title: Knockdown_of_FBgn0038551_CG7357_using_DRSC16234_replicate1

source_name: KO of FBgn0038551 CG7357 using DRSC16234


title: Knockdown_of_FBgn0039019_HP1c_using_DRSC16166_replicate1

status: Public on Sep 24 2016

type: SRA

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

country: USA

institute: NIDDK, NIH

library_source: transcriptomic

data_processing:
We performed base calling using CASAVA version 1.8.2 (Illumina, San Diego, CA).
We mapped RNA-Seq reads to the Drosophila genome assembly (Release 6) with ERCC spike-in sequences (Jiang et al., 2011. PMID: 21816910) using TopHat 2.0.10 (Trapnell et al., 2009. PMID: 19289445). We used -g 1 and -G parameters. We removed measurements for those problematic controls in our submission. A gene model is required for this setting (-G). We used FlyBase (version 6.06). Only major chromosome arms (chr2L, chr2R, chr3L, chr3R, chr4, chrX, chrY, and chrM) were used for mapping.
Read counts were obtained using HTseq (Anders et al., 2014. PMID: 25260700) using default parameters. We calculated normalized, gene level, expression using Cufflinks 2.2.1 (Trapnell et al., 2010. PMID: 20436464) that gave us Fragments per Kilobase per Million mapped reads (FPKM) values. -G, -b, and -u parameters were used.
Genome_build: BDGP release 6 (obtained from FlyBase (http://www.flybase.org)
Supplementary_files_format_and_content: Tab limited text files contain transcript abundance information, generated from HTseq and Cufflink. HTseq results contain read counts, and Cufflinks results contain FPKM values at the gene level.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: KO of FBgn0039019 HP1c using DRSC16166

growth_protocol: Drosophila S2R+ cells were grown at the Harvard Drosophila RNAi Screen Center (DRSC, Boston, MA) using protocol (Ramadan et al., 2007. PMID: 17853882. Also, refer to http://www.flyrnai.org/DRSC-PRC.html)

extract_protocol:
We isolated total RNA with RNeasy 96 kits (Qiagen, Valencia, CA) according to the manufacturer's protocol (Protocol for Isolation of Total RNA from Animal Cells using spin technology, Cat#19504).
We constructed PolyA+ RNA-Seq libraries as in Lee et al (doi:10.1101/032920 and Gene Expression Omnibus GSE73920) without modification. Briefly, we used Dynabeads Oligo(dT)25 (Life Technologies, Grand Island, NY) for polyA+ selection. We fragmented polyA+ RNA in the presence of External RNA Control Consortium (ERCC) spike-ins (Baker et al., 2005. PMID: 16179916).  For lacZ sham RNAi control samples we used ERCC pool 78A, and for the rest of samples we used pool 78B RNAs transcribed from Standard Reference Material 2374 (Zook et al., 2012. PMID: 22859977).  We performed reverse transcription and dUTP was incorporated into DNA during the second strand synthesis step to generate strand-specific libraries. We added 24 different barcoded adapters from TruSeq v2 kit (Illumina, San Diego, CA) for ligation for multiplex sequencing. We digested dUTP-incorporated strands of DNA before PCR amplification. We sequenced our libraries with Illumina HiSeq 2500 (Illumina, San Diego, CA).

treatment_protocol: We added 2.7 ug of dsRNA (27 uL at 100ng/uL) to 96-well assay plates before the cells. Confluent S2R+ cells were spun down at 1,300 rpm for 3 minutes. Media was removed and cells were re-suspended in serum free media and diluted to 1e5 cells/mL (100 cells/16 square on a hemocytometer). 53 uL of suspension, approximately 5,300 cells, were dispensed using a multichannel pipette into the dsRNA-containing 96 well assay plates. Cells were allowed to settle for 30 minutes. After 30 minutes, 160 uL of complete media (10% FBS) was added per well. Plates were placed in humidified chamber at 25oC incubator for 24 h. Media was removed from wells using a 12-well vacuuming wand. 150 uL of RLT buffer (Qiagen, Valencia, CA, Cat. No. 79216) was added to each well. We pipetted up and down 5 times to facilitate cell lysis. Plates were sealed and stored at -80oC until RNA extraction.

tag: cell line

tag: RNAi target gene id (flybase)

tag: RNAi target gene name

tag: RNAi reagent from harvard drosophila rnai screening center


title: Knockdown_of_FBgn0039712_CG15514_using_DRSC15053_replicate1

source_name: KO of FBgn0039712 CG15514 using DRSC15053


title: Knockdown_of_FBgn0051388_CG31388_using_DRSC15254_replicate1

source_name: KO of FBgn0051388 CG31388 using DRSC15254


title: Knockdown_of_FBgn0020493_Dad_using_DRSC16642_replicate1

source_name: KO of FBgn0020493 Dad using DRSC16642

value: Dad


title: Knockdown_of_FBgn0038301_CG6654_using_DRSC16084_replicate1

source_name: KO of FBgn0038301 CG6654 using DRSC16084


title: Knockdown_of_FBgn0037109_MED1_using_DRSC11808_replicate1

source_name: KO of FBgn0037109 MED1 using DRSC11808


title: Knockdown_of_FBgn0030699_CG8578_using_DRSC20114_replicate1

source_name: KO of FBgn0030699 CG8578 using DRSC20114


title: Knockdown_of_FBgn0030003_CG2116_using_DRSC18206_replicate1

source_name: KO of FBgn0030003 CG2116 using DRSC18206


title: Knockdown_of_FBgn0031874_CG13775_using_DRSC02279_replicate1

source_name: KO of FBgn0031874 CG13775 using DRSC02279


title: Knockdown_of_FBgn0001341_l[1]1Bi_using_DRSC18788_replicate1

source_name: KO of FBgn0001341 l[1]1Bi using DRSC18788


title: Knockdown_of_FBgn0038768_CG4936_using_DRSC15680_replicate1

source_name: KO of FBgn0038768 CG4936 using DRSC15680


title: Knockdown_of_FBgn0004597_CycC_using_DRSC16619_replicate1

source_name: KO of FBgn0004597 CycC using DRSC16619

value: CycC


title: Knockdown_of_FBgn0003862_trx_using_DRSC17089_replicate1

source_name: KO of FBgn0003862 trx using DRSC17089

value: trx


title: Knockdown_of_FBgn0016917_Stat92E_using_DRSC16870_replicate1

source_name: KO of FBgn0016917 Stat92E using DRSC16870


title: Knockdown_of_FBgn0030963_CG7101_using_DRSC20023_replicate1

source_name: KO of FBgn0030963 CG7101 using DRSC20023


title: Knockdown_of_FBgn0037031_CG11456_using_DRSC11665_replicate1

source_name: KO of FBgn0037031 CG11456 using DRSC11665


title: Knockdown_of_FBgn0032150_CG13123_using_DRSC02219_replicate1

source_name: KO of FBgn0032150 CG13123 using DRSC02219


title: Knockdown_of_FBgn0037920_CG14710_using_DRSC14933_replicate1

source_name: KO of FBgn0037920 CG14710 using DRSC14933


title: Knockdown_of_FBgn0022361_Pur-alpha_using_DRSC17166_replicate1

source_name: KO of FBgn0022361 Pur-alpha using DRSC17166

value: Pur-alpha


title: Knockdown_of_FBgn0003511_Sry-beta_using_DRSC16868_replicate1

source_name: KO of FBgn0003511 Sry-beta using DRSC16868

value: Sry-beta


title: Knockdown_of_FBgn0264075_tgo_using_DRSC17077_replicate1

source_name: KO of FBgn0264075 tgo using DRSC17077

value: tgo


title: Knockdown_of_FBgn0000283_Cp190_using_DRSC16607_replicate1

source_name: KO of FBgn0000283 Cp190 using DRSC16607


title: Knockdown_of_FBgn0044324_Chro_using_DRSC11630_replicate1

source_name: KO of FBgn0044324 Chro using DRSC11630

value: Chro


title: Knockdown_of_FBgn0085432_pan_using_DRSC17176_replicate1

source_name: KO of FBgn0085432 pan using DRSC17176

value: pan


title: Knockdown_of_FBgnNA_LacZ_using_DRSCNA_replicate1 [Plate2-1_F3]

source_name: KO of FBgnNA LacZ using DRSCNA

value: FBgnNA

value: LacZ


title: Knockdown_of_FBgn0013531_MED20_using_DRSC03463_replicate1

source_name: KO of FBgn0013531 MED20 using DRSC03463


title: Knockdown_of_FBgn0010282_TfIIFalpha_using_DRSC12608_replicate1

source_name: KO of FBgn0010282 TfIIFalpha using DRSC12608

value: TfIIFalpha


title: Knockdown_of_FBgn0030010_CG10959_using_DRSC17769_replicate1

source_name: KO of FBgn0030010 CG10959 using DRSC17769


title: Knockdown_of_FBgn0039904_Hcf_using_DRSC17143_replicate1

source_name: KO of FBgn0039904 Hcf using DRSC17143

value: Hcf


title: Knockdown_of_FBgn0037794_CG6254_using_DRSC16002_replicate1

source_name: KO of FBgn0037794 CG6254 using DRSC16002


title: Knockdown_of_FBgn0261573_CoRest_using_DRSC19881_replicate1

source_name: KO of FBgn0261573 CoRest using DRSC19881

value: CoRest


title: Knockdown_of_FBgn0015240_Hr96_using_DRSC16707_replicate1

source_name: KO of FBgn0015240 Hr96 using DRSC16707


title: Knockdown_of_FBgn0000520_dwg_using_DRSC18766_replicate1

source_name: KO of FBgn0000520 dwg using DRSC18766

value: dwg


title: Knockdown_of_FBgn0038046_CG5641_using_DRSC15852_replicate1

source_name: KO of FBgn0038046 CG5641 using DRSC15852


title: Knockdown_of_FBgn0037621_M1BP_using_DRSC16566_replicate1

source_name: KO of FBgn0037621 M1BP using DRSC16566


title: Knockdown_of_FBgn0015799_Rbf_using_DRSC18704_replicate1

source_name: KO of FBgn0015799 Rbf using DRSC18704

value: Rbf


title: Knockdown_of_FBgn0003567_su[Hw]_using_DRSC17074_replicate1

source_name: KO of FBgn0003567 su[Hw] using DRSC17074

value: su[Hw]


title: Knockdown_of_FBgn0030486_Set2_using_DRSC19765_replicate1

source_name: KO of FBgn0030486 Set2 using DRSC19765


title: Knockdown_of_FBgn0037445_CG9727_using_DRSC12585_replicate1

source_name: KO of FBgn0037445 CG9727 using DRSC12585


title: Knockdown_of_FBgn0011648_Mad_using_DRSC00759_replicate1

source_name: KO of FBgn0011648 Mad using DRSC00759

value: Mad


title: Knockdown_of_FBgn0010287_Trf_using_DRSC03462_replicate1

source_name: KO of FBgn0010287 Trf using DRSC03462

value: Trf


title: Knockdown_of_FBgn0051365_CG31365_using_DRSC15610_replicate1

source_name: KO of FBgn0051365 CG31365 using DRSC15610


title: Knockdown_of_FBgn0002733_E[spl]mbeta-HLH_using_DRSC16697_replicate1

source_name: KO of FBgn0002733 E[spl]mbeta-HLH using DRSC16697

value: E[spl]mbeta-HLH


title: Knockdown_of_FBgn0005642_wdn_using_DRSC17095_replicate1

source_name: KO of FBgn0005642 wdn using DRSC17095

value: wdn


title: Knockdown_of_FBgn0028398_Taf10_using_DRSC00793_replicate1

source_name: KO of FBgn0028398 Taf10 using DRSC00793


title: Knockdown_of_FBgn0003117_pnr_using_DRSC17027_replicate1

source_name: KO of FBgn0003117 pnr using DRSC17027

value: pnr


title: Knockdown_of_FBgn0038765_CG4424_using_DRSC15576_replicate1

source_name: KO of FBgn0038765 CG4424 using DRSC15576


title: Knockdown_of_FBgn0039338_XNP_using_DRSC15594_replicate1

source_name: KO of FBgn0039338 XNP using DRSC15594

value: XNP


title: Knockdown_of_FBgn0024330_MED6_using_DRSC16500_replicate1

source_name: KO of FBgn0024330 MED6 using DRSC16500


title: Knockdown_of_FBgn0030314_CG11696_using_DRSC19417_replicate1

source_name: KO of FBgn0030314 CG11696 using DRSC19417


title: Knockdown_of_FBgn0038472_CG3995_using_DRSC15532_replicate1

source_name: KO of FBgn0038472 CG3995 using DRSC15532


title: Knockdown_of_FBgn0005386_ash1_using_DRSC11325_replicate1

source_name: KO of FBgn0005386 ash1 using DRSC11325


title: Knockdown_of_FBgn0037446_Zif_using_DRSC12514_replicate1

source_name: KO of FBgn0037446 Zif using DRSC12514

value: Zif


title: Knockdown_of_FBgn0011291_Taf11_using_DRSC03448_replicate1

source_name: KO of FBgn0011291 Taf11 using DRSC03448


title: Knockdown_of_FBgn0011290_Taf12_using_DRSC16879_replicate1

source_name: KO of FBgn0011290 Taf12 using DRSC16879


title: Knockdown_of_FBgn0039509_bigmax_using_DRSC15481_replicate1

source_name: KO of FBgn0039509 bigmax using DRSC15481

value: bigmax


title: Knockdown_of_FBgn0038244_CG7987_using_DRSC16357_replicate1

source_name: KO of FBgn0038244 CG7987 using DRSC16357


title: Knockdown_of_FBgn0039044_p53_using_DRSC17024_replicate1

source_name: KO of FBgn0039044 p53 using DRSC17024


title: Knockdown_of_FBgn0026080_Tip60_using_DRSC18661_replicate1

source_name: KO of FBgn0026080 Tip60 using DRSC18661


title: Knockdown_of_FBgn0010417_Taf6_using_DRSC11299_replicate1

source_name: KO of FBgn0010417 Taf6 using DRSC11299


title: Knockdown_of_FBgn0017578_Max_using_DRSC11218_replicate1

source_name: KO of FBgn0017578 Max using DRSC11218

value: Max


title: Knockdown_of_FBgn0024975_CG2712_using_DRSC18589_replicate1

source_name: KO of FBgn0024975 CG2712 using DRSC18589


title: Knockdown_of_FBgn0039740_CG7928_using_DRSC16349_replicate1

source_name: KO of FBgn0039740 CG7928 using DRSC16349


title: Knockdown_of_FBgn0025463_Bap60_using_DRSC19337_replicate1

source_name: KO of FBgn0025463 Bap60 using DRSC19337


title: Knockdown_of_FBgn0031613_HP6_using_DRSC00471_replicate1

source_name: KO of FBgn0031613 HP6 using DRSC00471


title: Knockdown_of_FBgn0011715_Snr1_using_DRSC12369_replicate1

source_name: KO of FBgn0011715 Snr1 using DRSC12369


title: Knockdown_of_FBgn0051224_CG31224_using_DRSC16290_replicate1

source_name: KO of FBgn0051224 CG31224 using DRSC16290


title: Knockdown_of_FBgn0029173_fu2_using_DRSC03324_replicate1

source_name: KO of FBgn0029173 fu2 using DRSC03324


title: Knockdown_of_FBgn0260741_CG3281_using_DRSC15470_replicate1

source_name: KO of FBgn0260741 CG3281 using DRSC15470


title: Knockdown_of_FBgn0261885_osa_using_DRSC17022_replicate1

source_name: KO of FBgn0261885 osa using DRSC17022

value: osa


title: Knockdown_of_FBgn0262975_cnc_using_DRSC15289_replicate1

source_name: KO of FBgn0262975 cnc using DRSC15289

value: cnc


title: Knockdown_of_FBgn0014018_Rel_using_DRSC16819_replicate1

source_name: KO of FBgn0014018 Rel using DRSC16819

value: Rel


title: Knockdown_of_FBgn0037918_CG6791_using_DRSC16118_replicate1

source_name: KO of FBgn0037918 CG6791 using DRSC16118


title: Knockdown_of_FBgn0052772_CG32772_using_DRSC18406_replicate1

source_name: KO of FBgn0052772 CG32772 using DRSC18406


title: Knockdown_of_FBgn0038197_foxo_using_DRSC15463_replicate1

source_name: KO of FBgn0038197 foxo using DRSC15463

value: foxo


title: Knockdown_of_FBgn0015239_Hr78_using_DRSC11866_replicate1

source_name: KO of FBgn0015239 Hr78 using DRSC11866


title: Knockdown_of_FBgn0031894_CG4496_using_DRSC02753_replicate1

source_name: KO of FBgn0031894 CG4496 using DRSC02753


title: Knockdown_of_FBgn0031623_Taf12L_using_DRSC00467_replicate1

source_name: KO of FBgn0031623 Taf12L using DRSC00467


title: Knockdown_of_FBgn0259234_Camta_using_DRSC07272_replicate2

source_name: KO of FBgn0259234 Camta using DRSC07272

value: Camta


title: Knockdown_of_FBgn0033971_CG10209_using_DRSC05980_replicate2

source_name: KO of FBgn0033971 CG10209 using DRSC05980


title: Knockdown_of_FBgn0035137_CG1233_using_DRSC08269_replicate2

source_name: KO of FBgn0035137 CG1233 using DRSC08269


title: Knockdown_of_FBgn0036661_CG9705_using_DRSC11094_replicate1

source_name: KO of FBgn0036661 CG9705 using DRSC11094


title: Knockdown_of_FBgn0261617_nej_using_DRSC18801_replicate1

source_name: KO of FBgn0261617 nej using DRSC18801

value: nej


title: Knockdown_of_FBgn0033459_CG12744_using_DRSC06164_replicate2

source_name: KO of FBgn0033459 CG12744 using DRSC06164


title: Knockdown_of_FBgn0003607_Su[var]205_using_DRSC03446_replicate2

source_name: KO of FBgn0003607 Su[var]205 using DRSC03446


title: Knockdown_of_FBgn0034599_CG9437_using_DRSC04555_replicate2

source_name: KO of FBgn0034599 CG9437 using DRSC04555


title: Knockdown_of_FBgn0015602_BEAF-32_using_DRSC05927_replicate2

source_name: KO of FBgn0015602 BEAF-32 using DRSC05927


title: Knockdown_of_FBgn0035145_MED14_using_DRSC08235_replicate2

source_name: KO of FBgn0035145 MED14 using DRSC08235


title: Knockdown_of_FBgn0001324_kto_using_DRSC10983_replicate2

source_name: KO of FBgn0001324 kto using DRSC10983

value: kto


title: Knockdown_of_FBgn0015618_Cdk8_using_DRSC11113_replicate2

source_name: KO of FBgn0015618 Cdk8 using DRSC11113


title: Knockdown_of_FBgn0270924_zf30C_using_DRSC03641_replicate2

source_name: KO of FBgn0270924 zf30C using DRSC03641


title: Knockdown_of_FBgn0250786_Chd1_using_DRSC00745_replicate2

source_name: KO of FBgn0250786 Chd1 using DRSC00745


title: Knockdown_of_FBgn0033581_CG12391_using_DRSC06147_replicate2

source_name: KO of FBgn0033581 CG12391 using DRSC06147


title: Knockdown_of_FBgn0026582_CG9418_using_DRSC04554_replicate2

source_name: KO of FBgn0026582 CG9418 using DRSC04554


title: Knockdown_of_FBgn0267792_rgr_using_DRSC07229_replicate2

source_name: KO of FBgn0267792 rgr using DRSC07229

value: rgr


title: Knockdown_of_FBgn0035754_MED4_using_DRSC11014_replicate2

source_name: KO of FBgn0035754 MED4 using DRSC11014


title: Knockdown_of_FBgn0041111_lilli_using_DRSC00708_replicate2

source_name: KO of FBgn0041111 lilli using DRSC00708

value: lilli


title: Knockdown_of_FBgn0036775_CG5147_using_DRSC10485_replicate2

source_name: KO of FBgn0036775 CG5147 using DRSC10485


title: Knockdown_of_FBgn0032517_CG7099_using_DRSC03006_replicate2

source_name: KO of FBgn0032517 CG7099 using DRSC03006


title: Knockdown_of_FBgn0032401_Plzf_using_DRSC02994_replicate2

source_name: KO of FBgn0032401 Plzf using DRSC02994

value: Plzf


title: Knockdown_of_FBgn0261239_Hr39_using_DRSC03346_replicate2

source_name: KO of FBgn0261239 Hr39 using DRSC03346


title: Knockdown_of_FBgn0015805_Rpd3_using_DRSC08696_replicate2

source_name: KO of FBgn0015805 Rpd3 using DRSC08696


title: Knockdown_of_FBgn0001222_Hsf_using_DRSC07443_replicate2

source_name: KO of FBgn0001222 Hsf using DRSC07443

value: Hsf


title: Knockdown_of_FBgnNA_LacZ_using_DRSCNA_replicate2 [Plate1-2_F3]

source_name: KO of FBgnNA LacZ using DRSCNA

value: FBgnNA

value: LacZ


title: Knockdown_of_FBgn0035690_CG10274_using_DRSC09716_replicate2

source_name: KO of FBgn0035690 CG10274 using DRSC09716


title: Knockdown_of_FBgn0003612_Su[var]2-10_using_DRSC07721_replicate2

source_name: KO of FBgn0003612 Su[var]2-10 using DRSC07721


title: Knockdown_of_FBgn0261938_mtRNApol_using_DRSC00660_replicate2

source_name: KO of FBgn0261938 mtRNApol using DRSC00660

value: mtRNApol


title: Knockdown_of_FBgn0001978_stc_using_DRSC03620_replicate2

source_name: KO of FBgn0001978 stc using DRSC03620

value: stc


title: Knockdown_of_FBgn0085436_Not1_using_DRSC06794_replicate2

source_name: KO of FBgn0085436 Not1 using DRSC06794


title: Knockdown_of_FBgn0050011_gem_using_DRSC06093_replicate2

source_name: KO of FBgn0050011 gem using DRSC06093

value: gem


title: Knockdown_of_FBgn0034722_Rtf1_using_DRSC04085_replicate2

source_name: KO of FBgn0034722 Rtf1 using DRSC04085


title: Knockdown_of_FBgn0035769_CTCF_using_DRSC11004_replicate2

source_name: KO of FBgn0035769 CTCF using DRSC11004

value: CTCF


title: Knockdown_of_FBgn0262732_mbf1_using_DRSC11365_replicate2

source_name: KO of FBgn0262732 mbf1 using DRSC11365


title: Knockdown_of_FBgn0033155_Br140_using_DRSC06755_replicate2

source_name: KO of FBgn0033155 Br140 using DRSC06755


title: Knockdown_of_FBgn0032223_GATAd_using_DRSC02803_replicate2

source_name: KO of FBgn0032223 GATAd using DRSC02803

value: GATAd


title: Knockdown_of_FBgn0035036_CG4707_using_DRSC04483_replicate2

source_name: KO of FBgn0035036 CG4707 using DRSC04483


title: Knockdown_of_FBgn0003396_shn_using_DRSC07681_replicate2

source_name: KO of FBgn0003396 shn using DRSC07681

value: shn


title: Knockdown_of_FBgn0086655_jing_using_DRSC05000_replicate2

source_name: KO of FBgn0086655 jing using DRSC05000

value: jing


title: Knockdown_of_FBgn0011763_Dp_using_DRSC07402_replicate2

source_name: KO of FBgn0011763 Dp using DRSC07402

value: Dp


title: Knockdown_of_FBgn0024371_E2f2_using_DRSC03320_replicate2

source_name: KO of FBgn0024371 E2f2 using DRSC03320


title: Knockdown_of_FBgn0032475_Sfmbt_using_DRSC02552_replicate2

source_name: KO of FBgn0032475 Sfmbt using DRSC02552

value: Sfmbt


title: Knockdown_of_FBgn0022238_lolal_using_DRSC06948_replicate2

source_name: KO of FBgn0022238 lolal using DRSC06948

value: lolal


title: Knockdown_of_FBgn0267978_ap_using_DRSC04917_replicate2

source_name: KO of FBgn0267978 ap using DRSC04917

value: ap


title: Knockdown_of_FBgn0000541_E[bx]_using_DRSC08583_replicate2

source_name: KO of FBgn0000541 E[bx] using DRSC08583

value: E[bx]


title: Knockdown_of_FBgn0043364_cbt_using_DRSC00655_replicate2

source_name: KO of FBgn0043364 cbt using DRSC00655

value: cbt


title: Knockdown_of_FBgn0025185_az2_using_DRSC07580_replicate2

source_name: KO of FBgn0025185 az2 using DRSC07580


title: Knockdown_of_FBgn0001179_hay_using_DRSC11354_replicate2

source_name: KO of FBgn0001179 hay using DRSC11354

value: hay


title: Knockdown_of_FBgn0033185_CG1603_using_DRSC06602_replicate2

source_name: KO of FBgn0033185 CG1603 using DRSC06602


title: Knockdown_of_FBgn0035849_ERR_using_DRSC10840_replicate2

source_name: KO of FBgn0035849 ERR using DRSC10840

value: ERR


title: Knockdown_of_FBgn0034878_pita_using_DRSC04435_replicate2

source_name: KO of FBgn0034878 pita using DRSC04435

value: pita


title: Knockdown_of_FBgn0263667_Lpt_using_DRSC04515_replicate2

source_name: KO of FBgn0263667 Lpt using DRSC04515

value: Lpt


title: Knockdown_of_FBgn0031573_CG3407_using_DRSC00603_replicate2

source_name: KO of FBgn0031573 CG3407 using DRSC00603


title: Knockdown_of_FBgn0262937_Rabex-5_using_DRSC08628_replicate2

source_name: KO of FBgn0262937 Rabex-5 using DRSC08628


title: Knockdown_of_FBgn0001990_wek_using_DRSC03561_replicate2

source_name: KO of FBgn0001990 wek using DRSC03561

value: wek


title: Knockdown_of_FBgn0010280_Taf4_using_DRSC11297_replicate2

source_name: KO of FBgn0010280 Taf4 using DRSC11297


title: Knockdown_of_FBgn0032817_CG10631_using_DRSC02081_replicate2

source_name: KO of FBgn0032817 CG10631 using DRSC02081


title: Knockdown_of_FBgn0036522_CG7372_using_DRSC10827_replicate2

source_name: KO of FBgn0036522 CG7372 using DRSC10827


title: Knockdown_of_FBgn0015664_Dref_using_DRSC03319_replicate2

source_name: KO of FBgn0015664 Dref using DRSC03319

value: Dref


title: Knockdown_of_FBgn0034114_CG4282_using_DRSC06865_replicate2

source_name: KO of FBgn0034114 CG4282 using DRSC06865


title: Knockdown_of_FBgn0022764_Sin3A_using_DRSC07552_replicate2

source_name: KO of FBgn0022764 Sin3A using DRSC07552


title: Knockdown_of_FBgn0001185_her_using_DRSC03543_replicate2

source_name: KO of FBgn0001185 her using DRSC03543

value: her


title: Knockdown_of_FBgn0033233_Kdm4A_using_DRSC06586_replicate2

source_name: KO of FBgn0033233 Kdm4A using DRSC06586


title: Knockdown_of_FBgn0041205_key_using_DRSC04285_replicate2

source_name: KO of FBgn0041205 key using DRSC04285

value: key


title: Knockdown_of_FBgn0261278_grp_using_DRSC03541_replicate2

source_name: KO of FBgn0261278 grp using DRSC03541

value: grp


title: Knockdown_of_FBgn0000546_EcR_using_DRSC04910_replicate2

source_name: KO of FBgn0000546 EcR using DRSC04910

value: EcR


title: Knockdown_of_FBgn0265574_Cdc5_using_DRSC08577_replicate2

source_name: KO of FBgn0265574 Cdc5 using DRSC08577


title: Knockdown_of_FBgn0032815_CG10462_using_DRSC02058_replicate2

source_name: KO of FBgn0032815 CG10462 using DRSC02058


title: Knockdown_of_FBgn0031597_CG17612_using_DRSC00505_replicate2

source_name: KO of FBgn0031597 CG17612 using DRSC00505


title: Knockdown_of_FBgn0034217_Lhr_using_DRSC06759_replicate2

source_name: KO of FBgn0034217 Lhr using DRSC06759

value: Lhr


title: Knockdown_of_FBgn0036423_CG3919_using_DRSC10389_replicate2

source_name: KO of FBgn0036423 CG3919 using DRSC10389


title: Knockdown_of_FBgn0011656_Mef2_using_DRSC07468_replicate2

source_name: KO of FBgn0011656 Mef2 using DRSC07468


title: Knockdown_of_FBgn0020388_Gcn5_using_DRSC11248_replicate2

source_name: KO of FBgn0020388 Gcn5 using DRSC11248


title: Knockdown_of_FBgn0015391_glu_using_DRSC03539_replicate2

source_name: KO of FBgn0015391 glu using DRSC03539

value: glu


title: Knockdown_of_FBgn0032814_CG10366_using_DRSC02046_replicate2

source_name: KO of FBgn0032814 CG10366 using DRSC02046


title: Knockdown_of_FBgn0022935_D19A_using_DRSC11133_replicate2

source_name: KO of FBgn0022935 D19A using DRSC11133


title: Knockdown_of_FBgn0267792_rgr_using_DRSC06487_replicate2

source_name: KO of FBgn0267792 rgr using DRSC06487

value: rgr


title: Knockdown_of_FBgn0031610_CG15436_using_DRSC00451_replicate2

source_name: KO of FBgn0031610 CG15436 using DRSC00451


title: Knockdown_of_FBgn0036004_Jarid2_using_DRSC10372_replicate2

source_name: KO of FBgn0036004 Jarid2 using DRSC10372


title: Knockdown_of_FBgn0261850_Xpd_using_DRSC04666_replicate2

source_name: KO of FBgn0261850 Xpd using DRSC04666

value: Xpd


title: Knockdown_of_FBgn0031759_lid_using_DRSC03133_replicate2

source_name: KO of FBgn0031759 lid using DRSC03133

value: lid


title: Knockdown_of_FBgn0035213_CG2199_using_DRSC08558_replicate2

source_name: KO of FBgn0035213 CG2199 using DRSC08558


title: Knockdown_of_FBgn0001291_Jra_using_DRSC07447_replicate2

source_name: KO of FBgn0001291 Jra using DRSC07447

value: Jra


title: Knockdown_of_FBgn0032512_CG9305_using_DRSC03192_replicate2

source_name: KO of FBgn0032512 CG9305 using DRSC03192


title: Pputida_untreated_K

city: Cambridge

first: Junjie

last: Guo

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

description: rRNA-depleted RNA

data_processing:
Library strategy: DMS-seq
The six random nucleotides of the RT primer reduced circLigase bias and enabled the removal of PCR-duplicated sequences.
After removing these duplicates, the first six nucleotides and the 3′-adapter sequences were trimmed using FASTX tools.
The trimmed sequences were aligned to the reference transcriptome using Bowtie, requiring unique mapping and allowing one mismatch.
For each read, the nucleotide immediately upstream of the first aligned position was annotated as an RT stop.
At each position i of the transcriptome with ≥ 3 RT-stop reads, a fold-enrichment value (f) for RT stops was calculated as the ratio between the number of reads stalled at position i and the average number of reads over all positions of the same nucleotide within the same transcript (e.g. all G nucleotides) using an in-house perl script.
Genome_build: mm10 RefSeq, hg19 RefSeq, Saccharomyces Genome Database version 2015-1-13, E. coli RefSeq
Supplementary_files_format_and_content: Tab-delimited files containing the position of RT stop, base identity, raw RT-stop read count and fold enrichment.

molecule: total RNA

organism: Pseudomonas putida

extract_protocol:
Cells were treated with lysozyme at RT for 5 min. Total RNA was extracted with hot acid phenol.
The DMS-seq protocol (Rouskin et al. 2014) was adapted to detect RT stops in unmodified RNA. Poly(A)-selected RNA was denatured at 95°C for 2 minutes. 1X RNA-fragmentation reagent (Ambion) was added and mixed at 95°C for additional 1 minute before 20 mM EDTA was added to the mixture to stop the fragmentation. After ethanol precipitation, RNA fragments were dephosphorylated at their 3′ ends using T4 polynucleotide kinase (New England BioLabs). 60−80 nt RNA fragments were gel-purified and ligated to a pre-adenylated 3′ DNA adapter (AppTCGTATGCCGTCTTCTGCTTGddC). Products of the expected size (82−102 nt) were gel-purified and resuspended in 6 µl water. For reverse transcription, 1 µl 0.2 M Tris-Cl (pH 7.5), 1 µl 1.5 M KCl (or NaCl or LiCl), 0.5 µl 60 mM MgCl2, 0.5 µl 10 mM dNTP mix and 0.5 µl 1 µM 5′-radiolabeled primer (32p-NNNNNNGATCGTCGGACTGTAGAACTCTGAACCTGTCG/iSp18/CAAGCAGAAGACGGCATACG, in which N is any nucleotide, and iSp18 is an 18-atom hexa-ethyleneglycol spacer, IDT) were added to the RNA template. The mixture was incubated at 80°C for 2 minutes then cooled down to 42°C and incubated for additional 2 minutes before adding 100 U SuperScript III reverse transcriptase (Invitrogen). After incubation at 42°C for 10 minutes, the reaction was stopped with addition of 1 µl 1 M NaOH, and the mixture was heated at 98°C for 15 minutes to hydrolyze the RNA. cDNAs from extension that stalled after addition of 20−45 nt were separated from primers and full-length cDNAs on a 10% urea gel, eluted and precipitated. Purified cDNA fragments were circularized using 50 U CircLigase (Epicentre) at 60°C for 4 hours before inactivation at 80°C for 10 minutes. Circularized cDNAs were amplified using a 5′ indexed primer (AATGATACGGCGACCACCGACAGGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACxxxxxxATCCGACAGGTTCAGAGTTCTACAGTCCGA, in which xxxxxx is the multiplexing index), a common 3′ primer (CAAGCAGAAGACGGCATACGA), and Platinum Taq DNA Polymerase High Fidelity (Invitrogen) for 10–13 cycles of PCR. Libraries were purified on an 8% formamide gel and sequenced on a HiSeq 2000 sequencing machine (Illumina; 40 cycles, single-end mode).

tag: probe

tag: conditions

tag: rt cation


title: Pputida_untreated_Na

description: rRNA-depleted RNA

value: 150mM Na+


title: Knockdown_of_FBgn0032016_CG7818_using_DRSC03073_replicate2

source_name: KO of FBgn0032016 CG7818 using DRSC03073


title: Pputida_DMS_vivo

description: rRNA-depleted RNA

value: 8% DMS

value: In vivo, 37°C, 5min


title: Knockdown_of_FBgn0013764_Chi_using_DRSC04602_replicate2

source_name: KO of FBgn0013764 Chi using DRSC04602

value: Chi


title: Knockdown_of_FBgn0010422_TfIIS_using_DRSC03455_replicate2

source_name: KO of FBgn0010422 TfIIS using DRSC03455

value: TfIIS


title: Knockdown_of_FBgn0003963_ush_using_DRSC00843_replicate2

source_name: KO of FBgn0003963 ush using DRSC00843

value: ush


title: Knockdown_of_FBgn0035024_CG11414_using_DRSC04110_replicate2

source_name: KO of FBgn0035024 CG11414 using DRSC04110


title: Knockdown_of_FBgn0004396_CrebA_using_DRSC11122_replicate2

source_name: KO of FBgn0004396 CrebA using DRSC11122

value: CrebA


title: Knockdown_of_FBgn0035997_phol_using_DRSC10367_replicate2

source_name: KO of FBgn0035997 phol using DRSC10367

value: phol


title: Knockdown_of_FBgn0031391_CG11723_using_DRSC00324_replicate2

source_name: KO of FBgn0031391 CG11723 using DRSC00324


title: Knockdown_of_FBgn0035137_CG1233_using_DRSC08269_replicate1

source_name: KO of FBgn0035137 CG1233 using DRSC08269


title: Pputida_DMS_vitro_K150

description: rRNA-depleted RNA


title: Knockdown_of_FBgn0015371_chn_using_DRSC06086_replicate2

source_name: KO of FBgn0015371 chn using DRSC06086

value: chn


title: Knockdown_of_FBgn0033459_CG12744_using_DRSC06164_replicate1

source_name: KO of FBgn0033459 CG12744 using DRSC06164


title: Knockdown_of_FBgn0001324_kto_using_DRSC10983_replicate1

source_name: KO of FBgn0001324 kto using DRSC10983

value: kto


title: Knockdown_of_FBgn0032517_CG7099_using_DRSC03006_replicate1

source_name: KO of FBgn0032517 CG7099 using DRSC03006


title: Knockdown_of_FBgn0034975_enok_using_DRSC04096_replicate2

source_name: KO of FBgn0034975 enok using DRSC04096

value: enok


title: Knockdown_of_FBgn0034722_Rtf1_using_DRSC04085_replicate1

source_name: KO of FBgn0034722 Rtf1 using DRSC04085


title: Knockdown_of_FBgn0259234_Camta_using_DRSC07272_replicate1

source_name: KO of FBgn0259234 Camta using DRSC07272

value: Camta


title: Knockdown_of_FBgn0033569_CG12942_using_DRSC06253_replicate2

source_name: KO of FBgn0033569 CG12942 using DRSC06253


title: Knockdown_of_FBgn0034599_CG9437_using_DRSC04555_replicate1

source_name: KO of FBgn0034599 CG9437 using DRSC04555


title: Knockdown_of_FBgn0003607_Su[var]205_using_DRSC03446_replicate1

source_name: KO of FBgn0003607 Su[var]205 using DRSC03446


title: Knockdown_of_FBgn0267792_rgr_using_DRSC07229_replicate1

source_name: KO of FBgn0267792 rgr using DRSC07229


title: Knockdown_of_FBgn0250786_Chd1_using_DRSC00745_replicate1

source_name: KO of FBgn0250786 Chd1 using DRSC00745


title: Knockdown_of_FBgn0035690_CG10274_using_DRSC09716_replicate1

source_name: KO of FBgn0035690 CG10274 using DRSC09716


title: Knockdown_of_FBgn0033581_CG12391_using_DRSC06147_replicate1

source_name: KO of FBgn0033581 CG12391 using DRSC06147


title: 10T1P

city: Houston

first: Arindam

last: Chaudhury

state: TX

address: One Baylor Plaza / MS BCM335

department: Molecular Physiology and Biophysics

institute: Baylor College of Medicine

description:
total mRNA
10TP_biological replicate
10_quant_gene_reads_normalized.txt; 10gsa_result_filter120.xlsx

data_processing:
Running and Basecalls Performed on an Ion Proton Sequencer using Torrent Suite v3.6
Fastq files extracted from Torrent Suite output and fed into Partek Flow Suite
Within Partek Flow Suite, align to hg19 using Tophat2 and Bowtie2, normalize and analye for differential relative representation using Partek Gene Specific Analysis Feature
Partek GSA outputs imported to Excel, filtered to require 120 total observed reads across all conditions for a given cell type (ave 10/library), and compound enrichments calculated
Genome_build: hg19
Supplementary_files_format_and_content: .txt files - Partek GSA raw output.  .xlsx files - import of Partek GSA raw output, compound enrichment calculation.

organism: Homo sapiens

source_name: MCF10A cells

growth_protocol: see characteristics: Culture Medium above

extract_protocol:
Cells lysed in 10 mM Tris-Cl, pH 7.4, 5 mM MgCl2, 100 mM KCl, 1% (v/v) Triton X-100, 0.5% (w/v) deoxycholate, 1000 U/ml RNasin, 2mM DTT and 100 µg/ml Cycloheximide.  Total RNA and RNA from polysomal fractions were isolated with Trizol LS as per manufacturer's instructions. Poly(A) RNA was isolated using Dynabeads mRNA DIRECT Micro Kit (Life Technologies) according to manufacturer’s instructions.
Ion Total RNA-Seq Kit v2 (Life Technologies) was used according to manufacturer’s recommendations to prepare libraries.  the Ion PI Template OT2 200 Kit v2 (Life Technologies) was used as per manufacturer’s instructions to generate template Ion PI Ion Sphere particles using the Ion OneTouch 2 System. Ion PI Chip preparation was done using the Ion PI Sequencing 200 Kit v2 (Life Technologies) and sequenced on the Ion Proton Sequencer platform.
Single-read RNA-seq

treatment_protocol: Cells were treated with 5 ng/mL of TGF-b or vehicle control for 72 hours.

tag: cell type

value: breast epithelium

tag: treatment

value: TGFb, 5 ng/mL, 72h

tag: culture medium

value: DMEMF12, 5% Horse Serum, 20 ng/mL EGF, 0.5 mg/mL Hydrocortisone, 100 ng/mL Cholera Toxin, 10 mg/ml Insulin, Pen/Strep


title: 10T3P


title: Knockdown_of_FBgn0270924_zf30C_using_DRSC03641_replicate1

source_name: KO of FBgn0270924 zf30C using DRSC03641


title: Knockdown_of_FBgn0033971_CG10209_using_DRSC05980_replicate1

source_name: KO of FBgn0033971 CG10209 using DRSC05980


title: 10T2M

description:
total mRNA
10TM_biological replicate
10_quant_gene_reads_normalized.txt; 10gsa_result_filter120.xlsx

value: vehicle control, 72h


title: 10T3M


title: 10T2P


title: Knockdown_of_FBgn0261239_Hr39_using_DRSC03346_replicate1

source_name: KO of FBgn0261239 Hr39 using DRSC03346


title: Knockdown_of_FBgn0035518_CG15011_using_DRSC08464_replicate2

source_name: KO of FBgn0035518 CG15011 using DRSC08464


title: 10T1M


title: Knockdown_of_FBgn0035145_MED14_using_DRSC08235_replicate1

source_name: KO of FBgn0035145 MED14 using DRSC08235


title: Knockdown_of_FBgn0015602_BEAF-32_using_DRSC05927_replicate1

source_name: KO of FBgn0015602 BEAF-32 using DRSC05927


title: Knockdown_of_FBgn0015618_Cdk8_using_DRSC11113_replicate1

source_name: KO of FBgn0015618 Cdk8 using DRSC11113


title: 10E3P

description:
polysomal mRNA
10EP_biological replicate
10_quant_gene_reads_normalized.txt; 10gsa_result_filter120.xlsx


title: Knockdown_of_FBgn0041111_lilli_using_DRSC00708_replicate1

source_name: KO of FBgn0041111 lilli using DRSC00708

value: lilli


title: 10E2P


title: 10E1P


title: Knockdown_of_FBgn0035754_MED4_using_DRSC11014_replicate1

source_name: KO of FBgn0035754 MED4 using DRSC11014


title: Knockdown_of_FBgn0036775_CG5147_using_DRSC10485_replicate1

source_name: KO of FBgn0036775 CG5147 using DRSC10485


title: 10E3M

description:
polysomal mRNA
10EM_biological replicate
10_quant_gene_reads_normalized.txt; 10gsa_result_filter120.xlsx


title: Knockdown_of_FBgn0015805_Rpd3_using_DRSC08696_replicate1

source_name: KO of FBgn0015805 Rpd3 using DRSC08696


title: Knockdown_of_FBgn0026582_CG9418_using_DRSC04554_replicate1

source_name: KO of FBgn0026582 CG9418 using DRSC04554


title: Knockdown_of_FBgn0003612_Su[var]2-10_using_DRSC07721_replicate1

source_name: KO of FBgn0003612 Su[var]2-10 using DRSC07721


title: 7T3P

description:
total mRNA
7TP_biological replicate
7_quant_gene_reads_normalized.txt; 7gsa_result_filter120.xlsx

source_name: MCF7 cells

value: DMEM, 10% FBS, Pen/Strep


title: Knockdown_of_FBgn0001222_Hsf_using_DRSC07443_replicate1

source_name: KO of FBgn0001222 Hsf using DRSC07443

value: Hsf


title: 10E2M


title: 10E1M


title: Knockdown_of_FBgn0085436_Not1_using_DRSC06794_replicate1

source_name: KO of FBgn0085436 Not1 using DRSC06794


title: Pputida_DMS_vitro_K0

description: rRNA-depleted RNA

value: 8% DMS

value: 0mM K+, 37°C, 5min


title: 7T2M

description:
total mRNA
7TM_biological replicate
7_quant_gene_reads_normalized.txt; 7gsa_result_filter120.xlsx


title: 7T1M


title: Knockdown_of_FBgn0263667_Lpt_using_DRSC04515_replicate1

source_name: KO of FBgn0263667 Lpt using DRSC04515

value: Lpt


title: 7T1P


title: Knockdown_of_FBgn0032223_GATAd_using_DRSC02803_replicate1

source_name: KO of FBgn0032223 GATAd using DRSC02803

value: GATAd


title: 7T2P


title: Knockdown_of_FBgn0032401_Plzf_using_DRSC02994_replicate1

source_name: KO of FBgn0032401 Plzf using DRSC02994

value: Plzf


title: Knockdown_of_FBgn0050011_gem_using_DRSC06093_replicate1

source_name: KO of FBgn0050011 gem using DRSC06093

value: gem


title: Knockdown_of_FBgn0001978_stc_using_DRSC03620_replicate1

source_name: KO of FBgn0001978 stc using DRSC03620

value: stc


title: 7T3M


title: Knockdown_of_FBgn0261938_mtRNApol_using_DRSC00660_replicate1

source_name: KO of FBgn0261938 mtRNApol using DRSC00660

value: mtRNApol


title: Knockdown_of_FBgn0262732_mbf1_using_DRSC11365_replicate1

source_name: KO of FBgn0262732 mbf1 using DRSC11365


title: Knockdown_of_FBgnNA_LacZ_using_DRSCNA_replicate1 [Plate1-1_F3]

source_name: KO of FBgnNA LacZ using DRSCNA

value: FBgnNA

value: LacZ


title: 7E1P

description:
polysomal mRNA
7EP_biological replicate
7_quant_gene_reads_normalized.txt; 7gsa_result_filter120.xlsx

value: breast epithelium


title: 7E2P

value: TGFb, 5 ng/mL, 72h


title: 7E1M

description:
polysomal mRNA
7EM_biological replicate
7_quant_gene_reads_normalized.txt; 7gsa_result_filter120.xlsx


title: 7E3M


title: Knockdown_of_FBgn0035769_CTCF_using_DRSC11004_replicate1

source_name: KO of FBgn0035769 CTCF using DRSC11004

value: CTCF


title: 7E2M

value: vehicle control, 72h


title: Knockdown_of_FBgn0003396_shn_using_DRSC07681_replicate1

source_name: KO of FBgn0003396 shn using DRSC07681

value: shn


title: Knockdown_of_FBgn0011763_Dp_using_DRSC07402_replicate1

source_name: KO of FBgn0011763 Dp using DRSC07402

value: Dp


title: Knockdown_of_FBgn0033155_Br140_using_DRSC06755_replicate1

source_name: KO of FBgn0033155 Br140 using DRSC06755


title: Knockdown_of_FBgn0086655_jing_using_DRSC05000_replicate1

source_name: KO of FBgn0086655 jing using DRSC05000

value: jing


title: 7E3P

value: DMEM, 10% FBS, Pen/Strep


title: Knockdown_of_FBgn0035036_CG4707_using_DRSC04483_replicate1

source_name: KO of FBgn0035036 CG4707 using DRSC04483


title: SAFA positive CLIP

city: Pasadena

first: Mario

middle: R

last: Blanco

state: CA

address: 1200 E California Blvd

institute: Caltech

data_processing:
Base-calling was performed using Illumina software
Sequenced paired-end reads were aligned to mm9 genome with Bowtie2 using the following parameters: -k 1 -p 12 --very-sensitive-local --maxins 2000 --fr --no-discordant --no-mixed –no-unal
We identified protein binding sites on the Xist RNA by identifying regions that were enriched relative to the same region in the input control (“differential enrichment”) and also was enriched relative to all other regions on the remainder of the Xist RNA (“local enrichment”).
Genome_build: mm9
Supplementary_files_format_and_content: .bedgraph files coverage across genome

organism: Mus musculus

source_name: mouse ES cells

extract_protocol:
We crosslinked 6 hour doxycycline-induced pSM33 mouse male ES cells with 0.4 J/cm2 of UV254. Cells were lysed and RNA was digested with RNase I to achieve a size range of 100-500 nucleotides in length. For each CLIP sample, target proteins were immunoprecipitated from 20 million cells with antibody pre-coupled with Protein G beads. Samples were then washed and RNAs were eluted with NLS elution buffer with 100 mM DTT. Samples were then run through a standard SDS-PAGE gel and transferred to a nitrocellulose membrane, and a region 75 kDa above the molecular size of the protein of interest was isolated and treated with protease followed by phenol/chloroform/isoamyl alcohol extraction to isolate the RNAs.
The purified RNA in each sample was dephosphorylated and ligated to a mixture of barcoded adapters in which each adapter had a unique barcode identifier and Illumina sequencing libraries were generated according to our Massively Multiplexed RNA Sequencing method.

tag: binding site

value: SAFA

tag: gender

value: male


title: DKC negative control

value: DKC negative control


title: hnrnpK positive CLIP

value: hnrnpK


title: Knockdown_of_FBgn0001990_wek_using_DRSC03561_replicate1

source_name: KO of FBgn0001990 wek using DRSC03561

value: wek


title: Ecoli_DMS_vivo

description: rRNA-depleted RNA

organism: Escherichia coli

value: 8% DMS

value: In vivo, 37°C, 5min


title: Ecoli_DMS_vitro_K0

description: rRNA-depleted RNA

value: 0mM K+, 37°C, 5min


title: Knockdown_of_FBgn0262937_Rabex-5_using_DRSC08628_replicate1

source_name: KO of FBgn0262937 Rabex-5 using DRSC08628


title: Ecoli_DMS_vitro_K150

description: rRNA-depleted RNA


title: Ecoli_untreated_Na

description: rRNA-depleted RNA

value: 150mM Na+


title: Knockdown_of_FBgn0024371_E2f2_using_DRSC03320_replicate1

source_name: KO of FBgn0024371 E2f2 using DRSC03320


title: Knockdown_of_FBgn0035849_ERR_using_DRSC10840_replicate1

source_name: KO of FBgn0035849 ERR using DRSC10840

value: ERR


title: Knockdown_of_FBgn0001179_hay_using_DRSC11354_replicate1

source_name: KO of FBgn0001179 hay using DRSC11354

value: hay


title: Knockdown_of_FBgn0032475_Sfmbt_using_DRSC02552_replicate1

source_name: KO of FBgn0032475 Sfmbt using DRSC02552

value: Sfmbt


title: Knockdown_of_FBgn0043364_cbt_using_DRSC00655_replicate1

source_name: KO of FBgn0043364 cbt using DRSC00655

value: cbt


title: Knockdown_of_FBgn0000541_E[bx]_using_DRSC08583_replicate1

source_name: KO of FBgn0000541 E[bx] using DRSC08583

value: E[bx]


title: Knockdown_of_FBgn0022238_lolal_using_DRSC06948_replicate1

source_name: KO of FBgn0022238 lolal using DRSC06948

value: lolal


title: Knockdown_of_FBgn0025185_az2_using_DRSC07580_replicate1

source_name: KO of FBgn0025185 az2 using DRSC07580


title: Knockdown_of_FBgn0034878_pita_using_DRSC04435_replicate1

source_name: KO of FBgn0034878 pita using DRSC04435

value: pita


title: Knockdown_of_FBgn0267978_ap_using_DRSC04917_replicate1

source_name: KO of FBgn0267978 ap using DRSC04917

value: ap


title: Knockdown_of_FBgn0033185_CG1603_using_DRSC06602_replicate1

source_name: KO of FBgn0033185 CG1603 using DRSC06602


title: Knockdown_of_FBgn0015664_Dref_using_DRSC03319_replicate1

source_name: KO of FBgn0015664 Dref using DRSC03319

value: Dref


title: Knockdown_of_FBgn0001185_her_using_DRSC03543_replicate1

source_name: KO of FBgn0001185 her using DRSC03543

value: her


title: Knockdown_of_FBgn0032817_CG10631_using_DRSC02081_replicate1

source_name: KO of FBgn0032817 CG10631 using DRSC02081


title: Knockdown_of_FBgn0010280_Taf4_using_DRSC11297_replicate1

source_name: KO of FBgn0010280 Taf4 using DRSC11297


title: Knockdown_of_FBgn0265574_Cdc5_using_DRSC08577_replicate1

source_name: KO of FBgn0265574 Cdc5 using DRSC08577


title: Knockdown_of_FBgn0034114_CG4282_using_DRSC06865_replicate1

source_name: KO of FBgn0034114 CG4282 using DRSC06865


title: Knockdown_of_FBgn0000546_EcR_using_DRSC04910_replicate1

source_name: KO of FBgn0000546 EcR using DRSC04910

value: EcR


title: Knockdown_of_FBgn0022764_Sin3A_using_DRSC07552_replicate1

source_name: KO of FBgn0022764 Sin3A using DRSC07552


title: Knockdown_of_FBgn0041205_key_using_DRSC04285_replicate1

source_name: KO of FBgn0041205 key using DRSC04285

value: key


title: Ecoli_untreated_K

description: rRNA-depleted RNA


title: Knockdown_of_FBgn0032815_CG10462_using_DRSC02058_replicate1

source_name: KO of FBgn0032815 CG10462 using DRSC02058


title: Knockdown_of_FBgn0036522_CG7372_using_DRSC10827_replicate1

source_name: KO of FBgn0036522 CG7372 using DRSC10827


title: Knockdown_of_FBgn0261278_grp_using_DRSC03541_replicate1

source_name: KO of FBgn0261278 grp using DRSC03541

value: grp


title: Knockdown_of_FBgn0031597_CG17612_using_DRSC00505_replicate1

source_name: KO of FBgn0031597 CG17612 using DRSC00505


title: Knockdown_of_FBgn0032512_CG9305_using_DRSC03192_replicate1

source_name: KO of FBgn0032512 CG9305 using DRSC03192


title: Knockdown_of_FBgn0036423_CG3919_using_DRSC10389_replicate1

source_name: KO of FBgn0036423 CG3919 using DRSC10389


title: Knockdown_of_FBgn0020388_Gcn5_using_DRSC11248_replicate1

source_name: KO of FBgn0020388 Gcn5 using DRSC11248


title: Knockdown_of_FBgn0034217_Lhr_using_DRSC06759_replicate1

source_name: KO of FBgn0034217 Lhr using DRSC06759

value: Lhr


title: Knockdown_of_FBgn0035024_CG11414_using_DRSC04110_replicate1

source_name: KO of FBgn0035024 CG11414 using DRSC04110


title: Knockdown_of_FBgn0261850_Xpd_using_DRSC04666_replicate1

source_name: KO of FBgn0261850 Xpd using DRSC04666

value: Xpd


title: Knockdown_of_FBgn0267792_rgr_using_DRSC06487_replicate1

source_name: KO of FBgn0267792 rgr using DRSC06487

value: rgr


title: Knockdown_of_FBgn0031759_lid_using_DRSC03133_replicate1

source_name: KO of FBgn0031759 lid using DRSC03133

value: lid


title: Knockdown_of_FBgn0031573_CG3407_using_DRSC00603_replicate1

source_name: KO of FBgn0031573 CG3407 using DRSC00603


title: Knockdown_of_FBgn0015391_glu_using_DRSC03539_replicate1

source_name: KO of FBgn0015391 glu using DRSC03539

value: glu


title: Knockdown_of_FBgn0031610_CG15436_using_DRSC00451_replicate1

source_name: KO of FBgn0031610 CG15436 using DRSC00451


title: Knockdown_of_FBgn0036004_Jarid2_using_DRSC10372_replicate1

source_name: KO of FBgn0036004 Jarid2 using DRSC10372


title: Knockdown_of_FBgn0015371_chn_using_DRSC06086_replicate1

source_name: KO of FBgn0015371 chn using DRSC06086

value: chn


title: Knockdown_of_FBgn0035213_CG2199_using_DRSC08558_replicate1

source_name: KO of FBgn0035213 CG2199 using DRSC08558


title: Knockdown_of_FBgn0001291_Jra_using_DRSC07447_replicate1

source_name: KO of FBgn0001291 Jra using DRSC07447

value: Jra


title: Knockdown_of_FBgn0022935_D19A_using_DRSC11133_replicate1

source_name: KO of FBgn0022935 D19A using DRSC11133


title: Knockdown_of_FBgn0033569_CG12942_using_DRSC06253_replicate1

source_name: KO of FBgn0033569 CG12942 using DRSC06253


title: Knockdown_of_FBgn0013764_Chi_using_DRSC04602_replicate1

source_name: KO of FBgn0013764 Chi using DRSC04602

value: Chi


title: Knockdown_of_FBgn0034975_enok_using_DRSC04096_replicate1

source_name: KO of FBgn0034975 enok using DRSC04096

value: enok


title: Knockdown_of_FBgn0011656_Mef2_using_DRSC07468_replicate1

source_name: KO of FBgn0011656 Mef2 using DRSC07468


title: Knockdown_of_FBgn0003963_ush_using_DRSC00843_replicate1

source_name: KO of FBgn0003963 ush using DRSC00843

value: ush


title: Knockdown_of_FBgn0010422_TfIIS_using_DRSC03455_replicate1

source_name: KO of FBgn0010422 TfIIS using DRSC03455

value: TfIIS


title: Knockdown_of_FBgn0035997_phol_using_DRSC10367_replicate1

source_name: KO of FBgn0035997 phol using DRSC10367

value: phol


title: Knockdown_of_FBgn0031391_CG11723_using_DRSC00324_replicate1

source_name: KO of FBgn0031391 CG11723 using DRSC00324


title: Knockdown_of_FBgn0004396_CrebA_using_DRSC11122_replicate1

source_name: KO of FBgn0004396 CrebA using DRSC11122

value: CrebA


title: Knockdown_of_FBgn0035518_CG15011_using_DRSC08464_replicate1

source_name: KO of FBgn0035518 CG15011 using DRSC08464


title: Knockdown_of_FBgn0030316_CG11695_using_DRSC33720_replicate2

source_name: KO of FBgn0030316 CG11695 using DRSC33720


title: Knockdown_of_FBgn0032814_CG10366_using_DRSC02046_replicate1

source_name: KO of FBgn0032814 CG10366 using DRSC02046


title: Knockdown_of_FBgn0024975_CG2712_using_DRSC35047_replicate2

source_name: KO of FBgn0024975 CG2712 using DRSC35047


title: Knockdown_of_FBgn0265298_SC35_using_DRSC27081_replicate2

source_name: KO of FBgn0265298 SC35 using DRSC27081


title: Knockdown_of_FBgn0034570_CG10543_using_DRSC04081_replicate2

source_name: KO of FBgn0034570 CG10543 using DRSC04081


title: Knockdown_of_FBgn0034534_maf-S_using_DRSC35830_replicate2

source_name: KO of FBgn0034534 maf-S using DRSC35830

value: maf-S


title: Knockdown_of_FBgn0035993_Nf-YA_using_DRSC31581_replicate2

source_name: KO of FBgn0035993 Nf-YA using DRSC31581

value: Nf-YA


title: Knockdown_of_FBgn0000054_Adf1_using_DRSC30750_replicate2

source_name: KO of FBgn0000054 Adf1 using DRSC30750


title: Knockdown_of_FBgn0038551_CG7357_using_DRSC34531_replicate2

source_name: KO of FBgn0038551 CG7357 using DRSC34531


title: Knockdown_of_FBgn0003607_Su[var]205_using_DRSC37257_replicate2

source_name: KO of FBgn0003607 Su[var]205 using DRSC37257


title: Knockdown_of_FBgn0029711_Usf_using_DRSC18129_replicate2

source_name: KO of FBgn0029711 Usf using DRSC18129

value: Usf


title: Knockdown_of_FBgn0003042_Pc_using_DRSC32757_replicate2

source_name: KO of FBgn0003042 Pc using DRSC32757

value: Pc


title: Knockdown_of_FBgn0026080_Tip60_using_DRSC31333_replicate2

source_name: KO of FBgn0026080 Tip60 using DRSC31333


title: Knockdown_of_FBgn0034425_CG11906_using_DRSC33744_replicate2

source_name: KO of FBgn0034425 CG11906 using DRSC33744


title: Knockdown_of_FBgn0036248_ssp_using_DRSC34498_replicate2

source_name: KO of FBgn0036248 ssp using DRSC34498

value: ssp


title: Knockdown_of_FBgn0032016_CG7818_using_DRSC03073_replicate1

source_name: KO of FBgn0032016 CG7818 using DRSC03073


title: Knockdown_of_FBgn0011715_Snr1_using_DRSC32770_replicate2

source_name: KO of FBgn0011715 Snr1 using DRSC32770


title: Knockdown_of_FBgn0040918_schlank_using_DRSC40082_replicate2

source_name: KO of FBgn0040918 schlank using DRSC40082

value: schlank


title: Knockdown_of_FBgn0011655_Med_using_DRSC31858_replicate2

source_name: KO of FBgn0011655 Med using DRSC31858

value: Med


title: Knockdown_of_FBgn0004855_RpII15_using_DRSC31867_replicate2

source_name: KO of FBgn0004855 RpII15 using DRSC31867


title: Knockdown_of_FBgn0022893_Df31_using_DRSC22163_replicate2

source_name: KO of FBgn0022893 Df31 using DRSC22163


title: Knockdown_of_FBgn0028647_CG11902_using_DRSC14434_replicate2

source_name: KO of FBgn0028647 CG11902 using DRSC14434


title: Knockdown_of_FBgn0004597_CycC_using_DRSC36640_replicate2

source_name: KO of FBgn0004597 CycC using DRSC36640

value: CycC


title: Knockdown_of_FBgn0000286_Cf2_using_DRSC00744_replicate2

source_name: KO of FBgn0000286 Cf2 using DRSC00744


title: Knockdown_of_FBgn0263048_CG43343_using_DRSC37196_replicate2

source_name: KO of FBgn0263048 CG43343 using DRSC37196


title: Knockdown_of_FBgn0022893_Df31_using_DRSC35687_replicate2

source_name: KO of FBgn0022893 Df31 using DRSC35687


title: Knockdown_of_FBgn0022238_lolal_using_DRSC32751_replicate2

source_name: KO of FBgn0022238 lolal using DRSC32751

value: lolal


title: Knockdown_of_FBgn0033233_Kdm4A_using_DRSC06586_replicate1

source_name: KO of FBgn0033233 Kdm4A using DRSC06586


title: Knockdown_of_FBgn0037466_CG1965_using_DRSC34371_replicate2

source_name: KO of FBgn0037466 CG1965 using DRSC34371


title: Knockdown_of_FBgn0003687_Tbp_using_DRSC33210_replicate2

source_name: KO of FBgn0003687 Tbp using DRSC33210

value: Tbp


title: Knockdown_of_FBgn0037359_MED27_using_DRSC31307_replicate2

source_name: KO of FBgn0037359 MED27 using DRSC31307


title: HeLa_untreated_Na

description: polyA-selected RNA

source_name: HeLa

extract_protocol:
Cells were lyzed in TRI Reagent and total RNA extracted as instructed.
The DMS-seq protocol (Rouskin et al. 2014) was adapted to detect RT stops in unmodified RNA. Poly(A)-selected RNA was denatured at 95°C for 2 minutes. 1X RNA-fragmentation reagent (Ambion) was added and mixed at 95°C for additional 1 minute before 20 mM EDTA was added to the mixture to stop the fragmentation. After ethanol precipitation, RNA fragments were dephosphorylated at their 3′ ends using T4 polynucleotide kinase (New England BioLabs). 60−80 nt RNA fragments were gel-purified and ligated to a pre-adenylated 3′ DNA adapter (AppTCGTATGCCGTCTTCTGCTTGddC). Products of the expected size (82−102 nt) were gel-purified and resuspended in 6 µl water. For reverse transcription, 1 µl 0.2 M Tris-Cl (pH 7.5), 1 µl 1.5 M KCl (or NaCl or LiCl), 0.5 µl 60 mM MgCl2, 0.5 µl 10 mM dNTP mix and 0.5 µl 1 µM 5′-radiolabeled primer (32p-NNNNNNGATCGTCGGACTGTAGAACTCTGAACCTGTCG/iSp18/CAAGCAGAAGACGGCATACG, in which N is any nucleotide, and iSp18 is an 18-atom hexa-ethyleneglycol spacer, IDT) were added to the RNA template. The mixture was incubated at 80°C for 2 minutes then cooled down to 42°C and incubated for additional 2 minutes before adding 100 U SuperScript III reverse transcriptase (Invitrogen). After incubation at 42°C for 10 minutes, the reaction was stopped with addition of 1 µl 1 M NaOH, and the mixture was heated at 98°C for 15 minutes to hydrolyze the RNA. cDNAs from extension that stalled after addition of 20−45 nt were separated from primers and full-length cDNAs on a 10% urea gel, eluted and precipitated. Purified cDNA fragments were circularized using 50 U CircLigase (Epicentre) at 60°C for 4 hours before inactivation at 80°C for 10 minutes. Circularized cDNAs were amplified using a 5′ indexed primer (AATGATACGGCGACCACCGACAGGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACxxxxxxATCCGACAGGTTCAGAGTTCTACAGTCCGA, in which xxxxxx is the multiplexing index), a common 3′ primer (CAAGCAGAAGACGGCATACGA), and Platinum Taq DNA Polymerase High Fidelity (Invitrogen) for 10–13 cycles of PCR. Libraries were purified on an 8% formamide gel and sequenced on a HiSeq 2000 sequencing machine (Illumina; 40 cycles, single-end mode).

value: HeLa

value: 150mM Na+


title: Knockdown_of_FBgn0004050_z_using_DRSC40820_replicate2

source_name: KO of FBgn0004050 z using DRSC40820

value: z


title: HeLa_untreated_K

description: polyA-selected RNA


title: HEK293T_untreated_Na

description: polyA-selected RNA


title: Knockdown_of_FBgnNA_LacZ_using_DRSCNA_replicate2 [Plate10-2_F3]

source_name: KO of FBgnNA LacZ using DRSCNA

value: FBgnNA

value: LacZ


title: Knockdown_of_FBgn0003512_Sry-delta_using_DRSC16869_replicate2

source_name: KO of FBgn0003512 Sry-delta using DRSC16869

value: Sry-delta


title: Knockdown_of_FBgn0265276_l[3]neo38_using_DRSC14946_replicate2

source_name: KO of FBgn0265276 l[3]neo38 using DRSC14946


title: Knockdown_of_FBgn0022724_Taf8_using_DRSC33209_replicate2

source_name: KO of FBgn0022724 Taf8 using DRSC33209


title: Knockdown_of_FBgn0010328_woc_using_DRSC36479_replicate2

source_name: KO of FBgn0010328 woc using DRSC36479

value: woc


title: Knockdown_of_FBgn0029905_Nf-YC_using_DRSC31731_replicate2

source_name: KO of FBgn0029905 Nf-YC using DRSC31731

value: Nf-YC


title: Knockdown_of_FBgn0003507_srp_using_DRSC34303_replicate2

source_name: KO of FBgn0003507 srp using DRSC34303

value: srp


title: Knockdown_of_FBgn0016917_Stat92E_using_DRSC32774_replicate2

source_name: KO of FBgn0016917 Stat92E using DRSC32774


title: Knockdown_of_FBgn0028683_spt4_using_DRSC41571_replicate2

source_name: KO of FBgn0028683 spt4 using DRSC41571


title: Knockdown_of_FBgn0261278_grp_using_DRSC40694_replicate2

source_name: KO of FBgn0261278 grp using DRSC40694

value: grp


title: Knockdown_of_FBgn0024321_NK7.1_using_DRSC16755_replicate2

source_name: KO of FBgn0024321 NK7.1 using DRSC16755


title: Knockdown_of_FBgn0265574_Cdc5_using_DRSC31796_replicate2

source_name: KO of FBgn0265574 Cdc5 using DRSC31796


title: Knockdown_of_FBgn0038767_trem_using_DRSC35325_replicate2

source_name: KO of FBgn0038767 trem using DRSC35325

value: trem


title: Knockdown_of_FBgn0036395_CG17361_using_DRSC10266_replicate2

source_name: KO of FBgn0036395 CG17361 using DRSC10266


title: Knockdown_of_FBgn0000618_e[y]2_using_DRSC36363_replicate2

source_name: KO of FBgn0000618 e[y]2 using DRSC36363


title: Knockdown_of_FBgn0003507_srp_using_DRSC34304_replicate2

source_name: KO of FBgn0003507 srp using DRSC34304


title: Knockdown_of_FBgn0000097_aop_using_DRSC32788_replicate2

source_name: KO of FBgn0000097 aop using DRSC32788

value: aop


title: Knockdown_of_FBgn0010278_Ssrp_using_DRSC33199_replicate2

source_name: KO of FBgn0010278 Ssrp using DRSC33199

value: Ssrp


title: Knockdown_of_FBgn0004606_zfh1_using_DRSC31027_replicate2

source_name: KO of FBgn0004606 zfh1 using DRSC31027


title: HEK293T_untreated_K

description: polyA-selected RNA


title: Knockdown_of_FBgn0011291_Taf11_using_DRSC42501_replicate2

source_name: KO of FBgn0011291 Taf11 using DRSC42501


title: Knockdown_of_FBgn0259785_pzg_using_DRSC31702_replicate2

source_name: KO of FBgn0259785 pzg using DRSC31702

value: pzg


title: Knockdown_of_FBgn0024807_DIP1_using_DRSC20818_replicate2

source_name: KO of FBgn0024807 DIP1 using DRSC20818


title: Knockdown_of_FBgn0029504_CHES-1-like_using_DRSC35636_replicate2

source_name: KO of FBgn0029504 CHES-1-like using DRSC35636


title: Knockdown_of_FBgn0086350_tef_using_DRSC07301_replicate2

source_name: KO of FBgn0086350 tef using DRSC07301

value: tef


title: Knockdown_of_FBgn0052133_ptip_using_DRSC11048_replicate2

source_name: KO of FBgn0052133 ptip using DRSC11048

value: ptip


title: Knockdown_of_FBgn0021872_Xbp1_using_DRSC40918_replicate2

source_name: KO of FBgn0021872 Xbp1 using DRSC40918


title: Knockdown_of_FBgn0001978_stc_using_DRSC40850_replicate2

source_name: KO of FBgn0001978 stc using DRSC40850

value: stc


title: Knockdown_of_FBgn0037555_Ada2b_using_DRSC31319_replicate2

source_name: KO of FBgn0037555 Ada2b using DRSC31319


title: Knockdown_of_FBgn0003964_usp_using_DRSC36079_replicate2

source_name: KO of FBgn0003964 usp using DRSC36079

value: usp


title: Knockdown_of_FBgn0086908_egg_using_DRSC35080_replicate2

source_name: KO of FBgn0086908 egg using DRSC35080

value: egg


title: Knockdown_of_FBgn0278608_Dsp1_using_DRSC34259_replicate2

source_name: KO of FBgn0278608 Dsp1 using DRSC34259


title: Knockdown_of_FBgn0037262_MED31_using_DRSC33069_replicate2

source_name: KO of FBgn0037262 MED31 using DRSC33069


title: Knockdown_of_FBgn0015240_Hr96_using_DRSC41040_replicate2

source_name: KO of FBgn0015240 Hr96 using DRSC41040


title: Knockdown_of_FBgn0026869_Thd1_using_DRSC38683_replicate2

source_name: KO of FBgn0026869 Thd1 using DRSC38683


title: Knockdown_of_FBgn0041092_tai_using_DRSC31682_replicate2

source_name: KO of FBgn0041092 tai using DRSC31682

value: tai


title: Knockdown_of_FBgn0265784_CrebB_using_DRSC20232_replicate2

source_name: KO of FBgn0265784 CrebB using DRSC20232

value: CrebB


title: Knockdown_of_FBgn0039218_Rpb10_using_DRSC30955_replicate2

source_name: KO of FBgn0039218 Rpb10 using DRSC30955


title: Knockdown_of_FBgn0001276_ix_using_DRSC06325_replicate2

source_name: KO of FBgn0001276 ix using DRSC06325

value: ix


title: Knockdown_of_FBgn0025463_Bap60_using_DRSC32656_replicate2

source_name: KO of FBgn0025463 Bap60 using DRSC32656


title: Knockdown_of_FBgn0013531_MED20_using_DRSC33063_replicate2

source_name: KO of FBgn0013531 MED20 using DRSC33063


title: Knockdown_of_FBgn0004198_ct_using_DRSC40438_replicate2

source_name: KO of FBgn0004198 ct using DRSC40438

value: ct


title: Knockdown_of_FBgn0040339_MED22_using_DRSC35840_replicate2

source_name: KO of FBgn0040339 MED22 using DRSC35840


title: Knockdown_of_FBgn0028683_spt4_using_DRSC07696_replicate2

source_name: KO of FBgn0028683 spt4 using DRSC07696


title: Knockdown_of_FBgn0040305_MTF-1_using_DRSC31967_replicate2

source_name: KO of FBgn0040305 MTF-1 using DRSC31967


title: Knockdown_of_FBgn0034012_Hr51_using_DRSC30770_replicate2

source_name: KO of FBgn0034012 Hr51 using DRSC30770


title: Knockdown_of_FBgn0051612_CG31612_using_DRSC03697_replicate2

source_name: KO of FBgn0051612 CG31612 using DRSC03697


title: Knockdown_of_FBgn0033185_CG1603_using_DRSC34162_replicate2

source_name: KO of FBgn0033185 CG1603 using DRSC34162


title: Knockdown_of_FBgn0010282_TfIIFalpha_using_DRSC38961_replicate2

source_name: KO of FBgn0010282 TfIIFalpha using DRSC38961

value: TfIIFalpha


title: Knockdown_of_FBgn0000568_Eip75B_using_DRSC31610_replicate2

source_name: KO of FBgn0000568 Eip75B using DRSC31610


title: Knockdown_of_FBgn0033491_CG18011_using_DRSC34991_replicate2

source_name: KO of FBgn0033491 CG18011 using DRSC34991


title: Knockdown_of_FBgn0038741_CG17186_using_DRSC27612_replicate2

source_name: KO of FBgn0038741 CG17186 using DRSC27612


title: Knockdown_of_FBgn0052767_CG32767_using_DRSC18386_replicate2

source_name: KO of FBgn0052767 CG32767 using DRSC18386


title: Knockdown_of_FBgn0036581_MED10_using_DRSC35839_replicate2

source_name: KO of FBgn0036581 MED10 using DRSC35839


title: Knockdown_of_FBgn0053213_CG33213_using_DRSC40340_replicate2

source_name: KO of FBgn0053213 CG33213 using DRSC40340


title: Knockdown_of_FBgn0033458_CG18446_using_DRSC37446_replicate2

source_name: KO of FBgn0033458 CG18446 using DRSC37446


title: Knockdown_of_FBgn0005660_Ets21C_using_DRSC37546_replicate2

source_name: KO of FBgn0005660 Ets21C using DRSC37546


title: Knockdown_of_FBgn0261641_CG42724_using_DRSC25154_replicate2

source_name: KO of FBgn0261641 CG42724 using DRSC25154


title: Yeast_DMS_vitro_K10

description: polyA-selected RNA

organism: Saccharomyces cerevisiae

source_name: Budding yeast

extract_protocol:
Cells were stored in RNAlater at -80°C. Total RNA was extracted with hot acid phenol.
The DMS-seq protocol (Rouskin et al. 2014) was adapted to detect RT stops in unmodified RNA. Poly(A)-selected RNA was denatured at 95°C for 2 minutes. 1X RNA-fragmentation reagent (Ambion) was added and mixed at 95°C for additional 1 minute before 20 mM EDTA was added to the mixture to stop the fragmentation. After ethanol precipitation, RNA fragments were dephosphorylated at their 3′ ends using T4 polynucleotide kinase (New England BioLabs). 60−80 nt RNA fragments were gel-purified and ligated to a pre-adenylated 3′ DNA adapter (AppTCGTATGCCGTCTTCTGCTTGddC). Products of the expected size (82−102 nt) were gel-purified and resuspended in 6 µl water. For reverse transcription, 1 µl 0.2 M Tris-Cl (pH 7.5), 1 µl 1.5 M KCl (or NaCl or LiCl), 0.5 µl 60 mM MgCl2, 0.5 µl 10 mM dNTP mix and 0.5 µl 1 µM 5′-radiolabeled primer (32p-NNNNNNGATCGTCGGACTGTAGAACTCTGAACCTGTCG/iSp18/CAAGCAGAAGACGGCATACG, in which N is any nucleotide, and iSp18 is an 18-atom hexa-ethyleneglycol spacer, IDT) were added to the RNA template. The mixture was incubated at 80°C for 2 minutes then cooled down to 42°C and incubated for additional 2 minutes before adding 100 U SuperScript III reverse transcriptase (Invitrogen). After incubation at 42°C for 10 minutes, the reaction was stopped with addition of 1 µl 1 M NaOH, and the mixture was heated at 98°C for 15 minutes to hydrolyze the RNA. cDNAs from extension that stalled after addition of 20−45 nt were separated from primers and full-length cDNAs on a 10% urea gel, eluted and precipitated. Purified cDNA fragments were circularized using 50 U CircLigase (Epicentre) at 60°C for 4 hours before inactivation at 80°C for 10 minutes. Circularized cDNAs were amplified using a 5′ indexed primer (AATGATACGGCGACCACCGACAGGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACxxxxxxATCCGACAGGTTCAGAGTTCTACAGTCCGA, in which xxxxxx is the multiplexing index), a common 3′ primer (CAAGCAGAAGACGGCATACGA), and Platinum Taq DNA Polymerase High Fidelity (Invitrogen) for 10–13 cycles of PCR. Libraries were purified on an 8% formamide gel and sequenced on a HiSeq 2000 sequencing machine (Illumina; 40 cycles, single-end mode).

value: 8% DMS

value: 0mM K+, 30°C, 5min


title: Knockdown_of_FBgn0086908_egg_using_DRSC04119_replicate2

source_name: KO of FBgn0086908 egg using DRSC04119


title: Yeast_DMS_vitro_K150

description: polyA-selected RNA


title: Knockdown_of_FBgn0038047_CG5245_using_DRSC29337_replicate2

source_name: KO of FBgn0038047 CG5245 using DRSC29337


title: Knockdown_of_FBgn0037672_sage_using_DRSC28200_replicate2

source_name: KO of FBgn0037672 sage using DRSC28200

value: sage


title: Yeast_untreated_Na

description: polyA-selected RNA

value: 150mM Na+


title: Yeast_DMS_vivo

description: polyA-selected RNA

value: In vivo, 30°C, 5min


title: Knockdown_of_FBgn0015903_apt_using_DRSC26181_replicate2

source_name: KO of FBgn0015903 apt using DRSC26181

value: apt


title: Yeast_untreated_K

description: polyA-selected RNA


title: Knockdown_of_FBgn0003042_Pc_using_DRSC24966_replicate2

source_name: KO of FBgn0003042 Pc using DRSC24966

value: Pc


title: Knockdown_of_FBgn0039831_CG12054_using_DRSC23137_replicate2

source_name: KO of FBgn0039831 CG12054 using DRSC23137


title: Knockdown_of_FBgn0032202_CG18619_using_DRSC40331_replicate2

source_name: KO of FBgn0032202 CG18619 using DRSC40331


title: Knockdown_of_FBgn0037109_MED1_using_DRSC35838_replicate2

source_name: KO of FBgn0037109 MED1 using DRSC35838


title: Knockdown_of_FBgn0013799_Deaf1_using_DRSC34905_replicate2

source_name: KO of FBgn0013799 Deaf1 using DRSC34905


title: Knockdown_of_FBgn0004855_RpII15_using_DRSC31867_replicate1

source_name: KO of FBgn0004855 RpII15 using DRSC31867


title: Knockdown_of_FBgn0035993_Nf-YA_using_DRSC31581_replicate1

source_name: KO of FBgn0035993 Nf-YA using DRSC31581

value: Nf-YA


title: Knockdown_of_FBgn0000054_Adf1_using_DRSC30750_replicate1

source_name: KO of FBgn0000054 Adf1 using DRSC30750


title: Knockdown_of_FBgn0265298_SC35_using_DRSC27081_replicate1

source_name: KO of FBgn0265298 SC35 using DRSC27081


title: Knockdown_of_FBgn0036248_ssp_using_DRSC34498_replicate1

source_name: KO of FBgn0036248 ssp using DRSC34498

value: ssp


title: Knockdown_of_FBgn0034570_CG10543_using_DRSC04081_replicate1

source_name: KO of FBgn0034570 CG10543 using DRSC04081


title: Knockdown_of_FBgn0030316_CG11695_using_DRSC33720_replicate1

source_name: KO of FBgn0030316 CG11695 using DRSC33720


title: Knockdown_of_FBgn0024975_CG2712_using_DRSC35047_replicate1

source_name: KO of FBgn0024975 CG2712 using DRSC35047


title: Knockdown_of_FBgn0003607_Su[var]205_using_DRSC37257_replicate1

source_name: KO of FBgn0003607 Su[var]205 using DRSC37257


title: Knockdown_of_FBgn0034425_CG11906_using_DRSC33744_replicate1

source_name: KO of FBgn0034425 CG11906 using DRSC33744


title: Knockdown_of_FBgn0034534_maf-S_using_DRSC35830_replicate1

source_name: KO of FBgn0034534 maf-S using DRSC35830

value: maf-S


title: Knockdown_of_FBgn0011715_Snr1_using_DRSC32770_replicate1

source_name: KO of FBgn0011715 Snr1 using DRSC32770


title: Knockdown_of_FBgn0011655_Med_using_DRSC31858_replicate1

source_name: KO of FBgn0011655 Med using DRSC31858

value: Med


title: Knockdown_of_FBgn0040918_schlank_using_DRSC40082_replicate1

source_name: KO of FBgn0040918 schlank using DRSC40082

value: schlank


title: Knockdown_of_FBgn0028647_CG11902_using_DRSC14434_replicate1

source_name: KO of FBgn0028647 CG11902 using DRSC14434


title: Knockdown_of_FBgn0038551_CG7357_using_DRSC34531_replicate1

source_name: KO of FBgn0038551 CG7357 using DRSC34531


title: Knockdown_of_FBgn0037466_CG1965_using_DRSC34371_replicate1

source_name: KO of FBgn0037466 CG1965 using DRSC34371


title: Knockdown_of_FBgn0022893_Df31_using_DRSC22163_replicate1

source_name: KO of FBgn0022893 Df31 using DRSC22163


title: Knockdown_of_FBgn0263048_CG43343_using_DRSC37196_replicate1

source_name: KO of FBgn0263048 CG43343 using DRSC37196


title: Knockdown_of_FBgn0004597_CycC_using_DRSC36640_replicate1

source_name: KO of FBgn0004597 CycC using DRSC36640

value: CycC


title: Knockdown_of_FBgn0022893_Df31_using_DRSC35687_replicate1

source_name: KO of FBgn0022893 Df31 using DRSC35687


title: Knockdown_of_FBgn0265574_Cdc5_using_DRSC31796_replicate1

source_name: KO of FBgn0265574 Cdc5 using DRSC31796


title: Knockdown_of_FBgn0000286_Cf2_using_DRSC00744_replicate1

source_name: KO of FBgn0000286 Cf2 using DRSC00744


title: Knockdown_of_FBgn0037359_MED27_using_DRSC31307_replicate1

source_name: KO of FBgn0037359 MED27 using DRSC31307


title: Knockdown_of_FBgn0003687_Tbp_using_DRSC33210_replicate1

source_name: KO of FBgn0003687 Tbp using DRSC33210

value: Tbp


title: Knockdown_of_FBgn0003042_Pc_using_DRSC32757_replicate1

source_name: KO of FBgn0003042 Pc using DRSC32757


title: Knockdown_of_FBgn0004050_z_using_DRSC40820_replicate1

source_name: KO of FBgn0004050 z using DRSC40820

value: z


title: Knockdown_of_FBgn0022238_lolal_using_DRSC32751_replicate1

source_name: KO of FBgn0022238 lolal using DRSC32751

value: lolal


title: Knockdown_of_FBgn0029711_Usf_using_DRSC18129_replicate1

source_name: KO of FBgn0029711 Usf using DRSC18129

value: Usf


title: Knockdown_of_FBgn0026080_Tip60_using_DRSC31333_replicate1

source_name: KO of FBgn0026080 Tip60 using DRSC31333


title: Knockdown_of_FBgn0265276_l[3]neo38_using_DRSC14946_replicate1

source_name: KO of FBgn0265276 l[3]neo38 using DRSC14946


title: Knockdown_of_FBgn0022724_Taf8_using_DRSC33209_replicate1

source_name: KO of FBgn0022724 Taf8 using DRSC33209


title: Knockdown_of_FBgn0003507_srp_using_DRSC34303_replicate1

source_name: KO of FBgn0003507 srp using DRSC34303

value: srp


title: Knockdown_of_FBgn0037555_Ada2b_using_DRSC31319_replicate1

source_name: KO of FBgn0037555 Ada2b using DRSC31319


title: Knockdown_of_FBgn0010328_woc_using_DRSC36479_replicate1

source_name: KO of FBgn0010328 woc using DRSC36479

value: woc


title: Knockdown_of_FBgn0011291_Taf11_using_DRSC42501_replicate1

source_name: KO of FBgn0011291 Taf11 using DRSC42501


title: Knockdown_of_FBgn0016917_Stat92E_using_DRSC32774_replicate1

source_name: KO of FBgn0016917 Stat92E using DRSC32774


title: Knockdown_of_FBgn0028683_spt4_using_DRSC41571_replicate1

source_name: KO of FBgn0028683 spt4 using DRSC41571


title: Knockdown_of_FBgn0029504_CHES-1-like_using_DRSC35636_replicate1

source_name: KO of FBgn0029504 CHES-1-like using DRSC35636


title: Knockdown_of_FBgn0029905_Nf-YC_using_DRSC31731_replicate1

source_name: KO of FBgn0029905 Nf-YC using DRSC31731

value: Nf-YC


title: Knockdown_of_FBgn0261278_grp_using_DRSC40694_replicate1

source_name: KO of FBgn0261278 grp using DRSC40694

value: grp


title: Knockdown_of_FBgn0015240_Hr96_using_DRSC41040_replicate1

source_name: KO of FBgn0015240 Hr96 using DRSC41040


title: Knockdown_of_FBgn0036395_CG17361_using_DRSC10266_replicate1

source_name: KO of FBgn0036395 CG17361 using DRSC10266


title: Knockdown_of_FBgn0024321_NK7.1_using_DRSC16755_replicate1

source_name: KO of FBgn0024321 NK7.1 using DRSC16755


title: Knockdown_of_FBgn0000618_e[y]2_using_DRSC36363_replicate1

source_name: KO of FBgn0000618 e[y]2 using DRSC36363


title: Knockdown_of_FBgnNA_LacZ_using_DRSCNA_replicate1 [Plate10-1_F3]

source_name: KO of FBgnNA LacZ using DRSCNA

value: FBgnNA

value: LacZ


title: Knockdown_of_FBgn0038767_trem_using_DRSC35325_replicate1

source_name: KO of FBgn0038767 trem using DRSC35325

value: trem


title: Knockdown_of_FBgn0003507_srp_using_DRSC34304_replicate1

source_name: KO of FBgn0003507 srp using DRSC34304


title: Knockdown_of_FBgn0010278_Ssrp_using_DRSC33199_replicate1

source_name: KO of FBgn0010278 Ssrp using DRSC33199

value: Ssrp


title: Knockdown_of_FBgn0000097_aop_using_DRSC32788_replicate1

source_name: KO of FBgn0000097 aop using DRSC32788

value: aop


title: Knockdown_of_FBgn0259785_pzg_using_DRSC31702_replicate1

source_name: KO of FBgn0259785 pzg using DRSC31702

value: pzg


title: Knockdown_of_FBgn0052133_ptip_using_DRSC11048_replicate1

source_name: KO of FBgn0052133 ptip using DRSC11048

value: ptip


title: Knockdown_of_FBgn0003512_Sry-delta_using_DRSC16869_replicate1

source_name: KO of FBgn0003512 Sry-delta using DRSC16869

value: Sry-delta


title: Knockdown_of_FBgn0004606_zfh1_using_DRSC31027_replicate1

source_name: KO of FBgn0004606 zfh1 using DRSC31027


title: Knockdown_of_FBgn0024807_DIP1_using_DRSC20818_replicate1

source_name: KO of FBgn0024807 DIP1 using DRSC20818


title: Knockdown_of_FBgn0086350_tef_using_DRSC07301_replicate1

source_name: KO of FBgn0086350 tef using DRSC07301

value: tef


title: Knockdown_of_FBgn0003964_usp_using_DRSC36079_replicate1

source_name: KO of FBgn0003964 usp using DRSC36079

value: usp


title: Knockdown_of_FBgn0021872_Xbp1_using_DRSC40918_replicate1

source_name: KO of FBgn0021872 Xbp1 using DRSC40918


title: Knockdown_of_FBgn0086908_egg_using_DRSC35080_replicate1

source_name: KO of FBgn0086908 egg using DRSC35080

value: egg


title: Knockdown_of_FBgn0037262_MED31_using_DRSC33069_replicate1

source_name: KO of FBgn0037262 MED31 using DRSC33069


title: Knockdown_of_FBgn0025463_Bap60_using_DRSC32656_replicate1

source_name: KO of FBgn0025463 Bap60 using DRSC32656


title: Knockdown_of_FBgn0265784_CrebB_using_DRSC20232_replicate1

source_name: KO of FBgn0265784 CrebB using DRSC20232

value: CrebB


title: Knockdown_of_FBgn0001276_ix_using_DRSC06325_replicate1

source_name: KO of FBgn0001276 ix using DRSC06325

value: ix


title: Knockdown_of_FBgn0028683_spt4_using_DRSC07696_replicate1

source_name: KO of FBgn0028683 spt4 using DRSC07696


title: Knockdown_of_FBgn0040339_MED22_using_DRSC35840_replicate1

source_name: KO of FBgn0040339 MED22 using DRSC35840


title: Knockdown_of_FBgn0033185_CG1603_using_DRSC34162_replicate1

source_name: KO of FBgn0033185 CG1603 using DRSC34162


title: Knockdown_of_FBgn0041092_tai_using_DRSC31682_replicate1

source_name: KO of FBgn0041092 tai using DRSC31682

value: tai


title: Knockdown_of_FBgn0004198_ct_using_DRSC40438_replicate1

source_name: KO of FBgn0004198 ct using DRSC40438

value: ct


title: Knockdown_of_FBgn0278608_Dsp1_using_DRSC34259_replicate1

source_name: KO of FBgn0278608 Dsp1 using DRSC34259


title: Knockdown_of_FBgn0013531_MED20_using_DRSC33063_replicate1

source_name: KO of FBgn0013531 MED20 using DRSC33063


title: Knockdown_of_FBgn0001978_stc_using_DRSC40850_replicate1

source_name: KO of FBgn0001978 stc using DRSC40850

value: stc


title: Knockdown_of_FBgn0039218_Rpb10_using_DRSC30955_replicate1

source_name: KO of FBgn0039218 Rpb10 using DRSC30955


title: Knockdown_of_FBgn0036581_MED10_using_DRSC35839_replicate1

source_name: KO of FBgn0036581 MED10 using DRSC35839


title: Knockdown_of_FBgn0034012_Hr51_using_DRSC30770_replicate1

source_name: KO of FBgn0034012 Hr51 using DRSC30770


title: Knockdown_of_FBgn0086908_egg_using_DRSC04119_replicate1

source_name: KO of FBgn0086908 egg using DRSC04119


title: Knockdown_of_FBgn0010282_TfIIFalpha_using_DRSC38961_replicate1

source_name: KO of FBgn0010282 TfIIFalpha using DRSC38961

value: TfIIFalpha


title: Knockdown_of_FBgn0033491_CG18011_using_DRSC34991_replicate1

source_name: KO of FBgn0033491 CG18011 using DRSC34991


title: Knockdown_of_FBgn0053213_CG33213_using_DRSC40340_replicate1

source_name: KO of FBgn0053213 CG33213 using DRSC40340


title: Knockdown_of_FBgn0261641_CG42724_using_DRSC25154_replicate1

source_name: KO of FBgn0261641 CG42724 using DRSC25154


title: Knockdown_of_FBgn0033458_CG18446_using_DRSC37446_replicate1

source_name: KO of FBgn0033458 CG18446 using DRSC37446


title: Knockdown_of_FBgn0037672_sage_using_DRSC28200_replicate1

source_name: KO of FBgn0037672 sage using DRSC28200

value: sage


title: Knockdown_of_FBgn0000568_Eip75B_using_DRSC31610_replicate1

source_name: KO of FBgn0000568 Eip75B using DRSC31610


title: Knockdown_of_FBgn0003042_Pc_using_DRSC24966_replicate1

source_name: KO of FBgn0003042 Pc using DRSC24966

value: Pc


title: Knockdown_of_FBgn0040305_MTF-1_using_DRSC31967_replicate1

source_name: KO of FBgn0040305 MTF-1 using DRSC31967


title: Knockdown_of_FBgn0039831_CG12054_using_DRSC23137_replicate1

source_name: KO of FBgn0039831 CG12054 using DRSC23137


title: Knockdown_of_FBgn0052767_CG32767_using_DRSC18386_replicate1

source_name: KO of FBgn0052767 CG32767 using DRSC18386


title: Knockdown_of_FBgn0051612_CG31612_using_DRSC03697_replicate1

source_name: KO of FBgn0051612 CG31612 using DRSC03697


title: Knockdown_of_FBgn0032202_CG18619_using_DRSC40331_replicate1

source_name: KO of FBgn0032202 CG18619 using DRSC40331


title: Knockdown_of_FBgn0038741_CG17186_using_DRSC27612_replicate1

source_name: KO of FBgn0038741 CG17186 using DRSC27612


title: 4C-Sample_endel15-invdel24-2

city: North Bethesda

first: sandip

last: de

address: 6 center drive

department: rm 3B-331, bldg 6B

institute: NICHD/NIH

description: processed data file: 4C-Sample_endel15.invdel24-scale-mean.bedgraph

library_source: genomic

data_processing:
Library strategy: 4C-seq
Basecalls performed using CASAVA version 1.8
NGS reads were aligned to the Drosophila reference genome (release 5.22/6.02)
TDF files were generated from BAM files via IGV tools, analysis of 4C-seq data were carried out using DESeq2 software
Genome_build: release 5.22/6.02
Supplementary_files_format_and_content: igvtools package (count command) generates a binary read count density file in TDF format. DESeq2 analyzed the 4C-seq data generating BED files for vizualization.

molecule: genomic DNA

source_name: 3rd instar brains and imaginal disks

growth_protocol: All flies were grown at 25°C, 3rd instar larvae were dissected for brains and imaginal discs

extract_protocol: 4C-seq libraries were prepared from 3rd instar larval brains and disks, Chromatin was crosslinked in the presence of 2% formaldehyde. The primary restriction enzyme used was EcoRI (New England Biolabs, R0101L) and the secondary restriction enzyme was DpnII (New England Biolabs, R0543L).

tag: genotype

value: ry- invPREs-enPREs deleted

tag: tissue

value: CNS and imaginal disks

tag: developmental stage

value: 3rd instar


title: 4C-Sample_endel15-2

description: processed data file: 4C-Sample_endel15-scale-mean.bedgraph

value: ry- enPREs deleted


title: 4C-Sample_invdel24-1

description: processed data file: 4C-Sample_invdel24-scale-mean.bedgraph

value: ry- invPREs deleted


title: 4C-Sample_endel15-invdel24-1


title: 4C-Sample_invdel24-2


title: 4C-Sample_ry-2

description: processed data file: 4C-Sample_ry-scale-mean.bedgraph

value: ry- wild type


title: antiH3K27-del15-del24-2

description: processed data file: Sample_antiH3K27-del15-del24-1.sorted.bam.tdf

data_processing:
Basecalls performed using CASAVA version 1.8
NGS reads were aligned to the Drosophila reference genome (release 5.22/6.02)
TDF files were generated from BAM files via IGV tools, analysis of 4C-seq data were carried out using DESeq2 software
Genome_build: release 5.22/6.02
Supplementary_files_format_and_content: igvtools package (count command) generates a binary read count density file in TDF format. DESeq2 analyzed the 4C-seq data generating BED files for vizualization.

extract_protocol: Fixed brains and imaginal discs were dissected from 10 third instar larvae, and sonicated chromatin incubated with anti ChIP was performed with 1:100 dilutions of anti-Pho [custom made], anti-Ph (a kind gift from Donna Arndt-Jovin) antibodies and 1:200 dilutions of anti-H3K27me3 (Millipore, 17-622) antibodies.

tag: chip antibody


title: Knockdown_of_FBgn0005660_Ets21C_using_DRSC37546_replicate1

source_name: KO of FBgn0005660 Ets21C using DRSC37546


title: 4C-Sample_ry-1


title: 4C-Sample_endel15-1


title: Knockdown_of_FBgn0038047_CG5245_using_DRSC29337_replicate1

source_name: KO of FBgn0038047 CG5245 using DRSC29337


title: antiH3K27-del15-del24-1


title: antiPhLarvae-del15-del24-2

description: processed data file: Sample_antiPhLarvae-del15-del24-1.sorted.bam.tdf

value: anti-Ph


title: antiPhinv_dt_24-1-Input

description: no processed data file (input)


title: antiPhLarvae-del15-del24-1


title: antiPhinv_dt_24-2

description: processed data file: Sample_antiPhinv_dt_24-2.sorted.bam.tdf


title: Knockdown_of_FBgn0015903_apt_using_DRSC26181_replicate1

source_name: KO of FBgn0015903 apt using DRSC26181

value: apt


title: antiPhinv_dt_24-1


title: antiPhen_dt_15-1-Input

description: no processed data file (input)


title: Knockdown_of_FBgn0037109_MED1_using_DRSC35838_replicate1

source_name: KO of FBgn0037109 MED1 using DRSC35838


title: antiPhen_dt_15-2

description: processed data file: Sample_antiPhen_dt_15-1.sorted.bam.tdf


title: antiPhen_dt_15-1


title: Knockdown_of_FBgn0013799_Deaf1_using_DRSC34905_replicate1

source_name: KO of FBgn0013799 Deaf1 using DRSC34905


title: antiPhoen∆1.5-inv∆24_2

description: processed data file: Sample_antiPhoLarvae-del15-del24-2.sorted.bam.tdf

value: anti-Pho


title: mESC_DMS_vivo_PDS

description: polyA-selected RNA

source_name: mESC

value: mESC

value: 8% DMS

value: In vivo (2μM PDS), 37°C, 5min


title: mESC_NAI_vitro_K150

description: polyA-selected RNA

value: 100mM NAI

value: 150mM Na+


title: antiPhoen∆1.5-inv∆24_1


title: mESC_DMS_vivo_rep2

description: polyA-selected RNA

value: In vivo, 37°C, 5min


title: mESC_DMS_vivo_rep1

description: polyA-selected RNA


title: antiPhoinv∆24_1

description: processed data file: Sample_antiPhoinvdel24_1.sorted.bam.tdf


title: mESC_DMS_vitro_K150

description: polyA-selected RNA


title: antiPhoen∆1.5_1

description: processed data file: Sample_antiPhoendel15_2.sorted.bam.tdf


title: Synechococcus_DMS_vitro_K0

description: rRNA-depleted RNA

organism: Parasynechococcus marenigrum WH 8102

source_name: Synechococcus

value: 0mM K+, RT, 5min


title: antiPhoenen∆1.5_2


title: antiPhoinv∆24_2


title: mESC_DMS_vitro_K0

description: polyA-selected RNA

value: 0mM K+, 37°C, 5min


title: Synechococcus_DMS_vitro_K150

description: rRNA-depleted RNA

value: 150mM K+, RT, 5min


title: Synechococcus_untreated_K

description: rRNA-depleted RNA


title: mESC_untreated_Li

description: polyA-selected RNA

value: 150mM Li+


title: mESC_NAI_vivo

description: polyA-selected RNA

value: In vivo, 37°C, 15min


title: mESC_untreated_Na

description: polyA-selected RNA


title: NorHep.treatment_BS-seq

status: Public on Sep 23 2016

city: BeiJing

first: Wang

last: Yan

address: 16# LinCui Road

country: China

institute: Institute of Psychology

data_processing:
Trimmed RNA raw reads  were aligned  with TopHat 2.0.9.  Aligned bam files were assessed using cufflinks v.2.2.1(34) to generate a transcriptome assembly and to estimate the expression level (FPKM) of all detected isoforms.
Raw data from capure bisulfite sequencing were trimmed using Trimmomatic0.30(37) and aligned with BSMAP2.74, methylation ratios were extracted using python script methratio.py from the BSMAP package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample, tab-delimited text files include methylation information for each sample

source_name: normal primary liver cells

growth_protocol: HepG2 and SkHep1 cells were maintained in MEM medium (Gibco), supplemented with 2 mmol/L glutamine (Sigma-Aldrich), 10% fetal bovine serum (FBS; Gibco), 1 U/mL penicillin, and 1 μg/mL streptomycin (Gibco). NorHep cells were maintained in human hepatocyte cell culture complete medium (Celprogen). Cells were grown in a humidified atmosphere of 5% carbon dioxide at 370C.

extract_protocol:
DNA and RNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer’s protocol. One microgram of total RNA served as a template for cDNA synthesis using 20U of AMV reverse transcriptase (Roche Diagnostics), as recommended by the manufacturer.
RNA (4 µg) from SAM and SAM buffer (control) treated cells was prepared for sequencing using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, USA) following the manufacturer’s protocol.DNA (5µg) from SAM and SAM buffer (control) treated cells was used for preparation of DNA capture bisulfite sequencing library. The DNA libraries were prepared using Illumina's paired-end sequencing DNA sample preparation kit according to the manufacturer's protocol. Target DNA fragments were captured using the human SeqCap Epi CpGiant Enrichment Kit (Nimbergen, USA) according to the manufacturer's recommendations.

treatment_protocol: For S-Adenosylmethionine treatment, S-adenosylmethionine chloride (SAM), (Life Science Laboratories, Lakewood, NJ) was prepared in buffer containing 0.005M sulphuric acid and 10% ethanol. 200μm SAM or equivalent volume of buffer (control) were added to regular culture medium. Media were refreshed daily over a period of 5 days.

value: NorHep


title: mESC_untreated_K

description: polyA-selected RNA


title: mESC_DMS_vitro_95C

description: polyA-selected RNA

value: 0mM K+,  95°C, 1min


title: Skhep1.ctrl_BS-seq

source_name: hepatocellular carcinoma cell line


title: NorHep.ctrl_BS-seq


title: Skhep1.treatment_BS-seq


title: Knockdown_of_FBgn0026869_Thd1_using_DRSC38683_replicate1

source_name: KO of FBgn0026869 Thd1 using DRSC38683


title: HepG2.ctrl_BS-seq


title: NorHep.treatment.RNA-seq

tag: tag


title: NorHep.ctrl.RNA-seq


title: Skhep1.ctrl.RNA-seq


title: HepG2.ctrl.RNA-seq


title: HepG2.treatment.RNA-seq


title: Skhep1.treatment.RNA-seq


title: Synechococcus_untreated_Na

description: rRNA-depleted RNA


title: Malathion treated D. suzukii lab population rep 2

city: Athens

first: Ruchir

last: Mishra

state: GA

address: 120 Cedar St

department: Entomology

institute: University of Georgia

data_processing:
Base calling, de-multiplexing and adapter removal were performed using Illumina BaseSpace. The encoding version is Illumina 1.9
Due to high sequencing base quality at both 3’ and 5’ ends according to the FastQC output  and availability of reference genome, preprocessing steps were not performed
The 24 samples (paired-end reads, including  replicates) were independently mapped onto the D. suzukii genome (SpottedWingFlybase v.1) by using Tophat v2.0.13 with parameters -p 4 -r 105 (or -r 113 (for F10, F11 and F12 samples)) --no-novel-juncs
After the alignment, Cufflinks v2.2.1 was used to estimate the expression values of the transcripts in FPKM (Fragments Per Kilobase per Million mapped reads) with the Cuffdiff 2 default geometric normalization
Genome_build: SpottedWingFlybase v.1 downloaded from (http://spottedwingflybase.oregonstate.edu/)
Supplementary_files_format_and_content: tab-delimited text files gene_exp.diff from Cuffdiff output  containing FPKM values and differentially expressed genes

organism: Drosophila suzukii

source_name: Whole organism

extract_protocol:
Total RNA was extracted from the whole organism (D. suzukii) using TRIzol reagent (Ambion) and quantified with NanoDrop Spectrophotometer (N-  1000). KAPA Stranded mRNA-Seq Kit (KK8420) was used to create paired-end sequencing   libraries
RNA libraries were prepared for sequencing using KAPA Stranded mRNA-Seq Kit (KK8420) protocol
RNA-Seq (NGS Stranded RNA)

tag: strain

value: Lab

value: Whole organism

tag: age

value: 5-7 days old Adults

value: Wild type


title: IgG control result

city: Duarte

first: Xiaochun

last: Yu

address: 1500 E. Duarte Rd, Rm 202, Lippman-Graff Bldg

department: Internal Medicine

institute: city of hope

data_processing:
The read quality of each sample was determined by FastQC software. After prefiltering the raw data by removing sequenced adapters and low quality reads, the tags were mapped to the human genome (assembly hg19) by Bowtie software. Parameter settings were as follows: -v, 3 (reported alignments with at most 3 mismatches), -5, 3 and -3, 3 (trim3 bases from 5’ and 3’ end to remove low-quality bases). Peak detection was performed using MACS software from Galaxy browser (www.galaxy.psu.edu). Parameters settings were as follows: tag size with 25bp, band width with 300bp, P-value cutoff for peak detection was set to 1e-03. The peaks obtained from ChIP sequencing were matched to the annotated reference genome (mouse mm9) using Cisgenome 2.0
Genome_build: hg19
Supplementary_files_format_and_content: bed

source_name: HEK 293T cells

extract_protocol:
293T cells were crosslinked with formaldehyde treatment. The chromatin were isolated from 1 × 10^8 cells and fragmented to 200 to 400 bp by sonication.  .
DNA were repaired to blunt ends by T4 DNA polymerase and phosphorylated with T4 polynucleotide kinase using the END-IT kit (Epicentre). A single “A” base was added to 3’ end with Klenow. Double-stranded adaptors were ligated to the fragments with DNA ligase. Ligation products between 200 and 600 bp were gel purified on 2% agarose to remove unligated adaptors and subjected to 20 PCR cycles.Following ligation of a pair of adaptors to the repaired ends, the fragments around 160 bp to 370 bp were isolated from agarose gel.

tag: cell line

value: HEK 294T

value: IgG antibody (Abcam, #ab171870)


title: Malathion treated D. suzukii lab population rep 3


title: m_ostdl1a_S7_3

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: ostdl1a mutant, anther development stage 7 (S7), rep 3.

data_processing:
For data processing, the adapter sequences were trimmed from raw sequence reads. The small RNA sequences were further trimmed to the lengths between 18 and 34 nucleotides. RNA-seq sequences were maintained at the length after adapter trimming.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: Rice Genome Annotation Project 7.0
Supplementary_files_format_and_content: tag count file

organism: Oryza sativa

source_name: Rice spikelets

extract_protocol:
Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by TRIzol (Invitrogen) according to manufacturer's protocol.
Small RNA libraries were constructed from 1 microgram of  total RNA using Illumina Truseq small RNA sample preparation kit (RS-200-0012). RNA-seq libraries were constructed using the Illumina TruSeq RNA sample preparation kit (RS-122-2001).

value: ostdl1a mutant

value: anther development stage 7 (S7)


title: m_ostdl1a_S7_1

description: ostdl1a mutant, anther development stage 7 (S7), rep 1.


title: m_ostdl1a_S7_2

description: ostdl1a mutant, anther development stage 7 (S7), rep 2.


title: m_ostdl1a_S5_2

description: ostdl1a mutant, anther development stage 5 (S5), rep 2.

value: anther development stage 5 (S5)


title: HepG2.treatment_BS-seq


title: zeta-cypermethrin treated D. suzukii lab population rep 3

description: Control_Zeta-cypermethrin_Lab_gene_exp.diff.txt


title: m_ostdl1a_S5_3

description: ostdl1a mutant, anther development stage 5 (S5), rep 3.


title: zeta-cypermethrin treated D. suzukii lab population rep 1


title: Malathion treated D. suzukii lab population rep 1


title: zeta-cypermethrin treated D. suzukii lab population rep 2


title: Spinosad treated D. suzukii lab population rep 2


title: Spinosad treated D. suzukii lab population rep 3


title: m_ostdl1a_S5_1

description: ostdl1a mutant, anther development stage 5 (S5), rep 1.


title: mESC_NAI_vitro_K0

description: polyA-selected RNA

value: mESC

value: 100mM NAI

value: 150mM Na+


title: Spinosad treated D. suzukii lab population rep 1


title: Control (untreated) D. suzukii lab population rep3

description: Control_Zeta-cypermethrin_Lab_gene_exp.diff.txt, Control_Spinosad_Lab_gene_exp.diff.txt, Control_Malathion_Lab_gene_exp.diff.txt


title: m_ostdl1a_S3_2

description: ostdl1a mutant, anther development stage 3 (S3), rep 2.

value: anther development stage 3 (S3)


title: m_ostdl1a_S3_3

description: ostdl1a mutant, anther development stage 3 (S3), rep 3.


title: Lar_Mut_cg_2

city: Rehovot

first: Lilach

last: Gilboa

address: 234 Herzl Street,

department: Biological Regulation

country: Israel

institute: Weizmann Institute of Science

data_processing:
The data was processed using UMI-4C pipeline (https://bitbucket.org/tanaylab/umi4cpackage). With default parameters.
Processed reads were mapped with bowtie2 with the parameters:  --reorder --end-to-end.
Genome_build: dm6
Supplementary_files_format_and_content: The processed adj files are a 4 columns tab delimited table with headers: viewpoint (bait), fragment end id1 (fend1), fragment end id2 (fend2), UMI count (count)

source_name: Larva discs

extract_protocol:
5X10^6 cells used to generate the primary 3C template. Cells were collected, centrifuged at 1200rpm, the supernatant was removed and are resuspended in PBS/10% FBS. Then the cells are cross-linked with formaldehyde to final concentration of 2% for 10min. The reaction was quenched by addition of glycine to final concentration of 0.125M. The cells were centrifuged and resuspended in cold lysis buffer (50 mM Tris–HCl, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% TX-100, 1 tbl Protease inhibitor). The nuclei are extracted and resuspended in 450µl UPW. For digestion, we add 60µl DpnII buffer, 15µl 10% SDS and incubate on a Thermomixer (Eppendorf) 37c, 60 minutes. 75µl of 20% TX-100 are added and the tube is incubated again 37c, 60 minutes. The chromatin is then digested with HC DpnII (NEB R0543M) in three rounds as following: 200U for 2 hours, 200U overnight and 200U for 2 hours. An aliquot is taken from the tube and run on gel to inspect digestion efficiency. The enzyme is then inactivated by incubating 65c, 20min. Next, the chromatin is ligated with 15µl of HC T4 ligase (NEB M0202M), with 10x ligase buffer to final volume of 7mL and incubated overnight at 16c. Aliquot is taken from the sample and ran on gel to inspect ligation efficiency. The chromatin is then reverse cross-linked overnight at 65c with 30ul proteinase K (Sigma-Aldrich), and then 30ul  of RNase A are added and incubated for 45 minutes, 37c. The 3C DNA is then extracted by Ampure beads. Inverted head segments of  400 OR (wild type) or 200 cgKG000882/cg1 (mutant)  animals were fixed in 2% formaldehyde in PBS (20 min., Room Temperature). Fixed tissue was then washed twice with PBS/125mM Glycine/0.01% Triton]X]100, and a third time with PBS. Samples were  washed again with PBS/1% protease inhibitor cocktail (P8340,Sigma).Wing Imaginal discs were then dissected out and placed in an eppendorf tube. Excess fluid was removed and tissues were snap freezed in Liquid Nitrogen and stored at 80 C. To prepare DNA, discs were thawed on ice   and centrifuged at 13,000 rpm for 20 sec. Excess fluid was discarded. Discs were resuspended  in  50  ul  lysis  buffer (10  mM  Tris]HCl  pH  8.0,  10  mM  NaCl,  0.2%   Igepal CA360 (Sigma I8896)), and 10 ul/ml of protease Inhibitors (Sigma"P8340).Discs were  homogenized  with  a  plastic motorized  pestle  (3X2min) and continuation of the 4C protocol was as performed for KC cells.
5-10ug DNA in 200µl Elution Buffter (EB, 10mM Tris-HCl, pH 8) of 3C template is sonicated at 4°c using Bioruptor program: 5 cycles of 30s on, 60s off. The sonicated material is inspected by running 10µl on agarose gel to assure size distribution of 500-550 bps. The sonicated DNA is subjected to end-repair reaction - 20µl 10X end-repair buffer and 10µl end-repair mix (NEB E6050L) are added to the mix and incubated at 20°c for 30 minutes. The DNA is cleaned by x2.2 AmpureXP beads (Beckman Coulter) and eluted in 76µl EB. Two nested PCR reactions are used for UMI-4C library construction. The PCR reactions are performed in 50ul volume with the following reagents: 10ul GoTaq Flexi buffer (promga M792A), 3ul MgCl 25mM (promega A3511), 0.2mM dNTPs, 2µl 10mM bait primer (0.4mM final concentration), 2µl 10mM Illumina enrichment primer 2 (0.4mM final concentration), 1ul GoTaq (promga M3008) and 200ng UMI-4C DNA template. PCR program is 2 minutes 95°c, 20 cycles of 30s 95°c, 30s 56°c, 60s 72°c, final extension of 5min 72°c. Following the PCR reaction we clean the amplified DNA with x1 SPRI beads and use 75% of the eluate to a second PCR reaction. The second PCR reaction is identical to the first. The only difference is the use of the bait primer with the Illumina dangling adapter (As shown in figure 1B). In the second PCR reaction 15-18 cycles are used instead of 20. Then, A-tailing reaction is performed with 10µl NEBbuffer2, 4µl Klenow (NEB M0212M), and 10µl 10nM dATP. Following A-tailing, the 5’ ends of the DNA are dephosphorylated with 2µl of Alkaline Phosphatase (NEB M0290S) 50°c for 60 minutes, and the DNA is cleaned with AmpureXP beads (x2) and eluted in 67µl EB. The DNA template is ligated with 5µl 15µM Illumina indexed adapters (final concentration 0.4µM), 10µl ligase mix and 80µl 10X buffer (NEB M2200). To release the non-ligated strand of the adapter, the DNA is denatured at 95°c for 2 minutes and cleaned with SPRI beads x1.

value: Imaginal discs

tag: lineage

tag: genotype/variation

value: Mut

tag: viewpoint


title: Lar_Mut_cg_3


title: Lar_WT_3

value: WT


title: Control (untreated) D. suzukii lab population rep2


title: Lar_Mut_cg_1


title: Control (untreated) D. suzukii lab population rep1


title: Lar_WT_1


title: Lar_WT_2


title: KC_cgRNAi_EC_12_3

value: Embryonic cells

tag: conditions

value: cgRNAi EC


title: m_msp1_S7_3

description: msp1 mutant, anther development stage 7 (S7), rep 3.

value: msp1 mutant


title: Malathion treated D. suzukii field population rep 3

description: Control_Malathion_Field_gene_exp.diff.txt

value: Field

value: Whole organism

value: 5-7 days old Adults


title: KC_cgRNAi_12_3

tag: cell type

value: cgRNAi


title: KC_LacZ_E_12_3

value: LacZ EC


title: KC_cgRNAi_EC_13_2


title: m_msp1_S5_2

description: msp1 mutant, anther development stage 5 (S5), rep 2.


title: m_msp1_S7_1

description: msp1 mutant, anther development stage 7 (S7), rep 1.

value: anther development stage 7 (S7)


title: m_msp1_S5_3

description: msp1 mutant, anther development stage 5 (S5), rep 3.

value: anther development stage 5 (S5)


title: KC_LacZ_12_3

value: LacZ


title: KC_cgRNAi_13_2


title: Malathion treated D. suzukii field population rep 2

value: Wild type


title: KC_LacZ_13_2


title: Malathion treated D. suzukii field population rep 1


title: m_ostdl1a_S3_1

description: ostdl1a mutant, anther development stage 3 (S3), rep 1.

value: ostdl1a mutant


title: zeta-cypermethrin treated D. suzukii field population rep 3

description: Control_Zeta-cypermethrin_Field_gene_exp.diff.txt


title: KC_LacZ_E_5_4


title: zeta-cypermethrin treated D. suzukii field population rep 2


title: m_msp1_S5_1

description: msp1 mutant, anther development stage 5 (S5), rep 1.


title: KC_cgRNAi_5_4


title: zeta-cypermethrin treated D. suzukii field population rep 1


title: KC_cgRNAi_EC_5_4


title: KC_cgRNAi_3_4


title: KC_cgRNAi_EC_3_4


title: KC_LacZ_5_4


title: m_msp1_S3_3

description: msp1 mutant, anther development stage 3 (S3), rep 3.

value: anther development stage 3 (S3)


title: KC_LacZ_E_13_2


title: Spinosad treated D. suzukii field population rep 3

description: Control_Spinosad_Field_gene_exp.diff.txt


title: m_msp1_S3_2

description: msp1 mutant, anther development stage 3 (S3), rep 2.


title: KC_LacZ_E_3_4


title: KC_LacZ_3_4


title: m_msp1_S7_2

description: msp1 mutant, anther development stage 7 (S7), rep 2.


title: KC_cgRNAi_EC_13_1


title: KC_LacZ_13_1


title: KC_LacZ_E_13_1


title: Control (untreated) D. suzukii field population rep3

description: Control_Zeta-cypermethrin_Field_gene_exp.diff.txt, Control_Spinosad_Field_gene_exp.diff.txt, Control_Malathion_Field_gene_exp.diff.txt


title: Spinosad treated D. suzukii field population rep 1


title: KC_cgRNAi_EC_12_2


title: KC_cgRNAi_12_2


title: m_9522_S7_2

description: Wild type 9522, anther development stage 7 (S7), rep 2.

value: Wild type 9522