title: Mouse E15.5 liver mesothelium

value: liver mesothelium


title: HKC-8Normoxia21O2rep2

status: Public on Oct 06 2018

type: SRA

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

description: sample split over two lanes

library_source: transcriptomic

data_processing:
Illumina adaptor sequences were trimmed using Trimgalore (0.3.3)
Reads were aligned to GRCh37 using Tophat 2.0.8b (http://ccb.jhu.edu/software/tophat/index.shtml) and bowtie 1.0.0 (http://bowtie-bio.sourceforge.net/index.shtml) and non-uniquely mapping fragments excluded using SAMtools (0.1.19)
Total read counts for each UCSC defined gene were extracted using HTSeq (0.5.4p3) with ‘intersection-strict’ mode
Significantly regulated genes were identified using DESeq2
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: tab-delimited text files from htseq

molecule: polyA RNA

organism: Homo sapiens

source_name: kidney proximal tubule cell line

growth_protocol: Cell lines were grown in Dulbecco’s modified Eagle’s Medium, 100 U/ml penicillin, 100 μg/ml streptomycin and 10% fetal bovine serum (Sigma Aldrich) and regularly tested for mycoplasma infection.

extract_protocol:
Total RNA was prepared using the mirVana miRNA Isolation Kit (Ambion; Life Technologies Ltd, Paisley, UK) and treated with DNaseI (TURBO DNA‐free, Ambion).
PolyA+ RNA libraries were then prepared using the ScriptSeq v2 RNA‐Seq kit (Epicentre, Madison, WI, USA).
All RNA-seq experiments were performed in triplicate in accordance with ENCODE consortium guidelines

treatment_protocol: Hypoxic incubations were performed for the specified duration and ambient oxygen concentration in an In Vivo2 400 Hypoxia Work Station (Ruskinn Technology).

tag: cell line

tag: tissue

value: kidney proximal tubule cell line

tag: degree of hypoxia

value: normoxia

tag: duration of hypoxia


title: HKC8Hypoxia0.1O2rep2

description: sample split over two lanes

value: 16 hours


title: Mouse E15.5 lung mesothelium

city: Athens

first: Stephen

last: Dalton

state: GA

address: 325 Riverbend Rd

department: Biochemistry & Molecular Biology

country: USA

institute: University of Georgia

data_processing:
Basecalls were performed on the illumina Hiseq 2500 v4 platform
Processed reads were mapped to hg19 using tophat 2.0.13, HIAST2 2.1.0 and Bowtie 2.2.9 using default parameters
Reads over ENSEMBL genes were counted using Subread 1.4.2 with the following parameters featureCounts -p -t exon -g gene_id
Differential gene expression was performed using R studio (v 0.6.1p1)
ChIP-seq peaks were called using MACS2 2.1.1
Genome_build: hg19

molecule: total RNA

organism: Mus musculus

source_name: Mouse Embryo

growth_protocol: WA09 hESCs were maintained in chemically-defined media (CDM) consisting of DMEM/F12 w/o glutamine supplemented with 1x nonessential amino acids, 1x antimycotic/antibiotic, 1x trace elements A, B and C, 2 mM L-alanyl-L-glutamine, 10 mg/ml transferrin (HOLO), human plasma, tissue culture grade, 2% Probumin® bovine serum albumin life science grade, 0.1 mM b-mercaptoethanol, 50 μg/mL ascorbic acid, 10 ng/ml rhHeregulin b-1, 200 ng/ml LONG® R3 IGF-I human, 10 ng/ml rhActivin A and 8 ng/ml rhFGF basic on 1:200 Geltrex coated plates. For splanchnic mesoderm (SplM) induction, hPSCs were seeded at 50,000 cells/cm2 onto Geltrex coated plates into CDM supplemented with 25 ng/ml rhWNT3a and 100 ng/ml rhBMP4 for 4 days with media changed daily. For MesoT induction, CDM is supplemented with 25 ng/ml rhWNT3a, 50 ng/ml rhBMP4 and 4 μM all-trans retinoic acid for an additional 14 – 18 days. To self-renew MesoT (FCS), cells were passaged with collagenase type IV (800 units/ml) followed by 1x TrypLE Select and cultured with 10% fetal bovine serum, Minimal Essential Media, Alpha, 1x antibiotic/antimycotic, 2 mM L-alanyl-L-glutamine and 8 ng/ml FGF2 at an initial seeding density of 50,000 cells/cm2 on plastic then 10,000 cells/cm2 for subsequent passages using 1x TrypLE Select. Media was changed every day. For generation of mesothelium-like cells (MLCs), SplM is passed with 1x TrypLE select then replated at 150,000 cells/cm2 in CDM -FGF2 -Activin A +20 μM SB431542 +4 μM retinoic acid for 18 days total with media changed daily. SplM-derived smooth muscle was left in culture for 16-18 days. MesoT-derived MLCs were generated by replating MesT cells at 150,000 cell/cm2 using MLC media above.

extract_protocol:
Cells were collected using collagenase type IV (MesoT) and/or TrypLE Select (MesoT, MesoT FCS, MLC, smooth muscle). The outer mesothelial layer of mouse organs were digested by exposing intact organs to a dissociation buffer containing 1 mg/ml collagenase IV and 0.05% trypsin. All cells were homogenized with Omega Homogenizer Columns (HCR003). Total RNA were extracted using Trizol and purified with RNeasy mini kit (Qiagen) according to manufacture's protocol.
Samples with an RNA integrity number (RIN) above 0.9 were selected and sent out for standard RNA-Seq application, including poly A enrichment, adaptor ligation, bar-coding, library amplification, etc (Hudsonalpha, AL, US) and Georgia Genomics Facility (University of Georiga, US).
RNA-Seq, 50bp and 75bp pair-end, at least 25 million reads per sample; ChIP-seq, 50bp single-end, 25 millioms reads per sample

treatment_protocol: Wt1creERT2/+ Rosa26tdT/+ embryonic mice were generated by crossing Wt1creERT2/+ mice8 with a knock-in of tamoxifen inducible cre-recombinase in the Wt1 locus (Jackson Laboratory Stock #010912) and Rosa26tdT/tdT (Jackson Laboratory Stock #007914) mice with a loxP-flanked STOP cassette preventing transcription of a CAG promoter-driven red fluorescent protein variant, tdTomato{Madisen:2010fi}. At E12.5, pregnant dams were injected with 300 l of 10 mg/ml tamoxifen/corn oil solution intra-peritoneally at 24 hour intervals for three consecutive days. Embryos were harvested at E15.5 and the heart, lung, liver and gut were carefully isolated using sterile technique. The outer mesothelial layer was digested by exposing intact organs to a dissociation buffer containing 1 mg/ml collagenase IV and 0.05% trypsin and tdTomato+ fractions were sorted.

value: lung mesothelium


title: HKC8Hypoxia0.1O2rep1

description: sample split over two lanes


title: HepG2_16hrs 0.5% O2_HIF-2a (PM9)_Rep 2

library_source: genomic

data_processing:
Illumina adaptor sequences were trimmed using Trimgalore (0.3.3) and reads were aligned to Genome Reference Consortium GRCh37 (hg19) using BWA (0.7.5a-r405). Low quality mapping was removed (MapQ < 15) using SAMtools (0.1.19)
Low quality mapping was removed (MapQ < 15) using SAMtools (0.1.19) and reads mapping to Duke Encode black list regions (http://hgwdev.cse.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeMapability) were excluded using BEDTools (2.17.0)
Duplicate reads were marked for exclusion using Picard tools (1.106) (http://picard.sourceforge.net/).
ChIP-seq peaks were identified using T-PIC (Tree shape Peak Identification for ChIP-Seq) and MACS (Model-based analysis of ChIP-Seq) in control mode
Peaks detected by both peak callers were filtered quantitatively using the total count under the peak to include only peaks that were above the 99.99th percentile of random background regions selected from the ENCODE DNASE II cluster (p-value < 0.0001).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bigwig and bed files of called peaks

molecule: genomic DNA

source_name: hepatocellular cancer cell line

extract_protocol:
Chromatin immunoprecipitation (ChIP) experiments were performed using antibodies directed against HIF-1a (rabbit polyclonal, PM14), HIF-2a (rabbit polyclonal, PM9), or HIF-1b (rabbit polyclonal, Novus Biologicals, NB100-110).
Libraries were prepared from immunoprecipitated chromatin using the Illumina ChIP-Seq kit
All ChIP-seq experiments were performed in duplicate in accordance with ENCODE consortium guidelines

value: hepatocellular cancer cell line

tag: chip antibody

value: HIF2a (PM9)


title: HKC-8Normoxia21O2rep1

description: sample split over two lanes


title: HepG2_16hrs 0.5% O2_HIF-1a (PM14)_Rep 2

value: HIF1a (PM14)


title: HepG2_16hrs 0.5% O2_HIF-2a (PM9)_Rep 1


title: Mouse E15.5 heart mesothelium

value: heart mesothelium


title: HepG2_16hrs 0.5% O2_HIF-1b (Novus NB100-110)_Rep 2

value: HIF1b (Novus NB100-110)


title: HepG2_16hrs 0.5% O2_HIF-1a (PM14)_Rep 1


title: HepG2_16hrs 0.5% O2_HIF-1b (Novus NB100-110)_Rep 1


title: HepG2_16hrs 0.5% O2_Input_Rep 1

value: input chromatin


title: HepG2_16hrs 0.5% O2_Input_Rep 2


title: RCC4_Normoxia_INPUT repeat 2

source_name: kidney cancer cell line

value: kidney cancer cell line


title: RCC4_Normoxia_INPUT repeat 3


title: RCC4_Normoxia_Input_Rep 2


title: RCC4_Normoxia_HIF1b (Novus NB-100-110) repeat 3


title: RCC4_Normoxia_HIF1b (Novus NB-100-110) repeat 2


title: HKC-8Normoxia21O2rep3

description: sample split over two lanes


title: RCC4_Normoxia_HIF-2a (PM9)_Rep 2


title: RCC4_Normoxia_HIF-1a (PM14)_Rep 1


title: RCC4_Normoxia_Input_Rep 1


title: RCC4_Normoxia_HIF-1a (PM14)_Rep 2


title: RCC4_Normoxia_HIF-2a (PM9)_Rep 1


title: S17_1aKO-1bChIP(2)

description: sample split over two lanes


title: S19_2aKO-1bChIP(2)

description: sample split over two lanes


title: S18_1aKO-2aChIP(2)

description: sample split over two lanes


title: S15_WT-1aChIP(2)

description: sample split over two lanes


title: S16_WT-2aChIP(2)

description: sample split over two lanes


title: S14_WT-1bChIP(2)

description: sample split over two lanes


title: NSCinput

city: Utrecht

first: Paul

middle: J

last: Coffer

address: Uppsalalaan 6

department: Regenerative Medicine Center

country: Netherlands

institute: UMC Utrecht

description: input ChIP-seq

data_processing:
ChIP-sequencing reads were mapped with Bowtie 2.1.0 against the reference genome (mm10) using default settings (Langmead and Salzberg, 2012).
Peaks were called with HOMER software using the input as a control (Fold over local region=8, Fold over input=2) (Heinz et al., 2010).
Mapped fragments were extended according to the average fragment size and converted to TDF files, visualized with IGV tools v2.3.36 and represented as coverage normalized tracks (Robinson et al., 2011). SAMtools was used for manipulation of SAM and BAM files; manipulation of BED file format was performed with BEDtools (Li et al., 2009; Quinlan and Hall, 2010).
Motif discovery, peak annotation and generation of histograms were performed using HOMER software. For motif discovery the 200 bp sequence surrounding each peak was examined and motifs with length of 8, 10 and 12 nt were searched. Motifs were identified through de novo motif discovery.
For functional annotation of peaks the software GREAT was used (McLean et al., 2010).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

source_name: Emrbyonic neural stem cells

growth_protocol: NSCs were grown as neurospheres in presence of EGF and bFGF

extract_protocol:
Crosslink was performed with disuccinimidyl glutarate (DSG) (Thermo Scientifis) for 45 minutes followed by 30 minutes incubation with formaldehyde 1%. The reaction was blocked with glycine 100 mM. Shearing was performed using Covaris S2 (Covaris, Woburn, MA) for 8 min at maximum intensity. The sonicated chromatin was incubated O/N at 4°C in presence of 10µg of anti-SOX4 (Diagenode, CS-129-100) coupled to A/G sepharose beads (Santa Cruz Biotechnology).
Kapa Hyper Prep Kit (Kapa Biosystems, Wilmington, MA) was used for End-repair, A-tailing and ligation of sequence adaptors. Samples were amplified by PCR and the libraries were size-selected in the 200-500 bp range.

tag: strain

tag: age

tag: cell type

value: embryonic neural stem cells


title: S12_2aKO-1bChIP(1)

description: sample split over two lanes


title: MLC rep2

source_name: Human Embryonic Stem Cells

tag: passages


title: NSCSox4

value: rabbit anti-SOX4 (Diagenode, CS-129-100)


title: S20_2aKO-1aChIP(2)

description: sample split over two lanes


title: S11_1aKO-2aChIP(1)

description: sample split over two lanes


title: TRP1low_M9

city: Boston

first: Stephanie

last: Dougan

state: MA

address: 1 Jimmy Fund Way

department: Cancer Immunology & Virology

institute: Dana-Farber Cancer Institute

description: TRP1low T cells stimulated with M9 peptide

data_processing:
Reads were mapped to the mm10 transcriptome using Salmon (0.8.2) with default flags.
Transcript-level quantifications were transformed to gene-level quantifications in R using the tximport (1.8.0) package.
Genes that had less than 10 reads in total across all samples were filtered out.
DESeq2 (1.20.0) was used to perform differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: CSV of log2 normalized counts for each gene (one file per sample)

source_name: T cell

extract_protocol:
T cells were isolated from co-culture with B cells by Fluorescence-Activated Cell Sorting, and RNA from those cells was prepared using a Qiagen kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tcr


title: MLC rep1


title: S10_1aKO-1bChIP(1)

description: sample split over two lanes


title: S13_2aKO-1aChIP(1)

description: sample split over two lanes


title: TRP1low_K8

description: TRP1low T cells stimulated with K8 peptide


title: S09_WT-2aChIP(1)

description: sample split over two lanes


title: TRP1high_K8

description: TRP1high T cells stimulated with K8 peptide


title: TRP1high_M9

description: TRP1high T cells stimulated with M9 peptide


title: S08_WT-1aChIP(1)

description: sample split over two lanes


title: LPS+ISRIB_16h_RiboSeq [DY8]

city: Indianapolis

first: Takashi

last: Hato

state: IN

address: 950 W. Walnut St. R2 202

department: Medicine

institute: Indiana University

data_processing:
Library strategy: Ribo-Seq
For the Ion Proton data, the raw data in bam format were first converted to fastq with Picard (2.18.0).
Adapter sequences were removed with cutadapt (1.14+)
Reads after adapter removal were mapped to rRNA/tRNA with bowtie 2 (2.3.2).
Reads passed rRNA/tRNA filter were aligned to mouse referece genome mm10 using STAR-2.5.2b with parameters ajusted to short reads.
Genome_build: mm10

source_name: Kidney

extract_protocol:
Kidneys were snap frozen and pulverized under liquid nitrogen. Cryo-lysis was done using a Precellys tissue homogenizer in a polysome buffer consisting of Illumina TruSeq Polysome Buffer, Riboguard (Lucigen), Triton X-100, DTT, DNAse I, cycloheximide and NP40. Tissue lysates were centrifuged at 20,000 g for 10 min. Equal volumes of supernatant aliquots were made for ribo-seq and RNA-seq workflows.
RNA libraries were prepared for sequencing using standard Illumina protocols and Ion Torrent protocols

tag: timepoint

tag: treatment

value: LPS 5mg/kg + ISRIB

tag: gender

value: male

tag: genotype

value: WT


title: LPS_16h_RiboSeq [DY5]

value: LPS 5mg/kg


title: S07_WT-1bChIP(1)

description: sample split over two lanes

value: kidney proximal tubule cell line


title: LPS+ISRIB_16h_RiboSeq [DY6]


title: LPS+ISRIB_16h_RiboSeq [DY7]


title: LPS_16h_RiboSeq [DY4]


title: LPS_16h_RiboSeq [DY3]


title: S06_2aKOInput(2)

description: sample split over two lanes


title: H3_T-DM1

city: Basel

first: Ulrike

last: Menzel

address: Mattenstrasse 26

department: Department of Biosystems Science and Engineering

country: Switzerland

institute: ETH Zürich

data_processing:
Starting from the raw fastq files (1x81bp), the reads were mapped against the mouse reference genome and simultaneously soft-clipped using the STAR aligner (version 2.4.2a). Standard quality control (Picard, RSeQC, QoRTs) was run to assess the quality of the resulting alignments.
Subsequently, strand-specific (reversely stranded) read counting was performed using featureCount (subread, version 1.5.0). The library size of the 24 samples was of reasonably good quality. To avoid technical artifacts the data were filtered such that genes were removed where the average read depth over all samples was <5 counts.
Transcripts were further mapped to gene symbols and ENTREZID's using the org.Mm.eg.db package version 3.4.0.
Immunoglobulin CDR3 information was extracted using the MiXCR software package for bulk RNA-seq data using the recommended parameter settings (Bolotin, Nat Biotech 2017).
Genome_build: mm10
Supplementary_files_format_and_content: raw_counts.txt: raw read counts
Supplementary_files_format_and_content: Data_norm.txt: log-transformed and normalized abundance measurement (rlog from DESeq2)
Supplementary_files_format_and_content: MiXCR output.xlt: MiXCR clonotype output

source_name: CD45+ bead enriched cells

growth_protocol: 1 million EMT6-hHER2 cells were injected into the mammary fat pad of immunocompetent female Balb/c mice (8-10 weeks old, housed in specific-pathogen free environment).

extract_protocol:
Tumors were harvested 10 days after treatment (d10) and mechanically digested with accutase (PAA), collagenase IV (Worthington), hyaluronidase (Sigma), and deoxy-ribonuclease type IV (Sigma). Single-cell suspensions were then prepared and CD45-positive cells were enriched using the EasySep Mouse PE Positive Selection Kit (STEMCELL Technologies).
RNA of CD45+ cells was extracted and RNA-seq libraries were prepared using the Truseq stranded mRNA Library Prep Kit from Illumina with 200 ng input material. Samples were run on an Illumina NextSeq SR81 using the NextSeq 500/550 High Output v2 kit (75 cycles).

treatment_protocol: Once implanted tumors reached a volume of 80mm3 (d0), mice (n=6) were treated with T-PNU (1 mg/kg), T-DM1 (15 mg/kg) or trastuzumab (20 mg/kg) by intravenous injection; a fourth cohort received no treatment.

value: Balb/c

value: tumor-derived immune cells

tag: agent

value: T-DM1 (15 mg/kg)

value: 10-12 weeks


title: G3_T-DM1


title: S05_1aKOInput(2)

description: sample split over two lanes

value: 16 hours


title: Control_RiboSeq [DY2]

value: control


title: S04_WTInput(2)

description: sample split over two lanes


title: Control_RiboSeq [DY1]


title: F3_T-DM1


title: S03_2aKOInput(1)

description: sample split over two lanes


title: D3_T-DM1


title: E3_T-DM1


title: C3_T-DM1


title: S02_1aKOInput(1)

description: sample split over two lanes


title: S01_WTInput(1)

description: sample split over two lanes


title: B3_Tras

value: trastuzumab (20 mg/kg)


title: A3_Tras


title: HKC8_3_6hr_input

value: 6 hours


title: H2_Tras


title: HKC8_3_6hr_HIF1b_rep1

value: HIF1b (Novus NB100-110)


title: G2_Tras


title: HKC8_3_6hr_HIF2a_rep2

value: HIF2a (PM9)


title: F2_Tras


title: HKC8_3_6hr_HIF2a_rep1


title: E2_Tras


title: HKC8_3_6hr_HIF1a_rep2

value: HIF1a (PM14)


title: D2_T-PNU

value: T-PNU (1 mg/kg)


title: HKC8_3_6hr_HIF1b_rep2


title: HKC8_3_6hr_HIF1a_rep1


title: C2_T-PNU


title: B2_T-PNU


title: HKC8_0.5_48hr_input

value: 48 hours

value: input chromatin


title: HKC8_0.5_48hr_HIF1b_rep2


title: A2_T-PNU

value: WT


title: HKC8_0.5_48hr_HIF1b_rep1


title: H1_T-PNU


title: HKC8_0.5_48hr_HIF2a_rep2


title: 7PP15

type: RNA

city: Edinburgh

first: Filip

middle: J.

last: Wymeersch

address: 5, Little France Drive

department: MRC Centre for Regenerative Medicine, Institute for Stem Cell Research

institute: University of Edinburgh

description: Replicate 2/2

hyb_protocol: Standard Illumina hybridization protocol (performed by the Wellcome Trust Clinical Research Facility, Edinburgh)

scan_protocol: Standard Illumina scanning protocol (performed by the Wellcome Trust Clinical Research Facility, Edinburgh)

data_processing: Data normalisation was performed using the lumi package in the R statistical environment. Pre-processing steps consisted of a background adjustment, followed by Variance-Stabilizing Transformation (VST) and Robust Spline Normalization (RSN). A final quality control step was carried out to detect outliers and probes that were not expressed were filtered from any samples (21712 out of 45281; detection p-value<0.01). ComBat analysis was used to correct for any batch effects.

label: biotin

source_name: Dissected embryonic cells

label_protocol: RNA was labelled and amplified using the Illumina TotalPrep RNA Amplification Kit (Life Technologies) according to the manufacturer's instructions.

extract_protocol: RNA was isolated using the RNeasy Micro Kit (Qiagen) according to manufacturers' instructions.

treatment_protocol: Embryos were dissected in M2 medium (SIGMA) and dissections were performed under a 3h time limit. Pooled dissected regions kept were kept on ice.

tag: Stage

value: Headfold

tag: region

value: Proximal posterior

tag: no. regions/sample

tag: array

value: Array 6

tag: batch

value: Batch 3


title: 7PP10

description: Replicate 1/2


title: genomic DNA from primary adult diaphragm_rep1

type: genomic

description: Sample 37

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using HiScan using standard recommended Illumina scanner setting

data_processing:
Illumina IDATS were read directly into R and analyses were performed using subset-quantile within array normalization (PMID:22703947)
Normalization was performed in R using subset-quantile array normalization (SWAN) (PMID:22703947)

label: Cy5 and Cy3

source_name: Primary adult diaphragm

label_protocol: Standard Illumina Protocol

growth_protocol: WA09 hESCs were maintained in chemically-defined media (CDM) consisting of DMEM/F12 w/o glutamine supplemented with 1x nonessential amino acids, 1x antimycotic/antibiotic, 1x trace elements A, B and C, 2 mM L-alanyl-L-glutamine, 10 mg/ml transferrin (HOLO), human plasma, tissue culture grade, 2% Probumin® bovine serum albumin life science grade, 0.1 mM b-mercaptoethanol, 50 μg/mL ascorbic acid, 10 ng/ml rhHeregulin b-1, 200 ng/ml LONG® R3 IGF-I human, 10 ng/ml rhActivin A and 8 ng/ml rhFGF basic on 1:200 Geltrex coated plates. For splanchnic mesoderm (SplM) induction, hESCs were seeded at 50,000 cells/cm2 onto Geltrex coated plates into CDM supplemented with 25 ng/ml rhWNT3a and 100 ng/ml rhBMP4 for 4 days with media changed daily. For mesothelium (MesoT) induction, CDM is supplemented with 25 ng/ml rhWNT3a, 50 ng/ml rhBMP4 and 4 μM all-trans retinoic acid for an additional 14 days after SplM without replating. WA07-derived Cardiomyocytes monolayers were generated by seeding 100,000 cells/cm2 onto Matrigel- coated plates (Growth Factor Reduced Matrigel, BD Biosciences) in MEF-CM plus 8 ng/ml basic fibroblast growth factor (bFGF) for 6 d, with daily media changes. To induce cardiac differentiation, MEF-CM was replaced with RPMI-B27 medium (Invitrogen) supplemented with 100 ng/ml human recombinant activin A (R&D Systems) for 24 h, followed by 10 ng/ml human recombinant BMP4 (R&D Systems) for 4 days. The medium was then exchanged for RPMI-B27 without supplementary cytokines for 3 days

extract_protocol: WA09 hESCs, SplM and MesoT cell genomic DNA was extracted using the Zymo Research EZ DNA Methyation Kit per manufacturer's instructions. WA07 Cardiomyocytes and all primary tissue sample genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions.

tag: tissue

value: Primary adult diaphragm

tag: sample type

value: tissue

tag: developmental stage

value: 47 year old caucasian female

value: female


title: 7A3

description: Replicate 3/3

tag: strain

tag: age

value: Anterior


title: genomic DNA from primary fetal thymus_rep3

description: Sample 36

source_name: Primary fetal thymus 20 week

value: Primary fetal thymus 20 week

value: fetus


title: genomic DNA from primary fetal intestine_rep3

description: Sample 35

source_name: Primary fetal small intestine 20 week

value: Primary fetal small intestine 20 week


title: 9P2

description: Replicate 2/2

value: 22-25 somites

value: Posterior to CNH


title: genomic DNA from primary adult duodenum_rep1

description: Sample 38

source_name: Primary adult duodenum

value: Primary adult duodenum


title: G1_T-PNU

value: Balb/c

value: tumor-derived immune cells

value: T-PNU (1 mg/kg)

value: 10-12 weeks


title: HKC8_0.5_48hr_HIF2a_rep1

tag: cell line

value: kidney proximal tubule cell line

tag: degree of hypoxia

tag: duration of hypoxia

value: 48 hours

tag: chip antibody

value: HIF2a (PM9)


title: F1_untreated

value: WT


title: genomic DNA from primary fetal intestine_rep1

description: Sample 33

source_name: Primary fetal small intestine 15 week_rep1

value: tissue


title: HKC8_0.5_48hr_HIF1a_rep1

value: HIF1a (PM14)


title: genomic DNA from primary pancreatic islet_rep5

description: Sample 29

source_name: Primary pancreatic islet_rep5

value: Primary pancreatic islet_rep5

value: primary cell

value: 51 year old adult


title: 11P2

description: Replicate 2/2

value: 40-45 somites

value: Array 6

value: Batch 3


title: E1_untreated


title: D1_untreated


title: 12M2

description: Replicate 2/2

value: 50-55 somites

value: Chordoneural Hinge (CNH)

value: Array 5


title: 8L3

description: Replicate 3/3

value: 2-5 somites

value: Caudal Lateral Epiblast (CLE)


title: genomic DNA from primary fetal intestine_rep2

description: Sample 34

source_name: Primary fetal small intestine 15 week_rep2

value: fetus


title: HKC8_0.5_16hr_input

source_name: kidney proximal tubule cell line

value: kidney proximal tubule cell line

value: 16 hours

value: input chromatin


title: 13M2

description: Replicate 2/2

value: 60-63 somites


title: C1_untreated

value: Balb/c

value: tumor-derived immune cells

value: WT

value: 10-12 weeks


title: genomic DNA from primary pancreatic islet_rep3

description: Sample 27

source_name: Primary pancreatic islet_rep3

value: Primary pancreatic islet_rep3

value: primary cell

value: 52 year old adult


title: HKC8_0.5_16hr_HIF1b_rep2

value: HIF1b (Novus NB100-110)


title: 11M3

description: Replicate 3/3

value: 40-45 somites

value: Chordoneural Hinge (CNH)

value: Batch 3


title: genomic DNA from primary pancreatic islet_rep4

description: Sample 28

source_name: Primary pancreatic islet_rep4

value: Primary pancreatic islet_rep4

value: 12 year old child


title: genomic DNA from primary fetal umbilical cord_rep1

description: Sample 30

source_name: Primary fetal umbilical cord 20 week_rep1

value: fetus


title: B1_untreated


title: A1_untreated


title: HKC8_0.5_16hr_HIF1b_rep1

value: kidney proximal tubule cell line

value: 16 hours


title: genomic DNA from primary fetal umbilical cord_rep2

description: Sample 31

source_name: Primary fetal umbilical cord 18 week

value: Primary fetal umbilical cord 18 week


title: genomic DNA from primary fetal umbilical cord_rep3

description: Sample 32

source_name: Primary fetal umbilical cord 20 week_rep2

value: tissue


title: genomic DNA from primary fetal pancreas_rep4

description: Sample 24

source_name: Primary fetal pancreas 20 week_rep3

value: Primary fetal pancreas 20 week_rep3


title: genomic DNA from primary fetal pancreas_rep1

description: Sample 21

source_name: Primary fetal pancreas 18 week

value: Primary fetal pancreas 18 week


title: 11P1

description: Replicate 1/2

value: Posterior to CNH

value: Array 5


title: 8B3

description: Replicate 3/3

value: 2-5 somites

value: Node-Streak Border (NSB)


title: LPS_16h_LTM_RNAseq [DM8 control]

data_processing:
For the Ion Proton data, the raw data in bam format were first converted to fastq with Picard (2.18.0).
Adapter sequences were removed with cutadapt (1.14+)
Reads after adapter removal were mapped to rRNA/tRNA with bowtie 2 (2.3.2).
Reads passed rRNA/tRNA filter were aligned to mouse referece genome mm10 using STAR-2.5.2b with parameters ajusted to short reads.
Genome_build: mm10

source_name: Kidney

tag: timepoint

tag: treatment

value: LPS+LTM+puromycin

tag: gender

value: male

value: WT


title: HKC8_0.5_16hr_HIF2a_rep2

value: HIF2a (PM9)


title: 8L2

description: Replicate 2/3

source_name: Dissected embryonic cells

tag: Stage

value: Caudal Lateral Epiblast (CLE)

value: Batch 3


title: HKC8_0.5_48hr_HIF1a_rep2

value: 48 hours

value: HIF1a (PM14)


title: genomic DNA from primary pancreatic islet_rep2

description: Sample 26

source_name: Primary pancreatic islet_rep2

value: Primary pancreatic islet_rep2

value: primary cell

value: 55 year old adult


title: LPS_16h_LTM_RiboSeq [DM8]

tag: genotype


title: HKC8_0.5_16hr_HIF2a_rep1

value: kidney proximal tubule cell line

value: 16 hours


title: HKC8_0.5_16hr_HIF1a_rep2


title: genomic DNA from primary fetal pancreas_rep3

description: Sample 23

source_name: Primary fetal pancreas 20 week_rep2

value: Primary fetal pancreas 20 week_rep2

value: tissue

value: fetus


title: LPS_4h_LTM_RNAseq [DM7 control]


title: HKC8_0.5_6hr_input

value: 6 hours

value: input chromatin


title: genomic DNA from primary adult brain_rep2

description: Sample 20

source_name: Primary adult brain_rep2

value: Primary adult brain_rep2

value: adult


title: genomic DNA from primary fetal brain_rep8

description: Sample 16

source_name: Primary fetal brain 19 week

value: Primary fetal brain 19 week


title: Control_LTM_RNAseq [DM6 control]

value: LTM+puromycin

value: male

value: WT


title: genomic DNA from primary pancreatic islet_rep1

description: Sample 25

source_name: Primary pancreatic islet_rep1

value: Primary pancreatic islet_rep1

value: 35 year old adult


title: genomic DNA from primary fetal brain_rep12

description: Sample 18

source_name: Primary fetal brain 20 week_rep4

value: Primary fetal brain 20 week_rep4


title: genomic DNA from primary fetal pancreas_rep2

description: Sample 22

source_name: Primary fetal pancreas 20 week_rep1

value: Primary fetal pancreas 20 week_rep1


title: 9P1

description: Replicate 1/2

value: 22-25 somites

tag: region

value: Posterior to CNH

tag: no. regions/sample

value: Array 4

value: Batch 2


title: genomic DNA from primary fetal brain_rep13

description: Sample 19

source_name: Primary fetal brain 20 week_rep5

value: Primary fetal brain 20 week_rep5

value: tissue

value: fetus


title: HKC8_0.5_16hr_HIF1a_rep1

source_name: kidney proximal tubule cell line

value: kidney proximal tubule cell line

value: 16 hours

value: HIF1a (PM14)


title: LPS_4h_LTM_RiboSeq [DM7]

value: LPS+LTM+puromycin


title: genomic DNA from primary fetal brain_rep11

description: Sample 17

source_name: Primary fetal brain 20 week_rep3

value: Primary fetal brain 20 week_rep3


title: HKC8_0.5_6hr_HIF1b_rep2

value: 6 hours

value: HIF1b (Novus NB100-110)


title: LPS_28h_RNAseq [DM5 control]

value: LPS 5mg/kg

value: male

value: WT


title: HKC8_0.5_6hr_HIF1b_rep1


title: 8L1

description: Replicate 1/3

value: 2-5 somites

value: Caudal Lateral Epiblast (CLE)

tag: array

tag: batch


title: 11M1

description: Replicate 1/3

value: 40-45 somites

value: Chordoneural Hinge (CNH)

value: Array 4


title: Control_LTM_RiboSeq [DM6]

value: LTM+puromycin


title: 11M2

description: Replicate 2/3

value: Batch 2


title: LPS_28h_RiboSeq [DM5]


title: HKC8_0.5_6hr_HIF2a_rep1

tag: tissue

value: kidney proximal tubule cell line

value: HIF2a (PM9)


title: 12M1

description: Replicate 1/2

value: 50-55 somites


title: LPS_16h_RNAseq [DM4 control]


title: 13M1

description: Replicate 1/2

value: 60-63 somites


title: 9M2

description: Replicate 2/2

value: 22-25 somites

value: Array 3


title: HKC8_0.5_6hr_HIF1a_rep2

value: 6 hours

value: HIF1a (PM14)


title: genomic DNA from primary fetal brain_rep6

description: Sample 14

source_name: Primary fetal brain 18 week_rep2

value: Primary fetal brain 18 week_rep2

tag: sample type

value: tissue

tag: developmental stage

value: fetus


title: HKC8_0.5_6hr_HIF2a_rep2


title: LPS_16h_RiboSeq [DM4]

tag: strain

value: LPS 5mg/kg

value: male

value: WT


title: genomic DNA from primary fetal brain_rep7

description: Sample 15

source_name: Primary fetal brain 18 week_rep3

value: Primary fetal brain 18 week_rep3


title: LPS_4h_RNAseq [DM3 control]


title: HKC8_0.5_6hr_HIF1a_rep1

tag: cell line


title: genomic DNA from primary fetal brain_rep2

description: Sample 12

source_name: Primary fetal brain 14 week

value: Primary fetal brain 14 week


title: LPS_4h_RiboSeq [DM3]


title: LPS_1h_RNAseq [DM2 control]


title: 9M1

description: Replicate 1/2

tag: age

value: Chordoneural Hinge (CNH)

value: Batch 2


title: genomic DNA from primary human aortic smooth muscle

description: Sample 10

source_name: Primary smooth muscle aortic

value: Primary smooth muscle aortic

value: primary cell


title: InR_RU486_F3

city: Auburn

first: Rita

middle: M.

last: Graze

state: AL

address: 101 ROUSE LIFE SCIENCES BLDG, AUBURN UNIVERSITY

department: Biological Sciences

institute: Auburn University

description:
F_RU486_3
PolyA RNA
processed data file: processed_normalized_counts.csv

data_processing:
Basecalls performed using CASAVA version 1.8.4.
Duplicate reads were removed prior to mapping using a custom python script.
Distinct reads (no duplicate reads) were aligned to the D. melanogaster FlyBase Release 5 genome (v5.51) using bwa v0.7.15 (bwa mem -M).
Reads mapping uniquely were retained for read counts using a custom python script.
Using FlyBase annotations (v5.51), overlapping exons regardless of strand were combined into the maximum exonic region.
Expression was estimated for each exonic region as the natural log of the Reads Per Kilobase Per Million Mapped Reads (ln-RPKM).
Exonic Regions with low coverage (average per nucleotide coverage less than five in more than half of the replicates, for all four sample types) and regions corresponding to multiple gene annotations were not considered in the analysis.
Genome_build: FlyBase 5.51
Supplementary_files_format_and_content: processed_normalized_counts.csv: Comma-separated text file with the following columns: exonic region id, gene symbol (FlyBase v5.51), FlyBase gene id (FBgn), chromosome, start position, end position, sample id, number of mapped reads, number of reads in the exonic region, average per nucleotide coverage (APN), RPKM, ln-RPKM.

organism: Drosophila melanogaster

source_name: Head tissues

growth_protocol: Flies were raised on standard cornmeal food medium (33 L H2O, 237g Agar, 825g dried deactivated yeast, 1560 g cornmeal, 3300 g dextrose, 52.5 g 9 Tegosept in 270 ml 95% ethanol and 60 ml Propionic acid). The incubator conditions are 25˚C on a 12 hour light: 12 hour dark cycle.

extract_protocol:
Adult heads were separated from the body by mechanical tapping in the cryovial and then separated while frozen on a piece of plexiglass cooled on dry ice. Frozen heads were immediately transferred to Trizol reagent. Total RNA was extracted using the Trizol reagent protocol (Thermo Fisher) and was DNase treated with Turbo DNase and purified  (Zymo).
RNA-seq libraries were generated using 2ug total RNA. The NEBNext Ultra RNA Library Prep Kit for Illumina, with the polyA purification module (New England Biolabs Inc. E7530L), was used for Illumina library generation.

treatment_protocol: Virgin male and female F1 flies are collected soon after eclosion and aged for 3 days. On day four the flies are transferred to food medium with either 200 uM RU486 (80% ethanol is the solvent) or with the same volume of 80% ethanol for four days. Flies are then snap frozen in liquid nitrogen and stored at -80℃.

tag: genotype/variation

value: Head

value: RU486 Drug (InRDN expressing)

tag: Sex

value: Female

value: Adult 7d


title: InR_RU486_F4

description:
F_RU486_4
PolyA RNA
processed data file: processed_normalized_counts.csv


title: genomic DNA from primary fetal brain_rep1

description: Sample 11

source_name: Primary fetal brain 10 week

value: Primary fetal brain 10 week


title: InR_RU486_F2

description:
F_RU486_2
PolyA RNA
processed data file: processed_normalized_counts.csv


title: genomic DNA from primary fetal brain_rep4

description: Sample 13

source_name: Primary fetal brain 17 week

value: Primary fetal brain 17 week


title: LPS_1h_RiboSeq [DM2]

source_name: Kidney

tag: timepoint


title: 7A1

description: Replicate 1/3

source_name: Dissected embryonic cells

value: Headfold

value: Anterior

value: Array 3


title: 7P2

description: Replicate 2/2

value: Posterior


title: 7P1

description: Replicate 1/2


title: MCNH-2

description: Replicate 2/2

value: 32-35 somites

value: Array 2

value: Batch 1


title: genomic DNA from WA07 Cardiomyocyte_rep2

description: Sample 9

source_name: Human Embryonic Stem Cells

value: Human Embryonic Stem Cells

value: WA07 embryonic stem cell

value: Cardiomyocyte

value: female


title: 7A2

description: Replicate 2/3

value: Batch 2


title: Delta Hfq Replicate 3 sRNA library

city: Austin

first: Mia

last: Mihailovic

state: Texas

address: 200 E Dean Keeton St

department: McKetta Dept of Chem Eng

institute: UT Austin

data_processing:
trimming adaptors with cutadapt (1.14)
alignment to reference genome with bwa (0.7.16a) mem option (reference genome indexed using bwtsw option)
for sRNA library data ONLY, excluding multimapped (XA) or chimeric (SA) tags using 'grep'
converting .sam file to .bam and sorting by unique ID using samtools (1.1) view
converting .bam files to .bed using bedtools (2.26.0) bamtobed
filtering out R1 reads that do not contain at least 7 nucleotides (from the 5' end) of the asRNA sequence using 'grep'
separating R1 and R2 reads within each sample using 'awk'
sorting by unique ID and joining R1 and R2 files by unique ID using linux sort and join commands
Genome_build: Genome for gI intron INTERFACE = groupI_O-INTERFACE_genome.fa. Genome for sRNA INTERFACE=sRNA_INTERFACE_genome.fa. Genomes are "built" to consist of one "gene" for each asRNA in the library; in order of: (i) upstream promoter sequence (variable), (ii)asRNA sequence, (iii)downstream assay components (RSE, linker, RBS, truncated GFP = 'TACCATTCACCTCTTGGATTTGGGTATTAAAGAGGAGAAAGGTACCATGAATATCTTACATATATGTGTGACCTCAAAATGGTTCAATATTGACAACAAAATTGTCGATCACCGCCCTTGATTTGCCCTTCTGTAGCCATCACCAATGAGTCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCCACACAATCTGCCCTTTCGAAAGATCCCAACGAAAAGAGAGACCACATGGTCCTTCTTGAGTTTGTAACAGCTGCTGGGATTACACATGGCATGGATGATCTCTACAAATAA')
Supplementary_files_format_and_content: Processed data (.bed) files consist of lines corresponding to a unique read (column 1), the synthetic gene to which it maps (column 2 & 8), the starts and ends of each R1 (columns 3,4 for the sRNA library and columns 9,10 for the gI intron library, respectively) and R2 (columns 9,10 for the sRNA library and columns 3,4 for the gI intron library, respectively), as well as read quality.

organism: Escherichia coli

growth_protocol: 20 mL LB cultures, induced with arabinose (0.8% w/v final conc) and aTc (100 ng/mL final conc) for gI intron samples and arabinose only (0.8% w/v final conc) for sRNA samples in early exponential growth phase, sampled in exponential growth phase (OD~0.7)

extract_protocol:
RNA was harvested using Trizol reagent.NEBNext Multiplex Small RNA Library Prep set for Illumina (NEB E7330) was used with 0.5-1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols, with some exceptions: importantly, NO FRAGMENTATION was performed to preserve the ability to assign transcript length to each unique asRNA. Sequencing facility additionally performed a Pippin Prep (Sage Science) to select for transcript sizes between 120 and 310 nucleotides.

value: delta Hfq (knockout)


title: Delta Hfq Replicate 2 sRNA library


title: Control_RNAseq [DM1 control]

tag: treatment

value: control

value: male

value: WT


title: InR_EtOH_F3

description:
F_EtOH_3
PolyA RNA
processed data file: processed_normalized_counts.csv

value: Head

value: EtOH Control

value: Female

value: Adult 7d


title: Control_RiboSeq [DM1]

tag: gender


title: Delta Hfq  Replicate 1 sRNA library


title: PCNH-2

description: Replicate 2/2

tag: Stage

value: Posterior to CNH


title: Replicate 2 sRNA library

tag: genotype

value: wild type


title: genomic DNA from WA09 Mesothelium (MesoT)_rep2

description: Sample 6

value: WA09 embryonic stem cell

value: Mesothelium


title: Replicate 3 sRNA library


title: InR_EtOH_F1

description:
F_EtOH_1
PolyA RNA
processed data file: processed_normalized_counts.csv


title: InR_RU486_M4

description:
M_RU486_4
PolyA RNA
processed data file: processed_normalized_counts.csv

value: RU486 Drug (InRDN expressing)

value: Male


title: genomic DNA from WA09 Mesothelium (MesoT)_rep3

description: Sample 7

value: Human Embryonic Stem Cells


title: RN-2

description: Replicate 2/2

value: 2-5 somites

tag: region

value: Rostral node (RN)

value: Array 2

value: Batch 1


title: Bord-2

description: Replicate 2/3

value: Node-Streak Border (NSB)

tag: no. regions/sample


title: InR_RU486_M3

description:
M_RU486_3
PolyA RNA
processed data file: processed_normalized_counts.csv


title: genomic DNA from WA07 Cardiomyocyte_rep1

description: Sample 8

value: WA07 embryonic stem cell

value: Cardiomyocyte

value: female


title: Replicate 1 sRNA library


title: InR_RU486_M2

description:
M_RU486_2
PolyA RNA
processed data file: processed_normalized_counts.csv

value: Head


title: St5-2

description: Replicate 2/2

value: Posterior streak (St5)

tag: array


title: genomic DNA from WA09 Mesothelium (MesoT)_rep1

description: Sample 5


title: Replicate 3 gI intron induced


title: InR_RU486_M1

description:
M_RU486_1
PolyA RNA
processed data file: processed_normalized_counts.csv

value: Adult 7d


title: genomic DNA from WA09 Splanchnic.Mesoderm_rep2

description: Sample 4


title: Replicate 3 gI intron uninduced

value: wild type


title: Replicate 2 gI intron induced


title: InR_EtOH_M4

description:
M_EtOH_4
PolyA RNA
processed data file: processed_normalized_counts.csv

value: EtOH Control


title: MCNH-1

description: Replicate 1/2

value: 32-35 somites

value: Chordoneural Hinge (CNH)

value: Array 1

tag: batch


title: St1-2

description: Replicate 2/2

value: Anterior streak (St1)


title: Replicate 2 gI intron uninduced


title: Replicate 1 gI intron induced


title: InR_EtOH_M3

description:
M_EtOH_3
PolyA RNA
processed data file: processed_normalized_counts.csv

tag: tissue

value: Male


title: InR_EtOH_M1

description:
M_EtOH_1
PolyA RNA
processed data file: processed_normalized_counts.csv


title: Replicate 1 gI intron uninduced


title: PCNH-1

description: Replicate 1/2

value: Posterior to CNH


title: genomic DNA from WA09 hESC_rep1

description: Sample 1

value: Human Embryonic Stem Cells

tag: sample type

value: WA09 embryonic stem cell

value: embryonic stem cell


title: genomic DNA from WA09 Splanchnic.Mesoderm_rep1

description: Sample 3

tag: developmental stage


title: genomic DNA from WA09 hESC_rep2

description: Sample 2


title: InR_EtOH_M2

description:
M_EtOH_2
PolyA RNA
processed data file: processed_normalized_counts.csv


title: RN-1

description: Replicate 1/2

tag: strain

value: 2-5 somites

value: Rostral node (RN)

value: Batch 1


title: Lcell_replicate_T3Dpos_Dropseq_0

status: Public on Oct 05 2018

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: 301 Weill Hall

department: Meinig School of Biomedical Engineering

institute: Cornell University

description: Capture of host messenger RNA only.

data_processing:
Paired-end fastq files were analylzed for quality (adpater dimers and k-mer representation).
Reads were de-duplicated using UMI (from read 1) and sequences were trimmed.
Reads were tagged with cell barcodes and aligned to host transcriptome usign STAR aligner. Exonic alignments were extracted.
Aligned reads underwent quality control for possible bead synthesis errors.
Digital expression was calculated across cells passing filter.
Genome_build: mm10 or hg19
Supplementary_files_format_and_content: tab-delimited text files indicating number of counted transcripts for detected genes in each cell

source_name: 2500 Murine L929 cells

growth_protocol: L929 cells were infected with recominant type 3 Dearing orthoreovirus at an MOI of 10 and incubated for 15 hours. PBMCs were purchased from Zen-Bio (SER-PBMC-F) and thawed when ready to perform experiment.

extract_protocol: The following steps are identical to those performed using standard Drop-seq protocol (Macasko, 2015). Briefly, droplets containing beads and lysed cells were broken and washed. Complementary DNA was created using Maxima Reverse Transcriptase (Thermo Fisher) and a transcript switch oligomer. cDNA was amplified using 15 cycles of PCR. Amplified cDNA libraried were tagmented and amplified using Nextera. Illumina sequencing was performed on the libaries using 20x130 paired-end sequencing.

treatment_protocol:
Cells were washed three times with PBS + 0.01% BSA. In the case of the L929 cells, 300,000 cells were resuspended in 1 mL of PBS-BSA. In the case of PBMCs, 150,000 cells were resuspended in 1 mL of PBS-BSA.
Cells were injected into a microfluidic device and coencapsulated with either Drop-seq or DART-seq beads which were resuspended in a lysis buffer.

tag: cell type

value: Lcell T3Dpos

tag: capture

value: Drop-seq bead


title: Lcell_replicate_T3Dneg_Dropseq_0

description: Capture of host messenger RNA only.

value: Lcell T3Dneg


title: Lcell_replicate_T3Dpos_DARTseq_0

description: Capture of host messenger RNA and viral messenger and positive-stranded genomic RNA. Each of ten reovirus genomic segments was targeted at one locus.

value: DART-seq bead


title: Lcell_replicate_T3Dneg_DARTseq_0

description: Capture of host messenger RNA in an uninfected cell. This sample serves as a negative control, as all ten segments of  the viral RNA genome were targeted at one loci each, but no virus was present in the cells.


title: Bord-1

description: Replicate 1/3

tag: age

value: Node-Streak Border (NSB)


title: NanogKD_50cells_NoAb_rep2

city: Pittsburgh

first: Sarah

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

data_processing:
Library strategy: CUT&RUN
Barcode adapter sequences removed
Reads mapped to mm10 genome using Bowtie2, and allowing 1 mismatch
Picard used to remove duplicates
Low quality reads were removed (MAPQ <10)
Reads divded into size classes: 1-120 or 150-500
Aligned reads were processed in HOMER by using the “annotatePeaks” command to make 20 bp bins over regions of interest and sum the reads within each window.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

source_name: murine embryonic stem cells

growth_protocol: E14 mouse embryonic stem cells (ESCs) were cultured on gelatin-coated dishes without feeder cells in high-glucose DMEM medium (Sigma) containing 10% serum (Corning) and LIF at 37°C with 5% CO2.

extract_protocol:
The CUT&RUN protocol was modified from Skene and Henikoff (eLife 2017), who made their modified protocol available online (http://blocks.fhcrc.org/steveh/papers/CUT&RUN_protocol.htm). Mouse ES cells were counted using a TC-10 cell counter (Biorad) and diluted manually to respective cell amounts. Cells were pelleted at 600g for 3 minutes at 4°C, the supernatant was discard and cells were washed with 1mL cold PBS. Cells were pelleted at 600g for 3 minutes at 4°C, the supernatant was discard and cells were resuspended in 1mL cold nuclear extraction (NE) buffer (20mM HEPES-KOH, pH 7.9, 10mM KCl, 0.5mM Spermidine, 0.1% TritonX-100, 20% glycerol, freshly added protease inhibitors). Cells were pelleted at 600g for 3min at 4°C, the supernatant was discard and cells were resuspended in 600uL NE buffer. During the cell washes, Concanavalin A beads (Polysciences) were prepared. For 500,000 cells 200uL bead slurry were used, for 50,000 cells 150uL bead slurry were used, for 5,000 cells, 100uL bead slurry were used, for 500 cells and 50 cells 50uL bead slurry were used, and for 10 cells 20uL bead slurry were used. Beads were withdrawn and transferred to a microfuge tube containing 3X volume cold Binding buffer (20mM HEPES-KOH, pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2). Beads were washed twice in 1mL cold Binding buffer and resuspended in 300uL binding buffer. Extracted nuclei were added to beads with gentle vortexing and incubated for 10 minutes at room temperature. After nuclei binding, cytosolic fraction was discarded and beads were blocked with 1mL cold Blocking buffer (20mM HEPES, pH 7.5, 150mM NaCl, 0.5mM Spermidine, 0.1% BSA, 2mM EDTA, freshly added protease inhibitors) which was added with repeated gentle pipetting and incubated for 5 minutes at room temperature. Supernatant was discarded and nuclei/beads were washed in 1mL cold Wash Buffer (20mM HEPES, pH 7.5, 150mM NaCl, 0.5mM Spermidine, 0.1% BSA, freshly added protease inhibitors) and resuspended in 250uL cold Wash Buffer. Primary antibody was added with gentle vortexing of the nuclei in 250uL cold Wash Buffer to a final concentration of 1:100. Samples were incubated with rotation at 4°C for 2 hours. Supernatant was discarded and samples were washed twice in 1mL cold Wash Buffer. Supernatant was discarded and samples were resuspended in 250uL cold Wash Buffer. ProteinA-MNase (kindly provided by Steven Henikoff) was added with gentle vortexing of the nuclei in 250uL cold Wash Buffer to a final concentration of 1:400. Samples were incubated with rotation at 4°C for 1 hour. Supernatant was discarded and samples were washed twice in 1mL cold Wash Buffer. Supernatant was discarded and samples were resuspended in 150uL cold Wash Buffer. Samples were equilibrated to 0°C on ice water for 5-10 minutes. 3uL 100mM CalC2 was added during gentle vortexing, samples were flicked quickly to mix and returned to 0C on ice water. After 5 minutes of digestion, reactions were stopped with addition of 150uL 2XSTOP buffer (200mM NaCl, 20mM EDTA, 4mM EGTA, 50ug/mL RNaseA, 40ug/mL glycogen, 10pg/mL yeast spike-in DNA). Samples were incubated at 37°C for 20 minutes to activate RNase and release fragments. Samples were centrifuged at 16,000g for 5minutes and supernatants were transferred to a new microfuge tube while pellets and beads were discarded. Following addition of 3uL 10% SDS and 2.5uL 20m/gmL ProteinaseK, samples were mixed by inversion and incubated at 70°C for 10 minutes. DNA was cleaned using PCI followed by chloroform extraction, and precipitated with glycogen and ethanol. DNA was pelleted with a high speed spin at 4C, washed, air dried for ~5 minutes and resuspended in 36.5uL 0.1XTE.
Libraries were prepared using a modification of the Henikoff available protocol. DNA end-repair, phosphorylation, and A-tailing was performed in a single reaction, as follows. T4 DNA Polymerase (NEB) was diluted 1:20. 5uL 10X T4 DNA ligase buffer (NEB), 2.5uL 10mM dNTPs, 1.25uL 10mM ATP, 3.13uL 40% PEG4000, 0.63uL T4 PNK (NEB), 0.5uL diluted T4 DNA Polymerase, and 0.5uL Taq polymerase (homemade) was added to 36.5uL of CUT&RUN enriched DNA. Samples were incubated at 12°C for 15 minutes, 37°C for 15 minutes, followed by 72°C for 20 minutes in a thermocycler. Samples were put on ice immediately and the following adapter ligation reaction was performed. PE inline Illumina adapters were used for these experiments. 55uL of 1X Quick ligase buffer (NEB), 5uL Quick ligase (NEB), and 5uL of 1.5uM adapter mix was added to 50uL of A-tailed DNA and samples were incubated at 20°C for 15 minutes in a thermocycler. Immediately following adapter ligation, samples were cleaned using Ampure XP beads (Beckman Coulter). Beads were warmed to room temperature during adapter ligation and 38uL well-mixed beads were added to libraries. Samples were mixed thoroughly and incubated for 15 minutes at room temperature. Following solution clearing on a magnetic rack, supernatants were discarded and beads were washed two times with 200uL 80% EtOH. Samples were briefly spun, residual liquid was discarded, and beads were allowed to air dry for ~5 minutes. DNA was eluted from beads by resuspending beads in 30uL 10mM Tris-HCL pH 8.0 and incubation at room temperature for 2 minutes. Following solution clearing on a magnetic rack, 27.5uL DNA was transferred to a 0.2mL PCR tube and library enrichment was performed. Libraries were enriched for 14-19 cycles of PCR, with the following conditions. 10uL 5X KAPA buffer, 1.5uL 10mM dNTPs, 5uL 20uM PE PCR 1.0, 20uM PE PCR 2.0, 1uL KAPA hotstart HiFi polymerase (KAPA) was added to 27.5uL of library DNA. The following PCR program was used to enrich the samples: 98°C 45 seconds, 98°C 15 seconds, 60°C 10 seconds, steps two and three were repeated specified number of times, 72°C 1 minute. Following library enrichment, samples were loaded on an agarose gel and DNA corresponding to 150-700 bases was extracted using the Qiagen extraction buffer and Econospin columns. Size distribution of libraries was determined using a Fragment analyzer, and libraries were sequenced on an Illumina NextSeq 500.

treatment_protocol: Unfixed nuclei were bound to ConcanavalinA beads, washed, followed by successive addition of primary antibodie followed by proteinA-Mnase. Cleavage of Mnase was initiated by Ca** addition and stopped by chelation. Fragments were released and deep sequencing libraries were prepared.

value: E14 mouse embryonic stem cells (ESCs)

value: One 10cm dish was transiently transfected with esiRNAs and lipofectamine 2000 and cultured 48 hours post transfection

tag: primary antibody, vendor, catalog number and batch

tag: secondary antibody

value: proteinA-MNase generated by Fazzio lab, used at 1:200


title: NanogKD_50cells_Nanog_rep2

tag: treatment

value: anti-Nanog, Active Motif, Cat# 61419, Lot 04613001, used at 1:100 final


title: NanogKD_50cells_Nanog_rep1


title: Lcell_replicate_T3Dpos_DARTseq_1

description: Capture of host messenger RNA and viral messenger and positive-stranded genomic RNA. Reovirus genomic segment S2 (encoding mRNA for protein sigma-2) was targeted at seven loci.


title: Brg1KD_50cells_Nanog_rep1


title: St5-1

description: Replicate 1/2

value: Posterior streak (St5)

value: Array 1


title: Brg1KD_50cells_NoAb_rep2


title: Brg1KD_50cells_NoAb_rep1


title: GFPKD_50cells_Nanog_rep2


title: GFPKD_50cells_Nanog_rep1


title: GFPKD_50cells_NoAb_rep2


title: GFPKD_50cells_NoAb_rep1


title: Brg1KD_50cells_Nanog_rep2


title: St1-1

description: Replicate 1/2

value: Anterior streak (St1)


title: NanogKD_50cells_NoAb_rep1


title: NanogKD_50,000cells_Nanog_rep1


title: Brg1KD_50,000cells_Nanog_rep2


title: NanogKD_50,000cells_NoAb_rep2


title: Brg1KD_50,000cells_Nanog_rep1


title: NanogKD_50,000cells_NoAb_rep1


title: Brg1KD_50,000cells_NoAb_rep1


title: Brg1KD_50,000cells_NoAb_rep2


title: GFPKD_50,000cells_Nanog_rep1


title: GFPKD_50,000cells_Nanog_rep2


title: Sox2_1cell_rep24

value: anti-Sox2, Active Motif, Cat# 39843, Lot 19710001, used at 1:100 final


title: GFPKD_50,000cells_NoAb_rep2


title: GFPKD_50,000cells_NoAb_rep1


title: Sox2_1cell_rep21


title: Sox2_1cell_rep22


title: NanogKD_50,000cells_Nanog_rep2


title: Sox2_1cell_rep26


title: Sox2_1cell_rep23


title: InR_EtOH_F4

description:
F_EtOH_4
PolyA RNA
processed data file: processed_normalized_counts.csv

tag: genotype/variation

value: Head

value: EtOH Control

tag: Sex

value: Female

value: Adult 7d


title: Sox2_1cell_rep25


title: Sox2_1cell_rep20


title: Sox2_1cell_rep17


title: Sox2_1cell_rep18


title: Sox2_1cell_rep19


title: Sox2_1cell_rep16


title: Sox2_1cell_rep14


title: Sox2_1cell_rep15


title: Sox2_1cell_rep11


title: Sox2_1cell_rep12


title: Sox2_1cell_rep9


title: Sox2_1cell_rep10


title: Sox2_1cell_rep7


title: Sox2_1cell_rep8


title: Sox2_1cell_rep6


title: Sox2_1cell_rep4


title: Nanog_1cell_rep25


title: Nanog_1cell_rep23


title: Nanog_1cell_rep26


title: Sox2_1cell_rep3


title: Nanog_1cell_rep22


title: Nanog_1cell_rep20


title: Nanog_1cell_rep21


title: Nanog_1cell_rep17


title: Nanog_1cell_rep19


title: Nanog_1cell_rep24


title: Nanog_1cell_rep16


title: Sox2_1cell_rep13


title: Nanog_1cell_rep15


title: Nanog_1cell_rep14


title: Nanog_1cell_rep9


title: Nanog_1cell_rep10


title: Nanog_1cell_rep11


title: Nanog_1cell_rep8


title: Sox2_1cell_rep5


title: Nanog_1cell_rep18


title: Nanog_1cell_rep4


title: Nanog_1cell_rep7


title: Nanog_1cell_rep5


title: Nanog_1cell_rep6


title: NoAb_1cell_forN&S_rep7


title: NoAb_1cell_forN&S_rep10


title: NoAb_1cell_forN&S_rep9


title: Nanog_1cell_rep3


title: NoAb_1cell_forN&S_rep11


title: NoAb_1cell_forN&S_rep12


title: NoAb_1cell_forN&S_rep8


title: CTCF_1cell_rep119

value: anti-CTCF, millipore, Cat# 07-729, lot 2971000, used at 1:100 final


title: Nanog_1cell_rep13


title: NoAb_1cell_forN&S_rep6


title: Nanog_1cell_rep12


title: CTCF_1cell_rep117


title: CTCF_1cell_rep118


title: CTCF_1cell_rep120


title: NoAb_1cell_forN&S_rep5


title: CTCF_1cell_rep116


title: NoAb_1cell_forN&S_rep4


title: NoAb_1cell_forN&S_rep1


title: NoAb_1cell_forN&S_rep3


title: CTCF_1cell_rep113


title: CTCF_1cell_rep111


title: CTCF_1cell_rep115


title: NoAb_1cell_forN&S_rep2


title: CTCF_1cell_rep108


title: CTCF_1cell_rep114


title: CTCF_1cell_rep112


title: CTCF_1cell_rep109


title: CTCF_1cell_rep101


title: CTCF_1cell_rep98


title: CTCF_1cell_rep106


title: CTCF_1cell_rep103


title: CTCF_1cell_rep96


title: CTCF_1cell_rep104


title: CTCF_1cell_rep105


title: CTCF_1cell_rep110


title: CTCF_1cell_rep102


title: CTCF_1cell_rep107


title: CTCF_1cell_rep86


title: CTCF_1cell_rep100


title: CTCF_1cell_rep87


title: CTCF_1cell_rep84


title: CTCF_1cell_rep99


title: CTCF_1cell_rep97


title: CTCF_1cell_rep81


title: CTCF_1cell_rep78


title: CTCF_1cell_rep77


title: CTCF_1cell_rep94


title: CTCF_1cell_rep75


title: CTCF_1cell_rep93


title: CTCF_1cell_rep95


title: CTCF_1cell_rep91


title: CTCF_1cell_rep89


title: CTCF_1cell_rep74


title: CTCF_1cell_rep88


title: CTCF_1cell_rep85


title: CTCF_1cell_rep83


title: CTCF_1cell_rep82


title: CTCF_1cell_rep90


title: CTCF_1cell_rep66


title: CTCF_1cell_rep65


title: CTCF_1cell_rep69


title: CTCF_1cell_rep80


title: CTCF_1cell_rep79


title: CTCF_1cell_rep73


title: CTCF_1cell_rep76


title: CTCF_1cell_rep72


title: CTCF_1cell_rep92


title: CTCF_1cell_rep71


title: CTCF_1cell_rep70


title: CTCF_1cell_rep68


title: CTCF_1cell_rep64


title: CTCF_1cell_rep67


title: CTCF_1cell_rep48


title: CTCF_1cell_rep45


title: CTCF_1cell_rep60


title: CTCF_1cell_rep58


title: CTCF_1cell_rep54


title: CTCF_1cell_rep56


title: CTCF_1cell_rep53


title: CTCF_1cell_rep62


title: CTCF_1cell_rep50


title: CTCF_1cell_rep52


title: CTCF_1cell_rep49


title: CTCF_1cell_rep55


title: CTCF_1cell_rep46


title: CTCF_1cell_rep47


title: CTCF_1cell_rep51


title: CTCF_1cell_rep61


title: CTCF_1cell_rep41


title: CTCF_1cell_rep59


title: CTCF_1cell_rep63


title: CTCF_1cell_rep57


title: CTCF_1cell_rep44


title: CTCF_1cell_rep42


title: CTCF_1cell_rep43


title: CTCF_1cell_rep35


title: CTCF_1cell_rep38


title: CTCF_1cell_rep39


title: CTCF_1cell_rep34


title: CTCF_1cell_rep40


title: CTCF_1cell_rep37


title: CTCF_1cell_rep36


title: CTCF_1cell_rep33


title: CTCF_1cell_rep25


title: CTCF_1cell_rep28


title: CTCF_1cell_rep32


title: CTCF_1cell_rep27


title: CTCF_1cell_rep31


title: CTCF_1cell_rep26


title: CTCF_1cell_rep29


title: CTCF_1cell_rep30


title: CTCF_1cell_rep24


title: CTCF_1cell_rep22


title: CTCF_1cell_rep19


title: CTCF_1cell_rep23


title: CTCF_1cell_rep21


title: CTCF_1cell_rep20


title: CTCF_1cell_rep16


title: CTCF_1cell_rep14


title: CTCF_1cell_rep15


title: CTCF_1cell_rep17


title: NoAb_1cell_rep44


title: CTCF_1cell_rep13


title: NoAb_1cell_rep40


title: NoAb_1cell_rep46


title: NoAb_1cell_rep41


title: NoAb_1cell_rep47


title: CTCF_1cell_rep18


title: NoAb_1cell_rep45


title: NoAb_1cell_rep32


title: NoAb_1cell_rep43


title: NoAb_1cell_rep31


title: NoAb_1cell_rep29


title: NoAb_1cell_rep28


title: NoAb_1cell_rep39


title: NoAb_1cell_rep30


title: NoAb_1cell_rep37


title: NoAb_1cell_rep22


title: NoAb_1cell_rep20


title: NoAb_1cell_rep36


title: NoAb_1cell_rep21


title: NoAb_1cell_rep35


title: NoAb_1cell_rep34


title: NoAb_1cell_rep33


title: NoAb_1cell_rep18


title: NoAb_1cell_rep27


title: NoAb_1cell_rep25


title: NoAb_1cell_rep24


title: NoAb_1cell_rep23


title: NoAb_1cell_rep26


title: NoAb_1cell_rep42


title: IgG_50cells_rep2

value: anti-Brg1, Bethyl, Cat# A300-813A, Lot 3, used at 1:100 final


title: NoAb_forIgG_50cells_rep2


title: IgG_50000cells


title: Suz12_50cells


title: NoAb_1cell_rep19


title: H3K27me3_50cells_rep2

value: anti-H3K27me3, Millipore, Cat# 07449, Lot JBC1873477, used at 1:100 final


title: Brg1_50cells_rep2


title: NoAb_1cell_rep15


title: NoAb_forIgG_50cells


title: NoAb_1cell_rep38


title: NoAb_1cell_rep13


title: Sox2_50000cells_rep2


title: NoAb_1cell_rep16


title: Fig2_NoAb_50cells_rep2


title: NoAb_1cell_rep17


title: IgG_50cells


title: IgG_50000cells_rep2


title: H3K4me3_10cells_rep2

value: anti-H3K4me3, millipore, Cat# 05-745R, lot 2848536, used at 1:100 final


title: NoAb_1cell_rep12


title: Suz12_50000cells_rep2


title: NoAb_forIgG_50000cells_rep2


title: Oct4_50cells_rep2

value: anti-Oct4, Invitrogen, Cat# A13998, lot RK2423646, used at 1:100 final


title: Suz12_50cells_rep2

value: E14 mouse embryonic stem cells (ESCs)


title: Suz12_50000cells


title: H3K27ac_50cells_rep2

value: anti-H3K27ac, abcam, Cat# ab4729, Lot GR104852-1, used at 1:100 final


title: Brg1_50000cells_rep2

value: proteinA-MNase generated by Fazzio lab, used at 1:200


title: H3K27me3_50000cells_rep2


title: CTCF_500000cells_rep2

value: anti-CTCF, millipore, Cat# 07-729, lot 2475698, used at 1:100 final


title: CTCF_5000cells_rep2


title: Sox2_50cells_rep2


title: NoAb_1cell_rep14


title: NoAb_50000cells_rep2


title: Nanog_50000cells_rep2

value: anti-Nanog, Active Motif, Cat# 61419, Lot 04613001, used at 1:100 final


title: Nanog_50cells_rep2


title: NoAb_500000cells_rep2


title: H3K27ac_50000cells_rep2


title: NoAb_forIgG_50000cells


title: Fig2_NoAb_50000cells_rep2


title: H3K4me3_50cells_rep2


title: H3K4me3_500cells_rep2


title: iDF_mH2A2GFP_24h_RNA-seq_rep3

city: New York

first: Emily

last: Bernstein

state: NY

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

description: processed data file: iDF_mH2A2GFP_24h_over_0h_gene_exp.diff

data_processing:
Sequenced reads were aligned to mouse Ensembl genes 85 version (GRCm38.p4) with STAR (2.5.2b) using default parameters. Pileup bedgraph files (reads per million) was generated with STAR and converted to bigwig file using bedGraphToBigWig from the UCSC unitilites. Identification of differentially expressed genes with a cutoff of 0.05 for FDR was performed with the Cuffdiff program in the Cufflinks (2.2.1) package. Gene expression level as FPKM (fragments per kilobase per million) was determined by Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files contain the ChIP/input fold enrichment scores across the genome generated by MACS2 bdgcmp module (2.1.0). Bed files contains the genomic positions of significant peaks called by SICER (1.1). Tab files contains read counts per gene generated by STAR --quantMode GeneCounts (2.5.2b). Diff files contains results of differential gene expression analysis by Cuffdiff module from the Cufflinks package (2.2.1).

growth_protocol: iDFs were grown in DMEM with 10% FBS and 1% Penicillin/Streptomycin

extract_protocol:
Cells were grown to less than 80% confluency in 6-well dishes for RNA isolation. Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturer’s protocol.
Quality control of extracted RNA was performed using Agilent RNA 6000 Nano Kit and all samples have RNA Integrity Number (RIN) higher than 9.8. Poly(A) mRNA was selected from 1.5 ug total input RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to manufacturer’s protocol. Directional, strand specific RNA libraries were prepared using the NEXTflex Rapid Directional RNA-seq Kit (Bioo Scientific) according manufacturer’s protocol. The quality of the library was analyzed by Agilent bioanalyzer. The barcoded libraries were subject to 80-bp, single-end sequencing with an Illumina NextSeq 500 instrument.

treatment_protocol: treated with 0.5 ug/ml dox for 24 hours

tag: strain background

value: male

value: SV40 immortalized neonatal (P0) dermal fibroblast (iDF)

tag: passages

value: macroH2A1/2 double knockout with dox-inducible macroH2A2-GFP transgene

tag: treated with

value: 0.5 ug/ml dox for 24 hours


title: Oct4_50000cells_rep2


title: iDF_mH2A2GFP_0h_RNA-seq_rep3

treatment_protocol: no treatment

value: no treatment


title: H3K4me3_50000cells_rep2


title: iDF_mH2A2GFP_24h_RNA-seq_rep1


title: iDF_mH2A2GFP_24h_GSK126_ChIP-seq

data_processing:
Sequenced reads were aligned to the GRCm38 (mm10) assembly of mouse genome using Bowtie (1.1.2) using “-n 2 -l 65 -k 1 -M 5 --best” parameters. Redundant reads were removed using MACS2 (2.1.0) filterdup option with default parameters. Pileup tracks were generated using MACS2 callpeak module and ChIP/input fold enrichment pileups were further created with the MACS2 bdgcmp module using “-m FE” parameter. Conversion to bigwig files was performed using bedGraphToBigWig program (v4) from the UCSC utilities. Peaks for macroH2A and H3K27me3 were called with SICER (1.1) using “fragment size 150 bp, window size 200 bp, gap size 800 bp and FDR < 0.01” parameters. MCDs were called with SICER using “fragment size 150 bp, window size 1000 bp, gap size 4000 bp and FDR < 0.01” parameters.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files contain the ChIP/input fold enrichment scores across the genome generated by MACS2 bdgcmp module (2.1.0). Bed files contains the genomic positions of significant peaks called by SICER (1.1). Tab files contains read counts per gene generated by STAR --quantMode GeneCounts (2.5.2b). Diff files contains results of differential gene expression analysis by Cuffdiff module from the Cufflinks package (2.2.1).

extract_protocol:
Nuclei isolation for nChIP was performed as previously described (Fontanals-Cirera et al., 2017). Nuclei were resuspended with 100 ul Buffer A (0.32 M sucrose, 50 mM Tris, pH 7.5, 4 mM MgCl2 and 1 mM CaCl2) per 10 million cells. For each ChIP, an aliquot of 5 million cells was used and diluted with 350 ul of Buffer A. CaCl2 was added to a final concentration of 3 mM. 8.5 U MNase (Affymetrix, 70196Y) was added and the reaction was incubated at 37ºC for 10 min. The reaction was stopped by adding EGTA to a final concentration of 10 mM. Nuclei were spun down at 10,000g for 7 min. The supernatant, which contains mostly mononucleosomes, was collected as S1. The pellet was gently resuspended with 400 ul of Buffer B (50 mM Tris, pH 7.5, 300 mM NaCl, 2 mM EDTA and 0.1% NP-40) and incubated at 4ºC for 2 hours with head-to-head rotation. Nuclei were spun down at 10,000g for 7 min and the supernatant was collected as S2, which contains longer chromatin fragments. S1 and S2 were pooled, OD260 was taken and 100 ug chromatin was usde for each ChIP. The material was further clarified at maximum speed for 5 min and the supernatant was collected and diluted with Buffer C (50 mM Tris, pH 7.5, 150 mM NaCl, 2 mM EDTA, 0.05% NP-40) to 1 ml. 50 ul of the resulting material was taken as input. For GFP IP, 20 ul GFP-Trap_MA (ChromoTek) bead slurry was equilibrated and added to the material followed by a 2.5 hour incubation at 4ºC with head-to-head rotation. Beads were collected using a magnetic rack and washed once with Buffer G 150 (50 mM Tris, pH 7.5, 150 mM NaCl, 0.5% NP-40), twice with Buffer G 250 (50 mM Tris, pH 7.5, 250 mM NaCl, 0.5% NP-40), and once with TE buffer (10 mM Tris, pH 7.5 and 1 mM EDTA). Input and beads were incubated with 50 ug/ml RNase A for 1 hour at 37ºC in 200 ul TE. SDS was then added to 0.5% and Proteinase K 500 ug/ml. Samples were incubated overnight at 56ºC with constant vortexing at 800 r.p.m. in a thermomixer. The supernatant was collected and purified with QIAquick PCR purification columns (Qiagen). The input and ChIP DNA were subsequently analyzed and quantified using the Agilent 2100 Bioanalyzer High Sensitivity Kit.
nChIP-seq libraries were prepared as previously described with minor changes (Fontanals-Cirera et. al., 2017). Briefly, 8-10 ng input or ChIP DNA was end-repaired with T4 DNA polymerase (NEB), DNA polymerase I large (Klenow) fragment (NEB) and T4 polynucleotide kinase (NEB) in the presence of dNTPs (Roche). Next, dA-tailing was performed using Klenow fragment (3’->5’ exo-, NEB) with dATP (Roche) in NEB Buffer 2. Illumina Truseq adaptors with barcodes were ligated using Quick Ligase (NEB). Libraries were size-selected at the 300-400 bp range through agarose gel electrophoresis corresponding to mononucleosomal DNA. The libraries were then amplified using KAPA HiFi DNA Polymerase (KAPA biosystems). Optimal number of PCR cycles was determined by qPCR as described (Buenrostro et al., 2015). The size distribution and level of amplification were further controlled by analysis with the Agilent bioanalyzer and Qubit quantification. Resulting libraries were subject to 80-bp, single-end sequencing with an Illumina NextSeq 500 instrument.

treatment_protocol: treated with 5 uM GSK126 for 10 days and then 0.5 ug/ml dox for 24 hours

tag: chip-antibody

value: GFP-trap (ChromoTek)


title: H3K4me3_500000cells_rep2


title: CTCF_500cells_rep2


title: CTCF_50cells_rep2


title: CTCF_10cells_rep2


title: iDF_mH2A2GFP_6h_RNA-seq_rep1

description: processed data file: iDF_mH2A2GFP_6h_over_0h_gene_exp.diff

treatment_protocol: treated with 0.5 ug/ml dox for 6 hours

value: 0.5 ug/ml dox for 6 hours


title: H3K4me3_5000cells_rep2


title: iDF_input DNA

source_name: iDF_input DNA


title: NoAb_5000cells_rep2


title: NoAb_10cells_rep2


title: NoAb_500cells_rep2


title: PBMC-deep_DARTseq_0

description: Capture of messenger RNA and human B lymphocyte cell light and heavy chain constant regions (eight loci in total). Very deep sequencing of the transcriptome.

source_name: 5000 Commercial human peripheral blood mononuclear cells

value: PBMC

value: DART-seq bead


title: CTCF_50000cells_rep2


title: NoAb_50cells_rep2


title: OCI-AML-20_Rep3

city: Toronto

first: Mark

middle: D

last: Minden

state: Ontario

address: 610 University Avenue

department: Medical Oncology & Hematology

country: Canada

institute: Princess Margaret Cancer Centre

description: replicate 3

data_processing:
RNA-Seq reads were aligned to the GRCh38 reference genome using a two-pass method with STAR2 (v2.5.3a) [PMID: 23104886].
Post alignment, reads where quality filtered with SAMtools (v1.3.1) [PMID: 25260700] and mapped reads enumerated using HT-Seq count (v0.9.1)[PMID: 19505943] with GENCODE v22 annotations.
Genome_build: GRCh38
Supplementary_files_format_and_content: Text files containing read counts for transcripts in GENCODEv22.

source_name: Acute Myeloid Leukemia

growth_protocol: OCI-AML-20 cells were cultured in IMDM media with 10% FBS and 20ng/mL GM-CSF in 6 well format on confluent OP9 stromal cells.

extract_protocol:
RNA was collected using TRIzol (Invitrogen) extraction and integrity assessed using a Bioanalyzer (Agilent).
Sample libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kit (Illumina).
Sequencing was performed using Illumina NextSeq500 using 75-cycle paired-end protocol and multiplexing at the Princess Margaret Genomics Centre.

tag: cell line

tag: disease

value: Acute Myeloid Leukemia

tag: genotype


title: OCI-AML-20_Rep2

description: replicate 2


title: iDF_mH2A2GFP_24h_RNA-seq_rep2


title: iDF_mH2A2GFP_6h_RNA-seq_rep2


title: Post_P30

city: Cambridge

first: Keren

last: Yizhak

address: 415 Main street

institute: Broad Institute of MIT and Harvard

data_processing:
FASTQ files were aligned to the NCBI Human Reference Genome Build GRCh37 (hg19) using STAR
Expression levels were quantified as Transcripts Per Million (TPM) and were computed by the RSEM tool. Data were annotated using GENCODE v19.
For each cell we used three quality control (QC) measures. We excluded: (1) cells with a zero expression of both CD45; (2) cells expressing less than 1000 genes; (3) cells with an average expression of housekeeping genes, log2(TPM+1) < 2.5.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: tab-delimited text file containing log2(TPM+1) values (transcript-per-million reads) for 55,737 transcripts (rows) and 16,291 cells (columns)

source_name: Melanoma single cell

growth_protocol: We performed scRNA-seq on 48 tumor biopsies from 32 metastatic melanoma patients treated with checkpoint therapy (with 35 anti-PD1;  11 anti-CTLA4+PD1; and 2 anti-CTLA4 samples). This cohort includes 11 patients with longitudinal biopsies taken at baseline (e.g. Pre) and during treatment (e.g. Post), 1 patient with 2 biopsies taken at one time point, and 20 patients with one sample each, taken at baseline (Pre) or during treatment (Post). We used the following patient response categories defined by RECIST criteria: complete response (CR) and partial response (PR) for responders, or stable disease (SD) and progressive disease (PD) for non-responders (Eisenhauer et al., 2009).

extract_protocol:
Libraries from single cell lysates were generated with the Smart-Seq2 protocol (Picelli et al., 2013) with some modifications in the reverse transcription step as recently described (Villani et al., 2017). 96-well plates containing cell lysates were thawed on ice, spun down at 1500 rpm for 30 seconds, and mixed with Agencourt RNAClean XP SPRI beads (Beckman Coulter) for RNA purification. Purified RNA was resuspended in 4µl of Mix-1 (containing RT primers, dNTPS, recombinant RNase inhibitor and nuclease free water) , denatured at 72oC for 3 min and placed immediately on ice for 1 min before 7µl of Mix-2 was added (5X RT buffer, Betaine, MgCl2, TSO primer, recombinant RNase inhibitor and Maxima H Minus reverse trascriptase). Reverse transcription was carried out at 50oC for 90 min, followed by 5 min incubation at 85oC. 14µl of Mix-3 (nuclease free water, ISPCR primers and 2x KAPA HiFi Hotstart readymix) was added in each well and the whole-transcriptome amplification step was performed at 98oC for 3 min, followed by 21 cycles at (98oC for 15 sec, 67oC for 20 sec and 72oC for 6 min), and final extension at 72oC for 5min. cDNA was then purified with Agencourt AMPureXP SPRI beads (Beckman Coulter) as described (Villani et al., 2017), to remove all primer dimers residues. Quality control steps were performed on samples before library construction and included the following steps: (1) concentration measurements, using the Qubit dsDNA high sensitivity assay kit on the Synergy H1 Hybrid Microplate Reader (BioTek); (2) cDNA size distribution using the High-Sensitivity Bioanalyzer Kit.
Libraries were generated using the Nextera XT Library Prep kit (Illumina) with custom indexing adapters (Villani et al., 2017) in a 384-well PCR plate, followed by a cleanup step to remove residual primer dimers. Combined libraries from 384 cells were then sequenced on a NextSeq 500 sequencer (Illumina), using paired-end 38-base reads.

treatment_protocol: Fresh isolated tumor samples were collected immediately after surgery and were dissociated within 1 hour using the human tumor dissociation kit (Miltenyi Biotec; 130-095-929) with the following modifications. Tissue was minced into small pieces using a scalpel and put into a 1.5ml eppendorf tube containing 100µl of enzyme H, 50µl of enzyme R, 12.5µl of enzyme A (all provided in the kit), and 837.5µl of RPMI, followed by a 20 minute incubation in a thermomixer (Eppendorf; F1.5) at 37oC, 600 rpm. After incubation, debris were removed by filtering through a 70µm cell strainer, followed by mincing of the remaining tissue left on the strainer with a plunger in order to increase cell yield. Dissociated cells were subsequently washed with cold 1X PBS containing 1.5% heat inactivated FCS, spun down at 1300 rpm, 4°C for 5 minutes, resuspended, and counted for yield and viability with trypan blue using a Countess automated cell counter (Invitrogen). For cell sorting, Human TrueStain FcX (Biolegend, 422302) was used for blocking Fc receptors before labeling cells. To discriminate live from dead cells, we used Zombie Violet Dye (Biolegend, 77477) for 15 min at 4oC, followed by surface labelling of cells for 30 min at 4oC, using standard protocols. The antibodies used for cell surface labelling were PE anti-human CD45 (Biolegend, 304008), APC anti-human CD3 (Biolegend, 300412), FITC anti-human HLA-A,B,C (Biolegend, 311426), APC/Cy7 anti-human CD235a (Biolegend, 349116). Sorting of single cells was performed on a BD Fusion instrument using the following antibody panel: Zombie dye, CD45, CD235a, CD3 and HLA-A,B,C. CD45+ cells from dissociated samples were sorted into 96-well plates (Eppendorf, 951020401) containing 10µl of lysis buffer (TCL buffer, Qiagen 1031576, supplemented with 1% β-mercaptoethanol), sealed, vortexed, spun down at 2500 rpm for 30 seconds, immediately placed on dry ice, and then stored at -80oC until processing with the Smart-Seq2 protocol.

tag: patient id (pre=baseline; post=on treatment)

tag: response

value: Non-responder

tag: therapy


title: Post_P28_2


title: Post_P28


title: PBMC_replicate_Dropseq_0

description: Capture of messenger RNA only.

tag: cell type

tag: capture

value: Drop-seq bead


title: iDF_mH2A2GFP_0h_RNA-seq_rep1


title: iDF_mH2A2GFP_6h_GSK126_ChIP-seq

treatment_protocol: treated with 5 uM GSK126 for 10 days and then 0.5 ug/ml dox for 6 hours


title: iDF_mH2A2GFP_6h_RNA-seq_rep3


title: Post_P21

value: Responder


title: iDF_mH2A2GFP_5d_ChIP-seq

treatment_protocol: treated with 0.5 ug/ml dox for 5 days

value: 0.5 ug/ml dox for 5 days


title: iDF_mH2A2GFP_24h_FP_ChIP-seq

treatment_protocol: treated with 0.5 ug/ml dox for 24 hours with the last 18 hours under 0.5 uM flavopiridol treatment


title: iDF_mH2A2GFP_0h_RNA-seq_rep2


title: iDF_mH2A2GFP_24h_ChIP-seq


title: Post_P14


title: iDF_mH2A2GFP_6h_ChIP-seq


title: Post_P13


title: Post_P8


title: Bcell_Dropseq_0

description: Capture of messenger RNA only.

value: B cell


title: Post_P5


title: PBMC_replicate_DARTseq_0

description: Capture of messenger RNA and human B lymphocyte cell light and heavy chain constant regions (eight loci in total).


title: Post_P5_2


title: iDF_mH2A2GFP_0h_ChIP-seq


title: OCI-AML-20_Rep1

description: replicate 1


title: Post_P12


title: Bcell_DARTseq_0


title: Post_P23


title: Post_P23_2


title: Pre_P35


title: Pre_P33


title: Post_P20


title: Post_P17


title: Pre_P29


title: Post_P19


title: Post_P15


title: Post_P18


title: Pre_P26


title: Pre_P20


title: Post_P16


title: Post_P11


title: Post_P6


title: Post_P7


title: Post_P22


title: Post_P1_2


title: Post_P3_2


title: Post_P1


title: Post_P10


title: NCR65_325: HP1b-86 rep1

city: Birmingham

first: Nicole

middle: Christina

last: Riddle

address: 1720 2nd Ave South CH464

department: Biology

institute: University of Alabama at Birmingham

data_processing:
Basecalls performed using bcl2fastq version 2.18.0.12
Raw fastq files were trimmed with TrimGalore! Version 0.4.1 with parameters --paired --trim1
Trimmed fastq files were then aligned to the reference genome using TopHat version 2.1.1 with parameters -r 150, --keep-fasta-order, --library-type fr-firststrand
Cufflinks version 2.2.1 was used to estimated transcript abundances and calculate differential expression
Genome_build: UCSC dm3
Supplementary_files_format_and_content: tab-delimited Excel file containing FPKM values for each sample and gene sequenced

source_name: Third instar larvae

growth_protocol: Drosophila were grown at 25C in an incubator with ~70% humidity on Jazzmix food (Fisher Scientific).

extract_protocol:
Total RNA was isolated using Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Third instar larvae

tag: strain


title: Pre_P31


title: Pre_P4


title: Post_P2


title: HP1b-16-2: HP1b-16 rep2


title: Pre_P1


title: Post_P3


title: Post_P4


title: Pre_P3


title: Pre_P27


title: Pre_P25


title: Pre_P15


title: Pre_P24


title: RAW_mafk_chip_2

city: Haifa

first: Nitsan

last: Fourier

address: Technion

country: Israel

institute: Technion

data_processing:
Library quality-control was performed using FASTQ software (version 0.11.5).
For quality and adapter trimming trim_galore (cutadapt version 1.9) was used
Sequencing reads were mapped using BWA aln v0.7.12.
Peak calling was carried out by MACS2 v2.1.1 (20160309)
Peak merging was carried out by DiffBind v2.0.2 (R package)
Annotation were performed using ChIPseeker v1.8.3 (R package).
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files are track files of the peak regions.

growth_protocol: NIH3T3 and RAW cell-lines were maintained in DMEM supplemented with 10% FCS, 2.5 μg/ml Amphotericin and 50 μg/ml Gentamycin Sulfate. Cells were re-plated every 72 hrs before reaching maximum confluency

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the Illumina TruSeq Nano DNA Library Prep Kit.

value: Murine monocytes/macrophages-like

tag: chip antibody

value: MafK (Santa Cruz, CAT#sc-22831, Lot#12804)


title: Pre_P12


title: Pre_P8


title: HP1b-16-1: HP1b-16 rep1


title: Pre_P7


title: YW-2: yw rep2

value: yw


title: Pre_P6


title: NIH3T3_mafk_chip_4

value: Mouse embryo fibroblast


title: YW-1: yw rep1


title: WT rep2 dataset #2

city: Strasbourg

first: Dominique

last: Gagliardi

address: 12, rue du General Zimmer

department: IBMP

country: France

institute: CNRS

data_processing:
After initial data processing by the MiSeq Control Software v 2.5. (Illumina), base calls were retrieved and further analysed by a suite of home made python scripts (v2.7) using biopython (v1.63) and regex (v2.4) libraries.
Data processing pipeline was adapted from (Sikorska et al., 2017). Reads with low quality bases (=<Q10) within the 15 –base random sequence of the read 2 or within the 20 bases downstream the delimiter sequence, were filtered out.
Sequences with identical nucleotides in 15 –base random sequence were deduplicated.
Next, the sequences AAGAATTCTCGTCGCCTGAA and GCCAGAGCTATGTTGTTGGT were searched into reads 1 to identify MYB33 and SPL13 corresponding reads, respectively. One mismatch was tolerated. Matched reads 1 and their corresponding reads 2 were extracted and annotated.
Reads 2 that contain the delimiter sequence were selected and subsequently trimmed from their random and delimiter sequences.
In order to map 3’ extremities of target 5’ RISC generated fragments, the 20 nucleotide sequences downstream the read 2 delimiter sequence were mapped to the corresponding reference sequence, which goes from the first nucleotide of the transcript that maps the forward PCR primer MYB33_RISC_fw2 or SPL13_RISC_fw2 to the last nucleotide of the miRNA binding site.
To map the 3’ end position of reads 2 with untemplated tails, the sequences of the unmatched reads 2 were successively trimmed from their 3′ end, with a 1 nt trimming step, until successfully mapped to the reference sequence or until a maximum of 30 nt has been removed.
For each successfully mapped read 2, untemplated nucleotides at the 3‘ end were extracted and analyzed for their size and composition. 3’ modifications longer than 1 were considered only if composed of at least of 50 % of the same base (i.e. 50% U, 50% A, 50% C or 50% G).
As explained in the related paper, the sites cleaved by RISC were deduced from PARE-seq datasets to map the 5’ most nucleotide of the 3’ fragment. A single cleavage site was determined for MYB33, i.e. between nucleotides at position 0 and position +1. By contrast to two cleavage sites for SPL13, i.e. a major site between 0 and +1 and a minor site between +1 and +2. Because position +1 in SPL13 is a uridine, we could not determine whether this U is encoded or added post-transcriptionally and SPL13 graphs were generated by considering only U-tails>2.
Finally, a supplemental deduplication was performed to increase stringency: sequences with 13 or more identical nucleotides in the 15 –base random sequence were deduplicated.
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed data are provided for each genotype and biological replicate in separate file. Each line corresponds to one individual reads.
Supplementary_files_format_and_content: For each read, we indicate the read ID, gene name, 3' end position, encoded sequence, modification sequence, modification size, random sequence and a tag indicating is the tail is U, A, C or G rich.
Supplementary_files_format_and_content: Position 0 corresponds to the nucleotide of the MYB33 transcript that precedes the cleavage site.

organism: Arabidopsis thaliana

source_name: 24 day-old plantlets

growth_protocol: Arabidopsis plantlets of Col-0 accession were grown for 24 days in vitro on Murashige & Skoog media with 0.8% agar and 12h light (22°C)/12h darkness cycles (18°C)

extract_protocol:
Total RNA was extracted from 24 days plantlets with TRI Reagent® (Molecular Research Center) according to manufacturer’s instructions
3' RACE-seq
3'RACEseq protocol is based on the ligation of a primer at the 3’ end of RNA, and the subsequent targeted amplification by PCR of amplicons suitable for Illumina sequencing.

value: WT

tag: replicate

value: replicate 2

tag: dataset

tag: reference sequence


title: late EMP

city: Hangzhou

first: ZHI

middle: QING

last: LI

address: 866 Yuhangtang Road

country: China

institute: Zhejiang University School of Medicine

description:
E8_5Runx1
Skin mast cells were sorted from Runx1Cre/EYFP mice pulsed with 4’OHT at E8.5.
processed data file: mast cells with distinct origins.FPKM.txt

data_processing:
cDNA library construction and sequencing were performed by Beijing Genomics Institute using Illumina HiSeq platform.
High-quality reads were aligned to the mouse reference genome (UCSC_mm10) using Bowtie2.
The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM) using RNA-Seq by Expectation Maximization (RSEM).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: mast cells with distinct origins.FPKM.txt: Tab-delimited text file includes FPKMs.

source_name: skin mast cells

extract_protocol:
Total RNA was extracted from sorted cells using TRIzol reagent (Invitrogen) according to manufacturer’s protocol.
cDNA library construction and sequencing were performed by Beijing Genomics Institute using Illumina HiSeq platform.

treatment_protocol: Skin mast cells were sorted from Csf1rCre/EYFP mice pulsed with 4’OHT at E8.5 and from Runx1Cre/EYFP mice pulsed with 4’OHT at E8.5 and E9.5, 1 week postnatal respectively.

tag: strain/background

tag: age

value: 1 week postnatal

value: skin mast cells

tag: origin

value: late EMP


title: heso1 urt1 SIL # 3a dataset #2

value: heso1 urt1 SIL

value: replicate 1


title: NCR65_328: HP1b-86 rep2


title: NIH3T3_mafk_chip_3

tag: cell line


title: Pre_P2

value: Non-responder


title: Pre_P28


title: heso1 urt1 SIL # 2a dataset #2


title: fetal HSC

description:
E9_5Runx1
Skin mast cells were sorted from Runx1Cre/EYFP mice pulsed with 4’OHT at E9.5.
processed data file: mast cells with distinct origins.FPKM.txt

value: fetal HSC


title: heso1 urt1 SIL # 3b dataset #2


title: urt1 SIL  rep2 dataset #2

value: urt1 SIL


title: heso1 urt1 SIL # 2b dataset #2


title: early EMP

description:
ctrl
Skin mast cells were sorted from Csf1rCre/EYFP mice pulsed with 4’OHT at E8.5.
processed data file: mast cells with distinct origins.FPKM.txt

value: early EMP


title: RAW_mafk_chip_3


title: heso1 urt1 SIL # 1b dataset #2


title: urt1 rep2 dataset #2


title: heso1 rep4 dataset #1

value: replicate 4


title: RAW_input


title: WT rep3 dataset #1

value: replicate 3


title: heso1 rep1 dataset #1


title: heso1 rep2 dataset #2


title: heso1 rep2 dataset #1


title: CWR22Rv1 DMSO

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

description: Illimuna next-generation sequencing (2x150bp, paired-end)

data_processing:
The FASTQ-formatted sequence data was analyzed using a standard HISAT-Cufflinks workflow. In brief, raw sequence reads (FASTQ format) were aligned to the reference human genome assembly (Dec. 2013, GRCh38) using HISAT (hierarchical indexing for spliced alignment of transcripts) software. Gene- and transcript-level expression were comprehensively quantified with Cufflinks software, which performed 1) transcript assembly, 2) identification of splice variants, 3) quantification of expression as FPKM (fragments per kilobase of transcript per million mapped reads) values, and 4) normalization. Normalized FPKM values (Cuffnorm output) were utilized for downstream analysis steps.
Processed data are Cufflinks-Cuffnorm output files and contain Gene Symbol (Ensembl ID), FPKM values, and FPKM status.
Genome_build: GRCh38, Dec. 2013
Supplementary_files_format_and_content: Tab-delimited text files include Gene_Symbol (Ensembl ID), FPKM values, and FPKM status for each transcript and were prepared from the Cufflinks-Cuffnorm gene-level output files.

source_name: CWR22Rv1 cells cultured in medium with DMSO vehicle control.

growth_protocol: CWR22Rv1 cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin and 0.1 mg/ml streptomycin. C4-2B MDVR cells were maintained in the same medium containing enzalutamide (20 μM).

extract_protocol:
Total RNA was isolated using the TRIzol Reagent (Invitrogen) from C4-2b-MDVR and CWR22Rv1 cells treated with DMSO, Apoptozole, or VER155008 for 48 hours.
Indexed RNA-Seq libraries were prepared from 200 ng total RNA using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems, Inc.) according to the manufacturer’s protocol. Poly-adenylated mRNA was purified by binding to oligo(dT) beads and to remove rRNA, which was followed by fragmentation by incubation at 94ºC in the presence of magnesium. Double-stranded cDNA was then generated by random-primed first-strand synthesis and second strand synthesis in the presence of dUTP for strand marking. Subsequently, the cDNA was 3’-A tailed and indexed, Illumina-compatible adapters were ligated. The libraries were then enriched by high-fidelity PCR amplification (13 cycles) with KAPA HiFi HotStart DNA Polymerase and adapter-specific primers.

treatment_protocol: C4-2B MDVR and CWR22Rv1 cells were treated with vehicle or the HSP70 inhibitors APO (10 μM) and VER (10 μM) for 48 h before RNA extraction.

value: human castration-resistant prostate carcinoma

value: Parental cell line


title: RAW_mafk_chip_1

value: Murine monocytes/macrophages-like

value: MafK (Santa Cruz, CAT#sc-22831, Lot#12804)


title: NIH3T3_mafk_chip_2

value: Mouse embryo fibroblast


title: C4-2B MDVR VER

source_name: LNCaP-C4-2B cells cultured in medium with VER155008


title: heso1 urt1 SIL # 1a dataset #2


title: lung: NCI-H2227 ATAC-seq

city: Los Angeles

first: Owen

middle: N

last: Witte

address: 675 Charles E Young Dr S, 5720 MRL Bldg; MC 729022

department: MIMG

institute: UCLA

data_processing:
ENCODE processing pipeline (https://www.encodeproject.org/atac-seq/)
Genome_build: hg38 human genome
Supplementary_files_format_and_content: bigwig

source_name: lung

value: lung

value: small cell lung cancer

tag: transplant


title: C4-2B MDVR DMSO

source_name: LNCaP-C4-2B cells cultured in medium with DMSO vehicle control.


title: NIH3T3_input


title: urt1 SIL  rep1 dataset #2

tag: genotype


title: heso1 rep1 dataset #2


title: NIH3T3_mafk_chip_1


title: WT rep4 dataset #1

value: WT


title: WT rep1 dataset #2


title: urt1 rep1 dataset #2


title: prostate: ARCB6 ATAC-seq

source_name: prostate

value: prostate

value: transformed prostate basal epithelial

value: NSG mice


title: prostate: ARCB5 ATAC-seq


title: heso1 rep3 dataset #1


title: WT rep2 dataset #1

value: replicate 2


title: prostate: PACB3 ATAC-seq


title: CWR22Rv1 VER

source_name: CWR22Rv1 cells cultured in medium with VER155008


title: lung: NCI-H1436 ATAC-seq


title: CWR22Rv1 APO

source_name: CWR22Rv1 cells cultured in medium with Apoptozole


title: prostate: PACB1 ATAC-seq


title: prostate: ACB5 ATAC-seq


title: C4-2B MDVR APO

source_name: LNCaP-C4-2B cells cultured in medium with Apoptozole


title: C42B-Parental

description: Affymetrix microarray gene expression profiling data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix Genechip Human Genome U133 Plus 2 arrays using Affymetrix hybridization kit reagents. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using protocol  FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using GeneSpring GX 12.0 software.  Probe intensity values (CEL files) were background-corrected, summarized, and normalized using the Robust Multi-array Average (RMA) algorithm (Irizarry et al., 2003).

source_name: LNCaP-C42B parental cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, Rev3, Affymetrix).

growth_protocol: C4-2B parental cells were were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and 100 units/ml penicillin and 0.1 mg/ml streptomycin. The C4-2B MDVR (C4-2B enzalutamide resistant) and C4-2B AbiR (C4-2B abiraterone resistant) were maintained in medium containing 20 μM enzalutamide or 10 μM abiraterone acetate, respectively.

extract_protocol: Total RNA was isolated from each cell line using the using TRIzol reagent (Invitrogen).

treatment_protocol: C4-2B parental, C4-2B MDVR, and C4-2B AbiR cells were were cultured according the conditions described in the growth protocol above, and harvested for RNA isolation.


title: AR2754_03: Ex vivo Fibroblast of LS rep2

city: Shimotsuke-shi

first: Akihiko

last: Miyauchi

state: Tochigi

address: 3311-1 Yakushiji

department: Pediatrics

country: Japan

institute: Jichi Medical University

description: Gene expression in fibroblast of Leigh syndrome patient

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Fibroblast of LS, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Fibroblasts from Leigh syndrome patient were maintained in 1.0 g/L low-glucose DMEM supplemented with 10% FBS.

extract_protocol: Total RNA was extracted from the fibroblasts using RNeasy Mini Kit (QIAGEN).

treatment_protocol: We treated the fibroblast of Leigh syndrome patient (LSND3) with or without compound. The cultures were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: fibroblast

tag: diagnosis

value: Leigh syndrome


title: prostate: ACB4 ATAC-seq


title: AR2754_02: Ex vivo Fibroblast of LS with compound rep1

description: Gene expression in compound-treated fibroblast of Leigh syndrome patient

source_name: Fibroblast of LS, 1uM compound, replicate 1


title: WT rep1 dataset #1

value: replicate 1


title: lung: NCI-H1963 ATAC-seq


title: lung: NCI-H2171 ATAC-seq


title: prostate: ARCB4 ATAC-seq


title: prostate: ACB2 ATAC-seq


title: BiV-HF_LV5

first: Christoph

middle: Daniel

last: Rau

state: United States

address: 675 Charles E Young Drive S

data_processing:
Remove Adapters and low quality reads using Cutadapt
Reads mapped to genome using HISAT2 with standard parameters
Transcripts assembled using StringTie and merged together with gtfcompare to create unified mRNA expression profile
Differentially expressed mRNAs identified using Ballgown
Genome_build: hg38
Supplementary_files_format_and_content: CSV file with FPKMs and raw counts of each mapped gene

source_name: Left Ventricle

extract_protocol:
Human ventricular myocardium was obtained from end-stage ischemic cardiomyopathic hearts explanted at the time of cardiac transplantation. Non-failing donor hearts that had been deemed unsuitable for transplantation were used as control. Prior to explant, hearts underwent intra-operative antegrade coronary perfusion with 4:1 blood cardioplegia solution. Following arrest, hearts were explanted and placed into cold Ca2+-free, modified Krebs-Henseleit solution as previously described (120). Samples were taken from mid-myocardial regions of the left ventricular free wall and the right ventricular free wall, in areas void of scar tissue. Tissue samples were rapidly frozen in liquid nitrogen and stored at -80°C until RNA isolation. Prospective written informed consent for research use of heart tissue was obtained from all transplant recipients or next of kin (non-failing donors). Patient consent, sample collection and preparation, and clinical data collection were performed according to a human subject research protocol approved by the Institutional Review Board of the Lewis Katz School of Medicine at Temple University (PI: Tsai).
Sequencing libraries were generated using a NEBNext Ultra™ RNA Library Prep Kit for Illumina  following the manufacturer’s recommendations

value: Left Ventricle

tag: condition

value: BiVentricular Heart Failure


title: LV-HF_LV5

value: Left Ventricle Heart Failure


title: BiV-HF_LV2


title: BiV-HF_LV3


title: BiV-HF_LV4


title: prostate: ACB3 ATAC-seq