title: HTGTS_PB_ZFN_DRB_ASISI

description: control: HTGTS_PB_ZFN_NT_ASISI.fastq.gz

data_processing:
Reads were aligned to the GRCm38p2/mm10 genome assembly
Sites that underwent chromosomal translocations to the bait site, residing at chr6:41554860-41555099, were identified as described (Hu et al., 2016).
For ETO treated and non-treated experiments, data from two experiments was aggregated. To avoid proximity bias, reads that resided within 10 kilobases from the bait site were discarded. The remaining reads were clustered using bedtools merge function with the parameter -d 5000; that is, reads within 5kb from each other were merged. To avoid background reads, clusters that contained less than 5 reads were discarded. TOP2 lesions, or AsiSI breaks that overlapped with at least one cluster, were defined to be translocated. For translocations within genes, the total number of reads that overlapped with genes was calculated.
Genome_build: GRCm38p2/mm10
Supplementary_files_format_and_content: tlx files were generated using HTGTS pipeline (Hu et al. 2016)

extract_protocol:
DNA was extracted by digesting overnight at 55C in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, before DNA fragmentation.
HTGTS was performed as described in Hu et al., 2016. Primers and adapters used (with minor modifications from Hu et al., 2016): ZNF-bio,/5Biosg/CAGAAGCCTTCAGTATGCACCA, I7-ZNF-nested-barcode3,CTCGGCATTCCTGCTGAACCGCTCTTCCGATCTAGGCAGAATTCCACTTAACCCCAACTCCAG, I7-ZNF-nested-barcode4,CTCGGCATTCCTGCTGAACCGCTCTTCCGATCTTCCTGAGCTTCCACTTAACCCCAACTCCAG, Adapter-upper,GGTACACGACGCTCTTCCGATCTNNNNNN/3AmMO/, Adapter-lower-mod,/5Phos/AGATCGGAAGAGCGTCGTGTACC/3AmMO/, I5-bridge,AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T, P5-I5c,AATGATACGGCGACCACCGAGATCTACACTCTTT*C, P7-I7c,CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTT*C. Libraries (fragment size 500 – 1,000 bp) were purified and sequenced using Illumina MiSeq. For translocation analysis the standard LAM-HTGTS bioinformatic pipeline was used (Hu et al., 2016).
High-throughput genome wide translocation sequencing (HTGTS)

treatment_protocol: Pre-cells were arrested in G1 by treatment with 3 mM imatinib for 48 hours, ZFN was induced by treating with doxycycline at 1 μg/ml (starting after 24 hours of imatinib). Then cells pre-treated or not with drugs affecting transcription and treated with etoposide (50uM) for 2.5 hours or untreated or AsiSI was induced (starting after 24 hours of imatinib, with doxocycline (1 μg/ml) and 20 hours later with tamoxifen (1uM)). After 2.5 hours with etoposide, pre-B cells were washed 3 times in cold media and cultured for 12 hours in media. For transcription inhibition or stimulation, drug pre-treatment was performed for 2 hours with 150 mM DRB (D-ribofuranosylbenzimidazole, Sigma) prior to etoposide treatment or induction of AsiSI. All drugs were maintained during the treatment with etoposide or induction of AsiSI.


title: HTGTS_PB_ZFN_DRB_NT_TOPO

status: Public on Apr 24 2019

type: SRA

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Abelson-transformed pre-B cell

growth_protocol: Abelson pre-B cell lines were cultured DMEM supplemented 10% FBS, with 2 mM L-glutamine, 1 mM Sodium piruvate, non-essential amino acids, 0.05 mM β-mercaptoethanol, penicillin (100 U/ml) and streptomycin (100 U/ml) (Invitrogen).

tag: strain

tag: genotype/variation

tag: cell type

value: Abelson-transformed pre-B cell


title: HK-2 ATAC-seq null replicate 2

city: Bethesda

first: Benjamin

last: Carter

state: MD

address: 10 Center Drive

department: NHLBI

country: USA

institute: National Institutes of Health

description:
ATAC_HK2_inc_HOMER.txt
ATAC_HK2_dec_HOMER.txt

data_processing:
RNA-seq reads were trimmed using Trimmomatic and aligned to the appropriate reference genome using STAR with the following parameters: readFilesCommand zcat outFilterType BySJout outSJfilterCountUniqueMin -1 2 2 2 outSJfilterCountTotalMin -1 2 2 2 outFilterIntronMotifs RemoveNoncanonical. ATAC-seq reads were trimmed using Trimmomatic and mapped to the appropriate reference genome using Bowtie2 in very sensitive end-to-end mode.
For RNA-seq, gene expression levels were computed using htseq-count using default parameters. For ATAC-seq, BAM files were converted to BED files using BEDtools.
For RNA-seq, differential expression analysis was performed with DESeq2 using default parameters. For ATAC-seq, peaks of differential enrichment were identified using SICER-df with a false discovery rate threshold of 0.05. The annotatePeaks utility of HOMER was used to annotate statistically significant peaks.
Genome_build: hg19 for Caki1, Caki2, and HK2. mm10 for NMuMG.
Supplementary_files_format_and_content: For RNA-seq, files are tab-delimted text with the differential expression output from DESeq2. For ATAC-seq, files are tab-delimited text containing the annotated peaks obtained from HOMER.

organism: Homo sapiens

source_name: HK-2 cells

growth_protocol: Caki1 and Caki2 cells were cultured in McCoy’s 5A supplemented with 10% FBS, 1% nonessential amino acids, and 1% L-glutamine. HK-2 cells were cultured in RPMI supplemented with 10% FBS and 1% L -glutamine. NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10 µM/mL insulin, 1% L -glutamine, and 1% sodium pyruvate. All cell lines were grown at 37°C in a humidified atmosphere in a 5% CO2 incubator.

extract_protocol:
RNA was extracted using TRIzol reagent (Life Technologies Corporation, Grand Island, NY) according to the manufacturer’s instructions and cleaned up using RNeasy Mini Kit (Qiagen Inc., Valencia, CA). Genomic DNA for ATAC-seq was obtained according to the ENCODE ATAC-seq pipeline.
RNA and DNA libraries were prepared for sequencing using standard Illumina protocols.

tag: treatment

value: Lentiviral transfection of empty vector


title: smallRNA seq data from pancreatic cancer patient P32

city: Seoul

first: Kwondo

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description: small RNA

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and low-quality sequence using Trimmomatic-0.32
Trimmed reads with the length not in range within 16~35bp were filtered out.
Reads were aligned against miRBase v21 and quantified using miRDeep2
Genome_build: miRBase v21
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

molecule: total RNA

source_name: Serum

extract_protocol:
Serum samples were collected in 10-mL BD serum tubes and centrifuged at 4°C for 20 minutes at 3000 rpm. The supernatant serum was then aliquoted and total RNA containing miRNA was extracted from the samples using the Serum miRNA purification kit (Genolution, Seoul, Korea) according to the manufacturer’s instructions.
The libraries were prepared for 50bp single-end sequencing using the NEXTflex Small RNA-Seq Kit (Bioo Scientific Corp.). Namely, smallRNA molecules were isolated from 1μg of total RNA via the adapter ligation. The isolated smallRNAs were synthesized as single-stranded cDNAs through the RT (Reverse transcription) priming. By applying this as a template for second strand synthesis, double-stranded cDNA was prepared through PCR (Polymerase Chain Reaction). And, the fragments of ~150bp were extracted for sequencing through size selection by gel electrophoresis. Quality of these cDNA libraries was evaluated with the Agilent 2100 BioAnalyzer (Agilent, CA, USA) followed by quantification with the KAPA library quantification kit (Kapa Biosystems, MA, USA) according to the manufacturer’s protocol. Following cluster amplification of denatured templates, sequencing was progressed as single-end (50bp) using Illumina HiSeq2500 (Illumina, CA, USA).

tag: group

value: pancreatic cancer


title: HTGTS_PB_ZFN_DRB_ETO_TOPO

description: control: HTGTS_PB_ZFN_ETO_NT_1_TOPO.fastq.gz


title: 100_PDAC3-5

city: Boston

first: David

middle: T

last: Ting

state: MA

address: 149 E 13th street

department: Cancer Center

institute: Massachusetts General Hospital

description: cntPdac.csv

data_processing:
The paired-end reads from the three sequencing runs were combined and aligned to the hg38 genome from http://genome.ucsc.edu using the STAR v2.4.0h aligner with default settings. Reads that did not map or mapped to multiple locations were discarded.
Duplicate reads were marked using the MarkDuplicates tool in picard-tools-1.8.4 and were removed.
The uniquely aligned reads were counted using htseq-count in the intersection-strict mode against the Homo_sapiens.GRCh38.79.gtf annotation table from http://www.ensembl.org.
Genome_build: hg38
Supplementary_files_format_and_content: The raw read counts described above are available in two tables, one for the PDAC samples (cntPdac.csv) and one for the CAF samples (cntCAF.csv).

molecule: polyA RNA

source_name: primary pancreatic ductal adenocarcinoma cell line

growth_protocol: PDAC cells and CAFs were seeded in 6-well plates in 5 different ratios: 100% PDAC, 50:50 PDAC:CAF, 30:70 PDAC:CAF, 10:90 PDAC:CAF, and 100% CAF. DMEM (high glucose, pyruvate) with 10% fetal bovine serum (FBS) and 100 U/mL Penicillin and 100 mg/mL Streptomycin was used for all cultures.

extract_protocol:
After 72 hours of culture, cells were trypsinized and resuspended in PBS solution, and micromanipulated. PDAC cells or CAFs were then individually micromanipulated using a 10 μm transfer tip on an Eppendorf TransferMan NK2 micromanipulator, transferred into PCR tubes containing RNA protective lysis buffer (Clontech Laboratories), and flash frozen in liquid nitrogen.
Amplified cDNA was synthesized from the entire cell lysate using the SMARTer Ultra Low Input RNA Kit for Sequencing - v3 kit (Clontech Laboratories). PCR amplification following second strand synthesis was run for 18 cycles. 1 ng of amplified cDNA was loaded into the Nextera XT kit. Normalization was done using the KAPA SYBR® FAST Universal qPCR Kit (Kapa Biosystems) rather than the bead-based normalization in the Nextera XT kit.

value: single PDAC cell

tag: culture condition

value: 100% PDAC


title: 100_PDAC3-4

description: cntPdac.csv


title: smallRNA seq data from pancreatic cancer patient P18

description: small RNA


title: HTGTS_PB_ZFN_IFN_ETO_TOPO


title: smallRNA seq data from pancreatic cancer patient P31

description: small RNA


title: smallRNA seq data from pancreatic cancer patient P29

description: small RNA


title: HK-2 ATAC-seq null replicate 1


title: HTGTS_PB_ZFN_ETO_NT_1_TOPO

description: control: HTGTS_PB_ZFN_NT_NT_1_TOPO.fastq.gz


title: HTGTS_PB_ZFN_ETO_NT_2_TOPO

description: control: HTGTS_PB_ZFN_NT_NT_2_TOPO.fastq.gz


title: smallRNA seq data from pancreatic cancer patient P15

description: small RNA


title: smallRNA seq data from pancreatic cancer patient P28

description: small RNA


title: smallRNA seq data from pancreatic cancer patient P25

description: small RNA


title: HTGTS_PB_ZFN_NT_NT_1_TOPO


title: smallRNA seq data from pancreatic cancer patient P22

description: small RNA


title: HTGTS_PB_ZFN_NT_ASISI


title: smallRNA seq data from pancreatic cancer patient P21

description: small RNA


title: smallRNA seq data from pancreatic cancer patient P27

description: small RNA


title: Sample_Epi-CLL-11

city: Daegu

first: Ri

last: Ryu

address: 80 Daehak-ro

department: Food Science and Nutrition

institute: Kyungpook National University

description: CLE added high-fat diet_mRNA

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence
Mapped to M. musculus whole genome using the aligner bowtie2 version 2.2.3 with tophat 2.0.12
Transcripts were assembled and quantitated using Cufflinks v2.2.1
Genome_build: M. musculus Ensembl 77
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for "ND","HFD", "CLL" and "LU" sample.

source_name: Mouse epididymal adipose tissue

growth_protocol: Forty male C57BL/6J mice (four-week-old, male) were obtained from the Jackson Laboratories (Bar Harbor, ME, USA). All mice were individually housed under a constant temperature (24°C) and 12-h light/dark cycle and, fed a normal chow diet for acclimation for 1 week after arrival.

extract_protocol:
Total RNA was extracted from epididymal adipose tissue using TRIZOL reagent (Invitrogen Life Technologies, NY) according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser.
Libraries were constructed from mRNA using the Illumina TruSeq RNA Sample Prep Kit following  manufacturer's protocols.

treatment_protocol: At 5 weeks of age, they were randomly divided into 4 groups and fed a normal diet (ND), high-fat diet (HFD), HFD + 1.5% (w/w) chrysanthemum leaf ethanol extract (CLE), HFD + 0.003% (w/w) luteolin (LU) for 16 weeks

tag: age

value: 21 weeks

tag: tissue

value: Epididymal adipose tissue


title: Sample_Epi-LU-8

description: LU added high-fat diet_mRNA


title: HTGTS_PB_ZFN_IFN_NT_TOPO


title: HTGTS_PB_ZFN_NT_NT_2_TOPO


title: smallRNA seq data from pancreatic cancer patient P16

description: small RNA


title: smallRNA seq data from pancreatic cancer patient P14

description: small RNA


title: smallRNA seq data from pancreatic cancer patient P12

description: small RNA


title: smallRNA seq data from pancreatic cancer patient P20

description: small RNA


title: smallRNA seq data from pancreatic cancer patient P11

description: small RNA


title: Sample_Epi-HFD-18

description: High-fat diet_mRNA


title: Sample_Epi-LU-3

description: LU added high-fat diet_mRNA


title: Sample_Epi-HFD-15

description: High-fat diet_mRNA


title: smallRNA seq data from healthy control N15

description: small RNA

value: healthy control


title: smallRNA seq data from pancreatic cancer patient P09

description: small RNA


title: smallRNA seq data from healthy control N16

description: small RNA


title: smallRNA seq data from healthy control N21

description: small RNA


title: smallRNA seq data from pancreatic cancer patient P10

description: small RNA


title: smallRNA seq data from healthy control N14

description: small RNA


title: Sample_Epi-CLL-2

description: CLE added high-fat diet_mRNA


title: smallRNA seq data from pancreatic cancer patient P13

description: small RNA


title: Sample_Epi-R-LU-2

description: LU added high-fat diet_mRNA


title: Sample_Epi-R-ND-3

description: Normal diet_mRNA


title: Sample_Epi-R-CLL-4

description: CLE added high-fat diet_mRNA


title: smallRNA seq data from healthy control N18

description: small RNA


title: smallRNA seq data from healthy control N12

description: small RNA


title: smallRNA seq data from healthy control N09

description: small RNA


title: smallRNA seq data from healthy control N17

description: small RNA


title: Sample_Epi-HFD-12

description: High-fat diet_mRNA


title: smallRNA seq data from healthy control N20

description: small RNA


title: smallRNA seq data from healthy control N08

description: small RNA


title: smallRNA seq data from healthy control N13

description: small RNA


title: 805_KOC (Rep2)

city: Rehovot

first: Eran

last: Hornstein

address: 234 Herzl St.

department: Molecular Genetics

institute: Weizmann Institute of Science

data_processing:
Reads for each sample were mapped independently using TopHat2 version (v2.0.10)  against the mouse genome build mm9. Approximately, 85-90% mapping rate was observed.
Only uniquely mapped reads were used to determine the number of reads falling into each gene with the HTSeq-count script (0.6.1p1).
Differentially expressed genes were calculated with the DESeq2 package (v1.4.5).
Genome_build: mm9
Supplementary_files_format_and_content: Excel file - tabs include raw data read counts, normalized data_read counts, and DEseq2 output.

source_name: langerhans islets

extract_protocol:
Islets were isolated and RNA was harvested using Trizol reagent. Extraction of total RNA was carried out by the miRNeasy Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: langerhans islets

tag: genotype

value: miR-17-92/106 Control


title: Sample_Epi-ND-2

description: Normal diet_mRNA


title: 992_KOC (Rep6)


title: 817_KOC (Rep5)


title: smallRNA seq data from healthy control N11

description: small RNA


title: 701_KO (Rep5)


title: 703_KO (Rep6)


title: smallRNA seq data from healthy control N05

description: small RNA


title: smallRNA seq data from healthy control N02

description: small RNA


title: 813_KOC (Rep3)


title: smallRNA seq data from healthy control N10

description: small RNA


title: AKM39 input N2 DPY-27 RNAi emb ChIP-seq

city: New York City

first: Lena

middle: Annika

last: Street

state: NY

address: 100 Washington Square East

department: Biology

institute: New York University

data_processing:
Basecalls were performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the WS220 genome assembly using bowtie version 1.2.0 using default parameters for allowing mismatches in the seed (-n option) and suppressing alignments for reads with more than 4 reportable alignments.
Peaks were called using MACS version 1.4.3 with the following setting: input, genome size (-g ce), format (-f BAM), p-value (-p 1e-10 and -p 1e-5)
Genome coverage was estimated using MACS version 1.4.3 with the following setting: genome size (-g ce), format (-f BAM), output in wiggle format (-w), whole genome output (-S), resolution (--space=1)
Coverage per base was normalized to the genome-wide median coverage (excluding the mitochondrial chromosome). Final ChIP enrichment score per base was obtained by subtracting matching input coverage.
Replicates were merged by averaging coverage at each base position. To determine a set of final peaks, reads from the replicates were combined using the BEDTools utility mergeBam version 2.13.442, and MACS was used to call peaks (see above, p-value -p 1e-10). Only those peaks present in the majority of the individual replicates identified below p-value 1e-5 were included in the final peak set.
RNA-seq reads were aligned to the WS220 genome assembly using tophat version 2.1.1 using default parameters, specifying first strand alignment.
Resultant RNA-seq bam files were converted to sam files using samtools version 1.6. Sam files were used to generate count data using htseq-cout version 0.6.1.
Genome_build: WS220
Supplementary_files_format_and_content: BigWig files were generated by converting wiggle files using the UCSC wigToBigWig utility. Wiggle files were generated using MACS version 1.4.3, normalized according to the genome-wide mean coverage and then input subtracted. Scores represent the average coverage of each replicate at each base position.
Supplementary_files_format_and_content: Bed files were generated by combining replicate reads and using MACS version 1.4.3 at two different p-values. Only peaks at the more stringend cut-off were inlcuded in the final set that were overlapping with the majority of peaks of each of the replicates at the less stringend p-value.
Supplementary_files_format_and_content: Counts files were generated using Htseq-counts version 0.6.1.

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Embryos were isolated by bleaching gravid adults grown on plates at 20C.

extract_protocol:
Embryos were washed and dounced in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). 0.1 sarkosyl was added before sonicating to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of embryo extract and 3-5 ug of antibody was used per ChIP.
Half of the ChIP DNA were ligated to Illumina or home-made multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

treatment_protocol: Embryos were treated with 2% formaldehyde for 30 minutes, washed with M9, and collected by centifugation and freezing at -80C until extract preparation.

value: whole worms

tag: developmental stage

value: mixed embryo

tag: antibody target

value: INPUT

tag: antibody (vendor, cat#, lot#)

tag: antibody antigen

tag: antibody (host, clone)

tag: matching input


title: smallRNA seq data from healthy control N07

description: small RNA


title: Sample_Epi-R-ND-4

description: Normal diet_mRNA


title: 660_KO (Rep2)


title: 706_KOC (Rep1)


title: smallRNA seq data from healthy control N01

description: small RNA


title: 659_KO (Rep1)


title: smallRNA seq data from healthy control N06

description: small RNA


title: smallRNA seq data from healthy control N04

description: small RNA


title: TGF-α + Gefitinib 2

city: Hangzhou

first: Heng

last: Sun

state: Zhejiang

address: 866# Yuhangtang Road

department: Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine

country: China

institute: Zhejiang University School of Medicine

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
MapSplice mapping to reference genome
read counting
Genome_build: GRCm38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Femoral epiphysis

growth_protocol: P2 mouse epiphyseal chondrocytes cultured in DMEM/F12 medium with 10% FBS

extract_protocol:
RNA extraction protocol not provided.
RNA libraries were prepared for sequencing using standard Ion Proton protocols

treatment_protocol: Control: 0.1% DMSO for 48 h; TGF-a: 0.1% DMSO + 10 ng/ml TGF-a for 48 h; T+G: 0.1% DMSO + 10 μM Gefitinib for 30 min in advance, then 0.1% DMSO + 10 ng/ml TGF-a + 10 μM Gefitinib for 48 h

value: Femoral epiphysis

value: chondrocytes

value: post natal day 1


title: smallRNA seq data from healthy control N03

description: small RNA


title: KO_810_4

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

description: KO_810_4__SergioMenchero_RNA_Seq_SMARTER_ACTGAGCG_L002

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2.
Sequencing adaptor contaminations were removed from reads using Cutadapt v1.3.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3.
Genome_build: GRCm38 assembly, Ensembl genebuild 76
Supplementary_files_format_and_content: matrix_table.xls file contains ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.

source_name: Single embryo

growth_protocol: Experiments were conducted using E2.5 mouse embryos in an outbred genetic background

extract_protocol:
RNA from single embryos was isolated using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems)
cDNA libraries were generated using SMART-Seq Ultra Low Input RNA Kit (Clontech).
RNASeq libraries were sequenced (single-end mode and length of 60 bp) on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.

tag: strain/background

value: outbred

value: single embryo

tag: litter


title: 662_KO (Rep4)

tag: strain


title: 661_KO (Rep3)


title: H3 N2 DPY-27 RNAi emb rep3 ChIP-seq

value: Abcam, ab1791

value: Human Histone H3 aa 100 to the C-terminus conjugated to Keyhole Limpet Haemocyanin (KLH)

value: Rabbit, polyclonal


title: smallRNA seq data from bilirary tract cancer patient B15

description: small RNA

value: biliary tract cancer


title: Control 1


title: Control 2


title: smallRNA seq data from bilirary tract cancer patient B14

description: small RNA


title: smallRNA seq data from bilirary tract cancer patient B17

description: small RNA


title: TGF-α + Gefitinib 1


title: WT_808_1

description:
PolyA RNA
processed data file: matrix_table.txt

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2.
Sequencing adaptor contaminations were removed from reads using Cutadapt v1.3.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3.
Genome_build: GRCm38 assembly, Ensembl gene build 76
Supplementary_files_format_and_content: matrix_table.xls file contains ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.

growth_protocol: Experiments were conducted using E2.5 mouse embryos in an outbred genetic background.

extract_protocol:
RNA from single embryos was isolated using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems).
cDNA libraries were generated using SMART-Seq Ultra Low Input RNA Kit (Clontech).
RNASeq libraries were sequenced (single-end mode and length of 60 bp) on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.

tag: genotype/variation


title: smallRNA seq data from bilirary tract cancer patient B16

description: small RNA


title: TGF-α 2

tag: cell type


title: smallRNA seq data from bilirary tract cancer patient B13

description: small RNA


title: WT_808_4


title: H3 N2 DPY-27 RNAi emb rep1 ChIP-seq


title: H3 N2 DPY-27 RNAi emb rep2 ChIP-seq


title: smallRNA seq data from bilirary tract cancer patient B12

description: small RNA


title: TGF-α 1


title: P9715_125

city: Stockholm

first: Mikael

last: Svensson

state: Stockholm

address: Solnavägen 30

department: Clinical neuroscience

country: Sweden

institute: Karolinska Institutet

data_processing:
FastQC (v0.11.5)
Trim Galore! (v0.4.1)
Star (v2.5.1)
StringTie (v1.3.3)
Preseq (v0.1.0)
featureCounts (v1.5.1)
dupRadar (v1.0.0)
Picard MarkDuplicates (v2.0.1)
Nextflow (v0.25.7)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include counts for each sample

organism: Rattus norvegicus

source_name: Neural Progenitor Cells (NPCs)

extract_protocol:
Trizol (manufacturer’s protocol). Contaminating genomic DNA was removed during the RNA isolation by on-column digestion with DNAse (DNAse I Qiagen, 79254). RNA clean-up was conducted using the RNeasy micro kit (Qiagen, 74004).
SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian kit (Clontech)

tag: exposure


title: P9715_123


title: P9715_122


title: WT_808_3


title: P9715_128


title: 814_KOC (Rep4)


title: P9715_121


title: P9715_127


title: P9715_126


title: KO_808_7


title: P9715_124


title: P9715_119


title: P9715_120


title: smallRNA seq data from bilirary tract cancer patient B09

description: small RNA

tag: group


title: NMuMG ATAC-seq shPBRM1 replicate 1

description:
ATAC_NMuMG_inc_HOMER.txt
ATAC_NMuMG_dec_HOMER.txt

source_name: NMuMG cells

tag: treatment

value: Lentiviral transfection of shPBRM1


title: smallRNA seq data from bilirary tract cancer patient B07

description: small RNA


title: KO_808_6


title: smallRNA seq data from bilirary tract cancer patient B11

description: small RNA


title: smallRNA seq data from bilirary tract cancer patient B10

description: small RNA


title: NMuMG ATAC-seq shPBRM1 replicate 2


title: NMuMG ATAC-seq shPBRM1 replicate 3


title: P9715_118


title: P9715_117


title: P9715_106


title: P9715_114


title: P9715_116


title: NMuMG ATAC-seq null replicate 2

value: Lentiviral transfection of empty vector


title: P9715_105


title: P9715_103


title: NMuMG ATAC-seq null replicate 3


title: P9715_111


title: NMuMG ATAC-seq null replicate 1


title: iPS MNase-Seq

city: Cardiff

first: Adrian

middle: J.

last: Harwood

address: Hadyn Ellis Building, Maindy Road,

department: Neuroscience & Mental Health Research Institute

country: United Kingdom

institute: Cardiff University

data_processing:
Paired end mode sequencing of size-fractionated DNA was performed on a Illumina HiSeq 2000 platform (HiSeq) using a read-length of 50 bp. Base calling and quality control of the sequencing data was performed using Real Time Analysis (RTA) 1.09, CASAVA 1.8 software.
Reads were aligned to the human genome assembly hg19 using Bowtie version 0.12.8
Paired-end reads obtained from Bowtie alignments in .sam format were sorted into separate chromosome-specific files, the mid-point of each insert was determined and the reads were filtered according the insert size. Three size classes of reads were generated for each cell type: 112-137 bp, 138-161 bp and 161-188 bp.   Frequency distributions for the mid-point position of the paired read insert size values counting reads at 10 bp resolution were derived and the data was smoothed using a 3bin moving average.
Whole genome particle.sgr files were generated from the autosomal data and the NPC maps were normalised according to read depth.
Genome_build: hg19
Supplementary_files_format_and_content: Frequency distributions for the autosomal genomes were output  in .sgr format. Sgr files are tab-delimited graph files in the format: chromosome identification: chromosomal location of the start of each 10 bp bin: frequency of the paired-read midpoint values that fall within that 10 bp bin.

source_name: 34D6, male, human iPS cell line

growth_protocol: The 34D6, male, human iPS cell line was cultured in mTeSR1 (Stem Cell Technologies) following the manufacturer’s instructions. Tissue culture plates (Nunclon, Invitrogen) were coated for at least 2 hours with MatrigelTM (BD Biosciences) diluted 1:75 with DMEM (Invitrogen). 34D6 iPS cells were plated at a density of ~106 cells/10cm plate in complete mTeSR1TM medium containing 10μM Y27632 (Tocris) and incubated at 37oC in a standard 5% CO2, humidified incubator (Binder).  iPS cells were passaged by treatment with 10μM Y27632 for 2hrs, then washed with Ca2+/Mg2+- free PBS and cell colonies lifted from the plate by incubation with Dispase (Stem cell technologies) containing 10μM Y27632 (Tocris). Colonies were fragmented by gentle trituration, collected by centrifugation (180 x g) and resuspended in medium for re-plating.

extract_protocol:
Chromatin was prepared from human iPS cells and NPC cells as described previously (Kent, Adams et al. 2011). Three bio-replicates for each cell type were treated independently with MNase.  The cell membranes and nuclei were made permeable to MNase using the detergent NP-40 (Stewart, Reik et al. 1991, Kent and Mellor 1995) and treated by in vivo digestion with 300U/ml MNase at room temperature for 4 minutes. DNA fragments were purified from the MNase treated samples and then the samples for each cell type were pooled in equimolar amounts. DNA extracted from chromatin samples was size-fractionated on agarose gels. 25-35ug of DNA less than 300 bp was size-selected for each cell type.
All of the DNA fragments less than 300 bp in size, generated after MNase digestion, were utilised for sequencing. A standard Illumina paired-end mode sequencing protocol was used, apart from the omission of the nebulisation step and the addition of a further gel purification step to eliminate any excess concatenated linkers after the ligation of linker DNA to the sample.

treatment_protocol: For neural differentiation a dual SMAD inhibition protocol was used (Chambers, Fasano et al. 2009). 34D6 iPS cells were harvested as described above for iPS cell passaging. 34D6 iPS cell colony fragments were plated in non-adherent bacteriological grade culture dishes in ADF differentiation medium to allow for embryoid body formation. ADF differentiation medium comprised advanced DMEM/ F12TM media (Invitrogen) supplemented with penicillin/streptomycin (5μg/l, Invitrogen), L-glutamine (200mM, Invitrogen), 1x Lipid concentrate (Invitrogen), 7.5μg/ml holo-transferrin (Sigma), 14μg/ml Insulin (Roche), 10μM β- mercaptoethanol (Sigma). Medium was supplemented with 10μM Y27632 (Tocris) for the first 2 days, with 10μM SB-431542 (Tocris) until day 4 of differentiation and 0.5μM LDN193189 (Miltenyi) until day 8 of differentiation. Medium was changed every 2 days. At day8, neuralised embryoid bodies were washed with Ca2+/Mg2+-free PBS and then dissociated by incubation at 37oC with accutase (PAA laboratories). A single cell suspension was obtained by gentle trituration and cells washed with ADF medium and harvested by centrifugation at 1000rpm. Neural progenitors were then plated onto tissue culture plates coated with 0.1μg/ml Poly-L-Lysine (Sigma) and 10μg/ml Laminin (Sigma) in ADF medium + 5ng/ml FGF2. 34D6- derived neural progenitors were grown to sub-confluency and passaged once by dissociated with accutase and re-plating. The 34D6 iPS cells derived neural progenitors were harvested for nucleosome preparation on day 16 of differentiation.

value: induced pluripotent cells

tag: cell line

tag: gender

value: male


title: P9715_104


title: P9715_112


title: P9715_113


title: KD_Akt1_siRNAPool4_1 [VEIT10]

city: PARIS

first: Anne Laure

last: Todeschini

address: 15 rue hélène brion

country: France

institute: CNRS/Université Paris Cité

data_processing:
bcl2fastq2 v2.15.0 (Demultiplexing)
Fastqc 0.11.5 (read quality)
Cutadapt-1.9.1 (adaptor trimming)
TopHat2 (mapping) Only reads longer than 10pb were kept for analysis (about 10,000,000 reads per sample)
featureCounts 1.5.0-p2 (counting) and DESeq2 (differential expression analysis)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include logFoldChange for pool siRNA versus scramble.

growth_protocol: Cells were transiently transfected in 6-well plates with 30 pmoles of a pool of 3 different siRNAs against Akt1 (Dharmacon, Lafayette, Colorado, USA; ON-TARGETplus siRNAs, pool KD1: J-040709-06-0005, J-040709-07-0005, J-040709-08-0005, KD2: J-040709-06-0005, J-040709-08-0005, J-040709-09-0005, KD3: J-040709-06-0005, J-040709-07-0005, J-040709-09-0005 and KD4: J-040709-07-0005, J-040709-08-0005, J-040709-09-0005) or an equal amount of the nontargeting/scrambled siRNA (Dharmacon, D-001810-10-05) using Lipofectamine RNAiMax (Thermo Fisher Scientific). 5 hr after transfection, the mix was replaced by culture medium and cells were allowed to grow for 25 hr before performing subsequent experiments.

extract_protocol:
RNA extraction was performed 30 hr after of transfection, following the TRI-reagent supplier’s instructions and 1.3 μg of total RNAs underwent high throughput sequencing.
TruSeq mRNA Stranded library prep kit and library quality was assessed on an Agilent Bioanalyzer 2100, using an Agilent High Sensitivity DNA Kit.

treatment_protocol: Lipofectamine RNAiMax (supplier’s instructions)

tag: strain background

value: primary ovarian granulosa cells

value: siRNAs against Akt1


title: EcR_6hAPF_CUTnRUN_Rep1

city: New York

first: Christopher

middle: Mitsuo

last: Uyehara

address: 413 E 69th St

department: Meyer Cancer Center

institute: Weill Cornell Medicine

data_processing:
Library strategy: CUT&RUN
CUT&RUN - Adapter sequences were removed using bbmap (v37.50) using parameters ktrim=r ref=adapters rcomp=t tpe=t tbo=t hdist=1 mink=11
CUT&RUN - trimmed reads were aligned to the genome using bowtie (v2.2.8) using parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
CUT&RUN - reads with a qual score less than 5 were removed using samtools (v1.3.1)
CUT&RUN - PCR duplicates were remove using Picard (v2.2.4)
CUT&RUN - Bam files were converted to bed files using bedtools (v2.25.0) with parameter -bedpe
CUT&RUN - fragments were split into 20-120bp and 150-700 bp fragment lengths using awk
CUT&RUN - samples were merged by concatenating the reads together into a single file
CUT&RUN - peaks were called using MACS2 (v. 2.1.1.20160309) on individual replicates and merged bed files with 20-120bp fragments with parameters --nomodel --seed 123 -g 121400000
CUT&RUN - a final peak set was obtained by taking peaks that were called in the merged bed files peak calls and at least one replicate
CUT&RUN - bigwigs were generated by first generating bedgraphs using bedtools (v2.25.0) and then converting them to bigwigs using ucsctools (v320)
CUT&RUN - bigwigs were z-normalized using a custom R-script. Z-normalization of each chromosome arm was performed seperately.
processed data files format and content: z-normalized bigwigs for each merged CUT&RUN sample for the 20-120bp fragments
processed data files format and content: bed files that contain peaks locations for -6hAPF and +6hAPF. MACS2 narrowpeak (BED6+4) format is used.
Genome_build: dm3

organism: Drosophila melanogaster

source_name: +6hAPF wings

growth_protocol: Animals were raised at 25C. For the -6hAPF time point, wandering (3LW) larvae were used. For the +6hAPF time point, animals were staged at the white, pre-pupae stage.

extract_protocol: Wings were individually dissected in 1XPBS  and then transferred to a 9-well dissecting dish on ice.

tag: developmental stage

tag: genotype

value: w/w; EcR[GFSTF] / Df(2R)BSC313

tag: tissue

value: wing

value: EcR-GFSTF

tag: cut&run antibody

value: mouse anti-FLAG (Sigma F1804)

tag: Sex

value: female

tag: library construction

value: Rubicon Thruplex 12S DNAseq Kit


title: KD_Akt1_siRNAPool3_1 [VEIT8]


title: P9715_101


title: P9715_110


title: KD_Akt1_siRNAPool2_2 [VEIT7]


title: NPC MNase-Seq

source_name: 34D6 iPS cells-derived neural progenitors

value: neural progenitor cells


title: P9715_109


title: P9715_107


title: P9715_108


title: KD_Akt1_siRNAPool4_2 [VEIT11]


title: KD_Akt1_siRNAPool1_2 [VEIT5]


title: P9715_102


title: KD_Akt1_siRNAPool1_1 [VEIT4]


title: EcR_6hAPF_CUTnRUN_Rep2


title: KD_Akt1_Scramble_3 [VEIT3]

value: nontargeting/scrambled siRNA


title: KD_Akt1_siRNAPool3_2 [VEIT9]


title: P9715_115


title: EcR_3LW_CUTnRUN_Rep1

source_name: -6hAPF wings


title: EcR_3LW_CUTnRUN_Rep2


title: KD_Akt1_siRNAPool2_1 [VEIT6]


title: bronchiolar Club cells, rep2

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
Raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Reaper version 13-100 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides (Davis et al., Kraken: A set of tools for quality control and analysis of high-throughput sequence data). Only reads between 30 and 150 nucleotides were cleared for further analyses
Trimmed and filtered reads were aligned versus Ensembl mouse genome version mm10 (GRCm38) using STAR 2.4.0a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%
). The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include library size normlized counts per peak

source_name: lung tissue

extract_protocol:
Total RNA was isolated from FACS sorted cells using the miRNeasy micro Kit (Qiagen)
100pg of total RNA was used as input for SMARTer® Stranded Total RNA-Seq Kit - Pico Input Mammalian (Takara Clontech).

treatment_protocol: Primary murine lung epithelial cells were isolated based on endogenous reporter expression by FACS from CD31/CD45-depleted lung homogenates

value: primary bronchiolar Club cells

tag: marker profile

value: CCSP-mCherry+

tag: age

value: 8 weeks


title: KD_Akt1_Scramble_2 [VEIT2]


title: KD_Akt1_Scramble_1 [VEIT1]


title: bronchioalveolar stem cells, rep2

value: primary bronchioalveolar stem cells

value: CCSP-mCherry+/SPC-YFP+


title: F3_T_B: Fragment 3 Total RNA Replicate B

type: RNA

city: São Paulo

first: Glaucia

last: Hajj

state: SP

address: Rua Taguá 440

country: Brazil

institute: AC Camargo Cancer Center

description: Technical Replicate B

hyb_protocol: About 825ng of each test sample was combined at 825ng of the reference sample. 10X Blocking Agent, 25X Fragmentation Buffer and water were added to a final volume of 55μL. The hybridization mixture (100μL) was added to the slides and they remained in the hybridization oven for 16 hours at 37 ° C and 20rpm. Washing of slides occurred in consecutive baths in Wash Buffer 1, Wash Buffer 2, Acetonitrile (Sigma-Aldrich, MO, USA) and Stabilization and drying solution.

scan_protocol: Fluorescence signals were captured on the Agilent scanner using Scan Control 8.1 software (Agilent Technologies, CA, USA). All cases met the manufacturer's quality criteria, which includes, in particular, background analysis, hybridization uniformity, green and red signal strength, and variation of the duplicates.

data_processing: Agilent Feature Extraction result text files were processed with limma package using loess normalization and minimum background correction.

source_name: test sample

label_protocol: Sampling, hybridization and detection procedures followed the Two-color microarray-based gene expression analysis protocol using the Quick Amp Labeling Kit (Agilent Technologies, CA, USA). The cDNA pre-synthesis was performed using 800ng of total RNA, 2μL of the dilution of Spikes A and B and 1.2μL of T7 Promoter Primer. The cDNA synthesis consisted of the addition of 5X First Strand Buffer, 0.1M DTT, dNTP mix, 0.5μL of the RNase Out enzyme and 1μL of the MMLV-RT enzyme. Transcription of cDNA to cRNA occurred by reaction containing 15.3μL sterile water, 4X Transcription Buffer, 50% PEG, 0.1M DDT, 8μL NTP mix, 0.5μL RNase Out, 0.6μL Inorganic Pyrophosphatase, 2 , 4μL of Cy3 or Cy5 and 0.8μL of the T7 RNA Polymerase enzyme. The probes were purified using the RNeasy Mini Kit (Quiagen, TE, USA), following the manufacturer's specifications. The labeling intensity and reaction yield were evaluated for all samples using NanoDrop 1000 (Thermo Fisher Scientific Inc., MA, USA).

extract_protocol: The tissues were lysed in a Polytron with 400 ml of lysis buffer (20 mM Tris-HCl pH 7.5, 100 mM NaCl, 10 mM MgCl2, 1% Triton X-100, 1 mM DTT, 100 μg/mL cycloheximide, 100 units of RNAse inhibitor (Promega) and 1X protease inhibitor cocktail (EDTA-free)). The lysates were incubated on ice for 10 minutes, then centrifuged at 10.000 xg for 10 minutes at 4 °C. The supernatants were collected, 60 ml were reserved for total RNA extraction and 300 µL were loaded into 7–47% sucrose gradients (20 mM Tris-HCl pH 7.5, 100 mM NaCl, 10 mM MgCl2, 1 mM DTT). Each gradient was formed by mixing 5.5 mL of the indicated concentration of sucrose in a Beckman Centrifuge tube (14×89 mm; Beckman Instruments #3311372, CA, USA) using a Labconco pump (Kansas City, MO, USA). Gradients were placed in a Beckman SW41Ti rotor and centrifuged at 39,000 rpm for 2.5 hours at 4 °C. The absorbance at 254 nm was measured in a continuous flow and fractions were collected (1 mL each). Translational rates were measured by the ratio between the area under the curve of the polysome and 80S peaks, using Image J software (U. S. National Institutes of Health, Bethesda, MD, USA).

value: Glioblastoma

tag: histological grade

value: high

tag: rna type

value: total

source_name: reference sample

value: glioblastoma cell line LN-229


title: F5_P_B: Fragment 5 Polysome RNA Replicate B

description: Technical Replicate B

value: low

value: polysome associated


title: F8_T_B: Fragment 8 Total RNA Replicate B

description: Technical Replicate B


title: F3_P_B: Fragment 3 Polysome RNA Replicate B

description: Technical Replicate B


title: F8_P_A: Fragment 8 Polysome RNA Replicate A

description: Technical Replicate A


title: F4_P_A: Fragment 4 Polysome RNA Replicate A

description: Technical Replicate A


title: F4_T_B: Fragment 4 Total RNA Replicate B

description: Technical Replicate B


title: smallRNA seq data from healthy control N19

description: small RNA

value: healthy control


title: F5_T_B: Fragment 5 Total RNA Replicate B

description: Technical Replicate B


title: F4_P_B: Fragment 4 Polysome RNA Replicate B

description: Technical Replicate B


title: F8_T_A: Fragment 8 Total RNA Replicate A

description: Technical Replicate A


title: F1_T_B: Fragment 1 Total RNA Replicate B

description: Technical Replicate B


title: F4_T_A: Fragment 4 Total RNA Replicate A

description: Technical Replicate A


title: F8_P_B: Fragment 8 Polysome RNA Replicate B

description: Technical Replicate B


title: alveolar type 2 cells, rep2

tag: cell type

value: primary alveolar type 2 cells

value: SPC-YFP+


title: bronchiolar Club cells, rep1


title: alveolar type 2 cells, rep1


title: F3_P_A: Fragment 3 Polysome RNA Replicate A

description: Technical Replicate A


title: bronchioalveolar stem cells, rep1


title: T022: roots, experimental group (100mg/kg Cd)

city: Chengdu

first: Zhenyu

last: Bai

address: 211 Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: http://www.mbkbase.org/Pinku1/
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Verbena bonariensis

source_name: roots, experimental group (100mg/kg Cd)

growth_protocol: Verbena bonariensis seeds were available from Benary Manufacturer and grown in the greenhouse (14 h photoperiod, 24±3℃ temperature)

extract_protocol:
Verbena bonariensis roots were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The control group （T01）did not add Cd solution, the concentration of Cd in the experimental group was 100mg/kg(T02). 20 days after Cd stress, all the plants were harvested. In this experiment, the seedings were grown in ambient conditions with a photoperiod of 14 h at 25℃ and a relative humidity of 75%.  The roots samples were immediately frozen in liquid nitrogen and stored at -80°C.It’s three biological replicates per treatment for subsequent RNA extraction and analysis.

tag: strain

value: Finesse

value: roots


title: T023: roots, experimental group (100mg/kg Cd)


title: F7_T_B: Fragment 7 Total RNA Replicate B

description: Technical Replicate B


title: F1_P_A: Fragment 1 Polysome RNA Replicate A

description: Technical Replicate A


title: F3_T_A: Fragment 3 Total RNA Replicate A

description: Technical Replicate A


title: T021: roots, experimental group (100mg/kg Cd)


title: F7_P_B: Fragment 7 Polysome RNA Replicate B

description: Technical Replicate B


title: T013: roots, control group (no Cd solution)

source_name: roots, control group (no Cd solution)


title: T012: roots, control group (no Cd solution)


title: F1_T_A: Fragment 1 Total RNA Replicate A

description: Technical Replicate A


title: F1_P_B: Fragment 1 Polysome RNA Replicate B

description: Technical Replicate B


title: F7_T_A: Fragment 7 Total RNA Replicate A

description: Technical Replicate A


title: F7_P_A: Fragment 7 Polysome RNA Replicate A

description: Technical Replicate A


title: F5_T_A: Fragment 5 Total RNA Replicate A

description: Technical Replicate A


title: Celnbuteol 3

city: Kagoshima

first: Daichi

last: Ijiri

address: Korimoto 1-21-24

country: Japan

institute: Kagoshima University

description:
C2C12_T2-3
Test3ProcessedSignal

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 18 hr at 48C on Affymetrix GeneChip microRNA 4.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: C2C12_stimulated with 1μM clenbuterol

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: C2C12 myoblast cells were cultured in DMEM supplemented with 10 % FBS and 1 % P/S. Then,  to induce myotube formation, the medium was replaced with DMEM supplemented with 2 % HS and 1 % P/S.

extract_protocol: RNA was isolated using the mirVana™ miRNA Isolation Kit (Ambion, Austin, TX, USA).

treatment_protocol: C2C12 myotubes were treated with clenbuterol (1 μM) for 1 hour.

value: myoblast cells

value: 1μM clenbuterol


title: F5_P_A: Fragment 5 Polysome RNA Replicate A

description: Technical Replicate A


title: T011: roots, control group (no Cd solution)


title: Input-DR8dex2_Luc

city: Beijing

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

description: Input of DR8_dex2 hMSCs transduced with Luc.

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human refference genome using bowtie2 software.
For peak callling, MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files that we uploaded are MACS2 called peak files. And, all of the processed data files are xls format.

source_name: Mesenchymal stem cell

growth_protocol: Human MSCs (hMSCs) derived from hESCs were cultured in MEMa (Thermo Fisher Scientific) medium supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific (Cat:10099-141, Lot:1616964)), 0.1 mM non-essential amino acids (Thermo Fisher Scientific), 1% penicillin/streptomycin (Thermo Fisher Scientific), and 1 ng/mL bFGF (Joint Protein Central, JPC).

extract_protocol:
DNA was isolated using phenol-chloroform-isoamylalcohol extraction and ethanol precipitation.
The H3K9me3 enriched fragments were contructed into libararies via KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series(KK8504) following the manuals.

value: ESC-derived mesenchymal stem cell

tag: genotype/variation

value: transduced with Luc


title: Input-DR8dex2_MT

description: Input of DR8_dex2 hMSCs transduced with DR8-mtDRBD.

value: transduced with DR8-mtDRBD


title: Podocytes_SMPDL3b OE 3

city: Miami

first: Shamroop

middle: kumar

last: Mallela

state: Florida

address: 1580 NW 10th Ave

department: Medicine

institute: University of Miami

description: Differential expression of SMPDL3b OE to Ctrl

data_processing:
Raw sequence data were processed by the on-instrument Real Time Analysis software (v.2.7.7) to basecall files. These were converted to de-multiplexed FASTQ files with the Illumina supplied scripts in the BCL2FASTQ software (v2.17).
The quality of the reads was determined with FASTQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) for per base sequence quality, duplication rates, and overrepresented k-mers. Illumina adapters were trimmed from the ends of the reads using Trim Galore! package (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Reads were aligned to the human reference genome (hg19) with the STAR aligner (v2.5.0a)7. Gene count quantification for total RNA was performed using the GeneCounts function within STAR against the GENCODE v19 transcript gtf file.
Gene count data were input into edgeR software8 for differential expression analysis. Briefly, gene counts were normalized against total aligned reads for each sample to generate counts per million (cpm) expression value for each gene in each sample. Given the relatively small sample size per group for comparison (n=3 in each group) the exact test implemented in edgeR was used to determine differential expression including a false discovery rate p-value.
Supplementary_files_format_and_content: Raw Counts, Normalized CPM Values

growth_protocol: Human podocytes were differentiated at 37C for 14 days

extract_protocol:
RNA was extracted using Rneasy plus mini kit from Qiagen
Preparation and sequencing of RNA libraries was carried out in the John P. Hussman Institute for Human Genomics Center for Genome Technology. Briefly, total RNA was quantified and qualified using the Agilent Bioanalyzer to have an RNA integrity score (RIN) above 7. For each of the six samples, 500 ng of total RNA was used as input for the Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero to create ribosomal RNA depleted sequencing libraries. Each sample had a unique barcode to allow for multiplexing and >35 million raw reads in a 2x100 paired end sequencing run on the Illumina HiSeq 3000 were obtained

value: Immortalized, differentiated podocytes

value: SMPDL3b OE


title: Input-DR8dex2_WT

description: Input of DR8_dex2 hMSCs transduced with DR8-WT.

value: transduced with DR8-WT


title: Podocytes_SMPDL3b OE 2


title: Podocytes_SMPDL3b OE 1


title: ChIP-DR8dex2_WT-4

description: H3K9me3 ChIP-seq profile of DR8_dex2 hMSCs transduced with DR8-WT.


title: Celnbuteol 1

description:
C2C12_T2-1
Test1ProcessedSignal

tag: treatment


title: Control 3

description:
C2C12_T1-3
Control3ProcessedSignal

source_name: No treatment control of C2C12

value: none (control)


title: Control 2

description:
C2C12_T1-2
Control2ProcessedSignal


title: Control 1

description:
C2C12_T1-1
Control1ProcessedSignal


title: Podocytes_Ctrl 3

value: control


title: Celnbuteol 2

description:
C2C12_T2-2
Test2ProcessedSignal


title: ChIP-DR8dex2_WT-2


title: Podocytes_Ctrl 2


title: ChIP-DR8dex2_WT-3


title: ChIP-DR8dex2_MT-4

description: H3K9me3 ChIP-seq profile of DR8_dex2 hMSCs transduced with DR8-mtDRBD.


title: Podocytes_Ctrl 1


title: KO_HFD_3_female

city: Clemson

first: William

middle: S

last: Baldwin

state: South Carolina

address: 230 Parkway Dr

department: Biological Sciences

institute: Clemson University

description: Rawcounts_Female_Cyp2bnull_HFD_study.txt

data_processing:
Illumina Control Software/Real-Time Analysis (RTA) was used for base-calling.
Samples were sequenced to an average sequencing depth of 20,000,000 read pairs with a 2 x 150 paired-end module.
Quality metrics were checked using FastQC on all samples sequenced, and Trimmomatic was used to trim low quality bases.
Trimmed reads were aligned to the Mus musculus reference genome (GCF_000001635.25_GRCm38.p5) using GSNAP.  Subread feature counts software finds reads that aligned with known genes.
Raw read counts and EdgeR were used to determine differential gene expression.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Tab-deliminated text file includes raw counts for each sample.

source_name: liver

extract_protocol:
Livers were removed and stored at -80 degrees C. RNA was extracted from each treatment group (n=3) using Trizol.
Libraries were prepared using NEB Next Ultra RNA Library Prep kit.

treatment_protocol: WT and Cyp2b-null mice were fed either a normal chow diet (ND) or high fat diet (HFD, 60 % fat) for 10 weeks.

value: Cyp2b9/10/13-null (Cyp2bnull)

value: female

value: liver


title: KO_HFD_2_female


title: ChIP-DR8dex2_MT-2


title: KO_HFD_1_female


title: KO_ND_3_female

value: wild type (WT)


title: ChIP-DR8dex2_MT-1


title: Primary oral melanoma_metastasising_rep5

city: Newmarket

first: Mike

last: Starkey

address: Lanwades Park

institute: Animal Health Trust

hyb_protocol: 3µg of each labelled cDNA was included in a 120µl 'hybridisation cocktail' comprising 1 x Hyb Add 1, 30pM Control Oligo B2, 1 x Hybridisation Controls, 1 x WT Hyb Add 4 and 1 x WT Hyb Add 6. The cocktail was incubated at 99°C for 5 min and then at 48°C for 5 min, and centrifuged for 5s to remove insoluble material. Hybridisation was performed at 48°C for 20h in the GeneAtlas Hybridisation Station. Post-hybridisation washing and staining (‘42C_20m.xml’ washing and staining protocol; IVT/WT Wash/Stain and Imaging Tray maps) was performed using the GeneAtlas System Fluidics Station.

scan_protocol: Arrays were scanned using the GeneAtlas System Imaging Station.

data_processing:
Gene-level probe set expression values were generated by quantile normalisation, log2 transformation and signal summarisation, performed using the Robust Multichip Analysis algorithm, implemented within ‘Affymetrix Expression Console Software 1.3’.
probe group file: CanGene-1_1-st-v1.na36.canfam2.probeset.csv
meta-probeset file: CanGene-1_1-st-v1.na36.canfam2.transcript.csv

label: Biotin

organism: Canis lupus familiaris

source_name: Primary oral melanoma, metastasising

label_protocol: Fragmented, biotinylated single-stranded cDNA was prepared from 5.1ng of each total RNA sample using the GeneChip WT Pico Reagent Kit (ThermoFisher Scientific).

extract_protocol: Total RNA was isolated using the RecoverAll Total Nucleic Acid Isolation Kit. RNA was further purified by spin column filtration (OneStep PCR Inhibitor Removal Kit), and subject to further DNase digestion (TURBO DNA-free kit).

tag: metastatic status

value: Metastasising

tag: breed

value: Labrador Retriever


title: ChIP-DR8dex2_Luc-4

description: H3K9me3 ChIP-seq profile of DR8_dex2 hMSCs transduced with Luc.


title: ChIP-DR8dex2_WT-1


title: Primary oral melanoma_metastasising_rep2


title: Primary oral melanoma_non-metastasising_rep5

source_name: Primary oral melanoma, non-metastasising

value: Non-metastasising


title: ChIP-DR8dex2_Luc-3


title: KO_ND_1_female


title: Primary oral melanoma_non-metastasising_rep4


title: WT_HFD_3_female


title: ChIP-DR8dex2_Luc-2


title: Primary oral melanoma_non-metastasising_rep9

value: Golden Retriever


title: Primary oral melanoma_metastasising_rep7


title: Primary oral melanoma_non-metastasising_rep6


title: Primary oral melanoma_non-metastasising_rep3


title: Primary oral melanoma_non-metastasising_rep2


title: Primary oral melanoma_metastasising_rep15


title: ChIP-DR8dex2_MT-3


title: WT_HFD_2_female


title: Primary oral melanoma_non-metastasising_rep7

value: Irish Terrier


title: Primary oral melanoma_metastasising_rep10


title: Primary oral melanoma_metastasising_rep14


title: Primary oral melanoma_metastasising_rep8


title: ChIP-DR8dex2_Luc-1

value: ESC-derived mesenchymal stem cell


title: WT_HFD_1_female


title: KO_ND_2_female


title: WT_ND_3_female


title: WT_ND_2_female


title: WT_ND_1_female


title: B200CK: 200uM Fe2(SO4)3

first: Qin

last: Yao

state: Sichuan

address: Huimin Road

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: http://www.mbkbase.org/Pinku1/
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Triticum polonicum

source_name: dwarf Polish wheat

extract_protocol:
Fresh roots frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The groups treated with two fertilizers and CdCl2 solution before collected.The samples were collected after one week treatment. The roots samples were immediately frozen in liquid nitrogen and stored at -80°C.It’s three biological replicates per treatment for subsequent RNA extraction and analysis.

value: roots

value: 4weeks seedlings


title: B200Cd: 50uM Fe2(SO4)3+80uM CdCl2

value: 50uM Fe2(SO4)3+80uM CdCl2


title: B50Cd: 50uM Fe2(SO4)3


title: Primary oral melanoma_metastasising_rep6

value: Dachshund


title: B50CK: 200uM Fe2(SO4)3+80uM CdCl2

value: 200uM Fe2(SO4)3+80uM CdCl2


title: Primary oral melanoma_non-metastasising_rep1

value: Great Dane


title: Primary oral melanoma_metastasising_rep1


title: CreTW_4

city: Cologne

first: Bent

last: Brachvogel

address: Joseph-Stelzmann Street 52

institute: University of Cologne

hyb_protocol: Agilent Gene Expression Hybridization Kit

scan_protocol: Agilent G5761A Scanner

data_processing: Genespring 14.9

source_name: CreTW

label_protocol: Agilent low-Input QuickAmp Labeling Kit

extract_protocol: Trizol for RNA isolation

value: growth plate cartilage

value: CreTW


title: Primary oral melanoma_non-metastasising_rep10

value: Cross breed


title: Cre_3

source_name: Cre

value: Cre


title: A200Cd: 200uM FeCl3+80uM CdCl2

value: 200uM FeCl3+80uM CdCl2


title: CreTW_3


title: Cre_4


title: Cre_2


title: d_25

first: li

last: lei

address: xiashas street num 6

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to  whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Citrullus lanatus subsp. vulgaris cv. 97103
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Citrullus lanatus

source_name: watermelon leaf

growth_protocol: Watermelon leaves at two-true stage

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Watermelon leaves were inoculated with CGMMV and sampled at ck, 48h and 25d post CGMMV infection

tag: time

value: leaf at 25d post CGMMV inoculation


title: CreTW_2


title: A200CK: 200uM FeCl3

tag: developmental stage

value: 200uM FeCl3


title: Primary oral melanoma_metastasising_rep13

value: Metastasising


title: h_48

value: leaf at 48h post CGMMV inoculation


title: ck

value: leaf at 0h post CGMMV inoculation


title: A50Cd: 50uM FeCl3+80uM CdCl2

value: 50uM FeCl3+80uM CdCl2


title: CreTW_1


title: A50CK: 50uM FeCl3

value: roots

value: 50uM FeCl3


title: Primary oral melanoma_metastasising_rep11


title: Primary oral melanoma_metastasising_rep17


title: Cre_1


title: END_seq_HCT116__RAD21_AID_0_5h

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

institute: Bar-Ilan University

description: control: END_seq_HCT116_NT.fastq.gz

data_processing:
mouse and human END-seq reads were aligned to the GRCm38p2/mm10 and  GRCh37/hg19 genome assemblies,respectively.
Alignment done using bowtie version 0.12.7, with the parameters:   --best --all --strata  -n 3 -k1 -l 50
END-seq peaks were called using MACS 1.4.3  with the parameters: --nolambda,-- nomodel and –keep-dup=all (keep all redundant reads). For Etoposide-treated END-seq data peak calling, we used the corresponding non-treated samples as control, keeping >10 fold-enriched peaks.
END-seq data from pre-B cells, where cells with ZFN break were spiked-in to the library at a 1:50 (2%) ratio, the RPKM value for each peak was divided by the signal around the spiked-in breaks and then multiplied by 2, to get values as cell-percentage. From this value, X, the #cells per lesion were calculated as 100/X.
Genome_build: GRCm38p2/mm10 for mouse and  GRCh37/hg19 for human
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

growth_protocol: Abelson pre-B cell lines were cultured DMEM supplemented 10% FBS, with 2 mM L-glutamine, 1 mM Sodium piruvate, non-essential amino acids, 0.05 mM β-mercaptoethanol, penicillin (100 U/ml) and streptomycin (100 U/ml) (Invitrogen). MEFS were cultured and floxed alleles deleted as described (Busslinger et al., 2017). Mature WT and  Top2b-/- B-cells were generated by bone marrow reconstitution of lethally irradiated recipient mice with fetal liver cells derived from WT and Top2b-/- embryos, respectively. Recipient mice were irradiated with 950 rads, 4 hours before injection of 3 million donor fetal liver cells. Between 6 to 12 weeks after reconstitution mature resting B cells were isolated from recipient mouse spleen with anti-CD43 MicroBeads (Miltenyi Biotech). B cells were activated with LPS (25 mg/ml; Sigma), IL-4 (5 ng/ml; Sigma) and RP105 (0.5 mg/ml; BD) for 12 hr as described (Callen et al., 2013) and treated for 30 minutes with 50uM of etoposide.HCT116 cells were obtained from (Natsume et al., 2016), arrested in G1 by the treatment with 20uM of lovastatin for 24 hours and treated with auxin for 4 hours before 50uM etoposide treatment for 30 minutes.

extract_protocol:
Single cell suspensions of pre-B cells (40 million per agarose plug),  MEFS (4 million per agarose plug), and HCT116 (15 million per 2 agarose plugs) were washed in PBS, embedded in agarose and transferred into plug molds (Bio-Rad CHEF Mammalian Genomic DNA plug kit) and processed as previously described (Canela et al., 2016)
END-seq was performed as described in Canela et al., 2017. Agarose plugs were made using the Bio-Rad CHEF Mammalian Genomic DNA plug kit. Embedded cells were lysed and digested using Proteinase K (50º C, 1 hour then  37ºC for 7 hours). Plugs were rinsed in TE buffer and treated with RNase A at 37ºC, 1 hour. The next enzymatic reactions were performed with the DNA in agarose plugs to prevent shearing. DNA ends were blunted for 1 hour at 37C with Exonuclease VII followed by Exonuclease T (NEB) for 1 hour at 25ºC to detect all TOP2 lesions, or only with Exonuclease T (NEB) 1 hour at 25C to detect only DSBs, "ExoT END-seq". After blunting, A-tailing was performed, followed by ligation of “END-seq hairpin adaptor 1”, 5′-Phos-GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGUU[Biotin-dT]U[Biotin-dT]UUACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3′ [*phosphorothioate bond], using NEB Quick Ligase.  Agarose plugs were then melted and dialyzed and DNA was sonicated to a median shear length of 170bp using Covaris S220 sonicator. DNA was ethanol-precipitated and dissolved in 70 ul TE buffer. Biotinylated DNA was isolated using MyOne Streptavidin C1 Beads (ThermoFisher #650-01), followed by end repair and dA-tailing. The second end was ligated to “END-seq hairpin adaptor 2”, 5′-Phos-GATCGGAAGAGCACACGTCUUUUUUUUAGACGTGTGCTCTTCCGATC*T-3′ [*phosphorothioate bond], using NEB Quick Ligase. Hairpins were digested using USER (NEB), and the resulting DNA fragments were PCR amplified using TruSeq barcoded primer p5, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATC*T and TruSeq barcoded primer p7, CAAGCAGAAGACGGCATACGAGANNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T, (NNNNNNNN represents barcode and * a phosphothiorate bond).  PCR fragments were isolated by size selection from agarose gel, selecting 200-500 bp fragments followed by DNA purification using QIAquick Gel Extraction Kit. Libraries were quantified using KAPA Library Quantification Kit and sequenced using Illumina NextSeq 500 or 550.

treatment_protocol: Pre-cells were arrested in G1 by treatment with 3 mM imatinib for 48 hr and then treated with etoposide for the times indicated. MEFs, after 10 days in confluence and serum starvation (2% charcoaltreated FBS) were treated with 50uM of etoposide during 30 minutes and 2 hours and 30 minutes. HCT116 cells were arrested in G1 by the treatment with 20uM of lovastatin for 24 hours and treated with auxin for 4 hours before 50uM etoposide treatment for 30 minutes. For transcription inhibition or stimulation, and proteasome inhibition drug pre-treatment was performed for 2 hours with 150 mM DRB (D-ribofuranosylbenzimidazole, Sigma) or 2uM of epoxomicin (Sigma) prior to etoposide treatment. Drugs were maintained during the treatment with etoposide.

tag: genotype

value: RAD21 AID


title: Primary oral melanoma_metastasising_rep3


title: END_seq_HCT116_NT (control)

description: control: N/A

value: WT


title: Primary oral melanoma_metastasising_rep4


title: Primary oral melanoma_metastasising_rep16

value: Bullmastiff


title: RNA-seq_ETV4KO2_E2

status: Public on Apr 23 2019

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

data_processing:
Reads were aligned to the human genome using HISAT2
Sam files were then converted to bam files and sorted via Samtools
Read counts for each gene were determined from alignments to hg19 UCSC knownGene gene models using featuresCounts from the SubRead package
Normalization and differential expression analysis were performed using DeSeq2
Genome_build: hg19
Supplementary_files_format_and_content: Gene counts in a text file

source_name: Endometrioid adenocarcinoma_1 hr 10nM E2

growth_protocol: Ishikawa cells (Sigma-Aldrich) were grown in full media (RPMI-1640 (Gibco), 10% fetal bovine serum (Gibco), and 1% penicillin-streptomycin (Gibco)).  Five days prior to induction, cells were moved to hormone-depleted media with phenol-red free RPMI-1640(Gibco), 10% charcoal-dextran treated fetal bovine serum (Sigma-Aldrich), and 1% penicillin-streptomycin(Gibco).

extract_protocol:
Cells were harvested from 10cm dishes in 600mL RLT Plus (Qiagen) supplemented with 1% beta-mercaptoethanol after an 8 hour induction with 10nM E2 or DMSO.  RNA purification was performed using RNA Clean and Concentrator (Zymo Research) with the optional DNase I treatment.
The KAPA Stranded mRNA-seq kit (Kapa Biosystems) was used to create Poly(A) selected libraries from 1mg total RNA.

treatment_protocol: Inductions involved treating cells with 0.1% DMSO, as a vehicle control, or 10nM E2 (Sigma-Aldrich) for 8 hours

tag: cell line

value: Ishikawa ETV4 KO clone 2

value: Endometrioid adenocarcinoma

value: 1 hr 10nM E2


title: RNA-seq_ETV4KO1_E2

value: Ishikawa ETV4 KO clone 1


title: RNA-seq_ETV4KO2_DMSO

source_name: Endometrioid adenocarcinoma_1 hr 0.1% DMSO

value: 1 hr 0.1% DMSO


title: Primary oral melanoma_metastasising_rep18

value: Border Collie


title: Primary oral melanoma_metastasising_rep12

value: Cross breed


title: ChIP-seq_Ishi_T47D_ETV4_FLAG

description: FLAG-ETV4 ChIP-seq

data_processing:
Reads were aligned using Bowtie with the parameters: -m 1  -t –best -q -S -l 32 -e 80 -n 2
Peaks were called using MACS2 with a p-value cutoff of 1e-10 and the mfold parameter constrained between 15 and 100.
To determine read depth of peaks called, bedtools coverage was used to calculate the counts
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph, narrowpeaks

source_name: FLAG-ETV4 ChIP-seq

growth_protocol: Ishikawa cells (Sigma-Aldrich) and T-47D cells (ATCC) were grown in full media (RPMI-1640 (Gibco), 10% fetal bovine serum (Gibco), and 1% penicillin-streptomycin (Gibco)).  Five days prior to induction, cells were moved to hormone-depleted media with phenol-red free RPMI-1640(Gibco), 10% charcoal-dextran treated fetal bovine serum (Sigma-Aldrich), and 1% penicillin-streptomycin(Gibco).

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Crosslinking was stopped with 125mM Glycine and cells were washed and scraped in cold PBS. IP was done as described in Reddy et al 2009 using Santa Cruz ERα (HC-20)
TruSeq library construction as described in Reddy et al 2009

treatment_protocol: Inductions involved treating cells with 0.1% DMSO, as a vehicle control, or 10nM E2 (Sigma-Aldrich) for 1 hour

value: T-47D ETV4 ectopic expression

value: ER+ breast ductal carcinoma cell line

tag: chip antibody

value: Sigma FLAG M2

value: ETV4 ectopic expression


title: ChIP-seq_Ishi_ETV4KO2_Rescue_ER_E2

description: ER ChIP-seq

source_name: ER ChIP-seq

value: Ishikawa ETV4 KO clone 2, ETV4 ectopic expression

value: Endometrioid adenocarcinoma cell line

value: Santa Cruz ERalpha (HC-20)

value: ETV4 KO, ETV4 ectopic expression


title: ChIP-seq_Ishi_ETV4KO1_Rescue_ER_E2

description: ER ChIP-seq

value: Ishikawa ETV4 KO clone1, ETV4 ectopic expression


title: ChIP-seq_Ishi_T47D_DMSO_Input

description: ER ChIP-seq

value: WT


title: ChIP-seq_Ishi_WT_ETV4Overexpression_ER_E2

description: ER ChIP-seq

value: Ishikawa ETV4 ectopic expression


title: Primary oral melanoma_non-metastasising_rep8

value: Non-metastasising

value: Bouvier des Flandres


title: Acd: 80uM CdCl2

tag: tissue

value: roots

value: 4weeks seedlings

value: 80uM CdCl2


title: ChIP-seq_Ishi_ETV4KO2_E21hr_ER_B

description: ER ChIP-seq

value: Ishikawa ETV4 KO clone 2

value: 1 hr 10nM E2

value: ETV4 KO


title: ChIP-seq_Ishi_ETV4KO1_E21hr_ER_B

description: ER ChIP-seq

value: Ishikawa ETV4 KO clone 1


title: ChIP-seq_Ishi_Ishi_E21hr_ER_B

description: ER ChIP-seq

value: Ishikawa


title: ACK: Null


title: Yl growth in SM TH- vs Yl growth in SM TH+ 4

city: Thiverval Grignon

first: Reine

last: Malek

address: Avenue Lucien Brétignières

institute: INRA, UMR 1319 MICALIS

hyb_protocol: Hybridizations were performed for 17h at 65°C in dedicated micro-chambers with 300 ng of the different labelled samples.hybridization buffer was from Agilent (ref 5188-5242)

scan_protocol: Agilent G2565 Scanner in extended dynamic range with a resolution of 5nm per pixel

data_processing:
Intensity-dependent normalization was performed with the LOESS procedure followed by subtraction of the log-ratio median calculated over the values for an entire block from each individual log-ratio using the anapuce package of R. Differential analysis was performed with the varmixt package of R.
the raw P values were adjusted by the Bonferroni method
genes with both a P-value < 0,05 and a ratio higher than 2 were considered as diffrentially expressed

organism: Yarrowia lipolytica

source_name: growth of Y. lipolytica on SM TH+

label_protocol: RNA was labeled using two different fluorescent dyes: cyanine 3-CTP and cyanine 5-CTP as described in the Agilent Low Input Quick Amp labeling Kit.

growth_protocol: Yarrowia lipolytica was grown in a Synthetic agar Medium (SM) with or without THiamin (TH+ or TH-), for 14 days of culture, at 25°C.

extract_protocol: Total RNA was extracted by trizol treatment (Invitrogen, Carlsbad, CA, USA) for Yl cultivated on SM TH+, and by the mini Kit RNeasy (Qiagen, Courtaboeuf, France) for Yl cultivated on SM TH-, according to manufacturer’s instructions.

tag: growth condition

value: SM TH+

source_name: growth of Y. lipolytica on SM TH-

value: SM TH-


title: Yl growth in SM TH- vs Yl growth in SM TH+ 1


title: ChIP-seq_Ishi_Ishi_DMSO_Input

description: ER ChIP-seq

value: Endometrioid adenocarcinoma cell line

value: Santa Cruz ERalpha (HC-20)

value: 1 hr 0.1% DMSO


title: Yl growth in SM TH- vs Yl growth in SM TH+ 2


title: RNA-seq_WTIshikawa_E2

value: Endometrioid adenocarcinoma


title: Yl growth in SM TH- vs Yl growth in SM TH+ 3


title: ChIP-seq_Ishi_ETV4KO1_E21hr_ER

description: ER ChIP-seq


title: RNA-seq_WTIshikawa_DMSO


title: ChIP-seq_Ishi_ETV4KO2_E21hr_ER

description: ER ChIP-seq


title: ChIP-seq_Ishi_T47D_ER_E2

description: ER ChIP-seq

value: T-47D ETV4 ectopic expression

value: ER+ breast ductal carcinoma cell line

value: ETV4 ectopic expression


title: ChIP-seq_Ishi_E21hr_ER

description: ER ChIP-seq

value: WT


title: ATAC-seq_ETV4KO1_DMSO

data_processing:
Sequencing reads were aligned by Bowtie to the hg19 build of the human genome using the following parameters: -m 1  -t –best -q -S -l 32 -e 80 -n 2
Read counts were calculated using featureCounts from the SubRead package
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph

extract_protocol:
250,000 cells were collected and ATAC assay was performed as described in Buenrostro, et al. 2013.
Library was constructed as described in Buenrostro, et al. 2013.

treatment_protocol: Inductions involved treating cells with 0.1% DMSO, as a vehicle control, or 10nM E2 (Sigma-Aldrich) for 1 hour.


title: ATAC-seq_ETV4KO1_1hrE2


title: ATAC-seq_ETV4KO2_1hrE2


title: ATAC-seq_ETV4KO2_DMSO


title: ATAC-seq_WTIshikawa_1hrE2


title: ATAC-seq_WTIshikawa_DMSO


title: HET1

city: München

first: Friederike

last: Matheus

address: Ingolstädter Landstrasse 1

department: Institute for Stem Cell Research

institute: Helmholtz Center Munich

data_processing:
For Fastq manipulation steps, tools on the public server at usegalaxy.org were used.
Qualtiy was assessed using the FastQC tool
Reads were mapped to the hg19 genome using STAR software
Read quantification was performed using Cufflinks 2.2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes read counts for all samples
Supplementary_files_format_and_content: gene expression raw count matrix

source_name: neural crest differentiation culture

growth_protocol: Human embryonic stem cell lines were differentiated according to a protocol by Bajpai et al (Nature 463, 958-962).

extract_protocol:
RNA was isolated from cultures at day 7 of neural crest differentiation using the Qiagen RNeasy Mini Kit (Cat.#4104). QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (SKU015.24) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the Lexogen protocol

value: embryonic stem cell-derived neuronal crest progenitor culture

tag: day of protocol

value: day 7

value: heterozygous 500 bp deletion in ASXL1


title: HET3


title: Wildtype2

value: wildtype


title: Wildtype3


title: HET2


title: Wildtype1


title: MSC-EC-Vehicle_1

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description:
bone marrow microvascular niches (MVNs)
Cell culture and reagents. Freshly isolated human umbilical vein endothelial cells (ECs) were provided kindly by Dr. Andrew Putnam (University of Michigan) and propagated in fully supplemented EGM-2 growth medium (Lonza). Bone marrow-derived human MSCs were obtained commercially (ScienCell) and propagated in low glucose DMEM supplemented with 10% fetal bovine serum (ThermoFisher). All primary human cells were used in experiments by passage 11. Malignant HMT-3522-T4-2 (T4-2) cells were grown in H14 medium on collagen-coated tissue culture flasks 54. MCF-7 cells were grown in high glucose DMEM supplemented with 10% FBS.   mCherry-E4orf1-ECs were generated as described previously 41. YFP-T4-2 and -MCF-7 were generated by infection of tumor cells with pLentiCMV/YFP lentivirus followed by selection for 96h with 1 µg/ml puromycin. tdTomato-mVenus-p27K- T4-2 cells were generated by sequential infection with pLentiCMV/tdTomato lentivirus, selection for 96h with 1 µg/ml puromycin, and retroviral infection with pMXs-IRES-puro/mVenus-p27K- (ref. 45) generously provided by the Paddison Laboratory (Fred Hutchinson Cancer Research Center). As reported previously, this vector encodes for a mutant form of p27 that lacks cyclin-dependent kinase inhibitory activity 45. Cells were starved to drive them into a quiescent state and then mVenus-positive cells were flow sorted to establish a stable population of tdTomato-mVenus-p27K- T4-2 cells.     Generation of bone marrow microvascular niches. Bone marrow microvascular niches (MVNs) were generated as previously detailed (Nat Cell Biol. 2013 Jul;15(7):807-17.) MSCs were seeded alone at a density of 5x10¬4 cells/well in 96-well culture plates or with mCherry-E4-ECs at a 5:1 ratio to generate bone marrow MVNs. Cells were suspended in EGM-2 at a concentration 5x10¬4 cells/100 µl (stroma only) or 6x10¬4 cells/100 µl (stroma+ECs). After depositing 100 µl of cellular suspension per well of a 96-well plate, plates were left undisturbed on a flat surface for 20 min to allow even cell seeding prior to incubation.    After 10 days, YFP tumour cells were suspended in unsupplemented DMEM/F12 (500 cells/ml). YFP tumour cells were seeded (100 µl/well) after washing cultures thrice with PBS. Cells were allowed to settle for 15-25 min at room temperature, then a “drip50” of LrECM in DMEM/F12 was slowly added to each well (final concentration=20%). The LrECM drip condensed for 10-15min at room temperature before polymerizing fully at 37ºC.  Cultures were maintained with media changes every 72h. Cultures were treated at Day -12 and -15 post-seeding of tumour cells with vehicles (ddH2O or DMSO.)

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.66.3 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Reads were mapped to the hg19 human genome build using TopHat v2.1.0 and bowtie2 v2.2.6.
Mean and standard deviation of fragment size were calculated with picard-tools v2.18.1
Transcript abundance was determined from the TopHat alignments in R using the Genomic Alignments Bioconductor package v1.6.3 using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: hg19
Supplementary_files_format_and_content: *_processed_data.txt: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: bone marrow microvascular niches (MVNs)

extract_protocol:
Ten wells per replicate were pooled for RNAseq. Total RNA was isolated using Qiagen RNeasy mini kit, catalog no. 74104. RNA yield and purity was obtained by NanoDrop 2000 (Thermo Fisher Scientific).  RNA Integrity was evaluated by 2100 Bioanalyzer (Agilent Technologies).
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.
Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 generating 50 bp paired end reads.

value: bone marrow microvascular niches (MVNs)


title: MSC-Vehicle_1

description:
bone marrow mesenchymal stem cells (MSCs)
Cell culture and reagents. Freshly isolated human umbilical vein endothelial cells (ECs) were provided kindly by Dr. Andrew Putnam (University of Michigan) and propagated in fully supplemented EGM-2 growth medium (Lonza). Bone marrow-derived human MSCs were obtained commercially (ScienCell) and propagated in low glucose DMEM supplemented with 10% fetal bovine serum (ThermoFisher). All primary human cells were used in experiments by passage 11. Malignant HMT-3522-T4-2 (T4-2) cells were grown in H14 medium on collagen-coated tissue culture flasks 54. MCF-7 cells were grown in high glucose DMEM supplemented with 10% FBS.   mCherry-E4orf1-ECs were generated as described previously 41. YFP-T4-2 and -MCF-7 were generated by infection of tumor cells with pLentiCMV/YFP lentivirus followed by selection for 96h with 1 µg/ml puromycin. tdTomato-mVenus-p27K- T4-2 cells were generated by sequential infection with pLentiCMV/tdTomato lentivirus, selection for 96h with 1 µg/ml puromycin, and retroviral infection with pMXs-IRES-puro/mVenus-p27K- (ref. 45) generously provided by the Paddison Laboratory (Fred Hutchinson Cancer Research Center). As reported previously, this vector encodes for a mutant form of p27 that lacks cyclin-dependent kinase inhibitory activity 45. Cells were starved to drive them into a quiescent state and then mVenus-positive cells were flow sorted to establish a stable population of tdTomato-mVenus-p27K- T4-2 cells.     Generation of bone marrow microvascular niches. Bone marrow microvascular niches (MVNs) were generated as previously detailed (Nat Cell Biol. 2013 Jul;15(7):807-17.) MSCs were seeded alone at a density of 5x10¬4 cells/well in 96-well culture plates or with mCherry-E4-ECs at a 5:1 ratio to generate bone marrow MVNs. Cells were suspended in EGM-2 at a concentration 5x10¬4 cells/100 µl (stroma only) or 6x10¬4 cells/100 µl (stroma+ECs). After depositing 100 µl of cellular suspension per well of a 96-well plate, plates were left undisturbed on a flat surface for 20 min to allow even cell seeding prior to incubation.    After 10 days, YFP tumour cells were suspended in unsupplemented DMEM/F12 (500 cells/ml). YFP tumour cells were seeded (100 µl/well) after washing cultures thrice with PBS. Cells were allowed to settle for 15-25 min at room temperature, then a “drip50” of LrECM in DMEM/F12 was slowly added to each well (final concentration=20%). The LrECM drip condensed for 10-15min at room temperature before polymerizing fully at 37ºC.  Cultures were maintained with media changes every 72h. Cultures were treated at Day -12 and -15 post-seeding of tumour cells with vehicles (ddH2O or DMSO.)


title: MSC-Vehicle_2

source_name: bone marrow mesenchymal stem cells (MSCs)


title: MSC-EC-Vehicle_2


title: Time course_Growing_9779_L003_N712_N502

city: Providence

first: Nicola

last: Neretti

state: RI

address: 70 Ship St

department: Department of Molecular Biology, Cell Biology & Biochemistry

institute: Brown University

description:
Single cell mRNA
Not included in downstream analysis

data_processing:
(Smart-seq2 time course experiment):Paired-end reads were quality trimmed using Trim galore and subsequently aligned to the human reference genome, hg19, and ERCC spike-in sequences using HISAT2. Cells that have less than 200,000 hg19 aligned reads, and a ratio of ERCC RNA spike-in control aligned reads to total aligned reads that is greater than 0.5 were filtered out. 232 IMR90 cells (100 growing cells, 41 day 2 cells, 43 day 4 cells and 48 senescent cells) passed this first filtering step. Subsequently, hg19 aligned reads were randomly downsampled to 200,000 reads. Genes were quantified using HTSeq-Count[25]. Cells that have more than 80,000 total gene counts and at least 500 genes with at least one count were used for downstream analysis. 224 IMR90 cells (100 Growing cells, 41 Day2 cells, 42 Day4 cells and 41 senescent cells) passed this second filtering step. Downstream analyses were done on the 224 cells as indicated in the sample description field
(10x Co-culture experiment): Cell Ranger 2.0.1 was used to align 10x Chromium RNA-seq reads  to hg19, TurboGFP and  puromycin sequence from pGIPZ and neomycin sequence from pLNCX2-ER-ras_neo, using the default parameters, and to generate gene-cell matrices. The data were subsequently processed using Seurat 2.3.0 to generate t-SNE plots and three clusters were identified using sparcl 1.0.3 (https://cran.r-project.org/web/packages/sparcl/index.html).
(Smart-seq2 hepatocyte): Paired-end reads were quality trimmed using Trim galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and subsequently aligned to the mouse reference genome mm10 and ERCC spike-in sequences using HISAT2. The mm10 aligned reads were randomly downsampled to 50,000 and cells that have less than 50,000 reads were removed. 75 single cells from the induced and uninduced hepatocyte passed this filter. Subsequently, cells that have less than 20,000 gene count and less than 500 genes with at least one read detected were removed. 43 single cells from the induced hepatocytes and 21 cells from the uninduced hepatocytes were retained. Lastly, cells with the log-transformed number of expressed genes and library size of 3 median absolute deviation below the median value were removed [19]. 39 single cells from the induced hepatocytes and 19 cells from the uninduced hepatocytes passed these filters.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: csv file contains FPKM values (Time_course_FPKM.csv) and tab-delimited files contain counts from HTSeq after downsampling (Hepatocyte_downsampled_Htseq.txt and Time_course_downsampled_HTSeq)
Supplementary_files_format_and_content: Mdm2_deleted_hepatocyte_HTSeq.txt: counts from HTSeq for cells that passed the filter (Induced_hepatocyte)
Supplementary_files_format_and_content: timecourse_HTSeq.txt: counts from HTSeq for cells that passed the filter
Supplementary_files_format_and_content: timecourse_FPKM.csv: FPKM for cells that passed the filter
Supplementary_files_format_and_content: Growing_Sen_10x_count.txt contains UMI counts from 10x dataset and Growing_Sen_10x_metadata.txt contains the metadata for the UMI counts

extract_protocol:
Single-cell RNA-seq was performed using Smart-seq2 or 10x chromium as indicated by each experiemnt
Smart-seq2 or 10x Genomics 3' expression protocol

treatment_protocol: (Smart-seq2 Time course experiment): ER:RasG12V -expressing cells were induced into senescence for 7 days with 4-hydroxytamoxifen (4-OHT) and were isolated as single cells using FACS. Single cells that were not induced with 4-OHT were used as control. Single cells were also collected at another two time points, day 2 and day 4, before they became fully senescent on day 7. (10x Co-culture experiment): GFP cells are co-cultured with ER:Ras expressing cells and were induced into senescence with 4-OHT. Single cell 3' gene expression was generated using 10x Genomics Chromium.  (Smart-seq2 Hepatocyte experiment): Ex vivo primary hepatocytes were isolated using a modified retrograde perfusion technique as previously described[27]. Briefly, following perfusion with Perfusion Medium (Gibco) for 5 min, and Liver Digest Medium (Gibco) for 10 min, the liver was excised and the capsule disrupted to yield a cell suspension that was collected in Williams' E Medium supplemented with 2% FCS. Hepatocytes were purified by pelleting through a 40% (v:v) percoll gradient prior to FACS analysis.

tag: protocol used


title: Time course_Growing_9779_L003_N712_N508


title: Time course_Growing_9779_L003_N711_N508


title: Time course_Growing_9779_L003_N710_N517


title: Time course_Growing_9779_L003_N712_N503


title: Time course_Growing_9779_L003_N712_N507


title: Time course_Growing_9779_L003_N711_N517


title: Time course_Growing_9779_L003_N712_N517


title: Time course_Growing_9779_L003_N711_N502


title: Time course_Growing_9779_L003_N711_N507


title: Time course_Growing_9779_L003_N710_N508


title: Primary oral melanoma_metastasising_rep9

value: Metastasising

value: Cocker Spaniel


title: Time course_Growing_9779_L003_N710_N505


title: Time course_Growing_9779_L003_N710_N506


title: Time course_Growing_9779_L003_N708_N508


title: Time course_Growing_9779_L003_N709_N517


title: Time course_Growing_9779_L003_N710_N503


title: Time course_Growing_9779_L003_N709_N507


title: Time course_Growing_9779_L003_N709_N508


title: Time course_Growing_9779_L003_N707_N507


title: Time course_Growing_9779_L003_N707_N502


title: Time course_Growing_9779_L003_N712_N505


title: Time course_Growing_9779_L003_N707_N504


title: Time course_Growing_9779_L003_N707_N503


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title: Time course_day2_9787_L004_N712_N502


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title: Time course_day2_9787_L004_N711_N501


title: Time course_day2_9787_L004_N712_N501


title: Time course_day2_9787_L004_N711_N503


title: Time course_day2_9787_L004_N711_N508


title: Time course_day2_9787_L004_N712_N504


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title: Time course_day2_9787_L004_N710_N506


title: Time course_day2_9787_L004_N710_N503


title: Time course_day2_9787_L004_N710_N508


title: Time course_day2_9787_L004_N709_N507


title: Time course_day2_9787_L004_N710_N505


title: Time course_day2_9787_L004_N710_N501


title: Time course_day2_9787_L004_N709_N508


title: Time course_day2_9787_L004_N712_N505


title: Time course_day2_9787_L004_N709_N505


title: Time course_day2_9787_L004_N709_N503


title: Time course_day2_9787_L004_N709_N502


title: Time course_day2_9787_L004_N709_N501


title: Time course_day2_9787_L004_N711_N506


title: Time course_day2_9787_L004_N707_N508


title: Time course_day2_9787_L004_N707_N507


title: Time course_day2_9787_L004_N708_N504


title: Time course_day2_9787_L004_N707_N505


title: Time course_day2_9787_L004_N708_N508


title: Time course_day2_9787_L004_N708_N503


title: Time course_day2_9787_L004_N706_N508


title: Time course_day2_9787_L004_N705_N505


title: Time course_day2_9787_L004_N705_N503


title: Time course_day2_9787_L004_N706_N506


title: Time course_day2_9787_L004_N706_N502


title: Time course_day2_9787_L004_N706_N505


title: Time course_day2_9787_L004_N705_N504


title: Time course_day2_9787_L004_N704_N505


title: Time course_day2_9787_L004_N704_N503


title: Time course_day2_9787_L004_N705_N501


title: Time course_day2_9787_L004_N704_N502


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title: Time course_day2_9787_L004_N704_N501


title: Time course_day2_9787_L004_N702_N506


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title: Time course_day2_9787_L004_N703_N508


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title: END_seq_HCT116_0_5h

department: Azrieli Faculty of Medicine

description: control: END_seq_HCT116_NT.fastq.gz


title: Time course_day2_9787_L004_N708_N507


title: Time course_day2_9787_L004_N701_N503


title: Time course_Growing_9779_L003_N712_N506

description:
Single cell mRNA
Passed filtering and included in downstream analysis


title: Time course_day2_9787_L004_N701_N505


title: Time course_day2_9787_L004_N702_N501


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title: Time course_Growing_9779_L003_N708_N505


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title: Time course_day2_9787_L004_N701_N506


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title: Time course_Growing_9779_L003_N708_N506


title: Time course_Growing_9779_L003_N708_N504


title: Time course_Growing_9779_L003_N708_N502


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title: Time course_day2_9787_L004_N702_N504


title: Time course_Growing_9779_L003_N706_N502


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title: Time course_Growing_9779_L003_N704_N507


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title: Time course_Growing_9779_L003_N711_N504


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title: Time course_Growing_9779_L003_N703_N507


title: Time course_Growing_9779_L003_N709_N505


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title: Time course_Growing_9779_L003_N702_N507


title: Time course_day2_9787_L004_N711_N507


title: Time course_day2_9787_L004_N711_N504


title: Time course_Growing_9779_L003_N701_N503


title: Time course_day2_9787_L004_N711_N505


title: Time course_day2_9787_L004_N710_N507


title: Time course_day2_9787_L004_N710_N504