UserGuide:RNASeqFPKMGraph

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Users can download a file of FPKM data with developmental ontology terms from here: http://caltech.wormbase.org/pub/wormbase/spell_download/tables/modENCODE_FPKM.tgz

The file is 420M in zipped format. Here are the columns of the data:

Gene ID Gene Name Life Stage ID Life Stage FPKM Analysis
WBGene00000001 aap-1 WBls:0000699 770 min post first-cleavage Ce 5.911170 RNASeq.elegans.WBStrain00000001.WBls:0000699.Hermaphrodite.WBbt:0007833.SRP029448.SRX343210
WBGene00000001 aap-1 WBls:0000031 L2d-dauer molt Ce 22.847700 RNASeq.elegans.WBStrain00004309.WBls:0000031.Hermaphrodite.WBbt:0007833.SRP000401.SRX103274
WBGene00000001 aap-1 WBls:0000031 L2d-dauer molt Ce 26.271799 RNASeq.elegans.WBStrain00004309.WBls:0000031.Hermaphrodite.WBbt:0007833.SRP000401.SRX103275
WBGene00000001 aap-1 WBls:0000031 L2d-dauer molt Ce 20.627800 RNASeq.elegans.WBStrain00004309.WBls:0000031.Hermaphrodite.WBbt:0007833.SRP000401.SRX047470
WBGene00000001 aap-1 WBls:0000031 L2d-dauer molt Ce 24.492100 RNASeq.elegans.WBStrain00004309.WBls:0000031.Hermaphrodite.WBbt:0007833.SRP000401.SRX103273
WBGene00000001 aap-1 WBls:0000031 L2d-dauer molt Ce 12.759100 RNASeq.elegans.WBStrain00004309.WBls:0000031.Hermaphrodite.WBbt:0007833.SRP000401.SRX008139
WBGene00000001 aap-1 WBls:0000031 L2d-dauer molt Ce 27.917601 RNASeq.elegans.WBStrain00004309.WBls:0000031.Hermaphrodite.WBbt:0007833.SRP000401.SRX103276
WBGene00000001 aap-1 WBls:0000031 L2d-dauer molt Ce 38.173801 RNASeq.elegans.WBStrain00004309.WBls:0000031.Hermaphrodite.WBbt:0007833.SRP000401.SRX103277 ...

Github repository for processing RNAseq values: https://github.com/WormBase/wormbase-pipeline/tree/master/scripts/RNAseq

The FPKM graphs on the WormBase Gene pages are based on the RNASeq from the modENCODE project (PMID: 21177976 - Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project.)
RNASeq data from the modENCODE project are stored in the SRA under the Project ID: SRP000401.
We then analysed this data, using it to produce the expression values for the graph.

This RNASeq data was aligned against the N2 assembly sequence using the STAR aligner and FPKM values were produced using Cufflinks. A subset of this data using poly-A and ribozero selection protocols that did not involve conditions like a challenge by pathogens were selected. The graph is produced as part of the WormBase web interface.

We ended up using the following data. The columns are:


SRA Experiment ID
Embryo age in minutes or classical development stage.
Selection protocol
Library name


        SRX092477 => ['0','polyA', 'N2_EE_50-0'],
        SRX092478 => ['0','polyA', 'N2_EE_50-0'],
        SRX099902 => ['0','polyA', 'N2_EE_50-0'],
        SRX099901 => ['0','polyA', 'N2_EE_50-0'],
        SRX103649 => ['0','polyA', 'N2_EE_50-0'],
       SRX1022600 => ['0','ribozero', '20120411_EMB-0'],
        SRX1020637 => ['0','ribozero', '20120223_EMB-0'],
        SRX1020636 => ['0','ribozero', '20120223_EMB-0'],
        SRX092371 => ['30','polyA', 'N2_EE_50-30'],
        SRX092372 => ['30','polyA', 'N2_EE_50-30'],
        SRX099908 => ['30','polyA', 'N2_EE_50-30'],
        SRX099907 => ['30','polyA', 'N2_EE_50-30'],
        SRX103650 => ['30','polyA', 'N2_EE_50-30'],
        SRX1020634 => ['30','ribozero', '20120223_EMB-30'],
        SRX1022610 => ['30','ribozero', '20120419_EMB-30'],
        SRX1020635 => ['30','ribozero', '20120223_EMB-30'],
        SRX085112 => ['60','polyA', 'N2_EE_50-60'],
       SRX085111 => ['60','polyA', 'N2_EE_50-60'],
        SRX1022599 => ['60','ribozero', '20120411_EMB-60'],
        SRX1020638 => ['60','ribozero', '20120223_EMB-60'],
        SRX1020639 => ['60','ribozero', '20120223_EMB-60'],
        SRX092480 => ['90','polyA', 'N2_EE_50-90'],
        SRX092479 => ['90','polyA', 'N2_EE_50-90'],
        SRX099915 => ['90','polyA', 'N2_EE_50-90'],
        SRX103651 => ['90','polyA', 'N2_EE_50-90'],
        SRX1022605 => ['90','ribozero', '20120411_EMB-90'],
        SRX1020640 => ['90','ribozero', '20120223_EMB-90'],
        SRX1020641 => ['90','ribozero', '20120223_EMB-90'],
        SRX1022611 => ['90','ribozero', '20120419_EMB-90'],
        SRX085217 => ['120','polyA', 'N2_EE_50-120'],
        SRX085218 => ['120','polyA', 'N2_EE_50-120'],
        SRX1022602 => ['120','ribozero', '20120411_EMB-120'],
        SRX1022645 => ['120','ribozero', '20120419_EMB-120'],
        SRX1020630 => ['120','ribozero', '20120223_EMB-120'],
        SRX1020631 => ['120','ribozero', '20120223_EMB-120'],
        SRX099995 => ['150','polyA', 'N2_EE_50-150'],
        SRX1022601 => ['150','ribozero', '20120411_EMB-150'],
        SRX1020632 => ['150','ribozero', '20120223_EMB-150'],
        SRX1020633 => ['150','ribozero', '20120223_EMB-150'],
        SRX1022646 => ['150','ribozero', '20120419_EMB-150'],
        SRX099985 => ['180','polyA', 'N2_EE_50-180'],
        SRX1022603 => ['180','ribozero', '20120411_EMB-180'],
        SRX1022584 => ['180','ribozero', '20120223_EMB-180'],
        SRX1022585 => ['180','ribozero', '20120223_EMB-180'],
        SRX1022647 => ['180','ribozero', '20120419_EMB-180'],
        SRX099996 => ['210','polyA', 'N2_EE_50-210'],
        SRX099997 => ['210','polyA', 'N2_EE_50-210'],
        SRX099998 => ['210','polyA', 'N2_EE_50-210'],
        SRX103652 => ['210','polyA', 'N2_EE_50-210'],
        SRX1022570 => ['210','ribozero', '20120223_EMB-210'],
        SRX1022571 => ['210','ribozero', '20120223_EMB-210'],
        SRX099986 => ['240','polyA', 'N2_EE_50-240'],
        SRX099987 => ['240','polyA', 'N2_EE_50-240'],
        SRX103653 => ['240','polyA', 'N2_EE_50-240'],
        SRX1022604 => ['240','ribozero', '20120411_EMB-240'],
        SRX1022566 => ['240','ribozero', '20120223_EMB-240'],
        SRX1022567 => ['240','ribozero', '20120223_EMB-240'],
        SRX1022648 => ['240','ribozero', '20120419_EMB-240'],
        SRX099999 => ['270','polyA', 'N2_EE_50-270'],
        SRX100000 => ['270','polyA', 'N2_EE_50-270'],
        SRX100001 => ['270','polyA', 'N2_EE_50-270'],
        SRX103677 => ['270','polyA', 'N2_EE_50-270'],
        SRX1022568 => ['270','ribozero', '20120223_EMB-270'],
        SRX1022569 => ['270','ribozero', '20120223_EMB-270'],
        SRX1022649 => ['270','ribozero', '20120419_EMB-270'],
        SRX100819 => ['300','polyA', 'N2_EE_50-300'],
        SRX1022580 => ['300','ribozero', '20120223_EMB-300'],
        SRX1022581 => ['300','ribozero', '20120223_EMB-300'],
        SRX1022608 => ['300','ribozero', '20120411_EMB-300'],
        SRX1022650 => ['300','ribozero', '20120419_EMB-300'],
        SRX099980 => ['330','polyA', 'N2_EE_50-330'],
        SRX1022572 => ['330','ribozero', '20120223_EMB-330'],
        SRX1022573 => ['330','ribozero', '20120223_EMB-330'],
        SRX1022651 => ['330','ribozero', '20120419_EMB-330'],
        SRX099981 => ['360','polyA', 'N2_EE_50-360'],
        SRX1022574 => ['360','ribozero', '20120223_EMB-360'],
        SRX1022575 => ['360','ribozero', '20120223_EMB-360'],
        SRX1022607 => ['360','ribozero', '20120411_EMB-360'],
        SRX1022652 => ['360','ribozero', '20120419_EMB-360'],
        SRX099982 => ['390','polyA', 'N2_EE_50-390'],
        SRX099983 => ['390','polyA', 'N2_EE_50-390'],
        SRX1022576 => ['390','ribozero', '20120223_EMB-390'],
        SRX1022577 => ['390','ribozero', '20120223_EMB-390'],
        SRX099984 => ['420','polyA', 'N2_EE_50-420'],
        SRX1022578 => ['420','ribozero', '20120223_EMB-420'],
        SRX1022579 => ['420','ribozero', '20120223_EMB-420'],
        SRX1022653 => ['420','ribozero', '20120419_EMB-420'],
        SRX100002 => ['450','polyA', 'N2_EE_50-450'],
        SRX1022582 => ['450','ribozero', '20120223_EMB-450'],
        SRX1022583 => ['450','ribozero', '20120223_EMB-450'],
        SRX1022654 => ['450','ribozero', '20120419_EMB-450'],
        SRX099988 => ['480','polyA', 'N2_EE_50-480'],
        SRX099989 => ['480','polyA', 'N2_EE_50-480'],
        SRX099990 => ['480','polyA', 'N2_EE_50-480'],
        SRX103672 => ['480','polyA', 'N2_EE_50-480'],
        SRX1022586 => ['480','ribozero', '20120223_EMB-480'],
        SRX1022587 => ['480','ribozero', '20120223_EMB-480'],
        SRX100003 => ['510','polyA', 'N2_EE_50-510'],
        SRX100004 => ['510','polyA', 'N2_EE_50-510'],
        SRX100005 => ['510','polyA', 'N2_EE_50-510'],
        SRX103673 => ['510','polyA', 'N2_EE_50-510'],
        SRX1022588 => ['510','ribozero', '20120223_EMB-510'],
        SRX1022589 => ['510','ribozero', '20120223_EMB-510'],
        SRX099991 => ['540','polyA', 'N2_EE_50-540'],
        SRX099992 => ['540','polyA', 'N2_EE_50-540'],
        SRX099993 => ['540','polyA', 'N2_EE_50-540'],
        SRX103669 => ['540','polyA', 'N2_EE_50-540'],
        SRX1022592 => ['540','ribozero', '20120223_EMB-540'],
        SRX1022593 => ['540','ribozero', '20120223_EMB-540'],
        SRX099973 => ['570','polyA', 'N2_EE_50-570'],
        SRX099974 => ['570','polyA', 'N2_EE_50-570'],
        SRX103671 => ['570','polyA', 'N2_EE_50-570'],
        SRX1022597 => ['570','ribozero', '20120223_EMB-570'],
        SRX1022598 => ['570','ribozero', '20120223_EMB-570'],
        SRX099975 => ['600','polyA', 'N2_EE_50-600'],
        SRX099976 => ['600','polyA', 'N2_EE_50-600'],
        SRX099977 => ['600','polyA', 'N2_EE_50-600'],
        SRX103670 => ['600','polyA', 'N2_EE_50-600'],
        SRX1022596 => ['600','ribozero', '20120223_EMB-600'],
        SRX1022595 => ['600','ribozero', '20120223_EMB-600'],
        SRX1022609 => ['600','ribozero', '20120411_EMB-600'],
        SRX099978 => ['630','polyA', 'N2_EE_50-630'],
        SRX099979 => ['660','polyA', 'N2_EE_50-660'],
        SRX099994 => ['690','polyA', 'N2_EE_50-690'],
        SRX100006 => ['720','polyA', 'N2_EE_50-720'],
        SRX004863 => ['EE','polyA', 'EE_ce0128_rw005'],
        SRX004864 => ['EE','polyA', 'EE_ce1003_rw005'],
        SRX037186 => ['EE','polyA', 'N2_EE-2'],
        SRX004866 => ['EE','polyA', 'EE_ce0129_rw006'], # checked with LaDeana Hillier - she says this is an early embryo
        SRX145660 => ['EE','ribozero', 'N2_EE_RZ-54'],
        SRX190369 => ['EE','ribozero', 'N2_EE_RZ-54'],
        SRX004865 => ['LE','polyA', 'LE_ce0129_rw006'],
        SRX047446 => ['LE','polyA', 'N2_LE-1'],
        SRX004867 => ['L1','polyA', 'L1_ce0132_rw007'],
        SRX037288 => ['L1','polyA', 'N2_L1-1'],
        SRX001872 => ['L2','polyA', 'L2_ce0109_rw001'],
        SRX047653 => ['L2','polyA', 'N2_L2-4'],
        SRX190370 => ['L2','ribozero', 'N2_L2_RZ-53'],
        SRX145661 => ['L2','ribozero', 'N2_L2_RZ-53'],
        SRX001875 => ['L3','polyA', 'L3_ce0120_rw002'],
        SRX036881 => ['L3','polyA', 'N2_L3-1'],
        SRX008144 => ['L4','polyA', 'L4_ce1009_rw1001'],
        SRX001874 => ['L4','polyA', 'L4_ce0121_rw003'],
        SRX001873 => ['YA','polyA', 'YA_ce0122_rw004'],
        SRX047787 => ['YA','polyA', 'N2_Yad-1'],
        SRX103986 => ['YA','ribozero', 'N2_YA_RZ-1'],
        SRX103987 => ['YA','ribozero', 'N2_YA_RZ-1'],
        SRX103988 => ['YA','ribozero', 'N2_YA_RZ-1'],
        SRX103989 => ['YA','ribozero', 'N2_YA_RZ-1'],
        SRX011569 => ['Male EM','polyA', 'EmMalesHIM8_ce1005_rw1001'],
        SRX037198 => ['Male EM','polyA', 'EmMalesHIM8-2'],
        SRX004868 => ['Male L4','polyA', 'L4_ce1001_rw1001'],
        SRX047469 => ['Male L4','polyA', 'L4MALE5'],
        SRX014010 => ['Soma L4','polyA', 'L4JK1107soma_ce1014_rw1001'],
        SRX037200 => ['Soma L4','polyA', 'L4JK1107soma-2'],
        SRX008139 => ['Dauer entry','polyA', 'DauerEntryDAF2_ce1007_rw1001'],
        SRX047470 => ['Dauer entry','polyA', 'DauerEntryDAF2-2'],
        SRX103273 => ['Dauer entry','polyA', 'DauerEntryDAF2-1-1'],
        SRX103274 => ['Dauer entry','polyA', 'DauerEntryDAF2-1-1'],
        SRX103275 => ['Dauer entry','polyA', 'DauerEntryDAF2-1-1'],
        SRX103276 => ['Dauer entry','polyA', 'DauerEntryDAF2-1-1'],
        SRX103277 => ['Dauer entry','polyA', 'DauerEntryDAF2-4-1'],
        SRX008138 => ['Dauer','polyA', 'DauerDAF2_ce1006_rw1001'],
        SRX103983 => ['Dauer','polyA', 'DauerDAF2-2-1'],
        SRX103984 => ['Dauer','polyA', 'DauerDAF2-2'],
        SRX103985 => ['Dauer','polyA', 'DauerDAF2-5-1'],
        SRX008140 => ['Dauer exit','polyA', 'DauerExitDAF2_ce1008_rw1001'],
        SRX037199 => ['Dauer exit','polyA', 'DauerExitDAF2-2'],
        SRX103269 => ['Dauer exit','polyA', 'DauerExitDAF2-3-1'],
        SRX103270 => ['Dauer exit','polyA', 'DauerExitDAF2-3-1'],
        SRX103271 => ['Dauer exit','polyA', 'DauerExitDAF2-3-1'],
        SRX103272 => ['Dauer exit','polyA', 'DauerExitDAF2-3-1'],
        SRX103278 => ['Dauer exit','polyA', 'DauerExitDAF2-6-1'],
        SRX103281 => ['Dauer exit','polyA', 'DauerExitDAF2-6-1'],
        SRX103280 => ['Dauer exit','polyA', 'DauerExitDAF2-6-1'],
        SRX103279 => ['Dauer exit','polyA', 'DauerExitDAF2-6-1'],