title: MS male inject CER mouse 79


title: MS male inject BNST mouse 79

status: Public on Apr 22 2020

type: SRA

city: Munich

first: Janine

last: Arloth

address: Kraepelinstr. 2-10

country: Germany

institute: Max Planck Institute of Psychiatry

library_source: transcriptomic

data_processing:
After sequencing with the MiSeq Sequencer (V3 chemistry for 150 cycles), sequencing quality was analyzed with FastQC. Low-quality reads with phred scores lower than 20 or a length smaller than 25 bp were removed using PRINSEQ (PReprocessing and INformation of SEQuence data) lite Version 0.20.4. Subsequently, the reads were aligned with Burrows-Wheeler Aligner (BWA) Version 0.7.12 with default settings (allowing a maximum of three mismatches) and the manifest file provided by Illumina as reference. Gene expression quantification was inferred from the alignment. Genes with low overall coverage, i.e. <2000 reads across all samples, were excluded from further analysis (n = 5). The data were then normalized using DESeq2. Finally, surrogate variable analysis (SVA) from the R/Bioconductor package sva was applied to identify hidden technical batches.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including expression values for each sample.

molecule: total RNA

organism: Mus musculus

source_name: BNST

extract_protocol:
Frozen micropunches were lysed quickly in 500 µl Trizol (QIAzol) reagent and homogenized by repeated passing through an insulin syringe (29G). Subsequently, samples were kept at room temperature for at least 3 min before adding 100 µl chloroform. The remaining steps were conducted according to the miRNeasy Mini Kit (Qiagen, Hilden, Germany) protocol. Elution was performed with 30 µl RNAse-free water with a second round using the eluate from the first round.
TruSeq Targeted RNA sequencing (Illumina, San Diego, USA) was carried out according to the manufacturer’s protocol.

tag: strain

value: Male Balb/c mice

tag: tissue

value: BNST

tag: age

value: post natal day 9

tag: animal

tag: status

tag: injection


title: MS male inject AMY mouse 79

source_name: AMY

value: AMY


title: Co male inject dDG mouse 267

source_name: dDG

value: dDG


title: Co male inject Pit mouse 267

source_name: Pit

value: Pit


title: Co male inject PVN mouse 267

source_name: PVN

value: PVN


title: Co male inject BNST mouse 267


title: Co male inject CER mouse 267

source_name: CER

value: CER


title: Co Male naive vDG mouse 259

source_name: vDG

value: vDG


title: Co male inject AMY mouse 267


title: Co Male naive vCA3 mouse 259


title: Co Male naive vCA1 mouse 259


title: Co Male naive PVN mouse 259


title: Co male inject vCA3 mouse 267


title: Co Male naive Pit mouse 259


title: Co Male naive dDG mouse 259


title: Co Male naive PFC mouse 259

source_name: PFC

value: PFC


title: Co Male naive CER mouse 259


title: Co Male naive dCA1 mouse 259


title: Co Male naive dCA3 mouse 259


title: Co male inject dCA3 mouse 267


title: Co male inject dCA1 mouse 267


title: Co Male naive vDG mouse 255


title: Co Male naive AMY mouse 259


title: Co male inject vCA1 mouse 267


title: Co male inject PFC mouse 267


title: Co Male naive vCA3 mouse 255


title: Co Male naive vCA1 mouse 255


title: Co Male naive PVN mouse 255


title: Co Male naive Pit mouse 255


title: Co Male naive BNST mouse 259


title: Co Male naive PFC mouse 255


title: Co Male naive dDG mouse 255


title: Co Male naive dCA3 mouse 255


title: Pds5-GFP_ChIP_in_clr4_cells

type: genomic

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

country: USA

institute: NCI

description: Pds5-GFP ChIP clr4 deletion

hyb_protocol: Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software (CHIP-v1_95_May07 or ChIP-v1_10_Apr08 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: logarithmic growing cells

label_protocol: ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA). Cultures were grown at 30˚C.

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication to 500-1000bp fragments and immunoprecipitated with H3K9dime antibody (Abcam, ab1220) or GFP antibody (Abcam, ab290). Immunoprecipitated DNA was recovered by incubation with protein A/G slurry and reversed-crosslinked at 65˚C.

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at 30˚C. DMA was also added to the fixation of cells to be used in Pds5 ChIPs. Prior fixation cells were incubated at 18˚C for 2h (Pds5 ChIPs).

tag: genotype/variation

tag: sample type

value: Pds5-GFP immunoprecipitated DNA

tag: chip antibody

value: GFP (Abcam, ab290)

value: Whole-cell extract DNA


title: Co Male naive dCA1 mouse 255


title: Pds5-GFP_ChIP_in_wt_cells, rep2

description: Pds5-GFP ChIP wt_rep2

value: Wild type


title: 293T.2.m6A.seal.input.500ng

city: Los Angeles

first: Ye

last: Wang

state: California

address: 611 Charles E Young Dr E

department: Bioinformatics

institute: UCLA

description: No antibody(chemical assisted enrichment)

data_processing:
Library strategy: m6A-SEAL
Single-end and paired-end sequencing data were trimmed by single-end and paired-end model of cutadapt (v1.18) software respectively. Reads longer than 20 bp were retained for mapping.
Trimmed reads were aligned to hg38 genome assembly by hisat2 (v2.1.0) software using the default parameter for single or pair-end model
Peakcalling were performed by macs2(v3.8), the enrichment fold threshold is 1, FDR threshold is 0.05.
Comparision of m6A sites from MeRIP-m6A-seq and m6A-SEAL are performed by intersectBed in BEDtools.
Peaks from input and IP samples in both MeRIP-m6A-seq and m6A-SEAL are converted to bigwig files by bamCoverage script in deepTools for visualization and analysis.
Genome_build: hg38

molecule: polyA RNA

organism: Homo sapiens

source_name: HEK293T cells

growth_protocol: HEK293T cell were cultured by DMEM medium(10% FBS) and 1% Penicillin Streptomycin in 15cm dish under 37℃, 5%CO2.   Rice were cultivated in a half-strength Kiruma B solution (pH 5.6, changed every two days.) at 28℃ and 80% relative humidity for 15 days.

extract_protocol:
Total RNA was first extracted from HEK293T cells or rice tissue by Trizol reagent, The polyA RNA was then purified with oligo d(T)25 magnetic beads
PolyA RNA was fragmented by NEBNext Magnesium RNA Fragmentation Module. A portion of fragmented RNA was reserved as m6A input sample.For MeRIP-m6A-seq,  the left RNA was incubated with anti-m6A antibody and then eluted to get the m6A IP sample. For m6A-SEAL, the left RNA was enzymatically oxidized by FTO and then conjugated with biotin by dithiothreitol under acidic aqueous solution. The biotinylated RNA are enriched by streptavidin beads and then eluted by dithiothreitol to get m6A IP sample. Both input and m6A IP samples were prepared for next-generation sequencing library by standard protocol of NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.
m6A-SEAL and MeRIP-m6A-seq. Library was sequenced in PE150 model on Illumina X-Ten platform or in SR75 model on Illumina NextSeq 500 platform.

tag: cell line

value: HEK293T cells


title: Co Male naive CER mouse 255


title: Pds5-GFP_ChIP_in_swi6_cells

description: Pds5-GFP ChIP swi6 deletion


title: Pds5-GFP_ChIP_in_wt_cells, rep1

description: Pds5-GFP ChIP wt_rep1


title: H3K9me2_ChIP_in_pds5_cells

description: H3K9me2 ChIP pds5 deletion

value: H3K9me2 immunoprecipitated DNA

value: H3K9me2 (Abcam, ab1220)


title: Co Male naive BNST mouse 255

value: Male Balb/c mice


title: Co Male naive vDG mouse 253


title: Noggin doxycycline 72h 2

type: RNA

city: Freiburg

first: Antoine

last: Devisme

address: Breisacherstr. 153

institute: Institute of Medical Bioinformatics and Systems Medicine

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All arrays were normalized together using the quantile normalization algorithm without background subtraction using the R Bioconductor beadarray package

label: Biotin

source_name: LS174T-Snail1-HA, mNoggin + Dox, 72 h

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: LS174T-Snail1-HA were cultivated at 37 °C and 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% (v/v) FCS, 0.01 M HEPES/KOH, 1x MEM non-essential amino acids solution and 1x Penicillin/Streptomycin.

extract_protocol: Total RNA was extracted using the PeqGOLD total RNA kit (#732–2871, Peqlab/VWR Life Science, Bruchsal, Germany) according to manufacturer's instructions.

treatment_protocol: Cells were treated with 0.1 µg/ml-1 doxycycline and DMSO, 50 nM LDN193189 or 100 ng ml-1 mNoggin as indicated. If necessary media were refreshed after 48 h.

value: Colorectal cancer cell line


title: H3K9me2_ChIP_in_wt_cells

description: H3K9me2 ChIP wt


title: Noggin uninduced 72h 2

description: replicate 2

source_name: LS174T-Snail1-HA, mNoggin, 27 h


title: Noggin doxycycline 72h 1

description: replicate 1


title: Noggin uninduced 24h 2

description: replicate 2

source_name: LS174T-Snail1-HA, mNoggin, 24 h


title: Noggin doxycycline 6h 1

description: replicate 1

source_name: LS174T-Snail1-HA, mNoggin + Dox 6 h


title: Co Male naive vCA3 mouse 253

value: post natal day 9


title: Noggin uninduced 24h 1

description: replicate 1


title: Noggin doxycycline 24h 1

description: replicate 1

source_name: LS174T-Snail1-HA, mNoggin + Dox, 24 h


title: Noggin uninduced 6h 2

description: replicate 2

source_name: LS174T-Snail1-HA, mNoggin, 6 h


title: Noggin doxycycline 24h 2

description: replicate 2


title: Co Male naive vCA1 mouse 253


title: Noggin uninduced 72h 1

description: replicate 1

source_name: LS174T-Snail1-HA, mNoggin, 72 h


title: Co Male naive PVN mouse 253


title: Noggin doxycycline 6h 2

description: replicate 2

source_name: LS174T-Snail1-HA, mNoggin + Dox, 6 h


title: Noggin uninduced 6h 1

description: replicate 1


title: LDN doxycycline 24h 2

description: replicate 2

source_name: LS174T-Snail1-HA, LDN193189 + Dox, 24 h


title: Co Male naive Pit mouse 253


title: Co Male naive PFC mouse 253


title: Co Male naive dDG mouse 253

source_name: dDG


title: Co Male naive dCA3 mouse 253


title: LDN doxycycline 24h 1

description: replicate 1


title: LDN doxycycline 72h 1

description: replicate 1

source_name: LS174T-Snail1-HA, LDN193189 + Dox, 72 h


title: Co Male naive AMY mouse 255

source_name: AMY

value: AMY


title: Co Male naive CER mouse 253

source_name: CER


title: Co Male naive dCA1 mouse 253


title: Co Male naive BNST mouse 253

source_name: BNST

value: BNST


title: Co Male naive AMY mouse 253


title: Co Male naive vDG mouse 251

source_name: vDG


title: LDN uninduced 72h 2

description: replicate 2


title: Co Male naive vCA3 mouse 251


title: LDN doxycycline 6h 2

description: replicate 2

source_name: LS174T-Snail1-HA, LDN193189 + Dox, 6 h


title: Co Male naive PVN mouse 251

source_name: PVN


title: LDN doxycycline 6h 1

description: replicate 1

source_name: LS174T-Snail1-HA, LDN193189 + Dox 6 h


title: LDN uninduced 6h 2

description: replicate 2


title: LDN uninduced 72h 1

description: replicate 1


title: Co Male naive vCA1 mouse 251


title: LDN doxycycline 72h 2

description: replicate 2


title: LDN uninduced 24h 2

description: replicate 2


title: LDN uninduced 6h 1

description: replicate 1


title: Co Male naive PFC mouse 251

source_name: PFC


title: DMSO doxycycline 72h 1

description: replicate 1

source_name: LS174T-Snail1-HA, DMSO + Dox, 72 h


title: Co Male naive Pit mouse 251

source_name: Pit

value: Pit


title: DMSO doxycycline 72h 2

description: replicate 2


title: Co Male naive dDG mouse 251

value: dDG


title: Co Male naive dCA3 mouse 251


title: Co Male naive dCA1 mouse 251


title: DMSO doxycycline 24h 1

description: replicate 1

source_name: LS174T-Snail1-HA, DMSO + Dox, 24 h


title: Co Male naive BNST mouse 251


title: Co Male naive CER mouse 251

value: CER


title: Co male inject vDG mouse 249

value: vDG


title: Co Male naive AMY mouse 251


title: Co male inject Pit mouse 249


title: Co male inject vCA1 mouse 249


title: Co male inject PVN mouse 249

value: PVN


title: Co male inject dDG mouse 249


title: Co male inject dCA1 mouse 249


title: DMSO doxycycline 6h 1

description: replicate 1

source_name: LS174T-Snail1-HA, DMSO + Dox 6 h


title: DMSO doxycycline 24h 2

description: replicate 2


title: DMSO uninduced 24h 2

description: replicate 2

source_name: LS174T-Snail1-HA, DMSO, 24 h


title: DMSO uninduced 24h 1

description: replicate 1


title: DMSO uninduced 72h 2

description: replicate 2

source_name: LS174T-Snail1-HA, DMSO, 72 h


title: DMSO uninduced 72h 1

description: replicate 1


title: Co male inject BNST mouse 249


title: Co male inject AMY mouse 249


title: DMSO uninduced 6h 2

description: replicate 2

source_name: LS174T-Snail1-HA, DMSO, 6 h


title: LDN uninduced 24h 1

description: replicate 1


title: Co male inject PFC mouse 249

value: PFC


title: Co male inject vCA1 mouse 247


title: Co male inject vCA3 mouse 247


title: Co male inject vDG mouse 247


title: Co male inject PVN mouse 247


title: DMSO doxycycline 6h 2

description: replicate 2

source_name: LS174T-Snail1-HA, DMSO + Dox, 6 h


title: Co male inject Pit mouse 247


title: Co male inject dDG mouse 247

source_name: dDG


title: Co male inject dCA3 mouse 249


title: Co male inject CER mouse 249


title: Co male inject vCA3 mouse 249


title: Co male inject dCA3 mouse 247


title: Co male inject dCA1 mouse 247


title: Co male inject CER mouse 247


title: Co male inject BNST mouse 247


title: Co male inject vDG mouse 245


title: Co male inject vCA3 mouse 245


title: Co male inject PFC mouse 247


title: Co male inject PFC mouse 245


title: Co male inject vCA1 mouse 245


title: Co male inject Pit mouse 245


title: Co male inject dDG mouse 245


title: Co male inject vCA3 mouse 243


title: Co male inject CER mouse 245


title: Co male inject BNST mouse 245


title: Co male inject AMY mouse 245

source_name: AMY


title: Co male inject dCA1 mouse 245


title: Co male inject dCA3 mouse 245


title: Co male inject vDG mouse 243


title: Co male inject PVN mouse 245


title: Co male inject PVN mouse 243


title: Co male inject vCA1 mouse 243


title: Co male inject dDG mouse 243


title: Co male inject dCA3 mouse 243


title: Co male inject CER mouse 243

source_name: CER


title: Co male inject Pit mouse 243


title: Co male inject PFC mouse 243


title: Co male inject dCA1 mouse 243


title: Co male inject AMY mouse 243


title: Co Male naive PVN mouse 241


title: Co Male naive vDG mouse 241


title: Co Male naive vCA3 mouse 241


title: Co male inject AMY mouse 247


title: Co male inject BNST mouse 243

description: sample has no processed data

source_name: BNST


title: Co Male naive Pit mouse 241


title: Co Male naive dCA3 mouse 241


title: Co Male naive PFC mouse 241


title: Co Male naive dDG mouse 241


title: Co Male naive CER mouse 241


title: Co Male naive vCA3 mouse 239


title: Co Male naive vDG mouse 239

source_name: vDG


title: Co Male naive BNST mouse 241


title: Co Male naive AMY mouse 241


title: DMSO uninduced 6h 1

description: replicate 1


title: Co Male naive PVN mouse 239


title: Co Male naive PFC mouse 239


title: Co Male naive Pit mouse 239


title: Co Male naive dCA1 mouse 241


title: Co Male naive dCA3 mouse 239


title: Co Male naive AMY mouse 239


title: Co Male naive vCA1 mouse 241


title: Co Male naive BNST mouse 239


title: Co Male naive dCA1 mouse 239


title: Co Male naive vCA1 mouse 239


title: Co Male naive CER mouse 239


title: Co male inject vDG mouse 237


title: Co male inject vCA1 mouse 237


title: Co male inject Pit mouse 237


title: Co male inject PVN mouse 237


title: Co male inject dDG mouse 237


title: Co male inject PFC mouse 237


title: Co male inject dCA3 mouse 237


title: Co male inject CER mouse 237


title: Co male inject AMY mouse 237


title: Co male inject BNST mouse 237


title: Co male inject vDG mouse 235


title: Co Male naive dDG mouse 239


title: Co male inject dCA3 mouse 235


title: Co male inject dDG mouse 235


title: Co male inject PVN mouse 235


title: Co male inject vCA3 mouse 235


title: Co male inject CER mouse 235


title: Co male inject BNST mouse 235


title: Co male inject PFC mouse 235


title: Co male inject Pit mouse 235


title: Co male inject vCA1 mouse 235


title: Co male inject dCA1 mouse 235


title: Co male inject PVN mouse 233


title: Co male inject vCA1 mouse 233


title: Co male inject vCA3 mouse 233


title: Co male inject vDG mouse 233


title: Co male inject Pit mouse 233


title: Co male inject dCA1 mouse 233


title: Co male inject PFC mouse 233


title: Co male inject BNST mouse 233


title: Co male inject dCA1 mouse 237


title: Co male inject CER mouse 233


title: Co male inject AMY mouse 233


title: Co Male naive vDG mouse 229

description: sample has no processed data


title: Co Male naive vCA3 mouse 229


title: Co Male naive vCA1 mouse 229


title: Co Male naive Pit mouse 229


title: Co male inject AMY mouse 235


title: Co Male naive dCA1 mouse 229


title: Co Male naive dCA3 mouse 229


title: Co Male naive PVN mouse 229


title: Co Male naive vDG mouse 227


title: Co Male naive BNST mouse 229


title: Co Male naive AMY mouse 229


title: Co Male naive PFC mouse 229


title: Co Male naive CER mouse 229


title: Co Male naive dDG mouse 229


title: Co male inject dDG mouse 233


title: Co Male naive vCA3 mouse 227


title: Co Male naive PVN mouse 227


title: Co Male naive vCA1 mouse 227


title: Co Male naive dDG mouse 227


title: Co Male naive PFC mouse 227


title: Co male inject dCA3 mouse 233


title: Co Male naive dCA3 mouse 227


title: Co Male naive dCA1 mouse 227


title: Co Male naive CER mouse 227


title: Co Male naive BNST mouse 227


title: Co Male naive AMY mouse 227


title: MS male naive vDG mouse 109


title: MS male naive PVN mouse 109

description: sample has no processed data


title: MS male naive Pit mouse 109


title: Co Male naive Pit mouse 227


title: MS male naive vCA3 mouse 109


title: MS male naive dDG mouse 109


title: MS male naive vCA1 mouse 109


title: MS male naive dCA3 mouse 109


title: MS male naive PFC mouse 109


title: MS male naive dCA1 mouse 109


title: MS male naive CER mouse 109


title: MS male naive BNST mouse 109


title: MS male naive vDG mouse 107


title: ATAC-seq_Zebrafish_EGFP-121-3_BL

city: Leuven

first: Stein

last: Aerts

address: O&N4 Herestraat 49 PO Box 602

country: Belgium

institute: KU Leuven

library_source: genomic

data_processing:
Data processing of human melanoma baseline OmniATAC-seq samples: Paired-end reads were mapped to the human genome (hg19-Gencode v18) using bowtie2 (v2.2.6). Mapped reads were sorted using SAMtools (v1.8) and duplicates were removed using Picard MarkDuplicates (v1.134). Reads were filtered by removing chromosomal reads and filtering for Q>30 using SAMtools. Bam files of technical replicates of the same cell line were merged at this point using samtools merge. Peaks were called using MACS2 (v2.1.2) callpeak using the parameters -q 0.05, --nomodel, --call-summits, --shift -75 --keep-dup all and --extsize 150 per sample. Chromosomal peaks, blacklisted regions (ENCODE) and peaks overlapping with alternative chromosomes were removed. Summits were extended by 250bp up- and downstream using slopBed (bedtools; v2.28.0), providing human chromosome sizes. Peaks were normalised for the library size using a custom script and overlapping peaks were filtered using the peak score by keeping the peak with the highest score. For visualisation in IGV, normalised bigWigs were made by bamCoverage (Deeptools, v3.3.1), using as parameters --normalizeUsing None, -bl EncodeBlackListedRegions --effectiveGenomeSize 2913022398 and as scaling parameter (-scaleFactor) 1/(RIP/1E6), where the RIP stands for the number of reads in peaks.
Data processing of non-human (Omni)ATAC-seq samples, and of human SOX10 and TFAP2A knock-down OmniATAC-seq data: Adapter sequences were trimmed from the fastq files using fastq-mcf (as part of eautils; v1.05) and the read quality was checked using FastQC (v0.11.8). Reads were mapped using STAR (v2.5.1b) (for the zebrafish samples paired-end reads were mapped) to the genome which were downloaded from UCSC (http://hgdownload.cse.ucsc.edu/goldenPath/) (for human: hg19-Gencode v18; for dog: canFam3; for horse: equCab2; for pig: susScr11; for mouse: mm10; for zebrafish: danRer10) and by applying the parameters --alignIntronMax 1 and --aslignIntronMin 2. Mapped reads were filtered for quality using SAMtools (v1.2) view with parameter –q4, sorted with SAMtools sort and indexed using SAMtools index. Peaks were called using MACS2 (v2.1.2) callpeak using the parameters -q 0.05, --nomodel, --call-summits, --shift -75 --keep-dup all and with the genome size for the correct species in --g, and this for each sample per species separately. Summits were extended by 250bp up- and downstream using slopBed (bedtools; v2.28.0), providing the chromosome sizes for the specific species. Per sample, peaks were normalised for the library size using a custom script and overlapping peaks were filtered using the peak score (keeping the highest scoring peak). Normalised bedGraphs were produced by genomeCoverageBed (as part of bedtools; v2.28.0) using as scaling parameter (-scale) 1E6/(number of non-chromosomal mapping reads). BedGraphs were converted to bigWigs by the bedtools suit functions bedSort to sort the bedGraphs, followed by bedGraphToBigWig to create the bigWigs, which were used in IGV for visualisation.
Genome_build: For human: hg19-Gencode v18; for dog: canFam3; for horse: equCab2; for pig: susScr11; for mouse: mm10; for zebrafish: danRer10.
Supplementary_files_format_and_content: bigWig files represent the coverage of the ATAC-seq signal.

organism: Danio rerio

source_name: Melanoma cell line

growth_protocol:
Cells were cultured in DMEM medium (Life Technologies) supplemented with 10% heat-inactivated FBS (Atlanta Biologicals), 1X GlutaMAX (Life Technologies) and 1% Penicillin-Streptomycin (Life Technologies), at 28°C, 5% CO2.
Mentioned per sample in the SAMPLE section.

extract_protocol:
Cells were washed, trypsinised, spun down at 1000 RPM for 5 min, medium was removed and the cells were resuspended in 1 mL medium. Cells were counted and experiments were only continued when a viability of above 90% was observed. 50,000 cells were used per sample. OmniATAC-seq was performed as described previously in Corces et al., 2017; and ATAC-seq as described in Buenrostro et al., 2015.
Library prep was performed as described before in Corces et al., 2017 for OmniATAC-seq samplas; and as in Buenrostro et al., 2013 for ATAC-seq samples.

treatment_protocol: For the knock-down data: SOX10, TFAP2A and the control knockdown was performed in MM001 using respectively a SMARTpool of four siRNAs against, respectively, SOX10 (SMARTpool: ON-TARGETplus SOX10 siRNA, number L017192-00-0005, Dharmacon), TFAP2A (SMARTpool: ON-TARGETplus TFAP2A siRNA, number L-006348-02-0005, Dharmacon) and a negative control pool (ON-TARGETplus non-targeting pool, number D-001810-10-05, Dharmacon) at a concentration of 20 nM for SOX10-KD, and 40 nM for TFAP2A-KD and the control using as medium Opti-MEM (Thermo Fisher Scientific) and omitting antibiotics. The cells were incubated for 72 h before processing.

tag: tissue type

value: Melanoma form MiniCoopR zebrafish model

tag: condition

value: Baseline


title: MS male naive vCA1 mouse 107


title: Co male inject vCA3 mouse 237


title: MS male naive AMY mouse 109


title: ATAC-seq_Zebrafish_EGFP-121-5_BL


title: ATAC-seq_Zebrafish_EGFP-121-1_BL


title: MS male naive vCA3 mouse 107


title: MS male naive PVN mouse 107

source_name: PVN


title: MS male naive Pit mouse 107


title: MS male naive PFC mouse 107


title: 542_PB21_C2

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

data_processing:
Library strategy: Bar-Seq
Barcode sequences were extracted with the TagDust software (v2.33)
Extracted barcode sequences were processed with an ad-hoc script to merge similar (erroneous) barcodes
Supplementary_files_format_and_content: Tab-separated matrix with barcode counts

source_name: PBMCs from xenotransplanted NSG mice

extract_protocol:
QIAamp DNA Micro Kit (QIAGEN)
Custom library construction protocol. PCR amplicons for each individual sample were generated by nested PCR starting from >50-100 ng of purified gDNA. The first PCR step was performed with GoTaq Hot Start Polymerase (Promega) according to manufacturer instruction using the following amplification protocol: 95°C x 5’, (95°C x 0.5’, 60°C x 0.5’, 72°C x 0.5’) x 20 cycles, 72°C x 5’. Forward primers were designed to bind donor template upstream the BAR sequence, while the reverse primers annealed outside the homology region, thus amplifying 328 bp of the on-target integrated cassette. Exclusively for targeted sequencing of the transfer vector plasmid and AAV library, the reverse primer annealed to the downstream homology region. The second PCR step was performed with GoTaq G2 DNA Polymerase (Promega) according to manufacturer instruction using 5 µl of the first-step PCR product and the following amplification protocol: 95°C x 5’, (95°C x 0.5’, 60°C x 0.5’, 72°C x 0.5’) x 20 cycles, 72°C x 5’. Second-step PCR primers were endowed with tails containing P5/P7 sequence, i5/i7 Illumina tag to allow multiplexed sequencing and R1/R2 primer complementary sequence. PCR library amplicons were separately purified using MinElute PCR Purification kit (QIAGEN) and AmpPure XP beads (Invitrogen).
NextTera Illumina

tag: cell type

value: Peripheral blood mononuclear cells

tag: timepoint

value: 18-21 wks post-transplant

tag: facs sorting

value: no


title: 542_PB21_C0


title: MS male naive dDG mouse 107


title: 542_PB21_A4


title: 542_PB21_C3


title: 542_PB21_A3


title: ATAC-seq_Zebrafish_ZMEL1_BL


title: MS male naive dCA3 mouse 107


title: MS male naive CER mouse 107


title: 542_PB21_A1


title: 542_PB21_A0


title: MS male naive dCA1 mouse 107


title: MS male naive BNST mouse 107


title: 542_BM_C3

source_name: Total bone marrow-derived cells from xenotransplanted NSG mice

value: Bone-marrow derived cells


title: 542_BM_C2


title: 542_PB21_C1


title: MS male naive AMY mouse 107

value: Male Balb/c mice


title: 542_BM_A4


title: MS male naive vDG mouse 105


title: 542_BM_C1


title: MS male naive vCA3 mouse 105


title: MS male naive vCA1 mouse 105


title: 542_BM_A0


title: MS male naive Pit mouse 105


title: 542_PB21_A2


title: 583_E3

source_name: Total human splenocyte from xenotransplanted NSG mice

value: Splenocytes

value: yes


title: MS male naive PFC mouse 105

source_name: PFC

value: post natal day 9


title: MS male naive PVN mouse 105


title: 583_E2


title: MS male naive dDG mouse 105


title: 583_E1


title: MS male naive dCA3 mouse 105


title: FFPE_tumour_4

city: Dublin 4

first: Antoinette

last: Perry

address: Belfield

country: Ireland

institute: University College Dublin

description: Prostate tumour tissue

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

scan_protocol: iScan

label: Cy3, Cy5

source_name: prostate

label_protocol: Cy3, Cy5

extract_protocol: Genomic DNA from tissue biopsies were subjected to deparaffinisation, macro-dissection and extracted using QIAamp DNA FFPE tissue kit. cfDNA was isolated from 3 ml of plasma, using the QIAamp Circulating Nucleic Acid (Qiagen). DNA from urine sediments was extracted using the AllPrep DNA/RNA/mRNA Universal kit (Qiagen).

treatment_protocol: All samples were bisulfite modified using the Zymo EZ DNA methylation kit.

tag: patient id

value: Patient 4

tag: gender

value: Male

tag: age at diagnosis (years)

tag: psa (ng/ml)

tag: metastases location

value: Bone

tag: gleason score

value: 5+5 (LHS and RHS)


title: MS male naive dCA1 mouse 105

tag: strain

tag: tissue

tag: age

tag: animal

tag: status


title: FFPE_tumour_2

description: Prostate tumour tissue

value: Patient 2


title: MS male naive CER mouse 105

value: CER

tag: injection


title: 583_C2


title: 583_C3


title: 583_C1


title: Urine_sediment_2

description: Urine Sediment

source_name: urine sediment


title: MS male naive vDG mouse 103

value: vDG


title: 583_C0


title: 583_B3


title: FFPE_benign_2

description: Prostate matched normal tissue


title: MS male naive BNST mouse 105

value: BNST


title: MS male naive vCA1 mouse 103


title: Urine_sediment_3

description: Urine Sediment

value: Patient 3


title: 583_B2


title: 583_B0


title: 542_BM_A1


title: MS male naive AMY mouse 105

value: AMY


title: MS male naive PVN mouse 103

value: PVN


title: MS male naive Pit mouse 103

source_name: Pit

value: Pit


title: 583_A3

value: 18-21 wks post-transplant


title: FFPE_benign_3

description: Prostate matched normal tissue


title: MS male naive PFC mouse 103

value: Male Balb/c mice

value: PFC


title: 583_A2

value: Splenocytes

value: yes


title: Urine_sediment_4

description: Urine Sediment

value: Patient 4


title: FFPE_tumour_3

description: Prostate tumour tissue

value: Male


title: Plasma_cfDNA_4

description: Plasma sample

source_name: blood plasma

value: Bone


title: 583_A1


title: Plasma_cfDNA_3

description: Plasma sample


title: MS male naive dCA3 mouse 103

value: post natal day 9


title: Urine_sediment_1

description: Urine Sediment

value: Patient 1

value: 4+4 (LHS and RHS)


title: 583_A0


title: Plasma_cfDNA_1

description: Plasma sample


title: MS male naive CER mouse 103

value: CER


title: FFPE_benign_1

description: Prostate matched normal tissue


title: 577_SPL_F2


title: MS male naive BNST mouse 103

value: BNST


title: 577_SPL_F3


title: 577_SPL_F0


title: FFPE_benign_4

description: Prostate matched normal tissue

value: 5+5 (LHS and RHS)


title: MS male naive vDG mouse 101

value: vDG


title: 577_SPL_E2


title: Plasma_cfDNA_2

description: Plasma sample

value: Patient 2


title: MS male naive vCA3 mouse 101


title: 577_SPL_E1


title: 577_SPL_D2


title: MS male naive PVN mouse 101

value: PVN


title: MS male naive AMY mouse 103

value: AMY


title: FFPE_tumour_1

description: Prostate tumour tissue


title: 577_SPL_D1

value: 18-21 wks post-transplant


title: MS male naive Pit mouse 101

value: Male Balb/c mice

value: Pit


title: 577_SPL_E3

value: Splenocytes

value: yes


title: 577_SPL_D0


title: 577_SPL_C2


title: MS male naive PFC mouse 101

value: PFC


title: MS male naive dCA3 mouse 101


title: 577_SPL_C0


title: MS male naive dCA1 mouse 101


title: MS male naive dCA1 mouse 103


title: 577_SPL_C1


title: MS male naive CER mouse 101


title: MS male naive dDG mouse 103

value: dDG


title: 577_SPL_B2


title: MS male naive dDG mouse 101

value: post natal day 9


title: MS male naive vCA1 mouse 101


title: 732_SPL_B4

source_name: Total splenocyte from xenotransplanted NSG mice

value: no


title: 577_SPL_B0


title: MS male naive AMY mouse 101


title: 732_SPL_B3


title: 583_E0


title: 732_SPL_B2


title: 577_SPL_C3


title: 577_SPL_B1


title: 732_SPL_B1


title: 577_SPL_B3


title: 732_SPL_B0


title: 732_SPL_A2


title: 732_SPL_A3


title: MS male naive BNST mouse 101


title: 732_SPL_A1


title: 732_BM_B4

value: Bone-marrow derived cells


title: 732_SPL_A0


title: FTO CLIP-seq

city: philadelphia

first: Fange

last: Liu

state: PA

address: 415 curie blvd, Clinical Research Building Rm 350

institute: UPENN

data_processing:
exomePeak was used to call m6A different peaks between siTRMT10A and siCtrl.
CTK was used to call TRMT10A CLIP peaks.
PARalyzer was used to call FTO CLIP peaks.
Gene expression levels were normalized using DEseq2
Genome_build: hg38
Supplementary_files_format_and_content: m6A_diff_peak file contains different m6A peaks between siTRMT10A and siCtrl, *xlsx files include CLIP peaks

growth_protocol: HEK293T cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% FBS and 1% Pen/Strep in 37 °C, 5% CO2 incubator.

extract_protocol:
For m6A-IP,total RNA was purified by TRIzol reagent (Invitrogen), following the manufacture’s instruction. mRNA was extracted from the total RNA by using Dynabeads mRNA Purification Kit (Ambion) following the instruction. The rRNA was further removed by RiboMinus Eukaryote Kit (Invitrogen). mRNA was fragmented by sonication. The m6A-immunoprecipitation was performed using NEB EpiMark N6-Methyladenosine Enrichment Kit (E1610S). For CLIP, FTO or TRMT10A overexpression cells were UV crosslinked three times in a Stratagene Stratalinker 2400 UV Crosslinker. After irradiation, cells were harvested by cell lifter and pelleted by centrifugation at 500g for 4 min at 4 ℃. The pellet was then resuspended in lysis buffer (1 x PBS supplemented with 0.1% SDS, 1% Nonidet P-40, 0.5% Sodium Deoxycholate, Protease Inhibitor Cocktail) and kept on ice for 15 min. T1 digestion was carried out under 2 U/μl for 15 min at 22 °C. 200 μl anti-Flag beads (Millipore, M8823) were subsequently added to the supernatant and kept at 4 °C for overnight with rotation. The beads were then washed for 3 times with 1 ml of high salt buffer (5 x PBS supplemented with 0.1% SDS, 1% Nonidet P-40 and 0.5% Sodium Deoxycholate) and another 3 times with 1 ml of wash buffer (20 mM Tris-HCl, pH 7.4, 10 mM MgCl2 and 0.2% Tween-20). The RNAs were then isolated by 200 μl of elution buffer (100 mM Tris-HCl, pH 7.4, 10 mM EDTA, and 1% SDS) containing 2 mg/ml proteinase K under incubation at 37 °C for 40 min. The beads were removed and RNAs were recovered by RNA Clean & Concentrator (Zymo Research).
m6A profiling libraries were constructed by TruSeq stranded mRNA samples preparation kit from Illumina. CLIP-seq libraries were constructed by NEBNext® Small RNA Library Prep Set for Illumina (NEB7330).

treatment_protocol: Cells were treated with TRMT10A siRNA or control siRNA.

tag: cell line

tag: genotype

value: FTO overexpression


title: TRMT10A CLIP-seq rep3

value: TRMT10A overexpression


title: 583_B1

tag: cell type


title: 732_BM_B2

tag: timepoint


title: 732_BM_B1

tag: facs sorting


title: 732_BM_B3


title: 732_BM_B0


title: MS male naive vCA3 mouse 103


title: TRMT10A CLIP-seq rep1


title: 732_BM_A3


title: PRKAB2-/- clone 2 [8489R5_20_IndexD703-D504_CGCTCATT+GGCTCTGA]

city: Frankfurt am Main

first: Daniel

last: Margerie

address: Industrial Park Hoechst, Building H831

department: R&D, Digital Data Sciences

institute: Sanofi-Aventis Deutschland GmbH

description: 8489R5_20_IndexD703-D504_CGCTCATT+GGCTCTGA_L001

data_processing:
Bioinformatics analysis of RNASeq raw data has been performed using the Array Studio software package version 10.1.2.9 from OmicSoft (QIAGEN).
Mapping of RNASeq reads (fastq files) to the human genome has been done using Omicsoft gene model 20130723 with human B37.3 as reference genome and OSA4 as aligner.
To detect differentially expressed genes the DESeq2 statistical test has been applied to the comparison between the PRKAB1-/- and PRKAB2-/- clones vs. wildtpye. P-values were adjusted using the Benjamini-Hochberg procedure to control false discovery rates.
Genome_build: human B37.3
Supplementary_files_format_and_content: abundance measurements

source_name: PRKAB2-/-_human iPSCs_clone 2

growth_protocol: iPS cells were grown in mTeSR1 medium (Stemcell Technologies) and cultured according to the manufacturer's instructions

extract_protocol: total RNA was isolated using the RNeasy® Mini Kit (QIAGEN)

value: human induced pluripotent stem cells (iPSCs)

tag: genotype/variation

tag: developmental stage

value: undifferentiated


title: PDGF exosome

city: Incheon

first: Hara

last: Kang

address: 119 Academy-ro

country: South Korea

institute: Incheon National University

data_processing:
bcl2fastq v1.8.4 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To identify miRNA sequences, the unique sequences found after clustering were searched on the miRBase database by blast.
For non-miRNA sequences of unmatched trimmed read excluded from miRBase, they are blasted to non-miRNA of Rfam database.
Genome_build: hg38
Supplementary_files_format_and_content: Excel files include Read counts for each Sample

source_name: exosomes derived from human pulmonary artery smooth muscle cells

extract_protocol:
RNAs were extracted from exosomes isolated from  human pulmonary artery smooth muscle cell medium. Poly(A) mRNA using the Illumina  TruSeq RNA Sample Prep Kit v2, according to the manufacturer’s instructions.
Libraries were prepared for multiplex sequencing using Illumina TruSeq RNA Sample Prep Kit , according to the manufacturer’s protocol.

value: Cultured smooth muscle cell

value: Control


title: MOCK exosome


title: PRKAB2-/- clone 2 [8489R5_19_IndexD703-D503_CGCTCATT+CCTATCCT]

description: 8489R5_19_IndexD703-D503_CGCTCATT+CCTATCCT_L001


title: 732_BM_A2


title: 732_BM_A1


title: PAX7Venus 3wks_biological rep1

city: Boston

first: Olivier

last: Pourquie

state: MASSACHUSETTS

address: 60 Fenwood Road

department: Department of Pathology

institute: Brigham and Women’s Hospital

description:
Gene expression data from iPS-derived skeletal muscle cells
PAX7Venus_3wks-1  RMA Signal

hyb_protocol: Following fragmentation, cRNAs were hybridized on GeneChip Human Gene 2.0ST Arrays. Each microarray was then washed and stained on a GeneChip fluidics station 450 and further scanned with a GeneChip Scanner 3000 7G.

scan_protocol: Raw data (CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip Command Console (AGCC) version 1.4.1.46

data_processing: Initial filtering and preprocessing, including background correction, quantile normalization and summarization, was performed using both RMA and MAS with the R Bioconductor package (R version 2.12.1, Bioconductor version 2.8). Expression sets were then filtered according to Calls information. Probe sets expression fold changes between conditions (biological triplicates) were calculated using the “Comparative Marker Selection” module of GenePattern (Reich et al., 2006). Volcano and FcFc scatter plots were generated using the Multiplot application of GenePattern. Histogram expression profiles of gene probe sets were generated from MAS values. Further analysis was performed using the Manteia database (Tassy and Pourquie, 2014) and DAVID Functional Annotation tools (Huang da et al., 2009). Hierarchical clustering was performed on Microarray RMA data. Clustering was computed with an Average linkage method and Euclidean distances. Both an Approximately unbiased (AU) and Bootstrap probability (BP) P values were calculated (pvclust, R package).

label: biotin

source_name: FASC sorted PAX7-Venus cells at 3 weeks of myogenic differentiation

label_protocol: Biotinylated cRNA targets were prepared from total RNA using a double amplification protocol according to the GeneChip Expression Analysis Technical Manual: Two-Cycle Target Labeling Assay (P/N 701021 Rev.5, Affymetrix, Santa Clara, USA).

growth_protocol: iPS cells were cultured on Matrigel (BD Biosciences)-coated dishes in mTesR1 media (Stem Cell Technologies). Cells were passaged as aggregates or as single cells.

extract_protocol: Cells were purified by FACS from differentiated cultures using an Aria (BD Biosciences) or a S3 cell sorter (Bio-Rad). Gating was determined for each reporter line using corresponding undifferentiated culture as a baseline control.

treatment_protocol: Serum-free myogenic differentiation of human iPS lines was performed as described previously (Chal et al., 2016; Chal et al., 2015)

tag: cells

value: human iPS-derived PAX7


title: TRMT10A CLIP-seq rep2


title: PRKAB2-/- clone 2 [8489R5_18_IndexD703-D502_CGCTCATT+ATAGAGGC]

description: 8489R5_18_IndexD703-D502_CGCTCATT+ATAGAGGC_L001


title: 732_BM_A0

value: 18-21 wks post-transplant


title: PRKAB2-/- clone 2 [8489R5_17_IndexD703-D501_CGCTCATT+TATAGCCT]

description: 8489R5_17_IndexD703-D501_CGCTCATT+TATAGCCT_L001


title: up 200+ moi 10

city: Seoul

first: Mukesh

middle: Kumar

last: Yadav

state: Seoul

department: Institute for Medical Device Clinical Trials

institute: Korea University

data_processing:
The raw .cel file generated through above procedure meant expression intensity data used for expression data generation by Affymetrix Expression Console software version1.1. For the normalization, RMA (Robust Multi-Average) algorithm implemented in Affymetrix Expression Console software was used.
The change of gene expressions by 2-fold in treated samples with respect to control sample (untreated) was considered significant. The gene ontology (GO) and KEEG pathway analysis was performed using DAVID (http://david.abcc.ncifcrf.gov/), string and Medline databases (http://www.ncbi.nlm.nih.gov/).

source_name: Human middle ear epithelial cells treated with streptococcus pneumonaie+ uraban particles (up200+moi 10)

label_protocol: The cDNA was fragmented by UDG and APE 1 restriction endonucleases and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide. Fragmented end-labeled cDNA was hybridized to the GeneChip® Human Gene 2.0 ST arrays for 16 hours at 45°C at 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix). After hybridization, the chips were stained using SAPE (Streptavidin Phycoerythrin) and washed in a Genechip Fluidics Station 450 (Affymetrix). After the final wash and staining, the Affymetrix GeneChip® Human Gene 2.0 ST oligonucleotide array was scanned using Affymetrix Model 3000 G7 scanner and the image data was extracted through Affymetrix Commnad Console software1.1.

growth_protocol: The HMEECs were maintain and routinely culture in airway epithelial cell growth medium (PromoCell GmbH, Sickingenstr Heidelberg Germany) supplemented with bovine pituitary extract (0.004 mL/mL), epidermal growth factor (10 ng/mL), insulin (5 µg/mL), hydrocortisone (0.5 µg/mL), epinephrine (0.5 µg/mL), triiodo-L-thyronine (6.7 ng/mL), transferrin (10 µg/mL), retinoic Acid (0.1 ng/mL) and 1% fetal bovine serum and 5% CO2. 1× 10^4 HMEECs were seeded in 96-well plate and incubated at 37°C with 5% CO2 for 24 h.

extract_protocol: Total RNA of HMEECs was extracted using Trizol reagent (Invitrogen, USA), and RNA quality was assessed by Agilent 2100 bioanalyser (Agilent Technologies, USA), and quantity was determined by ND-1000 spectrophotometer (NanoDrop Technologies, USA).

treatment_protocol: Following incubation cells were washed with PBS and medium was replaced with UP (200 µg/mL) containing medium (antibiotic free medium) and further incubated for 8 h or the HMEECs pre-exposed to UP were infected with S. pneumoniae (MOI 10) for 15 h.

value: HMEECs

tag: agent

value: treated with streptococcus pneumonaie+urban perticles


title: hiPS undif_biological rep1 [re-analyzed]

description:
Gene expression data from undifferentiated iPS cells (Pluripotent)
hiPS_undif-1  RMA Signal

source_name: Undifferentiated iPS cells (Pluripotent)

value: human iPS (NCRM-1, RUCDR)


title: UP 200

hyb_protocol: Fragmented end-labeled cDNA was hybridized to the GeneChip® Human Gene 2.0 ST arrays for 16 hours at 45°C at 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix). After hybridization, the chips were stained using SAPE (Streptavidin Phycoerythrin) and washed in a Genechip Fluidics Station 450 (Affymetrix). After the final wash and staining, the Affymetrix GeneChip® Human Gene 2.0 ST oligonucleotide array was scanned using Affymetrix Model 3000 G7 scanner and the image data was extracted through Affymetrix Commnad Console software1.1.

source_name: Human middle ear epithelial cells with urban particles 200ug/ml(up 200)

value: treated with urban particles


title: 732_12_B4

value: Peripheral blood mononuclear cells

value: 12 wks post-transplant


title: PRKAB2-/- clone 1 [8489R5_16_IndexD702-D508_TCCGGAGA+GTACTGAC]

description: 8489R5_16_IndexD702-D508_TCCGGAGA+GTACTGAC_L001

source_name: PRKAB2-/-_human iPSCs_clone 1


title: Control

scan_protocol: After the final wash and staining, the Affymetrix GeneChip® Human Gene 2.0 ST oligonucleotide array was scanned using Affymetrix Model 3000 G7 scanner and the image data was extracted through Affymetrix Commnad Console software1.1.

source_name: Human middle ear epithelial cells untreated

value: untreated


title: PAX7Venus 3wks_biological rep2

description:
Gene expression data from iPS-derived skeletal muscle cells
PAX7Venus_3wks-2  RMA Signal


title: MOI 10

source_name: Human middle ear epithelial cells threated with streptococcus pneumonaie (moi10)

value: treated with streptococcus pneumoniae


title: hiPS undif_biological rep2 [re-analyzed]

description:
Gene expression data from undifferentiated iPS cells (Pluripotent)
hiPS_undif-2  RMA Signal


title: PAX7Venus 3wks_biological rep3

description:
Gene expression data from iPS-derived skeletal muscle cells
PAX7Venus_3wks-3  RMA Signal


title: 732_12_B3

source_name: PBMCs from xenotransplanted NSG mice

value: no


title: PRKAB2-/- clone 1 [8489R5_15_IndexD702-D507_TCCGGAGA+CAGGACGT]

description: 8489R5_15_IndexD702-D507_TCCGGAGA+CAGGACGT_L001


title: PRKAB2-/- clone 1 [8489R5_14_IndexD702-D506_TCCGGAGA+TAATCTTA]

description: 8489R5_14_IndexD702-D506_TCCGGAGA+TAATCTTA_L001


title: 732_12_B1


title: 732_12_B2


title: PRKAB1-/- clone 2 [8489R5_12_IndexD702-D504_TCCGGAGA+GGCTCTGA]

description: 8489R5_12_IndexD702-D504_TCCGGAGA+GGCTCTGA_L001

source_name: PRKAB1-/-_human iPSCs_clone 2


title: hiPS undif_biological rep3 [re-analyzed]

description:
Gene expression data from undifferentiated iPS cells (Pluripotent)
hiPS_undif-3  RMA Signal


title: 732_12_A2


title: PRKAB1-/- clone 2 [8489R5_10_IndexD702-D502_TCCGGAGA+ATAGAGGC]

description: 8489R5_10_IndexD702-D502_TCCGGAGA+ATAGAGGC_L001


title: PRKAB1-/- clone 2 [8489R5_09_IndexD702-D501_TCCGGAGA+TATAGCCT]

description: 8489R5_09_IndexD702-D501_TCCGGAGA+TATAGCCT_L001


title: PRKAB1-/- clone 2 [8489R5_11_IndexD702-D503_TCCGGAGA+CCTATCCT]

description: 8489R5_11_IndexD702-D503_TCCGGAGA+CCTATCCT_L001


title: 732_12_A1


title: 732_8_B4

value: 8 wks post-transplant


title: PRKAB1-/- clone 1 [8489R5_08_IndexD701-D508_ATTACTCG+GTACTGAC]

description: 8489R5_08_IndexD701-D508_ATTACTCG+GTACTGAC_L001

source_name: PRKAB1-/-_human iPSCs_clone 1


title: 732_12_A0


title: PRKAB1-/- clone 1 [8489R5_07_IndexD701-D507_ATTACTCG+CAGGACGT]

description: 8489R5_07_IndexD701-D507_ATTACTCG+CAGGACGT_L001


title: 732_8_B3


title: 732_8_B2


title: PRKAB1-/- clone 1 [8489R5_06_IndexD701-D506_ATTACTCG+TAATCTTA]

description: 8489R5_06_IndexD701-D506_ATTACTCG+TAATCTTA_L001


title: PRKAB1-/- clone 1 [8489R5_05_IndexD701-D505_ATTACTCG+AGGCGAAG]

description: 8489R5_05_IndexD701-D505_ATTACTCG+AGGCGAAG_L001


title: WT [8489R5_04_IndexD701-D504_ATTACTCG+GGCTCTGA]

description: 8489R5_04_IndexD701-D504_ATTACTCG+GGCTCTGA_L001

source_name: WT_human iPSCs

value: WT


title: WT [8489R5_03_IndexD701-D503_ATTACTCG+CCTATCCT]

description: 8489R5_03_IndexD701-D503_ATTACTCG+CCTATCCT_L001

value: human induced pluripotent stem cells (iPSCs)


title: WT [8489R5_02_IndexD701-D502_ATTACTCG+ATAGAGGC]

description: 8489R5_02_IndexD701-D502_ATTACTCG+ATAGAGGC_L001

value: undifferentiated


title: 732_8_A2


title: 732_8_A3


title: WT [8489R5_01_IndexD710-D502_TCCGCGAA+ATAGAGGC]

description: 8489R5_01_IndexD710-D502_TCCGCGAA+ATAGAGGC_L001


title: 732_8_B1


title: 732_8_A1


title: 732_8_A0


title: RPE190_Con_RNAseq

city: Stanford

first: Tomek

last: Swigut

state: CA

address: 265 Campus Dr

department: Chemical and Systems Biology

institute: Stanford University

description: RNAseq of human RPE

data_processing:
Basecalls performed using CASAVA
Reads were aligned to hg19 with top hat 2.2.14 using default settings
Transcript model coverage (GENCODE V24) was calculated with featureCounts.
TPM were calculated TPM using formula without read length correction.
Genome_build: hg19
Supplementary_files_format_and_content: CSV of TPM (transcripts per million)

source_name: Retinal Pigmented Epithelial Cells

growth_protocol: Human whole globes and posterior shells (globes without anterior segments) from donors aged 36-90 years within 40 hours of death were obtained from the National Disease Research Interchange, Philadelphia, PA., the Eye-Bank for Sight Restoration, Inc., New York, NY, the Lions Eye Bank, Albany, NY and Miracle In Sight, Winston-Salem, NC. Eye dissection and culture protocols were as published (Blenkinsop et al., 2013; Fernandes M., 2018). RPE cells were isolated and plated on tissue culture plates coated with Synthemax II (Corning) in RPE medium with 10% FBS and 10mMNAM, and fed 3x/week;after the first week, FBS was reduced to 2%.

extract_protocol:
RNA was isolated with TRIZOL
Sequencing libraries were prepared starting from ~30ng polyA enriched cDNA with NEBNext Multiplex Oligos for Illumina kit

treatment_protocol: RPE cultures were treated with 0.25% Trypsin for 5 mins., washed and replated at 3x104 cells per 1.9mm2 in a 24-well plate in DMEM/F12+5%FBS, L-Glutamine, Na-Pyruvate, NEAA, Pen/Strep. After 24 hrs, 10ng/ml TGFβ1 or 10ng/ml TNFα, or 10ng/ml of each (TNT) were added versus vehicle as control, and cultures were fed every other day for 5 days.

value: Retinal Pigmented Epithelial Cells

tag: treatment


title: 566_2nd_CD34_H3

source_name: Human bone marrow-derived HSPCs from xenotransplanted NSG mice (secondary recipients)

value: Hematopoietic stem/progenitor cells

value: 15 wks post secondary transplant

value: yes


title: PRKAB2-/- clone 1 [8489R5_13_IndexD702-D505_TCCGGAGA+AGGCGAAG]

description: 8489R5_13_IndexD702-D505_TCCGGAGA+AGGCGAAG_L001


title: 566_2nd_CD34_H2


title: 566_2nd_CD34_H1


title: 732_12_B0


title: 732_12_A3


title: RPE188_TnT_RNAseq

description: RNAseq of human RPE treated with TNF-alpha and TGF-beta

value: TNF-alpha + TGF-beta


title: RPE188_Con_RNAseq

description: RNAseq of human RPE


title: OmniATAC-seq_Horse_HoMel-A1_BL

organism: Equus caballus

source_name: Melanoma cell line

growth_protocol:
Cells were cultured at 37°C with 5% CO2 in Roswell Park Memorial Institute (RPMI) medium (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS; Invitrogen) and 1% penicillin/streptomycin (Thermo Fisher Scientific).
Mentioned per sample in the SAMPLE section.

tag: tissue type

value: Dermal–epidermal skin melanoma metastasis from a Shagya-Arabian mare

tag: condition

value: Baseline


title: 566_2nd_CD34_H0


title: 566_2nd_CD34_G1


title: 732_8_B0


title: OmniATAC-seq_Horse_HoMel-L1_BL

value: Primary dermal melanoma from a Lipizzaner stallion


title: RPE190_TnT_H3K27ac ChIP-Seq

data_processing:
Basecalls performed using CASAVA
Reads were aligned to hg19 with bowtie 2.2.4 using default settings
genome coverage was calculated with genomeCoverageBed -bg -scale, with scaling factor 10^-6*total aligned reads
genome coverage file was converted to bigwig with bedGraphToBigWig (Kent tools)
Genome_build: hg19
Supplementary_files_format_and_content: BigWig of normalized  ChIP read density: reads per base per million

extract_protocol:
ChIPs were performed using approximately 10^7 cells fixed with 1% formaldehyde for 10 min at room temp.
Sequencing libraries were prepared starting from ~30ng of ChIP DNA with NEBNext Multiplex Oligos for Illumina kit

tag: tissue

tag: antibody

value: H3K27ac (39133, Active Motif)


title: 566_2nd_CD34_G0


title: RPE190_TnT_ChIP-Seq input


title: 566_2nd_CD34_F1


title: RPE190_Con_H3K27ac ChIP-Seq


title: 566_2nd_CD34_F0


title: PIP025mut

city: Ann Arbor

first: Michelle

last: Brinkmeier

state: MI

address: 1241 Catherine St., 5704 MSII

department: Human Genetics

institute: University of Michigan

data_processing:
Sequencing reads were analyzed by the University of Michigan Bioinformatics Core.  The quality of the raw reads data for each sample was confirmed using FastQC (version 0.10.1) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content, etc.).
The Tuxedo Suite software package was utilized for alignment, differential expression analysis, and post-analysis diagnostics
Reads were aligned to the combined reference mRNA and lncRNA total transcriptome (UCSC mm10) (http://genome.ucsc.edu/) using TopHat (version 2.0.9) and Bowtie (version 2.1.0.).  Default parameter settings were used for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments.
FastQC was used for a second round of quality control (post-alignment), to ensure that only high-quality data would be input to expression quantitation and differential expression analysis.
Cufflinks/CuffDiff (version 2.1.1) was used for expression quantitation, normalization, and differential expression analysis, using UCSC mm10.fa as the reference genome sequence. For this analysis, the parameter settings: “--multi-read-correct” were used to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile –norm” for normalization of expression values.
We used locally developed scripts to format and annotate the differential expression data output from CuffDiff. Briefly, we identified genes and transcripts as being differentially expressed based on three criteria: test status = “OK”, FDR 0.05 and fold change ≥ ± 1.5.
Genome_build: NCBI Refseq Release 73
Supplementary_files_format_and_content: Both files are excel spreadsheets.  WT_v_Mutant_DE.xlsx gives a list of differentially expressed genes between the combined WT set and the combined Mutant set.  BrinkmeierRNAseq_individual_sample_FPKM.xlsx gives a list of differentially expressed genes showing FPKM values of individual samples.

source_name: whole P0 pituitary, posterior lobe removed

extract_protocol:
RNAqueso Micro Total RNA Kit,  Ambion
Libraries were prepared from the RNA using the TruSeq RNA Library Prep Kit v2 (Illumina) by the University of Michigan Sequencing Core.  The quality of the library preps was confirmed using the Bioanalyzer 2200 (Agilent, Santa Clara, CA).

value: whole pituitary, posterior lobe removed

value: Postnatal day 0

tag: sample id


title: RPE190_TnT_RNAseq


title: PIP030mut


title: PIP026mut


title: 566_2nd_CD33_H3

source_name: Human splenic myeloid cells from xenotransplanted NSG mice (secondary recipients)

value: Myeloid cells


title: RPE190_Con_ChIP-Seq input


title: 566_2nd_CD33_H2


title: PIP021mut


title: 566_2nd_CD33_H1


title: 566_2nd_CD33_H0


title: 566_2nd_CD33_G1


title: PIP014mut


title: RPE188_TnT_H3K4me3 ChIP-Seq

value: H3K4me3 (39159, Active Motif)


title: RPE188_TnT_H3K4me1 ChIP-Seq

value: H3K4me1 (ab8895, Abcam)


title: 566_2nd_CD33_G0


title: 566_2nd_CD33_F3


title: RPE188_TnT_H3K27ac ChIP-Seq


title: 566_2nd_CD33_F2


title: 566_2nd_CD34_F3


title: 566_2nd_CD34_F2


title: 566_2nd_CD33_F1


title: PIP037wt


title: RPE188_TnT_ChIP-Seq Input


title: 566_2nd_CD33_F0


title: 566_2nd_CD19_H3

source_name: Human splenic B cells from xenotransplanted NSG mice (secondary recipients)

value: B cells


title: PIP035wt


title: 566_2nd_CD19_H2


title: PIP024wt


title: 566_2nd_CD19_H1


title: PIP012wt


title: 566_2nd_CD19_G1


title: RPE188_Con_H3K4me3 ChIP-Seq


title: RPE188_Con_H3K4me1 ChIP-Seq


title: RPE188_Con_H3K27ac ChIP-Seq


title: PIP03wt


title: 566_2nd_CD19_G0


title: 566_2nd_CD19_F3


title: PIP010mut


title: RPE188_Con_ChIP-Seq Input


title: 566_2nd_CD19_F2


title: 566_2nd_CD19_F0


title: 3-3 p30

city: changchun

first: xia

last: he

address: xinmin street

country: China

institute: Key laboratory of pathobiology

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The mRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: ciXEN

growth_protocol: MEFs and ciXEN cells are cultured using DMEM basic medium and knockout DMEM, respectively

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

value: ciXEN

tag: passages

tag: strain

tag: group


title: 566_2nd_CD19_F1


title: WT_S: WT sinusoidal endothelial cells

city: Frederick

first: Brad

middle: LaMar

last: Jakubison

address: 1050 Boyles St., Building 539, Room 106

department: Mouse Cancer Genetics

institute: National Cancer Institute

data_processing:
10X Genomics CellRanger toolkit was used to perform demultiplexing, allowing for 1 mismatch in the barcodes.
Barcode reads were aligned to the mm10 transcriptome.
Pre-processing, removal of highly variable genes and contaminating immune cells, dimensionality reduction, and clustering analyses were performed using seurat R package.
Mitochondrial counts were removed, data was normalized by scaling by 10,000 then log transformed.  Dimensionality reduction was performed using principal component analysis followed byclustering of t-SNE.
DEGs, which represent atleast 25% of each cluster, were visualized in heatmaps and analyzed further using bioinformatics.
Genome_build: mm10

source_name: Lineage- CD31+ VECadherin+ Endomucin+ Sca-

extract_protocol:
FACs sorted H vessls and sinusoidal endothelial cells were captured using 10X Genomics Chromium
Single cell barcoded cDNA libraries were sequenced on the NeXtSeq 500
The sequencing run was set-up as 26 cycles + 57 cyclces in a non-symmetric run.

treatment_protocol: Mice were I.P. injected with tamoxifen for 5 consecutive days to induce deletion of the ID1 locus

value: Sinusoidal Cell

tag: genotype


title: 566_2nd_9WKS_H2

source_name: PBMCs from xenotransplanted NSG mice (secondary recipients)

tag: cell type

value: Peripheral blood mononuclear cells

value: 9 wks post secondary transplant

value: no


title: WT_H: WT H vessls

source_name: Lineage- CD31+ VECadherin+ Endomucin+ Sca+

value: H vessel cell


title: 566_2nd_9WKS_H1

tag: timepoint


title: 2-1 p30


title: 566_2nd_9WKS_H0

tag: facs sorting


title: 566_2nd_9WKS_G1


title: KO_S: ID1-/-ID3-/- sinusoidal endothelial cells


title: 566_2nd_CD19_H0

value: 15 wks post secondary transplant

value: yes


title: 1-1 p30


title: KO_H: ID1-/-ID3-/- H vessls


title: 3-3 p5


title: 566_2nd_9WKS_F3


title: 566_2nd_9WKS_G0


title: C57BL/6J retina

city: Dallas

first: Rafael

last: Ufret-Vincenty

state: TX

address: 5323 Harry Hines Blvd, Rm E7.244

department: Ophthalmology

institute: UT Southwestern

data_processing:
BCL files were demultiplexed using cellranger(v3.0.0)
Alignment, barcode counting, UMI counting were performed using cellranger(v3.0.0)
PCA, clustering, and differential expression was performed using Seurat
Genome_build: mm10
Supplementary_files_format_and_content: count matrix in a sparse matrix format
Supplementary_files_format_and_content: barcode id of the sample
Supplementary_files_format_and_content: gene ids of the sample

source_name: Retina

extract_protocol:
Retinas were removed from enucleated mouse eyes and the retina cells were dissociated using the Papain dissociation sysytem according to manufacturer's protocol
The library was generated according to manufacturer's instructions (10X Genomics).

value: Retina

tag: age

value: 3-4 month old


title: 566_2nd_9WKS_F1


title: 566_2nd_9WKS_F0


title: 566_2nd_9WKS_F2


title: 1-1 p5


title: 566_T_E5

source_name: Human splenic T cells from xenotransplanted NSG mice

value: T cells

value: 18-21 wks post-transplant


title: 2-1 p5


title: 566_T_E4


title: MEFs-3

source_name: MEFs

value: MEFs

value: control


title: PIP02wt

value: whole pituitary, posterior lobe removed

tag: developmental stage

value: Postnatal day 0


title: 566_T_E3


title: 566_2nd_9WKS_H3


title: 566_T_E2


title: MEFs-2


title: 566_T_E1


title: 566_T_E0


title: 566_T_C2


title: MEFs-1


title: 566_T_C1


title: 566_T_A5


title: 566_T_C0


title: Leukemia In-Vivo CRISPR Reya (InV)

city: La Jolla

first: Roman

last: Sasik

address: 9500 Gilman Dr.

department: Center for Computational Biology and Bioinformatics

institute: UCSD

description: Spleen leukemic cells, 7 days post transplantation, before the onset of full-blown disease

data_processing:
Reads were counted by first searching for the CACCG sequence in the primary read file that appears in the vector 5’ to all sgRNA inserts. The next 20 nts are the sgRNA insert, which was then mapped to a reference file of all possible sgRNAs present in the library.
Supplementary_files_format_and_content: tab-delimited text file, includes sgRNA code and count

source_name: splenic CML cells

growth_protocol: We generated lentiviral particles from the Brie library (Addgene #73633) and infected 300 million freshly isolated Cas9-GFP+ Lineage- blast crisis CML (bcCML) stem cells from the spleen of pre-morbid mice at an MOI of 0.25 such that a single cell is infected with only one virus carrying one gRNA.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions for HiSeq4000 sequencing.

treatment_protocol:
The cells were then selected for 48h in puromycin to enrich for cells carrying gRNAs (AfS sample).
60 hours post spinfection, an aliquot of cells was collected and represented a pool of infected cells with about 200 cells/guide (BeS sample). The cells were then selected for 48h in puromycin to enrich for cells carrying gRNAs (AfS sample).
35 million cells were transplanted in sub-lethally irradiated recipients (1 million cells/mouse) to ensure a coverage of >400 cells/guide. The recipient mice were sacrificed 7 days post-transplant, before the onset of full-blown disease. The cells from the spleen of all 35 mice were pooled into one sample (InV) after sorting for equal numbers (~1.1 million cells/mouse) of leukemic cells.

value: Spleen leukemic cells

tag: receptor strain

tag: donor strain


title: 566_T_A2


title: 566_T_A3


title: Leukemia In-Vivo CRISPR Reya (Pre-Sel)

description: Cas9-GFP+ Lineage- blast crisis CML (bcCML) stem cells infected with the genome-wide Brie library, pre-selection by puromycin

source_name: blast crisis CML cells


title: 566_T_A4


title: 566_T_A1


title: 566_T_A0


title: 566_P6_E5

source_name: Human splenic B cells from xenotransplanted NSG mice

value: B cells


title: 566_P6_E3


title: PPK1_D

city: Ottawa

first: Michael

last: Downey

state: Ont

address: 451 Smyth Rd.

department: Department of Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

description: transfected (48 hours)

data_processing:
The Illumina control software was HCS HD 3.4.0.38. Real-time anaylsis was RTA v. 2.7.7. The bcl2fastq v2.20 program to demultiplex samples and generate fastq reads.
Paired-ends sequencing reads were clipped for adapter sequence, trimmed (min quality (Q30) in 3'), filtered (min length 32 bp – Trimmomatic). Surviving read pairs aligned to the Genome Reference Consortium Human Build 38 with STAR (the two-passes method).
Gene quantification (gene-level count-based) against Ensembl annotations was done with HT-seq count (mode used: intersection-nonempty) and exploratory analysis conducted with various functions and packages from R and the Bioconductor project.
Differential expression done with edgeR and DEseq.
Gene Ontology enrichment done with the GOseq R package with an FDR threshold of 0.05. Transcript-level assembly, quantification and differential expression analysis done with Cufflinks and Cuffdiff.  Processing steps done through GenPipes framework.
genome build: Genome Reference Consortium Human Build 38
processed data files format and content: raw counts, log CPM, FC

source_name: HEK293T cell line

growth_protocol: The HEK293T cell lines used in this study were obtained from the American Type Culture Collection (ATCC CRL-3216). Cells were grown at 37°C and 5% CO2 to ~70% confluency in DMEM (Wisent Multicell) supplemented with supplemented with 10% Fetal Bovine Serum (Wisent Multicell), 1mM sodium pyruvate (Wisent Multicell), and Penicillin-Streptomycin-Amphotericin B solution (Wisent Multicell). Final concentrations of Penicillin, Streptomycin, and Amphotericin B were 50,000 IU/500 mL, 50 mgs/500 mL and 125 μg/500 mL, respectively. All cell lines used were regularly tested for mycoplasma contamination using a PCR Mycoplasma Detection Kit (Applied Biological Materials).

extract_protocol:
RNA for RNA-seq was extracted using an miRNeasy Mini Kit (Qiagen, 217004). Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed on a 2100 Bioanalyzer (Agilent Technologies).
Libraries were generated from 250 ng of total RNA as following: mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps of library preparation were done using and the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs.
Libraries were quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument.

treatment_protocol: HEK293T cells were grown to ~70% confluency and transiently transfected with 2-28 μg of either control plasmid (pcDNA3.1-) or ppk1+ expression plasmids (pcDNA3.1-ppk1+), (pcDNA3.1-HAppk1+) using Lipofectamine 2000 or Lipofectamine LTX Reagent (Invitrogen). Transfected cells were grown for 48 hours in OptiMeM (Fisher) and then harvested.

value: human embryonic kidney 293 cells, and contains the SV40 T-antigen

value: five to ten

tag: transfection

value: pcDNA3.1-ppk1 (Addgene Plasmid #108850)

tag: cell line


title: PPK1_C

description: transfected (48 hours)


title: 566_P6_E1


title: 566_P6_E2


title: PPK1_B

description: transfected (48 hours)


title: 566_P6_E4


title: 566_P6_C2


title: 566_P6_C1


title: 566_P6_C0


title: 566_P6_A5


title: CTRL_C

description: transfected (48 hours)


title: CTRL_B

description: transfected (48 hours)


title: 566_P6_A3


title: 566_P6_A1


title: Calu3 H3K27Ac ChIP-seq Rep2

city: Cleveland

first: Ann

last: Harris

state: OH

address: 10900 Euclid Ave

institute: Case Western Reserve Uni

data_processing:
Libraries were sequenced on Illumina HiSeq4000 machines.
Data was analyzed using ENCODE (phase-3) transcription factor and histone ChIP-seq pipeline https://github.com/ENCODE-DCC/chip-seq-pipeline2
Genome_build: hg19

growth_protocol: Cells were grown in indicated medias using standard methods

extract_protocol:
Cells were lysed in lysis buffer (5mM PIPES pH 8.0, 85mM KCL, 0.5% NP-40, 1x Protease Inhibitor Cocktail (Roche)). Nuclei were isolated by centrifugation, lysed in RIPA buffer (1x PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, Protease Inhibitor Cocktail), and sonicated. Protein-DNA complexes were isolated with antibodies.
DNA ends were blunted using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. Next, DNA was incubated with Klenow exo- to add 5’ adenine overhangs. Multiplex adaptors were then ligated to the ends and converted to dsDNA using 5 cycles of PCR. DNA was size-selected to contain fragments between 200 and 300bp and PCR amplified for 5 cycles. DNA was purified with 1.2x AMPure XP beads. Sequencing was performed on an Illumina Hi-Seq.

value: Human lung adenocarcinoma cells

tag: chip antibody

value: H3K27ac (Millipore 07-360)

tag: growth media

value: DMEM + 10% FBS


title: Leukemia In-Vivo CRISPR Reya (Post-Sel)

description: Cas9-GFP+ Lineage- blast crisis CML (bcCML) stem cells infected with the genome-wide Brie library, post 48h puromycin selection


title: 566_P6_A0

value: yes


title: 566_P5_E5

source_name: Human splenic myeloid cells from xenotransplanted NSG mice

value: Myeloid cells


title: Calu3 H3K27Ac ChIP-seq Rep1


title: Calu3 RNAPII ChIP-seq Rep1

value: RNA polymerase II (RNAPII) Rpb1 NTD (D8L4Y) (Cell Signaling 14958S)


title: Calu3 RNAPII ChIP-seq Rep2


title: 566_P5_E1


title: 566_P5_E0


title: CTRL_D

description: transfected (48 hours)


title: Caco2 RNAPII ChIP-seq Rep2

value: Human Colorectal adenocarcinoma cells


title: 566_P5_E2

value: 18-21 wks post-transplant


title: 566_P5_C1


title: 566_P5_C2


title: Caco2 RNAPII ChIP-seq Rep1


title: 16HBE14o- RNAPII ChIP-seq Rep2

value: Human bronchial epithelial cells


title: 566_P5_E4


title: 566_P5_C0


title: 566_P5_A5


title: 566_P5_E3


title: 566_P5_A3


title: 566_P5_A2


title: 566_P5_A1


title: 566_P6_A4


title: 566_P5_A0


title: 16HBE14o- H3K27Ac ChIP-seq Rep2


title: 566_18_E5

source_name: PBMCs from xenotransplanted NSG mice

value: Peripheral blood mononuclear cells

value: 18 wks post-transplant

value: no


title: Calu3 Omni ATAC rep2

data_processing:
Libraries were sequenced on Illumina HiSeq4000 machines.
Data was analyzed using ENCODE pipeline https://github.com/kundajelab/atac-seq-pipeline
Genome_build: hg19

extract_protocol:
Cells were lysed and isolated nuclei transposed using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962.
Libraries were construced using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962. With the following exception: Final libraries were purfied with Agencourt AMPure XP magnetic beads (Beckman-Coulter) at a sample to bead ratio of 1:1.2, following the manufacturer’s protocol, and eluted into 20 μL Buffer EB (Qiagen).

treatment_protocol: 50,000 cells were isolated prior to lysing/transpostion


title: 566_18_E4

extract_protocol:
QIAamp DNA Micro Kit (QIAGEN)
Custom library construction protocol. PCR amplicons for each individual sample were generated by nested PCR starting from >50-100 ng of purified gDNA. The first PCR step was performed with GoTaq Hot Start Polymerase (Promega) according to manufacturer instruction using the following amplification protocol: 95°C x 5’, (95°C x 0.5’, 60°C x 0.5’, 72°C x 0.5’) x 20 cycles, 72°C x 5’. Forward primers were designed to bind donor template upstream the BAR sequence, while the reverse primers annealed outside the homology region, thus amplifying 328 bp of the on-target integrated cassette. Exclusively for targeted sequencing of the transfer vector plasmid and AAV library, the reverse primer annealed to the downstream homology region. The second PCR step was performed with GoTaq G2 DNA Polymerase (Promega) according to manufacturer instruction using 5 µl of the first-step PCR product and the following amplification protocol: 95°C x 5’, (95°C x 0.5’, 60°C x 0.5’, 72°C x 0.5’) x 20 cycles, 72°C x 5’. Second-step PCR primers were endowed with tails containing P5/P7 sequence, i5/i7 Illumina tag to allow multiplexed sequencing and R1/R2 primer complementary sequence. PCR library amplicons were separately purified using MinElute PCR Purification kit (QIAGEN) and AmpPure XP beads (Invitrogen).
NextTera Illumina


title: 566_18_E3


title: Calu3 Omni ATAC rep1


title: 566_18_E2


title: 566_18_E1


title: 566_18_E0


title: OmniATAC-seq_MM001_SOX10_KD

data_processing:
Data processing of human melanoma baseline OmniATAC-seq samples: Paired-end reads were mapped to the human genome (hg19-Gencode v18) using bowtie2 (v2.2.6). Mapped reads were sorted using SAMtools (v1.8) and duplicates were removed using Picard MarkDuplicates (v1.134). Reads were filtered by removing chromosomal reads and filtering for Q>30 using SAMtools. Bam files of technical replicates of the same cell line were merged at this point using samtools merge. Peaks were called using MACS2 (v2.1.2) callpeak using the parameters -q 0.05, --nomodel, --call-summits, --shift -75 --keep-dup all and --extsize 150 per sample. Chromosomal peaks, blacklisted regions (ENCODE) and peaks overlapping with alternative chromosomes were removed. Summits were extended by 250bp up- and downstream using slopBed (bedtools; v2.28.0), providing human chromosome sizes. Peaks were normalised for the library size using a custom script and overlapping peaks were filtered using the peak score by keeping the peak with the highest score. For visualisation in IGV, normalised bigWigs were made by bamCoverage (Deeptools, v3.3.1), using as parameters --normalizeUsing None, -bl EncodeBlackListedRegions --effectiveGenomeSize 2913022398 and as scaling parameter (-scaleFactor) 1/(RIP/1E6), where the RIP stands for the number of reads in peaks.
Data processing of non-human (Omni)ATAC-seq samples, and of human SOX10 and TFAP2A knock-down OmniATAC-seq data: Adapter sequences were trimmed from the fastq files using fastq-mcf (as part of eautils; v1.05) and the read quality was checked using FastQC (v0.11.8). Reads were mapped using STAR (v2.5.1b) (for the zebrafish samples paired-end reads were mapped) to the genome which were downloaded from UCSC (http://hgdownload.cse.ucsc.edu/goldenPath/) (for human: hg19-Gencode v18; for dog: canFam3; for horse: equCab2; for pig: susScr11; for mouse: mm10; for zebrafish: danRer10) and by applying the parameters --alignIntronMax 1 and --aslignIntronMin 2. Mapped reads were filtered for quality using SAMtools (v1.2) view with parameter –q4, sorted with SAMtools sort and indexed using SAMtools index. Peaks were called using MACS2 (v2.1.2) callpeak using the parameters -q 0.05, --nomodel, --call-summits, --shift -75 --keep-dup all and with the genome size for the correct species in --g, and this for each sample per species separately. Summits were extended by 250bp up- and downstream using slopBed (bedtools; v2.28.0), providing the chromosome sizes for the specific species. Per sample, peaks were normalised for the library size using a custom script and overlapping peaks were filtered using the peak score (keeping the highest scoring peak). Normalised bedGraphs were produced by genomeCoverageBed (as part of bedtools; v2.28.0) using as scaling parameter (-scale) 1E6/(number of non-chromosomal mapping reads). BedGraphs were converted to bigWigs by the bedtools suit functions bedSort to sort the bedGraphs, followed by bedGraphToBigWig to create the bigWigs, which were used in IGV for visualisation.
Genome_build: For human: hg19-Gencode v18; for dog: canFam3; for horse: equCab2; for pig: susScr11; for mouse: mm10; for zebrafish: danRer10.
Supplementary_files_format_and_content: bigWig files represent the coverage of the ATAC-seq signal.

source_name: Melanoma cell line

growth_protocol:
Cells were cultured at 37°C with 5% CO2 and were maintained in Ham's F10 nutrient mix (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS; Invitrogen) and 100 µg ml-1 penicillin/streptomycin (Thermo Fisher Scientific).
Mentioned per sample in the SAMPLE section.

extract_protocol:
Cells were washed, trypsinised, spun down at 1000 RPM for 5 min, medium was removed and the cells were resuspended in 1 mL medium. Cells were counted and experiments were only continued when a viability of above 90% was observed. 50,000 cells were used per sample. OmniATAC-seq was performed as described previously in Corces et al., 2017; and ATAC-seq as described in Buenrostro et al., 2015.
Library prep was performed as described before in Corces et al., 2017 for OmniATAC-seq samplas; and as in Buenrostro et al., 2013 for ATAC-seq samples.

tag: tissue type

value: Cutaneous melanoma

tag: condition


title: 566_18_C2

data_processing:
Library strategy: Bar-Seq
Barcode sequences were extracted with the TagDust software (v2.33)
Extracted barcode sequences were processed with an ad-hoc script to merge similar (erroneous) barcodes
Supplementary_files_format_and_content: Tab-separated matrix with barcode counts


title: 566_P5_A4


title: OmniATAC-seq_MM001_NTC_KD


title: 566_18_C1


title: Gradient 2 Fraction 24

city: Gainesville

first: Eric

last: Wang

state: FL

address: 2033 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

description: highest density sucrose fraction

data_processing:
bcl2fastq/2.16.0.10 was used for basecalling.
Sequenced reads were trimmed for adaptor sequences
Reads were pseudo-aligned to mm10 and Transcripts Per Kilobase Million (TPM) counts were generated using the Kallisto package. Genes were filtered by a TPM greater than 1 for at least one fraction.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each fraction of the Atlas-Seq gradient

source_name: Liver

extract_protocol:
Wild-type FVB female mouse livers were dissected and washed in ice cold PBS. Tissue was placed in a tube containing 0.25 M buffered sucrose solution, 20mM Tris, water supplemented with protease inhibitor cocktail and 10 mM ribonucleoside-vanadyl complex (VRC) as a ribonuclease inhibitor) with 2.8 mm ceramic beads and placed in a bead homogenizer to homogenize tissue. Homogenized tissue was centrifuged at 5000 x g for 10 minutes to remove nuclei. A Biocomp Gradient Master™ was using to generate an 11 mL 10-50% sucrose gradient (with 10 mM VRC). Homogenate was layered onto the gradient, and components were resolved by ultracentrifugation in an SW41 rotor for 3 hours at 30,000 rpm (4° C). Twenty-four 0.5 ml fractions were collected from the gradient using the BioComp Piston Gradient Fractionator™. Fractions were split for RNA and protein extraction. RNA was extracted from each fraction by Direct-zol RNA miniprep kit. 10 equivalents of EDTA (relative to the VRC concentration) were added to each sample in Trizol-reagent before ethanol was added to remove the ribonucleoside-vanadyl complex. Protein concentrations were measured by the Pierce BCA protein assay kit.
RNA libraries were prepared for sequencing using the KAPA stranded RNA-Seq kit with RiboErase. Libraries were multiplexed and pooled.

tag: tissue

value: liver

value: wild type


title: 566_18_A2


title: 566_18_A0


title: 566_12_E5

value: 12 wks post-transplant


title: 566_12_E4


title: 566_12_E3


title: Gradient 2 Fraction 20


title: Gradient 2 Fraction 21


title: Gradient 2 Fraction 23


title: 566_12_E2


title: Gradient 2 Fraction 19


title: OmniATAC-seq_MM001_TFAP2A_KD

city: Leuven

first: Stein

last: Aerts

institute: KU Leuven


title: 566_12_E1

city: Segrate

first: Ivan

last: Merelli

institute: Consiglio Nazionale delle Ricerche


title: 566_12_E0


title: 566_12_C2


title: Gradient 2 Fraction 18


title: 566_12_C1


title: 566_18_A4


title: 566_12_C0


title: 566_18_A5


title: 566_12_A5


title: 566_12_A4


title: 566_18_A3


title: 566_18_C0


title: Gradient 2 Fraction 16


title: Gradient 2 Fraction 15


title: 566_12_A2


title: 566_12_A3


title: 566_18_A1


title: Gradient 2 Fraction 22


title: OmniATAC-seq_Mouse_BL

growth_protocol:
Cells were cultured at 37°C with 5% CO2 in Dulbecco's Modified Eagle Medium (DMEM) (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS; Invitrogen) and 1% penicillin/streptomycin (Thermo Fisher Scientific).
Mentioned per sample in the SAMPLE section.

value: Melanoma tumor from mouse with Tyr::Nras-/+/Ink4a-/-  background

value: Baseline


title: 566_12_A1


title: Gradient 2 Fraction 14


title: 566_12_A0


title: 566_8_E5

value: 8 wks post-transplant


title: 566_8_E4


title: Gradient 2 Fraction 13


title: 566_8_E3


title: Male tumor microglia GFP negative [MT-P5_S21]

city: Charlestown

first: Erik

last: Abels

state: Massachusetts

address: 149 13th Street

department: Neurology

institute: Massachusetts General Hospital

data_processing:
Total RNA was isolated and sequencing libraries were made using SMARTer Ultra Low Input RNA Kit. Sequencing was done using an Illumina NextSeq and bioinformatic analysis was performed using DESeq2 in R
Duplicate reads were marked using the MarkDuplicates tool in picard-tools-1.8.4 and removed.
The uniquely aligned reads were then counted against Gencode’s GRCm38.p3 GTF annotations using htseq-count in the intersection-strict mode
Data analysis of mapped counts was performed in R 3.2.3 using the DESeq2 package
Samples with less than 6000 genes with at least 5 mapped reads were excluded from analysis
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: tab-delimited text file with read counts per sample

source_name: Male tumor microglia GFP negative

extract_protocol:
Microglia are isolated from mouse brain following protocol described in Hickman et al. 2013. Total RNA was isolated using RNeasy Plus Micro kit (Qiagen) using the total RNA isolation protocol.
Total RNA was isolated and sequencing libraries were made using SMARTer Ultra Low Input RNA Kit. Sequencing was done using an Illumina NextSeq

tag: strain

tag: gender

value: male

value: 12 -18 weeks

value: microglia


title: Male tumor microglia GFP postive [MT-P6_S22]

source_name: Male tumor microglia GFP postive


title: Gradient 2 Fraction 12

tag: genotype


title: 566_8_E2

tag: cell type


title: Gradient 2 Fraction 17


title: Female tumor microglia GFP postive [FT-P6_S20]

source_name: Female tumor microglia GFP postive

value: female


title: 566_8_E1

tag: timepoint


title: 566_8_E0

tag: facs sorting


title: Gradient 2 Fraction 11


title: Female tumor microglia GFP negative [FT-P5_S19]

source_name: Female tumor microglia GFP negative

tag: age


title: Gradient 2 Fraction 10


title: 566_8_C1


title: 566_8_C0


title: Gradient 2 Fraction 9


title: 566_8_A5


title: Female tumor microglia GFP postive [FT1-P6_S26]


title: Female tumor microglia GFP negative [FT1-P5_S25]


title: 566_8_A3


title: 566_8_A2


title: Male control microglia [MC-P6_S27]

source_name: Male control microglia


title: Gradient 2 Fraction 7


title: 566_8_A1


title: 566_8_A0


title: Gradient 2 Fraction 6


title: 64_CD3p_D4

value: T cells

value: yes


title: Gradient 2 Fraction 8


title: 566_8_A4


title: Gradient 2 Fraction 5


title: 64_CD3p_D3

value: 18-21 wks post-transplant


title: 64_CD3p_D2


title: 64_CD3p_D1


title: sgn3-3_no_peptide_for_30min_batch3

city: Lausanne

first: Emanuel

last: Schmid-Siegert

address: UNIL Sorge

country: Switzerland

institute: UNIL

description: Samples were collected in March 2018 at Lausanne, Switzerland.

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v.0.11.1). Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013).
Reads were aligned against Arabidopsis thaliana TAIR10 genome using STAR (v. 2.5.3a, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using A. thaliana TAIR10 Ensembl 39 gene annotation.
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al. 2012).
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include gene-level read counts for each sample

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis thaliana ecotype Col-0 was grown at 22 Celsius degree under 16 h light/8 h dark vertically on solid half-strength Murashige-Skoog medium with mesh for 5 days in the same percival after 2-day startification at 4 Celsius degree.

extract_protocol:
RNA was extracted using a Trizol-adapted Reliaprep RNA extraction kit (Promega).
RNA quality was assessed on a Fragment Analyzer (Advanced Analytical Technologies, Inc., Ankeny, IA, USA).  RNA-seq libraries were prepared using 1000 ng of total RNA  and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA) on a Sciclone liquid handling robot (PerkinElmer; Waltham, Massachusetts, USA)   using a PerkinElmer-developed automated script. Cluster generation was performed with the resulting libraries using the Illumina TruSeq SR Cluster Kit v4 reagents and  sequenced on the Illumina HiSeq 2500 using TruSeq SBS Kit v4 reagents. Sequencing data were processed using the Illumina Pipeline Software version 2.20.

treatment_protocol: 5-day-old seedlings on mesh were transferred onto fresh half-strength medium with or without 100 nM CIF2 (Peptide Specialty Laboratories GmbH) for 30, 120, or 480 min. After the treatment, whole roots were collected and frozen in liquid nitrogen immediately.

tag: ecotype

tag: treatment

value: no peptide for 30 min


title: Gradient 2 Fraction 4


title: 64_CD3p_D0

address: via F.lli Cervi 93


title: sgn3-3_no_peptide_for_30min_batch2


title: 64_CD3p_C3


title: 566_8_C2

value: Peripheral blood mononuclear cells


title: Gradient 2 Fraction 3

description: lowest density sucrose fraction


title: Gradient 1 Fraction 21

description: highest density sucrose fraction


title: 64_CD3p_C2


title: 64_CD3p_C1


title: sgn3-3_no_peptide_for_30min_batch1


title: WT_no_peptide_for_30min_batch3

value: Wildtype


title: 64_CD3p_B4


title: 64_CD3p_C0


title: 64_CD3p_B2


title: 64_CD3p_B3


title: Female control microglia [FC1-P6_S23]

source_name: Female control microglia


title: cif1-2_cif2-2_100nM_CIF2_treatment_for_480min_batch3

value: cif1-2_cif2-2 (both are CRISPR alleles)

value: no peptide for 480 min


title: 64_CD3p_A1


title: 64_CD3p_B0


title: 64_CD3p_A0


title: 64_CD3p_A2


title: Female control microglia [FC2-P6_S24]


title: Gradient 1 Fraction 18

value: liver

value: wild type


title: WT_no_peptide_for_30min_batch2


title: 64_CD38m_D4

source_name: Human bone marrow-derived HSPCs from xenotransplanted NSG mice

value: Hematopoietic stem/progenitor cells


title: 64_CD3p_B1

source_name: Human splenic T cells from xenotransplanted NSG mice


title: Gradient 1 Fraction 16


title: Gradient 1 Fraction 15


title: WT_no_peptide_for_30min_batch1


title: Gradient 1 Fraction 19


title: cif1-2_cif2-2_100nM_CIF2_treatment_for_480min_batch2


title: cif1-2_cif2-2_no_peptide_for_480min_batch3


title: Gradient 1 Fraction 14


title: 64_CD38m_D2


title: 64_CD38m_D1


title: 64_CD38m_D3


title: cif1-2_cif2-2_no_peptide_for_480min_batch1


title: 64_CD38m_D0


title: 64_CD3p_A4


title: cif1-2_cif2-2_no_peptide_for_480min_batch2


title: Gradient 1 Fraction 17


title: 64_CD38m_C2


title: Gradient 1 Fraction 12


title: 64_CD38m_C1


title: Gradient 1 Fraction 11


title: sgn3-3_no_peptide_for_480min_batch3


title: sgn3-3_no_peptide_for_480min_batch2


title: 64_CD38m_C0


title: sgn3-3_no_peptide_for_480min_batch1


title: Gradient 1 Fraction 10


title: Gradient 1 Fraction 9


title: 64_CD38m_B1


title: 64_CD38m_B3


title: WT_no_peptide_for_480min_batch3


title: 64_CD38m_C3


title: 64_CD38m_B4


title: 64_CD38m_B0


title: Gradient 1 Fraction 7


title: Gradient 1 Fraction 13


title: Gradient 1 Fraction 8


title: WT_no_peptide_for_480min_batch2


title: 64_CD38m_A3


title: 64_CD38m_A4


title: WT_no_peptide_for_480min_batch1


title: 64_CD38m_B2


title: 64_CD38m_A2


title: 64_CD38m_A1


title: Gradient 1 Fraction 6


title: 64_CD38m_A0


title: 64_CD33p_D4

value: Myeloid cells


title: cif1-2_cif2-2_no_peptide_for_120min_batch3

value: no peptide for 120 min


title: Gradient 1 Fraction 5


title: 64_CD33p_D3


title: Gradient 1 Fraction 4

description: lowest density sucrose fraction


title: cif1-2_cif2-2_100nM_CIF2_treatment_for_480min_batch1


title: 64_CD33p_D0


title: 64_CD33p_D1


title: 64_CD33p_D2


title: 64_CD33p_C1


title: 64_CD33p_C3


title: s18_GSE56/Ad5-E4orf6/7 rep3

description:
18_S62
Heamtopoietic stem/progenitor cells cultured for 3 days and then electroporated with Cas9 RNP targeting the AAVS1 locus and the GSE56/Ad5-E4orf6/7 mRNA, and transduced with the cognate barcoded PGK.GFP AAV6 vector.

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trim_galore (options: "--quality 20 --length 25")
Trimmed reads were mapped to GRCh38 whole genome using STAR  v2.7.0d  (options: "--outSAMstrandField intronMotif --outSAMmultNmax 1 --outFilterMismatchNmax 10")
Gene counts of mapped reads were obtained with the Subread package ("featureCounts" function with options: "-g gene_name -s 0")
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file include counts of mapped reads for each Sample

growth_protocol: Human HSPCs were cultured CB-derived CD34+ HSPCs were seeded at the concentration of 5x10^5 cells/ml in serum-free StemSpan medium supplemented with penicillin, streptomycin, glutamine, hSCF, hFlt3-L, hTPO, hIL-6, 10 μM PGE2 (at the beginning of the culture), SR-1 and UM171.

extract_protocol:
miRNeasy Micro Kit
TruSeq Stranded mRNA (Illumina)

treatment_protocol: After Three days of prestimulation, cells were treated as specified in the section "overall design".

tag: cell tytpe

value: Human cord-blood derived hematopoietic stem/progenitor cells (HSPCs)

tag: nuclease

value: Cas9 RNP for AAVS1

tag: hdr template

value: Barcoded AAV6 for AAVS12

tag: electroporated mrna

value: GSE56 and Ad5-E4orf6/7


title: s14_Ad5-E4orf6/7 rep2

description:
14_S58
Heamtopoietic stem/progenitor cells cultured for 3 days and then electroporated with Cas9 RNP targeting the AAVS1 locus and the Ad5-E4orf6/7 mRNA, and transduced with the cognate barcoded PGK.GFP AAV6 vector.

value: Barcoded AAV6 for AAVS8


title: 64_CD33p_C2

value: yes


title: cif1-2_cif2-2_no_peptide_for_120min_batch1


title: 64_CD33p_B4

value: 18-21 wks post-transplant


title: s16_GSE56/Ad5-E4orf6/7 rep1

description:
16_S60
Heamtopoietic stem/progenitor cells cultured for 3 days and then electroporated with Cas9 RNP targeting the AAVS1 locus and the GSE56/Ad5-E4orf6/7 mRNA, and transduced with the cognate barcoded PGK.GFP AAV6 vector.

value: Barcoded AAV6 for AAVS10


title: s13_Ad5-E4orf6/7 rep1

description:
13_S57
Heamtopoietic stem/progenitor cells cultured for 3 days and then electroporated with Cas9 RNP targeting the AAVS1 locus and the Ad5-E4orf6/7 mRNA, and transduced with the cognate barcoded PGK.GFP AAV6 vector.

value: Barcoded AAV6 for AAVS7


title: 64_CD33p_B1


title: 64_CD33p_C0


title: sgn3-3_no_peptide_for_120min_batch3


title: s15_Ad5-E4orf6/7 rep3

description:
15_S59
Heamtopoietic stem/progenitor cells cultured for 3 days and then electroporated with Cas9 RNP targeting the AAVS1 locus and the Ad5-E4orf6/7 mRNA, and transduced with the cognate barcoded PGK.GFP AAV6 vector.

value: Barcoded AAV6 for AAVS9


title: cif1-2_cif2-2_no_peptide_for_120min_batch2

value: cif1-2_cif2-2 (both are CRISPR alleles)


title: 64_CD33p_B0


title: WT_no_peptide_for_120min_batch3

value: Wildtype


title: sgn3-3_no_peptide_for_120min_batch2


title: 64_CD33p_A3


title: 64_CD33p_B2


title: 64_CD33p_A1


title: sgn3-3_no_peptide_for_120min_batch1


title: 64_CD33p_A4


title: 64_CD19p_D4

value: B cells


title: 64_CD19p_D2


title: s8_RNP + AAV6 rep2

description:
8_S52
Heamtopoietic stem/progenitor cells cultured for 3 days and then electroporated with Cas9 RNP targeting the AAVS1 locus and transduced with the cognate barcoded PGK.GFP AAV6 vector.

source_name: HSPCs_RNP + AAV6

value: Barcoded AAV6 for AAVS2


title: 64_CD33p_A2


title: s9_RNP + AAV6 rep3

description:
9_S53
Heamtopoietic stem/progenitor cells cultured for 3 days and then electroporated with Cas9 RNP targeting the AAVS1 locus and transduced with the cognate barcoded PGK.GFP AAV6 vector.

value: Barcoded AAV6 for AAVS3


title: 64_CD19p_C2


title: s7_RNP + AAV6 rep1

description:
7_S51
Heamtopoietic stem/progenitor cells cultured for 3 days and then electroporated with Cas9 RNP targeting the AAVS1 locus and transduced with the cognate barcoded PGK.GFP AAV6 vector.

value: Barcoded AAV6 for AAVS1


title: WT_no_peptide_for_120min_batch1

value: no peptide for 120 min


title: s17_GSE56/Ad5-E4orf6/7 rep2

description:
17_S61
Heamtopoietic stem/progenitor cells cultured for 3 days and then electroporated with Cas9 RNP targeting the AAVS1 locus and the GSE56/Ad5-E4orf6/7 mRNA, and transduced with the cognate barcoded PGK.GFP AAV6 vector.

value: Human cord-blood derived hematopoietic stem/progenitor cells (HSPCs)

value: Barcoded AAV6 for AAVS11


title: cif1-2_cif2-2_100nM_CIF2_treatment_for_30min_batch3

value: 100 nM CIF2 for 30 min


title: s12_GSE56 rep3

description:
12_S56
Heamtopoietic stem/progenitor cells cultured for 3 days and then electroporated with Cas9 RNP targeting the AAVS1 locus and the GSE56 mRNA, and transduced with the cognate barcoded PGK.GFP AAV6 vector.

value: Cas9 RNP for AAVS1

value: Barcoded AAV6 for AAVS6


title: 64_CD19p_B4

value: yes


title: 64_CD19p_B3

value: 18-21 wks post-transplant


title: cif1-2_cif2-2_100nM_CIF2_treatment_for_30min_batch1


title: 64_CD19p_B2


title: s11_GSE56 rep2

description:
11_S55
Heamtopoietic stem/progenitor cells cultured for 3 days and then electroporated with Cas9 RNP targeting the AAVS1 locus and the GSE56 mRNA, and transduced with the cognate barcoded PGK.GFP AAV6 vector.

value: Barcoded AAV6 for AAVS5


title: 64_CD33p_B3

value: Myeloid cells


title: cif1-2_cif2-2_no_peptide_for_30min_batch3

value: no peptide for 30 min


title: 64_CD19p_D3


title: WT_no_peptide_for_120min_batch2


title: 64_CD19p_C3


title: cif1-2_cif2-2_no_peptide_for_30min_batch1

value: cif1-2_cif2-2 (both are CRISPR alleles)


title: s10_GSE56 rep1

description:
10_S54
Heamtopoietic stem/progenitor cells cultured for 3 days and then electroporated with Cas9 RNP targeting the AAVS1 locus and the GSE56 mRNA, and transduced with the cognate barcoded PGK.GFP AAV6 vector.

value: Barcoded AAV6 for AAVS4


title: cif1-2_cif2-2_no_peptide_for_30min_batch2


title: 64_CD19p_D1

value: B cells


title: s4_UT_electro rep1

description:
4_S48
Heamtopoietic stem/progenitor cells cultured for 3 days and then electroporated without adding any nucleic acid/protein component


title: 64_CD19p_B1


title: 64_CD19p_D0


title: 64_CD19p_B0


title: 64_CD19p_C1


title: s3_UT rep3

description:
3_S47
Heamtopoietic stem/progenitor cells cultured for 3.5 days


title: 64_CD33p_A0


title: 64_CD19p_C0


title: 64_CD19p_A2


title: cif1-2_cif2-2_100nM_CIF2_treatment_for_30min_batch2


title: 64_CD19p_A1


title: s5_UT_electro rep2

description:
5_S49
Heamtopoietic stem/progenitor cells cultured for 3 days and then electroporated without adding any nucleic acid/protein component


title: sgn3-3_100nM_CIF2_treatment_for_30min_batch3


title: s2_UT rep2

description:
2_S46
Heamtopoietic stem/progenitor cells cultured for 3.5 days


title: 64_18WKS_D4

value: Peripheral blood mononuclear cells

value: 18 wks post-transplant

value: no


title: s6_UT_electro rep3

description:
6_S50
Heamtopoietic stem/progenitor cells cultured for 3 days and then electroporated without adding any nucleic acid/protein component


title: sgn3-3_100nM_CIF2_treatment_for_30min_batch2

description: Samples were collected in March 2018 at Lausanne, Switzerland.


title: 64_CD19p_A4


title: WT_100nM_CIF2_treatment_for_30min_batch2

value: Wildtype


title: sgn3-3_100nM_CIF2_treatment_for_30min_batch1


title: 64_18WKS_D1


title: 64_CD19p_A3


title: 16HBE14o- del-20.9 cl.19 -80.1

description: 4C-seq library with the CFTR -80.1 kb region as the viewpoint

data_processing:
Library strategy: 4C-Seq
Libraries were sequenced on Illumina HiSeq2500 machines.
Data was analyzed using 4cseq pipeline http://compgenomics.weizmann.ac.il/tanay/?page_id=367
Genome_build: hg19
Supplementary_files_format_and_content: The processed data is a dataframe each genomic fragment and its measured interaction frequency with the viewpoint of interest. The processed data can be used to plot a dominogram to visualized these interaction frequencies.

source_name: Human lung

growth_protocol: Cells were grown in indicated media using standard methods

extract_protocol:
Nuclei were made as per the above Methods paper.
All libraries were constructed as per the above Methods paper.
4C-seq Barcoded libraries with Illumina sequencing adapters were made as per above Methods paper.

treatment_protocol: As per Splinter, E et al, 2012, Methods.

tag: cell line

value: Human bronchial epithelial cells

value: CRISPR/Cas9 mediated deletion of -20.9 kb CRE from the CFTR locus in 16HBE14o- clone # 19

tag: growth media

value: DMEM + 10% FBS


title: 64_CD19p_A0


title: 64_18WKS_D0


title: 16HBE14o- del-20.9 cl.19 Promoter

description: 4C-seq library with the CFTR CFTR promoter region as the viewpoint


title: sgn3-3_100nM_CIF2_treatment_for_480min_batch2

value: 100 nM CIF2 for 480 min


title: s1_UT rep1

description:
1_S45
Heamtopoietic stem/progenitor cells cultured for 3.5 days

value: Human cord-blood derived hematopoietic stem/progenitor cells (HSPCs)


title: 64_18WKS_D2


title: WT_100nM_CIF2_treatment_for_30min_batch3

value: 100 nM CIF2 for 30 min


title: 64_18WKS_D3