title: Met-seq of Ezh2 -/- mESC

source_name: Met-seq of Ezh2 -/- mESC


title: LNCaP DHT PSF-CLIP

status: Public on Dec 24 2017

type: SRA

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

library_source: transcriptomic

data_processing:
Library strategy: CLIP-Seq
To remove rRNA sequence, we used bowtie 2 version 2.2.6. Mapping to human genome (hg19) was performed using tophat 2.1.0.with bowtie.
Generate alignments in the SAM format from BAM given single-end reads. The reads were mapped to the human RefSeq mRNA database for RIP-seq data.
The expression levels of mapped transcripts were normalized into Reads Per Kilobase of exon per Million mapped reads (RPKM) to facilitate comparison among different samples.
For CLIP, signal scores were calculated using Model-based analysis of ChIP-seq (MACS; P-value < 10xE-4 or -5).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include RPKMs.
Supplementary_files_format_and_content: Bed files can be visualized by Integrative Genomics Viewer ver 2.3 (IGV ver 2.3). They include MACS signal scores.

molecule: total RNA

organism: Homo sapiens

source_name: prostate cancer cells LNCaP, DHT, PSF-CLIP

growth_protocol: LNCaP and 22Rv1 cells were cultured in RPMI 1640 containing 10% FBS. LTAD cells were treated with phenol-red free RPMI1640 containing 10% charcoal/dextran treated FBS. Before hormone treatment, cells were incubated in Phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days.

extract_protocol:
For RIP, cell lysates were immunoprecipitated using EZ-magna RIP RNA binding protein immunoprecipitation kit (Millipore 17-701). For CLIP, cells were crosslinked using UV crosslinker (150 mJ/cm2). Beads were prepared by mixing protein G beads with PSF specific antibodies. Harvested cells were lysed in lysis buffer (50mM Tris-HCl, PH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, proteinase inhibitors) and added RNase dilution and DNase to digest RNA and DNA. Cell lysates were immunoprecipitated by prepared protein G beads for 4 h. Beads were washed and suspended in SDS-PAGE sample buffer for SDS-PAGE electrophoresis. The protein-RNA complexes from the beads were transfered to a nitrocellulose membrane. Protein-RNA complexes were cut and isolated using PK buffer (100 mM Tris-HCl PH 7.4, 50 mM NaCl, 10 mM EDTA) and protein kinase K(10μl). Extracted RNA were collected for RNA-seq library construction.
SureSelect RNAXT RNA Target Enrichment for Illumina Multiplexed Sequencing (Agilent) was used for library construction according to the manufacturer's protocol.

treatment_protocol: LNCaP, 22Rv1 and LTAD cells were treated with vehicle or DHT 10 nM for 24 h.

tag: cell line

value: LNCaP

tag: cell type

value: prostate cancer cell line

tag: treatment

value: 24h DHT 10 nM

tag: antibody

value: PSF


title: LNCaP Et CLIP input

source_name: prostate cancer cells LNCaP, vehicle, input

value: 24h ethanol


title: LNCaP DHT CLIP input

source_name: prostate cancer cells LNCaP, DHT, input


title: LNCaP Et PSF-CLIP

source_name: prostate cancer cells LNCaP, vehicle, PSF-CLIP


title: LNCaP DHT PSF-RIP 2

description: Processed data file: refseq.hg19.lncap_dht_PSF_ripseq1_fr_vs_lncap_dht_input_ripseq_fr.txt

data_processing:
To remove rRNA sequence, we used bowtie 2 version 2.2.6. Mapping to human genome (hg19) was performed using tophat 2.1.0.with bowtie.
Generate alignments in the SAM format from BAM given single-end reads. The reads were mapped to the human RefSeq mRNA database for RIP-seq data.
The expression levels of mapped transcripts were normalized into Reads Per Kilobase of exon per Million mapped reads (RPKM) to facilitate comparison among different samples.
For CLIP, signal scores were calculated using Model-based analysis of ChIP-seq (MACS; P-value < 10xE-4 or -5).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include RPKMs.
Supplementary_files_format_and_content: Bed files can be visualized by Integrative Genomics Viewer ver 2.3 (IGV ver 2.3). They include MACS signal scores.

source_name: prostate cancer cells LNCaP, DHT, PSF-RIP


title: LNCaP DHT PSF-CLIP2


title: H3K27me3 ChIP-seq of Eed -/- mESC

city: Beijing

first: Yuanyuan

last: Li

address: Tsinghua University, Qinghua Yuan, Haidian District

country: China

institute: Tsinghua Universary

library_source: genomic

data_processing:
ChIP-seq reads were aligned to mm9 with Bowtie2 (version 2.2.2) with parameters -t -q -N 1 -L 25. All unmapped reads, multiplely mapped reads and PCR duplicates were removed. To generate the ChIP-Seq signals for each histone modification shown in the UCSC genome browser, we normalized the read counts by computing the number of reads per kilobase of bin per million reads sequenced (RPKM). To minimize the batch and cell type variation, the RPKM values were further normalized through Z-score transformation, by subtracting the mean of RPKM across the genome and divided by the standard deviation of RPKM across the genome.
RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11). The gene expression levels were calculated by Cufflinks (version 2.2.1). The expression levels for each transcript were quantified as Fragments Per Kilobase of transcript per Million mapped reads (FPKM).
MethylC-seq reads were aligned to mm9 using BSMAP with parameters –r 0 –w 100 –v 0.1 –A AGATCGGAAGAGC. Multiple-mapped reads and PCR duplicates were removed. After mapping, those reads with total CG coverage less than 5 within 200 bp were removed. Methylation level was calculated using methylated CpG versus total CpG in each bin.
4C-seq reads with 5’ end mapped to 4C forward primer were selected from total fastq file. The selected reads were mapped to mm9 assembly by Bowtie2 (version 2.2.2). The mapped reads were secondly mapped to HindIII sites by softeware fourSig. The fragment counts were finally normalized per one million reads.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited BEDGRAPH files including number of reads in 100bp bin in the genome for each ChIP-seq sample
Supplementary_files_format_and_content: Tab-delimited BEDGRAPH files for methylC-seq including the average mCG level in 200bp bins.
Supplementary_files_format_and_content: Tab-delimited txt files for RNA seq including FPKM values for each gene
Supplementary_files_format_and_content: Tab-delimited bedGraph files including number of reads for each HindIII fragment loci in the genome for each 4C-seq sample

molecule: genomic DNA

organism: Mus musculus

source_name: H3K27me3 ChIP-seq of Eed -/- mESC

growth_protocol: mESCs were passaged every 48-72h in DMEM(Gibco) supplemented with 15% FBS (HyClone), 1% non-essential amino acids(Gibco), 0.5% 2-mercaptoethanol(Gibco), 1% penicillin/streptomycin(Millipore), 0.01% leukemia inhibiting factor(LIF)(Millipore) and 1% glutamine(Gibco) on gelatinized plates.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at 37°C;Chromatin was fragmented by sonication to obtain fragments 100–700bp in length. For each ChIP assay,5 ug of antibodies were added and incubated at 4◦C overnight. Chromatin was reverse-crosslinked, purified and quantified with a Qubit fluorometer using the Quant-iT dsDNA HS assay kit
DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads or DNA purification kit according to the DNA amount. Library DNA was amplified by Phusion HF (NEB, Cat. M0530L). The amplified DNA was size selected using 2% agarose gel for 200-500bp DNA fragments.

tag: strain

tag: chip antibody

tag: genotype

value: Eed -/-

value: mESCs


title: H3K27ac ChIP-seq of Eed -/- mESC

source_name: H3K27ac ChIP-seq of Eed -/- mESC


title: LNCaP Et PSF-RIP 2


title: H3K27me3 ChIP-seq of WT mESC

source_name: H3K27me3 ChIP-seq of WT mESC

value: WT


title: H3K4me3 ChIP-seq of Eed -/- mESC

source_name: H3K4me3 ChIP-seq of Eed -/- mESC

value: H3K4me3(Millipore, Cat.04-745)


title: LNCaP DHT RIP input 2

description: Processed data file: refseq.hg19.lncap_Et_PSF_ripseq1_fr_vs_lncap_Et_input_ripseq_fr.txt


title: Met-seq of Tet TKO mESC

source_name: Met-seq of Tet TKO mESC

extract_protocol:
Cells were treated using Cell Lysis Solution (Qiagen, Cat. 1045723) and proteins were removed using Protein Precipitation Solution (Qiagen, Cat. 1045701). Genome DNA was precipitated by isopropyl alcohol and cleaned by wash with 75% ethanol.
A total amount of 6ug genomic DNA was mixed with 25ng lambda DNA and sonicated to 200-500bp.DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads or DNA purification kit according to the DNA amount. Bisulfite treatment is performed using commercial kit (Zymo research, Cat. D5005). DNA was amplified and 200-500bp fragments were gel selected.


title: H3K4me3 ChIP-seq of WT mESC

source_name: H3K4me3 ChIP-seq of WT mESC


title: LTAD Et PSF-RIP

source_name: prostate cancer cells LTAD, vehicle, PSF-RIP

value: LTAD


title: LNCaP Et RIP input 2


title: LTAD Et RIP input

source_name: prostate cancer cells LTAD, vehicle, input


title: LTAD DHT PSF-RIP

source_name: prostate cancer cells LTAD, DHT, PSF-RIP


title: LNCaP Et PSF-RIP

source_name: prostate cancer cells LNCaP, vehicle, PSF-RIP


title: LTAD DHT RIP input

source_name: prostate cancer cells LTAD, DHT, input


title: LNCaP DHT PSF-RIP


title: 22Rv1 Et PSF-RIP

source_name: prostate cancer cells 22Rv1, vehicle, PSF-RIP


title: 22Rv1 DHT PSF-RIP

source_name: prostate cancer cells 22Rv1, DHT, PSF-RIP


title: LNCaP Et RIP input

source_name: prostate cancer cells LNCaP, vehicle, input


title: LNCaP DHT RIP input

source_name: prostate cancer cells LNCaP, DHT, input


title: 22Rv1 Et RIP input

source_name: prostate cancer cells 22Rv1, vehicle, input


title: 22Rv1 DHT RIP input

source_name: prostate cancer cells 22Rv1, DHT, input


title: Uhrf1 cKO rep3

status: Public on Dec 23 2017

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

institute: Ehime University

data_processing:
Sequence data were mapped on the mouse genome (mm10) using Tophat and analyzed by Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: expression (method to generate expression levels not provided by the submitter)

source_name: Primary chondrocytes

growth_protocol: Knee cartilage obtained from post natal day 3 was sequentially digested by Collagenase D.

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen, USA) and an RNeasy spin column kit (Qiagen, USA), followed by treatment with DNase I (Qiagen). RNA samples with RNA integrity number (RIN) greater than 8 were normalized to 100 ng/μl before further analyses.
RNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Prep Kit setA (Illumina, San Diego CA) according to the manufacturer's instructions and subsequently validated for an average size of about 330-340 bp using a 2100 Bioanalyzer and the Agilent DNA1000 kit.for the construction of sequencing libraries.

treatment_protocol: Confluent cells were treated with 100 ng/ml of rhBMP-2 for 24 hours.

tag: tissue

value: knee cartilage

tag: age

value: post natal day 3


title: Control rep2


title: Uhrf1 cKO rep2


title: Uhrf1 cKO rep1


title: Control rep1


title: MEF4 WT

city: Dallas

first: Gokhul

middle: Krishna

last: Kilaru

state: TEXAS

address: 6000 Harry Hines Boulevard

department: Department of Neuroscience

country: USA

institute: University of Texas Southwestern Medical Center

description: IRF2 precipitated DNA

data_processing:
MEF ChIP-Seq samples from Illumina Next-Seq 500 were mapped to the mm10 genome assembly from UCSC using Bowtie2 version 2.1.0 (Langmead et al., 2012). Mapped reads containing mapping quality score greater than 10 were filtered using samtools. Duplicate reads were removed followed by extending the remaining reads to fragment size. Coverage tracks were made by normalizing to 10million reads. ChIP peaks for MEF samples were identified from uniquely mapped reads without duplicates using MACS (Zhang et al., 2008) with parameters "-p 1e-5 --gsize mm --nomodel True --wig --space=10" and relevant input chromatin samples as control data. MACS peaks were then subdivided using Peaksplitter with a valley cutoff of 0.7 and were later filtered for summit height greater than 6. To construct a master peak list from the four MEF samples, the peaks obtained after PeakSplitter and summit height filtering were merged, compared for overlaps and the peak with highest summit value was chosen if the summit coordinates were within the fragment size estimate of 192bp. Raw reads in the master peak regions were quantified using HOMER's (Heinz et al., 2010) annotatePeaks.pl program. The resultant counts matrix was used as input with DESEq2 (Love et al., 2014) and master peak regions with a FC >= 2 and FDR < 0.05 were considered differentially enriched and significant.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized bigWig files for visualizing ChIP binding. 6369 Masterpeaks identified using MACS, peaksplitter. 381 Differentially enriched masterpeaks identified from 6369 masterpeaks in bed format.

source_name: MEFs

growth_protocol: Primary MEFs were cultured in DMEM with 10% CBS until DIV3.

extract_protocol:
Associated DNA were precipitated with IRF2 antibody and purified with QiaQuick purification kit.
Libraries were prepared based on Illumina® TruSeq® ChIP Sample Preparation Kit.

value: MEFs

tag: developmental stage

tag: genotype/variation

value: wild type

tag: antibody vendor and catalog#

value: Santa Cruz/sc-498x


title: MEF2 Hcfc2 KO

description: IRF2 precipitated DNA

value: Hcfc2 KO


title: MEF1 Hcfc2 KO

description: IRF2 precipitated DNA


title: Control rep3


title: ChIP-seq LSD1 T0

city: Barcelona

first: Miguel

last: Beato

address: Aiguader 88

country: Spain

institute: CRG

data_processing:
Basecalls performed using Illumina pipeline version 1.4.0
ChIP-Seq Single-end reads were processed by aligning to the reference human genome (GRCh37/hg19) using Bowtie v1.0.0, an ultrafast short-read mapping program (Langmead et al. 2009), keeping only tags that mapped uniquely and with no more than two mismatches.
The integrated software MACS (Zhang et al. 2008) was used to detect peaks that were enriched from background reads with default parameters for BPTF, and a p-value of 1e-3 and no-model parameters set for HP1g and LSD1.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq data files are peak results “TSV” files with genomic coordinates of peaks
Supplementary_files_format_and_content: RPKM.H2A.hg19-proteinCoding-genes.txt: Homer v4.7.2 RPKM calculation for H2A ChIP-seq using hg19 protein-coding genes

source_name: Breast cancer cell line

growth_protocol: Cells were routinely grown in RPMI 1640 medium supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, and 100 mg/ml streptomycin

extract_protocol:
After hormone treatment, the medium was replaced by medium containing 1% formaldehyde and incubated 10 min at 37ºC for cross-linking. The reaction was stop by adding 125 mM glycine and incubated 5 min at room temperature. Cells were washed twice with cold PBS, and collected. Preparation of chromatin and ChIP experiments were performed as previously described (Strutt et al, Methods Mol Biol. 1999; 119:455-567). Immunoprecipitated DNA was purified by phenol:chloroform followed by ethanol precipitation
It was performed using the NEBNext DNA sample prep Reagents set 1

treatment_protocol: For the experiments, cells were plated in RPMI medium without phenol red supplemented with 10% dextran-coated charcoal-treated FBS and 48 hr later medium was replaced by fresh medium without serum. After 1 day in serum-free conditions, cells were incubated with R5020 (10 nM) for different times between 0 and 360 minutes

value: unstimulated cells

tag: chip-antibody

value: abcam anti-LSD1


title: ChIP-seq H2A T30

value: stimulated cells with 30 minutes

value: H2A; Kindly obtained from Stephan Dmitrov


title: ChIP-seq H2A T0


title: ChIP-seq H2A T60

value: stimulated cells with 60 minutes


title: ChIP-seq LSD1 T30


title: ChIP-seq HP1g T30

value: anti-HP1γ (Mab 3450)


title: 9496Hippo

city: Los Angeles

first: Yuichiro

last: Itoh

state: California

address: 635 Charles E. Young Drive South

department: Neurology

institute: UCLA

description:
mRNA co-immunoprecipitated with mouse monoclonal  anti-HA antibody
RNA from astrocyte

data_processing:
Data quality check was done on Illumina SAV
Demultiplexing was performed with Illumina CASAVA 1.8.2
The reads were mapped to the latest UCSC transcript set using the ultra fast high-throughput short read aligner Bowtie2 version 2.1.0
Gene expression levels were estimated using RSEM v1.2.15
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes count values for each Sample

source_name: Hippocampus

extract_protocol:
Spinal cord (Sc), cerebellum (Cb), cerebral cortex (Crx), and hippocampus (Hippo) were collected and snap-frozen by liquid nitrogen. After RNA co-immunoprecipitation process, RNA was isolated using RNeasy MicroKit (Qiagen).
Double-stranded cDNA was generated using a mixture of random hexamers and oligo dT with the Nugen Ovation RNA-Seq System V2 kit and the sequencing library was made using the Kapa LTP library kit.

value: hippocampus

value: astrocyte

tag: disease state

value: EAE

tag: rip antibody

value: anti-HA antibody


title: 9493Hippo


title: Hcfc2 KO MEF input

description: input DNA


title: 9268Hippo


title: 9223Hippo


title: WT MEF input

description: input DNA


title: 9120Hippo


title: ChIP-seq HP1g T0


title: 65Hippo

value: healthy control


title: 79Hippo


title: 154Hippo


title: 9496Crx

source_name: Cerebral cortex

value: cerebral cortex


title: 9493Crx


title: 9223Crx


title: MEF3 WT

description: IRF2 precipitated DNA


title: 9120Crx


title: 154Crx


title: 42Crx


title: 65Crx


title: 9496Cb

source_name: Cerebellum

value: cerebellum


title: 9223Cb


title: 9268Cb


title: 42Hippo


title: 79Cb


title: 154Cb


title: 9223HA

source_name: Spinal cord

value: spinal cord


title: 42Cb


title: 9496HA


title: 9493HA


title: 65Cb


title: 9493Cb


title: 154HA


title: 65HA


title: 9268Crx


title: 9496WT

description:
mRNA co-immunoprecipitated with rabbit anti-RPL22 antibody
RNA from all CNS cell types

value: all CNS cell types

value: anti-RPL22 antibody


title: 9493WT


title: 79Crx


title: 154WT


title: 79WT


title: 65WT


title: 9268HA


title: 42WT


title: 9120HA


title: EAE_4

description:
mRNA co-immunoprecipitated with mouse monoclonal  anti-HA antibody
RNA from astrocyte
mm10.gene_EAE_IP.txt

data_processing:
Data quality check was done on Illumina SAV
Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program
Qualities of raw sequence data were examined using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and Trimmomatic was used for cleaning.
R package “QuasR” was used for the read alignment to mouse genome (mm10) followed by the counting at gene level.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

source_name: Optic nerve

extract_protocol:
Due to the small quantity of tissue, both optic nerves from two mice within each group (EAE or control) were pooled to create each sample. Optic nerves were dissected out and rapidly snap frozen in liquid nitrogen. After RNA co-immunoprecipitation process, RNA was isolated using Direct-zol RNA microPrep (Zymo Research) .
Double-stranded cDNA was generated using a mixture of random hexamers and oligo dT with the Nugen Ovation RNA-Seq System V2 kit and the sequencing library was made using the Kapa LTP library kit.

value: optic nerve


title: CN_3

description:
mRNA co-immunoprecipitated with mouse monoclonal  anti-HA antibody
RNA from astrocyte
mm10.gene_CN_IP.txt


title: EAE_1


title: 9268WT


title: EAE_3


title: 42HA


title: NL84Opt

data_processing:
Data quality check was done on Illumina SAV
Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program
Qualities of raw sequence data were examined using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and Trimmomatic was used for cleaning.
R package “QuasR” was used for the read alignment to human genome (hg19) followed by the counting at gene level.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

source_name: Optic chiasm

extract_protocol:
Tissues were homogenized into Trizol Reagent (Thermo Fisher Scientific), and aqueous phase was collected after phase separation by adding chloroform. Further RNA purification was performed using Direct-zol™ RNA MiniPrep Plus (Zymo Research).
The RNA sequencing library was made using KAPA Stranded RNA-Seq Kit (Kapa Biosystems) which consists of mRNA enrichment, cDNA generation, end repair, A-tailing, adaptor ligation, strand selection, and PCR amplification.

value: optic chiasm


title: CN_4


title: NL90Opt


title: 9120Cb


title: 9223WT


title: CN_2


title: ChIP-seq BPTF T0

description:
BPTF_hormone-displaced_peaks.hg19.txt
BPTF_hormone-recruited_peaks.hg19.txt

value: unstimulated cells

value: BPTF; Kindly obtained from Ramin Shiekhattar


title: WT

city: Nagoya

first: Hossam

middle: Hassan

last: Shawki

state: Aichi

address: Mizuho Ward, Ōtachō, 3-chōme−1

department: Comparative and Experimental medicine

institute: Nagoya City University

data_processing:
Illumina Basespace Onsite software
FASTQ files were imported to CLC Genomics Workbench (Version 7.5.1), mapped to mm10 mouse genome and quantified for annotated genes in ENSEMBLE database to obtain RPKM values.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file format include RPKM values for each Sample ...

source_name: Sertoli cells

extract_protocol:
Total RNA was extracted by Nucleospin RNA XS kit (TaKaRa; 740902) according to the manufacturer's instructions. Concentration and purity of RNA were determined by automated optical density evaluation (OD 260/OD 280 ≥ 1.8 and OD 260/OD 230 ≥ 1.8) using Nanodrop.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Six weeks old mice carrying loxP-flanked Mafb allele with Cre-ERT2 as well as control wild type mice were received 75 mg tamoxifen/kg body weight intraperitoneally once daily for 5 consecutive days. Sertoli cells were sorted by FACs and the purity of the isolated cells was confirmed by immunocytochemical staining. Total RNA were then extracted and stored immediately in -80 C.

value: Wild Type (Control)

value: 3 months


title: NL66Opt


title: NL78Opt


title: NL72Opt


title: ChIP-seq BPTF T30

value: stimulated cells with 30 minutes


title: EAE_2


title: MS60Opt

value: MS


title: bsl1_mutant_rep2

city: St. Louis

first: Andrea

middle: L

last: Eveland

state: MO

address: 975 N. Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
Total RNA (1µg) was extracted (PicoPure RNA Isolation Kit; Thermo Fisher Scientific) and libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina, size-selected for 200 bp inserts and quantified on an Agilent bioanalyzer (Agilent) using a DNA 1000 chip.
We generated an average of 40M 100bp, single-end reads using the Illumina HiSeq 2500 platform at the University of Illinois at Urbana-Champaign W.M. Keck Center.
Read mapping and differential expression analysis were performed using the Tuxedo suite of open-source tools (Trapnell et al., 2013). Reads were mapped to the Setaria viridis A10.1 reference genome (http://phytozome.jgi.doe.gov; v1.1) using TopHat2 (v2.1.0) and an a priori set of 35,214 gene models. Gene-level expression values were represented by fragments per kilobase exon per million reads mapped (FPKM) and a consensus FPKM was determined for each gene based on its representation across biological replicates. Differential expression was determined using Cuffdiff (v 2.2.1)
Genome_build: Setaria viridis A10.1 reference genome v1.1
Supplementary_files_format_and_content: Single processed data file for RNAseq analysis includes expression information for all annotated S. viridis genes based on analysis with Cuffdiff v.2.2.1. Raw read counts for each sample and normalized fragments per kilobase per million reads (FPKM) are listed

organism: Setaria viridis

source_name: inflorescence primordia

growth_protocol: The bristleless1 (bsl1) mutant was identified by screening an N-Nitroso-N-methylurea (NMU) mutagenized M2 population of S. viridis. This mutant was selfed (M3) and then backcrossed to the reference line A10.1 and then the F1 selfed.  Homozygous mutants from this segregating F2 population were selfed and then used for the RNA-seq experiment.

extract_protocol:
Total RNA was extracted from pools of inflorescence tissue using the PicoPure RNA Isolation kit (Life Technologies), according to manufacturer instructions.  Messenger RNA was enriched by two successive purifications with oligo-dT coupled dynabeads (Invitrogen).
libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina, size-selected for 200 bp inserts and quantified on an Agilent bioanalyzer (Agilent) using a DNA 1000 chip.

treatment_protocol: Mutant and wild-type A10.1 seedlings were grown in a controlled environment to ~15 DAS (Days after sowing). Inflorescence primordia were hand-dissected and flash frozen in liquid N. ~10 representative inflorescence primordia were pooled into a single biological replicate.

value: 15 Days After Sowing

value: bsl1 mutant


title: bsl1_mutant_rep1


title: 79HA

value: astrocyte

value: anti-HA antibody


title: MafB-cKO

value: MafB knockout


title: MS54Opt


title: d1_leaf_rep_1.fastq.gz

city: University Park

first: Zhao

last: SU

state: PA

address: 354 N. Frear

department: Biology

institute: The Penn State University

description: replicate 1

data_processing:
Raw sequencing reads were examined using FastQC and adapter sequences were trimmed from both ends of the raw reads using Trimmomatic (Bolger, Lohse & Usadel, 2014). Low-quality base calls (Q < 30) were also trimmed from both the 5’ and 3’ ends of the reads. Reads from each of the four libraries were then mapped independently to the rice genome (IRGSP-1.0) using Tophat2, with a GTF (Gene Transfer File) annotation file supplied as an option. Transcript abundance and differential gene expression were calculated using Cufflinks. Gene expression levels were normalized using fragments per kilobase of exon per million mapped reads (FPKM). After confirming high correlation in transcriptome expression levels between biological replicates, data from the replicates were merged using Cuffmerge. Cuffdiff was used to calculate q values (FDR adjusted p-values) to identify differentially expressed (DE) genes between WT and d1. Differentially expressed genes (DE) were defined as those with q value less than 0.05 and with FPKM greater than 1 in either of datasets. DE genes with q values less than 0.05 were further divided into genes up-regulated in d1 as compared to WT control and genes down-regulated in d1 as compared to WT control.
Genome_build: ensemblgenomes_Oryza_sativa_release_31
Supplementary_files_format_and_content: excel file with FPKM data

organism: Oryza sativa

source_name: Leaf

growth_protocol: Wild-type (WT) and d1-1 mutant plants (henceforth referred to as d1) were grown in a greenhouse. Plants were grown individually in 2 US gallon pots containing Metro-mix 360 potting mixture (Sun Gro Horticulture Canada Ltd). Growth temperatures averaged 30˚C during the day with peaks of 35˚C at midday; night temperature was 25˚C. The day:night cycle was 16:8 with light supplied as natural daylight supplemented with 1000W metal halide lamps (Philips Lighting Co., Somerset, NJ) for the duration of the light cycle. Light intensity averaged 500 μmol m-2 s-1 PPFD. Plants were grown for 100 days before use in experiments.

extract_protocol:
Total RNA was extracted from each sample using the NucleoSpin RNA Plant kit. After examination of the quality (Bioanalyzer, Agilent) and quantity (NanoDrop 2000, ThermoFisher) of each RNA sample.
Total RNA samples were sent to the Genomics Core Facility at Penn State University for the standard RNA-seq library preparation and next generation sequencing (Hiseq 2500, Illumina).

value: two-month-old

value: leaf

value: d1-1 mutant


title: d1_leaf_rep_2.fastq.gz

description: replicate 2


title: wt_rep3

value: wild-type


title: MS48Opt


title: CN_1

value: optic nerve

value: healthy control


title: MS42Opt

value: optic chiasm


title: wt_rep1


title: WT_TC65_leaf_rep_1.fastq.gz

description: replicate 1

value: wild type


title: WT_TC65_leaf_rep_2.fastq.gz

description: replicate 2


title: wt_rep2


title: MS36Opt


title: cMYCoe_line2_r3

status: Public on Dec 22 2017

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Reads were aligned to a custom version of the zebrafish reference genome containing danRer10 references for all zebrafish chromosomes and "pseudochromosomes" created from the coding sequence of human c-Myc and n-Myc used in the experimental system
Reads were aligned using tophat with parameters --no-novel-juncs and in single-end mode
Read counts per RefSeq gene and human c-Myc and n-Myc were quantified using htseq-count using parameters --stranded=no, -i gene-name -f bam
Reads per kilobase of exon per million mapped reads were created from these readcounts by dividing by the number of kilobases in all isoforms with the same gene name and then by the millions of mapped reads
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

molecule: polyA RNA

organism: Danio rerio

source_name: Neuroblastoma tumor cells

growth_protocol: EGFP+ neuroblastoma cells were harvested from tumor-bearing MYCN and MYC transgenic zebrafish. Tumors were mechanically homogenized and EGFP+ cells were sorted directly into Trizol-LS

extract_protocol:
Sorted EGFP+ cells were sorted, then total RNA was extracted with Trizol-LS.
Total RNA was depleted of ribosomal RNA with the SMARTer Universal Low Input RNA Kit (Clontech). Enriched mRNA was then applied to library preparation according to manufacturer’s protocol (NEBNext Ultra). After repeated quality control for average DNA input size of 300 bp, the samples were sequenced on a HiSeq Illumina sequencer with 2x100bp paired-end reads.

value: EGFP+ transformed neuroblasts

tag: overexpression

value: c-Myc


title: MYCNoe_r4

value: n-Myc


title: MYCNoe_r2


title: 9120WT

value: spinal cord

value: all CNS cell types

value: EAE

value: anti-RPL22 antibody


title: MYCNoe_r1


title: cMYCoe_line2_r4


title: cMYCoe_line1_r1


title: cMYCoe_line2_r2


title: cMYCoe_line1_r2


title: cMYCoe_line1_r4


title: cMYCoe_line2_r1


title: SJNB3_input_MWZ4975 [Lab: Look]

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 75
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: Neuroblastoma

growth_protocol: Cells were cultured according to the suggested guidelines in RPMI media containing 10% FBS and 1% Penicillin-Streptomycin

extract_protocol:
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Lysates were clarified from sonicated nuclei and target bound fragments were isolated with antibody.


title: NB69_CTCF_MWZ4975 [Lab: Look]

value: CTCF

tag: antibody vendor

value: Abcam

tag: antibody catalog

tag: antibody lot


title: SJNB3_H3K27ac_MWZ4975 [Lab: Look]

tag: cell type


title: SKNAS_input_MWZ4975 [Lab: Look]

value: SK-N-AS


title: SKNAS_CTCF_MWZ4975 [Lab: Look]


title: NB69_input_MWZ4975 [Lab: Look]


title: SY5Y_input_MWZ4975 [Lab: Look]


title: SY5Y_CTCF_MWZ4975 [Lab: Look]


title: NB69 H3K27ac [Lab: Look]


title: NB69 input [Lab: Look]


title: MYCNoe_r3


title: SKNAS input [Lab: Look]

value: SKNAS


title: SKNAS ATAC [Lab: Look]

data_processing:
Each read file was separately aligned using bowtie with configuration --sam --best -k 1 -m 1 -l 75 and the resulting sam files were concatenated.
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

extract_protocol:
Libraries were generated using the Ad1 and Ad2.13–2.24 barcoded primers from and were amplified for 7–9 total cycles
DNA was simultaneously fragmented and tagged with sequencing adapters using the Nextera Tn5 transpoase kit
Nextera


title: cMYCoe_line1_r3


title: NB69 ATAC [Lab: Look]


title: SHSY5Y ATAC [Lab: Look]


title: AB2847

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample. Meta data file associating each single cell with its amplification batch and index sorting readouts is available on the series record in the file "metadata.txt".

source_name: PA-GFP spleen

growth_protocol: All mice were maintained under specific pathogen-free conditions

extract_protocol:
Murine tissues were treated with enzymes cocktail (Collagenase, Dispase and Dnase) at 37C. Cells were separated by Percoll gradient density centrifugation, filtered and stained with Flow cytometry antibodies.
Murin small intestines were flushed with PBS, treated with EDTA, Dispase and Dnase, filtered and stained with Flow cytometry antibodies.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol: Mice were sacrified by CO2

value: C57BL/6 PA-GFP

value: Spleen

tag: selection marker

tag: infection

value: LCMV

tag: treatment

tag: replicate id

tag: mouse age

value: 8-9 weeks


title: AB2843

tag: strain

tag: tissue


title: AB2631

value: C57BL/6 PA-GFP/Cx3cr1-GFP chimera

value: PA-GFP+

value: Photoactivation of marginal zone


title: AB2846


title: AB2632


title: SKNAS H3K27ac [Lab: Look]

tag: chip antibody


title: AB2845


title: AB2844


title: AB2630


title: AB2545


title: AB2544


title: AB2546


title: AB2482


title: AB2481


title: AB2480

value: Photoactivation of B area


title: AB2616

value: LCMV-GFP

value: Photoactivation of virus zone


title: AB2617


title: AB2614


title: AB2547


title: AB2478


title: AB2479


title: AB2615


title: AB2628


title: AB2629


title: AB2477


title: AB2476


title: AB2466


title: AB2424

value: Photoactivation of T area


title: AB2422


title: AB2465


title: AB2423


title: AB2419


title: AB2421


title: AB2280


title: AB2420


title: AB2279


title: AB2278


title: AB2277


title: AB2237


title: AB2236


title: AB2276


title: AB2234


title: AB2233


title: AB2235


title: AB2232


title: AB2223


title: AB2225


title: AB2475


title: AB2224


title: AB2087


title: AB2774


title: AB2773


title: AB2227


title: AB2772


title: AB2771


title: AB2769


title: AB2770


title: AB2621


title: AB2768


title: AB2620


title: AB2767


title: AB2619


title: AB2088


title: AB2226


title: AB2418


title: AB2414


title: AB2413


title: AB2416


title: AB1988


title: AB2618


title: AB2415


title: AB2240


title: AB2076


title: AB1983


title: AB2075


title: AB1986


title: AB1987


title: AB2241


title: AB1980


title: AB1979


title: AB1977


title: AB2239


title: AB2417


title: AB1978


title: AB2851

source_name: PA-GFP LN

value: Lymph node


title: AB1984


title: AB2853


title: AB1982


title: AB2238


title: AB2849


title: AB2850


title: AB1985


title: AB2848


title: AB2464


title: AB2469


title: AB2459


title: AB2468


title: AB1886


title: AB2460


title: AB2461


title: AB2462


title: AB1887


title: AB2463


title: AB2852


title: AB1881


title: AB1882


title: AB1879


title: AB1878


title: AB1884


title: AB1877


title: AB1875


title: AB1876


title: AB1873


title: AB1874


title: AB1758


title: AB1759


title: AB1757


title: AB2467


title: AB1885


title: AB2623


title: AB1880


title: AB2626


title: AB1981


title: AB2473


title: AB1883


title: AB2472


title: AB1658


title: AB2625


title: AB1659


title: AB1657


title: AB1655


title: AB1656


title: AB2471


title: DFL_E12_delattp-rel5d9lac_Cs65

city: Geneva

first: Eddie

last: Rodríguez-Carballo

address: 4, Boulevard d'Yvoy

department: Department of Genetics and Evolution

country: Switzerland

institute: Université de Genève

description: Distal forelimb mouse E12.5_del(attp-rel5)d9lac_Cs65 viewpoint

data_processing:
Library strategy: 4C-Seq
De-multiplexing, mapping and 4C-analysis were performed through HTSstation (David et al, 2014 and http://htsstation.epfl.ch/). Reads were mapped to the mm10 (GRCm38) mouse genome assembly with bowtie2 version 2.2.1 (Langmead et al, 2012) with parameters “--end-to-end --sensitive -k 20”. The segtofrag files were obtained after mapping the 4C data on in silico generated mutant genomes.
4C figures were made using a running mean algorithm with a window size of eleven fragments. Normalisation is done by dividing the fragment scores by the mean of fragments scores falling into a region defined as +/-5Mb around the centre of the bait coordinates, such as to see only changes in contact distribution and to minimize PCR complexity bias in each sample.
segtofrag files were obtain after mapping the 4C on the in-silico generated mutant genomes (added as complementary file in Dryad -datadryad.org- or Figshare -figshare.com-) and performing the 4C-analysis on HTSstation (David et al, 2014 and http://htsstation.epfl.ch). The resulting data was used to compute the cumulative sum over the specified region (Rodriguez-Carballo et al, 2017).
Genome_build: mm10 (for bedGraph of smoothed/normalized data) and mutant genomes (available at DOI: 10.6084/m9.figshare.5220637) for segToFrag bedGraph.
Supplementary_files_format_and_content: Smoothed/normalized data (bedGraph), one per viewpoint, per tissue.   Segtofrag are raw coverage of each fragment once mapped on the mutant genome.

source_name: Distal Forelimbs

extract_protocol:
Micro-dissected proximal and distal segments of E12.5 forelimbs either from wild type or mutant embryos (delHoxD(10-12), delHoxd(9-12), delHoxd(8-13)d11lac, delHoxd(8-13)rXII, delHoxd(1-13)d11lac, delHoxd(1-13)d9lac,delHoxD(attP-Rel5)d9lac). Tissues were dissected, dissociated with collagenase (Sigma Aldrich/Fluka) and filtered through a 35 micron mesh to isolate single cells. Cells were fixed with 2% formaldehyde (in PBS/10%FBS) for 10 min at room temperature and the reaction was quenched on ice with glycine. Cells were further lysed with 10 mM Tris pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EDTA, 1x Protease inhibitor cocktail to isolate nuclei and stored at -80°C. Nuclei from pools of at least 10 distal or proximal limbs were digested with NlaIII (New England Biolabs) and ligated with T4 DNA ligase HC (Promega) in diluted conditions to promote intramolecular ligation. Samples were digested again with DpnII (New England Biolabs) and ligated with T4 DNA ligase HC (Promega) in diluted conditions.
These templates were amplified using Expand long template (Roche) and inversed PCR primers flanked with adaptors allowing multiplexing. The illumina adaptors used were 5'-AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCT-3' for the inverse-forward primers located at the NlaII site and 5'-CAAGCAGAAGACGGCATACGA-3' for the inverse-reverse primers located at the DpnII site. Barcodes (4bp) were added between the illumina adaptor and the specific NlaIII primers when the same viewpoints were multiplexed in the same run. The barcode is mentioned in the raw file name being: A14 (ATCG), A24 (ACTT), C14 (CAGA), C44 (CTGT), G14 (GACA), G24 (GGTA), T14 (TGAC), T24 (TAGC) and T34 (TTAG). Specific primer information for each viewpoint is displayed in the related publication (Rodríguez-Carballo et al, 2017). Undigested and self-ligated fragments were discarded according to the sequences provided as an associated file named "Rodriguez-Carballo_2017_4C-seq_filtered_out_sequences.txt"

value: Distal Forelimbs

tag: genotype

tag: embryonic day


title: PFL_E12_delattp-rel5d9lac_lacZ

description: Proximal forelimb mouse E12.5_del(attp-rel5)d9lac_lacZ viewpoint

source_name: Proximal Forelimbs

value: Proximal Forelimbs


title: PFL_E12_Wt_Cs65

description: Proximal forelimb mouse E12.5 WT_Cs65 viewpoint

value: wild type


title: DFL_E12_Wt_Cs65

description: Distal forelimb mouse E12.5 WT_Cs65 viewpoint


title: DFL_E12_delattp-rel5d9lac_lacZ

description: Distal forelimb mouse E12.5_del(attp-rel5)d9lac_lacZ viewpoint


title: PFL_E12_delattp-rel5d9lac_Cs65

description: Proximal forelimb mouse E12.5_del(attp-rel5)d9lac_Cs65 viewpoint


title: PFL_E12_del1-13d11lac_Cs38

description: Proximal forelimb mouse E12.5_del(1-13)d11lac_Cs38 viewpoint


title: DFL_E12_del1-13d11lac_Cs38

description: Distal forelimb mouse E12.5_del(1-13)d11lac_Cs38 viewpoint


title: PFL_E12_delattp-rel5d9lac_Cs38

description: Proximal forelimb mouse E12.5_del(attp-rel5)d9lac_Cs38 viewpoint


title: DFL_E12_delattp-rel5d9lac_Cs38

description: Distal forelimb mouse E12.5_del(attp-rel5)d9lac_Cs38 viewpoint


title: AB1660


title: AB2627


title: AB2624


title: PFL_E12_del1-13d9lac_Cs38

description: Proximal forelimb mouse E12.5_del(1-13)d9lac_Cs38 viewpoint


title: AB2622


title: AB2474


title: PFL_E12_del8-13rXII_Cs38_2n

description: Proximal forelimb mouse E12.5_del(8-13)rXII_Cs38 viewpoint


title: PFL_E12_del1-10_CS38

description: Proximal forelimb mouse E12.5_del(1-10)_Cs38 viewpoint


title: DFL_E12_del1-10_CS38

description: Distal forelimb mouse E12.5_del(1-10)_Cs38 viewpoint


title: PFL_E12_del9-12_Cs38

description: Proximal forelimb mouse E12.5_del(9-12)_Cs38 viewpoint


title: PFL_E12_del8-13d11lac_Cs38

description: Proximal forelimb mouse E12.5_del(8-13)d11lac_Cs38 viewpoint


title: DFL_E12_del1-13d9lac_Cs38

description: Distal forelimb mouse E12.5_del(1-13)d9lac_Cs38 viewpoint


title: DFL_E12_Wt_Cs38_5n

description: Distal forelimb mouse E12.5 WT_Cs38 viewpoint


title: DFL_E12_del8-13d11lac_Cs38

description: Distal forelimb mouse E12.5_del(8-13)d11lac_Cs38 viewpoint


title: DFL_E12_del9-12_Cs38

description: Distal forelimb mouse E12.5_del(9-12)_Cs38 viewpoint


title: PFL_E12_del9-12_Hoxd4

description: Proximal forelimb mouse E12.5_del(9-12)_Hoxd4 viewpoint


title: PFL_E12_Wt_Cs38_5n

description: Proximal forelimb mouse E12.5 WT_Cs38 viewpoint


title: DFL_E12_del10-12_Cs38

description: Distal forelimb mouse E12.5_del(10-12)_Cs38 viewpoint


title: DFL_E12_del8-13rXII_Hoxd4_2n

description: Distal forelimb mouse E12.5_del(8-13)rXII_Hoxd4 viewpoint


title: PFL_E12_del10-12_Cs38

description: Proximal forelimb mouse E12.5_del(10-12)_Cs38 viewpoint


title: PFL_E12_del8-13rXII_Hoxd4_2n

description: Proximal forelimb mouse E12.5_del(8-13)rXII_Hoxd4 viewpoint


title: PFL_E12_del8-13d11lac_Hoxd4

description: Proximal forelimb mouse E12.5_del(8-13)d11lac_Hoxd4 viewpoint


title: DFL_E12_del9-12_Hoxd4

description: Distal forelimb mouse E12.5_del(9-12)_Hoxd4 viewpoint


title: PFL_E12_del1-10_Hoxd13

description: Proximal forelimb mouse E12.5_del(1-10)_Hoxd13 viewpoint


title: DFL_E12_del8-13d11lac_Hoxd4

description: Distal forelimb mouse E12.5_del(8-13)d11lac_Hoxd4 viewpoint


title: PFL_E12_del9-12_Hoxd13

description: Proximal forelimb mouse E12.5_del(9-12)_Hoxd13 viewpoint


title: DFL_E12_Wt_Hoxd4_3n

description: Distal forelimb mouse E12.5 WT_Hoxd4 viewpoint rep1


title: PFL_E12_Wt_Hoxd4_3n

description: Proximal forelimb mouse E12.5 WT_Hoxd4 viewpoint rep1


title: PFL_E12_del10-12_Hoxd13

description: Proximal forelimb mouse E12.5_del(10-12)_Hoxd13 viewpoint


title: DFL_E12_del9-12_Hoxd13

description: Distal forelimb mouse E12.5_del(9-12)_Hoxd13 viewpoint


title: DFL_E12_del10-12_Hoxd13

description: Distal forelimb mouse E12.5_del(10-12)_Hoxd13 viewpoint


title: DFL_E12_del8-13rXII_Cs38_2n

description: Distal forelimb mouse E12.5_del(8-13)rXII_Cs38 viewpoint


title: PFL_E12_Wt_Hoxd13_3n

description: Proximal forelimb mouse E12.5 WT_Hoxd13 viewpoint


title: PFL_E12_del1-13d11lac_Evx2

description: Proximal forelimb mouse E12.5_del(1-13)d11lac_Evx2 viewpoint


title: DFL_E12_Wt_Hoxd13_3n

description: Distal forelimb mouse E12.5 WT_Hoxd13 viewpoint


title: DFL_E12_del8-13rXII_Evx2

description: Distal forelimb mouse E12.5_del(8-13)rXII_Evx2 viewpoint


title: PFL_E12_del10-12_Evx2

description: Proximal forelimb mouse E12.5_del(10-12)_Evx2 viewpoint


title: PFL_E12_Wt_Evx2_3n

description: Proximal forelimb mouse E12.5 WT_Evx2 viewpoint


title: DFL_E12_del1-13d11lac_Evx2

description: Distal forelimb mouse E12.5_del(1-13)d11lac_Evx2 viewpoint


title: PFL_E12_del8-13rXII_Evx2

description: Proximal forelimb mouse E12.5_del(8-13)rXII_Evx2 viewpoint


title: PFL_E12_del1-10_Evx2

description: Proximal forelimb mouse E12.5_del(1-10)_Evx2 viewpoint


title: DFL_E12_del1-10_Evx2

description: Distal forelimb mouse E12.5_del(1-10)_Evx2 viewpoint


title: DFL_E12_del10-12_Evx2

description: Distal forelimb mouse E12.5_del(10-12)_Evx2 viewpoint


title: PFL_E12_delattp-rel5d9lac_Island4

description: Proximal forelimb mouse E12.5_del(attp-rel5)d9lac_Island4 viewpoint


title: DFL_E12_Wt_Evx2_3n

description: Distal forelimb mouse E12.5 WT_Evx2 viewpoint


title: PFL_E12_del1-13d11lac_Island4_2n

description: Distal forelimb mouse E12.5_del(1-13)d11lac_Island4 viewpoint


title: PFL_E12_del8-13d11lac_Island4

description: Proximal forelimb mouse E12.5_del(8-13)d11lac_Island4 viewpoint


title: DFL_E12_del1-13d9lac_Island4

description: Distal forelimb mouse E12.5_del(1-13)d9lac_Island4 viewpoint


title: DFL_E12_delattp-rel5d9lac_Island4

description: Distal forelimb mouse E12.5_del(attp-rel5)d9lac_Island4 viewpoint


title: DFL_E12_del1-13d11lac_Island4_2n


title: DFL_E12_del8-13d11lac_Island4

description: Distal forelimb mouse E12.5_del(8-13)d11lac_Island4 viewpoint


title: DFL_E12_del8-13rXII_Island4_2n

description: Distal forelimb mouse E12.5_del(8-13)rXII_Island4 viewpoint


title: PFL_E12_del8-13rXII_Island4_2n

description: Proximal forelimb mouse E12.5_del(8-13)rXII_Island4 viewpoint


title: PFL_E12_del1-10_Island4

description: Proximal forelimb mouse E12.5_del(1-10)_Island4 viewpoint


title: PFL_E12_del9-12_Island4

description: Proximal forelimb mouse E12.5_del(9-12)_Island4 viewpoint


title: DFL_E12_del1-10_Island4

description: Distal forelimb mouse E12.5_del(1-10)_Island4 viewpoint


title: DFL_E12_del9-12_Island4

description: Distal forelimb mouse E12.5_del(9-12)_Island4 viewpoint


title: PFL_E12_del1-13d9lac_Island4

description: Proximal forelimb mouse E12.5_del(1-13)d9lac_Island4 viewpoint


title: PFL_E12_del10-12_Island4

description: Proximal forelimb mouse E12.5_del(10-12)_Island4 viewpoint


title: DFL_E12_del10-12_Island4

description: Distal forelimb mouse E12.5_del(10-12)_Island4 viewpoint


title: PFL_E12_Wt_Island4_5n

description: Proximal forelimb mouse E12.5 WT_Island4 viewpoint


title: DFL_E12_Wt_Island4_5n

description: Distal forelimb mouse E12.5 WT_Island4 viewpoint


title: PFL_E12_attp-rel5_Island2

description: Proximal forelimb mouse E12.5 attp-rel5_Island2 viewpoint


title: DFL_E12_attp-rel5_Island2

description: Distal forelimb mouse E12.5 attp-rel5_Island2 viewpoint


title: PFL_E12_Wt_Island2

description: Proximal forelimb mouse E12.5 WT_Island2 viewpoint


title: DFL_E12_Wt_Island2

description: Distal forelimb mouse E12.5 WT_Island2 viewpoint


title: Il22-/- sham #3

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

data_processing:
low quality bases were trimmed with Trimmomatic 0.33 (parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Alignment and summarization were done using STAR 2.5.0a
Differential expression analysis was performed using DESeq2 1.14
Genome_build: GRCm38.84
Supplementary_files_format_and_content: tab-delimited text file containing normalized counts for all samples provided by DESeq2

source_name: liver tissue

extract_protocol:
Total RNA from liver tissues was isolated using Trizol reagent (Applied Biosystems®, Foster City, CA).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)

value: liver

value: sham surgery


title: Il22bp-/- sham #3


title: DFL_E12_del1-10_Hoxd13

description: Distal forelimb mouse E12.5_del(1-10)_Hoxd13 viewpoint


title: Il22bp-/- sham #1


title: Il22bp-/- sham #2


title: Il22-/- sham #1


title: Il22-/- sham #2


title: Wt sham #3

value: wt


title: Wt sham #2


title: Il22-/- IR #3

value: Ischemia reperfusion injury


title: Il22bp-/- IR #1


title: Il22bp-/- IR #3


title: Il22bp-/- IR #2


title: Il22-/- IR #2


title: Wt IR #3


title: Il22-/- IR #1


title: Wt IR #2


title: Wt IR #1


title: siRAD21_OHT_48h_rep2

city: Milan

first: Marco

middle: J.

last: Morelli

address: via Adamello 16

department: Center for Genomic Science of IIT@SEMM

country: Italy

institute: Istituto Italiano di Tecnologia

description: rRNA-depleted RNA (ribozero)

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v -i ; fastq_masker -Q33 -q 20 -r -N -v -i
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-inds --library-type fr-unstranded -G gtffile reffile fastqfile
removing duplicate reads: samtools rmdup -S bamfile
expression quantification with featureCounts 1.4.5 (options -T 2 -p -P) on hg19 standard gtf. Expression values, differently from regular RPKMs, were normalised to the total number of reads aligned on exons rather than library size.
Genome_build: hg19
Supplementary_files_format_and_content: csv file with RPKM normalised to exonic reads

source_name: Osteosarcoma U2OS cell line

growth_protocol: U2OS cells were grown in DMEM (Lonza) supplemented with 10% FBS, 1% penicillin/streptomycin (GIBCO) and 2 mM L-Glutamine.

extract_protocol:
Cells were lysed with QIAzol lysis reagent and total RNA was purified using RNeasy columns. DNase treatment was performed with RNase-free DNase on the column. 5 µg of purified RNA was first treated with Ribozero rRNA removal kit (Illumine) and then precipitated with ethanol. RNA quality and removal of rRNA were checked with the Agilent 2100 Bioanalyser (Agilent Technologies).
RNA-seq libraries were prepared with the TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer’s protocol.

treatment_protocol: U2OS-MycER cells were reverse-transfected with RNAiMAX lipofectamine and specific siRNAs. Cells were treated with OHT (400nM) or ethanol (as a control) simultaneously.

value: Osteosarcoma U2OS cell line


title: siRAD21_OHT_24h_rep1

description: rRNA-depleted RNA (ribozero)


title: siRAD21_OHT_48h_rep1

description: rRNA-depleted RNA (ribozero)


title: siRAD21_OHT_24h_rep2

description: rRNA-depleted RNA (ribozero)


title: Kras;Rank+/+ 2 [23944]

city: Vienna

first: Shuan

last: Rao

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

data_processing:
50-bp single-end Illumina mRNA sequencing reads were aligned using STAR 2.5.0a
aligned reads were counted with HTSeq
TPM estimation was performed with RSEM (v1.2.25) and differential expression analysis with DESeq2 (v 1.10.1)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample (standard output RSEM)

source_name: male primary pneumocytes

extract_protocol:
Total RNA was purified using RNAeasy mini Kit (Qiagen). poly-T selected RNA was isolated and dUTP-containing cDNA was generated.
Illumina TruSeq protocol

value: normal lung

tag: genotype/variation

value: Kras;rank+/+


title: Kras;Rank+/+ 1 [23943]


title: siRAD21_24h_rep2

description: rRNA-depleted RNA (ribozero)


title: Kras;Rankfl/fl 1 [23945]

value: Kras;rankfl/fl


title: Kras;Rankfl/fl 2 [23946]


title: siCtrl_OHT_48h_rep3

description: rRNA-depleted RNA (ribozero)


title: dsSSRP_80mM_MNaseSEQ_(2016-04-14,2016-05-17_SR_Dm_80mM_2)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Nuclei from Drosophila S2 cells exposed to dsRNA against SSRP were treated with Mnase, and extracted with low salt buffer. The low salt soluble chromatin was subjected to Illumina paired-end sequencing. Two technical replicates.

data_processing:
Genome_build: FlyBase r5.51
1. We used Novoalign (2.08.03 - 16 Oct 2012) to map paired-end 25bp reads to release r5.51 (May 2013) of the D.melanogaster genomic sequence obtained from FlyBase. If a read was mapped to multiple locations, one location was picked at random 2. We extracted properly paired reads (Supplementary file .bed) 3. We selected aligned paired-end fragments by insert size length for analysis.

organism: Drosophila melanogaster

source_name: MNase DNA

extract_protocol:
extract_protocol_2.rtf
PMID 25827087

tag: cell line

value: S2 DRSC


title: siCtrl_OHT_48h_rep2

description: rRNA-depleted RNA (ribozero)


title: siCtrl_OHT_48h_rep1

description: rRNA-depleted RNA (ribozero)


title: ChIP-Seq analysis of H2BK120-ub in mouse ESCs under shPhf5a knockdown treatment replicate 3

city: New York

first: Alexandros

last: Strikoudis

state: NY

address: 550 First Avenue, Smilow 1303

department: Pathology

institute: NYU Medical Center

data_processing:
Basecalls performed using Illumina bcl2fastq.
ChIP-seq reads were aligned to the mouse genome (build mm10) using Bowtie2.
MACS2 was used for peak discovery. GenomicTools was used for ChIP-seq profile construction.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig format containg genome-wide binding profile

source_name: ESC shPhf5a WITH LIF

growth_protocol: Embryonic stem cells (ESCs), cultured in LIF-containing ESC growth medium on gelatin coated plates. ESC strain used: KH2 ESC line (C57BL/6 X 129/Sv) Original ESC reference: Beard, C., et al. (2006). "Efficient method to generate single-copy transgenic mice by site-specific integration in embryonic stem cells." Genesis 44(1): 23-28.

extract_protocol:
Ten million cells were treated withmicrococcal nuclease to generate mono-nucleosomes and for the ChIP chromatin was precipitated using 10 micrograms of antibody against H2Bk120-ub, clone 56 (Millipore, 05-1312).
Libraries were generated as described before (Strikoudis A. et. al., 2016), including end-repair, A-tailing, adapter (Illumina Truseq system) ligation and PCR amplification.

treatment_protocol: ESCs cultured in the presence LIF were treated with inducible shControl or shPhf5a knockdown using doxycycline (2μg/mL) for 3 days

value: mouse embryonic stem cells


title: ChIP-Seq analysis of H2BK120-ub in mouse ESCs under shPhf5a knockdown treatment replicate 2

value: H2Bk120-ub, clone 56 (Millipore, 05-1312)


title: Wt sham #1


title: ChIP-Seq analysis of H2BK120-ub in mouse ESCs under shPhf5a knockdown treatment replicate 1


title: siRAD21_48h_rep2

description: rRNA-depleted RNA (ribozero)


title: ChIP-Seq analysis of H2BK120-ub in mouse ESCs under shControl knockdown treatment replicate 1

source_name: ESC shControl WITH LIF


title: siCtrl_OHT_24h_rep1

description: rRNA-depleted RNA (ribozero)


title: dsGFP_80mM_MNaseSEQ_(2016-04-14,2016-05-17_SR_Dm_80mM_4)

description: Nuclei from Drosophila S2 cells exposed to dsRNA against GFP were treated with Mnase, and extracted with low salt buffer. The low salt soluble chromatin was subjected to Illumina paired-end sequencing. Two technical replicates.


title: siRAD21_48h_rep1

description: rRNA-depleted RNA (ribozero)


title: 4hDox_3

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v ; fastq_masker -Q33 -q 20 -r -N -v
Read alignment with tophat 2.0.8: tophat -p 8 -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded R1.fastq R2.fastq
Read quantification with HTSeq (options -q --mode=intersection-nonempty) on mm9 standard gtf
Genome_build: mm9
Supplementary_files_format_and_content: text files with unnormalized read counts

source_name: tumor

extract_protocol:
Frozen tissue samples were homogenized with the GentleMACS Dissociator (Miltenyi Biotec), RNA was extracted in Trizol (Invitrogen) using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
5 μg of total RNA were depleted of ribosomal RNA with the Ribo-ZeroTM rRNA Removal Kit from Epicentre®. RNAseq libraries were prepared with the Illumina TruSeq RNA sample preparation kit v2 following the manufacturer’s protocol

treatment_protocol: CD1-nude ho mice, injected with transformed hepatoblasts containing the conditional shRNA vector (TtRMPVIR shST18) to silence ST18, were treated with Doxycycline to activate the knockdown of ST18. we administrated the first dose of 200mg/ml Doxycycline (Sigma) in 300µl of water by oral gavage and sacrificed them after 4h

value: CD1 nude ho

value: 4h Doxycycline

value: ST18 knockdown


title: siCtrl_48h_rep3

description: rRNA-depleted RNA (ribozero)


title: noDox_3

value: untreated


title: siRAD21_24h_rep1

description: rRNA-depleted RNA (ribozero)


title: noDox_1


title: noDox_2


title: siCtrl_48h_rep2

description: rRNA-depleted RNA (ribozero)


title: 4hDox_1


title: S2_ShortFragment_MNaseSEQ_(2014-06-17,2016-12-23_SR_Dm_total_SF)

description: Nuclei from Drosophila S2 cells were treated with Micrococcal nuclease and the DNA was extracted and subjected to paired-end Illumina sequencing. Two technical replicates.

extract_protocol:
extract_protocol_1.rtf
PMID 25827087


title: siCtrl_48h_rep1

description: rRNA-depleted RNA (ribozero)


title: siCtrl_24h_rep2

description: rRNA-depleted RNA (ribozero)


title: ChIP-Seq analysis of H2BK120-ub in mouse ESCs under shControl knockdown treatment replicate 3


title: ChIP-Seq analysis of H2BK120-ub in mouse ESCs under shControl knockdown treatment replicate 2


title: dsSpt16_80mM_MNaseSEQ_(2016-04-14,2016-05-17_SR_Dm_80mM_1)

description: Nuclei from Drosophila S2 cells exposed to dsRNA against Spt16 were treated with Mnase, and extracted with low salt buffer. The low salt soluble chromatin was subjected to Illumina paired-end sequencing. Two techinal replicates


title: siCtrl_OHT_24h_rep2

description: rRNA-depleted RNA (ribozero)


title: GK_NAC_2

first: Wen

last: Zhong

address: Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
Fastq files were aligned with Bowtie (v1.1.1)  to merged transcript sequences from the UCSC RefGene database. The parameter for the mapping program Bowtie was “-l25 -n2 –M3 -e 200 --best --strata --phred33-quals --trim5 4”.
The unmapped tags in the first round were then mapped to the rat genome (rn6)
For each gene, only tags uniquely mapped and localized in exons or exon-exon junctions were counted
Genome_build: rn6
Supplementary_files_format_and_content: bigwig files were generated using bedGraphToBigWig

organism: Rattus norvegicus

source_name: Pancreatic Islet cells

extract_protocol:
For RNA extraction, we used Trizol kit by following manufacturer's instructions
Trizol-isolated RNA was enriched for Poly(A+) RNA with biotinylated oligo(dT), converted to cDNA with Superscript III (Invitrogen). Next, a terminal transferase (NEB, cat.no.M0315S) was used to add a ddNTP to the 3’-end of the cDNA. After the second-strand cDNA synthesis, 23 cycles of PCR were performed to amplify the cDNA. The length of 200-400nt PCR product was subjected to deep sequencing.

tag: treat

value: NAC


title: GK_NAC_1


title: GK_control_3

value: control


title: GK_control_2


title: GK_control_1


title: S2_MNaseSEQ_(2014-06-17,2016-09-09_SR_Dm_total_All)


title: dsSpt6_80mM_MNaseSEQ_(2016-04-14,2016-05-17_SR_Dm_80mM_3)

description: Nuclei from Drosophila S2 cells exposed to dsRNA against Spt6 were treated with Mnase, and extracted with low salt buffer. The low salt soluble chromatin was subjected to Illumina paired-end sequencing. Two technical replicates.


title: 4hDox_2


title: WST_1st_24w

data_processing:
Fastq files were aligned with Bowtie (v1.1.1)  to merged transcript sequences from the UCSC RefGene database. The parameter for the mapping program Bowtie was “-l25 -n2 –M3 -e 200 --best --strata --phred33-quals --trim5 4”.
The unmapped tags in the first round were then mapped to the rat genome (rn6)
For each gene, only tags uniquely mapped and localized in exons or exon-exon junctions were counted
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include raw counts of genes for each sample

extract_protocol: Briefly, total RNA was extracted from islets using TRIzol reagent (Invitrogen , cat. no. 15596018). Poly(A+) RNAs were enriched with biotinylated oligo(dT) and converted to cDNA with Superscript III (Invitrogen, cat. no. 18080-051). A ddNTP was added to the 3’-end of the cDNA by a terminal transferase. After second-strand cDNA synthesis, 23 cycles of PCR were performed to amplify the cDNA. PCR products with lengths of 200-400 nt were subjected to deep sequencing on a HiSeq 2500 (Illumina).

value: Wistar

tag: age

value: week 24

value: Pancreatic Islet cells


title: GK_3rd_24w

value: GK


title: WST_2nd_24w


title: GK_2nd_24w


title: 11L_iF1

city: Crawley

first: Mohammed

last: Alsaweed

address: 35 stirling hwy

department: Biochemistry

country: Australia

institute: UWA

data_processing:
Illumina Casava1.7 software used for basecalling.
Cleaning reads: including getting rid of low quality reads, rid of reads with 5' primer contaminants, rid of reads without 3' primer, rid of reads without the insert tag, rid of reads with poly A, rid of reads shorter than 18nt.
Reads Per Kilobase of exon per Megabase of library size (RPKM) 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.
length distribution of all clean reads
Analysis of base composition and quality
map to human genome
reads aligned to miRBase database
Novel miRNA prediction
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files includ include reads for each identified SE50 molecules in each Sample

source_name: Human milk lipids

extract_protocol:
Human milk total cells and lipids were isolated by centrifugation of whole milk, then lipids were purified by further centrifugation, and total cells were washed three times using PBS, total RNA/miRNA was extracted using miRNeasy kit (Qiagen) for cells samples and Exiqon Biofluids kit was used for lipids samples.
RNA libraries were prepared for sequencing using standard Illumina protocols
Small RNA-Seq using illumina Hiseq 2000

tag: tag

value: Collected during different types of infections in mother/baby

tag: gender

value: female

value: Breastmilk

tag: fraction

value: Human milk lipids


title: WST_2nd_16w

city: Beijing

value: week 16


title: GK_3rd_16w


title: WST_3rd_16w


title: 11C_iF1

source_name: Total human milk cells

value: Total human milk cells


title: WST_3rd_24w


title: 10L_iF1


title: WST_1st_16w


title: siCtrl_24h_rep1

description: rRNA-depleted RNA (ribozero)

value: Osteosarcoma U2OS cell line


title: 10C_iF1


title: GK_1st_24w


title: 9L_iF1


title: 8L_iF1


title: WST_3rd_8w

value: week 8


title: 8C_iF1


title: GK_3rd_8w


title: 9C_iF1


title: GK_2nd_16w


title: GK_2nd_8w


title: WST_2nd_8w


title: GK_1st_16w


title: WST_1st_8w


title: 7L_iF1


title: WST_3rd_6w

value: week 6


title: WST_2nd_6w


title: 7C_iF1


title: GK_1st_8w


title: GK_3rd_6w


title: WST_1st_6w


title: GK_3rd_4w

value: week 4


title: GK_2nd_6w


title: GK_1st_6w


title: WST_2nd_4w


title: 6C_H1

value: Collected from healthy mother


title: 5L_H1


title: WST_1st_4w


title: GK_2nd_4w


title: GK_1st_4w


title: 4C_H1


title: 4L_H1


title: 3L_H1


title: 5C_H1


title: 3C_H1


title: 4L_iF1


title: 4C_iF1


title: 2L_H1


title: 1L_iF1


title: 6L_H1


title: 2C_H1


title: 1L_H1


title: 1C_H1


title: 35R_54B

city: Uppsala

first: Louise

middle: Sara

last: Andersson

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

data_processing:
Reads were aligned using GSNAP to the RefBeet 1.0 genome
Count data was generated from BAM files using standard procedures established at NCGR (National center for genome research)
FastQ files for each of the 36 samples were submitted to a Python script which determines nucleotide percentage by position of all reads as well as average quality (Phred) scores by position.
The R (version 3.2.3) package EDAseq was used for correction of GC bias and to predict read quality. Read quality was high across all samples.
Genome_build: RefBeet 1.0 and RefBeet 1.1 (http://bvseq.molgen.mpg.de/index.shtml)
Supplementary_files_format_and_content: csv-file showing the number of reads per sample and gene. Gene annotations for both RefBeet 1.0 and RefBeet 1.1 are included in the processed data file. The gff and fasta used for read counting (RefBeet 1.0) are available on the series record.

organism: Beta vulgaris

source_name: Susceptible genotype 2, 5 dpi

growth_protocol: Plants were grown for 13 weeks in a greenhouse 18/12 degrees C (day/night). After inoculation plants were moved to 24/18 degrees C.

extract_protocol:
Material were flash frozen in liquid nitrogen at harvest. Total RNA was extracted using the protocol from Puthoff and Smigocki. Plant Cell Rep, 2007. 26:71-84
RNA was cleaned with RiboPure RNA Purification Kit (Thermo Fisher Scientific). cDNA was prepared with a polyA tail and fragmented into 200bp fragments. Random primers and adaptors were added.10 cycles of PCR were conducted.

treatment_protocol: Plants were inoculated with R. solani AG2-2 IIIB BBA 69670 isolate and harvested at 0, 2 or 5 days post inoculation

value: root

value: Susceptible 2

tag: harvest time-point


title: 36R_54C


title: 34R_54A


title: 1C_iF1


title: 33R_53C

source_name: Susceptible genotype 1, 5 dpi

value: Susceptible 1


title: 32R_53B


title: 31R_53A


title: PL_HiC_E12_del1-13d9lac

description: Proximal limb mouse E12.5_del1-13d9lac_HiC

data_processing:
Reads were mapped, filtered and bias corrected as described before (Lajoie et al. Methods 2015, Giorgetti Nature 2016).
Briefly, read pairs were mapped independently, starting at 25bp and iterated every 5bp using bowtie2 (version 2.2.4 (Langmead et al. 2009)) (as described in Imakaev Nature methods 2012) with parameter: --very-sensitive, either on mouse genome (mm10), or on the mutant genomes generated in silico. Each read was assigned to a fragment using the 5’ mapped-position shifted 3 bp toward the 3’ position to assign correctly the reads overlapping the cutting sites. The fragment assignment and mapping strand from R1 and R2 was combined and used to filter out the single-side mapped pairs, dangling-end pairs, error pairs and self-circle pairs. For each condition (same tissue and same genotype), two replicates were merged (fifteen replicates for CH12) and the interactions were filtered to discard duplicates. Each fragment was assigned to a bin (40 or 20kb) based on the position of the middle of the fragment and each valid interaction was assigned to a couple pair of bins (one bin for the R1 and one bin for the R2) and reported in the raw matrix. Prior to the ICE normalization (Imakaev et al. 2012), the rows and columns were masked if the sum of reads in this region was 10 fold less the expectation with uniform coverage, or if the number of fragments covered by at least two reads in this region was less than half the number of the fragments of this region.
Genome_build: mm10 (for DL_Wt, PL_Wt, DL_delattP-Rel5d9lac, PL_delattP-Rel5d9lac, CH12 and mESC) and mutant genomes (for DL_delattP-Rel5d9lac, PL_delattP-Rel5d9lac, DL_del1-13d9lac and PL_del1-13d9lac which are available at DOI: 10.6084/m9.figshare.5220637)
Supplementary_files_format_and_content: validPair.txt.gz contains every valid pair (not asigned to the same fragments) for each dataset. Each line is a read, column 2 is the chromosome name of the first read, column 3 is the coordinate of this read, column 4 is the strand, column 5 is the read name, column 6 is the fragment number to which this read has been asigned, columns 8-12 are the same for the other read. This file is not filtered for duplicates.  __txt.tar contains all cis matrices of interactions in one folder for each resolution (20kb or 40kb bin size) and then one subfolder for the raw and one subfolder for the iced (normalised) matrices. At the 40kb resolution, cis interactions for all chromosomes are provided. At 20kb resolution, only the matrices for chr2 are provided.

source_name: Proximal forelimbs and proximal hindlimbs

extract_protocol: Hi-C libraries were generated using the HindIII enzyme as described in the protocol outlined in (Belton et al. 2012).


title: DL_HiC_E12_del1-13d9lac

description: Distal limb mouse E12.5_del1-13d9lac_HiC

source_name: Distal forelimbs and distal hindlimbs

value: Distal forelimbs and distal hindlimbs


title: PL_HiC_E12_delattP-Rel5d9lac

description: Proximal limb mouse E12.5_delattP-Rel5d9lac_HiC

value: Proximal forelimbs and proximal hindlimbs


title: 28R_52A

source_name: Resistant genotype 2, 5 dpi

value: Resistant 2


title: 29R_52B


title: 27R_51C

source_name: Resistant genotype 1, 5 dpi

value: Resistant 1


title: 26R_51B


title: DL_HiC_E12_delattP-Rel5d9lac

description: Distal limb mouse E12.5_delattP-Rel5d9lac_HiC


title: 30R_52C


title: 25R_51A


title: 24R_24C

source_name: Susceptible genotype 2, 2 dpi


title: 22R_24A


title: 21R_23C

source_name: Susceptible genotype 1, 2 dpi


title: 19R_23A


title: 18R_22C

source_name: Resistant genotype 2, 2 dpi


title: 20R_23B


title: AUTS2_KD_ChIPseq

city: Naples

first: Giovanni

last: D'Angelo

address: Via Pietro Castellino, 111

institute: Institute of Protein Biochemistry-National Research Council

data_processing:
AUTS2_KD, Gb3S_KD and mock sequence reads were generated by Illumina's HiSeq2500 platform.
Quality of the short reads of 50 bp were analysed and high quality reads were selected. They were aligned to the human reference genome (hg19) by using Bowtie2.
Data were filtered by uniquely aligned reads.
Peaks were called using MACS v.2.1.0. The sample enrichments were normalized for each specific input. MACS parameter settings were: --bw 200, -p 1e-4, -m 8,30 and --gsize hs.
Peaks were defined as common when a summit was located within 500bp of another one. The normalized ChIP signals for each peak in the three conditions were compared calculating the Log2-intensity ratio. Genomic annotation of peaks was achieved by Homer software (Heinz et al. 2010)
Genome_build: hg19
Supplementary_files_format_and_content: bed files including peaks and pileup values.

source_name: HeLa cells

growth_protocol: HeLa cells were obtained from the American Tissue Type Collection. HeLa cells were grown in Dulbecco’s modified Eagle’s medium (Gibco) supplemented with 4.5 g/L glucose, 2 mM L-glutamine, 100 U/mL penicillin and streptomycin, and 10% (v/v) foetal calf serum (FCS).

extract_protocol:
After cross-linking, crude nuclear extracts were isolated and subjected to sonication. After immunoprecipitation with the anti-acetyl H3 antibody , the histone-DNA immunocomplexes were purified by co-precipitation with protein A-Sepharose (GE Healthcare, UK).
Ovation Ultralow Library System v2’ kits (NuGEN, San Carlos, CA, USA) were used for the library preparation, according to the manufacturer instructions. The input and immunoprecipitated samples, as well as the final libraries were quantified by using a fluorometer (Qubit 2.0; Invitrogen, Carlsbad, CA, USA) and quality tested using an Agilent 2100 Bioanalyser RNA nanoassay (Agilent Technologies, Santa Clara, CA, USA) and real-time Stratagen Mx3000P (Agilent Technologies, Santa Clara, CA, USA). The libraries were then processed with Illumina cBot for cluster generation on a flowcell, according to the manufacturer instructions and sequenced on single-end mode at the multiplexing level requested on HiSeq2500 (Illumina, San Diego, CA, USA).

treatment_protocol: HeLa cells were plated at 30% confluence in  12-well plates, and transfected with 120 pmol of siRNAs with Oligofectamine (Invitrogen, USA), according to the manufacturer instructions. At 72 h after the initial treatment with the siRNAs, the cells were fixed with 1% formaldehyde and processed for chromatin immunoprecipitation.

value: HeLa

tag: passage

value: AUTS2 KD

value: anti acetyl-H3 Millipore 06-599


title: No-IgG Triple-crosslinked

first: David

middle: S

last: Gilmour

state: Pennsylvania

address: 465 North Frear

institute: Penn State University

description:
Protein-DNA complex
ChIP-exo

data_processing:
Basecalls performed using Bcl2FastQ version 2.16.0
Sequenced reads were masked for low-quality sequence, then mapped to dm3 whole genome using bwa mem 0.7.9a,0.7.12 with the default parameters.
Replicates were megred and  and only the 5' end of read1 was kept.
Tag directories were created in homer with a fragment length of 1.
BedGraph files were generated using the Homer makeUCSCfile command with reads normalized to 1E7
Genome_build: dm3
Supplementary_files_format_and_content: bedGraph files for each sample were generated using homer's makeUCSCfile function by normalizing to 1E7 and keeping strand information.

growth_protocol: M3+BPYE media at 25°C

extract_protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with rabbit IgG antibody.

treatment_protocol: Cells were crosslinked with dimethyl adipimidate and ethylene glycol bis(succinimidyl succinate) for at room temperature for 10 minutes prior to the addition of 1% formaldehyde followed by an additional 10 minute incubation at room temperature.

tag: antibody

value: No-IgG


title: INPUT_AUTS2_KD_ChIPseq


title: 17R_22B


title: PL_HiC_E12_Wt

description: Proximal limb mouse E12.5_Wt_HiC

value: wild type


title: Gb3S_KD_ChIPseq

value: Gb3S KD


title: 16R_22A


title: INPUT_Gb3S_KD_ChIPseq


title: Preimmune

description:
Protein-DNA complex
ChIP-exo

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 10 min and quenched with 250mM glycine.

value: Preimmune


title: 15R_21C

source_name: Resistant genotype 1, 2 dpi


title: GFZF

description:
Protein-DNA complex
ChIP-exo

value: GFZF


title: 14R_21B


title: Mock_ChIPseq

value: control


title: 10R_04A

source_name: Susceptible genotype 2, 0 dpi


title: 13R_21A


title: 12R_04C


title: 9R_03C

source_name: Susceptible genotype 1, 0 dpi


title: INPUT_Mock_ChIPseq


title: 23R_24B


title: 8R_03B


title: 7R_03A


title: 5R_02B

source_name: Resistant genotype 2, 0 dpi


title: 6R_02C


title: 4R_02A


title: 11R_04B


title: 3R_01C

source_name: Resistant genotype 1, 0 dpi


title: 2R_01B


title: GFZF Triple-crosslinked

description:
Protein-DNA complex
ChIP-exo


title: NET_DRB2_R10_60M_UV_1

status: Public on Dec 21 2017

city: Taichung

first: Yi-Ying

last: Chiou

address: No.145, Xingda Rd., South Dist.

department: Graduate Institute of Biochemistry

country: Taiwan

institute: National Chung Hsing University

description:
NET-seq, preDRB, release 10min, UV, 60 min Repair with DRB, Rep 1
RNAPII bound RNA

data_processing:
Library strategy: mNET-seq
Reads were trimmed by bbduk tool of BBMap (35.82)  and mapped to the genome by Bowtie2 (2.28) (XR-seq) using the option -- very-sensitive or BBMap (35.82) (NET-seq) using the options maxindel=100000 intronlen=10 ambig=random qin=33
For NET-seq, reads with proper pair were selected and the locations of RNAPII were defined as the positon of first base from the 3’-end of the isolated RNA
Aligned reads were strand-specifically assigned to the genes using Intersect tool of Bedtools (2.25.0) with the option: -c.  For intra-gene distribution, genes with RPKM >=  0.1 in all conditions and the length >= 50 kb were selected (1646 genes). Genes were separated into 250 base per bin and the aligned reads were assigned to each bin using Intersect tool of Bedtools with the options: -c -F 0.5.
Genome_build: human (hg19)
Supplementary_files_format_and_content: Bed files, Number of reads of each gene / each bin of gene

source_name: XP-C cells: GM15983

growth_protocol: All cells were grown in DMEM–high glucose (ThermoFisher) supplemented with 10% (v/v) fetal bovine serum (Sigma) and maintained at 37oC in 5% CO2

extract_protocol:
mNET-seq: protocol from (2016) Nature protocols 11, 413-428 using anti-RNAPII antibody MABI0601 from MEDICAL & BIOLOGICAL LABORATORIES
mNET-seq: NEBNext Small RNA Prep Set for Illumina

treatment_protocol:
UV irradiation: 20J/ m2 UVC
DRB regimens:
a. DMSO: 0.1% DMSO added after UV
b. DRB: 100 uM DRB added after UV
c. DRB2: 100 uM DRB added 2 hrs before UV, released by changing to fresh medium for 5 / 10 min, after UV, cells were incubated in the medium with 100 uM DRB

tag: cell type

value: skin fibroblast

value: XPC mutant


title: NET_DRB2_R10_60M_UV_2

description:
NET-seq, preDRB, release 10min, UV, 60 min Repair with DRB, Rep 2
RNAPII bound RNA


title: 1R_01A

value: root


title: NET_DRB2_R10_60M_Ctl_2

description:
NET-seq, preDRB, release 10min, mock, 60 min with DRB, Rep 2
RNAPII bound RNA


title: NET_DRB2_R10_30M_UV_2

description:
NET-seq, preDRB, release 10min, UV, 30 min Repair with DRB, Rep 2
RNAPII bound RNA


title: UACC_62_1

city: Madrid

first: Metehan

last: Cifdaloz

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology Program

institute: CNIO

data_processing:
RNA-seq processing:
RNA-seq data was analysed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/) as follows:
Reads are quality-checked with FastQC, and aligned to the human genome (GRCh37/hg19) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing two mismatches. Transcripts quantification and differential expression were calculated with Cufflinks 2.2.1, using the human GRCh37/hg19 transcript annotations from https://ccb.jhu.edu/software/tophat/igenomes.shtml.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM values calculated with Cufflinks

source_name: Human melanoma cell line UACC-62

growth_protocol: The melanoma cell lines were grown in DMEM medium supplemented with 10% fetal bovine serum, 1% penicillin and streptomycin (Gibco), and maintained at 37°C in humidified 5% CO2 atmosphere. Primary human melanocytes were cultured in Medium 254 supplemented with 1% melanocyte growth factors (HMGS, Cascade Biologics), 0.2 mM CaCl2 and 100 μg/mL Penicillin/Spreptomycin.

extract_protocol:
Total RNA was purified using RNeasy Mini kit (Qiagen) and digested with DNase (Qiagen).
1 µg of total RNA samples was used. Average sample RNA Integrity Number was 9.8 when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (10 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina HiSeq2500 by following manufacturer's protocols.

treatment_protocol: All cells were harvested by trypsination at a confluency of approx. 70% and the pellets were stored at -80ºC.

value: melanoma cell line

tag: Stage

value: metastatic


title: UACC_62_3


title: UACC_62_2


title: SK_MEL_147_2

source_name: Human melanoma cell line SK-Mel-147


title: NET_DRB2_R10_30M_Ctl_1

description:
NET-seq, preDRB, release 10min, mock, 30 min with DRB, Rep 1
RNAPII bound RNA


title: SK_MEL_28_2

source_name: Human melanoma cell line SK-Mel-28


title: NET_DRB2_R10_60M_Ctl_1

description:
NET-seq, preDRB, release 10min, mock, 60 min with DRB, Rep 1
RNAPII bound RNA


title: SK_MEL_28_3


title: SK_MEL_28_1


title: NET_DRB2_R10_30M_UV_1

description:
NET-seq, preDRB, release 10min, UV, 30 min Repair with DRB, Rep 1
RNAPII bound RNA


title: L15

first: Charles

last: Murphy

address: 1300 York Ave

institute: Weill Cornell Medicine

description: Liver RNA-seq sample from non-tumor-bearing mice that were fasted. Biological replicate 5.

data_processing:
The quality of the raw FASTQ files were checked with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), then mapped to human reference GRCm38 using STAR (v2.4.1d, 2-pass mode).
Gene expression was estimated using cufflinks (v2.2.1, default parameters) and HTSeq (v0.6.1). Differential expression analyses were performed using DESeq2 (v1.14.1).
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma-delimited files contain FPKM or counts for each sample.

extract_protocol:
Total RNA was extracted from liver (30-50mg) and gastrocnemius (whole muscle) using Trizol (Thermo Fisher, Waltham, MA) followed by clean-up using RNeasy kit (Qiagen, Hilden, Germany).
One microgram of total RNA of each sample was submitted to the WCM Genomics Resources Core Facility.

value: Mouse liver

tag: group

value: fasted

tag: sequencing strategy

value: 101bp single end RNAseq


title: NET_DRB2_R10_30M_Ctl_2

description:
NET-seq, preDRB, release 10min, mock, 30 min with DRB, Rep 2
RNAPII bound RNA


title: SK_MEL_147_1


title: M1BP

description:
Protein-DNA complex
ChIP-exo
Merged with M1BP ChIP-exo data from GSM2579179.
M1BP_25_17_14_read1_5prime_merged.ucsc.bedGraph


title: FM_2

source_name: Human melanocytes 2

value: normal melanocytes

value: primary melanocytes


title: FM_3

source_name: Human melanocytes 3


title: FM_1

source_name: Human melanocytes 1


title: L13

description: Liver RNA-seq sample from non-tumor-bearing mice that were fasted. Biological replicate 3.

tag: tissue


title: L10

description: Liver RNA-seq sample from tumor-bearing mice that did develop CACS. Biological replicate 5.

value: CACS


title: L14

description: Liver RNA-seq sample from non-tumor-bearing mice that were fasted. Biological replicate 4.


title: L7

description: Liver RNA-seq sample from tumor-bearing mice that did develop CACS. Biological replicate 2.


title: L11

description: Liver RNA-seq sample from non-tumor-bearing mice that were fasted. Biological replicate 1.


title: L8

description: Liver RNA-seq sample from tumor-bearing mice that did develop CACS. Biological replicate 3.


title: L6

description: Liver RNA-seq sample from tumor-bearing mice that did develop CACS. Biological replicate 1.


title: L12

description: Liver RNA-seq sample from non-tumor-bearing mice that were fasted. Biological replicate 2.


title: L5

description: Liver RNA-seq sample from tumor-bearing mice that did not develop CACS. Biological replicate 5.

value: non-CACS


title: SK_MEL_147_3


title: L3

description: Liver RNA-seq sample from tumor-bearing mice that did not develop CACS. Biological replicate 3.


title: L2

description: Liver RNA-seq sample from tumor-bearing mice that did not develop CACS. Biological replicate 2.


title: G15

description: Gastrocnemius muscle RNA-seq sample from non-tumor-bearing mice that were fasted. Biological replicate 5.

value: Mouse gastrocnemius muscle


title: G14

description: Gastrocnemius muscle RNA-seq sample from non-tumor-bearing mice that were fasted. Biological replicate 4.


title: G12

description: Gastrocnemius muscle RNA-seq sample from non-tumor-bearing mice that were fasted. Biological replicate 2.


title: G9

description: Gastrocnemius muscle RNA-seq sample from tumor-bearing mice that did develop CACS. Biological replicate 4.


title: G13

description: Gastrocnemius muscle RNA-seq sample from non-tumor-bearing mice that were fasted. Biological replicate 3.


title: G10

description: Gastrocnemius muscle RNA-seq sample from tumor-bearing mice that did develop CACS. Biological replicate 5.


title: G11

description: Gastrocnemius muscle RNA-seq sample from non-tumor-bearing mice that were fasted. Biological replicate 1.


title: G7

description: Gastrocnemius muscle RNA-seq sample from tumor-bearing mice that did develop CACS. Biological replicate 2.


title: G5

description: Gastrocnemius muscle RNA-seq sample from tumor-bearing mice that did not develop CACS. Biological replicate 5.


title: G4

description: Gastrocnemius muscle RNA-seq sample from tumor-bearing mice that did not develop CACS. Biological replicate 4.


title: G2

description: Gastrocnemius muscle RNA-seq sample from tumor-bearing mice that did not develop CACS. Biological replicate 2.


title: G3

description: Gastrocnemius muscle RNA-seq sample from tumor-bearing mice that did not develop CACS. Biological replicate 3.


title: G6

description: Gastrocnemius muscle RNA-seq sample from tumor-bearing mice that did develop CACS. Biological replicate 1.


title: L9

description: Liver RNA-seq sample from tumor-bearing mice that did develop CACS. Biological replicate 4.


title: G1

description: Gastrocnemius muscle RNA-seq sample from tumor-bearing mice that did not develop CACS. Biological replicate 1.


title: GHA501A115, Untreated single cell RNA-seq

city: London

first: Arsham

last: Ghahramani

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: Single cell

data_processing:
Reads were preprocessed using FastQC and Cutadapt. Sequences were aligned to the Mus Musculus genome (GRCm38) using Tophat discarding multiply-mapped reads. Gene level counts were extracted using featureCounts 53. Transcript levels were quantified as transcripts per million (TPM). Genes with a TPM greater than 1 were considered as expressed. We filtered cells for analyses on the basis of number of aligned reads (> 200,000), percentage of ribosomal reads (< 2%) and number of genes expressed (> 2000).
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV containing TPM normalized read count for each gene in each cell

source_name: Keratinocytes

growth_protocol: Keratinocytes were isolated and cultured from adult dorsal skin in FAD medium (one part Ham’s F12, three parts Dulbecco’s modified Eagle’s medium, 1.8×10-4 M adenine), supplemented with 10% foetal calf serum (FCS) and a cocktail of 0.5 μg/ml hydrocortisone, 5 μg/ml insulin, 1×10-10 M cholera enterotoxin and 10 ng/ml epidermal growth factor (HICE cocktail)

extract_protocol:
Wild type and K14ΔNβ-cateninER keratinocytes were cultured on 12 well plates in a ratio of 9:1 for a total of 200,000 cells per well and allowed to attach for 24 hours. Subsequently, cells were treated with 4-OHT (200nM) or DMSO as a control. After 24 hours of treatment cells were trypsinised and resuspended as a single cell suspension.
Single keratinocytes were captured on a medium-sized (10-17μm) microfluidic chip (C1, Fluidigm). Cells were assessed for viability (LIVE/DEAD assay, Life Technologies) and C1 capture sites were imaged by phase contrast to determine empty and doublet capture sites. Cells were loaded onto the chip at a concentration of 300 cells μl-1. Doublet or non-viable cells were excluded from later analysis. Cell lysis, reverse transcription, and cDNA amplification were performed on the C1 Single-Cell Auto Prep IFC, as per the manufacturer’s instructions. For cDNA synthesis the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) was used. Single cell Illumina NGS libraries were constructed with Nextera XT DNA Sample Prep kit (Illumina). Sequencing was performed on Illumina HiSeq4000 (Illumina) using 100bp paired-end reads.

treatment_protocol: Untreated; DMSO. Treated; 200nM 4OHT for 24 hours.

tag: treatment

value: UnTreated - 24 hours 4OHT - Control

value: Keratinocytes


title: GHA501A73, Treated single cell RNA-seq

description: Single cell

value: Treated - 24 hours 4OHT


title: GHA501A25, Treated single cell RNA-seq

description: Single cell


title: L1

description: Liver RNA-seq sample from tumor-bearing mice that did not develop CACS. Biological replicate 1.


title: GHA501A174, Untreated single cell RNA-seq

description: Single cell


title: GHA501A105, Untreated single cell RNA-seq

description: Single cell


title: L4

description: Liver RNA-seq sample from tumor-bearing mice that did not develop CACS. Biological replicate 4.


title: GHA501A31, Treated single cell RNA-seq

description: Single cell


title: GHA501A113, Untreated single cell RNA-seq

description: Single cell


title: G8

description: Gastrocnemius muscle RNA-seq sample from tumor-bearing mice that did develop CACS. Biological replicate 3.


title: GHA501A114, Untreated single cell RNA-seq

description: Single cell


title: GHA501A59, Treated single cell RNA-seq

description: Single cell


title: GHA501A118, Untreated single cell RNA-seq

description: Single cell


title: GHA501A108, Untreated single cell RNA-seq

description: Single cell


title: GHA501A74, Treated single cell RNA-seq

description: Single cell


title: GHA501A120, Untreated single cell RNA-seq

description: Single cell


title: GHA501A135, Untreated single cell RNA-seq

description: Single cell


title: GHA501A46, Treated single cell RNA-seq

description: Single cell


title: GHA501A16, Treated single cell RNA-seq

description: Single cell


title: GHA501A144, Untreated single cell RNA-seq

description: Single cell


title: GHA501A3, Treated single cell RNA-seq

description: Single cell


title: GHA501A167, Untreated single cell RNA-seq

description: Single cell


title: GHA501A14, Treated single cell RNA-seq

description: Single cell


title: GHA501A80, Treated single cell RNA-seq

description: Single cell


title: GHA501A171, Untreated single cell RNA-seq

description: Single cell


title: GHA501A35, Treated single cell RNA-seq

description: Single cell


title: GHA501A1, Treated single cell RNA-seq

description: Single cell


title: GHA501A81, Treated single cell RNA-seq

description: Single cell


title: GHA501A38, Treated single cell RNA-seq

description: Single cell


title: GHA501A67, Treated single cell RNA-seq

description: Single cell


title: GHA501A162, Untreated single cell RNA-seq

description: Single cell


title: GHA501A158, Untreated single cell RNA-seq

description: Single cell


title: GHA501A27, Treated single cell RNA-seq

description: Single cell


title: GHA501A122, Untreated single cell RNA-seq

description: Single cell


title: GHA501A29, Treated single cell RNA-seq

description: Single cell


title: GHA501A190, Untreated single cell RNA-seq

description: Single cell


title: GHA501A55, Treated single cell RNA-seq

description: Single cell


title: GHA501A142, Untreated single cell RNA-seq

description: Single cell


title: GHA501A110, Untreated single cell RNA-seq

description: Single cell


title: GHA501A139, Untreated single cell RNA-seq

description: Single cell


title: GHA501A157, Untreated single cell RNA-seq

description: Single cell


title: GHA501A126, Untreated single cell RNA-seq

description: Single cell


title: GHA501A48, Treated single cell RNA-seq

description: Single cell


title: GHA501A165, Untreated single cell RNA-seq

description: Single cell


title: GHA501A9, Treated single cell RNA-seq

description: Single cell


title: GHA501A146, Untreated single cell RNA-seq

description: Single cell


title: GHA501A69, Treated single cell RNA-seq

description: Single cell


title: GHA501A86, Treated single cell RNA-seq

description: Single cell


title: GHA501A39, Treated single cell RNA-seq

description: Single cell


title: GHA501A43, Treated single cell RNA-seq

description: Single cell


title: GHA501A129, Untreated single cell RNA-seq

description: Single cell


title: GHA501A84, Treated single cell RNA-seq

description: Single cell


title: GHA501A6, Treated single cell RNA-seq

description: Single cell


title: GHA501A166, Untreated single cell RNA-seq

description: Single cell


title: GHA501A61, Treated single cell RNA-seq

description: Single cell


title: GHA501A106, Untreated single cell RNA-seq

description: Single cell


title: GHA501A4, Treated single cell RNA-seq

description: Single cell


title: GHA501A63, Treated single cell RNA-seq

description: Single cell


title: GHA501A99, Untreated single cell RNA-seq

description: Single cell


title: GHA501A153, Untreated single cell RNA-seq

description: Single cell


title: GHA501A37, Treated single cell RNA-seq

description: Single cell


title: GHA501A42, Treated single cell RNA-seq

description: Single cell


title: GHA501A128, Untreated single cell RNA-seq

description: Single cell


title: GHA501A140, Untreated single cell RNA-seq

description: Single cell


title: GHA501A119, Untreated single cell RNA-seq

description: Single cell


title: GHA501A104, Untreated single cell RNA-seq

description: Single cell


title: GHA501A116, Untreated single cell RNA-seq

description: Single cell


title: GHA501A88, Treated single cell RNA-seq

description: Single cell


title: GHA501A47, Treated single cell RNA-seq

description: Single cell


title: GHA501A76, Treated single cell RNA-seq

description: Single cell


title: GHA501A176, Untreated single cell RNA-seq

description: Single cell


title: GHA501A186, Untreated single cell RNA-seq

description: Single cell


title: GHA501A125, Untreated single cell RNA-seq

description: Single cell


title: GHA501A98, Untreated single cell RNA-seq

description: Single cell


title: GHA501A23, Treated single cell RNA-seq

description: Single cell


title: GHA501A161, Untreated single cell RNA-seq

description: Single cell


title: GHA501A28, Treated single cell RNA-seq

description: Single cell


title: GHA501A20, Treated single cell RNA-seq

description: Single cell


title: GHA501A169, Untreated single cell RNA-seq

description: Single cell


title: GHA501A154, Untreated single cell RNA-seq

description: Single cell


title: GHA501A70, Treated single cell RNA-seq

description: Single cell


title: GHA501A66, Treated single cell RNA-seq

description: Single cell


title: GHA501A137, Untreated single cell RNA-seq

description: Single cell


title: GHA501A18, Treated single cell RNA-seq

description: Single cell


title: GHA501A133, Untreated single cell RNA-seq

description: Single cell


title: GHA501A170, Untreated single cell RNA-seq

description: Single cell


title: GHA501A34, Treated single cell RNA-seq

description: Single cell


title: GHA501A152, Untreated single cell RNA-seq

description: Single cell


title: GHA501A111, Untreated single cell RNA-seq

description: Single cell


title: GHA501A44, Treated single cell RNA-seq

description: Single cell


title: GHA501A156, Untreated single cell RNA-seq

description: Single cell


title: GHA501A62, Treated single cell RNA-seq

description: Single cell


title: GHA501A72, Treated single cell RNA-seq

description: Single cell


title: GHA501A159, Untreated single cell RNA-seq

description: Single cell


title: GHA501A181, Untreated single cell RNA-seq

description: Single cell


title: GHA501A33, Treated single cell RNA-seq

description: Single cell


title: GHA501A12, Treated single cell RNA-seq

description: Single cell


title: GHA501A13, Treated single cell RNA-seq

description: Single cell


title: GHA501A19, Treated single cell RNA-seq

description: Single cell


title: GHA501A149, Untreated single cell RNA-seq

description: Single cell


title: GHA501A187, Untreated single cell RNA-seq

description: Single cell


title: GHA501A30, Treated single cell RNA-seq

description: Single cell


title: GHA501A183, Untreated single cell RNA-seq

description: Single cell