title: 85_2i_Zfp532

city: Cologne

first: Andreas

last: Beyer

address: Joseph-Stelzmann-Str. 26

department: CECAD

institute: University of Cologne

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11798

data_processing:
STAR (version 2.5.3) was used to align single end reads and to retrieve raw counts
STAR(version 2.5.2b) was used to align paired end reads and to retrieve raw counts
FPKM values were calculated using DeSEQ2 (version 1.20.0).
TPM values were calculated using exon sizes from gencode.vM11.primary_assembly.annotation.gtf
Genome_build: mm10
Supplementary_files_format_and_content: CSV (raw counts of single and paired end data in separate files; FPKM of single end data; TPM of paired end data)

source_name: embryonic stem cells

growth_protocol: Cells were maintained in DMEM supplemented with 15% FCS (batch tested, Biowest), 1x Penicillin-Streptomycin (Sigma), 0.1mM NEEA, 1mM sodium pyruvate, 1mM L-glutamine, 0.05mM 2-mercatpoethanol (Gibco), 10ng/mL LIF (batch tested, in-house), 1.5µM CHIRON and 0.5µM PD0325901 (ESDMEM-2i) on gelatin coated plates.

extract_protocol:
RNA was extraced with the RNeasy Mini Kit (Qiagen) according to the manufacturer`s protocol.
[1] Single end data: mRNA was isolated from 1 ug total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturer’s instructions. Final elution was done in 15ul 2x first strand cDNA synthesis buffer (NEBnext, NEB). After chemical fragmentation by incubating for 15 min at 94°C the sample was directly subjected to the workflow for strand specific RNA-Seq library preparation (Ultra Directional RNA Library Prep, NEB). For ligation custom adaptors were used 1: (Adaptor-Oligo 5'-ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT-3', Adaptor-Oligo 2: 5'-P-GAT CGG AAG AGC ACA CGT CTG AAC TCC AGT CAC-3'). After ligation, adapters were depleted by an XP bead purification (Beckman Coulter) adding beads in a ratio of 1:1, followed by an index PCR (15 cycles) using Illumina compatible index primer. After double XP beads purifications (with beads added in a ratio 1:1) libraries were quantified on a Fragment Analyzer run with a NGS Assay Kit (Agilent) and loaded on a HiSeq 3000 flowcell with 50 cycles single end seqeuncing by pooling the samples in respect of their molarity aiming at 30 mio. reads per sample.
[2] paired-end data: Illumina TruSeq mRNA stranded

treatment_protocol: Differentiation medium (N2B27) consisted of a 1:1 mixture of DMEM/F12 and Neurobasal medium supplemented with 1x B27 (Gibco), 0.5x N2 (homemade), 0.1mM NEAA, 1mM L-glutamine, 1x Penicillin-Streptomycin and 0.05mM 2-mercaptoethanol. 24h before starting differentiation, medium was changed from maintenance ESDMEM-2i medium to N2B27 medium supplemented with 3µM CHIR99201 and 1µM PD0325901 (N2B27-2i). Cells were differentiated in parallel in duplicates for 2-32 hours in unsupplemented N2B27. The undifferentiated control samples were cultured in N2B27-2i.

tag: strain

value: Zfp532 KO

tag: medium

tag: time point

value: 0 h


title: 605_N1_Zfp423

status: Public on Dec 22 2020

type: SRA

country: Germany

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12598

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: genotype

value: Zfp423 KO


title: 607_N1_Kdm6a

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12600

data_processing:
STAR (version 2.5.3) was used to align single end reads and to retrieve raw counts
STAR(version 2.5.2b) was used to align paired end reads and to retrieve raw counts
FPKM values were calculated using DeSEQ2 (version 1.24.0).
TPM values were calculated using exon sizes from gencode.vM11.primary_assembly.annotation.gtf
Genome_build: mm10
Supplementary_files_format_and_content: CSV (raw counts of single and paired end data in separate files; FPKM of single end data; TPM of paired end data)

value: Kdm6a KO


title: 111_N1_Zfp532

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11756


title: 125_N1_Zfp532

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11862


title: 99_2i_Zfp532

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11734


title: 563_2i_Zfp423

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12410


title: 604_N1_Zfp423

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12597


title: PFBS50D0.17_688_S112_R1_001

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

data_processing:
bcl files were processed into fastq files with bcl2fastq v.2.17.1.14
Fastq files were processed with the manufacturer's script generate_reference.R and pete.star.script_3.0.R where tables of feature counts were generated for each samples.
Genome_build: Human TempO-Seq® Tox+ Surrogate (S1500+) custom probe annotation
Supplementary_files_format_and_content: table of probe counts for each sample, grouped by exposure length

organism: Homo sapiens

source_name: human liver spheroids Insphero

growth_protocol: 14 day in minimal media

extract_protocol:
not extracted, tempoSeq lysis buffer used to lyse cells, which were then frozen and 2ul used for TempO-Seq library building
Assay Principle
The TempO-Seq assay utilizes a detector oligo (DO) pool specific to the RNA targets to be monitored. BioSpyder offers fixed content and custom DO pools to measure focused sets of transcripts, up to whole transcriptomes. The assay can utilize purified RNA, cell lysates, tissue lysates, or FFPE tissue lysates (FFPE kit available separately). In addition, both positive and negative control samples can be included.
Samples are annealed to a matched pair of detector oligos (DOs), with each pair targeting a single gene. The DO pool targets up to tens of thousands of RNA sequences, depending on the targeted gene content of the assay, but all share the same pair of primer binding sequences (indicated in Fig 1. by the red and yellow sections of each DO). The DOs hybridize to sequences of the targeted RNA molecule such that their respective 3’ and 5’ ends are adjacent. Each UDO has an additional target-specific sequence at their 3’ end that hybridizes to the targeted RNA.
After DO annealing, excess oligos and mis-hybridized or weakly hybridized DOs are removed by nuclease digestion, and the annealed oligos are ligated to form amplifiable templates. The ligated DOs are amplified with one pair of primers (making each PCR reaction single-plex regardless of the number of genes measured), with a different combination of sample index/tag sequences assigned to each sample. The PCR products are pooled together into a sequencing library, which is then purified and run on an Illumina NGS to count the number of ligated detector oligo sequences per sample (ThermoFisher-compatible kit under development). Because TempO-Seq includes an end-point PCR reaction, quantitation of the amplified products before library pooling is not needed. Very low concentration and negative control samples are expected to show low reads in the sequencing data.
BioSyder -TempO-Seq protocol v2.1 sept 6,2017
Human S1500, index E,F,H,G were used for indexing

treatment_protocol: PFAS replenished every 3rd day with media change

tag: chemical

value: PFBS

tag: dose(um)

tag: time point (days)


title: 695_N1_Zfp281

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12573

value: Zfp281 KO


title: PFBS50D0.17_592_S16_R1_001


title: 693_N1_Zfp281

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12572


title: PFBS50D0.17_588_S12_R1_001


title: PFDS0.2_629_S53_R1_001

value: PFDS


title: PFBS20_696_S120_R1_001


title: 562_2i_Zfp423

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12409


title: 671_2i_Zfp281

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12559


title: 670_2i_Zfp281

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12558


title: PFBS20_600_S24_R1_001


title: PFBS20_692_S116_R1_001


title: 692_N1_Usp9x

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12570

value: Usp9x KO


title: 667_2i_Usp9x

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12555


title: 668_2i_Usp9x

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12556


title: PFBS2_712_S136_R1_001


title: 691_N1_Usp9x

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12569


title: 129_N1_Usp7

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11866

value: Usp7 KO


title: 91_2i_Usp7

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11742


title: PFBS100D0.3_580_S4_R1_001


title: PFBS100D0.3_676_S100_R1_001


title: 355_N1_Tsc2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12368

value: Tsc2 KO


title: PFBS2_612_S36_R1_001


title: PFBS10_704_S128_R1_001


title: 103_2i_Usp7

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11738


title: PFBS50D0.17_684_S108_R1_001


title: 117_N1_Usp7

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11762


title: 297_2i_Tsc2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12337


title: 354_N1_Tsc2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12367


title: PFBS10_700_S124_R1_001


title: PFBS100D0.3_680_S104_R1_001


title: 296_2i_Tsc2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12336


title: PFBS1_716_S140_R1_001


title: 199_N1_Trp53

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11916

value: Trp53 KO


title: PFBS1_624_S48_R1_001


title: 198_N1_Trp53

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11915


title: PFBS1_720_S144_R1_001


title: PFBS20_596_S20_R1_001


title: 165_2i_Trp53

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11882


title: PFBS2_708_S132_R1_001


title: PFBS1_620_S44_R1_001


title: 164_2i_Trp53

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11873


title: PFBS0.2_724_S148_R1_001


title: 690_N1_Trim71

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12568

value: Trim71 KO


title: PFBS0.2_728_S152_R1_001


title: PFBS100D0.3_584_S8_R1_001


title: PFBS0.2_632_S56_R1_001


title: 666_2i_Trim71

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12554


title: PFBS0.2_628_S52_R1_001


title: PFBS0.1_732_S156_R1_001


title: PFBS0.1_640_S64_R1_001


title: 665_2i_Trim71

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12553


title: PFBS0.1_636_S60_R1_001


title: 15_2i_Tet1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11825

value: Tet1 KO


title: 52_N1_Tet1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11791


title: 41_N1_Tet1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11780


title: 9_2i_Tcf7l1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11819

value: Tcf7l1 KO


title: PFBS0.02_744_S168_R1_001


title: PFBS0.02_740_S164_R1_001


title: PFBS0.02_648_S72_R1_001


title: PFBS0.02_644_S68_R1_001


title: 8_2i_Tcf7l1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11818


title: 34_N1_Tcf7l1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11773


title: 35_N1_Tcf7l1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11774


title: 613_N1_Suz12

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12606

value: Suz12 KO


title: 570_2i_Suz12

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12401


title: 609_N1_Sulf1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12602

value: Sulf1 KO


title: 571_2i_Suz12

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12402


title: 612_N1_Suz12

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12605


title: 608_N1_Sulf1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12601


title: 689_N1_Trim71

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12567


title: 566_2i_Sulf1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12413


title: 349_N1_Ssr2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12362

value: Ssr2 KO


title: 348_N1_Ssr2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12361


title: 291_2i_Ssr2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12335


title: 567_2i_Sulf1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12414


title: 26_2i_Tet1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11836


title: 290_2i_Ssr2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12334


title: 126_N1_Smg7

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11863

value: Smg7 KO


title: 100_2i_Smg7

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11735

value: 0 h


title: 112_N1_Smg7

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11757


title: 372_N1_Smg6

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12375

value: Smg6 KO


title: 86_2i_Smg7

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11799


title: 373_N1_Smg6

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12387


title: 352_N1_Smg5

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12365

value: Smg5 KO


title: 353_N1_Smg5

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12366


title: 314_2i_Smg6

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12344


title: 195_N1_Ski

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11896

value: Ski KO


title: 294_2i_Smg5

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11989


title: 295_2i_Smg5

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11990


title: 194_N1_Ski

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11895


title: 324_N1_Rps6ka1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12351

value: Rps6ka1 KO


title: 160_2i_Ski

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11869


title: DMSO0_659_S83_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_659

value: DMSO


title: 325_N1_Rps6ka1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12352


title: DMSO0_658_S82_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_658


title: PFOS20_502_S118_R1_001

value: PFOS


title: DMSO0_657_S81_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_657


title: PFOS20_406_S22_R1_001


title: 539_2i_RC9-2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12392


title: 267_2i_Rps6ka1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11978


title: 581_N1_RC9-2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12588


title: PFOS20_402_S18_R1_001


title: 374_N1_RC9-2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12388


title: 316_2i_RC9-2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11991


title: 315_2i_Smg6

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12345


title: PFOS20_498_S114_R1_001


title: 224_N1_RC9-2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11971


title: DMSO0_660_S84_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_660


title: 190_2i_RC9-2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11891


title: PFOS2_422_S38_R1_001


title: 161_2i_Ski

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11870


title: 23_2i_RC9-2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11833


title: PFOS10_510_S126_R1_001


title: PFOS10_506_S122_R1_001


title: 124_N1_RC9-2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11861


title: 49_N1_RC9-2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11788


title: PFOS10_414_S30_R1_001


title: 266_2i_Rps6ka1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11977


title: PFOS1_526_S142_R1_001


title: PFOS10_410_S26_R1_001


title: 98_2i_RC9-2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11749


title: 317_N1_RC9-1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12346


title: PFOS2_518_S134_R1_001


title: PFOS1_430_S46_R1_001


title: PFOS1_522_S138_R1_001


title: 157_2i_RC9-1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11868


title: PFOS0.2_534_S150_R1_001


title: PFOS2_514_S130_R1_001


title: PFOS0.2_530_S146_R1_001


title: PFOS1_426_S42_R1_001


title: 259_2i_RC9-1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11972


title: 16_2i_RC9-1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11826


title: PFOS2_418_S34_R1_001


title: 84_2i_RC9-1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11797


title: 580_N1_RC9-1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12587


title: 110_N1_RC9-1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11755


title: PFOS0.1_542_S158_R1_001


title: 42_N1_RC9-1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11781


title: L54675_N1_RC9

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L54675


title: 707_N1_RC-9_2b

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12578


title: PFOS0.1_538_S154_R1_001


title: L54674_2i_RC9

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L54674


title: PFOS0.02_550_S166_R1_001


title: PFOS0.2_434_S50_R1_001


title: 693_N1_RC-9_2a

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12571


title: L54672_N1_RC9

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L54672


title: L54679_2i_RC9

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L54679


title: PFOS0.02_546_S162_R1_001


title: PFOS0.1_446_S62_R1_001


title: PFOS0.02_454_S70_R1_001


title: 669_2i_RC-9_2a

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12557


title: PFOS0.02_450_S66_R1_001


title: 683_2i_RC-9_2b

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12564


title: 209_N1_Rbpms

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11910

value: Rbpms KO


title: PFOA50D0.17_491_S107_R1_001

value: PFOA


title: 538_2i_RC9-1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12391


title: PFOA50D0.17_395_S11_R1_001


title: 175_2i_Rbpms

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11876


title: PFOS0.2_438_S54_R1_001


title: PFOA20_499_S115_R1_001


title: PFOA20_407_S23_R1_001


title: 174_2i_Rbpms

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11875


title: 208_N1_Rbpms

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11909


title: 201_N1_Rbpj

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11918

value: Rbpj KO


title: PFOA2_519_S135_R1_001


title: 200_N1_Rbpj

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11917


title: 167_2i_Rbpj

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11884


title: 664_2i_Raf1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12552

value: Raf1 KO


title: PFOA100D0.3_391_S7_R1_001


title: 688_N1_Raf1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12566


title: 24_2i_Pum1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11834

value: Pum1 KO


title: PFOA50D0.17_399_S15_R1_001


title: PFOA10_411_S27_R1_001


title: 166_2i_Rbpj

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11883


title: PFOA2_419_S35_R1_001


title: PFOA2_423_S39_R1_001


title: PFOA10_507_S123_R1_001


title: PFOA1_527_S143_R1_001


title: 341_N1_Ptpn11

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12358

value: Ptpn11 KO


title: PFOA10_415_S31_R1_001


title: 687_N1_Raf1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12565


title: 31_N1_Pum1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11841


title: 663_2i_Raf1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12551


title: PFOA2_515_S131_R1_001


title: PFOA1_523_S139_R1_001


title: PFOA10_511_S127_R1_001


title: PFOA100D0.3_487_S103_R1_001


title: 50_N1_Pum1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11789


title: PFOA100D0.3_387_S3_R1_001


title: 5_2i_Pum1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11815


title: 340_N1_Ptpn11

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12357


title: 283_2i_Ptpn11

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11984


title: PFOA1_431_S47_R1_001


title: PFOA1_427_S43_R1_001


title: PFOA20_403_S19_R1_001


title: 282_2i_Ptpn11

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11983


title: PFOA0.2_535_S151_R1_001


title: 361_N1_Pten

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12370

value: Pten KO


title: 360_N1_Pten

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12369


title: PFOA0.2_531_S147_R1_001


title: 302_2i_Pten

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12338


title: PFOA0.1_539_S155_R1_001


title: 205_N1_Prkci

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11906

value: Prkci KO


title: PFOA0.1_543_S159_R1_001


title: PFOA0.2_435_S51_R1_001


title: 303_2i_Pten

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12339


title: PFOA0.2_439_S55_R1_001


title: 221_N1_Pitpnc1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11968

value: Pitpnc1 KO


title: PFOA0.02_547_S163_R1_001


title: PFOA0.02_455_S71_R1_001


title: 220_N1_Pitpnc1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11967


title: PFOA0.02_451_S67_R1_001


title: PFOA0.1_447_S63_R1_001


title: 170_2i_Prkci

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11887


title: PFOA0.02_551_S167_R1_001


title: 171_2i_Prkci

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11888


title: PFDS50D0.17_493_S109_R1_001

value: PFDS


title: 186_2i_Pitpnc1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11903

value: 0 h


title: PFDS50D0.17_489_S105_R1_001


title: PFDS50D0.17_397_S13_R1_001


title: 83_2i_Pecam1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11796

value: Pecam1 KO


title: 123_N1_Pecam1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11860


title: PFDS50D0.17_393_S9_R1_001


title: 109_N1_Pecam1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11754


title: PFDS20_501_S117_R1_001


title: 81_2i_Nsd1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11794

value: Nsd1 KO


title: PFDS2_517_S133_R1_001


title: PFDS2_513_S129_R1_001


title: PFDS2_417_S33_R1_001


title: 187_2i_Pitpnc1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11904


title: PFDS20_401_S17_R1_001


title: 611_N1_Nmt1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12604

value: Nmt1 KO


title: 107_N1_Nsd1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11752


title: 610_N1_Nmt1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12603


title: 108_N1_Nsd1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11753


title: 568_2i_Nmt1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12415


title: 569_2i_Nmt1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12416


title: PFDS100D0.3_481_S97_R1_001


title: PFDS2_421_S37_R1_001


title: 701_N1_Nmnat2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12577

value: Nmnat2 KO


title: PFDS10_509_S125_R1_001


title: 204_N1_Prkci

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11921


title: 677_2i_Nmnat2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12563


title: 97_2i_Pecam1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11748


title: PFDS10_505_S121_R1_001


title: 676_2i_Nmnat2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12562


title: PFDS20_497_S113_R1_001


title: 20_2i_Nes

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11830

value: Nes KO


title: PFDS10_409_S25_R1_001


title: 82_2i_Nsd1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11795


title: PFDS10_413_S29_R1_001


title: PFDS100D0.3_485_S101_R1_001


title: 700_N1_Nmnat2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L13224


title: PFDS1_525_S141_R1_001


title: 45_N1_Nes

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11784


title: PFDS100D0.3_389_S5_R1_001


title: 206_N1_Ncor1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11907

value: Ncor1 KO


title: PFDS1_521_S137_R1_001


title: 173_2i_Ncor1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11874


title: PFDS100D0.3_385_S1_R1_001


title: 172_2i_Ncor1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11889


title: PFDS0.2_529_S145_R1_001


title: 46_N1_Nes

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11785


title: PFDS1_429_S45_R1_001


title: PFDS0.2_437_S53_R1_001


title: PFDS1_425_S41_R1_001


title: 19_2i_Nes

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11829


title: PFDS0.2_533_S149_R1_001


title: 561_2i_Myo10

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12400

value: Myo10 KO


title: 603_N1_Myo10

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12596


title: 602_N1_Myo10

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12595


title: 560_2i_Myo10

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12399


title: PFDS0.1_537_S153_R1_001


title: PFDS0.1_445_S61_R1_001


title: PFDS0.1_541_S157_R1_001


title: PFDS0.2_433_S49_R1_001


title: 18_2i_Myc

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11828

value: Myc KO


title: PFDS0.02_549_S165_R1_001


title: 17_2i_Myc

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11827


title: 207_N1_Ncor1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11908


title: 44_N1_Myc

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11783


title: PFDS0.1_441_S57_R1_001


title: PFDS0.02_545_S161_R1_001


title: 43_N1_Myc

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11782


title: PFDS0.02_449_S65_R1_001


title: 279_2i_Mthfd1l

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11982

value: Mthfd1l KO


title: 336_N1_Mthfd1l

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12355


title: PFBS50D0.17_496_S112_R1_001

value: PFBS


title: 80_2i_Mta3v2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11793

value: Mta3v2 KO


title: 337_N1_Mthfd1l

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12356


title: PFDS0.02_453_S69_R1_001


title: 278_2i_Mthfd1l

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11981


title: PFBS50D0.17_396_S12_R1_001


title: PFBS50D0.17_400_S16_R1_001


title: PFBS50D0.17_492_S108_R1_001


title: 106_N1_Mta3v2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11751


title: 79_2i_Mta3v2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11792


title: 105_N1_Mta3v2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11750


title: PFBS20_408_S24_R1_001


title: 51_N1_Msi2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11790

value: Msi2 KO


title: PFBS20_500_S116_R1_001


title: PFBS2_520_S136_R1_001


title: PFBS2_516_S132_R1_001


title: 12_2i_Msi2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11822


title: 25_2i_Msi2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11835


title: 38_N1_Msi2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11777


title: 121_N1_Mbd3

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11858

value: Mbd3 KO


title: 122_N1_Mbd3

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11859


title: PFBS2_420_S36_R1_001


title: PFBS100D0.3_488_S104_R1_001


title: PFBS100D0.3_484_S100_R1_001


title: 95_2i_Mbd3

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11746


title: PFBS100D0.3_392_S8_R1_001


title: 21_2i_Mapk1-het

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11831

value: Mapk1-het KO


title: 96_2i_Mbd3

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11747


title: 22_2i_Mapk1-het

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11832


title: PFBS10_512_S128_R1_001


title: 48_N1_Mapk1-het

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11787


title: 367_N1_Macf1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12374

value: Macf1 KO


title: PFBS10_416_S32_R1_001


title: 47_N1_Mapk1-het

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11786


title: PFBS10_412_S28_R1_001


title: PFBS20_404_S20_R1_001


title: PFBS2_424_S40_R1_001


title: PFBS10_508_S124_R1_001


title: 308_2i_Macf1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12342


title: 309_2i_Macf1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12343


title: 579_N1_Lmna

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12408

value: Lmna KO


title: 366_N1_Macf1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12373


title: PFBS1_524_S140_R1_001


title: PFBS1_432_S48_R1_001


title: PFBS1_528_S144_R1_001


title: 578_N1_Lmna

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12407


title: PFBS1_428_S44_R1_001


title: 536_2i_Lmna

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12389

value: 0 h


title: 537_2i_Lmna

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12390


title: PFBS100D0.3_388_S4_R1_001


title: PFBS0.2_440_S56_R1_001


title: PFBS0.2_436_S52_R1_001


title: 363_N1_Leo1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12372

value: Leo1 KO


title: PFBS0.1_544_S160_R1_001


title: 362_N1_Leo1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12371


title: 305_2i_Leo1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12341


title: PFBS0.1_540_S156_R1_001


title: PFBS0.1_448_S64_R1_001


title: 304_2i_Leo1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12340


title: PFBS0.02_456_S72_R1_001


title: PFBS0.2_536_S152_R1_001


title: PFBS0.02_548_S164_R1_001


title: 601_N1_L3mbtl3

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12594

value: L3mbtl3 KO


title: 558_2i_L3mbtl3

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12397


title: PFBS0.02_452_S68_R1_001


title: 565_2i_Kdm6a

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12412

value: Kdm6a KO


title: 600_N1_L3mbtl3

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12593


title: 223_N1_Kdm6a

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11970


title: 559_2i_L3mbtl3

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12398


title: 189_2i_Kdm6a

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11890


title: DMSO0.3_557_S173_R1_001

description:
controls for dose 100
DMSO_3e-04_557

value: DMSO


title: DMSO0.3_554_S170_R1_001

description:
controls for dose 100
DMSO_3e-04_554


title: DMSO0.3_553_S169_R1_001

description:
controls for dose 100
DMSO_3e-04_553


title: PFBS0.2_532_S148_R1_001


title: 617_N1_Jmjd1c

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12610

value: Jmjd1c KO


title: 616_N1_Jmjd1c

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12609


title: DMSO0.3_462_S78_R1_001

description:
controls for dose 100
DMSO_3e-04_462


title: DMSO0.3_461_S77_R1_001

description:
controls for dose 100
DMSO_3e-04_461


title: DMSO0.3_458_S74_R1_001

description:
controls for dose 100
DMSO_3e-04_458


title: 574_2i_Jmjd1c

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12405


title: L54677_N1_Jarid2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L54677

value: Jarid2 KO


title: DMSO0.3_457_S73_R1_001

description:
controls for dose 100
DMSO_3e-04_457


title: PFBS0.1_444_S60_R1_001


title: L54678_2i_Jarid2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L54678


title: DMSO0.3_558_S174_R1_001

description:
controls for dose 100
DMSO_3e-04_558


title: DMSO0.17_556_S172_R1_001

description:
controls for dose 50
DMSO_0.00017_556


title: L54676_N1_Jarid2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L54676


title: 213_N1_Irak3

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11960

value: Irak3 KO


title: L54673_2i_Jarid2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L54673


title: DMSO0.17_555_S171_R1_001

description:
controls for dose 50
DMSO_0.00017_555


title: 179_2i_Irak3

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11880


title: 178_2i_Irak3

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11879


title: DMSO0.17_459_S75_R1_001

description:
controls for dose 50
DMSO_0.00017_459


title: 212_N1_Irak3

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11913


title: DMSO0.17_463_S79_R1_001

description:
controls for dose 50
DMSO_0.00017_463


title: DMSO0.17_460_S76_R1_001

description:
controls for dose 50
DMSO_0.00017_460


title: DMSO0.17_464_S80_R1_001

description:
controls for dose 50
DMSO_0.00017_464


title: 202_N1_Igf2bp1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11919

value: Igf2bp1 KO


title: DMSO0_572_S188_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_572


title: 203_N1_Igf2bp1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11920


title: 169_2i_Igf2bp1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11886


title: DMSO0_566_S182_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_566


title: 168_2i_Igf2bp1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11885


title: DMSO0_567_S183_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_567


title: DMSO0_565_S181_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_565


title: DMSO0.17_560_S176_R1_001

description:
controls for dose 50
DMSO_0.00017_560


title: DMSO0_564_S180_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_564


title: DMSO0_562_S178_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_562


title: 119_N1_Hprt

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11764

value: Hprt KO


title: DMSO0_561_S177_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_561


title: 94_2i_Hprt

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11745


title: 120_N1_Hprt

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11765


title: 93_2i_Hprt

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11744


title: 323_N1_Hnrnph1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12350

value: Hnrnph1 KO


title: DMSO0_476_S92_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_476


title: 322_N1_Hnrnph1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12349


title: DMSO0_480_S96_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_480


title: DMSO0_568_S184_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_568


title: DMSO0_472_S88_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_472


title: DMSO0_469_S85_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_469


title: 265_2i_Hnrnph1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11976


title: DMSO0_468_S84_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_468


title: 575_2i_Jmjd1c

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12406


title: DMSO0_471_S87_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_471


title: 264_2i_Hnrnph1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11975


title: DMSO0_467_S83_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_467


title: 185_2i_Gtfird1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11902

value: Gtfird1 KO


title: DMSO0_466_S82_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_466


title: DMSO0_465_S81_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_465


title: 343_N1_Gabbr1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12360

value: Gabbr1 KO


title: 184_2i_Gtfird1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11901


title: 342_N1_Gabbr1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12359


title: 285_2i_Gabbr1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11986


title: 284_2i_Gabbr1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11985


title: 90_2i_Fryl

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11803

value: Fryl KO


title: 89_2i_Fryl

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11802


title: miR_saline_4105

type: RNA

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

country: USA

institute: University of Washington

hyb_protocol: The standard hybridization protocol was used as recommended by Affymterix.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

data_processing: Bioconductor software, RMA normalization log2

label: biotin

organism: Macaca nemestrina

source_name: fetal membrane tissue

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Multispecies miRNA-2_0 Arrays through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: RNA extraction was performed by the CHDD Genomics Core Laboratory followed by the manufacturer’s protocols using the GeneChip platform by Affymetrix.

tag: tissue

value: chorioamnion

tag: treatment

value: saline


title: 218_N1_Gtfird1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11965


title: 219_N1_Gtfird1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11966


title: 333_N1_Foxp1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12354

value: Foxp1 KO


title: miR_saline_M99183


title: miR_saline_M05267


title: miR_saline_5081


title: miR_gbs_M02217

value: Group B Streptococcus


title: 275_2i_Foxp1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11980

value: 0 h


title: 274_2i_Foxp1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11979


title: 351_N1_Fgfr2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12364

value: Fgfr2 KO


title: 350_N1_Fgfr2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12363


title: miR_gbs_L99192


title: miR_gbs_5096


title: miR_gbs_K94129


title: miR_gbs_A03159


title: 292_2i_Fgfr2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11987


title: miR_saline_5109


title: 293_2i_Fgfr2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11988


title: 211_N1_Fgfr1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11912

value: Fgfr1 KO


title: 116_N1_Fryl

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11761


title: 115_N1_Fryl

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11760


title: 332_N1_Foxp1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12353


title: 210_N1_Fgfr1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11911


title: 176_2i_Fgfr1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11877


title: 192_N1_Fbxw7

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11893

value: Fbxw7 KO


title: Hep_Alb_CB1R_cKO4_SD

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: A total of 600 ng Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE3 Mouse 8x60k v1 gene expression microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were rinsed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and dried by slowly removing from Wash buffer 2.

scan_protocol: Following posthybridization rinses, arrays were scanned using an Agilent SureScan microarray Scanner at 5 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw microarray hybridization intensity data were log-transformed.  Raw microarray data were log transformed to yield z-scores. The z-ratio was calculated as the difference between the observed gene z-scores for the experimental and the control comparisons, and dividing by the standard deviation associated with the distribution of these differences. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a 5% false discovery rate (FDR) threshold. The complete set was tested for gene set enrichment using parametric analysis of gene set enrichment. For each pathway z-score, a p-value was computed using JMP 6.0 software to test for the statistical significance.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low-Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were evaluated with the NanoDrop ND-1000 Spectrophotometer (Wilmington, DE).

growth_protocol: All animals were housed at the National Institute on Aging (NIA). Hepatocyte-specific CB1−/− mice (hCNR1-/-) and control animal (hCNR1+/+) littermates were developed by breeding with mice carrying the albumin-Cre gene (Alb-Cre; Jackson Laboratories, Bar Harbor, ME) to CNR1flox/flox mice.

extract_protocol: Total RNA was purified from mouse hepatocytes using using a RNeasy Mini kit (Qiagen, Valencia, CA) according to the manufacturers instructions.

value: Hepatocytes

tag: diet

value: Standard

value: CNRO Alb-Cre

tag: age

value: 12-14 weeks

tag: Sex

value: Male


title: Hep_Alb_CB1R_cKO3_SD


title: Hep_Alb_CB1R_WT4_SD

value: CNRO


title: Hep_Alb_CB1R_cKO1_SD


title: 159_2i_Fbxw7

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11741


title: Hep_Alb_CB1R_WT2_SD


title: 158_2i_Fbxw7

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11740


title: Hep_Alb_CB1R_WT1_SD


title: 127_N1_Etv5

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11864

value: Etv5 KO


title: 87_2i_Etv5

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11800


title: Hep_Alb_CB1R_cKO2_SD


title: 113_N1_Etv5

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11758


title: 101_2i_Etv5

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11736


title: Hep_Alb_CB1R_WT3_SD


title: 215_N1_Etl4

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11962

value: Etl4 KO


title: 214_N1_Etl4

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11961


title: 180_2i_Etl4

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11881


title: 181_2i_Etl4

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11898


title: CKO_Resting_rep3

city: Sendai

first: Kyoko

last: Ochiai

address: 2-1, Seiryo-machi, Aobaku

department: Biochemistry

country: Japan

institute: Tohoku University School of Medicine

description: Gene expression without differentiation stimuli

hyb_protocol: A sureprint G3 mouse GE microarray slide was used for hybridization according to the manufacturer's instructions(Agilent).

scan_protocol: Agilent scan protocol

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20101029) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Splenic B cells from B1-8hi:Sub1fl/fl-Mb1-Cre

label_protocol: Total RNA was amplified with an Amino Allyl MessageAmpII aRNA Amplification Kit (Ambion) and was labeled with indocarbocyanine through the use of a CyDye post-labeling Reactive Dye Pack (Amersham).

extract_protocol: RNA was prepared using the RNeasy Plus Micro kit (QIAGEN) following the manufacturer's recommendations. RNA quantity and quality were measured with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Splenic B cells were cultured in RPMI-1640 medium supplemented with 100 U/mL IL-2, 5 ng/mL IL-4, 1.5 ng/mL IL-5, 0.2 ng/mL CD40 ligand, 0.01 ng/mL NP-ficoll, 10% FBS 10mM HEPES, 1 mM Na-Pyruvate, 0.1 mM non-essential amino acids and penicilli/streptmycin.

value: Splenic B cells

value: Naïve

tag: genotype/variation


title: CKO_Resting_rep2


title: CKO_Activated_rep3

description: Gene expression after 72 hours upon differentiation stimuli

value: Stimulated


title: CKO_Activated_rep1


title: CKO_Activated_rep2


title: CKO_Resting_rep1


title: WT_Activated_rep1

source_name: Splenic B cells from B1-8hi:Sub1fl/fl


title: HNSCC PRAS40 knockout 6-10B cells 1

city: Changsha

first: Gangcai

last: Zhu

state: M

address: Remin Road 132

country: China

institute: The Second Xiangya Hospital, Central South University

description:
in vitro
Pras40_1

data_processing:
Illumina HiSeq platform was used for sequencing
Clean Data was obtained after data quality control steps (remove joints, remove low quality, remove N bases, etc.)
In this project, we used Hisat2 to compare filtered Clean reads to the Reference Genome.
In this study, HTSeq software was used to analyze the gene expression level of each sample, and the model was UNION.
The number of genes and the expression level of individual genes at different expression levels were counted respectively.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with gene counts and fpkm for every gene and every sample.

source_name: HNSCC  6-10B cells

growth_protocol: 6‐10B cells were cultured in RPMI1640 medium(Cytiva, USA, Cat. No. SH30027.01). All media were supplemented with 10% fetal bovine serum (ThermoFisher, USA, Cat. No.16000044), 100 IU/mL penicillin, and 100 μg/mL streptomycin at 37°C with 5% CO2 in an incubator. Cells have been checked to ensure that all in free of contamination and exponential growth so that they were used for subsequent experiments.

extract_protocol:
According to the manufacturer's protocol, total RNA extracted from knockout and wildtype cells were reverse transcripted to cDNA by All‐in‐One First‐Strand cDNA Synthesis kit (GeneCopoeia, USA).
MRNA as template, synthesised single-stranded cDNA with six bases random primers (random hexamers), then added the buffer, dNTPs and DNA polymerase I, synthesised double-stranded cDNA. Then purified double-stranded cDNA with AMPure XP beads. Purified double-stranded cDNA sequence was repaired the end, added A tail and connected joint of sequencing, and then chose fragment size with AMPure XP beads. Finally got cDNA library after PCR enrichment.

treatment_protocol: The knockout of PRAS40 in 6-10B cell lines was achieved by CRISPR/Case9 system,The PRAS40 protein expression was confirmed as being knockout by western blot.

value: PRAS40 knockout


title: HNSCC WT 6-10B cells

description:
in vitro
qb610B

value: WT


title: 544_2i_Eed

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12394

value: Eed KO

value: 0 h


title: 584_N1_Eed

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12589


title: 130_N1_Dym

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11867

value: Dym KO


title: WT_Activated_rep3


title: WT_Resting_rep3


title: WI38slow-iCas9- pooled sgRNA cells, day 14 of iCas9 induction, repeat1

city: Rehovot

first: Roni

last: Rak

address: Herzl 229

department: Animal Science

country: Israel

institute: Agriculture Research Organization

description:
WI38slow_growth_D14_rep1
processed data file: sgRNAseq_growthCompetition_allSamples.csv

library_source: genomic

data_processing:
library strategy: amplicon library
Growth competition:  SeqPrep (https://github.com/jstjohn/SeqPrep) was used to merge paired reads into a single contig, to increase sequence fidelity over regions of dual coverage. The size of each contig was then compared to the amplicon’s length. Next, the forward and reverse primers were found on each contig (allowing for 2 mismatches) and trimmed out. This step was performed for both the forward and reverse complement sequences of the contig, to account for non-directional ligation of the adaptors during library preparation. After the primers were trimmed, the contig was tested again for its length to ensure no Indels had occurred. Contigs were then compared sequentially to all sgRNAs, comparing the sequence of each contig to the sequence of each sgRNA. Any contig without a matching sgRNA within two mismatches or less was discarded. Contigs with more than a single matching sgRNA with the same reliability were also discarded due to ambiguity.
Cell cycle arrest signals:  Reads were trimmed using Cutadapt and then clustered into unique sequences using vsearch (Rognes et al., 2016). Each unique read was then aligned to the matched sgRNA sequence, allowing up to two mismatches
Genome_build: sgRNA name sgRNA sequence  ArgACG-sgRNA GATTCCAGGTTCGACTCC  ProAGG-sgRNA GGGTATGATTCTCGCTTA  LeuCAG-sgRNA GTCTAAGGCGCTGCGTTC  TrpCCA-sgRNA GCGTGTTCAAATCACGTC  GlyCCC-sgRNA GAACCCGGGTCGCAAGAA  ArgCCG-sgRNA GGATAAGGCGTCTGATTC  SerCGA-sgRNA GTTGGACTCGAAATCCAA  ProCGG-sgRNA GGGTATGATTCTCGCTTC  ThrCGT-sgRNA GACCGACGCCTTACCACT  GlyGCC-sgRNA GGGCCGGGAATCGAACCC  IleAAT-sgRNA GTGGTGCTAATAACGCCA  AsnATT-sgRNA GCAATCGGTCAGAGCGTT  LeuCAA-sgRNA GGATGGCCGAGTGGTCTA  ValTAC-sgRNA GTCTGCTTTACACGCAGA  LeuTAG-sgRNA GTCTAAGGCGCTGGATTT  IleTAT-sgRNA GTGAGTTCGAGCCTCACC  ArgTCG-sgRNA GGATAAGGCGTCTGACTT  ArgTCT-sgRNA GCGCAATGGATAGCGCAT  GluTTC-sgRNA GATTCCTGGTTTTCACCC  LysTTT-sgRNA GGGTTCAAGTCCCTGTTC
Supplementary_files_format_and_content: read count of each sgRNA in each sample

molecule: genomic DNA

source_name: WI38slow-iCas9- pooled sgRNA

growth_protocol: Growth comeptition  HeLa- iCas9 with pooled sgRNAs  cells were grown in DMEM + NEAA (Life Technologies; 10938-025) - Dulbecco’s Modified Eagle medium with 4.5mg/ml D-Glucose and Non-Essential amino acids. Supplemented with 10% FBS, 1% penicillin/ streptomycin (P/S), 1% L-Glutamine and 1% Sodium Pyruvate. The medium was supplemented with 200µg/ml Hygromycin (for iCas9 selection, Thermo Fisher; 10687010), 2µg/ml Puromycin (for sgRNA selection, Sigma-Aldrich; 58-58-2) and 1µg/ml Doxycycline (for iCas9 induction, Sigma-Aldrich; 10592-13-9).   WI38 fast and slow iCas9 with pooled sgRNAs cells were grown in in MEM-EAGLE + NEAA– Earle’s salts base with Non-Essential amino acids (Biological Industries; 01-025-1A), supplemented with 10% FBS, 1% penicillin/ streptomycin (P/S) and 1% L-Glutamine. The medium was supplemented with 200µg/ml Hygromycin (for iCas9 selection, Thermo Fisher; 10687010), 2µg/ml Puromycin (for sgRNA selection, InvivoGen; BLL-38-02A. notice that WI38 dervied cells are already resistant to Puromycine, for more information see "Materials and Methods") and 1µg/ml Doxycycline (for iCas9 induction, Sigma-Aldrich; 10592-13-9).   Upon iCas9 induction, each cell population was samples every 3-4 days, and fresh medium containing all antibiotics was replaced every two days for 12 days.  Cell cycle arrest signals  WI38 fast iCas9- p21p-mCherry- pooled sgRNA cells were grown is previously described. The medium was supplemented with 200µg/ml Hygromycin (for iCas9 selection, Thermo Fisher; 10687010), 10 µg/ml Blasticidin  and 1µg/ml Doxycycline (for iCas9 induction, Sigma-Aldrich; 10592-13-9).

extract_protocol:
PureLink genomic DNA mini kit (Invitrogene; K182000)
Growth competition:  PCR reaction was conducted using iProof master mix (X2), 10µM of each primer and 20ng of genomic DNA in a 50µl total volume reaction, for 26 cycles, Tm = 64°C. The primers used to amplify the sgRNA region were:  Forward primer- GCTTACCGTAACTTGAAAGTATTTCGATTTCTTGG  Reverse primer- CTTTTTCAAGTTGATAACGGACTAGCCTTATTTTAAC   After PCR clean-up using Wizard SV Gel and PCR Clean-Up (Promega; A9281), samples were run in 2% agarose gel to ensure that the PCR product is compose of a single amplicon in the appropriate size. Next, Illumina HiSeq 2000 libraries were prepared using the sequencing library module from (Blecher-Gonen et al., 2013). Briefly, blunt ends were repaired, Adenine bases were added to the 3' end of the fragments, barcode adapters containing a T overhang were ligated, and finally the adapted fragments were amplified. The process was repeated for each sample with a different Illumina DNA barcode for multiplexing, and then all samples were pooled in equal amounts and sequenced.   Cell cycle arrest signals:  PCR reaction was conducted using 2X KAPA HiFi HotStart ReadyMix, 10µM of each primer and 20ng of genomic DNA extracted from the samples in a 50µl total volume reaction, for 20 cycles, Tm = 58°C. We used shifted primers to increase library complexity. PCR products were purified with SPRI-beads using left-side size selection protocol in which the PCR product and beads were mixed at 1:1.5 ratio. Then, each sample was barcoded with a different Illumina barcode while the Forward primer was fixed and the reverse primer included the different barcodes. The barcoding PCR reaction that was conducted using KAPA HiFi HotStart ReadyMixPCR Kit (X2), 10µM of Illumina primers and 0.35-0.7ng of PCR product in a 10µl total volume reaction, for 15 cycles. Additional clean-up step was performed using SPRI beads with left-side size selection protocol in which the PCR product and beads were mixed at 1:1.5 ratio. Samples were pooled in equal amounts and sequenced.

treatment_protocol: Cell cycle arrest signals:  following 3 days of iCas9 induction, ancestor cell population was split to three populations, in which each population was treated differently. To activate senescence, cells were grown with media containing 2.5uM Etoposide (Sigma-Aldrich; 33419-42-0). To active quiesence, cells were grown with serum- free media. The third population continued to grow without any treatment.   All samples:  Cells were centrifuged for 3 minutes at 2000rpm. The medium was removed and cell pellet was freezed at -80°C until genomic DNA extraction.

tag: cell line

tag: day of sampling

value: day 14 of iCas9 induction

tag: repeat

value: repeat 1


title: 118_N1_Dym

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11763


title: HNSCC PRAS40 knockout 6-10B cells 2

description:
in vitro
Pras40_2


title: WI38slow-iCas9- pooled sgRNA cells, day 14 of iCas9 induction, repeat2

description:
WI38slow_growth_D14_rep2
processed data file: sgRNAseq_growthCompetition_allSamples.csv

value: repeat 2


title: WI38slow-iCas9- pooled sgRNA cells, day 10 of iCas9 induction, repeat1

description:
WI38slow_growth_D10_rep1
processed data file: sgRNAseq_growthCompetition_allSamples.csv

value: day 10 of iCas9 induction


title: WI38slow-iCas9- pooled sgRNA cells, day 7 of iCas9 induction, repeat2

description:
WI38slow_growth_D7_rep2
processed data file: sgRNAseq_growthCompetition_allSamples.csv

value: day 7 of iCas9 induction


title: 586_N1_Eed

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12590


title: WT_Resting_rep1


title: WT_Activated_rep2


title: 92_2i_Dym

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11743


title: 30_N1_Dido1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11840

value: Dido1 KO


title: 104_2i_Dym

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11739


title: 4_2i_Dido1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11814


title: WT_Resting_rep2


title: WI38slow-iCas9- pooled sgRNA cells, day 7 of iCas9 induction, repeat1

description:
WI38slow_growth_D7_rep1
processed data file: sgRNAseq_growthCompetition_allSamples.csv


title: 29_N1_Dido1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11839


title: 542_2i_Eed

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12393


title: WI38slow-iCas9- pooled sgRNA cells, day 10 of iCas9 induction, repeat2

description:
WI38slow_growth_D10_rep2
processed data file: sgRNAseq_growthCompetition_allSamples.csv


title: 3_2i_Dido1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11813


title: 197_N1_Ctbp2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11914

value: Ctbp2 KO


title: WI38slow-iCas9- pooled sgRNA cells, before iCas9 induction, repeat2

description:
WI38slow_growth_D0_rep2
processed data file: sgRNAseq_growthCompetition_allSamples.csv

value: before iCas9 induction


title: WI38fast-iCas9- pooled sgRNA cells, day 14 of iCas9 induction, repeat2

description:
WI38fast_growth_D14_rep2
processed data file: sgRNAseq_growthCompetition_allSamples.csv

source_name: WI38fast-iCas9- pooled sgRNA


title: WI38slow-iCas9- pooled sgRNA cells, day 4 of iCas9 induction, repeat2

description:
WI38slow_growth_D4_rep2
processed data file: sgRNAseq_growthCompetition_allSamples.csv

value: day 4 of iCas9 induction


title: WI38slow-iCas9- pooled sgRNA cells, before iCas9 induction, repeat1

description:
WI38slow_growth_D0_rep1
processed data file: sgRNAseq_growthCompetition_allSamples.csv


title: WI38fast-iCas9- pooled sgRNA cells, day 14 of iCas9 induction, repeat1

description:
WI38fast_growth_D14_rep1
processed data file: sgRNAseq_growthCompetition_allSamples.csv


title: 196_N1_Ctbp2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11897


title: 163_2i_Ctbp2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11872


title: WI38fast-iCas9- pooled sgRNA cells, day 10 of iCas9 induction, repeat1

description:
WI38fast_growth_D10_rep1
processed data file: sgRNAseq_growthCompetition_allSamples.csv


title: WI38fast-iCas9- pooled sgRNA cells, day 7 of iCas9 induction, repeat2

description:
WI38fast_growth_D7_rep2
processed data file: sgRNAseq_growthCompetition_allSamples.csv


title: 162_2i_Ctbp2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11871


title: WI38fast-iCas9- pooled sgRNA cells, day 10 of iCas9 induction, repeat2

description:
WI38fast_growth_D10_rep2
processed data file: sgRNAseq_growthCompetition_allSamples.csv


title: WI38slow-iCas9- pooled sgRNA cells, day 4 of iCas9 induction, repeat1

description:
WI38slow_growth_D4_rep1
processed data file: sgRNAseq_growthCompetition_allSamples.csv


title: 28_N1_Csnk1a1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11838

value: Csnk1a1 KO


title: 2_2i_Csnk1a1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11812


title: WI38fast-iCas9- pooled sgRNA cells, day 7 of iCas9 induction, repeat1

description:
WI38fast_growth_D7_rep1
processed data file: sgRNAseq_growthCompetition_allSamples.csv


title: 1_2i_Csnk1a1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11811


title: WI38fast-iCas9- pooled sgRNA cells, day 4 of iCas9 induction, repeat2

description:
WI38fast_growth_D4_rep2
processed data file: sgRNAseq_growthCompetition_allSamples.csv


title: 595_N1_Cdk8

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12592

value: Cdk8 KO


title: WI38fast-iCas9- pooled sgRNA cells, day 4 of iCas9 induction, repeat1

description:
WI38fast_growth_D4_rep1
processed data file: sgRNAseq_growthCompetition_allSamples.csv


title: 553_2i_Cdk8

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12396


title: WI38fast-iCas9- pooled sgRNA cells, before iCas9 induction, repeat2

description:
WI38fast_growth_D0_rep2
processed data file: sgRNAseq_growthCompetition_allSamples.csv


title: 594_N1_Cdk8

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12591


title: WI38fast-iCas9- pooled sgRNA cells, before iCas9 induction, repeat1

description:
WI38fast_growth_D0_rep1
processed data file: sgRNAseq_growthCompetition_allSamples.csv


title: HeLa-iCas9- pooled sgRNA cells, day 14 of iCas9 induction, repeat1

description:
HeLa_growth_D14_rep1
processed data file: sgRNAseq_growthCompetition_allSamples.csv

source_name: HeLa-iCas9- pooled sgRNA

value: HeLa


title: HeLa-iCas9- pooled sgRNA cells, day 14 of iCas9 induction, repeat2

description:
HeLa_growth_D14_rep2
processed data file: sgRNAseq_growthCompetition_allSamples.csv


title: 552_2i_Cdk8

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12395


title: HeLa-iCas9- pooled sgRNA cells, day 10 of iCas9 induction, repeat2

description:
HeLa_growth_D10_rep2
processed data file: sgRNAseq_growthCompetition_allSamples.csv


title: 7_2i_Cabin1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11817

value: Cabin1 KO


title: HeLa-iCas9- pooled sgRNA cells, day 10 of iCas9 induction, repeat1

description:
HeLa_growth_D10_rep1
processed data file: sgRNAseq_growthCompetition_allSamples.csv


title: 6_2i_Cabin1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11816


title: HeLa-iCas9- pooled sgRNA cells, day 7 of iCas9 induction, repeat1

description:
HeLa_growth_D7_rep1
processed data file: sgRNAseq_growthCompetition_allSamples.csv


title: HeLa-iCas9- pooled sgRNA cells, day 7 of iCas9 induction, repeat2

description:
HeLa_growth_D7_rep2
processed data file: sgRNAseq_growthCompetition_allSamples.csv


title: 217_N1_Bcor

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11964

value: Bcor KO


title: HeLa-iCas9- pooled sgRNA cells, day 4 of iCas9 induction, repeat2

description:
HeLa_growth_D4_rep2
processed data file: sgRNAseq_growthCompetition_allSamples.csv


title: 216_N1_Bcor

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11963


title: HeLa-iCas9- pooled sgRNA cells, day 4 of iCas9 induction, repeat1

description:
HeLa_growth_D4_rep1
processed data file: sgRNAseq_growthCompetition_allSamples.csv


title: HeLa-iCas9- pooled sgRNA cells, before iCas9 induction, repeat2

description:
HeLa_growth_D0_rep2
processed data file: sgRNAseq_growthCompetition_allSamples.csv


title: 183_2i_Bcor

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11900


title: HeLa-iCas9- pooled sgRNA cells, before iCas9 induction, repeat1

description:
HeLa_growth_D0_rep1
processed data file: sgRNAseq_growthCompetition_allSamples.csv


title: 331_N1_Atg13

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12614

value: Atg13 KO


title: UTE5 RNA-seq

city: Irvine

first: Farah

middle: B

last: Rahmatpanah

state: CA

address: D440 Medical Sciences I

department: Pathology and Laboratory Medicine

institute: University of California

data_processing:
Aligned to reference genomes hg19 with Strand NGS 3.1
Reads filtered on duplicates to remove PCR artifacts
Normalization of reads was performed using De-Seq method in Strand
Genome_build: hg19

source_name: Clear cell tumor

extract_protocol:
Tissue blocks were evaluated by a pathologist to identify the most homogeneous area of CCC from which RNA could be extracted. The FFPE RNA/DNA Purification Plus Kit (Cat # 54300, Norgen Biotek Corp) was used to isolate total RNA from patient specimens. RNA quality and quantity were assessed using an Agilent 2100 Bioanalyzer and a Qubit fluorimeter, respectively. All samples exhibited a DV200 metric of > 30% of RNA with fragment sizes > 200 nucleotides.
Prepared using standard Illumina protocols

tag: tumor stage

value: uterine clear cell carcinoma

tag: race

value: Black

tag: subgroup

tag: pd-l1 cps


title: 330_N1_Atg13

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12613

tag: strain

tag: genotype

tag: medium

tag: time point


title: 182_2i_Bcor

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11899

value: 0 h


title: UTE4 RNA-seq

tag: tissue

value: White


title: UTE2 RNA-seq


title: OVA11 RNA-seq

value: ovarian clear cell carcinoma


title: 27_N1_Csnk1a1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11837


title: UTE1 RNA-seq


title: UTE3 RNA-seq

value: Unknown


title: 261_2i_Arih2v2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11974

value: Arih2v2 KO


title: OVA9 RNA-seq


title: 319_N1_Arih2v2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12348


title: 318_N1_Arih2v2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12347


title: 33_N1_Cabin1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11772


title: 32_N1_Cabin1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11842


title: 177_2i_Fgfr1

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11878

value: Fgfr1 KO


title: OVA7 RNA-seq

value: Asian


title: 14_2i_Arid5b

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11824

value: Arid5b KO


title: 272_2i_Atg13

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12611


title: OVA10 RNA-seq


title: OVA6 RNA-seq


title: 40_N1_Arid5b

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11779


title: 39_N1_Arid5b

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11778


title: 615_N1_Apc

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12608

value: Apc KO


title: 273_2i_Atg13

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12612


title: 614_N1_Apc

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12607


title: OVA2 RNA-seq


title: OVA3 RNA-seq


title: OVA4 RNA-seq


title: 573_2i_Apc

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12404


title: OVA1 RNA-seq


title: OVA8 RNA-seq


title: 260_2i_Arih2v2

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11973


title: 572_2i_Apc

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12403


title: 13_2i_Arid5b

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11823


title: RMS_breast tumor_194 [VMT98]

city: Lyon

first: Virginie

last: MARCEL

address: 28 rue Laennec

country: France

institute: Cancer Research Center of Lyon

data_processing:
library strategy: RiboMethSeq
Adatper sequences were removed with Trimmomatic v0.36. Reads shorter than 17 nucleotides were discarded.
Reads were aligned to the human rRNA sequence with Bowtie 2.
5' end reads were counted at each rRNA nucleotide position
Genome_build: NR_046235
Supplementary_files_format_and_content: Raw counts of 5' end reads on each position of the rRNA subunits

source_name: RMS_breast tumor

extract_protocol:
RNAeasy kit (Qiagen)
Total RNA was first subjected to partial alkaline hydrolysis to generate RNA fragments ranging from 50 to 100 bp. Libraries were then prepared using NEBNext Multiplex Small RNA Library Prep Set

value: primary breast tumour

tag: subtype

tag: p53 status

value: MT

tag: Stage

tag: molecule subtype

value: ribosomal RNA


title: RMS_breast tumor_192 [VMT95]

value: TNBC

value: Stage 3


title: RMS_breast tumor_193 [VMT96]

value: LumiNAl

value: WT


title: 88_2i_Alg13

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11801

value: Alg13 KO


title: 114_N1_Alg13

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11759


title: 128_N1_Alg13

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11865


title: RMS_breast tumor_191 [VMT94]


title: RMS_breast tumor_195 [VMT99]


title: 697_N1_Aff3

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L13223

value: Aff3 KO


title: OVA5 RNA-seq


title: RMS_breast tumor_190 [VMT93]


title: RNA_ref_ctrl_4 [VMT333]

value: pool of different origins


title: 672_2i_Aff3

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12560

value: 0 h


title: RNA_ref_ctrl_5 [VMT331_VMT242]


title: RMS_breast tumor_188 [VMT331]

value: ER+ HER2-


title: 673_2i_Aff3

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12561


title: RMS_breast tumor_187 [VMT330]


title: RMS_breast tumor_186 [VMT329]


title: RMS_breast tumor_185 [VMT328]

value: Stage 2


title: 102_2i_Alg13

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11737


title: RMS_breast tumor_184 [VMT327]


title: 696_N1_Aff3

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L12574


title: RMS_breast tumor_181 [VMT324]


title: RMS_breast tumor_182 [VMT325]


title: RMS_breast tumor_189 [VMT92]

value: Stage 1


title: RMS_breast tumor_183 [VMT326]


title: RMS_breast tumor_180 [VMT323]


title: RMS_breast tumor_179 [VMT322]


title: RMS_breast tumor_178 [VMT321]


title: RMS_breast tumor_177 [VMT320]


title: RMS_breast tumor_175 [VMT318]


title: RMS_breast tumor_176 [VMT319]


title: RMS_breast tumor_173 [VMT316]


title: 193_N1_Fbxw7

description:
[1]
counts_KOs.csv
FPKM_KOs.csv
L11894

value: Fbxw7 KO


title: RMS_breast tumor_171 [VMT314]


title: RMS_breast tumor_170 [VMT313]


title: bic stimulation at 180 min, biological rep1

city: Maebashi

first: Yuichi

last: Uosaki

state: Gunma

address: 3-39-22 Showa-machi

department: Pediatrics

institute: Gunma university

hyb_protocol: Following fragmentation, cRNA were incubated for 14hrs at 45℃ on GeneChip mouse Genome array. GeneChips were washed and stained with Fluidics Station.

scan_protocol: GeneChip were scanned with 3000.

data_processing: Data analysis were performed in the Laboratory of Molecular Technology (NCI-Frederick).

label: Biotin

source_name: hippocampal neurons at 10DIV

label_protocol: Biotylated RNA was prepared according to the standard Affymetrix protocol from total RNA on the Mouse Gene ST1.0 (Affimetrix).

growth_protocol: Hippocampal neuros from ICR mice at E17.5 were cultured for 10 days.

extract_protocol: RNA samples were extracted using the RNAeasy kit (Qiagen) at 0, 30, 180, and 300 min after bicuculline stimulation according to manufactual instructions.

treatment_protocol: The neurons were stimulated with 50 μM of bicuculline for 0, 30, 180, and 300 min.

tag: treatment

value: bic stimulation at 180 min

value: ICR

tag: developmental stage

value: brain hippocampus


title: RMS_breast tumor_168 [VMT311]

value: primary breast tumour


title: bic stimulation at 0 min, biological rep1

value: bic stimulation at 0 min


title: bic stimulation at 30 min, biological rep2

value: bic stimulation at 30 min


title: bic stimulation at 0 min, biological rep2


title: bic stimulation at 180 min, biological rep2


title: bic stimulation at 30 min, biological rep1


title: bic stimulation at 300 min, biological rep2

value: bic stimulation at 300 min


title: bic stimulation at 300 min, biological rep1


title: RMS_breast tumor_167 [VMT310]

value: ribosomal RNA


title: RMS_breast tumor_165 [VMT307]

value: WT


title: RMS_breast tumor_166 [VMT309]

value: MT

value: Stage 3


title: RMS_breast tumor_164 [VMT306]


title: RMS_breast tumor_172 [VMT315]


title: RMS_breast tumor_163 [VMT304]


title: OE_3

city: Tianjin

first: Yajing

last: Chu

address: Nanjing Road 288

department: State Key Laboratory of Experimental Hematology

institute: Institute of Hematology, Chinese Academy of Medical Sciences

description:
RNAseq-batch 2
FPKM batch_2.txt
OE_3

data_processing:
Raw image data file from high-throughput sequencing (like Illumina HiSeqTM) was transformed to Sequenced Reads (called Raw Data or Raw Reads) by CASAVA 1.8 base recognition (Base Calling)
Raw reads were filtered as follows: 1) remove reads containing adaptors;2)remove reads containing N > 10% (N represents base that could not be determined);3) The Qscore (Quality value) of over 50% bases of the read is <=5.
Alignment was accomplished using TopHat2 (Kim et al, 2013)
FPKM (Fragments Per Kilo bases per Million reads) was used for estimating gene expression levels, which takes the effects of both sequencing depth and gene length on counting of fragments into consideration(Mortazavi et al. 2008).
Genome_build: mm10
Supplementary_files_format_and_content: FPKM files

source_name: c-Kit+ leukemic cells from bone marrow

extract_protocol:
c-Kit+ leukemic cells were enriched from bone marrows of moribund SUV-OE and control AML mice. Total RNA was isolated from these enriched c-Kit+ cells following standard protocol with TRIzol reagent (Invitrogen).
RNA-seq libraries were generated using the Illumina TruSeq RNA Sample Preparation Kit v2 following manufacturer's protocol.

value: bone marrow

tag: cell type

value: c-Kit+ leukemic cells from bone marrow

tag: mouse model

value: MLL-AF9 induce acute myeloid leukemia

value: Suv39h1-eGFP overexpression


title: OE_2

description:
RNAseq-batch 2
FPKM batch_2.txt
OE_2


title: CT_4

description:
RNAseq-batch 2
FPKM batch_2.txt
CT_4

value: control-eGFP overexpression


title: RMS_breast tumor_169 [VMT312]


title: lens_emmetropia_3

city: Shanghai

first: Yu

last: Du

address: 83 Fenyang Road

department: Ophthalmology

institute: Eye and Ear, Nose, and Throat Hospital of Fudan University

hyb_protocol: Array hybridization and wash were performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) following the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, GeneSpring Software12.6.1 (Agilent Technologies, Santa Clara, CA, US).

source_name: lens epithelium, emmetropia, axial length 22.99mm

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using GeneChip 3'IVT PLUS Reagent Kit (Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: Anterior lens epithelial cell membrane

tag: gender

value: Female

tag: age

value: 60 yrs

tag: diagnosis

value: Emmetropia


title: RMS_breast tumor_162 [VMT303]

value: primary breast tumour

value: ER+ HER2-

value: Stage 1


title: RMS_breast tumor_174 [VMT317]

value: Stage 2


title: WT w/ 3 μM MMC 2 hours

city: Frederick

first: Sandra

middle: Lynn

last: Wolin

address: Miller Drive

department: RNA Biology

institute: National Cancer Institute

data_processing:
Basecalling was performed using Illumina basecalling RTA 1.18.66.3.
Library complexity (i.e. percentage of non-duplicate reads) was determined by measuring the percentage of unique fragments in the mapped reads using Picard’s MarkDuplicate (version 1.84) utility.
Samples were trimmed of adapters and low quality sequence using Trimmomatic software before alignment with S. typhimirium (14028s) using Bowtie2
Bowtie2-build was used to generate an index from Salmonella enterica Typhimurium 14028S complete genome (GI: 267991652) and plasmid (GI: 267990039)
Sequenced reads were mapped to Salmonella enterica Typhimurium 14028S complete genome (GI: 267991652) + plasmid (GI: 267990039) using Bowtie2, with options: --very-sensitive-local.
Mapped BAM files were used as an input for Cuffdiff in order to determine differential gene expression between WT and WT-mmc samples.
Genome_build: Salmonella enterica Typhimurium 14028S complete genome (GI: 267991652) + plasmid (GI: 267990039)
Supplementary_files_format_and_content: XLSX file were generated from Cuffdiff output file

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: S. Typhimurium cells

growth_protocol: For treatment with DNA damaging agents, cells were grown in LB to OD600 = 0.9 and incubated with 3 μM (1 μg/ml) MMC (Sigma-Aldrich).  Afterwards, bacteria were centrifuged and RNA extracted using hot acid phenol.

extract_protocol:
Total RNAs were extracted using hot phenol and treated with RQ1 RNase-free DNAse.  RNA intergrity was checked by Bioanalyzer 2100.
The libary was constructed using the TruSeq RNA library kit from Illumina.  Ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. The RNA was fragmented into small pieces and the cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The resulting double-strand cDNA was used as the input to a standard Illumina library prep with end-repair, adapter ligation and PCR amplification being performed to give a sequencing ready library. The final purified product was then quantitated by qPCR before cluster generation and sequencing on the Illumina NextSeq 500 using TruSeq V2 chemistry, 75bp paired-end protocol.

treatment_protocol: Cells were treated with 3 μM (1 μg/ml) MMC (Sigma-Aldrich) for 2 hours.

value: 3 μM mitomycin C  for 2 h


title: RMS_breast tumor_161 [VMT302]

value: ribosomal RNA


title: WT w/o MMC


title: RMS_breast tumor_160 [VMT301]

value: WT


title: RMS_breast tumor_159 [VMT296]


title: LP1_sgAURKA-rep3

first: Liu

last: Zhiqiang

address: 22 Qxiangtai Rd

institute: Tianjin Medical University

data_processing:
Basecalls performed using BGISEQ-500
SOAPnuke was used to get the "clean reads".
Mapping clean reads to hg19 whole genome using BWA.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include fpkm, tpm, read count values for each Sample and diffexp

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using BGISEQ500 protocol

treatment_protocol:
LP-1 was innfected by virus sgRNA none targeting (NT Control),and cells were cultured with 10%FBS
LP-1 was innfected by virus sgRNA targeting AURKA gene (Aurora A-KO) ,and cells were cultured with 10%FBS

value: B lymphoblast

tag: tumor type

value: mutiple myeloma

tag: cell line

value: Aurora A-KO


title: RMS_breast tumor_158 [VMT293]

value: MT

value: Stage 3


title: CT_3

description:
RNAseq-batch 2
FPKM batch_2.txt
CT_3

tag: strain

value: bone marrow

value: c-Kit+ leukemic cells from bone marrow

value: MLL-AF9 induce acute myeloid leukemia

tag: genotype

value: control-eGFP overexpression


title: lens_emmetropia_1

source_name: lens epithelium, emmetropia, axial length 22.30mm

value: Anterior lens epithelial cell membrane

value: Male

value: 63 yrs

value: Emmetropia


title: LP1_sgAURKA-rep2

value: innfected by virus sgRNA targeting AURKA gene (Aurora A-KO)


title: lens_high myopia_3

source_name: lens epithelium, high myopia, axial length 34.74mm

value: 55 yrs

value: High myopia


title: RMS_breast tumor_157 [VMT288]

value: primary breast tumour

value: ER+ HER2-

value: WT

value: Stage 2

value: ribosomal RNA


title: dCas9_rep3_presort

city: Boston

last: Liu

state: MA

address: 300 Longwood Avenue

department: Hematology/Oncology

institute: Boston Children's Hospital

description:
dCas9_deconvolved_scores.bedgraph
dCas9_neglog10_pvals.bedgraph
dCas9_raw_scores.bed

data_processing:
Library strategy: CRISPR Screen
DESeq2 was then used to compare the sgRNA counts between sorted and unsorted samples
sgRNA counts were used as input into CRISPR-SURF Count with the following parameters: -nuclease cas9, -pert indel (for Cas9 samples) or -pert crispri (for dCas9 samples). With the resulting output, CRISPR-SURF Deconvolution was applied with the following parameters: -pert cas9, -sim_n 1000, and the perturbation range parameter -range 7 (for Cas9) or -range 20 (for dCas9). The CRISPR-SURF deconvolution analysis provides p-values and statistical power for the CRISPR dense perturbation data.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph contains the raw score, deconvoluted score, or p value of each sgRNA

source_name: HUDEP-2 cells

extract_protocol:
genomic DNA was extracted using the Qiagen Blood and Tissue kit. sgRNA integrant PCR to amplify spacer sequences was performed with Herculase II reaction buffer (1X), forward and reverse primers (0.5 μM each), dimethyl sulfoxide (DMSO) (8%), deoxynucleotide triphosphates (dNTPs) (0.25 μM each), Herculase II Fusion DNA Polymerase (0.5 reactions) using the following cycling conditions: 95°C for 2 min; 20 cycles of 95°C for 15 s, 60°C for 20 s, 72°C for 30 s; 72°C for 5 min. Multiple reactions of no more than 200 ng each were used to amplify from 6.6 ug gDNA (~1x106 cell genomes) per pool. Samples were subjected to additional rounds of PCR to add sequencing adaptors and indices before Illumina sequencing.
sgRNA integrant PCR to amplify spacer sequences was performed with Herculase II reaction buffer (1X), forward and reverse primers (0.5 μM each), dimethyl sulfoxide (DMSO) (8%), deoxynucleotide triphosphates (dNTPs) (0.25 μM each), Herculase II Fusion DNA Polymerase (0.5 reactions) using the following cycling conditions: 95°C for 2 min; 20 cycles of 95°C for 15 s, 60°C for 20 s, 72°C for 30 s; 72°C for 5 min. Multiple reactions of no more than 200 ng each were used to amplify from 6.6 ug gDNA (~1x106 cell genomes) per pool. Samples were subjected to additional rounds of PCR to add sequencing adaptors and indices before Illumina sequencing.

treatment_protocol: HUDEP-2 cells were transduced with lentivirus encoding various Cas9 or dCas9 variants to produce stably expressing cells. The cells were then transduced with the sgRNA lentivirus library and selected with 1 μg/ml puromycin. Cells were transduced at MOI of 0.3. Cell numbers were maintained throughout the experiment with at least 1000 cells per spacer sequence. After sgRNA transduction, cells were cultured in EDM2 medium for 12 days.

value: Erythroid

tag: crispr

tag: hbf-sorted population

value: presort

tag: differentiation stage

value: Day 12


title: lens_high myopia_2

source_name: lens epithelium, high myopia, axial length 31.54mm

tag: tissue

value: 68 yrs


title: 6498 VMM exponential phase 3

city: Zürich

first: Hans-Martin

last: Fischer

address: Vladimir-Prelog-Weg 4

department: Microbiology

country: Switzerland

institute: ETH Zürich

description: B. japonicum blr1880 mutant grown aerobically in VMM to exponential phase

hyb_protocol: Hybridisation, washing, staining, and scanning were done according to the Affymetrix manual using a gene chip fluidics station 450 (Affymetrix) and a gene chip scanner 3000 (Affymetrix). For hybridization of individual gene chips, 2–2.5 µg of labeled cDNA from culture-grown bacteria, and 6 -7.5 µg of total bacteroid cDNA were used in a total volume of 150 µl hybridization solution, which contained 7% DMSO (Sigma-Aldrich, St. Louis, USA) in addition to the described composition. Hybridization was done overnight at 48°C. The amount of bacteroid cDNA was estimated from the proportion of bacterial:plant RNA in nodules (Bioanalyzer, Agilent technologies, Palo Alto CA).

scan_protocol: Standard Affymetrix procedures

data_processing: Signal intensities were detected and analyzed using the mas5 algorithm described in the Affymetrix statistical algorithms description document (http://www.affymetrix.com). Normalized signal values from the arrays were then analyzed using Genespring GX 7.3 (Agilent Technologies,CA, USA). For culture-grown bacteria or bacteroids, only those genes which are “present” (i.e., expressed, based on the detection P-value ≤ 0.06) in 80% of all replicates were further considered. For experiments comparing different conditions amongst culture-grown bacteria or bacteroids, each chip was normalized to the median. Values below 0.01 were set to 0.01. For statistical comparisons, the student t-test with a P-value threshold of 0.01 was applied. Genes were considered as differentially expressed if the fold change (FC) was higher than 2, when comparing different conditions amongst culture-grown bacteria or symbiotic bacteria.

organism: Bradyrhizobium japonicum

source_name: B. japonicum blr1880 mutant grown in VMM until exponential phase

label_protocol: The fragmented cDNA was end-labeled with biotin-ddUTP in a final volume of 50 µl using terminal dexoynucleotidyl transferase (Promega) in combination with the gene chip labeling reagent (Affymetrix).  The double amounts of labeling reagent and terminal deoxynucleotide transferase was used for fragmented cDNA from bacteroids. The reaction was incubated for 75 min at 37°C and stopped by the addition of 2 µl of 0.5 M EDTA.

growth_protocol: Cells were grown to mid-exponential phase (OD600 of 0.4-0.5) and stationary phase (OD600 of 2) in VMM minimal medium. For harvesting, cultures were rapidly transferred to cold tubes containing one tenth of the culture volume of “stop solution” (10% Tris-HCl-buffered phenol [pH 8] in ethanol), centrifuged for 5 min (10,800 × g; 4°C), the supernatant was decanted, and cells were frozen in liquid nitrogen and stored at −80°C. Nodules from 5 soybean plants were collected for each GeneChip hybridization experiment. Nodules were harvested 21 post inoculation (dpi) and immediately frozen in liquid nitrogen.

extract_protocol: Total RNA was isolated using the hot phenol extraction procedure described previously (Babst et al. 1996). For RNA isolation from symbiotically grown bacteria, approximately 10 frozen nodules were placed in a 2-ml Eppendorf tube, disrupted and homogenized using a TissueLyzer (Qiagen, Valencia, CA) (3 times for 50 sec; 30 Hertz) with a tungsten carbide bead (3 mm; Qiagen) (Pessi et al. MPMI, 2007). RNA integrity was checked by agarose gel electrophoresis. Precipitated RNA (100 µg) was treated with 20 units of RQ1 DNase I (Promega, Madison, USA) for 30 min at 37°C in a reaction volume of 200 µl. SUPERase•InTM (100 units; Ambion,Huntingdon, UK) was included in the reaction to inhibit potential RNase activity. RNA samples were cleaned up with RNeasy spin columns (Qiagen). cDNA was synthesized. according to the Affymetrix antisense genome array protocol for E. coli (http://www.affymetrix.com). For reverse transcription, MMLV reverse transcriptase RNase H minus (Promega, Madison, USA) was used in the supplied reaction buffer. The resulting cDNA was spectrophotometrically quantified and fragmented according to the Affymetrix manual except that the time for fragmentation by DNase I was shortened to 3 min. For control, 200 ng of DNase I-treated cDNA were separated on a 4-to–20% acrylamide gradient gel and stained with SYBR green II (Molecular Probes, Inc., Eugene, OR, USA). Ideally, the fragmented cDNA migrated in a range that corresponded to 50–200 bp of the 50-bp ladder (Fermentas International Inc., Burlington, Canada). RNA was isolated from the roots of soybean plants as described above, and cDNA was fragmented and labeled according to the protocol for free-living bacteria.

tag: genotype/variation

value: blr1880 mutant

tag: growth condition

value: aerobic, exponential

tag: medium

value: VMM

tag: phase

value: exponential


title: lens_high myopia_1

source_name: lens epithelium, high myopia, axial length 29.98mm

value: Anterior lens epithelial cell membrane

value: Female

value: 53 yrs


title: 6498 VMM exponential phase 2


title: scribKD_Tet(+)_30hr

city: Bunkyo-ku

first: Motoyuki

last: Ogawa

state: Tokyo

department: Graduate School of Pharmaceutical Sciences

institute: The University of Tokyo

description: Gene expression at 30 hours after cultured with tetracycline

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Canine (V2) Gene Expression Microarray (Agilent, G2519F-021193) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides. Dye channel is set to Green and Green PMT is set to 100%.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Canis lupus familiaris

source_name: scribKD, 30hr, with Tet

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: MDCK-II scribKD cells were plated in a 12-well plate at a density of 154,000 cells/wel.  The cells were cultured in DMEM high glucose supplemented with 10% FBS and 100 units/ml penicillin G in a 5% CO2 atmosphere at 37℃.

extract_protocol: At the indicated time after tetracycline addtion, total RNA was extracted from three independent wells of the same condition and mixed using Isogen (Wako) according to the manufacturer's instructions.

treatment_protocol: The cells were treated with tetracycline at a final concentration of 5 µg/ml at 6 hours after plating.

value: Madin-Darby Canine Kidney (MDCK) cellls

tag: treatment condition

value: cultured with tetracycline for 30 hours


title: lens_emmetropia_2

source_name: lens epithelium, emmetropia, axial length 23.44mm

value: Emmetropia


title: scribKD_Tet(–)_60hr

description: Gene expression at 60 hours after cultured without tetracycline

source_name: scribKD, 60hr, without Tet

value: cultured without tetracycline for 60 hours


title: scribKD_Tet(+)_45hr

description: Gene expression at 45 hours after cultured with tetracycline

source_name: scribKD, 45hr, with Tet

value: cultured with tetracycline for 45 hours


title: RMS_breast tumor_156 [VMT287]

value: primary breast tumour

tag: subtype

tag: p53 status

value: WT

tag: Stage

value: Stage 1

tag: molecule subtype

value: ribosomal RNA


title: scribKD_Tet(+)_60hr

description: Gene expression at 60 hours after cultured with tetracycline

source_name: scribKD, 60hr, with Tet

value: cultured with tetracycline for 60 hours


title: 110spc4 VMM exponential phase 1

description: B. japonicum wild-type strain grown aerobically in VMM to exponential phase

source_name: B. japonicum wild-type strain grown in VMM until exponential phase

value: wild type


title: 110spc4 VMM exponential phase 2

value: aerobic, exponential


title: 6498 VMM  exponential phase 1

value: blr1880 mutant

value: VMM


title: 110spc4 VMM exponential phase 3

value: exponential


title: 110spc4 VMM exponential phase 4


title: dCas9_rep3_HbF_high

value: Erythroid

value: high

value: Day 12


title: scribKD_Tet(–)_45hr

description: Gene expression at 45 hours after cultured without tetracycline

source_name: scribKD, 45hr, without Tet

value: Madin-Darby Canine Kidney (MDCK) cellls

value: cultured without tetracycline for 45 hours


title: scribKD_Tet(–)_30hr

description: Gene expression at 30 hours after cultured without tetracycline

source_name: scribKD, 30hr, without Tet

value: cultured without tetracycline for 30 hours


title: LP1_Vector-rep3

tag: cell type

value: B lymphoblast

tag: tumor type

value: mutiple myeloma

tag: treatment

value: innfected by virus sgRNA none targeting (NT Control)

value: control


title: dCas9_rep2_presort

tag: cell line

value: presort


title: LP1_Vector-rep2

tag: genotype


title: RNA_ref_ctrl_3 [VMT283]

value: pool of different origins

value: ribosomal RNA


title: dCas9_rep2_HbF_high

tag: crispr

tag: hbf-sorted population


title: LP1_sgAURKA-rep1

value: innfected by virus sgRNA targeting AURKA gene (Aurora A-KO)

value: Aurora A-KO


title: RMS_breast tumor_155 [VMT285]

source_name: RMS_breast tumor

tag: tissue

value: primary breast tumour

value: WT

value: Stage 3


title: 6498 VMM stationary phase 2

description: B. japonicum blr1880 mutant grown aerobically in VMM to stationary phase

source_name: B. japonicum blr1880 mutant grown in VMM until stationary phase

tag: strain

tag: genotype/variation

value: blr1880 mutant

value: aerobic, stationary

value: VMM

value: stationary


title: LP1_Vector-rep1


title: 6498 VMM stationary phase 3

tag: growth condition

tag: medium


title: RMS_breast tumor_154 [VMT282]

value: MT


title: dCas9_rep1_presort

value: Erythroid

tag: differentiation stage

value: Day 12


title: RMS_breast tumor_153 [VMT281]

tag: subtype

value: ER+ HER2-

value: Stage 2


title: pAVICs- GSNO

city: Columbus

first: Vidu

last: Garg

state: OH

address: 700 Children's Drive WB4239

department: Cardiovascular Research

institute: Research Institute at Nationwide Children's Hospital

data_processing:
We used the 10X Genomics' Cell Ranger pipeline to demultiplex and convert Illumina bcl output into fastq files.
We mapped the fastq reads to the pig genome Sscrofa11 with Y sequences from WTSI_X_Y_pig V2 (GCF_000003025.6_Sscrofa11.1_genomic.fna) and gene annotation (GCF_000003025.6_Sscrofa11.1_genomic_genes.filtered.gtf) downloaded from NCBI (https://www.ncbi.nlm.nih.gov/assembly/GCF_000003025.6/).
scRNA-seq data with different treatments (control, GSNO, NO donor and NO donor withdrawal after three days) were combined using the cell ranger aggregate function yielding a total of 7037 cells (control: 1683, GSNO: 1966, NO donor: 1485 and NO donor withdrawal: 1903) with an average of 3397 genes per cell.
This data was processed using Seurat (version 3.0) to perform normalization and identification of genes with the highest variability.
Differential gene expression analysis was performed by splitting the pAVICs of one treatment into three sample groups of equal number of cells. These in silico replicates were then analyzed using DESeq254 to identify differentially expressed genes between conditions.
Genome_build: WTSI_X_Y_pig V2 (GCF_000003025.6_Sscrofa11.1_genomic.fna)
Supplementary_files_format_and_content: Normalized, Counts per million reads from 3 virtually split samples and Differentially expression analysis stats from DESeq2, (Format XLSX)

organism: Sus scrofa

source_name: Aortic valve interstitial cells

growth_protocol: Aortic valve Interstitial cells were grown as described in (PMID: 21248687)

extract_protocol:
pAVICs were dissociated with TrypLE Express, followed by filteration through a 40µm cell strainer (BD Falcon# 352340), and resuspension in 0.04% BSA. Cell viabilities (>85%) were measured using the Automated Cell Counter (ThermoFisher# AMQAF1000). Single-cell  droplet libraries from this suspension were generated in the 10XGenomics Chromium controller (~2000 target cell recovery/group) according to the manufacturer's instructions.
For each sample, the quality and integrity of cDNA and cDNA libraries were quantitated using the High Sensitivity D5000 and D1000 ScreenTape  (Agilent# 5067-5592 and 5067-5584) on the Agilent-2200 TapeStation.
All libraries were sequenced (150bp paired-end) in Illumina HiSeq4000 platform at The Steve and Cindy Rasmussen Institute for Genomic Medicine in Nationwide Children's Hospital.

treatment_protocol: Media were supplemented with either detaNONOate (NO donor: 150μM) (FisherScientific# AC328651000), or S-nitrosoglutathione (GSNO) (S-nitrosylating agent: 200μM) (MilliporeSigma# N4148) for the time periods indicated in the manuscript

tag: culture type

value: Primary culture

value: Aortic valve

value: Aortic valve interstitial cells

value: S-Nitrosylation donor (S-Nitrosoglutathione; GSNO) for five days


title: dCas9_rep1_HbF_high

value: high


title: pAVICs- Control

value: Control (five days culture)


title: RMS_breast tumor_151 [VMT278]

value: primary breast tumour

tag: p53 status

value: WT

tag: Stage

value: ribosomal RNA


title: VP64_rep3_HbF_high

description:
VP64_deconvolved_scores.bedgraph
VP64_neglog10_pvals.bedgraph
VP64_raw_scores.bed


title: VP64_rep3_presort

value: presort


title: RMS_breast tumor_152 [VMT279]

value: Stage 3

tag: molecule subtype


title: VP64_rep2_presort


title: pAVICs- Nitric oxide

tag: cell type

value: Nitric oxide donor (DETANONATE) for five days


title: RMS_breast tumor_149 [VMT276]

value: MT


title: VP64_rep2_HbF_high

value: Erythroid


title: RMS_breast tumor_148 [VMT275]


title: 6498 VMM stationary phase 1

value: blr1880 mutant

value: aerobic, stationary

value: VMM

tag: phase

value: stationary


title: 110spc4 VMM stationary phase 2

description: B. japonicum wild-type strain grown aerobically in VMM to stationary phase

source_name: B. japonicum wild-type strain grown in VMM until stationary phase

value: wild type


title: VP64_rep1_presort

tag: cell line

value: Day 12


title: Smg-pIC-2

first: Lvyun

state: Hunan

address: 109 Deya Road, Kaifu District

department: College of Liberal Arts and Sciences

institute: National University of Defense Technology

description: poly I:C, simulated microgravity, replicate 2

data_processing:
Sequence quality was examined using the FastQC software.
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to the reference genome using Hisat2 software (v2.0.4).
The transcript abundances for each sample were estimated with StringTie (v1.2.3), and the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0).
The differentially expressed genes and transcripts were filtered using R package Ballgown.
The novel genes and transcripts were predicted from assembled results by comparing them to the reference annotation using StringTie and Ballgown.
Genome_build: Danio rerio (assembly GRCz10)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Danio rerio

source_name: embryos

extract_protocol:
After 12 hours post fertilization (hpf), total RNA from each sample was extracted using TRIzol reagent and quantified by a NanoDrop ND-1000 instrument and agarose gel electrophoresis.
1–2 μg total RNA was used to prepare the sequencing library in the following steps: 1) Total RNA is enriched by oligo(dT) magnetic beads (rRNA removed); 2) RNA-seq library is prepared using a KAPA Stranded RNA-Seq Library Prep Kit, which incorporates dUTP into the second cDNA strand and renders the RNA-seq library strand-specific.

treatment_protocol: One-cell stage embryos were microinjected with 2 nL (1 mg/μL) poly I:C or microinjection buffer (0.5% phenol red, 240 mM KCl, and 40 mM HEPES at pH 7.4) control using a microinjector (ASI MPPI-3) and then subjected immediately to the simulated microgravity conditions generated by RCCS or the normal gravity conditions in cell culture dish.

value: Wild-type AB

tag: gravity conditoin

value: Simulated microgravity

tag: stimulation

value: poly I:C


title: Smg-pIC-3

description: poly I:C, simulated microgravity, replicate 3


title: 110spc4 nodules soybean 21 Days 4

description: nodules soybean 21 dpi infected by B. japonicum wild-type strain

value: nodules

value: soybean

tag: time

value: 21 Days


title: 110spc4 VMM stationary phase 3


title: 110spc4 nodules soybean 21 Days 3

source_name: nodules soybean 21 dpi infected by B. japonicum wild-type strain


title: pAVICs- Nitric oxide withdrawal (NC)

value: Primary culture

tag: tissue

value: Aortic valve

value: Aortic valve interstitial cells

tag: treatment

value: Nitric oxide donor (DETANONATE) for three days followed by without nitric oxide donor for two days


title: 110spc4 VMM stationary phase 1

tag: strain

tag: genotype/variation


title: Smg-pIC-1

description: poly I:C, simulated microgravity, replicate 1


title: VP64_rep1_HbF_high

source_name: HUDEP-2 cells

value: Erythroid

tag: crispr

tag: hbf-sorted population

value: high


title: 110spc4 nodules soybean 21 Days 1

tag: growth condition

tag: medium


title: RMS_breast tumor_147 [VMT274]

value: primary breast tumour

tag: subtype

tag: p53 status

value: MT

value: Stage 3

value: ribosomal RNA


title: RMS_breast tumor_150 [VMT277]

tag: Stage

tag: molecule subtype


title: RMS_breast tumor_146 [VMT273]

value: WT


title: Smg-3

description: Mock buffer, simulated microgravity, replicate 3

value: Wild-type AB

value: Mock buffer


title: Smg-2

description: Mock buffer, simulated microgravity, replicate 2

value: Simulated microgravity


title: RMS_breast tumor_145 [VMT272]

value: Stage 2


title: RMS_breast tumor_144 [VMT271]

value: TNBC


title: KRAB_rep3_HbF_high

description:
KRAB_deconvolved_scores.bedgraph
KRAB_neglog10_pvals.bedgraph
KRAB_raw_scores.bed

tag: differentiation stage

value: Day 12


title: KRAB_rep2_presort

tag: cell line

value: presort


title: Smg-1

description: Mock buffer, simulated microgravity, replicate 1

tag: gravity conditoin


title: 6498 nodules soybean 21 Days 3

description: nodules soybean 21 dpi infected by a B. japonicum blr1880 mutant

value: blr1880 mutant

value: nodules

value: soybean

value: 21 Days


title: RMS_breast tumor_143 [VMT270]


title: Ng-pIC-3

description: poly I:C, normal gravity, replicate 3

value: Normal gravity

tag: stimulation

value: poly I:C


title: KRAB_rep2_HbF_high

value: Erythroid

value: high


title: HUVEC RUX + IL-6 3

city: Albany

first: Alejandro

middle: Pablo

last: Adam

state: NY

address: 43 New Scotland Ave

department: Molecular and Cellular Physiology

institute: Albany Medical College

description: Non-ribosomal RNA

data_processing:
Trimming with trim galore v0.4.4
Alignment with salmon v 0.8.2
Import into R with tximport
Fold-change analysis with DESeq2
Annotation with biomart and EnsDb.Hsapiens.v86
Genome_build: Genome Reference Consortium Human Build 38
Supplementary_files_format_and_content: csv file with counts per million reads mapped (CPM)

source_name: HUVEC

growth_protocol: Grown at confluency in EGM-2 media

extract_protocol:
Trizol
GENEWIZ Riibo--Zero workflow

treatment_protocol: Post-confluent (48h) monolayers

tag: cell type

value: HUVEC


title: RMS_breast tumor_142 [VMT269]

tag: tissue

value: primary breast tumour

value: WT

value: Stage 3

value: ribosomal RNA


title: KRAB_rep3_presort


title: HUVEC RUX + IL-6 2

description: Non-ribosomal RNA

tag: treatment


title: Ng-pIC-2

description: poly I:C, normal gravity, replicate 2

tag: strain

value: Wild-type AB


title: KRAB_rep1_presort


title: 6498 nodules soybean 21 Days 1

source_name: nodules soybean 21 dpi infected by a B. japonicum blr1880 mutant

tag: genotype/variation

tag: time


title: 110spc4 nodules soybean 21 Days 2

value: wild type


title: RMS_breast tumor_141 [VMT268]


title: Ng-3

description: Mock buffer, normal gravity, replicate 3

value: Mock buffer


title: HUVEC RUX + IL-6 1

description: Non-ribosomal RNA


title: Cas9_rep_3_presort

description:
Cas9_deconvolved_scores.bedgraph
Cas9_neglog10_pvals.bedgraph
Cas9_raw_scores.bed

tag: crispr

tag: hbf-sorted population

value: presort

value: Day 12


title: Ng-pIC-1

description: poly I:C, normal gravity, replicate 1