title: H3K4me3_scChIPseq_Jurkat-Ramos

status: Public on Apr 12 2019

city: Paris

first: Kevin

last: Grosselin

address: 10 rue Vauquelin

department: CBI

institute: ESPCI Paris

description: R1 fastq file: nucleosomal sequence. R2 fastq file: single-cell barcode sequence (0 - 76 bp) and cell type specific sequence (Jurkat: TAGCTCGGTTAA ; Ramos: GTGATTGCTTGTGACTTAA)

data_processing:
scChIP-seq: Sequenced reads were mapped to hg38 or mm10 whole genome using bowtie v1.2.2 with parameters -p 8 -m 1
scChIP-seq: Barcodes were extracted from Reads #2 by first searching for the constant 4 bp linkers found between the 20-mer indices of the barcode allowing up to 1 mismatch in each linker. If the correct linkers were identified, the three interspersed 20-mer indices were extracted and concatenated together to form a 60 bp non-redundant barcode sequence. A library of all 884,736 combinations of the 3 sets of 96 indices (963) was used to map barcode sequences using the sensitive read mapper Cushaw3 (v3.0.3).
scChIP-seq: For each barcode, aligned reads were extended to 150 bp and all the reads falling in the same 150 bp window were stacked into one as reads possibly originating from PCR duplicates or from the same nucleosome. Then, reads were binned in non-overlapping 50 kb for H3K27me3 and 5 kb genomic bins for H3K4me3 spanning the genome to generate a n x m coverage matrix with n barcodes and m genomic bins used in downstream analysis
scChIP-seq: Single cells with a total number of uniquely mapped reads within the upper percentile were considered as outliers and removed. Genomic regions not represented in at least 1% of all cells were filtered out. The coverage matrix was then normalized by dividing counts by the total number of reads per cell and multiplying by the average number of reads across all cells.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read count for each cell in genes (scRNA-seq, TAR of MTX and TSV) or genomic bins (scChIP-seq)

organism: Homo sapiens

source_name: Jurkat-Ramos

growth_protocol: Human Jurkat and Ramos cell lines were grown in RPMI medium supplemented with 10% heat inactivated bovine serum and 1% Penicillin-Streptomycin.

extract_protocol:
Prior scChIP-seq and  scRNA-seq, PDX were digested at 37°C for 2h with a cocktail of Collagenase I (Roche, # 11088793001) and Hyaluronidase (Sigma, # H3506) as previously described (Petit et al, Lab Investigation 2013). Cells were further individualized at 37°C using a cocktail of 0.25% trypsin/Versen (ThermoFisher Scientific, #15040-033), Dispase II (Sigma, # D4693) and Dnase I (Roche, # 11284932001). Red Blood Cell lysis buffer (ThermoFisher Scientific, # 00-4333-57) was then added to degrade red blood cells. To increase the viability of the cell suspension, we removed dead cells using a Dead Cell Removal kit (Miltenyi Biotec). Cells were re-suspended in PBS/0.04% BSA (ThermoFisher Scientific, # AM2616).
After immunoprecipitation targeting H3K4me3 or H3K27me3, scChIP-seq libraries were prepared as following: barcoded-nucleosomes were amplified by in vitro transcription using the T7 MegaScript kit (ThermoFisher Scientific). The resulting amplified RNA was purified using 1x RNAClean XP beads (Beckman) and reverse transcribed by random priming in cDNA. After RNA digestion, DNA was amplified by PCR using with Illumina Primers for 12 cycles and library fragments ranging from 300 to 600 bp (single-cell barcode plus nucleosomal sequence + PCR primer sequence) were size-selected on an agarose gel. Single-cell ChIP-seq libraries were sequenced on Illumina NextSeq 500 MidOutput 150 cycles

value: Jurkat and Ramos cell lines


title: H3K27me3_scChIPseq_Jurkat-Ramos

type: SRA

country: France

description: R1 fastq file: nucleosomal sequence. R2 fastq file: single-cell barcode sequence (0 - 72 bp) and cell type specific sequence (Jurkat: TAGCTCGGTTAA ; Ramos: GTGATTGCTTGTGACTTAA)

library_source: genomic

molecule: genomic DNA

tag: tissue


title: Undeprived P5 barrel cortex [55RU_S7]

city: Worcester

first: Georgia

last: Gunner

state: Massachusetts

address: 364 Plantation Street, LRB 770 Y-Z

department: Neurobiology

country: USA

institute: UMass Medical School

library_source: transcriptomic

data_processing:
Raw sequencing data was processed using Illumina bcl2fastq2 Conversion Software v2.17.
Sequences were mapped using the TopHat2 package (v2.1.0)61
Reads were counted using HTSeq-count (v0.6.0) against the Ensembl v67 annotation.
The read alignment, read counting, and quality assessment were done using SPEctRA.
The raw counts were processed through VST procedure using the DESeq2 package.
Genome_build: mm9

molecule: total RNA

organism: Mus musculus

source_name: Right barrel cortex tissue from P5 Cx3cr1CreErt2/+;Eef1a1LSL.eGFPL10a/+ mice

extract_protocol:
RNA was isolated from right barrel cortex
cDNA was generated using Nugen Ovation V2 kit. Libraries were produced using TruSeq DNA Sample kit. Multiplexed libraries were directly loaded on NextSeq 500 (Ilumina) with High Output single read sequencing for 75 cycles.

treatment_protocol: Mice were treated with Tamoxifen at P1-3, whiskers on the right side were cauterized at P4.

tag: genotype/variation

tag: age

value: Right barrel cortex


title: Deprived P5 barrel cortex [54LU_S6]

source_name: Left barrel cortex tissue from P5 Cx3cr1CreErt2/CreErt2;Eef1a1LSL.eGFPL10a/+ mice

extract_protocol:
RNA was isolated from left barrel cortex
cDNA was generated using Nugen Ovation V2 kit. Libraries were produced using TruSeq DNA Sample kit. Multiplexed libraries were directly loaded on NextSeq 500 (Ilumina) with High Output single read sequencing for 75 cycles.

value: Left barrel cortex


title: Deprived P5 barrel cortex [55LU_S7]

source_name: Left barrel cortex tissue from P5 Cx3cr1CreErt2/+;Eef1a1LSL.eGFPL10a/+ mice


title: Undeprived P5 barrel cortex [54RU_S6]

source_name: Right barrel cortex tissue from P5 Cx3cr1CreErt2/CreErt2;Eef1a1LSL.eGFPL10a/+ mice


title: Undeprived P5 barrel cortex [4RU_S7]


title: Deprived P5 barrel cortex [4LU_S8]


title: Undeprived P5 barrel cortex [3RU_S5]


title: Deprived P5 barrel cortex [3LU_S6]


title: Undeprived P5 barrel cortex [1RU_S1]


title: Deprived P5 barrel cortex [1LU_S2]


title: LNCaP CUL4B knockdown

status: Public on Apr 13 2019

type: RNA

city: Jinan

first: meng

last: jiao

address: No.247, beiyuan street

country: China

institute: 2nd Hospital of Shandong University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human miRNA Microarrays (8*60K) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner using oneAgilentG3_miRNA setting for  8x60K  array slides.

data_processing: The scanned images were analyzed with Agilent Feature Extraction software V.11.5 using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: prostate cancer

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by Absolutely RNA miRNA Kit (Agilent p/n 400814)  following the manufacturer’s instructions.

value: prostate cancer

tag: cell line

value: LNCaP

tag: Sex

value: Male


title: LNCaP Negative Control

value: control


title: LNCaP Negative Control

description: Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51C with the denatured radi

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).Scanned images (TIFF format) were then imported into Agilent software (version 2.5) for grid alignment and expression data analysis.

data_processing: All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed genes were identified through Fold Change filtering.

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the Agilent Gene Expression Analysis protocol ( Agilent  Technologies,Inc. Waldbronn, Germany). Briefly, ds-cDNA was incubated with 4ug RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the epicentreTargetAmp 1-round aRNA amplification kit  was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (  Agilent  Technologies,Inc. Waldbronn, Germany). One ?g ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: Negative Control


title: Cumulus cells ET-1 0H

city: hangzhou

first: long

last: cui

address: xueshi Rd1#

institute: women's hospital school of medicine,zhejiang university

description: Gene expression data from cumulus cell treat with ET-1 for 18 h

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US).

data_processing: Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.

label: biotin

source_name: ET-1 treated 0 hours

label_protocol: Total RNA was amplified, labeled and purified by Affymetrix  WT PLUS Reagent Kit(Cat#902280， Affymetrix, Santa Clara, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA

growth_protocol: After being washed three-times in D-PBS, the cumulus cells were inoculated in 35mm culture dish (Falcon, BD), and cultured in minimum essential medium alpha (α-MEM) medium (Invitrogen)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cumulus cells were cultured in minimum essential medium alpha (α-MEM) medium (Invitrogen), either with or without 100ng/ml ET-1.when harvest, the cells were washed three-times in D-PBS.

tag: cell type

value: cumulus cells

tag: treatment

tag: time


title: LNCaP CUL4B knockdown

value: CUL4B knockdown


title: KHYG-1_1 RNA-seq

city: Boston

first: Samuel

last: Ng

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Paired-end RNASeq samples were mapped to the human genome reference assembly (hg19) with STAR 2.4.2a
Transcript expression estimated with Cufflinks 2.2.1
Gene expression calculated as sums of FPKM values with genes with transcripts <300 bp ignored
Genome_build: hg19
Supplementary_files_format_and_content: Cufflinks normalized abundance measurment

source_name: Aggressive NK-cell leukemia

extract_protocol: Processed per standard CCLE protocols (doi:10.1038/nature11003)


title: MTA_1 RNA-seq


title: Karpas-384_1 RNA-seq

source_name: Primary cutaneous gd T-cell lymphoma


title: NKL_1 RNA-seq

source_name: Chronic lymphoproliferative disorder of NK cells


title: DERL-2_1 RNA-seq

source_name: Hepatosplenic T-cell lymphoma


title: Autonomic 4

city: Zurich

first: Luis

last: Zurkirchen

state: Zurich

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

description: mouse primary material

hyb_protocol: 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).

scan_protocol: Scanning was done with the GeneChip® Scanner 3000 7G (Affymetrix) using the Affymetrix Command Console as instrument control software.

data_processing: Quality control and microarray data analysis was done using R/Bioconductor [Gentleman RC et al., 2004; R Development Core Team, 2011; http://www.bioconductor.org/]. Expression values were computed RMA (robust multi array average) [Irizarry et al., 2003a, b] as processing algorithm.

source_name: Neural Crest

label_protocol: Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.

growth_protocol: NCSC media as described in (Greenwood et al., 1999)

extract_protocol: Qiagen RNAeasy

treatment_protocol: Cells treated with instructive growth factors

value: NCSCs primed to neurons


title: cells with H5N1 infection, biological rep1

city: Beijing

first: Yanxin

last: Hu

state: Beijing

address: no. 2 Yuanmingyuan west road

institute: China Agricultural University

description: Gene expression data from mouse mast cells with H5N1 infection at12h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Genechip Scanner 3000.

data_processing: The data were analyzed with Affymetrix® GeneChip® Command Console® Software using Affymetrix default analysis settings method.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

value: mast cells

tag: agent


title: Mesenchymal 4

description: mouse primary material

value: NCSCs primed to mesenchyme


title: Mesenchymal 3

description: mouse primary material


title: OCILY12_1 RNA-seq

source_name: Peripheral T-cell lymphoma, NOS


title: Cumulus cells ET-1 18H

source_name: ET-1 treated 18 hours


title: Glia 4

description: mouse primary material

value: NCSCs primed to glia


title: Glia 1

description: mouse primary material


title: NCSCs 2

description: mouse primary material

value: NCSC not primed


title: NCSCs 4

description: mouse primary material


title: cells with no infection, biological rep1

description: Gene expression data from mouse mast cells with no infection at12h


title: Mesenchymal 2

description: mouse primary material


title: Mesenchymal 1

description: mouse primary material


title: Autonomic 2

description: mouse primary material


title: cells with H1N1 infection, biological rep1

description: Gene expression data from mouse mast cells with H1N1 infection at12h


title: OCILY132_1 RNA-seq

source_name: Anaplastic large-cell lymphoma, ALK-


title: Glia 2

description: mouse primary material


title: Autonomic 3

description: mouse primary material


title: Autonomic 1

description: mouse primary material


title: Glia 3

description: mouse primary material


title: NCSCs 3

description: mouse primary material


title: NCSCs 1

description: mouse primary material


title: cells with H7N2 infection, biological rep1

description: Gene expression data from mouse mast cells with H7N2 infection at12h


title: FEPD_1 RNA-seq


title: L82_1 RNA-seq

source_name: Anaplastic large-cell lymphoma, ALK+


title: MAC2A_1 RNA-seq


title: DL-40_1 RNA-seq


title: 2_U_4-4

city: AUSTIN

first: Meghan

last: Bloom

state: TX

address: 107 W DEAN KEETON ST

institute: THE UNIVERSITY OF TEXAS - AUSTIN

description:
U_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)

data_processing:
A step-by-step read me and executable scripts for reproducing analysis is available on "https://github.com/sachitsaksena/nfkb-tag-seq/". The readme allows for generation of commands across all samples, which can then be run in parallel, if computing resources permit.
TagSeq trimming was carried out using FASTX-Toolkit’s fastx-clipper with parameters to remove non-template bases introduced by reverse transcriptase on the 5’ end. First a script from the original TagSeq authors available at "https://github.com/z0on/tag-based_RNAseq/blob/master/tagseq_clipper.pl" was run to clip 5' leader off Illumina fastq reads. Then fastx-clipper (from FASTx-Toolkit) was run with the following parameters: 1) -a AAAAAAAA -l 20 -Q33, 2)  -a AGATCGGAAG -l 20 -Q33 and then fastq_quality_filter is run with the following parameters -Q33 -q 20 -p 90.
Reads were aligned against an assembly of cDNA sequences for the GRCm38 (mm10) assembly genome using Bowtie2 with the following parameters: -x Mus_musculus.GRCm38.cdna.all.fa -S "outdir" --no-hd --no-sq --no-unal -k 5. (all analysis following this step assumes bowtie2 was run in "k" mode!).
In order to generate raw (un-normalized)  counts, gene names are extracted from the cDNA reference file and a counting script from the original authors available at "https://github.com/z0on/tag-based_RNAseq/blob/master/samcount.pl" was run in order to generate a tab-seperated table of raw read counts.
We provide raw, unnormalized counts in order to allow users to use a variety of normalization schemes as suits their analysis and as keeps up-to-date with advances in RNA-seq read normalizaition.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each sample

source_name: 3T3 Fibroblast

growth_protocol: 3T3 mouse fibroblast cells were maintained in glucose containing Dulbecco's modified Eagle's medium supplemented with 10% bovine calf serum and penicillin-streptomycin (100 units/ml)

extract_protocol:
RNA extraction and purification were done using the Rneasy Mini Kit (cat. No. 74106) and Rnase-Free Dnase set (cat. No. 79256) (Quiagen, Hilden, Germany) according to the manufacterers instructions. Briefly, cells were lysed directly from the plate and homogenized by vortexing. All samples were treated with DNase. Precipitate was formed using 70% ethanol.
RNA samples were sent to the Genome Sequence and Analysis Facility at The University of Texas at Austin where libraries were constructed. Briefly, RNA fragmentation and RT primer annealing were done using 5X First Strand Buffer (Takara Bio USA, Inc., Mountain View, CA) at 95°C for 2.5 min. SmartScribe reverse transcriptase (Takara Bio USA, Inc., Mountain View, CA) was added to samples for cDNA synthesis. Titanium tag polymerase (Takara Bio USA, Inc., Mountain View, CA) was used in cDNA amplification master mix.
RNA TagSeq

treatment_protocol: Cells were pretreated with culture medium containing SC-514 (0, 25, 50 or 100 µM) 1 hour prior to stimulation. Cells were stimulated with either 1 ng/ml of IL-1β, or 10 ng/ml of TNF-α for 15, 30, 60, 120, and 360 min.

tag: stimulus

value: TNF-alpha (10ng/ml)

tag: sc-514 concentration

tag: time stimulated


title: SMZ-1_1 RNA-seq


title: 2_U_4-2


title: 2_U_3-3

description:
U_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_U_3-1


title: 2_U_4-3


title: 2_U_3-2


title: 2_U_3-4


title: S24hours.1

city: Bron

first: Sally

last: Badawi

address: 59 Bd Pinel

department: Biology

institute: Université Claude Bernard Lyon1

data_processing:
NCS 2.0.2 and RTA 2.4.11 Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using cutadapt v1.9.1 software, then mapped to mm10 whole genome using TopHat v2.1.0 software with default parameter (bowtie 2.2.9).
Signals were counted using htseq-count v0.6.0 software with unstranded parameter and tables gathering raw counts and RPK (Read Per Kilobase) were generated.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including raw count values matrix for all samples

molecule: polyA RNA

source_name: Heart

extract_protocol:
Hearts were removed and RNA was extracted using Tripure reagent solution and then purified by Rneasy minikit. NextFlex Rapid Directional mRNA-Seq (Bio-Scientific) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Heart

tag: time post surgery

value: 24 hours


title: 2_U_2-4

description:
U_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_U_4-1


title: 2_U_2-2


title: 2_U_2-3


title: 2_U_1-4

description:
U_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_U_2-1


title: 2_U_1-2


title: 2_U_1-3


title: 2_T_4-3

description:
T_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_T_4-4


title: 2_U_1-1


title: 2_T_3-3

description:
T_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_T_3-2


title: 2_T_4-1


title: 2_T_2-4

description:
T_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_T_3-1


title: 2_T_2-2


title: 2_T_4-2


title: 2_T_3-4


title: 2_T_2-3


title: 2_T_2-1


title: 2_T_1-2

description:
T_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_S_4-4

description:
S_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_S_2-4

description:
S_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_S_4-2


title: 2_S_3-4

description:
S_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_S_2-3


title: 2_T_1-3


title: 2_S_2-2


title: 2_S_2-1


title: 2_S_1-4

description:
S_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_S_3-2


title: 2_T_1-1


title: 2_S_4-3


title: 2_S_4-1


title: 2_S_1-1


title: 2_S_1-2


title: 2_S_3-1


title: 2_R_4-3

description:
R_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_R_4-4


title: 2_R_4-2


title: 2_R_3-2

description:
R_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_R_3-4


title: 2_R_3-3


title: 2_R_3-1


title: 2_R_2-4

description:
R_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_R_4-1


title: 2_R_2-3


title: 2_T_1-4


title: 2_S_3-3


title: 2_R_1-3

description:
R_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_R_1-2


title: 2_R_2-1


title: 2_R_2-2


title: 2_Q_4-3

description:
Q_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_R_1-1


title: 2_Q_4-2


title: 2_Q_4-4


title: 2_Q_4-1


title: 2_S_1-3


title: 2_Q_3-4

description:
Q_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_Q_3-2


title: 2_Q_3-1


title: 2_Q_2-4

description:
Q_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_Q_2-3


title: 2_Q_2-1


title: 2_Q_1-3

description:
Q_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_Q_1-4


title: 2_Q_1-2


title: 2_Q_1-1


title: 2_P_4-3

description:
P_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_P_4-2


title: 2_P_4-1


title: 2_P_3-3

description:
P_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_P_4-4


title: 2_R_1-4


title: 2_P_3-4


title: 2_P_3-2


title: 2_P_2-4

description:
P_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_P_3-1


title: 2_P_2-3


title: 2_Q_3-3


title: 2_P_2-1


title: 2_O_4-4

description:
O_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_P_1-2

description:
P_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_P_1-3


title: 2_P_1-1


title: 2_P_1-4


title: 2_Q_2-2


title: 2_O_4-3


title: 2_O_4-2


title: 2_O_4-1


title: 2_O_3-2

description:
O_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_O_1-3

description:
O_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_O_2-2

description:
O_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_O_1-4


title: 2_O_1-2


title: 2_O_3-1


title: 2_O_2-1


title: 2_N_4-4

description:
N_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_P_2-2


title: 2_O_2-3


title: 2_N_3-3

description:
N_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_N_3-4


title: 2_N_4-1


title: 2_N_3-2


title: 2_N_2-4

description:
N_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_N_3-1


title: 2_N_2-3


title: 2_N_2-2


title: 2_N_1-4

description:
N_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_N_4-2


title: 2_N_1-3


title: 2_N_2-1


title: 2_O_3-4


title: 2_M_4-4

description:
M_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_N_1-1


title: 2_O_2-4


title: 2_M_4-3


title: 2_O_1-1


title: 2_N_1-2


title: 2_N_4-3


title: 2_M_4-1


title: 2_M_3-1

description:
M_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_M_3-3


title: 2_M_3-2


title: 2_M_2-3

description:
M_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_M_2-4


title: 2_M_4-2


title: 2_M_3-4


title: 2_M_2-2


title: 2_M_1-4

description:
M_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_O_3-3


title: 2_L_4-4

description:
L_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_L_4-2


title: 2_L_4-3


title: 2_M_1-2


title: 2_L_3-4

description:
L_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_M_1-1


title: 2_L_3-1


title: 2_L_2-4

description:
L_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_L_3-3


title: 2_L_3-2


title: 2_L_2-2


title: 2_L_2-1


title: 2_L_1-4

description:
L_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_L_2-3


title: 2_L_1-2


title: 2_L_1-3


title: 2_L_1-1


title: 2_K_4-4

description:
K_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_M_1-3


title: 2_K_4-3


title: 2_K_3-3

description:
K_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_K_3-4


title: 2_K_4-1


title: 2_M_2-1


title: 2_K_2-4

description:
K_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_L_4-1


title: 2_K_1-3

description:
K_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_K_2-1


title: 2_K_1-1


title: 2_K_1-2


title: 2_K_3-2


title: 2_K_2-2


title: 2_J_4-4

description:
J_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_J_4-2


title: 2_J_4-3


title: 2_J_3-4

description:
J_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_J_3-1


title: 2_J_3-2


title: 2_J_4-1


title: 2_J_2-3

description:
J_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_J_2-4


title: 2_K_4-2


title: 2_J_2-2


title: 2_J_1-4

description:
J_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_J_1-3


title: 2_K_3-1


title: 2_I_4-4

description:
I_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_J_1-2


title: 2_J_1-1


title: 2_I_4-3


title: 2_K_2-3


title: 2_K_1-4


title: 2_I_4-2


title: 2_I_3-1

description:
I_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_I_4-1


title: 2_I_3-3


title: 2_I_3-4


title: 2_I_2-2

description:
I_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_I_3-2


title: 2_I_2-3


title: 2_J_3-3


title: 2_I_2-4


title: 2_I_1-3

description:
I_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_I_2-1


title: 2_H_4-2

description:
H_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_H_4-3


title: 2_J_2-1


title: 2_I_1-2


title: 2_I_1-1


title: 2_H_4-1


title: 2_H_3-4

description:
H_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_H_3-3


title: 2_H_3-2


title: 2_H_2-2

description:
H_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_H_1-4

description:
H_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_H_2-4


title: 2_H_2-1


title: 2_H_3-1


title: 2_H_1-3


title: 2_H_1-2


title: 2_H_1-1


title: 2_I_1-4


title: 2_G_4-2

description:
G_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_G_4-3


title: 2_G_4-1


title: 2_H_4-4


title: 2_G_3-4

description:
G_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_G_3-2


title: 2_G_4-4


title: 2_G_2-4

description:
G_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_G_3-3


title: 2_G_2-2


title: 2_G_2-3


title: 2_G_1-2

description:
G_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_G_1-4


title: 2_H_2-3


title: 2_F_4-4

description:
F_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_G_1-1


title: 2_F_3-3

description:
F_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_F_4-2


title: 2_F_4-1


title: 2_F_3-2


title: 2_F_4-3


title: 2_F_3-4


title: 2_F_3-1


title: 2_G_3-1


title: 2_F_2-1

description:
F_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_F_1-4

description:
F_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_F_1-3


title: 2_F_1-2


title: 2_F_2-4


title: 2_F_1-1


title: 2_E_4-1

description:
E_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_F_2-2


title: 2_E_4-2


title: 2_E_4-4


title: 2_G_2-1


title: 2_G_1-3


title: 2_E_4-3


title: 2_E_3-3

description:
E_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_E_3-2


title: 2_E_2-3

description:
E_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_E_2-4


title: 2_E_3-1


title: 2_E_2-2


title: 2_E_2-1


title: 2_E_1-4

description:
E_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_E_1-2


title: 2_E_1-3


title: 2_F_2-3


title: 2_D_4-3

description:
D_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_D_4-4


title: 2_D_4-2


title: 2_E_1-1


title: 2_D_3-4

description:
D_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_D_4-1


title: 2_D_3-3


title: 2_E_3-4


title: 2_D_1-3

description:
D_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_D_2-2

description:
D_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_D_2-4


title: 2_D_2-3


title: 2_D_2-1


title: 2_D_1-4


title: 2_D_3-1


title: 2_D_1-2


title: 2_D_1-1


title: 2_C_4-4

description:
C_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_C_4-3


title: 2_C_4-2


title: 2_C_3-4

description:
C_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_C_4-1


title: 2_C_3-3


title: 2_C_3-1


title: 2_C_2-4

description:
C_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_C_2-3


title: 2_C_1-4

description:
C_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_C_2-1


title: 2_C_2-2


title: 2_C_1-3


title: 2_D_3-2


title: 2_B_4-3

description:
B_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_B_4-1


title: 2_C_1-2


title: 2_B_4-4


title: 2_C_1-1


title: 2_B_2-4

description:
B_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_B_2-1


title: 2_B_3-3

description:
B_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_B_3-1


title: 2_B_1-3

description:
B_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 2_B_2-2


title: 2_B_2-3


title: 2_B_1-1


title: 2_B_3-2


title: 2_B_4-2


title: 2_C_3-2


title: 1_U_4-4

description:
2_U_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)

value: IL-1-beta (1ng/ml)


title: 1_U_4-2


title: 2_B_1-2


title: 2_B_3-4


title: 1_U_4-3


title: 2_B_1-4


title: 1_U_4-1


title: 1_U_3-4

description:
2_U_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_U_3-3


title: 1_U_3-2


title: 1_U_3-1


title: 1_U_2-4

description:
2_U_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_U_2-3


title: 1_U_2-2


title: 1_U_1-1

description:
2_U_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_U_1-4


title: 1_U_1-3


title: 1_U_2-1


title: 1_T_4-3

description:
2_T_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_T_4-4


title: 1_T_4-1


title: 1_T_3-3

description:
2_T_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_T_3-1


title: 1_T_3-4


title: 1_T_3-2


title: 1_U_1-2


title: 1_T_2-4

description:
2_T_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_T_1-3

description:
2_T_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_T_2-2


title: 1_T_2-1


title: 1_T_4-2


title: 1_T_1-1


title: 1_T_2-3


title: 1_T_1-4


title: 1_T_1-2


title: 1_S_4-4

description:
2_S_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_S_4-3


title: 1_S_4-2


title: 1_S_4-1


title: 1_S_2-4

description:
2_S_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_S_2-3


title: 1_S_2-1


title: 1_S_3-1

description:
2_S_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_S_3-4


title: 1_S_3-3


title: 1_S_1-4

description:
2_S_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_S_2-2


title: 1_S_1-1


title: 1_R_4-4

description:
2_R_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_S_1-3


title: 1_R_4-3


title: 1_R_4-2


title: 1_R_4-1


title: 1_R_3-4

description:
2_R_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_R_3-3


title: 1_R_2-4

description:
2_R_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_R_3-2


title: 1_R_3-1


title: 1_R_2-2


title: 1_R_2-3


title: 1_R_2-1


title: 1_S_3-2


title: 1_R_1-4

description:
2_R_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_R_1-2


title: 1_Q_4-4

description:
2_Q_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_R_1-1


title: 1_Q_4-2


title: 1_S_1-2


title: 1_Q_4-1


title: 1_Q_3-1

description:
2_Q_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_Q_3-4


title: 1_Q_3-2


title: 1_Q_2-3

description:
2_Q_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_Q_2-4


title: 1_Q_3-3


title: 1_Q_2-2


title: 1_Q_1-4

description:
2_Q_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_Q_2-1


title: 1_P_4-3

description:
2_P_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_Q_1-1


title: 1_P_4-4


title: 1_P_4-1


title: 1_P_4-2


title: 1_P_3-4

description:
2_P_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_R_1-3


title: 1_P_2-4

description:
2_P_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_Q_4-3


title: 1_P_2-3


title: 1_P_1-4

description:
2_P_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_Q_1-2


title: 1_P_2-2


title: 1_P_1-3


title: 1_O_4-4

description:
2_O_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_P_1-1


title: 1_O_4-1


title: 1_P_1-2


title: 1_O_3-4

description:
2_O_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_O_3-3


title: 1_P_3-2


title: 1_O_3-2


title: 1_O_3-1


title: 1_P_3-3


title: 1_O_4-2


title: 1_O_2-2

description:
2_O_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_Q_1-3


title: 1_O_2-1


title: 1_O_2-3


title: 1_O_1-3

description:
2_O_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_O_1-2


title: 1_N_4-4

description:
2_N_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_O_1-1


title: 1_P_3-1


title: 1_P_2-1


title: 1_N_4-3


title: 1_N_4-1


title: 1_N_3-4

description:
2_N_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_N_3-3


title: 1_N_3-2


title: 1_N_3-1


title: 1_N_2-3

description:
2_N_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_N_2-4


title: 1_N_1-4

description:
2_N_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_N_2-1


title: 1_O_2-4


title: 1_N_2-2


title: 1_O_1-4


title: 1_M_4-4

description:
2_M_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_M_4-3


title: 1_N_1-2


title: 1_M_3-3

description:
2_M_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_M_3-4


title: 1_M_4-2


title: 1_M_4-1


title: 1_N_1-1


title: 1_M_3-2


title: 1_M_3-1


title: 1_M_2-4

description:
2_M_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_M_2-3


title: 1_N_4-2


title: 1_M_1-4

description:
2_M_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_M_2-2


title: 1_M_2-1


title: 1_M_1-3


title: 1_M_1-2


title: 1_L_4-4

description:
2_L_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_M_1-1


title: 1_N_1-3


title: 1_L_4-3


title: 1_L_4-2


title: 1_L_3-3

description:
2_L_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_L_3-2


title: 1_L_3-1


title: 1_L_2-4

description:
2_L_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_L_2-2


title: 1_L_2-1


title: 1_L_2-3


title: 1_L_1-3

description:
2_L_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_K_4-4

description:
2_K_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_L_1-4


title: 1_L_1-1


title: 1_K_4-3


title: 1_K_4-2


title: 1_K_3-3

description:
2_K_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_K_4-1


title: 1_K_3-4


title: 1_L_3-4


title: 1_K_1-4

description:
2_K_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_K_2-1

description:
2_K_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_K_2-4


title: 1_K_3-2


title: 1_K_2-2


title: 1_L_4-1


title: 1_K_1-3


title: 1_K_1-1


title: 1_J_4-4

description:
2_J_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_J_4-1


title: 1_K_3-1


title: 1_J_4-2


title: 1_J_3-3

description:
2_J_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_L_1-2


title: 1_J_4-3


title: 1_J_3-2


title: 1_J_3-1


title: 1_J_2-2

description:
2_J_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_J_1-4

description:
2_J_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_J_2-4


title: 1_J_1-3


title: 1_J_1-2


title: 1_J_1-1


title: 1_K_2-3


title: 1_I_4-4

description:
2_I_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_I_4-1


title: 1_I_3-4

description:
2_I_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_I_4-3


title: 1_I_4-2


title: 1_I_3-2


title: 1_J_3-4


title: 1_I_3-1


title: 1_I_2-4

description:
2_I_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_I_2-3


title: 1_I_2-2


title: 1_I_2-1


title: 1_I_1-4

description:
2_I_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_J_2-1


title: 1_J_2-3


title: 1_I_1-1


title: 1_I_1-2


title: 1_H_4-2

description:
2_H_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_H_4-4


title: 1_H_4-1


title: 1_H_3-4

description:
2_H_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_H_3-3


title: 1_H_3-2


title: 1_H_3-1


title: 1_H_2-4

description:
2_H_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_I_3-3


title: 1_H_2-3


title: 1_H_2-2


title: 1_H_2-1


title: 1_H_1-4

description:
2_H_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_H_1-2


title: 1_H_1-1


title: 1_H_1-3


title: 1_I_1-3


title: 1_H_4-3


title: 1_G_4-4

description:
2_G_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_G_4-3


title: 1_G_3-4

description:
2_G_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_G_3-2


title: 1_G_2-4

description:
2_G_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_G_3-1


title: 1_G_4-1


title: 1_G_2-3


title: 1_G_1-4

description:
2_G_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_G_2-2


title: 1_G_1-2


title: 1_G_1-1


title: 1_F_4-4

description:
2_F_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_F_4-2


title: 1_F_3-3

description:
2_F_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_F_4-3


title: 1_F_4-1


title: 1_F_3-4


title: 1_G_4-2


title: 1_F_2-3

description:
2_F_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_F_2-4


title: 1_F_3-1


title: 1_F_2-2


title: 1_F_2-1


title: 1_F_1-4

description:
2_F_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_G_2-1


title: 1_E_4-3

description:
2_E_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_F_1-2


title: 1_E_4-4


title: 1_O_4-3

description:
2_O_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_F_1-1


title: 1_E_4-2


title: 1_E_3-4

description:
2_E_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_G_1-3


title: 1_G_3-3


title: 1_E_3-2


title: 1_E_4-1


title: 1_E_2-3

description:
2_E_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_E_3-1


title: 1_E_1-4

description:
2_E_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_E_1-3


title: 1_E_3-3


title: 1_E_2-4


title: 1_D_4-4

description:
2_D_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_E_2-2


title: 1_F_3-2


title: 1_D_4-2


title: 1_E_1-2


title: 1_E_2-1


title: 1_D_3-4

description:
2_D_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_D_3-3


title: 1_F_1-3


title: 1_D_4-3


title: 1_D_2-4

description:
2_D_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_D_4-1


title: 1_D_3-1


title: 1_D_3-2


title: 1_D_2-2


title: 1_D_2-3


title: 1_D_1-3

description:
2_D_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_D_2-1


title: 1_D_1-1


title: 1_D_1-2


title: 1_C_4-4

description:
2_C_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_E_1-1


title: 1_C_4-3


title: 1_C_3-4

description:
2_C_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_C_3-3


title: 1_C_4-2


title: 1_C_4-1


title: 1_C_3-2


title: 1_C_2-3

description:
2_C_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_C_3-1


title: 1_C_2-4


title: 1_C_2-1


title: 1_C_2-2


title: 1_D_1-4


title: 1_C_1-4

description:
2_C_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: loin_high_MM [Pi2]

city: Kraków

first: Tomasz

last: Szmatoła

address: Komuny Paryskiej, 4

country: Poland

institute: National Reseach Institute of Animal Production

description:
Pi2
processed data file: PAREsnip_results.xlxs
processed data file tab: PAREsnip LMM Pi2(2)

data_processing:
Basecalls performed using CASAVA version 1.8.2.
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove degradome adapters and shorten the reads to the required length.
Cleaned sequences were aligned to the Sus scrofa genome (assembly Sus Scrofa-11.0).
PARESNIP was used to find targets of small RNAs using the degradome.
Genome_build: Sus_scrofa 11
Supplementary_files_format_and_content: PAREsnip_results.xlsx: Excel file containing results obtained from PARESNIP.

organism: Sus scrofa

source_name: loin

growth_protocol: All pigs were female and they were maintained at Pig Test Station under the same feeding and housing conditions and were slaughtered when they reached 100±2 kg.

extract_protocol:
RNA was isolated by TRI Reagent™ Solution (Ambion, Cambridge, UK), homogenised by beads method and using 1-bromo-3-chloropropane (Sigma-Aldrich, Saint Louis, USA) instead of chloroform. The RIN values were over 7 what was estimated by TapeStation2200 and RNA tapes (Agilent, Palo Alto, USA).
The PARE libraries were prepared as described Zhai et al. (2014) with few modifications. TargetRT, 5` and 3` DNA PCR, FinalPCR, PAREseq primers and 5`RNA adapter were HPLC purified and purchased in Genomed (Poland). dsDNA_bottom and dsDNA_top were PAGE purified (Invitrogen). In addition, we used ready-to-use 10% Novex™ TBE Gels for both electrophoreses that were run on the XCell SureLock® Mini-Cell (Invitrogen, Carlsbad, USA) using 0.5% TBE. The PARE library quantification was assessed by TapeStation2200 (D1000 tape) (Agilent, Palo Alto, USA) and by Qubit™ using dsDNA HS Assay (Invitrogen, Carlsbad, USA). The final concentration of the PARE libraries was normalised to 10 nM.
The libraries were diluted according to a cluster generation protocol and loaded into a v3 Illumina flowcell.

tag: breed

value: Pietrain

tag: day

value: female

value: loin

tag: shear force

value: heavy

tag: replicate


title: loin_low_MM [Pi6]

description:
Pi6
processed data file: PAREsnip_results.xlxs
processed data file tab: PAREsnip HMM Pi3(6)

tag: tissue

value: light


title: loin_low_MM [Pi7]

description:
Pi7
processed data file: PAREsnip_results.xlxs
processed data file tab: PAREsnip HMM Pi4(7)


title: loin_high_MM [Pi1]

description:
Pi1
processed data file: PAREsnip_results.xlxs
processed data file tab: PAREsnip LMM Pi1(1)


title: 1_C_1-3


title: loin_high_MM [PLW5]

description:
PLW5
processed data file: PAREsnip_results.xlxs
processed data file tab: PAREsnip PLW3 HMM(5)

value: Polish Large White


title: loin_high_MM [PLW7]

description:
PLW7
processed data file: PAREsnip_results.xlxs
processed data file tab: PAREsnip PLW4 HMM(7)


title: 1_C_1-2


title: loin_low_MM [PLW2]

description:
PLW2
processed data file: PAREsnip_results.xlxs
processed data file tab: PLW2 LMM PAREsnipM(2)


title: 1_C_1-1


title: loin_high_MM [H9]

description:
H9
processed data file: PAREsnip_results.xlxs
processed data file tab: PAREsnip H3 HMM(9)

value: Hampshire


title: 1_B_4-4

description:
2_B_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: loin_high_MM [H10]

description:
H10
processed data file: PAREsnip_results.xlxs
processed data file tab: PAREsnip H4 HMM(10)


title: 1_K_1-2

description:
2_K_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: loin_low_MM [H3]

description:
H3
processed data file: PAREsnip_results.xlxs
processed data file tab: PAREsnip H2 LMM(3)


title: Chi-C_siRE_rep2

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

data_processing:
Quality of reads was verified using FASTQC analysis
The capture Hi-C paired-end sequencing reads were aligned using HiCUP tools (PMID: 26835000). The raw sequencing reads are separated and mapped against the positions of the human genome (hg38). The reads were then filtered for experimental artefacts and duplicate reads
Functions provided with HOMER (PMID: 20513432) were used for HiC data processing and to obtain interactions
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph files containing first principle component values of genome-wide coverage

source_name: Chi-C from Kasumi1 cell line siRE rep2

extract_protocol:
5× 10^7 Kasumi-1 cells were fixed via suspension in 37 ml of RPMI-1640 supplemented with 15% FBS and 2% formaldehyde. The cells were fixed for 10 minutes at room temperature while mixing. 6 ml of 1M glycine (0.125 M final concentration) was added to quench the reaction. Cells were incubated at room temperature for 5 min, followed by 15 minutes on ice. Cells were then pelleted by centrifugation at 400 x g for 10 minutes at 4 °C. The supernatant was discarded and cells were washed in ice cold PBS. The cells were then pelleted and after removing the supernatant, each sample was flash frozen in liquid nitrogen, and stored at −80 °C. Cells were lysed in a tight dounce homogeniser (ten cycles) with 3ml of cold lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 0.2% Igepal CA-630, one tablet protease inhibitor cocktail (Roche complete, EDTA-free, 11873580001)). Cells were left on ice for five minutes then homogenised another ten times. The lysed cells, in 3 ml lysis buffer, were added to 47ml of lysis buffer and incubated on ice for 30 minutes with occasional mixing.  The chromatin was pelleted at 1800 rpm for 5 minutes at 4°C and the supernatant discarded. The pellet was resuspended in 1ml of 1.25x NEBuffer 2 and split into four. Each sample was then pelleted at 1000 rpm and resuspended in 358 µl of 1.25x NEBuffer 2. 11 µl 10% SDS was added and each tube was incubated at 37°C for 60 minutes, rotating at 950 rpm. Samples were mixed by pipetting up and down every 15 minutes. The SDS was quenched with 75µl 10% Triton X-100 and incubated at 37˚C for 60 minutes, rotating at 950 rpm. During the incubation, samples were mixed by pipetting up and down every 15 minutes. The chromatin was digested overnight with 1500 units of HindIII (NEB R0104T), rotating (950 rpm) at 37 °C. The HindIII cleavage of its restriction site (5’ AAGCTT 3’) generates a 5’ overhang (5’-AGCT-3’), which was repaired to include a biotinylated nucleotide, allowing the enrichment of Hi-C ligation products. To do this, 6µl 10x NEB2, 2µl H2O, 1.5µl 10mM dCTP, 1.5µl 10mM dGTP, 1.5µl 10mM dTTP, 37.5µl 0.4mM biotin-14-dATP (Life Technologies 19524-016), and 10μl 5U/μl Klenow (DNA polymerase I large fragment, NEB M0210L) were added to each tube. Samples were mixed carefully and incubated for 60 minutes at 37˚C, with mixing by pipetting every ten minutes. The digested chromatin mixture was added to a falcon tube with 8 ml of ligation buffer (750µl 10x ligation buffer (NEB B0202S), 75 μl 10mg/ml BSA (NEB B9001S) and 50 μl  1U/μl T4 DNA ligase (Invitrogen 15224-025). These dilute conditions favour ligation of fragments crosslinked within the same chromatin complex (intra-molecular ligation). The tubes were mixed by inversion and incubated overnight at 16 °C. The following day, samples were incubated for a further 30 minutes at room temperature. Crosslinks were reversed and proteins degraded by incubating the tubes over night at 65 ˚C, with 60µl 10mg/ml proteinase K (Roche 03115879001). After the overnight incubation, another 60 µl of 10 mg/ml proteinase K per tube was added, followed by a 2 hour incubation at 65˚C. The reaction mixtures were cooled to room temperature and 12.5 µl of 10 mg/ml RNase A (Roche 10109142001) was added. Samples were incubated at 37˚C for 60 minutes. The DNA in these tubes was purified with two phenol extractions. After ethanol precipitation, the DNA pellets were resuspended in 25µl 1x TE and the four samples were pooled. The Quant-iT assay was used to determine the DNA concentration of the resultant HiC library using a Qubit® 3.0 Fluorometer (Thermo Scientific).
To check the library was sufficiently ligated, a 1/10 dilution was resolved on a 0.8% agarose gel. The majority of the library should run at around 10 kb. To confirm that blunt-end ligation was successful, the fact that fill-in and ligation of a HindIII site (AAGCTT) creates a NheI restriction site (GCTAGC) was exploited. A particular ligation product formed by the MYC promoter and a known 1.8 MB long range interaction was amplified with 3C PCR (see table 12 for primer sequences). The same was done for a ligation product formed by the MYC promoter and an adjacent restriction fragment. 200ng of the purified PCR products were split into four and digested with HindIII, NheI or both enzymes, with undigested DNA is used as a control. The resultant DNA samples were run on a 1.5% gel.  To avoid pulling down any non-ligated fragments, biotin was removed from free ends using the exonuclease activity of T4 DNA polymerase. 8 reactions of  5μg of Hi-C library, 0.5μl 10 mg/ml BSA, 5μl 10x NEBuffer 2, 2μl 2.5mM dATP, and 5μl T4 DNA polymerase (NEB M0203L) in a total volume of 50μl were made and incubated at 20˚C for 4 hours. The reaction was stopped by adding 2ml of 0.5M EDTA pH 8.0. Two reactions were pooled to generate four tubes of approximately 10ug DNA. The DNA was purified via phenol:chloroform extraction and ethanol precipitation. Each sample was reconstituted in 130 μl H2O. An E220 focused-ultrasonicator (Covaris) was used to fragment the DNA with the intensity set to 4, the duty cycle set to 10% and with 200 cycles per burst for 55 seconds. After sonication,  the entire volume of each sample was transferred into a fresh Eppendorf tube and 18μl 10x ligation buffer (NEB B0202S),18μl 2.5mM dNTP mix, 6.5μl T4 DNA polymerase (NEB M0203L),6.5μl T4 DNA Polynucleotide kinase (NEB M0201L) and 1.3μl Klenow (NEB M0210L) were added. The reaction was left for 30 minutes at room temperature. Each sample was then split into two and purified with a MinElute column (Qiagen 28004), according to the manufacturer’s instructions. Each column was eluted twice with 15 μl TLE (10mM Tris pH8.0, 0.1mM EDTA). To the sheared and end repaired DNA , 5 μl of NEBuffer 2 10x, 11.5 μl dATP 1mM and 3.5 μl Klenow exo- (NEB M0212L) were added. The reaction was incubated for 30 minutes at 37 ˚C. To inactivate the enzyme, each reaction was incubated at 65˚C for 20 minutes, and put on ice immediately afterwards. Fragments between 200 and 650 base pairs were size selected by double-sided SPRI bead (ampure) size selection (0.6x followed by 0.9x), following the manufacturers protocol.  All Hi-C library samples were then pooled and quantified with the Quant-iT™ High-Sensitivity DNA Assay Kit (Invitrogen) and assayed on the Qubit™ Fluorometer (Invitrogen). The biotin marked fragments were immobilized via MyOne Strapavidin C1 DynaBeads (Invitrogen) following manufacturers protocol. The fragments were ligated to illumina paired-end adaptors. The immobilized Hi-C fragments were amplified via PCR, using PE PCR primers 1 and 2 with 7 cycles. The Hi-C library was then purified twice with solid phase reversible immobilization (SPRI) beads (Beckman Coulter Ampure XP beads A63881) with a 1:1.8 DNA to SPRI bead ratio.

tag: genotype/variation


title: loin_low_MM [PLW1]

description:
PLW1
processed data file: PAREsnip_results.xlxs
processed data file tab: PAREsnip PLW1 LMM(1)


title: Chi-C_siRE_rep1

source_name: Chi-C from Kasumi1 cell line siRE rep1

tag: cell line


title: 1_B_4-1


title: loin_low_MM [H1]

description:
H1
processed data file: PAREsnip_results.xlxs
processed data file tab: PAREsnip H1 LMM(1)

tag: Sex


title: Chi-C_siMM_rep2

source_name: Chi-C from Kasumi1 cell line siMM rep2

value: mismatch control


title: 1_B_4-3


title: KO_H3K27me3_ChIPSeq

city: Los Angeles

first: Xiuju

last: Wu

state: CA

address: 650 Charles Young Dr East, CHS A2-237

institute: University of California, Los Angeles

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2.
Peaks were called using HOMER tools with the following setting: Histone ChIP threshold (0.001 FDR), KO versus WT Enrichment Fold (4), Sox2 ChIP threshold (0.05 FDR), KO versus WT Enrichment Fold (2).
Motifs were discovered using HOMER motif analysis function.
Genome_build: mm10

source_name: Brain EC

extract_protocol:
Isolation of cerebral endothelial cells (ECs) from Mgp KO and WT mice was performed by Fluorescence-activated cell sorting (FACS) analysis usng anti-CD31 antibodies. EC lysates were clarified from sonicated nuclei and ChIPs were performed by using specific antibodies for Sox2 (R&D system, MAB2018), H3K27me3 (Abcam, ab6002) and H3K4me3 (Abcam, ab8580).
Libraries were prepared according to manufacturer's instructions using KAPA DNA HyperPrep Kit (Kapa Biosystems).

value: Brain


title: 1_B_4-2


title: KO_H3K4me3_ChIPSeq


title: WT_H3K27me3_ChIPSeq


title: shRE JUND ChIP

description: transfection with RUNX1-ETO shRNA

data_processing:
The raw sequence reads in fastq format returned by the Illumina Pipeline was aligned to the hg38 human genome build using Bowtie
The reads in the resulting alignment files were used to generate density maps using bed-tools (Quinlan and Hall, 2010)
Regions of enrichment (peaks) of ChIP and DNAse1 sequencing data were identified using MACS (Zhang et al., 2008) and cisGenome (Ji et al., 2008) software. The resulting peaks common for the two peak calling methods were considered for further analysis
Genome_build: hg38
Supplementary_files_format_and_content: wiggle with read density data derived from bam files

source_name: shRE JUND ChIP after RUNX1/ETO knockdown from Kasumi1 cells

extract_protocol:
Chromatin Immunoprecipitation was carried out as described previously. Cells were re-suspended at 3.3x106 cells/ml and crosslinked for 45 minutes with 0.83 mg/ml Di(N-succinimidyl) glutarate (DSG – sigma). Cells were washed four times with PBS before re-suspending at 2x106 cells/ml and crosslinking for 10 minutes with 1% formaldehyde (Pierce) in PBS. Reactions were quenched with 0.4 M glycine, washed twice with PBS and incubated with Buffer A (10 mM HEPES pH 8.0, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100) at 4oC for 10 minutes followed by Buffer B (10 mM HEPES pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.01% Triton X-100, 0.25% SDS) at 4oC for 10 minutes. Chromatin was sheared (15 X 10 e6 cells/ml) in IP Buffer I (25 mM Tris 1 M, pH 8.0, 150 mM NaCl, 2 mM EDTA, pH 8.0, 1% TritonX-100 and 0.25 % SDS) using a PicorupterTM (Diagenode) to fragments of ~500bp. The supernatant was collected and diluted 3-fold in IP Buffer II (25 mM Tris, pH 8.0, 150 mM NaCl, 2 mM EDTA, pH 8.0, 1% TritonX-100, 7.5 % glycerol). Chromatin from 2x106 cells was incubated with 2 ug JunD (sc-74) coupled to 15 microliter protein G Dynabeads (Dynal) for 2 hours at 4oC. Beads were washed with Buffer 1 (20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 2 mM EDTA, pH 8.0, 1 % TritonX-100, 0.1 % SDS), twice with Buffer 2 (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, pH 8.0, 1 % TritonX100, 0.1 % SDS), LiCl buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1 mM EDTA, pH 8.0, 0.5 % NP40, 0.5 % Na-deoxycholate) and twice with TE/NaCl buffer (10 mM Tris-HCl pH 8.0, 50 mM NaCl, 1 mM EDTA). Samples were eluted in 100 microliter elution buffer (100 mM NaHCO3, 1% SDS) and crosslinks were reversed overnight at 65oC with proteinase K. DNA was purified using Agencourt AMPure (Beckman Coulter) according to the manufacturer’s instructions. Samples were analysed and validated by qPCR.
DNA libraries from the chromatin immunoprecipitation assays were prepared using the Kapa Hyper-Prep kit according the manufacturer’s guidelines. Libraries were indexed and then amplified by PCR. Libraries were gel purified to ensure the correct fragment lengths were sequenced (Qiagen Gel purification Kit). Fragments of 200-300bp were selected for DNase I libraries and 200-400bp for ChIP libraries. Libraries were validated by qPCR and quantified using the Kapa quantification kit before pooling and sequencing on NextSeq® 500/550 High Output kit v2 75 cycles (Illumina, FC 404-2005).

tag: chip target

value: JunD

tag: chip antibody

value: Jun D Antibody (329):sc-74

value: RUNX1/ETO knockdown


title: Chi-C_siMM_rep1

source_name: Chi-C from Kasumi1 cell line siMM rep1


title: WT_H3K4me3_ChIPSeq


title: KO_Sox2_ChIPSeq


title: 1_B_3-4

description:
2_B_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: Control JUND ChIP

description: transfection with scrambled shRNA

source_name: Control JUND ChIP from Kasumi1 cells

value: control (scrambled shRNA)


title: Dam::EMR-1_mrg-1_cec-4_rep3

city: Seville

first: Peter

last: Askjaer

address: UPO Carretera de Utrera km 1

country: Spain

institute: Centro Andaluz de Biología del Desarrollo

description:
processed data file:
DamID (identification of methylated GATC fragments)
mapped_reads_1kb_ce11.txt
mapped_reads_10kb_ce11.txt
mapped_reads_100kb_ce11.txt
log2_1kb_ce11.txt
log2_10kb_ce11.txt
log2_100kb_ce11.txt

data_processing:
Library strategy: DamID-seq
Most analyses were performed in R Studio (Version 1.0.153; RStudio Team 2016) using the damid.seq.R pipeline (Sharma et al, doi:10.1002/dvg.22925; available at github.com/damidseq/RDamIDSeq). This pipeline identifies and maps specifically those NGS reads that contain the DamID adapters (adapt.seq="CGCGGCCGAG”) and corresponds to genomic fragments flanked by GATC sites (restr.seq = "GATC"). Mapping was to the C. elegans genome release WBCel235 (species = "BSgenome.Celegans.UCSC.ce11"). The pipeline provides absolute and relative read counts both per GATC fragment and per user-defined bin size. 2.2-18.7 million uniquely mapped reads were obtained from each sample. Moreover, the pipeline computes the log2 ratio between relative Dam::EMR-1 and GFP::Dam reads across all replicas.
Genome_build: ce11
Supplementary_files_format_and_content: Output from the damid.seq.R pipeline organised in txt files. Pipeline used at 3 different bin sizes: 1 kb, 10 kb and 100 kb. Files named "mapped reads…" contain the number of reads of the individual samples. Files named "log2…" contain the log2 ratios between relative Dam::EMR-1 and GFP::Dam reads across all replicas.

organism: Caenorhabditis elegans

source_name: L1 larvae

growth_protocol: We used the promoter of the heat shock-inducible gene hsp-16.41, and performed the DamID experiments without induction, in order to have only trace expression levels of Dam::EMR-1. Strains expressing a nuclear GFP::Dam fusion were used as a standard control for the experiments. Plates full of mix-staged worms growing on Dam- plates were washed with M9 and collected in 15 ml tubes. Worms were pelleted by centrifugation at 500g for 2 min and washed twice before adding 2 ml of bleach solution (5 ml H2O, 2ml NaOH 5M, 3 ml bleach). Tubes were agitated until half of the worms are broken up (max. 4 min). M9 was added and released embryos were washed ten times. Finally, embryos were resuspended in M9 and let hatch overnight. ~1000 L1s per plate were seeded onto four 10cm plates (NGM plates + 1 mM IPTG + 100 μg/ml ampicillin) previously seeded with E. coli producing double-stranded control or mrg-1 RNA. Animals were incubated for 66h at 20°C to produce embryos, which were harvested by hypochlorite treatment, as described above, and hatched overnight at 20°C in the absence of food. Cultures were centrifuged and ~ 20000 L1s were incubated in 10ml liquid culture containing E. coli GM119 Dam- bacteria as food source for 2.5 hours at 20°C in an orbital shaker (120 rpm). L1 larvae were harvested by centrifugation, washed with M9 10 times and distributed in aliquots of 30 ul. Excess liquid was removed and aliquots were snap-frozen in liquid nitrogen and stored at -80°C. RNAi efficiency was verified by incubating L1s on mrg-1 RNAi plates for 2 generations, which produced 30-50% F1 adult sterility.

extract_protocol:
Genomic DNA (gDNA) extraction from ~30 μl L1s was performed by 5 rounds of rapid freeze/thaw cycles in liquid nitrogen and 37°C water bath to break the worm cuticle followed by purification using a DNeasy Blood and Tissue Kit (QIAGEN #69504). gDNA was eluted in two rounds in a total volume of 300 μl and precipitated using 0.1x volume NaAc 3M and 2.5x volume 96% ethanol. The final concentration after resuspension in 10 μl of 10mM Tris-Cl was measured by QUBIT.
200 ng gDNA were digested using 10 units DpnI (NEB #R0176S; cuts methylated GATC) in 10 μl for 6 hours at 37°C in a thermocycler. Next, DpnI was inactivated by heating to 80°C for 20 min. Double-stranded adaptors were prepared by heating a mixture of 50 μl primer AdRt (5’-CTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAGGA, 100 μM) and 50 μl AdRb (5’-TCCTCGGCCGCG; 100 μM) to 95°C and cooling slowly to room temperature. Next, 0.8 μl of the double-stranded adapters were ligated to the DpnI-digested gDNA in a volume of 20 μl at 16°C in a thermocycler overnight using T4 DNA ligase (Roche #10799009001), which later was inactivated by incubation for 10 min at 65°C. The ligated gDNA was purified with 1.8x volume Agencourt AMPure XP® beads (Beckman Coulter; #A63880) using a magnetic particle concentrator, washed with 180 μl of freshly prepared 70% ethanol and eluted in 20 μl elution buffer (EB; 10 mM Tris-Cl, pH 8.5). Unmethylated GATC sites were digested with 10 units of DpnII (NEB #R0543S) in a volume of 50 μl for 1 h at 37°C. Next, DpnII was inactivated by heating to 80°C for 20 min. The digested gDNA was re-purified with AMPure XP® beads as above and eluted in 25 μl. Methylated gDNA fragments were amplified using Taq DNA polymerase with ThermoPol buffer (NEB #M0267) in 50 μl reactions containing 5 μl 10x PCR reaction buffer, 25 μl DpnII digested DNA, 1.25 μl primer AdR (5’-NNNNGTGGTCGCGGCCGAGGATC; 50 μM), 4 μl dNTP mix (each 2.5 mM), 1 μl polymerase. PCR parameters were 1) 68°C 10 min; 2) 94°C 1 min; 3) 65°C 5 min; 4) 68°C 15 min; 5) 94°C 1 min; 6) 65°C 1 min; 7) 68°C 10 min; 8) Go to step 5 and repeat three times; 9) 94°C 1 min; 10) 65°C 1 min; 11) 68°C 2 min; 12) Go to step 9 and repeat 19 times. Five μl of each PCR reaction were analyzed by agarose gel electrophoresis: successful amplification of methylated DNA was confirmed by the presence of a 400–1000 bp smear which was not observed in controls without DpnI or T4 DNA ligase. Finally, the PCR products were purified using QIAquick PCR Purification Kit (QIAGEN #28104), eluted in 30 μl EB and their concentration was measured using QUBIT. 400 ng of PCR fragments were used as input in the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370). The manufacturer’s instructions were used with the following conditions. Size selection was performed by first adding 30 μl of resuspended SpeedBead Magnetic Carboxylate Modified Particles, Azide 0.05% (GE65152105050250) to the 100 μl ligation reaction. The beads were discarded and the supernatant was mixed with 60 μl resuspended SpeedBeads. Then, the supernatant was discarded and the beads were washed with ethanol and DNA was eluted in 17 μl of 10mM Tris. Eight PCR cycles were performed to amplify the samples. The quality of the samples was verified by agarose gel electrophoresis and QUBIT analysis as above.

tag: RNAi

value: intestine

tag: developmental stage

value: L1 larvae


title: GFP::Dam_mrg-1_cec-4_rep3


title: HH RNA-seq

source_name: Primary cutaneous anaplastic large-cell lymphoma

value: HH


title: 1_B_3-3

tag: stimulus

value: IL-1-beta (1ng/ml)


title: 1_B_3-2

tag: sc-514 concentration


title: WT_Sox2_ChIPSeq


title: MJ RNA-seq

source_name: Mycosis fungoides

value: MJ


title: GFP::Dam_cec-4_rep3

value: control


title: Dam::EMR-1_cec-4_rep3


title: 1_B_3-1

tag: time stimulated


title: My-La_1 RNA-seq


title: GFP::Dam_mrg-1_cec-4_rep2

tag: strain


title: 1_B_2-4

description:
2_B_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: Dam::EMR-1_mrg-1_cec-4_rep2


title: HuT_78 RNA-seq

source_name: Sézary syndrome


title: 1_B_2-3


title: Dam::EMR-1_mrg-1_rep3


title: GFP::Dam_mrg-1_rep3


title: Dam::EMR-1_wt_rep3


title: GFP::Dam_wt_rep3


title: 1_B_2-2


title: Dam::EMR-1_cec-4_rep2


title: Dam::EMR-1_mrg-1_rep2


title: SUP-M2 RNA-seq


title: GFP::Dam_cec-4_rep2


title: 1_B_1-4

description:
2_B_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: GFP::Dam_mrg-1_rep2


title: GFP::Dam_wt_rep2


title: Dam::EMR-1_mrg-1_cec-4_rep1


title: SU-DHL-1 RNA-seq


title: 1_B_2-1


title: Ki-JK RNA-seq

value: Ki-JK


title: Dam::EMR-1_cec-4_rep1


title: Neuron-PbControl-1

type: genomic

city: Ann Arbor

first: Kelly

last: Bakulski

state: MI

address: 1415 Washington Heights

department: Department of Epidemiology

institute: University of Michigan

description: mouse neuronal DNA from 10 months of age

hyb_protocol: Input and methylation enriched samples were hybridized to array per manufacturer's instructions.

scan_protocol: Arrays were scanned using NimbleGen MS 200 Microarray Scanner to generate image file.

data_processing: Scanned images were uploaded to Nimblegen DEVA Software to extract location and raw Cy3 and Cy5 intensity. Locally weighted polynomial regression (LOESS) spatial correction was performed to correct for position-dependent non-uniformity of signals. After position-dependent normalization, the DEVA software calculated log2(Cy5/Cy3) ratios for each probe, and values were centered around Tukey’s biweight mean for all probes.

source_name: MBD Enriched DNA

label_protocol: Input and methylation enriched samples labeled using the NimbleGen Dual-Color Labeling Kit.

extract_protocol: Nuclei from cortex tissue was FACS sorted for NeuN+ sample. DNA was extracted from cells by modifying previously established methods for DNA extraction from blood cells, described in Qiagen protocols. All reactions were scaled appropriately, but are reported here for 1 mL of FACS-sorted NeuN+ sample. Each sample was incubated with 100 μL of Proteinase K and 1.2 mL of proprietary Qiagen lysis buffer at 50oC overnight. One equivalent of 100% frozen ethanol was added, followed by centrifugation through a Qiagen DNA binding column. The solution was then washed three times with Qiagen wash buffer, and eluted in ~200 μL of 10 mM Tris/0.5 mM EDTA buffer. DNA samples were sonicated. For each pool, one portion was used as control genomic input, and another was enriched for methylated DNA through methyl-CpG binding domain-based capture using the EpiMark Methylated DNA Enrichment Kit.

tag: pb diet

tag: cell type

value: neuron

tag: age

value: 10 months of age

tag: fraction

value: MBD-enriched

source_name: Input DNA

value: input


title: Neuron-PbControl-2


title: KARPAS-299 RNA-seq

source_name: Anaplastic large-cell lymphoma, ALK+


title: GFP::Dam_mrg-1_cec-4_rep1


title: HFD rep1

city: Chengdu

first: Linyuan

last: Shen

state: Sichuan

address: 211# Huiming Road

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

data_processing:
Sequence  reads  that  fit  any  of  the  following  parameters  were  removed  with  following   standard quality control criteria: 1) The reads with N; more than 4 bases whose quality score   is lower  than  10 or more  than  6 bases whose quality  score is lower  than 13. 2) The  reads   with 5’ primer contaminants or without 3’ primer. 3) The reads without the insert tag. 4) The   reads with ploy A. 5) The reads shorter than 18nt. The clean reads were obtained after data   filtration.
Mapping to genome: Small RNA tags were mapped to rat genome (Rnor_5.0) by SOAP to analyze their distribution and expression on the genome.
Small RNA Annotation: Small RNA tags were annotated with miRNA, tRNA, rRNA and other  small  noncoding  RNA  from  miRBase19,  Genbank  and  Rfam  databases  using  blastn  with  standard parameters: ‐F F ‐e 0.01. rRNA reads were removed for length distribution analysis.
Differentially expressed TRFs were generated by DEGseq
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: Read content and tRFs sequence for each Sample
Supplementary_files_format_and_content: counts

organism: Rattus norvegicus

source_name: heart

extract_protocol:
Total RNAs are extracted by Trizol (Invitrogen). 1-2 μg total RNAs were separated by denatured 15% PAGE with 7M urea. The gel was stained with SYBR Green I solution (Invitrogen). Small RNAs sized at 15-40 nt were excised from the gel were uesd to construct small RNA-sequencing library and sequenced on an Illumina Hi-Seq 2500 apparatus.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 16 of 6-week-old male SD rats were randomly separated into two groups: LFD (normal chow, n=8) and HFD (high fat diet, 40% fat, n=8), feeding with 100 days.

value: Sprague Dawley

value: adipose

value: 8 weeks


title: Neuron-PbControl-3


title: Neuron-PbLow-1

value: low


title: GFP::Dam_cec-4_rep1


title: 1_B_1-1

source_name: 3T3 Fibroblast


title: Neuron-PbLow-3


title: Dam::EMR-1_wt_rep1


title: Dam::EMR-1_wt_rep2


title: Neuron-PbHigh-2

value: high


title: sftb-1(cer39)  rep1

city: Hospitalet de Llobregat

first: Julián

last: Cerón

state: Barcelona

address: Gran via 199, Hospital Duran i Reynals, planta 3

department: Cancer and Human Molecular Genetics

institute: IDIBELL

data_processing:
RNA-seq reads were mapped against C. elegans reference assembly (WBcel235.87) with STAR (Dobin et al., 2013). Genes and transcripts were quantified with RSEM (Li and Dewey, 2011).
Genome_build: WBcel235
Supplementary_files_format_and_content: transcripts and alternative splicing events significatively deregulatated

source_name: synchronized animal population

extract_protocol: Four RNA-Seq libraries – samples 1 to 4 – were prepared with KAPA Stranded mRNA-Seq Illumina® Platforms Kit (Kapa Biosystems), and mRNA purified by poly-A capture. Samples 6 to 10 were prepared using a the TruSeq™ Stranded Total RNA kit protocol (Illumina) and rRNA was depleted from 0.5 µg of total RNA using the Ribo-Zero Gold rRNA Removal Kit .

tag: developtmental stage

value: L2 stage


title: Neuron-PbHigh-1


title: 1_A_3-4

description:
1_A_3.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: HFD rep3

tag: tissue


title: Neuron-PbLow-2


title: sftb-1(cer6) rep2

tag: genotype/variation

value: cer6 is a deletion allele


title: sftb-1(cer6) rep1


title: 1_A_4-1

description:
1_A_4.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_A_3-2


title: WT-L2 rep2

value: Wildtype


title: Neuron-PbHigh 3


title: HFD rep2


title: sftb-1(cer7)  rep2

value: L4 stage


title: 1_B_1-3

value: IL-1-beta (1ng/ml)


title: 1_A_3-3


title: sftb-1(cer3)  rep1


title: WT-L2 rep1


title: 1_A_4-2


title: WT-L4 rep1

value: N2 from cer3 outcross


title: 1_A_3-1


title: SR-786 RNA-seq

tag: cell line


title: H3K27me3_scChIPseq_HBCx-22

description: R1 fastq file: nucleosomal sequence. R2 fastq file: single-cell barcode sequence (0 - 72 bp)

data_processing:
scChIP-seq: Sequenced reads were mapped to hg38 or mm10 whole genome using bowtie v1.2.2 with parameters -p 8 -m 1
scChIP-seq: Barcodes were extracted from Reads #2 by first searching for the constant 4 bp linkers found between the 20-mer indices of the barcode allowing up to 1 mismatch in each linker. If the correct linkers were identified, the three interspersed 20-mer indices were extracted and concatenated together to form a 60 bp non-redundant barcode sequence. A library of all 884,736 combinations of the 3 sets of 96 indices (963) was used to map barcode sequences using the sensitive read mapper Cushaw3 (v3.0.3).
scChIP-seq: For each barcode, aligned reads were extended to 150 bp and all the reads falling in the same 150 bp window were stacked into one as reads possibly originating from PCR duplicates or from the same nucleosome. Then, reads were binned in non-overlapping 50 kb for H3K27me3 and 5 kb genomic bins for H3K4me3 spanning the genome to generate a n x m coverage matrix with n barcodes and m genomic bins used in downstream analysis
scChIP-seq: Single cells with a total number of uniquely mapped reads within the upper percentile were considered as outliers and removed. Genomic regions not represented in at least 1% of all cells were filtered out. The coverage matrix was then normalized by dividing counts by the total number of reads per cell and multiplying by the average number of reads across all cells.
Genome_build: mm10, hg38
Supplementary_files_format_and_content: tab-delimited text files include read count for each cell in genes (scRNA-seq, TAR of MTX and TSV) or genomic bins (scChIP-seq)

organism:
Homo sapiens
Mus musculus

growth_protocol: Female Swiss nude mice were purchased from Charles River Laboratories and maintained under specific pathogen-free conditions. Their care and housing were in accordance with institutional guidelines and the rules of the French Ethics Committee (project authorization no. 02163.02). A PDX model of luminal breast cancer (HBCx-22) was previously established at Institut Curie from untreated early-stage luminal breast cancer with informed consent from the patient (Cottu et al, Breast Cancer Research Treatment, 2012). Acquisition of a resistant phenotype for a derivative of HBCx-22, HBCx-22-TamR, was previously established and maintained as previously described in Cottu et al, Clinical Cancer Research 2014. A PDX from a residual triple negative breast cancer post neo-adjuvant chemotherapy (HBCx-95) was previously established at Institut Curie with informed consent from the patient (Marangoni et al, Clinical Cancer Research, 2018). HBCx-95 xenografts were treated with Capecitabine (Xeloda, Roche Laboratories) orally at a dose of 540 mg/kg/day, 5 days a week for 6 weeks. Relative tumor volumes (RTV, mm^3) were calculated as previously described (Marangoni et al, Clinical Cancer Research, 2007). Mice with recurrent tumors were treated for a second round of Capecitabine when PDX reached a volume of over 200 mm^3. Mouse which did not respond to Capecitabine and PDX specimen was extracted at 1100mm^3 and tagged as HBCx-95-CapaR.

extract_protocol:
Prior scChIP-seq and  scRNA-seq, PDX were digested at 37°C for 2h with a cocktail of Collagenase I (Roche, # 11088793001) and Hyaluronidase (Sigma, # H3506) as previously described (Petit et al, Lab Investigation 2013). Cells were further individualized at 37°C using a cocktail of 0.25% trypsin/Versen (ThermoFisher Scientific, #15040-033), Dispase II (Sigma, # D4693) and Dnase I (Roche, # 11284932001). Red Blood Cell lysis buffer (ThermoFisher Scientific, # 00-4333-57) was then added to degrade red blood cells. To increase the viability of the cell suspension, we removed dead cells using a Dead Cell Removal kit (Miltenyi Biotec). Cells were re-suspended in PBS/0.04% BSA (ThermoFisher Scientific, # AM2616).
After immunoprecipitation targeting H3K4me3 or H3K27me3, scChIP-seq libraries were prepared as following: barcoded-nucleosomes were amplified by in vitro transcription using the T7 MegaScript kit (ThermoFisher Scientific). The resulting amplified RNA was purified using 1x RNAClean XP beads (Beckman) and reverse transcribed by random priming in cDNA. After RNA digestion, DNA was amplified by PCR using with Illumina Primers for 12 cycles and library fragments ranging from 300 to 600 bp (single-cell barcode plus nucleosomal sequence + PCR primer sequence) were size-selected on an agarose gel. Single-cell ChIP-seq libraries were sequenced on Illumina NextSeq 500 MidOutput 150 cycles

value: mouse PDX human tumor


title: 1_A_2-3

description:
1_A_2.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: 1_A_2-4


title: H3K27me3_scChIPseq_HBCx-95


title: GFP::Dam_wt_rep1

value: control

value: intestine

value: L1 larvae


title: sftb-1(cer39)  rep2


title: H3K27me3_scChIPseq_HBCx-22-TamR


title: LFD rep1


title: 1_B_1-2


title: H3K27me3_scChIPseq_HBCx-95-CapaR


title: LFD rep2


title: WT-L4 rep2

value: N2 from cer7 outcross


title: 1_A_2-2


title: 1_A_1-4

description:
1_A_1.fastq.trim.sam.counts
RNA TagSeq (3’ poly-A-directed mRNA-seq)


title: LFD rep3


title: 1_A_2-1


title: 1_A_1-3


title: 1_A_4-4


title: 1_A_4-3


title: 1_A_1-2


title: CRISPR-Cas9 screening experiment2 WT

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

description:
CRISPR-Cas9
processed data file: Screen2.count.txt.gz
processed data file: Screen2.gene_summary.txt.gz

data_processing:
Library strategy: CRISPR-Cas9 screen
The sequencing results were analyzed by MAGeCK package, which took into consideration of the magnitude of enrichment/depletion and the consistency of multiple sgRNAs targeting the same gene, to rank positive/negative regulators.
The generation of the processed data was done using the following command (Screen1 as example):
mageck count -l gRNA_lib_for_mageck.txt -n Screen1 --sample-label WT,2C --fastq Screen1_WT.fastq Screen1_2C.fastq --trim-5 22 --norm-method median
mageck test -k Screen1.count.txt -t 2C -c WT -n Screen1 --norm-method median
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.count.txt: Tab-delimited text files.
Supplementary_files_format_and_content: *.gene_summary.txt: Tab-delimited text files.

growth_protocol: ES-E14TG2a cells were cultured with medium consisted of DMEM (Gibco, Cat. # 11995) with 15% FBS (Sigma, Cat. #F6178), 1000 U/ml mouse leukemia inhibitory factor (Millipore, Cat. #ESG1107), 0.1 mM non-essential amino acids (Gibco, Cat. # 11140), 0.1mM β-mercaptoethanol (Gibco, Cat. # 21986023), 1 mM Glutamine-max (Gibco, Cat. # 25030), 1 mM sodium pyruvate (Gibco, Cat. # 11360)) and penicillin/streptomycin (100 U/ml) (Gibco, Cat, #15140).

extract_protocol:
Genomic DNA of 2C-positive and negative cells were extracted through Qiagen DNeasy Blood & Tissue Kit (Cat. No. 69504).
Around 1 million 2C-positive cells and 10 million 2C-negative cells were collected through FACS based on tdTomato reporter expression. Genomic DNA of 2C-positive and negative cells were extracted through Qiagen DNeasy Blood & Tissue Kit (Cat. No. 69504). gRNA sequences were then amplified using P5 primer (AATGATACGGCGACCACCGAGATCTACACTCTTT CCCTACACGACGCTCTTCCGATCTTTGTGGAAAGGACGAAACACCG) and P7 primer (5’CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCCAATTCCCACTCCTTTCAAGACCT; NNNNNNNN refers to 8bp index) through KAPA HiFi HotStart ReadyMix (Cat. No. KK2602). For each sample, 4 parallel PCR reactions were set up, and mixed products from 4 reactions were then purified through AMPure XP reagents (1.0x) and sequenced by an Illumina HiSeq 2500 Sequencer. Two screen replicates (independent Dux induction and FACS isolation) were performed.

treatment_protocol: CRISPR knockdown is performed as described in "Shalem O*, Sanjana NE*, Hartenian E, Shi X, Scott DA, Mikkelsen T, Heckl D, Ebert BL, Root DE, Doench JG, Zhang F (2014). Science, 343, 83-7. DOI: 10.1126/science.1247005".

value: embryonic stem cell

tag: dux induction

value: Yes

tag: cell population


title: CRISPR-Cas9 screening experiment1 2C

description:
CRISPR-Cas9
processed data file: Screen1.count.txt.gz
processed data file: Screen1.gene_summary.txt.gz


title: CRISPR-Cas9 screening experiment1 WT


title: RRBS_sggfp_D1_Rep2

data_processing:
DNA (1 ng) with 0.5% nonmethylated λ DNA spike-in was digested by MspI for 3.5 hours. DNA was then end-repaired, dA-tailed, and ligated with methylated adaptors. Bisulfite conversion was carried out using an EpiTect fast bisulfite conversion kit (Qiagen) according to the manufacturer’s instructions. Bisulfite-converted DNA was then amplified with five PCR cycles to obtain the final library. The RRBS libraries were subjected to pair-end (2 × 110 bp) sequencing on a HiSeq 2500 (Illumina). Raw reads were first trimmed using TrimGalor with paramters “--three_prime_clip_R1 2 --length 35” then mapped the mm10 genome using Bismark and bowtie2. Reads mapping to the positive and negative strand were extracted separately using samtools then the methylation levels were estimated using bismark_methylation_extractor. CpG sites overlapping with known SNPs were removed and sites with at least 5x coverage were used for the down-stream analysis. Promoters were defined as TSS ± 1kb and only promoters harboring at least 3CpG sites were considered.
Genome_build: mm10
Supplementary_files_format_and_content: bed

extract_protocol:
Cellular RNA and DNA was harvested using Qiagen Allprep RNA/DNA mini kit (Qiagen, Cat 80204).
The bulk RNA-seq library was prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, Cat E7420S). Drop-seq was performed as described in "Chen, R., Wu, X., Jiang, L. & Zhang, Y. Single-Cell RNA-Seq Reveals Hypothalamic Cell Diversity. Cell Rep 18, 3227-3241 (2017)." RRBS: DNA (1 ng) with 0.5% nonmethylated λ DNA spike-in was digested by MspI for 3.5 hours. DNA was then end-repaired, dA-tailed, and ligated with methylated adaptors. Bisulfite conversion was carried out using an EpiTect fast bisulfite conversion kit (Qiagen) according to the manufacturer’s instructions. Bisulfite-converted DNA was then amplified with five PCR cycles to obtain the final library.

treatment_protocol: Doxycycline is added to induce Dux transgene. CRISPR knockdown is performed as described in "Shalem O*, Sanjana NE*, Hartenian E, Shi X, Scott DA, Mikkelsen T, Heckl D, Ebert BL, Root DE,Doench JG, Zhang F (2014). Science, 343, 83-7. DOI: 10.1126/science.1247005".


title: CRISPR-Cas9 screening experiment2 2C


title: D2 2C- cells Rep2

data_processing:
Genes expression :Raw reads were first trimmed using Trimmomatic (v.0.36). Illumina sequence adaptors were removed, the leading and tailing low-quality base-pairs (less than 3) were trimmed, and a 4-bp sliding window was used to scan the reads and trim when the window mean quality dropped below 15. Only reads with more than 50-bp were kept. The resulting reads were mapped to the mm10 genome using STAR 33 (v.2.5.2b) with the following parameters: --outSAMtype BAM SortedByCoordinate –outSAMunmapped Within –outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --quantMode TranscriptomeSAM GeneCounts. The generated gene expression count files generated by STAR were then used for estimating gene expression.
Repeats expression :Multi-mapped reads and reads mapping to intronic or intergenic regions were extracted and then mapped to the repeats pseudo-genome. First, the TagReadWithGeneExon command of the dropseq tools was used to tag the reads into utr, coding, intergenic and intronic reads using the bam tag “XF”. Multi-mapped reads, intergenic and intronic reads were extracted and mapped to the repeats pseudo-genome using STAR. The STAR read counts were used as an estimate of repeats expression.
Analysis: For each sample, the genes and repeats expression matrices were merged together and then the “Trimmed Mean of M-values” normalization (TMM) method from the R/Bioconductor package edgeR package was used to calculate the normalized expression
Genome_build: mm10
Supplementary_files_format_and_content: tab

growth_protocol: ES-E14TG2a cells were cultured with medium consisted of DMEM (Gibco, Cat. # 11995) with 15% FBS (Sigma, Cat. #F6178), 1000 U/ml mouse leukemia inhibitory factor (Millipore, Cat. #ESG1107), 0.1 mM non-essential amino acids (Gibco, Cat. # 11140), 0.1mM β-mercaptoethanol (Gibco, Cat. #  21986023), 1 mM Glutamine-max (Gibco, Cat. # 25030), 1 mM sodium pyruvate (Gibco, Cat. # 11360)) and penicillin/streptomycin (100 U/ml) (Gibco, Cat, #15140).

extract_protocol:
Cellular RNA and DNA was harvested using Qiagen Allprep RNA/DNA mini kit (Qiagen, Cat 80204).
The bulk RNA-seq library was prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, Cat E7420S).

treatment_protocol: Doxycycline is added to induce Dux transgene. CRISPR knockdown is performed as described in "Shalem O*, Sanjana NE*, Hartenian E, Shi X, Scott DA, Mikkelsen T,  Heckl D, Ebert BL, Root DE,Doench JG, Zhang F (2014). Science, 343, 83-7. DOI: 10.1126/science.1247005".

value: No


title: D2 2C- cells Rep1


title: 1_A_1-1


title: RRBS_sggfp_D1_Rep1


title: monocultured SAEC at time 24 hr, biological replicate 3

city: Morgatown

first: Nancy

middle: Lan

last: Guo

state: WV

address: 2816 Health Sciences Center

department: Occupational and Environmental Health Sciences

institute: West Virginia University

description: Gene expression array

hyb_protocol: Following purification of labeled cRNAs, 825 ng of Cy3- and Cy5-labeled cRNAs were combined and hybridized for 17 h at 65°C in an Agilent hybridization oven.

scan_protocol: Microarrays were then washed and scanned using an Agilent DNA Microarray Scanner.

data_processing:
In vitro microarray data were exported using Feature Extraction v10 as tab-delimited text files after background subtraction, log transformation, and lowess normalization and reported as log or relative expression of sample compared to universal reference. Data were read from each file into R using a custom script (Guo et al. 2012).
For each array, values for control spots, spots which were saturated on either channel, spots which were reported by Feature Extraction as non-uniform outliers on either channel, and spots which were not well above background on at least one channel were considered unreliable and/or uninformative and replaced by “NA”. Values were collated into a single table, and probes for which fewer than 10 present values were available were removed. For probes spotted multiple times on the array, values were averaged across replicate probes. Missing data were imputed using the K-means nearest neighbor algorithm as implemented by the impute.knn function in the impute R package from Bioconductor.

label_protocol: Total RNA (250 ng) was used for labeling using a QuickAmp labeling kit (Agilent). Extracted RNA was labeled with cyanine (Cy)-3-CTP (PerkinElmer, Waltham, MA) and reference RNA with (Cy)-5-CTP.

growth_protocol: SAEC were a kind gift from Dr. Tom K. Hei (Columbia University, New York, NY) (Piao et al. 2005). SAEC were cultured in serum free complete SAGM medium supplemented with various growth factors supplied by the manufacturer (Lonza Walkersville, Inc., Walkersville, MD). HMVEC were a kind gift from Dr. Rong Shao (Biomedical Research Institute, Baystate Medical Center/University of Massachusetts, Amherst, Springfield, MA) (Shao and Guo 2004). HMVEC were cultured in endothelial basal medium-2 (EBM-2) (Lonza) and supplemented with 10% fetal bovine serum (Atlanta Biological, Lawrenceville, GA), 100 U/mL penicillin and 10 ug/mL streptomycin (Lonza), 0.01 ug/mL epidermal growth factor (Sigma), and 1 ug/mL hydrocortisone (Sigma). All cells were maintained in an incubator at 37°C with 5% CO2.

extract_protocol: Total RNA was isolated from SAEC and HMVEC using RNAprotect Cell Reagent and an RNeasy Mini Kit from Qiagen according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA concentrations were determined using a NanoDrop 1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE), and RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: To prepare cocultures, inserts were removed from 100 mm polycarbonate Transwell (Corning, Tewksbury, MA) dishes and hydrated in SAEC complete media in a companion 100 mm dish for at least 1 hour. HMVEC were plated at 1,000,000 cells in the bottom of each Transwell dish (growth area: 55 cm2) and allowed to adhere for at least 1 h without the apical chamber insert. Inserts were returned to the Transwell after hydration, and 1,000,000 SAEC were plated onto the Transwell insert (growth area: 44 cm2). Cells were maintained in 15 mL of complete EBM-2 media in the basolateral chamber and 10 mL of complete SAEC media in the apical chamber.

value: monocultured SAEC

tag: time point

value: 24 hr

tag: biological replicate

source_name: reference RNA

tag: reference

value: reference RNA


title: RRBS_sggfp_D0_Rep2


title: monocultured SAEC at time 24 hr, biological replicate 6

description: Gene expression array


title: Breast tumour T51

city: Gothenburg

first: Jana

last: Biermann

address: Medicinaregatan 1F

country: Sweden

institute: University of Gothenburg

description: Human breast tumour

hyb_protocol: Probes annealing and ligation on tumour DNA, amplification by PCR, probes digestion and DNA hybridization on each array were performed according to the manufacturer's instructions.

scan_protocol: Hybridized probes were captured by streptavidinphycoerythrin conjugates using Fluidics Station 450 and arrays were scanned using GeneChip Scanner 3000 7G.

data_processing:
CEL files were processed using the Chromosome Analysis Suite (ChAS; v.3.3.0.139) to produce OSCHP files. Weighted log2 ratios and B allele frequencies generated by ChAS were processed by the ‘copynumber’ R-package (v.1.22.0) to obtain allele-specific segmentation into regions of constantcopy numbers using Piecewise Constant Fitting.
Excel metadata file, CEL files, OSCHP files, copy number data

label: Biotin

source_name: Human breast tumour

label_protocol: Performed according to manufacturer's protocols.

growth_protocol: All samples were formalin-fixed paraffin-embedded (FFPE) tumours.

extract_protocol: Tumour tissues were sectioned and tumour DNA was extracted using the AllPrep DNA/RNA FFPE kit (Qiagen) with overnight Proteinase K treatment. The DNA concentration was determined with the Qubit Fluorometer.

tag: gender

value: Female


title: Breast tumour T48

description: Human breast tumour


title: Breast tumour T7

description: Human breast tumour


title: monocultured SAEC at time 24 hr, biological replicate 1

description: Gene expression array


title: monocultured SAEC at time 6 hr, biological replicate 5

description: Gene expression array

value: 6 hr


title: Breast tumour T6

description: Human breast tumour


title: monocultured SAEC at time 24 hr, biological replicate 2

description: Gene expression array


title: monocultured SAEC at time 6 hr, biological replicate 6

description: Gene expression array


title: monocultured SAEC at time 24 hr, biological replicate 5

description: Gene expression array


title: RRBS_sggfp_D0_Rep1


title: Breast tumour T37

description: Human breast tumour


title: monocultured SAEC at time 6 hr, biological replicate 4

description: Gene expression array


title: Breast tumour T46

description: Human breast tumour


title: monocultured SAEC at time 6 hr, biological replicate 3

description: Gene expression array


title: Breast tumour T32

description: Human breast tumour


title: Breast tumour T41

description: Human breast tumour


title: Breast tumour T23

description: Human breast tumour


title: RRBS_sgDnmt1_D1_Rep2


title: Breast tumour T39

description: Human breast tumour


title: Breast tumour T44

description: Human breast tumour


title: RRBS_sgDnmt1_D1_Rep1


title: Breast tumour T24

description: Human breast tumour


title: Breast tumour T28

description: Human breast tumour


title: RRBS_sgDnmt1_D0_Rep1


title: Breast tumour T38

description: Human breast tumour


title: RRBS_sgDnmt1_D0_Rep2


title: Drop-seq 36H collected cells

data_processing:
Read1 = Technical (Barcode position (bp): 1 - 12, UMI position (bp): 13-20)
Read2 = Biological
Quantification: For gene expression quantification in Drop-seq, the raw Drop-seq data were processed using dropseq tools. Reads were mapped against the mm10 genome (GRCm38) and the Ensemble GRCm38.85 transcriptome was used for gene annotation. Initially, the gene expression of the top 2,000 abundant cell barcodes was generated (DigitalExpression command of dropseq tools with the option NUM_CORE_BARCODES=2000). To estimate the repeats expression, the bam tag “XF” added by the dropseq tools’ TagReadWithGeneExon was used to extract non-mapped reads and reads mapping to intronic and intergenic. The extracted reads were mapped to the repeats pseudo-genome using dropseq tools. The expression matrix of the top 2,000 enriched cell barcodes were generated. For each time point, the expression matrix of the cell barcode detected in both the reads and genes were generated.
Analysis: Seurat R package (v2.3.0) was then used to load and pool all the dataset together. We filtered out cells with <800 detected transcripts and cells in which the mitochondrial transcriptome occupies >10% of the total transcripts. Genes expressed in less than 3 cells were excluded.
Genome_build: mm10
Supplementary_files_format_and_content: counts.csv (reporting raw counts) and meta.csv

source_name: 36H collected cells

tag: time


title: Drop-seq 24H collected cells

source_name: 24H collected cells


title: Breast tumour T25

description: Human breast tumour


title: monocultured SAEC DM control, biological replicate 6

description: Gene expression array

value: monocultured SAEC DM control


title: Drop-seq 12H collected cells

source_name: 12H collected cells


title: monocultured SAEC at time 6 hr, biological replicate 1

description: Gene expression array


title: monocultured SAEC at time 6 hr, biological replicate 2

description: Gene expression array


title: Drop-seq 0H collected cells

source_name: 0H collected cells


title: monocultured SAEC DM control, biological replicate 2

description: Gene expression array


title: monocultured SAEC DM control, biological replicate 3

description: Gene expression array


title: monocultured SAEC DM control, biological replicate 1

description: Gene expression array


title: monocultured HMVEC at time 24 hr, biological replicate 6

description: Gene expression array

value: monocultured HMVEC


title: monocultured HMVEC at time 24 hr, biological replicate 4

description: Gene expression array


title: monocultured HMVEC at time 24 hr, biological replicate 3

description: Gene expression array


title: monocultured SAEC DM control, biological replicate 5

description: Gene expression array