UserGuide:RNASeqFPKMGraph
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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, see: PMID: 21177976 Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project. RNASeq data from the modENCODE project is 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'],
