title: J.R1.LB.input

first: zhike

last: lu

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

data_processing:
All samples were sequenced by Illumina Hiseq 4000 with single-end 50-bp read length. The deep sequencing data were mapped to pig reference genome (Sscrofa10.2/susScr3).
Data analysis for each experiment: (1) for m6A-seq, reads were aligned to the reference genome using Tophat v2.0.14 with parameter -g 1 --library-type=fr-firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene had multiple isoforms. Aligned reads were extended to 150 bp (average fragments size) and converted from genome-based coordinates to isoform-based coordinates, in order to eliminate the interference from introns in peak calling. The peak calling method was modified from published work (Dominissini et al., 2012). To call m6A peaks, the longest isoform of each gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform, windows with read counts less than 1/20 of the top window in both m6A-IP and input sample were excluded. For each gene, the read counts in each window were normalized by the median count of all windows of that gene. A Fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the FDR < 0.01 and log2(Enrichment Score) >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak (or window): reads count of the IP samples in the current peak/window (a), median read counts of the IP sample in all 100 bp windows on the current mRNA (b), reads count of the input sample in the current peak/window (c), and median read counts of the input sample in all 100 bp windows on the current mRNA (d). The enrichment score of each window was calculated as (a×d)/(b×c). (2) for mRNA-seq (the input samples of m6A-seq), reads were mapped with Tophat and Cufflink (v2.2.1) was used to calculate the FPKM of each gene to represent their mRNA expression level.
Genome_build: pig reference genome (Sscrofa10.2/susScr3)
Supplementary_files_format_and_content: excel file containing processed FPKM from input samples and m6A peak list from IP samples

organism: Sus scrofa

source_name: pig adipose tissue

growth_protocol: Two males of the Landrace (a leaner breed) and Two males of the Jinhua (a fatty breed) at 180-day-old were used in this study.

extract_protocol:
total RNA was extracted from tissue by TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples, mRNA was sonicated and subjected to IP using m6A antibody (Synaptic Systems, 202003).
Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: adipose tissue

tag: breed

value: Jinhua


title: Lung_tumor [SVA492]

status: Public on Oct 05 2018

type: SRA

city: Minneapolis

first: Chris

middle: H

last: Wendt

state: MN

address: 420 Delaware St SE

department: Medicine

country: USA

institute: University of Minnesota

library_source: transcriptomic

data_processing:
50bp FastQ paired-end reads (n=XXX Million per sample) were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30
Quality control checks on raw sequence data for each sample were performed with FastQC
Read mapping was performed via Bowtie (v2.2.4.0)
Gene quantification was done via Cuffquant for FPKM values and Feature Counts for raw read counts
Genome_build: hg19
Supplementary_files_format_and_content: FPKM, raw read counts

molecule: total RNA

organism: Homo sapiens

source_name: Lung tumor tissue_LU2756A

extract_protocol:
Frozen lung tissue samples ranging in weight from 25-60 mg were individually ground to a fine powder using a liquid nitrogen cooled ceramic mortar and pestle. For RNA quality control (QC), approximately 20% of each sample was processed with TRI Reagent (Sigma Aldrich, St Louis, MO). Once the initial RNA QC was completed, polyribosome preparations were performed in random sample pairs. For this purpose, the remainder of each frozen powdered sample was solubilized in 100 µL of lysis buffer (10 mM Tris-HCl at pH 8.0, 150 mM NaCl, 5 mM MgCl2, 1% Nonidet-P40, 1% sodium deoxycholate, 40 mM dithiothreitol, 500 U/mL RNAsin (Promega, Madison, WI), 40 mM VRC (vanadyl ribonucleoside complex), and 150 µg/ml cycloheximide) and mixed by pipetting. Nuclei and insoluble material were removed by centrifugation (12,000 x g, 10 seconds, at 4°C). Extraction buffer (50 µL; 0.2 M Tris-HCl at pH 7.5, 0.3 M NaCl, 10 mM PMSF) was added to the supernatant and the sample was mixed by pipetting. The sample was centrifuged (12,000 x g, 5 min, at 4° C) and 25% of the supernatant was processed with TRI Reagent to generate a cytosolic total RNA sample. The remaining supernatant was layered onto a 5 mL, linear sucrose gradient (0.5–1.5 M), 10 mM Tris-HCl pH 7.5, 140 mM NaCl, 3 mM MgCl2, 10 mM DTT. Gradients were centrifuged (200,000 x g in a Beckman SW55Ti rotor for 80 minutes at 4o C) and the gradients were fractionated into ten, 0.5 mL fractions utilizing an ISCO density gradient fractionator with absorbance monitored at 254 nm. Each fraction was collected into a tube containing 50 µL 1%SDS and 20 µL 0.5 M EDTA. The polyribosomal mRNA from fractions 7, 8, 9 and 10 were individually processed with 1 mL of TRI Reagent and 200 µL chloroform and the resultant RNA pellets from these four fractions were combined to create the polyribosomal mRNA sample corresponding to each tissue sample. Polyribosomal mRNA and cytosolic RNA were sent to the University of Minnesota Genomics Core for quality assessment by Caliper High Sensitivity Lab Chip. Those samples passing the Caliper QC were processed into indexed library samples for analysis by RNA sequencing. This was accomplished using the SMART-Seq protocol.
Libraries were quantified using a fluorimetric PicoGreen assay. Library size was assessed using capillary electrophoresis on an Agilent BioAnalyzer 2100 and only libraries quantifying higher than 10 nM were analyzed. Libraries were pooled and assessed using Kapa qPCR to ensure adapters were ligated to DNA fragments and functional. Nextera libraries were hybridized to a single read flow cell and individual fragments were clonally amplified by bridge amplification on the Illumina cBot. Once clustering was complete, the flow cell was loaded on a HiSeq 2000 and sequenced using Illumina SBS chemistry. Upon completion of read 1, an 8-base pair index read for Index 1 was performed. The Index 1 product was removed and the template was reannealed to the flow cell surface. The run proceeded with 8 chemistry-only cycles, followed by an 8-base pair index read to read Index 2.

tag: tissue

value: Lung tissue

tag: fraction

value: Total RNA

tag: group


title: TPD40_p1-nega

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: PD-1 negative in T cells from blood

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: Nivolumab unbound peripheral blood CD8 T cells

growth_protocol: Mononuclear cells in freshly collected peripheral blood were enriched by Ficoll-Paque.

extract_protocol:
RNA was prepared from sorted CD8 T cells (2-5x104 cells/each population) by the miRNeasy Isolation kit.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: Nivolumab bound and unbound peripheral blood CD8 T cells (CD45+CD56-CD19-TCRab+CD8a+) was sorted by a BD FACSAria II.

tag: cell type

value: peripheral blood T cells


title: J.R2.LB.input

city: Chicago

state: IL


title: TPD40_p1+posi

description: PD-1 positive in T cells from blood

source_name: Nivolumab bound peripheral blood CD8 T cells


title: J.R2.LB.IP


title: C-7

city: Menlo Park

first: Christina

last: Fan

state: CALIFORNIA

address: 4040, Campbell Ave

institute: BD Biosciences

data_processing:
BD Rhapsody pipeline for whole transcriptome analysis was used to identify the molecular index sequences (position 49-56) and align reads to predfined cell label sequences (position 1-8,22-30,43-51) on Read1, and to align reads (Read2) to the human transcriptome (hg19, gencode annotation) using STAR with default parameters. A unique cell label is a combination of the cell label sequences in the 3 indicated positions on Read1.
cell label sequence for position 1-8: TTAACGCG,TGTGCTGA,TCGAGTTG,TTGGCGAT,GCATCCAA,TATACGCG,GAGTTCTG,ATGCTTGG,TCCTCAAC,CCTAATCC,CGAACGTT,TTGCCGTT,AGCTCAAC,ATCCGGTA,AAGCAAGC,CACTCAGA,CAAGGTTC,AGGATGGT,TAGGATGG,ACACACAC,CACATCTC,TCCACTTG,TCCATGCT,GCAAGGAT,GGATATGG,TTGCATCC,CAGACACT,GGATAACG,CTAGTGGT,TGTGACTG,TATAGCCG,TCTGGTCT,ATGGATGG,GCAAGGTA,TGGATGCT,CAACTCGA,GCATGCAT,TCCTTGGT,AAGCAACG,AACGCGAA,TCTCTGTG,AATACGCC,AACGATGG,TCGACAAC,TAGCCGAT,TGCACTTC,GATCCATG,TGGTTGGT,CAACGTAC,ATTAGCCG,TCCAACCT,CTTGGATG,ACGAACCT,CCATTAGG,GCAAGCTT,ACAGCACT,AGTCTCTC,AGTGAGTG,TTCCATGC,CCATAACG,TGGACTTG,TTAAGCCG,TCGACTTC,GCATGGTT,CTTCCAAC,CAACCATG,TCCTAGCT,GTGACACT,GCAATAGG,TGACACAC,TTGCCGAA,TTCCAAGG,AACCTAGC,AAGCCGTT,AACGCCTA,TTAACGGC,ATCCTTGC,GGTACGAA,AACGGCTT,CACTGAGT,GGTTCCTT,CTTCTCCT,CTAGGTTG,AAGGATGC,TCAGACTG,TGTGGACT,TTCCTTGG,TAGGTTCG,AGCTTGGT,ATTACGCG,AACCATGC,TGCAACGT,AGGTGAAC,TGTCTGTC,GATCTGGT,CTGACTGA,
cell label sequence for position 22-30: TGGTCTTC,CAACAGCT,GGTACGTT,TGGAGTTC,TTGCAAGC,TTATGGCG,CAACACGT,CCAACCAA,TCTCTGAC,CTTGTGCT,AGCTTCCT,AGTCCTCT,GAACCATC,CTTGACGA,CATCCTTG,CCTATTGC,TGGTTCCT,TGCATGGT,CCTAGCTT,GCATAAGG,CACATGAC,CCAATTCC,AAGCCGAA,ACTCAGAC,GCAATTCG,GATCTCCT,GACTCTGA,AGCAACGA,ACTGACTG,GCCGTTAA,CAACCAAC,AAGCTTGC,CAAGTGCT,GATGACCT,ACCTGATG,GTCTGTGA,CAACCTTC,AGGTACGA,ATCCAAGC,AGCTCATG,GTTCTGCT,TGCTTGCT,ACTGCTCT,ATGCCGTA,CCATATCC,AGTGGTCT,TGAGTCTG,CGATATGC,CGATTAGC,GATGACGA,TTCGATGG,GTTGCTTC,CTGAACTG,TAGCCGTA,ACCACAAC,GAACGATG,TGCTGTTC,AATTGCCG,TGTGCTCT,GGATGGAT,GATGGATG,GATGGTTC,ACGATGCT,CAAGGATG,GCAACGTT,TGCTCTTG,ATTACGGC,TGCTGATG,CTCAACTC,TGCACATG,CTTGGTTC,ACTGGACT,CTCTTCTC,TGGTTCGA,GTTCCATC,GGTTGCAT,TGGTACGT,GCGGTATT,GTTGTCCT,TTGCTTCG,ACACGACT,CATGGTAC,TCCTCATG,GGATGCAA,TTGCATGG,GATCCAAC,GATCAGCT,TGACCTGA,TGCATCCT,CGAATAGG,ATCCATCC,CTTCCTTC,AGGTCTTG,TGACTGAC,GGTTCGAT,GTTGCATG,
cell label sequence for position 43-51: CTGACTCT,GACTGACT,TAGCTTGG,CATGGTTG,CCATAAGC,TTCGAACG,CTCTCTGA,ACACTGTG,ATATGCCG,AACGGCAA,GCGGTTAT,ACTGTCTC,TGTCCACT,GAACTGCT,TCAGACAC,ACACACTG,ATAACGCC,GGTATTGC,CCAATACG,TCTCTCTC,TCTGACTC,AAGGTACG,GATGTGCT,GCCGTATA,TCTGTCTG,GTCTTCTG,TCGACATG,TCCTTCCT,CGATAAGG,TTGCAACG,GGTTCCAA,TGAGGAGT,GCATCCTT,CATCTGCT,CACACTCT,GATGAGGT,CGAACCAT,ACTGACAC,ACTCCACT,GCCGTAAT,TGAGGTCT,GTCTTGTC,AAGCATCC,CTGTTCTG,TCGAGTAC,CCTAATGG,CATGTCCT,GATGCTTG,GTGAGTCT,GCCGATAT,TCAGCTCT,GACTCTCT,CGAACGAA,TGCAAGCT,CAGAACTC,TCTGAGTG,ATGCATGC,AGTGGAGT,TGACCTCT,AGGAGTAC,TAGCTTCC,CTAGCAAC,GGTATTCG,CCTTCGAT,CTTCAGCT,TTCCGGTT,TCCAAGGT,GACATCTG,GGTTAAGG,GGATGGTA,TCCTGTTG,ACCTGAAC,ACTGAGTC,GTCTAGTG,ATGCGGTT,AACCAAGG,AGGACATG,AAGGTTGG,GCATTACG,TTGGTTGG,CGAATTGC,ACGACATC,CCAATAGC,ATGGTTGC,CTAGTCCT,TGACTCTC,GCAACCAT,AGGAGTTG,TCTGGTGA,AGCTGTTG,CTTGCTTG,CTCAAGTG,ATGCAAGG,CTAGGTAC,CCATGGTA,TATTGGCG,
Reads with the identical cell label, molecular index, and gene identity, are collapsed and counted as 1 molecule
Counts of molecule per gene per cell label are organized in a cell by gene matrix format, which is the final processed data file
Genome_build: hg19
Supplementary_files_format_and_content: Data tables containing number of molecules per gene per cell

source_name: C-7: hiPSC-derived 3D culture (pallium)

growth_protocol: Differentiation of human iPSC into hCS

extract_protocol:
Dissociated single cells from were loaded onto the BD Rhapsody single cell gene expression analysis system
mRNA from individual cells were captured by barcoded oligo probes on a BD Rhapsody bead. Capture probes contain cell labels (total of 27 bases) and molecule index (8 randomers) such that when cDNAs were extended by reverse transcriptase, each cDNA molecule was tagged with a cell specific sequence and a molecular index sequence. cDNA were then universally amplified following by adaptor ligation. 3' end of transcripts were enriched using random priming and sequenced on Illumina HiSeq2500.

treatment_protocol: Patterning for pallium; single cell trituration (no reporter used)


title: L.R2.LB.IP

value: Landrace


title: L.R2.LB.input


title: L.R1.LB.IP


title: L.R1.LB.input


title: D5 H3K4me3 IP

status: Public on Oct 04 2018

city: Duarte

first: Amy

last: Leung

address: 1500 E. Duarte Rd

department: Diabetes/Cancer

institute: Beckman Research Institute, City of Hope

library_source: genomic

data_processing:
ChIP-seq: Sequenced reads were aligned with Bowtie (Langmead, 2010) using default parameters except only uniquely mapping reads were retained (-m 1) for each H3K4me3 IP and input samples. MACS (Zhang, et al, 2008) with default parameters was used to identify H3K4me3 enriched peaks.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq: BED format

molecule: genomic DNA

source_name: CD19 B cells

extract_protocol: Libraries were prepared using Kapa Hyper Prep Kit (Kapa Biosystems)

treatment_protocol: B cells (CD19+) cells were isolated from fresh donor blood samples with Dyanbeads CD19 Pan B (Invitrogen). Isolated cells were immediately used for chromatin immunoprecipitation experiments.

value: CD19 B cells

tag: ID

value: Donor 5

tag: antibody

value: H3K4me3, ab8580 (Abcam)


title: 4s(TPD039p1_nega)

description: PD-1 negative in T cells from blood

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: hg19

extract_protocol:
RNA was prepared from sorted CD8 T cells (2-5x104 cells/each population) by the miRNeasy Isolation kit.
cDNA was generated using a Clontech SMART-Seq v4 Ultra Low Input RNA Kit (Takara Clontech, Mountain View, CA, USA). Each cDNA sample was sheared (200 - 500 bp) using the Covaris S220 (Covaris, Woburn, MA, USA) and prepared using KAPA Library Preparation Kits (Kapa Biosystems, Wilmington, MA) for 75 bp single-end reads, according to the manufacturer’s instructions.


title: 3s(OPD047p1_nega)

description: PD-1 negative in T cells from blood


title: D5 Input


title: D4 Input

value: Donor 4


title: D3 H3K4me3 IP

value: Donor 3


title: D3 Input


title: D4 H3K4me3 IP


title: Tumor_OV390

city: Gothenburg

first: Hanna

last: Engqvist

address: Medicinaregatan 1G

country: Sweden

institute: University of Gothenburg

description: Paired-end strand-specific RNA libraries

data_processing:
Quality control of FASTQ files using FastQC
Removal of adapter sequences using TrimGalore wrapper script
FASTQ files were mapped to the human reference genome hg19 using the STAR aligner and the resulting BAM-file was name-sorted
Raw read counts were calculated using htseq-count in htseq
Genome_build: hg19
Supplementary_files_format_and_content: The processed data file "OV106-391_counts.txt" is given in text format

source_name: Primary invasive ovarian carcinomas

extract_protocol:
Total RNA was extracted from the tumor samples using the RNeasy Lipid Tissue Mini Kit (Qiagen), followed by RNA concentration and integrity assessment using Nanodrop ND1000 (Nanodrop Technologies) in combination with QuBit (ThermoFisher Scientific) and the RNA 6000 Nano LabChip Kit with Agilent 2100 Bioanalyzer (Agilent Technologies), respectively. Samples with an RNA integrity number (RIN) of 6 or higher were used for sequencing.
Illumina TruSeq strand-specific RNA libraries (Ribosomal depletion using RiboZero human) containing 125 bp pair-end reads were obtained for each sample on a HiSeq2000 sequencer (Illumina). Paired-end sequencing was used.

value: early-stage primary invasive ovarian carcinoma

tag: figo stage

value: I

tag: age


title: Tumor_OV391

value: II


title: Tumor_OV389


title: DNA methylation in hormone-free T47D breast cancer cells

city: Barcelona

first: François

last: Le Dily

address: Dr. Aiguader, 88

country: Spain

institute: CRG-Centre for Genomic Regulation

data_processing:
Sequencing reads were mapped to the human genome v19 using Bowtie 1 with default parameters and only keeping uniquely-mapped reads. All duplicates were discarded after mapping.
Sequences mapped to regions of high-duplication were filtered out using guidelines from Pickrell et al., Bioinformatics. 2011 Aug 1;27(15):2144-6. doi: 10.1093/bioinformatics/btr354
The resulting SAM/BAM files containing the alignments were sorted and normalized genome-wide coverage profiles were generated using bwtool (Pohl and Beato, Bioinformatics. 2014 Jun 1;30(11):1618-9. doi: 10.1093/bioinformatics/btu056)
Genome_build: hg19

source_name: T47D breast cancer cells

extract_protocol:
Hormone-deprived T47D cell pellet has been resuspended in Tris-EDTA and 20 μg of proteinase K was added. The mix has been then incubated at 55°C for 16 hours and DNA was extracted using first 1 volume of phenol and the 1 volume of chloroform. The DNA was precipitated with ethanol and sodium acetate and then resuspended in Tris-EDTA containing 20 μg/ml RNAse A
The library has been prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) following manufacturer’s instructions.

value: T47D breast cancer cells


title: Tumor_OV388


title: J.R1.LB.IP


title: Tumor_OV385


title: Tumor_OV383


title: Tumor_OV387


title: Tumor_OV384


title: Tumor_OV382


title: Tumor_OV380


title: Tumor_OV378


title: Tumor_OV376


title: Tumor_OV375


title: Tumor_OV373


title: Tumor_OV372


title: Tumor_OV377


title: Tumor_OV368


title: Tumor_OV366


title: Tumor_OV365


title: Tumor_OV359


title: Tumor_OV364


title: Tumor_OV362


title: Tumor_OV360


title: Tumor_OV353


title: Tumor_OV357


title: Tumor_OV355


title: Tumor_OV356


title: Tumor_OV347


title: Tumor_OV352


title: Tumor_OV345


title: Tumor_OV348


title: Tumor_OV346


title: Tumor_OV349


title: Tumor_OV371


title: Tumor_OV339


title: Tumor_OV370


title: Tumor_OV341


title: Tumor_OV343


title: Tumor_OV342


title: Tumor_OV338


title: Tumor_OV363


title: Tumor_OV336


title: Tumor_OV358


title: Tumor_OV337


title: Tumor_OV333


title: Tumor_OV335


title: Tumor_OV332


title: Tumor_OV329


title: Tumor_OV331


title: Tumor_OV324


title: Tumor_OV344


title: Tumor_OV326


title: Tumor_OV327


title: Tumor_OV328


title: Control_tissue [SVA497]

source_name: Emphysematous lung from non-cancer lungs_276977

value: Heavy, Polyribosomal-bound RNA

value: Control


title: Tumor_OV323


title: Tumor_OV325


title: Tumor_OV314


title: Tumor_OV317


title: Tumor_OV340


title: Tumor_OV315


title: Tumor_OV318


title: Tumor_OV313


title: Tumor_OV311


title: Tumor_OV321


title: Tumor_OV310


title: Tumor_OV312


title: Tumor_OV308


title: Tumor_OV307


title: Tumor_OV309


title: Tumor_OV306


title: Tumor_OV304


title: Tumor_OV207


title: Tumor_OV301


title: Tumor_OV303


title: Tumor_OV206


title: Tumor_OV204


title: Tumor_OV205


title: Tumor_OV203


title: Tumor_OV188


title: Tumor_OV202


title: Tumor_OV169


title: Tumor_OV172


title: Tumor_OV185


title: Tumor_OV170


title: Tumor_OV163


title: Tumor_OV162


title: Tumor_OV151


title: Tumor_OV152


title: Tumor_OV106


title: Tumor_OV131


title: Tumor_OV135


title: Tumor_OV177


title: Tumor_OV178


title: Tumor_OV305


title: ATRi,18h_RPAChIPSeq rep2

city: Philadelphia

first: Nishita

last: Shastri

state: Pennsylvania

address: 421 Curie Boulevard

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
For basecalling and demultiplexing, Illumina bcl2fastq v2.17.1.14 was used
ChIP-seq reads were aligned to the mm10 genome assembly using STAR-2.5.2a with the following configurations: outFilterMultimapNmax 3, outFilterMultimapNmax 100, outReadsUnmapped Fastx
Alignment tracks were converted to bam and sorted using samtools-0.1.19. Unique, deduplicated, blacklist-regions-removed tracks were then derived from the sorted bams using samtools-0.1.19 view -bq 10 to get unique reads, ngsutils-0.5.7 bamutils filter -excluded to remove blacklisted regions according to the mm10 blacklisted track from ENCODE (https://sites.google.com/site/anshulkundaje/projects/blacklists), picard-tools-1.141 MarkDuplicates REMOVE_DUPLICATES=true to remove duplicates.
Conditions with at least two quality replicate peaks were called using IDR methodology (https://sites.google.com/site/anshulkundaje/projects/idr) with MACS2 version 2.1.0 with the following setting: -p 1e-3. Without replicates, MACS2 version 2.1.0 was used with -q 0.01.
Peaks that were within 5 kb were merged for each condition. Merged peaks were further selected by filtering for those that contained peaks with p-value <10-20 and >4-fold signal enrichment value. The final peak list was generated as a set intersection and subtraction from the DMSO-control peak list
Genome_build: mm10

organism: Mus musculus

source_name: Mouse embryonic fibroblasts

growth_protocol: MEFs were grown in 150 mm tissue-culture plates in DMEM containing high glucose 4.5gm/L and supplemented with 10% FBS, 2mM L-glutamine and Pen/Strep to obtain 15 x 106 cells upon collection for RPA ChIP-Seq.

extract_protocol:
Lysates were clarified from sonicated nuclei (sheared to obtain chromatin size <4 kb) and RPA-DNA complexes were isolated with anti-RPA32 antibody.
Libraries were prepared according to the NEBNext kit. Briefly, DNA was sonicated to ~200 bp. DNA was end-repaired using a combination of T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA fragments of ~200 bp (insert plus adaptor) were band isolated from a 2% agarose gel. The purified DNA was PCR amplified with Illumina primers for 18 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina HiSeq following the manufacturer's protocols.

value: ATR+/- MEFs

tag: cell line

value: Passage-immortalized

tag: treatment

value: 1 uM ATR-45 inhibitor for 18hrs

tag: chip antibody

value: anti-RPA32 (EMD Millipore, NA19L-100UG, lot D00153981)


title: ATRi+shTIM,18h_RPAChIPSeq rep2

data_processing:
For basecalling and demultiplexing, Illumina bcl2fastq v2.17.1.14 was used
ChIP-seq reads were aligned to the mm10 genome assembly using STAR-2.5.2a with the following configurations: outFilterMultimapNmax 3, outFilterMultimapNmax 100, outReadsUnmapped Fastx
Alignment tracks were converted to bam and sorted using samtools-0.1.19. Unique, deduplicated, blacklist-regions-removed tracks were then derived from the sorted bams using samtools-0.1.19 view -bq 10 to get unique reads, ngsutils-0.5.7 bamutils filter -excludebed to remove blacklisted regions according to the mm10 blacklisted track from ENCODE (https://sites.google.com/site/anshulkundaje/projects/blacklists), picard-tools-1.141 MarkDuplicates REMOVE_DUPLICATES=true to remove duplicates.
Conditions with at least two quality replicate peaks were called using IDR methodology (https://sites.google.com/site/anshulkundaje/projects/idr) with MACS2 version 2.1.0 with the following setting: -p 1e-3. Without replicates, MACS2 version 2.1.0 was used with -q 0.01.
Peaks that were within 2 kb were merged for each condition. Merged peaks were further selected by filtering for those that contained peaks with p-value <10^-3 and >4-fold signal enrichment value. The final peak list was generated as a set intersesction and subtraction from the DMSO-control peak list
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak

growth_protocol: MEFs were grown in 150 mm tissue-culture plates in DMEM containing high glucose 4.5gm/L and supplemented with 10% FBS, 2mM L-glutamine and Pen/Strep to obtain 15 x 10^6 cells upon collection for RPA ChIP-Seq.

value: Passage-immortalized MEFs

value: 1 uM ATR-45 inhibitor for 18hrs in TIM KD MEFs

value: anti-RPA32 (EMD Millipore, NA19L-100UG, lot D00144219)


title: ATRi+shTIM,18h_Input


title: APH,18h_RPAChIPSeq rep2

value: 0.2 uM aphidicolin for 18hrs

value: anti-RPA32 (EMD Millipore, NA19L-100UG, lot D00127062)


title: APH,18h_Input


title: Tumor_OV201


title: ATRi+shTIM,18h_RPAChIPSeq rep1


title: ATRi,18h_Input for rep1


title: ATRi,18h_RPAChIPSeq rep1


title: ATRi+APH,9h_RPAChIPSeq rep2

value: 1 uM ATR-45 inhibitor + 0.2 uM aphidicolin for 9hrs


title: ATRi+APH,9h_Input


title: Tumor_OV155


title: ATRi+APH,18h_Input for rep3

value: 1 uM ATR-45 inhibitor + 0.2 uM aphidicolin for 18hrs


title: ATRi+APH,18h_Input for rep1&2


title: ATRi+APH,18h_RPAChIPSeq rep3


title: DMSO,18h_RPAChIPSeq rep1

value: DMSO treatment for 18hrs


title: DMSO,18h_Input


title: ATRi+APH,18h_RPAChIPSeq rep1


title: DMSO,18h_RPAChIPSeq rep2


title: ATRi+APH,18h_RPAChIPSeq rep2


title: ATRi,18h_Input for rep2


title: PT_24hT_rep3

city: Berlin

first: Monika

last: Hilker

address: Haderslebener Str. 9

department: Institute of Biology

country: Germany

institute: Freie Universität Berlin

data_processing:
Illumina CASAVA Version ist 1.8.2 was used for basecalling.
Sequenced reads were trimmed and filtered using  Trimmomatic v0.33 with parameters PE ILLUMINACLIP:IPK.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50
Sequenced reads mapped using Soap v2.21 with parameters -r 0
Genome_build: Custom transcriptome assembly (included as processed data file: SOAPK75_Locus0Contings.fa)
Supplementary_files_format_and_content: comma-delimited text file includes number of mapped reads per sample and transcript

organism: Ulmus minor

growth_protocol: Ulmus minor trees of approximately 15-19 weeks age were used for the experiments. The trees were grown under greenhouse conditions after transferring shoots from a clonal in vitro culture to soil.

extract_protocol:
Approximately 100mg of leaf tissue around the treated site was harvested and flash frozen in liquid nitrogen. Extraction of RNA from the ground material was performed in 15 mL Falcon tubes according to a phenol-based protocol, modified from Ikoma et al., 1996: In short, the material was extracted with 5mL homogenization buffer (0.2 M boric acid, 10mM EDTA and 2% SDS, adjusted to pH7.6 with Tris base, 5% ß-mercaptoethanol, 25mM dithiothreitol). The homogenization step was followed by three steps of phenol:chloroform:isoamyl alcohol (P/C/I; 25:24:1, v/v/v) extraction. In the second PCI step, ca. 0.05g of polyvinylpolypyrrolidone (PVPP) was added. After the third PCI step, clean-up of polysaccharides was achieved by separation with ethanol (20%), 560mM potassium acetate and one volume of chloroform:isoamyl alcohol (C/I, 49:1, v/v). This was followed by extraction with C/I (49:1, v/v) and overnight precipitation with lithium chloride (LiCl, 2.67M). After washing the pellet with 2M cold LiCl and thereafter in cold 80% ethanol, the pellet was dissolved in nuclease-free water, transferred to 2mL tubes and extracted again with one volume C/I and precipitated with LiCl (2.67M) overnight. Finally the pellet was washed in 2M LiCl, twice in 80% ethanol, dried and dissolved in nuclease free water. DNase digestion was performed using the TURBO DNA-free™ Kit (Ambion, Life Technologies, Carlsbad, CA, USA) according to manufacturer’s protocol. The RNA integrity and quality was analyzed with an Agilent 2100 Bioanalyzer on a Nano RNA 6000 chip (Agilent Technologies, Palo Alto, CA, USA).
Illumina TruSeqRNA sample prep v2; polyA+ selection during library preparation; a gel-based size selection was used to obtain the final library

treatment_protocol: A full factorial design was used in which Ulmus minor leaves from clonal trees were treated with either simulated egg-deposition (priming stimulus) or larval feeding (triggering stimulus) or both. Additionally untreated control leaves were harvested. For the simulated egg-deposition, a 1.5 cm x 1 mm piece of leaf epidermis was scratched off with a scalpel and oviduct secretion obtained from freshly killed gravid elm leaf beetle females was applied onto this site. For the larval feeding treatment 5 neonate larvae per leaf were placed on the leaves using a soft brush. All treatments were done in triplicates.

tag: treatment [simulated egg-deposition (priming)]

value: yes

tag: treatment [larval feeding (triggering)]

tag: harvesting time

value: 24 hours after triggering

tag: genotype

value: wild type

value: leaf


title: PT_6hT_rep2

value: 6 hours after triggering


title: CT_24hT_rep2

value: no


title: CT_24hT_rep1


title: CT_6hT_rep2


title: CT_1hT_rep2

value: 1 hour after triggering


title: PT_6hT_rep3


title: CT_6hT_rep1


title: PC_24hT_rep3


title: ATRi+APH,9h_RPAChIPSeq rep1

value: ATR+/- MEFs


title: CT_1hT_rep1


title: PC_6hT_rep3


title: P_6hP_rep3

value: not in

value: 6 hours after priming


title: PC_6hT_rep2


title: PC_1hT_rep2


title: P_6hP_rep2


title: PC_24hT_rep1


title: PT_24hT_rep1


title: PT_6hT_rep1


title: PC_6hT_rep1


title: CT_24hT_rep3


title: PC_1hT_rep1


title: P_6hP_rep1


title: CC_6hT_rep4


title: P_24hP_rep1

value: 24 hours after priming


title: CC_24hT_rep3


title: CC_6hT_rep3


title: CC_1hT_rep3


title: C_1hP_rep3

value: 1 hour after priming


title: CC_24hT_rep2


title: PC_24hT_rep2


title: P_24hP_rep3


title: CC_1hT_rep2


title: C_6hP_rep3


title: C_24hP_rep2


title: C_6hP_rep2


title: CC_1hT_rep1


title: C_1hP_rep2


title: P_1hP_rep2


title: CC_6hT_rep1


title: C_6hP_rep1


title: C_24hP_rep1


title: PT_1hT_rep3


title: P_1hP_rep1


title: CC_24hT_rep1


title: P_24hP_rep2


title: C_1hP_rep1


title: PT_1hT_rep1


title: CT_6hT_rep3


title: PT_1hT_rep2


title: CT_1hT_rep3


title: PC_1hT_rep3


title: C_24hP_rep3


title: PT_24hT_rep2


title: dms denaturated uninfected

status: Public on Oct 03 2018

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

description:
processed files xud (# of mismatches) nud (total # of reads)
supplementary file: 0vs72.txt (human)

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded.
Wig files were then generated by summing the number of mismatches and total reads  obtained for each position in the human genome. For this, each read was counted for each bp.
Genome_build: refSeq Genome + NC_006273.2
Supplementary_files_format_and_content: txt files, contains aligned reads following the described pre-processing steps
Supplementary_files_format_and_content: files were filtered for positions with more than 10 reads total and that passed the untreat and denatured cutoffs.  x1,x2 first and second time points mismatches   n1,n2 first and second time points total reads   xu, xd #of mismatches for untreated and denatured samples (controls)   nu, nd: total reads for untreated and denatured samples respectively (controls)   pu. pd ratio (mismatches/total) for untreated and denatured

source_name: Primary fibroblasts

growth_protocol: HFFs cells were grown in DMED high glucose media in 37c  5%CO2. HFFs were either mock or 72h infected with HCMV Merlin strain passage 3 with MOI 5 prior to DMS treatment

extract_protocol:
total RNA was extracted using TRI ragent and phase separated using chloroform. mRNA was isolated using polyA selection kit (Ambion)
Small RNA fragments were size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circularized and PCR amplified.

treatment_protocol: 6% DMS for 5min in 37c. Discard medium and neutralization with 30% BME. Harvesting with TRI reagent

tag: infection

value: uninfected

value: DMS, denatured

value: Primary fibroblasts


title: dms rep1 72hr post infection

description:
processed files x3 (# of mismatches) n3 (total # of reads)
supplementary file: 0vs72.txt (human)

value: human cytomegalovirus (HCMV) - Merlin - 72 hours

value: DMS


title: not dms treated uninfected

description:
processed files  xuu (# of mismatches) nuu (total # of reads)
supplementary file: 0vs72.txt (human)

value: untreated


title: P_1hP_rep3

value: yes


title: P07

city: London

first: Lilach

last: Soreq

address: Queen Square

department: Molecular  Neuroscience

country: United Kingdom

institute: UCL

description: Barcode sequence: CAGATC

data_processing:
Base-calling was performed using bclTofastq
Casava, version 1.8.2, core parameters: nohup make -j N (Bcl conversion and demultiplexing), nohup make -j N r1 (Bcl conversion and demultiplexing for read 1.)
The workflow includes: FASTQ generation and multiplexing, alignment to the reference genome, and detecting variants and counting of RNA reads
Alignment was performed as follows:
ELAND v2, parameters: --bam (enables BAM output), --copy-references (copies the reference to the output directory), with core parameters:  - force exciting output files to be overwritten), --input-type <input format>, --log <path to log> (path to log file), --outputdirectory<output dir>, --output-prefix
<prefix>, --kagu-options <"options"> (Indicates paired-read analysis parameters to pass to
alignmentResolver. e.g. -ko "-c" enables circular reference sequence support), --remove-temps (removes all files except exports, BAM files, and log files upon successful completion), --seed-length <value> - Length of read substring (seed) used for ELAND alignment (defaults to the lower of read-length and 32), --use-bases <value> - Expanded mask to apply to the FASTQ file
two values if paired analysis. Defaults to Y*n --help -h Shows help text.
To determine the association between the population genes (N=23,881) and the experimental repopulation condition, we measured the fit of a Generalized Linear regression model (GLM) to the RPKM (Reads Per Kilobase of transcript per Million mapped reads) measurements as a function of the experimental condition (control, repopulated ) by a specific contrast interrogating control < repopulated for each gene independently. Additionally, we corrected for multiple comparison across all the coefficient terms for the specific contrast using false discovery rate (FDR, with q=0.05).
Genome_build: mm10
Supplementary_files_format_and_content: RPKMs and differential expression

source_name: frozen half brain

extract_protocol:
RNA was extracted and purified from frozen half brains using an RNA Plus Universal Mini Kit (Qiagen; Cat. #73404) per the manufacturer’s instructions.
RNA-Sequencing (RNA-Seq) libraries were produced intact half brain homogenate samples of 3 young control, 3 aged control, 3 aged eliminated and 3 aged repopulated mice, using Illumina hiSeq

treatment_protocol: The microglia  repopulated animals were on 2 wk PLX5622 to Eliminate microglia, 4 wk Control diet to Repopulate

tag: age group

value: young

tag: type

value: control

value: 5 months

tag: strain

tag: source

value: JAX

tag: date of birth

tag: diet

value: 6 wk Control diet


title: P12

description: Barcode sequence: CTTGTA

value: aged

value: 24 months

value: NIA


title: P09

description: Barcode sequence: GATCAG


title: UbiqC-A

city: New York

first: Mark

middle: Monroe

last: Emerson

state: NY

address: 160 Convent Ave

department: Biology

institute: The City College of New York

description: E5 20hr cultured explant

data_processing:
Reads were clipped for adapter sequences and any sequencing artifacts removed with FastX toolkit.
Paired reads were aligned to known and predicted RNA from the galgal5 NCBI refseq RNA dataset using kallisto (Bray et al, 2016)
Differential expression analysis was measured using sleuth (Pimentel et al, 2016) in gene aggregation mode.
Genome_build: galgal5
Supplementary_files_format_and_content: tab separated files include TPM values for each transcript; sleuth results in xls providing differential expression measurements (q value, fold change)

molecule: polyA RNA

organism: Gallus gallus

source_name: Retinal progenitor cells

growth_protocol: E5 chick retinal explants electroporated with ThrbCRM1-GFP and UbiqC-Tdt then cultured for approx. 20hrs on floating Nuclepore Track-Etch membranes (Whatman, Florham Park, NJ) in 10% fetal bovine serum (Invitrogen, Carlsbad, CA), 45% Dulbecco's modified Eagle's medium (DMEM; Invitrogen), 45% F12 nutrient mixture (Invitrogen), 100 U/mL penicillin (Invitrogen), 100 mg/mL streptomycin (Invitrogen), and 2 mM L-glutamine (Sigma, St. Louis, MO). Sorted by FACS into GFP+/TDT+ and TDT+ populations.

extract_protocol:
RNA was extracted with Qiagen RNAeasy kit.
Standard Illumina protocol

tag: tissue

value: retina

tag: cell population

value: UbiqC


title: ThrbCRM1-B

description: E5 20hr cultured explant


title: P11

description: Barcode sequence: GGCTAC

tag: age


title: 12_CK09_30S_4

city: Baltimore

first: Boris

last: Zinshteyn

state: Maryland

address: 725 N Wolfe St, PCTB 714

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

data_processing:
library strategy: DMS-MapSeq
adaptor removed with cutadapt
first 3 nt trimmed with FASTX trimmer
low quality bases trimmed (ShapeMapper)
Reads mapped to rRNA with Bowtie2 (ShapeMapper)
Coverage and mutations computed for each read (ShapeMapper)
Genome_build: E.coli rRNA operons B or H
Supplementary_files_format_and_content: tab-seperated text file of mutation rates (#mutations/coverage), a proxy for extent of DMS modification, for each nucleotide in each dataset.

organism: Escherichia coli

extract_protocol:
Modified ribosomes were isopropanol precipitated, phenol extracted, reprecipitated.
rRNA was fragmented with Zinc Chloride for 5' @ 94C. 3' ends were resolved by treatment with T4 PNK, and RNA was size-selected by gel for ~60-70nt fragments.Preadenylated IDT miRNA cloning linker 2 was ligated with T4 PNK, and the ligated products gel purified. RT was performed with TGIRTIII RT @ 60C for 1 hour, and full-length RT products were gel purified. cDNA was circularized with circ ligase, and amplified by 11-13 cycles of PCR.

treatment_protocol: Ribosomes were treated for 4 min with 100mM DMS, and quenched with βME buffer.

tag: genotype/variation

tag: dms concentration

tag: treatment time

value: 4 minutes

tag: molecule subtype

value: Purified ribosomes; 30S ribosomal RNA


title: P01

description: Barcode sequence: ATCACG

value: microglia repopulated

value: 2 wk PLX5622 to Eliminate microglia, 4 wk Control diet to Repopulate


title: P08

description: Barcode sequence: ACTTGA


title: UbiqC-B

description: E5 20hr cultured explant


title: ThrbCRM1-A

description: E5 20hr cultured explant


title: P10

description: Barcode sequence: TAGCTT


title: 6_CK09_30S_1


title: 4_CK09_30S_no_DMS_2

value: 0 mM


title: 11_CK07_30S_4


title: 2_CK09_30S_no_DMS_1


title: 8_CK09_30S_2


title: dms denaturated 72hr post infection

description: supplementary file: 0vs72.txt (human)

value: human cytomegalovirus (HCMV) - Merlin - 72 hours

tag: treatment

value: DMS, denatured

tag: cell type

value: Primary fibroblasts


title: 5_CK07_30S_1


title: 7_CK07_30S_2


title: dms rep1 uninfected

description:
processed files x1 (# of mismatches) n1 (total # of reads)
supplementary file: 0vs72.txt (human)

value: uninfected

value: DMS


title: 1_CK07_30S_no_DMS_1


title: P03

description: Barcode sequence: TTAGGC


title: P02

description: Barcode sequence: CGATGT


title: MCF7_2 (RRBS)

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
The raw reads from reduced representation bisulfite sequencing (RRBS), after trimming low quality ends and adaptor sequences, are aligned to version hg19 of human genome by using bsmap (PMID: 19635165) with parameters of “-v 0.05 -s 12 -S 1 -r 1”.
The DNA methylation beta values of all CpG sites are calculated and the CpG sites with lower than 5 reads covered are removed from the analyses.
Genome_build: hg19
Supplementary_files_format_and_content: bed files contain the beta values of CpG sites with more than 5 reads covered

source_name: breast cancer cells

growth_protocol: MCF7, C70R and C49R cells were cultured in DMEM supplemented with 10% FBS, 1% penicillin/streptomycin and 10 μg ml−1 insulin. FULVR and TAMR cells are cultured in RPMI without phenol red supplemented with 10% charcoal-stripped FBS, 1% penicillin/streptomycin and 10 μg ml−1 insulin.

extract_protocol: RRBS was performed according to a previously published protocol (Smith et al., 2009)

tag: cell line


title: BRKR.BQE.d02.3 (RNA-Seq)

data_processing:
Raw RNA-seq reads are aligned to version hg19 of human genome by using Tophat2 (PMID: 23618408) with the default parameters.
Gene counts are quantified by using RSEM with REFSEQ annotation.
Genome_build: hg19
Supplementary_files_format_and_content: Gene quantification files (*.genes.results) are generated using RSEM

growth_protocol: MCF7, C70R and C49R cells were cultured in DMEM supplemented with 10% FBS, 1% penicillin/streptomycin and 10 μg ml−1 insulin. FULVR and TAMR cells are cultured in RPMI without phenol red supplemented with 10% charcoal-stripped FBS, 1% penicillin/streptomycin and 10 μg ml−1 insulin. For the analysis between MCF7, FULVR and TAMR, MCF7 cells are cultured in RPMI without phenol red supplemented with 10% charcoal-stripped FBS, 1% penicillin/streptomycin and 10 μg ml−1 insulin. Cells were cultured in RPMI without phenol red supplemented with 10% charcoal-stripped FBS, 1% penicillin/streptomycin for E2 and its corresponding control.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols.

treatment_protocol: MCF7, C70R, C49R, FULVR and TAMR cells were treated with E2 (100 nM) or three different inhibitors: fulvestrant (1 μM), KDM5-C70 (10 μM) and KDM5-C49 (10 μM).

value: C49 2day


title: MCF7_1 (RRBS)


title: C49R_2 (RRBS)


title: TAMR_2 (RRBS)

value: TAMR


title: FULR_2 (RRBS)

value: FULR


title: C70R_2 (RRBS)


title: BRKR.BRK.d02.3 (RNA-Seq)

value: C70 2day


title: FULR_1 (RRBS)


title: BQER.BRK.d02.3 (RNA-Seq)


title: MCF7 (inDrop)

data_processing:
Single-cell RNA-seq data generated by inDrop version 3 were processed using the indrops pipeline developed by the Klein laboratory (https://github.com/indrops/indrops, v.0.3.1.1, commit 7979ee8a212fcec5ba726a8ccf8b7b8fa9db52cf, using Python 2.7, Rsem 1.3.0, Bowtie 1.1.1, Samtools 1.3.1, JDK 1.8.0_45) (https://www.ncbi.nlm.nih.gov/pubmed/27929523). Default parameters were applied (for Bowtie, m: 200, n: 1, l:15, e: 80; for Trimmomatic, LEADING: "28", SLIDINGWINDOW: "4:20", MINLEN: "16"; for UMI quantification, m: 10, u: 1, d: 600, split-ambigs: False, min_non_polyA: 15; for low complexity filter, max_low_complexity_fraction: 0.50; for output: output_unaligned_reads_to_other_fastq: False, filter_alignments_to_softmasked_regions: False).
Sequences originating from pooled libraries were demultiplexed using the following indices:
C70R, ATAGAGAG; MCF7.C70, CGGAGAGA, MCF7, TACTCCTT
Alignment was performed against cDNA from Ensembl GRCh38.85 release. Empty or improductive droplets were filtered out based on the low abundance of reads per barcode, with a threshold set manually for each dataset after inspection of the barcode abundance distribution.
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv files contain the raw UMIs for each gene

growth_protocol: MCF7 and C70R cells were cultured in DMEM supplemented with 10% FBS, 1% penicillin/streptomycin and 10 μg ml−1 insulin. FULVR cells are cultured in RPMI without phenol red supplemented with 10% charcoal-stripped FBS, 1% penicillin/streptomycin and 10 μg ml−1 insulin. SUM159 cells are cultured in DMEM/F12 supplemented with 5% FBS, 10 mM HEPES, 10 μg ml−1 hydrocortisone, 5 μg ml−1 insulin and 1% penicillin/streptomycin.

extract_protocol:
Single-cell RNA-seq was performed using the inDrop protocol on a custom system as described in [https://www.ncbi.nlm.nih.gov/pubmed/27929523]. Hydrogel beads with version 3 oligonucleotide design were purchased from the Harvard Single Cell Core (https://iccb.med.harvard.edu/single-cell-core). Microfluidic encapsulation chips were purchased from 1CellBio (part no. 10080; https://1cell-bio.com/).
Library preparation was performed as described in [https://www.ncbi.nlm.nih.gov/pubmed/27929523].

treatment_protocol: Cells were treated with inhibitors: fulvestrant (1 μM) or KDM5-C70 (10 μM).

tag: cell lines

value: MCF70 -none, MCF7.C70 - C70, C70R - none


title: BRKR.CTL.d00.3 (RNA-Seq)


title: BQER.CTL.d00.3 (RNA-Seq)


title: TAMR_1 (RRBS)


title: C49R_1 (RRBS)


title: BRKR.BRK.d02.2 (RNA-Seq)


title: pMCF7 (inDrop)

data_processing:
Single-cell RNA-seq data generated by inDrop version 3 were processed using the indrops pipeline developed by the Klein laboratory (https://github.com/indrops/indrops, v.0.3.1.1, commit 7979ee8a212fcec5ba726a8ccf8b7b8fa9db52cf, using Python 2.7, Rsem 1.3.0, Bowtie 1.1.1, Samtools 1.3.1, JDK 1.8.0_45) (https://www.ncbi.nlm.nih.gov/pubmed/27929523). Default parameters were applied (for Bowtie, m: 200, n: 1, l:15, e: 80; for Trimmomatic, LEADING: "28", SLIDINGWINDOW: "4:20", MINLEN: "16"; for UMI quantification, m: 10, u: 1, d: 600, split-ambigs: False, min_non_polyA: 15; for low complexity filter, max_low_complexity_fraction: 0.50; for output: output_unaligned_reads_to_other_fastq: False, filter_alignments_to_softmasked_regions: False).
Sequences originating from pooled libraries were demultiplexed using the following indices:
pMCF7-1, ATAGAGAG; pMCF7-FULV-1, AGAGGATA; FULVR-1, CTCCTTAC; FULVR.C70-1, TATGCAGT; SUM159-1, TACTCCTT; SUM159.C70-1, AGGCTTAG; MCF7-2, ATTAGACG; MCF7.FULV-2, CGGAGAGA; FULVR-2, CTAGTCGA; FULVR.C70-2, AGCTAGAA; SUM159-2, ACTCTAGG; SUM159.C70-2, TCTTACGC
Alignment was performed against cDNA from Ensembl GRCh38.85 release. Empty or improductive droplets were filtered out based on the low abundance of reads per barcode, with a threshold set manually for each dataset after inspection of the barcode abundance distribution.
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv files contain the raw UMIs for each gene

value: pMCF7 - none, PMCF7.FUL -Fulvestrant, FULR -none, FULR.C70 - C70, SUM159 - none, SUM159.C70 - C70


title: BQER.BQE.d02.3 (RNA-Seq)


title: BRKR.BQE.d02.2 (RNA-Seq)


title: 3_CK07_30S_no_DMS_2


title: BRKR.CTL.d00.2 (RNA-Seq)


title: BQER.BRK.d02.2 (RNA-Seq)


title: BQER.BQE.d02.2 (RNA-Seq)


title: BQER.CTL.d00.2 (RNA-Seq)


title: MCF7.E2.h06.3 (RNA-Seq)

value: E2 6hour


title: MCF7.E2.h03.3 (RNA-Seq)

value: E2 3hour


title: C70R_1 (RRBS)


title: BRKR.E2.h06.3 (RNA-Seq)


title: BRKR.E2.h03.3 (RNA-Seq)


title: BQER.E2.h06.3 (RNA-Seq)


title: MCF7.E2.h00.3 (RNA-Seq)


title: BRKR.E2.h00.2 (RNA-Seq)


title: MCF7.E2.h06.2 (RNA-Seq)


title: MCF7.E2.h03.2 (RNA-Seq)


title: MCF7.E2.h00.2 (RNA-Seq)


title: BQER.E2.h03.3 (RNA-Seq)


title: BRKR.E2.h03.2 (RNA-Seq)


title: BRKR.E2.h00.3 (RNA-Seq)


title: BQER.E2.h06.2 (RNA-Seq)


title: MCF7.CSS.3 (RNA-Seq)


title: BQER.E2.h00.2 (RNA-Seq)


title: MCF7.CSS.2 (RNA-Seq)


title: TAMR.3 (RNA-Seq)


title: MCF7.CSS.1 (RNA-Seq)


title: FulR.3 (RNA-Seq)


title: FulR.1 (RNA-Seq)


title: TAMR.2 (RNA-Seq)


title: FulR.2 (RNA-Seq)


title: BRKR.E2.h06.2 (RNA-Seq)


title: MCF7.E2.h03.1 (RNA-Seq)


title: MCF7.E2.h06.1 (RNA-Seq)


title: TAMR.1 (RNA-Seq)


title: BQER.E2.h00.3 (RNA-Seq)


title: BQER.E2.h03.2 (RNA-Seq)


title: MCF7.E2.h00.1 (RNA-Seq)


title: BRKR.E2.h06.1 (RNA-Seq)


title: APH,18h_RPAChIPSeq rep1

value: ATR+/- MEFs

value: Passage-immortalized MEFs

value: 0.2 uM aphidicolin for 18hrs

tag: chip antibody

value: anti-RPA32 (EMD Millipore, NA19L-100UG, lot D00127062)


title: BQER.E2.h06.1 (RNA-Seq)


title: BRKR.E2.h03.1 (RNA-Seq)


title: BRKR.E2.h00.1 (RNA-Seq)


title: BQER.E2.h03.1 (RNA-Seq)


title: BQER.E2.h00.1 (RNA-Seq)


title: MCF7.BRK.d07.3 (RNA-Seq)

value: C70 7day


title: MCF7.BQE.d07.3 (RNA-Seq)

value: C49 7day


title: MCF7.KDM5B.WT.1 (RNA-Seq)


title: MCF7.BQE.d02.3 (RNA-Seq)


title: MCF7.BRK.d02.3 (RNA-Seq)


title: MCF7.CTL.d00.3 (RNA-Seq)


title: MCF7.BRK.d14.3 (RNA-Seq)

value: C70 14day


title: BRKR.BQE.d02.1 (RNA-Seq)


title: BRKR.BRK.d02.1 (RNA-Seq)


title: BRKR.CTL.d00.1 (RNA-Seq)


title: BQER.BQE.d02.1 (RNA-Seq)


title: BQER.CTL.d00.1 (RNA-Seq)


title: BQER.BRK.d02.1 (RNA-Seq)


title: MCF7.BRK.d02.2 (RNA-Seq)


title: MCF7.BRK.d07.1 (RNA-Seq)


title: MCF7.BQE.d14.3 (RNA-Seq)

value: C49 14day


title: MCF7.BRK.d07.2 (RNA-Seq)


title: MCF7.BRK.d02.1 (RNA-Seq)


title: MCF7.BRK.d14.2 (RNA-Seq)


title: MCF7.BRK.d14.1 (RNA-Seq)


title: MCF7.BQE.d02.2 (RNA-Seq)


title: MCF7.BQE.d14.2 (RNA-Seq)


title: MCF7.CTL.d00.2 (RNA-Seq)


title: MCF7.BQE.d02.1 (RNA-Seq)


title: C70R (Exome-Seq)

data_processing:
Samples sequenced in the same lane were demultiplexed using the Picard tools. Read pairs were aligned to the hg19 reference sequence using the Burrows-Wheeler Aligner (Li and Durbin, 2009), and data were sorted and duplicate-marked using Picard tools. The alignments were further refined using the Genome Analysis Toolkit (GATK) (McKenna et al., 2010; DePristo et al., 2011) for localized realignment around indel sites (https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_indels_IndelRealigner.php). Recalibration of quality scores was also performed using the GATK (http://gatkforums.broadinstitute.org/discussion/44/base-quality-score-recalibration-bqsr). Mutation analysis for single nucleotide variants (SNV) was performed using MuTect v1.1.4 (Cibulskis et al., 2013) in paired mode using the CEPH as the “project normal,” and indel calling was performed using the GATK SomaticIndelDetector tool. SNVs and indels were annotated using Variant Effect Predictor (McLaren et al. 2010).
Copy number variants were identified using RobustCNV, an algorithm in development at the CCGD (manuscript in preparation). RobustCNV relies on localized changes in the mapping depth of sequenced reads to identify changes in copy number at the loci sampled during targeted capture. This strategy includes a normalization step in which systematic bias in mapping depth is reduced or removed using robust regression to fit the observed tumor mapping depth against a panel of normals (PoN) sampled with the same capture bait set. Observed values are then normalized against predicted values and expressed as log2ratios. A second normalization step is then done to remove GC bias using a loess fit. Finally, log2ratios are centered on segments determined to be diploid based on the allele fraction of heterozygous SNPs in the targeted panel.
Normalized coverage data is next segmented using Circular Binary Segmentation (Olshen et al., 2004) with the DNAcopy Bioconductor package. Finally, segments are assigned “gain,” “loss,” or “normal-copy” calls using a cutoff derived from the within-segment standard deviation of post-normalized mapping depths and a tuning parameter which was set based on comparisons to array-CGH calls in separate validation experiments.
Genome_build: hg19
Supplementary_files_format_and_content: xlsx file contains the SNV and CNV calling results

extract_protocol:
Genomic DNA was extracted from the frozen cell populations with a QIAamp DNA Mini Kit (Qiagen).
Sequencing libraries were prepared as previously described (Brastianos et al., 2013). Briefly, gDNA from five cell lines and one human CEPH normal (http://hapmap.ncbi.nlm.nih.gov/citinghapmap.html.en) were fragmented to 250 bp using Adaptive Focused Acoustics (AFA) ultra-sonication (Covaris Inc., Woburn, MA) and further purified using Agencourt AMPure XP beads (Beckman Coulter, Inc., Indianapolis, IN). A total of 50 ng of size-selected DNA was ligated to DNA barcoded adaptors during library preparation (KAPA HTP DNA Library Preparation Kit, KK8234, Kapa Biosystems, Inc., Wilmington, MA). Each library was made with sample-specific barcodes and quantified using an Illumina MiSeq Nano flow cell (Illumina Inc., San Diego, CA). For exome enrichment, the 6 libraries were pooled in 3 x 2-plex to a total of 750 ng per pool, and exonic regions were captured with the SureSelect Target Enrichment system using the Human All Exon V5 hybrid capture kit (Agilent Technologies, Santa Clara, CA). All captures were further pooled and sequenced in two lanes of the HiSeq 2500 system in Rapid Run Mode (Illumina Inc., San Diego, CA).
Exome-seq

value: C70 resistant MCF7


title: Group11_C70R_KDM5B (ChIP-Seq)

data_processing:
Adapter sequences of ChIP-seq raw reads are removed by using cutadapt (DOI:10.14806/ej.17.1.200).
Trimmed reads are aligned by bowtie2 using default parameters to version hg19 of human genome. The samtools (PMID: 19505943) and picard (http://broadinstitute.github.io/picard) are used to sort and remove duplicated reads to avoid PCR bias from the sequencing process.
Each group of libraries after the above pre-processing is down-sampled (without replacement) to a fixed number of reads, which shown in the file names, such as "ds20000000".
Peak calling (identification of regions of ChIP-seq enrichment over background) is performed by using MACS2 (PMID: 18798982) with parameters of “--extsize=146 –nomodel”.
The “broad peak” option is on when identifying binding regions of KDM5B, H3K4me3 and H3K4me2. The typical-enhancers and super-enhancers are identified from H3K27ac enrichment by using ROSE pipeline with parameters described in PMID: 23582322.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig of downsampled signals & bed files of called peaks are generated using MACS2

extract_protocol:
For KDM5B ChIP-seq, 1 × 107 cells were fixed with 2mM DSG (Thermo scientific 20593) for 30 min at room temperature. DSG was then removed and replaced with fixing buffer (50 mM HEPES-NaOH (pH 7.5), 100 mM NaCl, 1mM EDTA) containing 1% paraformaldehyde (Electron Microscopy Sciences, 15714) and crosslinked for 10 min at 37 °C.  For histone modification ChIP-seq, 5 × 106 cells were fixed with 1% paraformaldehyde for 10 min at room temperature. For ER ChIP-seq, 1 × 107 cells were fixed with 1% paraformaldehyde for 10 min at 37 °C. Crosslinking was quenched by adding glycine to a final concentration of 0.125 M. The cells were washed with ice-cold PBS, harvested in PBS. The nuclear fraction was extracted by first resuspending the pellet in 1 ml of lysis buffer (50 mM HEPES-NaOH (pH 8.0), 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) for 10 min at 4 °C. Cells were pelleted, and washed in 1 ml of wash buffer (10 mM Tris-HCL (pH 8.0), 200 mM NaCl, 1 mM EDTA) for 10 min at 4 °C. Cells were then pelleted and resuspended in 1 ml of shearing buffer (10 mM Tris-HCl (pH 8), 1 mM EDTA, 0.1% SDS) and sonicated in a Covaris sonicator. Lysate was centrifuged for 5 min at 14,000 rpm to purify the debris. Then 100 µl of 10% Triton X-100 and 30 µl of 5M NaCl were added. The sample was then incubated with 20 µl of Dynabeads Protein G (LifeTechnologies,10003D) for 1 h at 4 °C. Primary antibodies were added to each tube and immunoprecipitation (IP) was conducted overnight in the cold room. Cross-linked complexes were precipitated with Dynabeads Protein G for 2 hr at 4 °C. The beads were then washed in low salt wash buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C, high salt wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C and LiCl wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C. DNA was eluted in elution buffer (100 mM sodium bicarbonate and 1% SDS). Cross-links were reversed overnight at 65 °C. RNA and protein were digested with 0.2 mg ml−1 RNase A for 30 min at 37 °C followed by 0.2 mg ml−1 Proteinase K for 1 h at 55 °C. DNA was purified with phenol-chloroform extraction and isopropanol precipitation.
ChIP-seq libraries were prepared using the Rubicon ThruPLEX DNA-seq Kit from 1 ng of purified ChIP DNA or input DNA according to the manufacturer’s protocol.

treatment_protocol: MCF7, C70R, C49R, FULVR and TAMR cells were treated with E2 (100 nM) or three different inhibitors: fulvestrant (10 μM), KDM5-C70 (10 μM) and KDM5-C49 (10 μM).

tag: antibody

value: anti-KDM5B (Novus Biologicals, 22260002)


title: Group11_C70R_input (ChIP-Seq)


title: TAMR (Exome-Seq)

value: Tamoxifen resistant MCF7


title: C49R (Exome-Seq)

value: C49 resistant MCF7


title: FULR (Exome-Seq)

value: Fulvestrant resistant MCF7


title: MCF7 (Exome-Seq)


title: Group11_MCF7_C70_5day_KDM5B (ChIP-Seq)


title: Group11_MCF7_KDM5B (ChIP-Seq)


title: Group11_MCF7_input (ChIP-Seq)


title: Group10_FULR_FUL_KDM5B (ChIP-Seq)

value: FULR

value: Fulvestrant


title: Group10_FULR_C70plusFUL_KDM5B (ChIP-Seq)


title: Group10_FULR_KDM5B_input (ChIP-Seq)


title: Group9_FULR_ER_input (ChIP-Seq)


title: MCF7.BQE.d07.2 (RNA-Seq)


title: Group9_FULR_ER (ChIP-Seq)

value: anti-ERα (Cell signaling, 8644)


title: Group10_FULR_KDM5B (ChIP-Seq)


title: MCF7.BQE.d07.1 (RNA-Seq)


title: Group9_FULR_FUL_ER (ChIP-Seq)


title: Group10_FULR_C70_KDM5B (ChIP-Seq)


title: Group9_FULR_C70_ER (ChIP-Seq)


title: MCF7.BQE.d14.1 (RNA-Seq)


title: MCF7.CTL.d00.1 (RNA-Seq)


title: Group8_TAMR_CSS_KDM5B (ChIP-Seq)

value: TAMR


title: Group9_FULR_C70plusFUL_ER (ChIP-Seq)


title: Group8_TAMR_CSS_input (ChIP-Seq)


title: Group11_C70R_C70_5day_KDM5B (ChIP-Seq)


title: Group8_TAMR_CSS_E2_45min_KDM5B (ChIP-Seq)


title: Group8_MCF7_CSS_KDM5B (ChIP-Seq)


title: Group8_FULR_CSS_KDM5B (ChIP-Seq)


title: Group8_MCF7_CSS_E2_45min_KDM5B (ChIP-Seq)


title: Group8_MCF7_CSS_input (ChIP-Seq)


title: Group8_FULR_CSS_E2_45min_KDM5B (ChIP-Seq)


title: Group8_FULR_CSS_input (ChIP-Seq)


title: Group8_C70R_CSS_E2_45min_KDM5B (ChIP-Seq)


title: Group8_C70R_CSS_input (ChIP-Seq)


title: Group7_TAMR_CSSplusinsulin_input (ChIP-Seq)


title: Group7_MCF7_CSSplusinsulin_input (ChIP-Seq)


title: Group7_MCF7_FBS_input (ChIP-Seq)


title: Group7_MCF7_CSSplusinsulin_KDM5B (ChIP-Seq)


title: Group7_MCF7_FBS_KDM5B (ChIP-Seq)


title: Group7_TAMR_CSSplusinsulin_KDM5B (ChIP-Seq)


title: Group7_MCF7_CSS_input (ChIP-Seq)


title: Group7_MCF7_CSSplusE2_KDM5B (ChIP-Seq)


title: Group7_MCF7_CSS_KDM5B (ChIP-Seq)


title: Group6_TAMR_CSS_H3K4me3 (ChIP-Seq)

value: anti-H3K4me3 (abcam, ab1012)


title: Group7_FULR_CSSplusinsulin_input (ChIP-Seq)


title: Group6_TAMR_CSS_H3K4me2 (ChIP-Seq)

value: anti-H3K4me2 (Millipore, 07-030)


title: Group7_FULR_CSSplusinsulin_KDM5B (ChIP-Seq)


title: Group6_MCF7_CSS_H3K4me3 (ChIP-Seq)


title: Group6_MCF7_CSS_input (ChIP-Seq)


title: Group6_MCF7_CSS_H3K4me2 (ChIP-Seq)


title: 9_CK07_30S_3

value: 4 minutes

value: Purified ribosomes; 30S ribosomal RNA


title: Group8_C70R_CSS_KDM5B (ChIP-Seq)


title: Group6_FULR_CSS_input (ChIP-Seq)


title: Group6_FULR_CSS_H3K4me3 (ChIP-Seq)


title: Group7_MCF7_CSSplusE2_input (ChIP-Seq)


title: Group6_FULR_CSS_H3K4me2 (ChIP-Seq)


title: Group5_C70R_KDM5B (ChIP-Seq)


title: Group5_C49R_KDM5B (ChIP-Seq)


title: Group5_C70R_input (ChIP-Seq)


title: Group5_C49R_input (ChIP-Seq)


title: 10_CK09_30S_3


title: Group6_TAMR_CSS_input (ChIP-Seq)


title: Group4_MCF7_CSS_input (ChIP-Seq)


title: Group4_MCF7_CSS_ER (ChIP-Seq)


title: Group4_MCF7_E2_45min_ER (ChIP-Seq)


title: Group3_MCF7_C49_2day_H3K27ac (ChIP-Seq)

value: anti-H3K27Ac (abcam, ab4729)


title: Group4_C70R_E2_45min_ER (ChIP-Seq)


title: Group4_C70R_CSS_ER (ChIP-Seq)


title: Group3_MCF7_C70_2day_H3K27ac (ChIP-Seq)


title: Group4_C49R_CSS_ER (ChIP-Seq)


title: Group4_C49R_E2_45min_ER (ChIP-Seq)


title: Group2_C49R_C49_2day_H3K4me2 (ChIP-Seq)


title: Group2_C49R_input (ChIP-Seq)


title: Group3_C49R_input (ChIP-Seq)


title: Group2_C49R_H3K4me3 (ChIP-Seq)


title: Group2_C49R_C70_2day_H3K4me3 (ChIP-Seq)


title: Group3_C49R_C70_2day_H3K27ac (ChIP-Seq)


title: Group2_C49R_C70_2day_H3K4me2 (ChIP-Seq)


title: Group2_MCF7_0day_H3K4me3 (ChIP-Seq)


title: Group3_C70R_C70_2day_H3K27ac (ChIP-Seq)


title: Group3_C49R_0day_H3K27ac (ChIP-Seq)


title: Group3_C70R_C49_2day_H3K27ac (ChIP-Seq)


title: Group2_C49R_C49_2day_H3K4me3 (ChIP-Seq)


title: Group3_C49R_C49_2day_H3K27ac (ChIP-Seq)


title: Group2_C49R_H3K4me2 (ChIP-Seq)


title: Group2_MCF7_C49_2day_H3K4me3 (ChIP-Seq)


title: Group5_MCF7_KDM5B (ChIP-Seq)


title: Group5_MCF7_input (ChIP-Seq)


title: Group3_MCF7_0day_H3K27ac (ChIP-Seq)


title: Group3_C70R_0day_H3K27ac (ChIP-Seq)


title: Group2_MCF7_C70_2day_H3K4me3 (ChIP-Seq)


title: Group2_MCF7_C70_2day_H3K4me2 (ChIP-Seq)


title: Group2_MCF7_C49_2day_H3K4me2 (ChIP-Seq)


title: Group2_MCF7_input (ChIP-Seq)


title: not dms treated 72hr post infection

description:
processed files  xiu (# of mismatches) niu (total # of reads)
supplementary file: 0vs72.txt (human)

tag: infection

value: human cytomegalovirus (HCMV) - Merlin - 72 hours

value: untreated

value: Primary fibroblasts


title: Group2_C70R_C70_2day_H3K4me3 (ChIP-Seq)


title: Group2_C70R_C49_2day_H3K4me3 (ChIP-Seq)


title: dms rep2 72hr post infection

description:
processed files x4 (# of mismatches) n4 (total # of reads)
supplementary file: 0vs72.txt (human)

value: DMS


title: Group2_C70R_C70_2day_H3K4me2 (ChIP-Seq)


title: dms rep2 24hr post infection

description:
processed files x2 (# of mismatches) n2 (total # of reads)
supplementary file: 24vs72.txt (human) 24hr.plus.tab, 24hr.minus.tab (merlin)

value: human cytomegalovirus (HCMV) - Merlin - 24 hours


title: Group2_C70R_C49_2day_H3K4me2 (ChIP-Seq)


title: dms rep1 05hr post infection

description:
processed files x1 (# of mismatches) n1 (total # of reads)
supplementary file: 5vs72.txt (human) 5hr.plus.tab, 5hr.minus.tab (merlin)

value: human cytomegalovirus (HCMV) - Merlin - 5 hours


title: Group2_C70R_0day_H3K4me3 (ChIP-Seq)


title: Group2_C70R_input (ChIP-Seq)


title: dms rep2 05hr post infection

description:
processed files x2 (# of mismatches) n2 (total # of reads)
supplementary file: 5vs72.txt (human) 5hr.plus.tab, 5hr.minus.tab (merlin)


title: dms rep1 24hr post infection

description:
processed files x1 (# of mismatches) n1 (total # of reads)
supplementary file: 24vs72.txt (human) 24hr.plus.tab, 24hr.minus.tab (merlin)


title: Group1_MCF7_C70_7day_H3K4me3 (ChIP-Seq)


title: Group1_MCF7_C70_2day_H3K4me2 (ChIP-Seq)


title: dms rep2 uninfected

description:
processed files x2 (# of mismatches) n2 (total # of reads)
supplementary file: 0vs72.txt (human)

value: uninfected


title: Group1_MCF7_C70_7day_H3K4me2 (ChIP-Seq)


title: Group1_MCF7_C70_14day_H3K4me3 (ChIP-Seq)


title: Group1_MCF7_C70_14day_H3K4me2 (ChIP-Seq)


title: Group2_MCF7_0day_H3K4me2 (ChIP-Seq)


title: Dahomey Protein Rep4

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Indexed sample libraries were sequenced using the 75 cycle high output kit v2 chemistry for the Illumina Hiseq2000 sequencing instrument
Reads were aligned to the mouse genome by Rsubread version 1.16.1
Read counts were summarized by Entrez Gene ID using Rsubread featureCounts function and NCBI annotation
Genome_build: GCF 000001215.4 Release 6 plus ISO1 MT
Supplementary_files_format_and_content: tab-delimited text files were written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

organism: Drosophila melanogaster

source_name: Third instar larvae

extract_protocol:
Sorted cells were preserved in RNAlater (ThermoFisher Scientific) and frozen at -80°C, then RNA was isolated with RNeasyPlus Mini kit (Qiagen)
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions

tag: diet protein

value: carb ratio:1:2

tag: mitotype

value: Dahomey


title: Dahomey Carbohydrate Rep4

value: carb ratio:1:16


title: Dahomey Carbohydrate Rep3


title: Dahomey Protein Rep3


title: Group1_MCF7_C70_0day_H3K4me3 (ChIP-Seq)


title: Group1_MCF7_C70_0day_H3K4me2 (ChIP-Seq)


title: Dahomey Protein Rep2


title: Group1_MCF7_input (ChIP-Seq)


title: Group2_C70R_0day_H3K4me2 (ChIP-Seq)


title: Dahomey Protein Rep1


title: Dahomey Carbohydrate Rep2


title: Group1_MCF7_C70_2day_H3K4me3 (ChIP-Seq)


title: MCF7_p0_1 (Barcode)

data_processing:
We followed the method used in Bhang et al. 2015 with small modifications. In details, all sequencing reads are trimmed by using 3 prime adaptor sequence: AGCAGAGCTACGCACTCTATGCTAGTGCTAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCACGATCGTATCTCGTATGCCGTCTTCTGCTTG with minimum alignment length of 40-nt. The trimmed reads with Ns or less than 30-nt or without the WS x 15 pattern are removed. Then the 30-nt barcode sequences are extracted from the 3 prime end of the trimmed sequences. Barcodes with an estimated Phred quality score of at least 10 for all nucleotides and with an average Phred quality score greater than 30 are kept as qualified barcodes. The barcodes with only one count are excluded from the analyses to avoid the noise derived from the sequencing error.
Genome_build: hg19
Supplementary_files_format_and_content: tsv files contain the abundant of each barcode

growth_protocol: MCF7 cells were barcoded by lentiviral infection using high-complexity barcode library, ClonTracer. After a 24 h incubation with virus, infected cells were selected with 2 μg ml−1 puromycin. To ensure that the majority of cells were labeled with a single barcode per cell, for lentival infection we used a target m.o.i. of approximately 0.2, corresponding to 20% infectivity after puromycin selection. Infected cell populations were expanded in culture for the minimal time period to obtain a sufficient number of cells to set up replicate experiments. Cells were cultured in DMEM supplemented with 10% FBS, 1% penicillin/streptomycin and 10 μg ml−1 insulin for KDM5-C70, KDM5-C49 and their corresponding control or DMEM with 10% FBS, 1% penicillin/streptomycin and 10 μg ml−1 insulin for KDM5-C70, KDM5-C49 and their corresponding control or RPMI without phenol red supplemented with 10% charcoal-stripped FBS, 1% penicillin/streptomycin and 10 μg ml−1 insulin for fulvestrant, 4-OHT and their corresponding control.

extract_protocol:
Genomic DNA was extracted from the frozen cell populations with a QIAamp DNA Mini Kit (Qiagen).
We used PCR to amplify the barcode sequence for NGS by introducing Illumina adaptors and 5-bp-long index sequences.
Barcode_seq

treatment_protocol: Barcoded MCF7 cells were treated with four different inhibitors: fulvestrant (10 μM), 4-OHT (5 μM), KDM5-C70 (10 μM) and KDM5-C49 (10 μM). The control groups were treated with 0.1% DMSO. Each group was cultured in quadruplicate.

tag: passage


title: MCF7_p0_2 (Barcode)


title: C70R_p15_4 (Barcode)

value: C70 resistant MCF7


title: C70R_p15_3 (Barcode)


title: Alstonville Protein Rep4

value: Alstonville


title: Dahomey Carbohydrate Rep1


title: C49R_p15_4 (Barcode)

value: C49 resistant MCF7


title: C70R_p15_2 (Barcode)


title: Alstonville Carbohydrate Rep4


title: Alstonville Protein Rep3


title: Alstonville Carbohydrate Rep3


title: C49R_p15_2 (Barcode)


title: C70R_p15_1 (Barcode)


title: C49R_p15_3 (Barcode)


title: Alstonville Carbohydrate Rep2


title: C49R_p15_1 (Barcode)


title: MCF7_p15_1 (Barcode)


title: MCF7_p15_2 (Barcode)


title: TAMR_3 (Barcode)

value: Tamoxifen resistant MCF7


title: TAMR_4 (Barcode)


title: Alstonville Protein Rep1


title: Alstonville Carbohydrate Rep1


title: TAMR_1 (Barcode)


title: FULR_2 (Barcode)

value: Fulvestrant resistant MCF7


title: Alstonville Protein Rep2


title: TAMR_2 (Barcode)


title: FULR_4 (Barcode)


title: MCF7_3 (Barcode)


title: FULR_1 (Barcode)


title: DU145_si2

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

data_processing:
RNASeq raw data quality control by FastQC
RNASeq raw data clean performed by cutadapt
RNASeq data mapping to hg19 reference genome by tophat2 with at most 2 mismatch for each reads. Cuflinks was used for differential expression gene analysis,gene expression value with more than 2 fold change was defined differential expression genes.
Genome_build: hg19
Supplementary_files_format_and_content: txt format file for RNASeq gene expression level in each sample.

source_name: prostate; derived from metastatic site: brain

extract_protocol:
For RNASeq 10ug total RNA was used, and mRNA purification was performed using oligo-dT magnic beads(NEBNext PolyA mRAN magnetic isolation module # E7490). mRNA was fragmented and reverse transcript into 200-400bp dscDNA for library construction(NEB # E7525 # E6111).
Rubicon ThruPLEX DNA-seq 48D kit was used for RNASeq  library construction. Brifely, about 100ng dscDNA was used as initiation for end repair and prepared for adaptor ligation. After adaptor ligation, PCR amplification with 15 cycles for each library and gel selection was used for library size selection and purification.

tag: tissue

value: prostate

tag: disease

value: carcinoma


title: DU145_si1


title: 769-P_si2

source_name: kidney

value: kidney

value: renal cell adenocarcinoma


title: 769-P_si1


title: 769-P_NC


title: DU145_NC


title: MCF7_p15_4 (Barcode)


title: MCF7_p15_3 (Barcode)


title: shZFX_H3_1

status: Public on Oct 02 2018

city: Durham

first: Greg

last: Wang

state: NC

address: 3 Genome Court

department: Duke Department of Pharmacology and Cancer Biology  and Duke Cancer Institute

institute: Duke University School of Medicine, and Department of Biochemistry and Biophysics, UNC at Chapel Hill (adjunct)

data_processing:
Basecalls by Casava
Alignment by MapSplice2
Genome to transcriptome coordiantes by UBU (https://github.com/mozack/ubu/wiki)
Gene expression estimates by RSEM using Sept 2011 UCSC knownGene transcript definitions
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited matrix of normalized gene expression

growth_protocol: 22Rv1 cells were grown in RPMI plus 10% FBS.

extract_protocol:
RNA was extracted by using Qiagen RNeasy Mini Kit. Illumina Truseq sample prep kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For knocking down AR-FL, AR-V7 or vector experiment, 22Rv1 cells were infected with lentivirus encoding shAR-FL, or shAR-V7 or control vector, at 48 hrs post infection, cells were switched to phenol red free RPMI medium containing 10% charcoal-stripped FBS for a couple days before RNA was extracted. For knocking down ZFX or vector experiment, 22Rv1 cells were infected with lentivirus encoding shZFX or LKO control vector, at 48 hrs post infection, cells were switched to RPMI medium containing 2ug/ml puromycin for a couple days and then switched to phenol red free RPMI medium containing 10% charcoal-stripped FBS for 3 days before RNA was extracted. For drug treatment experiment, cells were cultured for 3 days in phenol red free RPMI medium containing 10% charcoal-stripped FBS, and then treated with DMSO as a vehicle control or DHT or DHT plus MDV3100 or DHT plus JQ1 for 24hrs before RNA was extracted.

value: prostate carcinoma epithelial cell line 22Rv1

value: shZFX


title: LKO_1

source_name: LKO

value: LKO control vector


title: cs_shVec_2

value: control vector


title: shZFX_H3_2


title: LKO_2


title: cs_shV7_2


title: FULR_3 (Barcode)


title: cs_shAR_2

value: shAR-FL


title: cs_shv7_1


title: cs_shAR_1


title: whiteFat DEL Rep4

first: Ashok

last: Ragavendran

address: 185 Cambridge St

department: Center for Human Genetic Research

data_processing:
Illumina Casava1.8 software used for basecalling.
sequenced reads were Qced using Fastqc, duplicates marked using Picard tools and aligned to Ensembl GRCm38 Mus musculus Reference using GSNAP version 2014-07-28 with the following parameters -s myRef.splicesites.iit -a off -N 1 --pairexpect=450   --gunzip -B 3 --query-unk-mismatch=1. The italics refers to the splicesites files created by gsnap
Counts of reads were generated using a custom procedure to account for strand-specificity using Bedtools multibamcov with the following options -s -f 0.96  -split -D
Genome_build: Ensembl Mus musculus GRCm38.75
Supplementary_files_format_and_content: Comma-seperated text files include CPM values for all Sample  within a specific tissue.

source_name: whiteFat

extract_protocol:
Total RNA extraction was performed from tissues using TRIzol (Invitrogen).  Detailed description of the protocol is presented in Blumenthal I, Ragavendran A, Erdin S, et al. Transcriptional Consequences of 16p11.2 Deletion and Duplication in Mouse Cortex and Multiplex Autism Families. American Journal of Human Genetics. 2014;94(6):870-883.
libraries were prepared with a customized version of the originally published, strand-specific dUTP method. Detailed description of the protocol is presented in Blumenthal I, Ragavendran A, Erdin S, et al. Transcriptional Consequences of 16p11.2 Deletion and Duplication in Mouse Cortex and Multiplex Autism Families. American Journal of Human Genetics. 2014;94(6):870-883.

tag: strain

value: whiteFat

tag: age

value: Post Natal day 53

tag: genotype

value: Deletion

tag: gender

value: F

tag: date of birth

tag: litter

tag: erccmix

tag: jax stock #

tag: animal id


title: MCF7_2 (Barcode)

tag: cell line


title: MCF7_1 (Barcode)


title: whiteFat DEL Rep2

value: M


title: whiteFat DEL Rep3


title: whiteFat DEL Rep1


title: whiteFat WT Rep8

value: Post Natal day 50

value: Wild Type


title: whiteFat WT Rep5


title: whiteFat WT Rep6


title: whiteFat DUP Rep4

value: Post Natal day 68

value: Duplication


title: whiteFat DUP Rep3


title: whiteFat DUP Rep2

value: Post Natal day 59


title: whiteFat WT Rep3


title: whiteFat WT Rep4


title: cs_shVec_1

tag: treatment


title: whiteFat DUP Rep1


title: Striatum DEL Rep1

source_name: Striatum

value: Striatum


title: whiteFat WT Rep1


title: whiteFat WT Rep2


title: Striatum DEL Rep4


title: Striatum WT Rep8


title: Striatum WT Rep7


title: Striatum WT Rep6


title: Striatum DEL Rep2


title: Striatum DUP Rep4


title: Striatum WT Rep5


title: Striatum DUP Rep3


title: Striatum DUP Rep2


title: Striatum DUP Rep1


title: Striatum WT Rep4


title: whiteFat WT Rep7


title: Striatum WT Rep3


title: Striatum WT Rep2


title: Liver DEL Rep3

source_name: Liver

value: Liver


title: Liver DEL Rep2


title: Liver WT Rep8


title: Liver DEL Rep4


title: Striatum WT Rep1


title: Liver DEL Rep1


title: Liver WT Rep7


title: Striatum DEL Rep3


title: Liver DUP Rep3


title: Liver WT Rep5


title: Liver DUP Rep4


title: Liver DUP Rep2


title: Liver WT Rep4


title: Liver DUP Rep1


title: Liver WT Rep3


title: Cortex DEL Rep3

source_name: Cortex

value: Cortex


title: Cortex DEL Rep4


title: Liver WT Rep2


title: Liver WT Rep1


title: Cortex DEL Rep2


title: Cortex DEL Rep1


title: Cortex WT Rep6


title: Cortex WT Rep5


title: Cortex DUP Rep3


title: Cortex DUP Rep2


title: Cortex WT Rep8


title: Cortex DUP Rep1


title: Cortex WT Rep3


title: Cortex WT Rep7


title: Cortex WT Rep2


title: Cortex DUP Rep4


title: Cerebellum DEL Rep4

source_name: Cerebellum

value: Cerebellum


title: Cortex WT Rep1


title: Liver WT Rep6


title: Cerebellum DEL Rep2


title: Cerebellum DEL Rep1


title: Cerebellum WT Rep7


title: Cerebellum WT Rep8


title: Cerebellum WT Rep6


title: Cerebellum DUP Rep2


title: Cerebellum WT Rep5


title: Cerebellum DUP Rep3


title: Cerebellum DUP Rep4


title: Cerebellum WT Rep4


title: Cerebellum DUP Rep1


title: Cortex WT Rep4


title: BrownFat DEL Rep4

source_name: BrownFat

value: BrownFat


title: Cerebellum WT Rep1


title: BrownFat DEL Rep3


title: Cerebellum WT Rep3


title: Cerebellum WT Rep2


title: BrownFat DEL Rep2


title: BrownFat WT Rep8


title: Cerebellum DEL Rep3


title: BrownFat DUP Rep4


title: BrownFat DUP Rep3


title: BrownFat WT Rep5


title: BrownFat DEL Rep1


title: BrownFat WT Rep7


title: BrownFat WT Rep6


title: BrownFat DUP Rep1


title: BrownFat WT Rep4


title: BrownFat WT Rep3


title: BrownFat WT Rep1


title: Input DNA

city: Bangalore

first: Manchanahalli

middle: Rangaswamy

last: Satyanarayana Rao

state: Karnataka

address: Jakkur, Bengaluru, Karnataka

department: Molecular Biology and Genetics Unit (MBGU)

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)

data_processing:
Quality Control Analysis and modification were performed in a three step procedure. Firstly, FASTQC was used to extract the sequence  quality measures from the raw files. Secondly, Adaptor(GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG)  clipping was done with a stringent overlap condition of 1bp using trim_galore.The pairs in which this step resulted in reduction of sequence length to below 20bp were removed. Finally, pairs where read quality was found to be less than 20 were removed.
Bowtie2 was used to align the paired end reads for each sample and during alignment all unpaired and discordant reads were removed. For this purpose UCSC Rattus  norvegicus genome (rn5; build: March, 2012) was used as a reference. SAM files were converted to  respective BAM files using SAMtools, which were subsequently sorted and filtered off PCR duplicates. Resulting processed  BAM files were the passed through another quality check using BAMQC. BED files were prepared with bedtools for visualisation and  peak identification corresponding to each BAM file.
Peak identification was done using macs14 for both the replicates using INPUT sample as control. Two cut-off p-values (1e-05 and 1e-10) were used in each case. Macs14 results were used for further analysis and visualisation of peaks identified. The peak files for the two samples (Run 2, p-value cut-off 1e-05) were used to find overlapping peaks using bedtools. Criterion for selection was a maximum distance of 100bp between peak summits in the two peak files
Overlap reigions were annotated to find basic annotations related to the overlaps using Homer
Regions with high enriched peaks were selected for ChIP-PCR
Genome_build: rn5; build: March, 2012

organism: Rattus norvegicus

source_name: testicular cells

extract_protocol:
Nuclei were prepared from 50-60 days old rat testis, decondensed and chromatin immunoprecipitation was done using anti-HILS1 antibodies.. Immunocomplexes were captured on 50 μl protein A Dynabeads. Beads with bound immunocomplexes were washed, eluted and reverse cross-linked at 65°C overnight and DNA was recovered using Qiagen PCR purification kit. Input was prepared with 5% of the sonicated chromatin.
Library DNA was purified using Qiagen DNA purification kit. Sequencing was performed with Illumina HiSeq 1000 system, and raw sequence reads containing adaptor sequences were trimmed and filtered with Phred quality threshold as 20. Read pairs falling below 20 bp after clipping were removed

tag: cell type

value: Elongating/condensing spermatids

tag: antibody


title: HILS1_ChIPSeq 2


title: 21NA

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

description: Sample 6

data_processing:
Illumina bcl2fastq 1.8.4 software used for basecalling.
RNA-Seq data analysis was done using the Eoulsan software version 1.2.2. Before mapping, poly N read tails were trimmed, reads ≤11 bases were removed, and reads with quality mean ≤12 were discarded. Reads were then aligned against the T. Weissflogii reference transcriptome using Bowtie mapper (version 0.12.9) using the "-n 2 -l 28 -e 70 -a –best" parameters. Only one alignment were kept in a given locus for each read and reads alignments matching on more than one locus were removed. To compute gene expression, T. Weissflogii transcriptome annotation was used.
Genome_build: Thalassiosira Weissflogii reference transcriptome (transcriptome assembly is linked as supplementary file on the Series record)
Supplementary_files_format_and_content: tab-delimited text files include transcripts counting for each Sample

organism: Conticribra weissflogii

source_name: Non-adapted strain, 21 ppm salinity

extract_protocol:
Total RNA was extracted using the Rneasy Lipid tissue kit (Qiagen). PolyA+ RNAs were purified from 800 µg of total RNA using oligo(dT)
Libraries were prepared using the non directional RNA-Seq library preparation TruSeq RNA Sample Prep Kits v2 (Illumina)

tag: salinity

value: 21 ppm

value: Non-adapted


title: 28A

description: Sample 3

source_name: adapted strain, 28 ppm salinity

value: 28 ppm

value: adapted


title: 28NA

description: Sample 7

source_name: Non-adapted strain, 28 ppm salinity


title: 21A

description: Sample 2

source_name: adapted strain, 21 ppm salinity


title: 35A

description: Sample 4

source_name: adapted strain, 35 ppm salinity

value: 35 ppm


title: Sox14_12h_C

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

institute: Weizmann Institute of Science

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
alignment: hisat 0.1.5  with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8).
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl DM6.gtf none -d [TAG DIR] -count 3utr -condenseGenes -strand +
Genome_build: DM6
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: pupae (12h after puparium formation)

growth_protocol: All fly strains were reared under standard laboratory conditions at 25°C on molasses containing food. Males and females were chosen at random. Developmental stage is referred to in the relevant places while adult refers to 3-5 days post eclosion.

extract_protocol:
Brains were dissected a cold Ringer’s solution, incubated with collagenase/dispase mix at 29ºC, washed in dissociation solution, mechanically dissociated into single cells and transferred via 35um mesh. 1000 DsRed+ positive cells were sorted directly into 100μl Pico-Pure RNA isolation kit extraction buffer followed by RNA extraction using the kit or stored in -80 for later use.
Library constracted using MARS-seq technique (Jaitin et al, Science 2014). Briefly mRNA was barcoded, converted into cDNA and linearly amplified by T7 in vitro transcription.
single end protocol ( samples used read2 to read molecule barcodes and UMI)

tag: organ

value: Brain

tag: selection marker

value: DsRed +

value: Isolated γ neurons expressing Sox14 RNAi

tag: developmental stage

value: pupae (12h after puparium formation)

value: Sox14 RNAi


title: BrownFat DUP Rep2

tag: strain

tag: tissue

value: Post Natal day 59

value: Duplication

value: F


title: HILS1_ChIPSeq 1

tag: age


title: Sox14_12h_B


title: Sox14_6h_C

source_name: pupae (6h after puparium formation)

value: pupae (6h after puparium formation)


title: Sox14_0h_B

source_name: pupae (0h after puparium formation)

value: pupae (0h after puparium formation)


title: Sox14_0h_C


title: Sox14_12h_A


title: Sox14_6h_A


title: Sox14_6h_B


title: BrownFat WT Rep2

value: BrownFat

tag: genotype

value: Wild Type

tag: gender


title: Sox14_L3_C

source_name: Third instar larvae

value: Third instar larvae


title: Sox14_0h_A


title: E75_6h_B

value: Isolated γ neurons expressing E75 RNAi

value: E75 RNAi


title: Sox14_L3_A


title: 35NA

description: Sample 8

source_name: Non-adapted strain, 35 ppm salinity

value: Non-adapted


title: E75_6h_A


title: E75_12h_C


title: E75_12h_A


title: E75_0h_B


title: E75_0h_A


title: Sox14_L3_B


title: E75_L3_B


title: E75_L3_A


title: E75_L3_C


title: EcR_0h_C

value: Isolated γ neurons expressing EcR-DN

value: EcR-DN


title: EcR_6h_C

value: Brain

value: DsRed +


title: E75_6h_C


title: EcR_6h_B


title: EcR_6h_A


title: EcR_12h_B

value: pupae (12h after puparium formation)


title: EcR_L3_A


title: EcR_12h_A


title: EcR_0h_B


title: EcR_L3_C


title: EcR_0h_A


title: Control_12h_A

value: Isolated γ neurons

value: y,w/+; UAS-RedStinger/+;71G10/+


title: Control_12h_C


title: Control_6h_A


title: Control_6h_C


title: Control_0h_B


title: EcR_L3_B


title: DM1

source_name: DM

value: prostate carcinoma epithelial cell line 22Rv1

value: DHT plus MDV3100


title: Control_L3_B


title: DM2


title: Control_0h_C


title: MCF7_4 (Barcode)

source_name: breast cancer cells

tag: passage


title: Control_0h_A


title: Control_12h_B


title: ALRM_Adult_3

source_name: Adult Flies

value: Astrocyte like cells

value: Adult Flies

value: UAS-RedStinger/cyo; alrm-Gal4, UAS-CD8:GFP, UAS-Dcr2/TM6, tb


title: ALRM_Adult_4


title: DJ1

source_name: DJ

value: DHT plus JQ1


title: DHT2

source_name: DHT

value: DHT


title: ALRM_Adult_1


title: Control_L3_C

value: Third instar larvae


title: ALRM_Adult_2


title: Mock2

source_name: Mock

value: DMSO (vehicle control)


title: C155_4

value: Non-MB neurons


title: C155_1


title: C155_3


title: NP3061_2

value: Isolated αβ  neurons

value: y,w/w; UAS-RedStinger/+;NP3061-GAL4/+


title: Adult_4

value: Brain


title: NP3061_1

value: DsRed +


title: Adult_1


title: NP3061_4


title: DHT1


title: Adult_2


title: Adult_3


title: 30h_3

source_name: pupae (30h after puparium formation)

value: pupae (30h after puparium formation)


title: C155_2


title: 27h_3

source_name: pupae (27h after puparium formation)

value: Isolated γ neurons

value: pupae (27h after puparium formation)


title: 30h_1

value: y,w/+; UAS-RedStinger/+;71G10/+


title: 30h_2


title: DJ2

value: prostate carcinoma epithelial cell line 22Rv1


title: 24h_3

source_name: pupae (24h after puparium formation)

value: pupae (24h after puparium formation)


title: Mock1


title: 27h_2


title: NP3061_3

value: Adult Flies


title: 24h_2


title: 24h_4


title: 24h_1


title: 21h_2

source_name: pupae (21h after puparium formation)

value: pupae (21h after puparium formation)


title: 21h_3


title: 30h_4


title: 21h_1


title: 18h_2

source_name: pupae (18h after puparium formation)

value: pupae (18h after puparium formation)


title: 18h_1


title: 15h_2

source_name: pupae (15h after puparium formation)

value: pupae (15h after puparium formation)


title: 12h_4

source_name: pupae (12h after puparium formation)

value: pupae (12h after puparium formation)


title: 15h_4


title: 15h_3


title: 18h_4


title: 27h_4


title: 15h_1


title: 12h_3


title: 27h_1


title: 12h_1


title: DO_FAKi_SSC_2_ATAC-seq

city: Stanford

first: Howard

last: Chang

state: CA

address: CCSR 2130, 269 Campus Drive

department: Dermatology

institute: Stanford University

data_processing:
ATAC adapters and barcodes were trimmed using CutAdapt Software
Sequences were aligned to the mm9 genome using Bowtie2 software
Non-concordant reads and reads mapping to the mm9 blacklist were filtered out
Peaks were called using Macs2 software with a no-shifting model
Peaks were filtered for enrichment and reads mapping to the ENCODE blacklist, repetitive elements, and segmental duplications were removed
Genome_build: mm9
Supplementary_files_format_and_content: Processed data file is a .bed file containing all peaks merged across samples for SSC, BCSP, and OPs

source_name: mouse mandibular cells isolated by FACS

growth_protocol: in vivo

extract_protocol:
Nuclei were isolated using NP-40, Tween-20, and Digitonin-containing buffer and subsequently transposed with adapter-loaded hyperactive Tn5 transposase (Illumina) in the presence of Tween and Digitonin.
Following clean-up transposed fragments were directly amplified and barcoded using Nextera indexes
Libraries were then sequenced using Illumina NextSeq 500 with 2x75 bp reads

tag: strain/background

value: male

value: skeletal stem cells sorted from distracted mandibular bone(3.0mm) treated with FAK inhibitor PF-573228 (POD 10)

tag: cell number


title: DO_FAKi_OP_1_ATAC-seq

value: osteogenic progenitor cells sorted from distracted mandibular bone(3.0mm) treated with FAK inhibitor PF-573228 (POD 10)


title: DO_FAKi_BCSP_2_ATAC-seq

value: skeletal progenitor cells sorted from distracted mandibular bone(3.0mm) treated with FAK inhibitor PF-573228 (POD 10)


title: 12h_2

value: Brain


title: DO_FAKi_OP_2_ATAC-seq


title: DO_FAKi_BCSP_1_ATAC-seq


title: DO_FAKi_SSC_1_ATAC-seq


title: 18h_3

value: DsRed +


title: 9h_3

source_name: pupae (9h after puparium formation)

value: pupae (9h after puparium formation)


title: DO_OP_1_ATAC-seq

value: osteogenic progenitor cells sorted from distracted mandibular bone(3.0mm) (POD 10)


title: 9h_1

value: Isolated γ neurons


title: DO_BCSP_2_ATAC-seq

value: skeletal progenitor cells sorted from distracted mandibular bone(3.0mm) (POD 10)


title: DO_SSC_2_ATAC-seq

value: skeletal stem cells sorted from distracted mandibular bone(3.0mm) (POD 10)


title: 6h_4

source_name: pupae (6h after puparium formation)

value: pupae (6h after puparium formation)

value: y,w/+; UAS-RedStinger/+;71G10/+


title: 9h_2


title: 6h_3


title: Fracture_OP_2_ATAC-seq

value: osteogenic progenitor cells sorted from fractured mandibular bone (POD 10)


title: 6h_2


title: DO_SSC_1_ATAC-seq


title: DO_BCSP_1_ATAC-seq


title: 3h_3

source_name: pupae (3h after puparium formation)

value: pupae (3h after puparium formation)


title: 3h_2


title: Fracture_OP_1_ATAC-seq


title: 6h_1


title: Fracture_BCSP_1_ATAC-seq

value: skeletal progenitor cells sorted from fractured mandibular bone (POD 10)


title: Fracture_BCSP_2_ATAC-seq


title: 0h_4

source_name: pupae (0h after puparium formation)

value: pupae (0h after puparium formation)


title: 3h_1


title: Fracture_SSC_2_ATAC-seq

value: male

value: skeletal stem cells sorted from fractured mandibular bone (POD 10)


title: Fracture_SSC_1_ATAC-seq


title: Uninjured_BCSP_2_ATAC-seq

value: skeletal progenitor cells sorted from injured mandibular bone


title: 9h_4


title: Uninjured_BCSP_1_ATAC-seq


title: 0h_3


title: 0h_2


title: 0h_1


title: Uninjured_SSC_2_ATAC-seq

value: skeletal stem cells sorted from injured mandibular bone


title: L3_4

source_name: Third instar larvae

value: Brain

value: Third instar larvae


title: Uninjured_SSC_1_ATAC-seq


title: L3_3

value: DsRed +


title: L2_2

source_name: Second instar larvae

value: Second instar larvae


title: L3_2

value: Isolated γ neurons


title: L2_1


title: ER_KO6

status: Public on Oct 01 2018

city: Lausanne

first: George

middle: A

last: Sflomos

address: SV 2815, Batiment SV, Station 19

department: ISREC

country: Switzerland

institute: EPFL

data_processing:
RNA-seq reads were aligned to the mm10 mouse genome using the RNA-Seq pipeline of the Bioinformatics and Biostatistics Core Facility (BBCF) HTS station http://htsstation.epfl.ch (David, FPA et al. HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis. PLoS ONE 9, e85879 (2014). We applied the ready-to-use pipeline ASAP (the Automated Single-cell Analysis Pipeline) https://asap.epfl.ch/ (https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btx337) to the RNA-seq analysis.
Genome_build: mm10

source_name: mammary gland

extract_protocol:
RNA was extracted from FACS sorted cells derived from intraductally engrafted WT.GFP+ or ERα-/-.GFP+ cells from contralateral glands of the pregnant NSG hosts using miRNeasy Mini Kit (Qiagen, cat.# 217004)
Libraries were prepared in 2 steps. The first step was performed according to Clontech's instructions accompanying the SMART-Seq v4 Ultra Low Input RNA Kit (Part# 634889). Briefly, 10 ng of RNA was reverse transcribed uning a oligo dT primer flanked with a proprietary adapter. Template switching mechanism was then used to append another proprietary adapter on the 3' end of the cDNA (corresponding to the beginning of the mRNA molecule). A PCR specific for the aforementionned adapters was used to create and amplify double-stranded cDNA molecules. The second step was performed according to Illumina's instructions accompanying the Nextera XT kit (Part# FC-131-1096). Briefly, tagmentation of the double-stranded cDNA with hyperactive Tn5 created fragments of a few hundred bp, flanked with Illumina proprietary adapters. DNA was then PCR amplified with Illumina primers for 8 cycles, generating final libraries of ~400 bp (insert plus adaptors). Libraries were sequenced on a NextSeq 500 instrument with single-end reads of 85 nt, following the manufacturer's protocols. Basecalls and Illumina adapters trimming performed using bcl2fastq v2.18. Clontech adapters trimming performed with CLC 9.

tag: genotype/variation

value: ER-alpha -/-. GFP+


title: ER_WT5


title: ER_WT3


title: ER_WT2


title: ER_KO2


title: Fc Treated_3

city: Irvine

first: Hosung

last: Bae

address: 839 Health Sciences Road Sprague Hall, Room 150

institute: UC Irvine

description: To administer indicated reagents intravitreally, 5 µg of reagent (5 mg/ml) was injected into the vitreal cavity using the micro-injector fitted with a glass capillary pipette.

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: RPE-choroidal complex

growth_protocol: 8-week-old male mice were used for generation of CNV. After dilation of the pupils with 5 mg/ml phenylephrine and 5 mg/ml tropicamide eye drops (Santen Pharmaceutical) and instillation of 0.5% proparacaine hydrochloride eye drops (Alcon) for topical anesthesia, laser photocoagulator (Lumenis Inc.) with a slit lamp delivery system was used with a glass coverslip as a contact lens to visualize the retina. Sufficient laser energy (532 nm wavelength, 250 mW power, 100 ms duration, 50 μm spot size) was delivered in 4 locations for each eye (the 3, 6, 9 and 12 o’clock positions of the posterior pole). Only burns that produced a bubble at the time of laser photocoagulation, indicating the rupture of the Bruch membrane, were included in this study. Spots containing hemorrhage at the laser site were excluded from the analysis.

extract_protocol:
collected using laser capture microdissection (PALM MicroBeam, Carl Zeiss)
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

tag: Sex


title: ABTAA_Treated_2

treatment_protocol: To administer indicated reagents intravitreally, 5 µg of reagent (5 mg/ml) was injected into the vitreal cavity using the micro-injector fitted with a glass capillary pipette.


title: Fc Treated_2


title: ABTAA_Treated_1


title: Fc Treated_1


title: VEGF Trap_Treated_2


title: naive colonic eos 2

city: Tel Aviv

first: Hadar

last: Reichman

address: 30 Haim Levanon

department: Microbiology & Immunology

institute: Tel Aviv University

data_processing:
reads mapping: RNA-STAR (v. 2.4.2a) PMCID: PMC3530905
RefSeq assignment: BioWardrobe
Differential gene expression analysis: DESeq (PMID: 20979621)
Genome_build: mm10
Supplementary_files_format_and_content: Data analysis was performed in BioWardrobe Experiment Management System (https://biowardrobe.com/)

source_name: naive colon

growth_protocol: Naive C57/BL6 WT mice

extract_protocol:
RNA extraction: Trizol
samples preparation: CEL-Seq, 3 technical replicates per sample using different primer pools

treatment_protocol: Colons were subjected to enzymatic digestion, then eosinophils were isolated using flow cytometry.

value: colon

value: eosinophil


title: naive colonic eos 1