title: KM12-luc, 1 uM, 24 h

city: Kamakura

first: Hiroshi

last: Tanaka

state: Kanagawa

address: 200 Kajiwara

institute: Chugai Pharmaceutical Co., Ltd.

data_processing:
100 bases were sequenced from both ends of the library using HiSeq 2500 Sequencing System (Illumina), HiSeq Control Software v2.2.38, Real Time Analysis v1.18.61 and bcl2fastq v1.8.4
RSEM software was used to align reads against RefSeq transcripts and calculate expression values (FPKM) for each gene.
Raw data has not been submitted due to patient privacy laws in Japan.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: An xlsx file include FPKM values for each sample

source_name: Colorectal cancer

growth_protocol: CUTO-3 and KM12-luc cell lines were cultured in RPMI-1640 supplemeted with 10% FBS and D-MEM supplemented with 10% FBS and 1mM sodium pyruvate, respectively.

extract_protocol:
Cellular RNA was extracted using miRNeasy Mini Kit (QIAGEN)
RNA samples were prepared for sequencing using TruSeq RNA Sample Prep Kit v2 (Illumina) to generate an mRNA library.

treatment_protocol: Cells were treated with DMSO or 1 uM CH7057288 for 4 and 24 hours

value: Colorectal cancer

tag: compound treated

tag: treatment time

value: 24 hours


title: KM12-luc, 0 uM, 24 h

status: Public on Sep 14 2018

type: SRA

country: Japan

description: Raw data has not been submitted due to patient privacy laws in Japan.

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell line

tag: tissue

value: DMSO


title: ChIPSeq_ATAC1_5D

city: Grand Rapids

first: Hong

last: Wen

state: Michigan

address: 333 Bostwick Ave. N.E.

department: Center for Epigenetics

country: USA

institute: Van Andel Research Institute

library_source: genomic

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie2 v2.1.0; RNA-seq reads were aligned to hg19 genome using tophat v2.0.10
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS-1.3.6+B102; Scores represent the ChIP-seq tag numbers; RNA-seq htseq file include differential significance across treatment and control and the tag numbers in all samples
Supplementary_files_format_and_content: RNA-seq read counts were calculated using HTSeq 0.6.1p1

molecule: genomic DNA

growth_protocol: Human H1299 cells (ATCC) were cultured in RPMI 1640 with 10% FBS (Cellgro) supplemented with 10% fetal bovine serum (Sigma), 5% CO2, 37 oC.

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.   mRNA was prepared using the RNeasy Plus kit (Qiagen) and reverse-transcribed using the iScript™ cDNA Synthesis Kit (Bio-Rad).
For ChIP-seq, sequencing libraries were prepared using the Illumina TruSeq DNA Sample Preparation Kit according to the manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor) were band isolated from an agarose gel. DNA fragments were sequenced using paired-end sequencing technology on Illumina HiSeq 2000 platform.  For RNA-seq, samples were prepared as instructed using the TruSeq mRNA Sample Preparation Kit v2 (Illumina, San Diego, CA) in accordance with the manufacturer's instructions. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles, DNA fragments were sequenced using single-end sequencing technology on Illumina paried-end on Illumina HiSeq2000 .

treatment_protocol: For shRNA knockdown, 293T cells were co-transfected with pMD2.G and pPAX2 (Addgene) together with pLKO-shRNA constructs or a non-targeting pLKO-shRNA (pLKO-shNT). Viral supernatants were harvested after 48 hrs. For infections, H1299 cells were incubated with viral supernatants in the presence of 8 µg/ml polybrene. After 48 hrs, puromycin (2 µg/ml) was added to the medium. Cells were grown with selection for 4-7 days to select for stable knockdown cells.

tag: cell

value: H1299 cells

tag: treatment

value: ATAC1 Knock Down + D824A rescue

tag: antibody

value: Rabbit 2616, Laszlo Tora lab


title: 6 dpl non-vascular niche replicate 3

type: RNA

city: Gdansk

first: Jakub

last: Mieczkowski

address: Debinki 12

country: Poland

institute: Medical University of Gdansk

description:
SAMPLE 6
replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: 6 dpl non-vascular niche

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Demyelination in rats was induced bilaterally by stereotaxic injection of 4 μL of 0.01% ethidium bromide  into the CCP as previously described (Woodruff and Franklin, 1999).

tag: gender

value: female

value: Rat cerebellar white matter (caudal cerebellar peduncle, CCP)

tag: niche

value: non-vascular niche

tag: time

value: 6 dpl


title: 6 dpl vascular niche replicate 2

description:
SAMPLE 3
replicate 2

source_name: 6 dpl vascular niche

value: vascular niche


title: 6 dpl vascular niche replicate 4

description:
SAMPLE 7
replicate 4


title: 6 dpl non-vascular niche replicate 1

description:
SAMPLE 2
replicate 1


title: Notch2-11cKO SRBC cDC2, replicate 2

city: Saint Louis

first: Carlos

middle: Gustavo

last: Briseno

state: Missouri

address: 660 S Euclid

institute: Washington University School of Medicine

hyb_protocol: Hybed onto Mouse Gene 1.0 ST Arrays (Affymetrix)

scan_protocol: not provided

data_processing: Data was analyzed using DNASTAR Arraystar Software

label: Biotin

organism: Mus musculus

source_name: CD11c-Cre Notch2f/f mouse spleen

label_protocol: Ambion WT Expression kit, Genechip WT Terminal Labeling and Controls Kit

growth_protocol: Spleens were digested with Collagenase B and DNAse 1 to make single cells suspensions

extract_protocol: Digestion of spleens with Collagenase B and DNAse1 followed by enrichment of CD11c+ cells prior to sorting

treatment_protocol: Mice were analyzed at steady state or 24 hours after treatment with 2x10^8 sheep red blood cells i.p.

tag: genotype

value: CD11c-Cre+ Notch2f/f

value: spleen

tag: cell type


title: Notch2-11cKO SRBC cDC2, replicate 3


title: Telomere_4_CD8TEMRA_sorted

city: Baltimore

first: Mary

last: Armanios

state: MD

address: 401 North Broadway

department: School of Medicine

institute: The Johns Hopkins University

hyb_protocol: 18hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing: Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  RMA normalization was used to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.

source_name: CD8+ TEMRA cell

label_protocol: NuGEN Ovation Pico WTA RNA amplification System 2.0 kit following manufacturer's protocol.

extract_protocol: Sorted cells were removed from -80 storage and thawed at room temperature. Samples were deposited in phase-lock heavy gel tubes and then supplemented with 200uL chloroform and then mixed. Tubes were spun at 14,000xg for 20 minutes at 4 degrees. The top (aqueous) layer was then transferred to a new tube. Total RNA extraction was completed using the Agencourt RNAdvance Tissue kit (Beckman Coulter) beginning with step 3 of manufacturer's instructions.

treatment_protocol: PBMCs isolated using Ficoll-Paque gradient in SepMate isolation tubes were thawed at 37 degrees. Samples underwent red cell lysis and were resuspended in 100uL PBS with 2% FBS. Cells were stained with CD3 APC, CD4 PE Cy5, CD8 FITC, CCR7 BV421, and CD45RA ACP Cy7 for for 20 minutes at 4 degrees. CD3+CD8+CCR7-CD45RA+ cells were sorted into cold TRIzol using a MoFlow XPD (Beckman Coulter)

value: Male

tag: age

tag: telomere length

value: <1st %ile, TERT mutation


title: Telomere_2_CD8TEMRA_sorted

value: Female


title: Telomere_1_CD8TEMRA_sorted

value: <1st %ile, TR mutation


title: 6 dpl vascular niche replicate 1

description:
SAMPLE 1
replicate 1


title: Old_3_CD8TEMRA_sorted

value: Normal


title: 6 dpl non-vascular niche replicate 2

description:
SAMPLE 4
replicate 2


title: Notch2-11cKO SRBC cDC2, replicate 1


title: Telomere_3_CD8TEMRA_sorted

value: <1st %ile, classic dyskeratosis congenita


title: Old_4_CD8TEMRA_sorted


title: Notch2-11cKO Untreated cDC2, replicate 2


title: Old_2_CD8TEMRA_sorted


title: CUTO-3, 0 uM, 24h

source_name: Lung cancer

value: Lung cancer

value: DMSO

value: 24 hours


title: ChIPSeq_ATAC1_4F

value: H1299 cells

value: ATAC1 Knock Down + F821A rescue

value: Rabbit 2616, Laszlo Tora lab


title: KM12-luc, 1 uM, 4 h

value: Colorectal cancer

value: 4 hours


title: WT SRBC cDC2, replicate 3

source_name: WT mouse spleen

value: WT


title: ChIPSeq_H3K4me3_Rep2

value: shNT control vector

value: Abcam, ab8580


title: Notch2-11cKO Untreated cDC2, replicate 1

value: CD11c-Cre+ Notch2f/f

value: spleen


title: ChIPSeq_H3K4me3_Rep1


title: KM12-luc, 0 uM, 4 h


title: Young_4_CD8TEMRA_sorted

value: Female


title: CUTO-3, 1 uM, 24h


title: ChIPSeq_H3K4ac

value: Active Motif, 39381


title: WT SRBC cDC2, replicate 2


title: CUTO-3, 1 uM, 4h


title: ChIPSeq_H3K9ac_Rep2

value: Active Motif, 61251


title: Young_3_CD8TEMRA_sorted

value: Male

value: Normal


title: WT SRBC cDC2, replicate 1


title: CUTO-3, 0 uM, 4h

value: Lung cancer

value: DMSO


title: Old_1_CD8TEMRA_sorted


title: Young_2_CD8TEMRA_sorted


title: ChIPSeq_ATAC1_Rep2

value: H1299 cells


title: HCT116_M12_DRB_NaCl10_CTD_180518

city: Aurora

first: David

last: Bentley

state: Colorado

department: BMG

institute: UCD AMC

data_processing:
Single-end 50 base reads (after removing barcodes) or 151 base reads (after removing barcodes) were mapped to the hg19 UCSC human genome with Bowtie2 version 2.3.2 (trim from 3 prime to 50 base pairs)
Genome_build: GRCh37/hg19 assembly

growth_protocol: HCT116 cells were grown in McCoy's medium 10% FCS and pen/strep

extract_protocol:
cross-linked Chromatin was sonicated with a Bioruptor
1-2 mg of cross-linked extract was immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, gel purification of ~200bp fragments, and amplification (18cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.

treatment_protocol: In some experiments  HCT116  were treated with 10mM NM-PP1 for 24 hr before cross-linking and harvesting for ChIP-seq, this drug treament should have no effect on these cells.

tag: cell line/genotype

tag: spike in

value: mouse M12

tag: growth conditions

value: McCoy's 10% FCS DRB 100mM 60min. add NaCl 230mM 10 min.

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)

tag: experiment

value: Chromatin IP against RNA pol II


title: EFT

city: Seville

first: Lucía

last: García

address: Avda. Reina Mercedes

country: Spain

institute: Universidad de Sevilla

description:
Sample 4
The bacteria constitutively express both stdE and stdF. StdF has the 3xFLAG tag.
processed data file: E_EFT_anotacion_picos.bed
processed data file: F_EFT_anotacion_picos.bed
processed data file: ChIP-seq_results.xlsx

data_processing:
BAM files reported by the sequencing facility of the Functional Genomics Core Facility were converted to FASTQ format with the BAM2FASTQ tool (http://www.hudsonalpha.org/gsl/information/software/bam2fastq).
The quality of the sequence reads was examined using FASTQC (Andrews, 2010) that reported the presence of Illumina adapters. The adapters were trimmed with the FASTX_CLIPPER tool of the FASTX-Toolkit suite (http://hannonlab.cshl.edu/fastx_toolkit/). Reads shorter than 40 nt were discarded.
Peaks were called using CisGenome version 2.0 (Ji et al., 2008) using default parameters.
The IGV browser (Thorvaldsdóttir et al., 2013) was used for data visualization.
Genes closest to a ChIP peak were identified using the bedtools suite (Quinlan & Hall, 2010). Peak boundaries sequences were extracted from the reference genome using the fastaFromBed utility from the BEDTools suite (Quinlan & Hall, 2010).
NCBI GCA_000210855.2 genome assembly of S. enterica SL1344 was used as reference genome. Mapping was performed with Bowtie (Langmead et al., 2009) allowing only two mismatches for unique alignment.
Genome_build: GCA_000210855.2 (ASM21085v2)
Supplementary_files_format_and_content: E_CEF_anotacion_picos.bed: Peaks in BED format. The obtained peaks for the IP sample (Sample 1) is compared with the peaks for the control sample (mock IP: Sample 3).
Supplementary_files_format_and_content: E_EFT_anotacion_picos.bed: Peaks in BED format. The obtained peaks for the IP sample (Sample 1) is compared with the peaks for the control sample (mock IP: Sample 4).
Supplementary_files_format_and_content: F_CEF_anotacion_picos.bed: Peaks in BED format. The obtained peaks for the IP sample (Sample 2) is compared with the peaks for the control sample (mock IP: Sample 3).
Supplementary_files_format_and_content: F_EFT_anotacion_picos.bed: Peaks in BED format. The obtained peaks for the IP sample (Sample 2) is compared with the peaks for the control sample (mock IP: Sample 4).
Supplementary_files_format_and_content: ChIP-seq results.xlsx: Peaks in Excel format. The obtained peaks for the IP samples (Sample 1 and 2) are compared with the peaks for the control samples (mock IP: Sample 3 and 4).

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Bacterial cells constitutively expressing stdEF::3xFLAG

growth_protocol: 20ml of the bacterial strain PLtetO-stdEF::3xFLAG, incubated with shaking (200rpm) at 37ºC until OD600∼2.

extract_protocol:
To immunoprecipitate StdE-DNA and StdF-DNA complexes, 800 μL of chromatin, 20 μL of Ultralink Immobilized protein A/G beads (Pierce) and 2 μL of the corresponding antibody were used (anti-StdE and anti-FLAG). Control sample (mock-IP) was performed with no antibody added. They were then incubated for 90 minutes at room temperature on a rotating wheel. Beads were transferred to a Spin-X column tube (Costar) and centrifuged at 3000rpm for 1min. Beads were gently re-suspended in 500 μL of IP buffer and incubated on wheel for additional 3min. Beads were washed with 500 μL of IP salt buffer, IP wash buffer and TE pH8.0 by resuspending and centrifuging the sample. The column was transferred to a fresh tube and the beads were resuspended in 100 μL of elution buffer (50 mM Tris-HCl at pH 7.5, 10 mM EDTA, and 1% SDS) and incubated at 65ºC for 20min. After centrifuging at 3000rpm for 1min, the flow-through was treated with 10μL of 40mg/mL Pronase (Roche) made up in TBS. The samples were heated at 42ºC for 2h and 65ºC for 6 hours. The reactions were then kept at 4ºC overnight. The samples were cleaned up by using a PCR clean up Kit (Promega) and resuspended in 50 μL of H2O.
NEBNext® Ultra DNA Library Prep Kit for Illumina; 50 nt SE sequencing.

treatment_protocol: Bacterial cells were collected and cross-linked with 1% formaldehyde at 37ºC for 25 min, followed by quenching of the unused formaldehyde with 450 mM glycine for an additional 5 min of incubation. Cross-linked cells were harvested and washed with 10 mL of TBS pH7.6 (2.42 g/l Trizma base, 8 g/l NaCl). The washed cells were resuspended in 1 mL of lysis buffer (10 mM Tris-HCl -pH 8, 20% sucrose, 50 mM NaCl, 10 mM EDTA) and after an additional centrifugation step, the cells were resuspended in 0.5mL of lysis buffer with lysozyme (20mg/ml; Sigma Chemical Co.). The cells were incubated for 30 min at 37°C and then treated with 4 mL of IP buffer (50mM HEPES-KOH-pH7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS and 1mg/mL PMSF). The lysate was then sonicated using a Bioruptor (Diagenode) with 5 cycles of 7 minutes (30″ON/30″OFF) at high setting. Cell debris was removed by centrifugation for 20 min at 4°C and the resulting supernatant was used as cell extract for the immunoprecipitation. The range of the DNA size resulting from the sonication procedure was 100-500 bp, and the average DNA size was 300 bp.

tag: genotype/variation

tag: chip antibody


title: WT Untreated cDC2, replicate 2

value: WT

tag: tissue


title: ChIPSeq_H3K9ac_Rep1

tag: cell

value: shNT control vector


title: HCT116_M12_DRB_NaCl5_CTD_180518

value: McCoy's 10% FCS DRB 100mM 60min. add NaCl 230mM 5 min.


title: HCT116_M12_DRB_CTD_180518

value: McCoy's 10% FCS DRB 100mM 60min.


title: ChIPSeq_ATAC1_Rep1

tag: treatment

value: Rabbit 2616, Laszlo Tora lab


title: StdF

description:
Sample 2
The bacteria constitutively express both stdE and stdF. StdF has the 3xFLAG tag.
processed data file: F_CEF_anotacion_picos.bed
processed data file: F_EFT_anotacion_picos.bed
processed data file: ChIP-seq_results.xlsx

value: Monoclonal anti-FLAG M2 (Sigma F1804)


title: CEF

description:
Sample 3
The bacteria constitutively express both stdE and stdF. StdF has the 3xFLAG tag.
processed data file: E_CEF_anotacion_picos.bed
processed data file: F_CEF_anotacion_picos.bed
processed data file: ChIP-seq_results.xlsx


title: HCT116_M12_DRB_NaCl2_CTD_180518

value: McCoy's 10% FCS DRB 100mM 60min. add NaCl 230mM 2 min.

tag: antibody


title: 359GG doxo 4

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

description: Gene expression after 4hr of doxorubicin in p53 mutated clls

hyb_protocol: The labelled RNA were hybridized to a microarray (Agilent Human whole genome 44K, Agilent Technologies) containing approximately 44,000 probes (~26,600 unique genes) in accordance with the manufacturer's instructions.

scan_protocol: The raw signal intensities were extracted from the arrays using Agilent Feature Extraction Software (Agilent Technologies)

data_processing: Only those array elements with signal intensities 1.4-fold higher than the local background were selected and normalized using the quantile method in R. The ratios from duplicated spots were averaged.

source_name: Human (fibroblasts cell line) induced pluripotent stem cell harboring TP53 c.359A>G mutation

label_protocol: The isolated RNA was amplified and labeled using the Low RNA Input Linear Amplification kit PLUS (Agilent Technologies).

extract_protocol: Total RNA from each sample was extracted using TRIzol and the RNeasy Mini Kit.

value: 0.2 uM treatment of doxorubicin

value: 4 hr

value: p53 mutated clls


title: WT Untreated cDC2, replicate 1

value: spleen


title: StdE

description:
Sample 1
The bacteria constitutively express both stdE and stdF. StdF has the 3xFLAG tag.
processed data file: E_CEF_anotacion_picos.bed
processed data file: E_EFT_anotacion_picos.bed
processed data file: ChIP-seq_results.xlsx

value: Anti-StdE (custom antibody produced by Biomedal S.L. Spain)


title: UMI-77.S

status: Public on Sep 13 2018

city: Birmingham Gardens

first: YUANYUAN

last: ZHANG

state: NSW

address: UNIVERSITY DRIVE, University Dr

country: Australia

institute: The University of Newcastle

data_processing:
Primary sequencing data that produced by Illumina HiseqTM 2000, called as raw reads, which will be filtered into clean reads by remove adaptor contained and low quality reads.
Reference annotation based assembly method was used to reconstruct the transcripts, while background noise would be reduced by using FPKM and coverage threshold.
The novel transcripts could be detected by comparing to the reference, then calculate the coding potential of these transcripts to identify the novel lncRNA.
Gene expression and differential expression analysis for both predicted novel lncRNA and lncRNA from the database
Genome_build: hg19
Supplementary_files_format_and_content: txt file includes gene ID, locus, FPKM values and gene name for each Sample

source_name: Melanoma cells

growth_protocol:
Melanoma cell lines were cultured using Dulbecco's modified Eagle's medium (DMEM) supplemented with 5% fetal calf serum (FCS)  at 37oC with 5% CO2.
ME4405 TRAIL-selected (TRAIL.S) cells were continously exposed to 25 ng/ml TRAIL in the culture medium
ME4405 UMI-77-selected (UMI-77.S) cells were continously exposed to 4 uM UMI-77 in the culture medium.

extract_protocol:
Total RNA was extracted by ISOLATE II RNA Mini Kit (Bioline) and 20 ul aliquots of RNA were dried by vacuum concentration for 30 min at room temperature in the presence of RNAstable (Biomatrica 93221-001)
After extracting the total RNA from samples, mRNA and non-coding RNAs are enriched by removing rRNA from the total
RNA with kit. By using the fragmentation buffer, the mRNAs and non-coding RNAs are fragmented into short fragments(about 200~500nt), then the first-strand cDNA is synthesized by
random hexamer-primer using the fragments as templates, and dTTP is substituted by dUTP during the synthesis of the second strand. Short fragments are purified and resolved with
EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters, then the second strand is degraded using
UNG(Uracil-N-Glycosylase) finally. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100
Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeq 2000.

value: primary melanoma

tag: cell line

value: ME4405 UMI-77-selected (UMI-77.S) cell sub-line


title: OTX015_anti-IgG

city: Guangzhou

first: Lingyun

last: Zheng

state: Guangdong

address: 280 Wai Huan Dong Lu, Guangzhou Higher Education Mega Center

department: School of Life Sciences and Biopharmaceutics

country: China

institute: Guangdong Pharmaceutical University

data_processing:
Basecalls performed using bcl2fastq version 2.18
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using HISAT2 v2.0.4
Ailgned sam files convert to bam by samtools, and extract mapped reads then remove duplicated mapped reads, use bedtools convert bam files to bed format.
peaks were called using SICER version 1.1 with the following setting: redundancy threshold (1), window size (200), gap size (400), FDR (0.05).
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated and normalized using SICER

extract_protocol:
Lysates were clarified from sonicated nuclei and DNA fragments were isolated with antibody.
Libraries were prepared according to VAHTS Universal DNA Library Prep Kit( ND604). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment(3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 10 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hiseq 2500  following the manufacturer's protocols.

tag: agent

value: IgG


title: Input_OTX015


title: OTX015_anti-BCL6


title: DMSO_anti-IgG

source_name: A549 DMSO

value: DMSO


title: Input_DMSO


title: DMSO_anti-BRD3


title: DMSO_anti-BCL6


title: p53 KO doxo 0

description: Gene expression after 4hr of doxorubicin in p53 knock-out cells

source_name: Human (fibroblasts cell line) induced pluripotent stem cell in p53 KO with deletion of exon 7

value: No treatment of doxorubicin

tag: time

value: 0 hr

value: p53 knock-out cells


title: L5-spleen

city: Wanju-Gun

first: woncheoul

last: park

state: Iseo-Myeon

address: 1500 kongjwipatjwi-Ro

department: Animal genomics and Bioinformatics

institute: National Institute of Animal Science

data_processing:
Quality of RNA-seq reads from all of the kidney tissues were checked using FastQC.
Reads passed the quality control were mapped to Gallus gallus genome (Galgal4) from ENSEMBL using Hisat2 (v2.0.4).
The reads were counted using featurecount tool
The reads were nomalized using FPKM by Cufflinks
DEGs were detacted by Cuffdiff(Cufflinks)
Genome_build: Galgal4
Supplementary_files_format_and_content: tab-delimited text files include raw counts of genes for each sample.

organism: Gallus gallus

source_name: Spleen tissue

extract_protocol:
RNA extraction using Isol
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Sample Preparation Guide

tag: breed

value: Low altitude

tag: phenotype

value: adapted to heat

value: Spleen


title: J774-CD1d

city: La Jolla

first: Shilpi

last: Chandra

state: California

address: 9420 Athena Circle

department: Division of Developmental Immunology

institute: La Jolla Institute for Allergy and Immunology

hyb_protocol: Affymetrix GeneChip Hybridization, Wash and Stain Kit according to the manufacturer's instructions

scan_protocol: Wash, Stain and Scan protocol using GeneChip Hybridization Wash and Stain Kit according to manufacturer's instructions

data_processing: Raw intensity data were normalized with the 'rma' function from oligo package v1.42.0 in R v3.4.2 with default parameters.

source_name: Cultured J774A.1 overexpressing Cd1d.1

label_protocol: Affymetrix GeneChip IVT Express Kit according to the manufactuer's instructions

growth_protocol: J774-CD1d cells were cultured in DMEM medium containing 10% heat-inactivated FBS, 100 U per ml penicillin, 100 U per ml streptomycin, 2 mM L-glutamine, 1 mM sodium pyruvate and 10 mM HEPES and F4/80+ cells were isolated from 6 weeks old Balb/c mice

extract_protocol: RNA was isolated using QIAGEN Rneasy mini kit according to the manufacturer's instructions

treatment_protocol: Not applicable

tag: cell type

value: macrophage cell line

tag: age

value: Not applicable

value: overexpressing Cd1d.1


title: L7-spleen


title: L9-spleen


title: L8-spleen


title: L4-spleen


title: p53 KO doxo 4

value: 0.2 uM treatment of doxorubicin

value: 4 hr


title: 359GG doxo 0

description: Gene expression after 0hr of doxorubicin in p53 mutated clls

value: p53 mutated clls


title: WT doxo 4

description: Gene expression after 4hr of doxorubicin in wild type cells

source_name: Human (fibroblasts cell line) induced pluripotent stem cell

value: Wide type cells


title: WT doxo 0

description: Gene expression after 0hr of doxorubicin in wild type cells


title: L3-spleen


title: ME4405

value: primary melanoma

value: ME4405 parental cells


title: TRAIL.S

value: ME4405 TRAIL-selected (TRAIL.S) cell sub-line


title: Young_1_CD8TEMRA_sorted

tag: gender

value: Female

tag: telomere length

value: Normal


title: L6-spleen


title: L2-spleen


title: H9-spleen

value: High altitude

value: not adapted to heat


title: L1-spleen

value: Low altitude


title: H5-spleen


title: H4-spleen


title: H2-spleen


title: H8-spleen


title: H6-spleen


title: L8-meat

source_name: breast muscle

value: adapted to heat

value: breast muscle


title: H1-spleen

value: Spleen


title: L7-meat


title: L6-meat


title: H3-spleen


title: iPSC-Hep_RNAseq 3

city: Orlando

first: Maddalena

last: Parafati

state: FL

address: 6400 Sanger rd

department: Conrad Prebys Center for Chemical Genomics

institute: SBPMRI

data_processing:
1. FastQC
2. Use tophat2 to align the reads to the genome
Reference: hg38
3. Use Partek to generate the reads count, RPKM and the mapping summary
4. Use DESeq to get differential expression list, FoldChange, log2FC, P-value and P-adj
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Human induced pluripotent stem cells (hiPSC)

growth_protocol: hiPSC cell–derived hepatocytes cells were routinely generated by two steps protocol plating cells at the stage of hepatoblasts  (typically 2–3 × 104 cells into a 384w plate) on collagen I coated plates in RPMI 1640 medium plus glutamine medium supplemented with 1X B27, 20 ng/ml Oncostatin M, 0.1 µM Dexamethasone, 25 µg/ml Gentamicin and iCell Hepatocytes 2.0 Medium supplement for 5 days. After 5 days of culturing, hepatic maturation was maintained with medium William`s E medium supplemented with 0.1 µM dexamethasone and hepatocytes maintenance supplement pack.

extract_protocol:
RNA was isolated from primary hepatocytes and hiPSC-derived hepatocytes using the RNeasy kit (Qiagen, Frederick, MD) and subsequently subjected to DNase Digestion (Qiagen). Total RNA was quantified using NanoDrop 8000 (Thermo Scientific).
RNA-Seq libraries were prepared using Truseq Stranded Total RNA Library preparation kit (Illumina, San Diego, CA) with 1 ug of total RNA.

treatment_protocol: For lipid induction in hiPSC-Hep, cells were treated with 15 µl of a 2x mixture of oleic acid, and palmitic acid or BSA in 30 µl. Fatty acids (FA) were used at 8:1 ratio palmitic to oleic acid. Thapsigargin was added in the presence and absence of FA and incubated for 18 h at 1 µM.

value: Cryopreserved hiPSC-derived Hepatocytes

tag: treatmnet

value: Lipid loading plus thapsigargin for 18 hrs

tag: genotype

value: Wild type ( cell line)


title: L9-meat


title: iPSC-Hep_RNAseq 1


title: iPSC-Hep_RNAseq 4

value: Pretreatment of hiPSC-Hep with OCA and lipid loading plus thapsigargin for 18 hrs


title: L5-meat


title: total RNA from RBM10 siRNA treated sample 3

city: Trivandrum

first: Rakesh

middle: S

last: Laishram

state: Kerala

address: Thycaud P O, Poojappura

department: Cardiovascular and Diabetes Biology Group

country: India

institute: Rajiv Gandhi Centre for Biotechnology(RGCB)

description: gene expression after treating with RBM10 siRNA

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to a Agilent designed Human Gene expression Microarray 8x60K (AMADID No: 39494) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

scan_protocol: The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327) and scanned using the Agilent Microarray Scanner (AgilentTechnologies, Part Number G2600D).

data_processing:
Data extraction from Images was done using Feature Extraction software Version 11.5 of Agilent. Images were quantified using Feature Extraction Software (Version-11.5 Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent.
Normalization of the data was done in GeneSpring GX using the 75th percentile shift (Percentile shift normalization is a global normalization, where the locations of all the spot intensities in an array are adjusted. [This normalization takes each column in an experiment independently, and computes the  percentile of the expression values for this array, across all spots (where n has a range from 0-100 and n=75 is the median). It subtracts this value from the expression value of each entity) and fold expression values were obtained with respect to Specific control Samples].

source_name: HEK 293 cell line

label_protocol: Samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasyMini kit columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: HEK 293 cell line was obtained from American Type Culture Collection and maintained in DMEM with 10% FBS and penicillin/streptomycin (50 U/ml) at 37°C in 5% CO2.

extract_protocol: Total RNA was extracted from HEK 293 cells transfected with RBM10 specific or control siRNA oligonucleotides using the RNeasy Mini Kit (Qiagen, Cat.No. 74004 ) with DNAse treatment as per manufacturer’s protocol. The RNA sample was eluted in 25uL of Nuclease free water. The concentration and purity of the RNA extracted were evaluated using the Nanodrop Spectrophotometer (Thermo Scientific; 1000).  The integrity of the extracted RNA were analysed on the Bioanalyzer (Agilent; 2100 expert). We considered RNA to be of good quality based on the 260/280 values (Nanodrop), rRNA 28S/18S ratios and RNA integrity number (RIN) (Bioanalyzer).The purity and integrity of RNA was checked using Nanodrop (Thermo Scientific) and Bioanalyzer (Agilent)

treatment_protocol: After reaching 60% of confluency, HEK 293 cells was transfected with siRNA oligos using Oligofectamine reagent and cells were harvested 48-hours post-transfection.

value: HEK 293

tag: sirna knockdown

value: RBM10 siRNA


title: total RNA from control siRNA treated sample 1

description: gene expression after treating with control siRNA

value: control siRNA


title: total RNA from RBM10 siRNA treated sample 1


title: F4/80+ Peritoneal macrophages

source_name: Isolated F4/80+ peritoneal macrophages from Balb/c mice

value: F4/80+ peritoneal macrophages

value: 6 weeks

tag: strain

value: Balb/c


title: L4-meat

tag: tissue


title: total RNA from control siRNA treated sample 3


title: L3-meat


title: iPSC-Hep_RNAseq 2


title: L2-meat


title: H9-meat


title: L1-meat


title: H7-spleen


title: total RNA from RBM10 siRNA treated sample 2


title: H8-meat


title: EpiSC, Rep 3

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

hyb_protocol: Labelled RNA was submitted to the WTCRF MRC Human Genetics Unit (University of Edinburgh) for further processing using standard Illumina protocols. cRNA quality was checked using a Agilent 2100 Bioanalyser and  hybridization performed on an MouseWG-6 v2 BeadChip (Illumina Cat # BD-201-0202).

data_processing: Quantile-normalization and low-quality probe filtering performed using the beadarray package in R, batch correction with ComBat

source_name: Mouse EpiSC

label_protocol: 100ng of RNA was reverse transcribed into double stranded cDNA and transcribed/amplified into biotin labelled cRNA using an Illumina TotalPrep RNA Amplification Kit (Ambion Cat # AMIL1791).

growth_protocol: E14Tg2a Esrrb-2a-GFPd-IBIH ESCs were cultured in GMEMb/b-mercaptoethanol/10%FCS/LIF as described (Smith, 1991). TNG Esrrb-2a-TdTomato EpiSC in were cultured in standard N2B27/Activin/FGF conditions.

extract_protocol: RNA was prepared from at least 106 sorted cells for each population and TNG Esrrb-2a-TdTomato EpiSC using a RNeasy minikit (Qiagen Cat # 74104).

treatment_protocol: E14Tg2a Esrrb-2a-GFPd-IBIH ESCs were plated at low density (3000/cm2) adnd cultured for 3 days. Cells were trypsinised, resuspended at 2 x 106 cells/ml in 10%FCS/PBS containing anti SSEA-1 mouse monoclonal antibody from ascitic fluids (DSHB Cat # MC-480) diluted 1:1000. Cells were incubated (on ice, 15 min), washed in ice-cold PBS, resuspended and incubated in 10%FCS/PBS containing goat anti-mouse IgM-Alexa647 secondary antibody (Molecular Probes Cat # A-21238) (on ice, 15 min), washed in ice-cold PBS and resuspended in 10%FCS/PBS. Cells were fractioned in GFPhigh,GFPmedium and GFPnegative cells using a FacsARIA cell sorter (Becton, Dickinson).

value: epiblast stem cells (EpiSC)

tag: array id


title: H7-meat

value: High altitude


title: ESC Esrrb high, Rep 3

source_name: Mouse ESC sorted for high Esrrb expression

value: embryonic stem cells (ESC)

tag: sort

value: Esrrb high


title: ESC Esrrb medium, Rep 1

source_name: Mouse ESC sorted for medium Esrrb expression

value: Esrrb medium


title: ESC Esrrb negative, Rep 1

source_name: Mouse ESC sorted for negative Esrrb expression

value: Esrrb negative


title: EpiSC, Rep 2


title: H6-meat

value: not adapted to heat

value: breast muscle


title: ESC Esrrb negative, Rep 2


title: ESC Esrrb negative, Rep 3


title: EpiSC, Rep 1


title: ESC Esrrb medium, Rep 2


title: ESC Esrrb high, Rep 1


title: Total Synchonized adult mouse testis Stages VIII-X replicate 2

city: Pullman

first: Estela

middle: Jasmin

last: Jauregui

state: WA

address: 1770 NE Stadium Way

department: School of  Molecular Biosciences

institute: Washington State University

description: Gene expression data from total  testis

hyb_protocol: Fragmented, bioting labeled cDNA was hybridized for 16 hr at 45C on GeneChip Mouse Gene ST 1.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Array output was normalized using the RMA algorith and data analaysis was conducted using Genespring (Version 12.6.1; Agilent Technologies)

source_name: Total testis transcripts Stages VIII-X

label_protocol: 100 ng of  RNA extracted from total testis or Leydig cell-only samples were used to generate cDNA using the Ovation RNA Amplification System V2 (NuGen, San Carlos, CA) according to the manufacturer's instructions. 3.74ug of the cDNA was then fragmented and labelled using the Encore Biotin Mocule (NuGEN, San Carlos, CA) accroding to the manufacturer's instructions.

growth_protocol: Mouse colonies used in this study were maintained in a temperature- and humidity-controlled environment with food and water provided ad libitum

extract_protocol: Testes from RiboTag-positive/Cyp17icre-positive experimental male mice from different time points were homogenized and immunoprecipitation (IP) was performed. Briefly, one testis per time point was homogenized in 3% weight/volume of homogenization buffer. For the total testis RNA samples, RNA from 50 ul of homogenized testis was extracted using the Qiagen RNeasy Mini Kit (catalog no. 74104; Qiagen; Hilden, Germany). The rest of the homogenized testis was used for IP sampling. For the IP RNA samples, five microliters of HA-tag antibody (catalog no. 90151, BioLegend; San Diego, CA) coupled to 400 ul of Dynabeads Potrein G (catalog no. 1004D; Life Technologies; Carlsbad, CA) were added to the homogenized testis and incubated overnight at 4C. The following day, the beads coupled to anti-HA antibody and bound to the HA-tagged polysomes were washed in high salt buffer and RNA extracted using the Qiagen RNeasy Mini Kit. The extracted IP and total RNA samples were quantified using a Nano Drop 1000 Spectrophotometer. The RNA samples were then stored at -80C until use.

treatment_protocol: Spermatogenesis was synchronized in RiboTag-positive/Cyp17icre-positive experimental male mice. Two days postpartum (dpp) male mice were treated with 100 μg/g body weight WIN 18,446 once daily for 7 consecutive days. The following day, at 9 dpp, mice were injected with 200 μg all-trans RA (atRA). Experimental animals were then left to recover and euthanized 42-50 days after injection. Testes were dissected and used for microarray analysis, immunohistochemistry (IHC), or analysis of synchronized spermatogenesis.

value: male

value: testis

tag: stages

value: Stages VIII-X


title: Total Synchonized adult mouse testis Stages X-XII replicate 2

description: Gene expression data from total  testis

source_name: Total testis transcripts Stages X-XII

value: Stages X-XII


title: ESC Esrrb high, Rep 2


title: Total Synchonized adult mouse testis Stages VI-VIII replicate 2

description: Gene expression data from total  testis

source_name: Total testis transcripts Stages VI-VIII

value: Stages VI-VIII


title: Total Synchonized adult mouse testis Stages II/III-VI replicate 2

description: Gene expression data from total  testis

source_name: Total testis transcripts Stages II/III-VI

value: Stages II/III-VI


title: ESC Esrrb medium, Rep 3


title: H4-meat


title: H3-meat


title: H2-meat


title: H1-meat


title: total RNA from control siRNA treated sample 2

tag: cell line

value: HEK 293

value: control siRNA


title: IP Synchonized adult mouse testis Stages X-XII replicate 2

description: Gene expression data from Leydig cells

source_name: Leydig cell transcripts Stages X-XII


title: IP Synchonized adult mouse testis Stages VI-VIII replicate 2

description: Gene expression data from Leydig cells

source_name: Leydig cell transcripts Stages VI-VIII


title: L8-Heart

source_name: Heart tissue

value: Low altitude

value: adapted to heat

value: Heart


title: L9-Heart


title: L7-Heart


title: IP Synchonized adult mouse testis Stages VIII-X replicate 2

description: Gene expression data from Leydig cells

source_name: Leydig cell transcripts Stages VIII-X


title: IP Synchonized adult mouse testis Stages II/III-VI replicate 2

description: Gene expression data from Leydig cells

source_name: Leydig cell transcripts Stages II/III-VI


title: IP Synchonized adult mouse testis Stages XII-II/III replicate 2

description: Gene expression data from Leydig cells

source_name: Leydig cell transcripts Stages XII-II/III

value: Stages XII-II/III


title: Total Synchonized adult mouse testis Stages XII-II/III replicate 2

description: Gene expression data from total  testis

source_name: Total testis transcripts Stages XII-II/III


title: L6-Heart


title: ChIP_Ring1b_KO_R2

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

institute: Center for Genomic Regulation (CRG)

data_processing:
Sequence reads were mapped to a synthetic genome constituted of the mouse and the human chromosomes (mm9+hg19) using BOWTIE (PubMed ID 19261174) with the option -m 1.
Peak detection was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIPseq genome-wide profiles are normalized by the total number of human reads of each sample.
Genome_build: mm9
Supplementary_files_format_and_content: Files *.bedgraph.gz: BedGraph, genome-wide ChIP profiles.
Supplementary_files_format_and_content: Files .bed: BED, signal enriched regions.

source_name: mouse Embryonic Stem Cells (mESCs)

growth_protocol: The Mll2F/F:CreERT2/+ ESCs were established from blastocysts of C57Bl/6 mice as previously described (Denissov et al, Development 2014). Cells were cultured in feeder-free 0.1% gelatin-coated dishes, in DMEM (SIGMA G5154) supplemented with 20% FBS (HyClone), with 0.2% β-mercaptoethanol (Gibco), 1% Pen/Strep (Gibco), 1% sodium pyruvate (Gibco), 1% non-essential amino acids (MEM NEAA, Gibco), 1% GlutaMAX™ (Gibco) and 1,000U/ml recombinant LIF (Millipore).

extract_protocol:
ChIPseq experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013). This ChIPseq includes spike-in control from human K562 cell line:  0.75ug (2.5%) of chromatin from crosslinked K562 cells was added to 30 ug of ESCs chromatin, together with 4ug of homemade RING1B-specific antibody during immunoprecipitation reactions.
Libraries were prepared according to Illumina instructions.

treatment_protocol: Induction of Cre-recombination was achieved by treating cells with 10-6 M 4-hydroxytamoxifen during 96 hours as previously described (Glaser et al., Epigenetics Chromatin 2009).

tag: strain/background

tag: mll2 status

value: KO

value: Embryonic Stem Cells

tag: chip antibody

value: Ring1b (Homemade (PubMed id:22226355))


title: L5-Heart

tag: breed

tag: phenotype


title: Total Synchonized adult mouse testis Stages VIII-X replicate 1

description: Gene expression data from total  testis


title: ChIP_Ring1b_WT_R2

extract_protocol: ChIPseq experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013). This ChIPseq includes spike-in control from human K562 cell line:  0.75ug (2.5%) of chromatin from crosslinked K562 cells was added to 30 ug of ESCs chromatin, together with 4ug of homemade RING1B-specific antibody during immunoprecipitation reactions. Libraries were prepared according to Illumina instructions.

value: WT

tag: cell type


title: Total Synchonized adult mouse testis Stages II/III-VI replicate 1

description: Gene expression data from total  testis

tag: gender


title: ESserum_oX

first: Thomas

last: Graf

address: c/Dr. Aiguader, 88. PRBB Building

institute: CRG (Center for Genomic Regulation)

data_processing:
We used the GEM mapper (Marco-Sola et al., 2012) with two modified versions each of the mouse (GRCm38) and viral reference genomes: one with all C’s changed to T’s and another with all G’s changed to A’s. Reads were fully converted in silico prior to mapping to the modified reference genomes, and the original reads were restored after mapping.
The first few bases from each read have been shown to have a slightly higher probability of being called as methylated (Schultz et al., 2015), so we trimmed the first ten bases from each read. Heterozygous positions, positions with a genotype error probability greater than 0.01, and positions with a read depth greater than 250 were filtered out. Only cytosines with six or more reads informative for methylation status were considered. On average, half of the reads from either strand will be informative for methylation status at a given position, so minimum coverage is tipically greater than 12.
Methylated and unmethylated cytosine conversion rates were determined from spiked-in bacteriophage DNA (fully methylated phage T7 and unmethylated phage lambda).
Methylated non-CGs were defined as those cytosines with at least two unconverted reads and a methylation probability greater than two SDs, where the probability of the following base being a guanine was at least two orders of magnitude smaller than the most probable base
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files used for browser exploration of the data.

source_name: embryo (inner cell mass)

growth_protocol: B and Ba cells were grown in 20%FBS-RPMI+IL7; D1-D4 in N2B27 medium. ES2i in N2B27+2i medium. ESserum in 15%FBS+LIF conditions.  All cells were grown on feeders (mitomycin-C treated mouse embryonic fibroblasts)

extract_protocol:
Cells were collected, seperated from feeders by pre-plating and genomic DNA was extracted using the Blood & Cell Culture DNA Mini kit (Qiagen).
High molecular weight DNA (400ng) was spiked with unmethylated bacteriophage ? DNA (5 ng of ? DNA per microgram of genomic DNA; Promega), with methylated T7 phage DNA (5 ng of T7 DNA per microgram of genomic DNA) and also with the manufacture’s digestion and sequencing control (each 20 ng per microgram of genomic DNA). Genomic DNA with the spike-in controls was sheared using Covaris LE220 focused-ultrasonicator to a mean fragment size of 800bp, purified, denatured and the sample was evenly split for the oxidation reaction and the mock-oxidation reaction where the oxidant solution was replaced by water. Both aliquots were then processed in parallel for all stages of the protocol. Illumina compatible adapters and library specific indexes were incorporated through ten PCR cycles. The quality control of the library was monitored using the Agilent 2100 Bioanalyzer DNA 7500 assay, and the concentration was estimated using the KAPA Library Quantification Kit for Illumina® Platforms, v1.14 (Kapa Biosystems).
WGBS and oxWGBS following the workflow of  CEGX TrueMethyl® Whole Genome kit, v3.1 (Cambridge Epigenetix) in HydroxyMethyl mode

treatment_protocol: C/EBPa was induced with beta-estradiol; OSKM with doxycycline.

tag: culture

value: low passage (p<10)


title: Total Synchonized adult mouse testis Stages X-XII replicate 1

description: Gene expression data from total  testis

value: male


title: ESserum_BS


title: Total Synchonized adult mouse testis Stages VI-VIII replicate 1

description: Gene expression data from total  testis

value: testis


title: IP Synchonized adult mouse testis Stages VIII-X replicate 1

description: Gene expression data from Leydig cells

value: Stages VIII-X


title: Total Synchonized adult mouse testis Stages XII-II/III replicate 1

description: Gene expression data from total  testis

source_name: Total testis transcripts Stages X-II/III


title: IP Synchonized adult mouse testis Stages II/III-VI replicate 1

description: Gene expression data from Leydig cells


title: ChIP_Suz12_KO_R2

data_processing:
Sequence reads were mapped to a synthetic genome constituted of the mouse and the fruit fly chromosomes (mm9+dm3) using BOWTIE (PubMed ID 19261174) with the option -m 1.
Peak detection was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIPseq genome-wide profiles are normalized by the total number of fly reads of each sample.
Genome_build: mm9
Supplementary_files_format_and_content: Files *.bedgraph.gz: BedGraph, genome-wide ChIP profiles.
Supplementary_files_format_and_content: Files .bed: BED, signal enriched regions.

extract_protocol:
ChIPseq experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013). These ChIPseq experiments include spike-in control: an equal amount of D. melanogaster S2 cell chromatin was added to each ChIP reaction (2.5% of the ESCs chromatin for histone modification ChIPs, and 0,08% for the rest of the ChIPs), together with 1 µg of an antibody against Drosophila-specific histone variant, H2Av, (Active Motif, Catalog No. 61686).
Libraries were prepared according to Illumina instructions.

value: Suz12 (Abcam, ab12073)


title: IP Synchonized adult mouse testis Stages XII-II/III replicate 1

description: Gene expression data from Leydig cells


title: IP Synchonized adult mouse testis Stages VI-VIII replicate 1

description: Gene expression data from Leydig cells

value: Stages VI-VIII


title: L4-Heart


title: ChIP_Suz12_WT_R2


title: IP Synchonized adult mouse testis Stages X-XII replicate 1

description: Gene expression data from Leydig cells

value: Stages X-XII


title: ChIP_H3K27me3_KO_R2

value: H3K27me3 (Millipore, 07-449)


title: ChIP_H3K27me3_WT_R2


title: L3-Heart


title: L2-Heart


title: ChIP_H3K4me3_KO_R2

value: H3K4me3 Diagenode C15410003


title: PRO_Mll2WT_R2

description:
PROseq experiment
Processed data file: PROseq_OH1-OH2-TAM1-TAM2_FPKMs.txt
WT2

data_processing:
Library strategy: PRO-seq
PROseq analysis: Raw fastq data were trimmed by cutadapt 1.14 (Martin, EMBnet.Journal, 2011) and Trimmomatic 0.33 (PubMed ID 24695404), then aligned on mm9 or dm3 genome by BOWTIE 1.1.2 (PubMed ID 19261174).
Expression: DeSeq2 (PubMedID 25516281) was run to quantify the expression in FPKMs of each annotated transcript in RefSeq. PROseq genome-wide profiles in plus/minus strands of mm9 are normalized by the number of fly spike-in reads of each sample.
Genome_build: mm9
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide PROseq profiles)
Files .txt (FPKMs): values for the replicates WT1, WT2, KO1 and KO2

extract_protocol:
PROseq: We followed the protocol as described previously (Mahat et al, Nat Protoc., 2016) with some modifications. After 4-hydroxytamoxifen treatment for 96 h, nuclei were isolated by Dounce homogenizer with loose pestle. ~10^7 nuclei were subjected to nuclear run-on (30 °C, 3 min) in the presence of 25 µM Biotin-11-ATP/GTP/CTP/UTP (PerkinElmer) and 6x10^5 Drosophila S2 spike-in nuclei. Total RNA were extracted and hydrolyzed in 0.2 M NaOH (on ice, 10 min). Biotinylated nascent RNA were purified by Dynabeads M-280 streptavidin (Invitrogen). After 3’ VRA3 adapter ligation and the 2nd purification by Dynabeads, 5’ cap and 5’ hydroxyl RNA were converted to 5’ monophosphorylated RNA by RppH (NEB) and PNK (NEB), respectively. After 5’ VRA5 adapter ligation and the 3rd purification by Dynabeads, cDNA were generated by reverse transcription with SuperScript III (Invitrogen) and RP1 primer. PCR by Phusion Hot Start (Thermo) and RP1/RPIx primer sets in 10 cycles amplified indexed DNA libraries. 140–350 bp DNA libraries were size-selected by Pippin HT with 2% gel cassette 20B (Sage Science) and then sequenced by NextSeq 500 system (illumina) with single-read runs.
Libraries were prepared according to Illumina instructions.

value: Embryonic stem cells


title: PRO_Mll2KO_R2

description:
PROseq experiment
Processed data file: PROseq_OH1-OH2-TAM1-TAM2_FPKMs.txt
KO2

data_processing:
Library strategy: PRO-seq
PROseq analysis: Raw fastq data were trimmed by cutadapt 1.14 (Martin, EMBnet.Journal, 2011) and Trimmomatic 0.33 (PubMed ID 24695404), then aligned on mm9 or dm3 genome by BOWTIE 1.1.2 (PubMed ID 19261174).
Expression: DeSeq2 (PubMedID 25516281) was run to quantify the expression in FPKMs of each annotated transcript in RefSeq. PROseq genome-wide profiles in plus/minus strands of mm9 are normalized by the number of fly spike-in reads of each sample.
Genome_build: mm9
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide ChIP and PROseq profiles)
Files .txt (FPKMs): values for the replicates WT1, WT2, KO1 and KO2


title: L1-Heart

value: Low altitude

value: adapted to heat


title: PRO_Mll2WT_R1

description:
PROseq experiment
Processed data file: PROseq_OH1-OH2-TAM1-TAM2_FPKMs.txt
WT1


title: H5-meat

source_name: breast muscle

value: High altitude

value: not adapted to heat

value: breast muscle


title: ChIP_H3K27me3_Mll2CD

description: ChIPseq experiment

data_processing:
ChIPseq analysis: Sequence reads were mapped to the Mouse genome (mm9, July 2007) using BOWTIE (PubMed ID 19261174) with the option -m 1. Peak-calling: Peak detection was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIPseq genome-wide profiles are normalized by the total number of reads of each sample.
Genome_build: mm9
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide ChIP)
Files .bed (BED, signal enriched regions)

growth_protocol: Wild-type and catalytic dead Mll2 cells were cultured in dishes coated with 0.1% gelatin and irradiated mouse embryonic fibroblasts (MEF) feeders, in 20% FBS DMEM media containing the abovementioned supplements and LIF. To remove contaminating feeder cells, ESCs cells where trypsinized and pre-plated for two rounds for 30 minutes each plating. Supernatant containing feeder-cleared ESCs was then collected and pelleted.

extract_protocol: ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013).

value: catalytic dead Mll2 (Y2602A mutant) embryonic stem cells (generated in A. Shilatifard Lab)


title: ChIP_H3K27me3_Mll2WT

description: ChIPseq experiment

value: WT


title: H6-Heart

value: Heart


title: H7-Heart


title: H8-Heart


title: ChIP_INPUT_Mll2WT

description: ChIPseq experiment


title: ChIP_H3K4me3_Mll2WT

description: ChIPseq experiment

value: H3K4me3 (Diagenode C15410003)


title: ChIP_H3K4me3_Mll2CD

description: ChIPseq experiment


title: H4-Heart


title: H2-Heart


title: H1-Heart


title: H5-Heart


title: ChIP_H3K4me3_WT_R2

value: Embryonic Stem Cells


title: PRO_Mll2KO_R1

description:
PROseq experiment
Processed data file: PROseq_OH1-OH2-TAM1-TAM2_FPKMs.txt
KO1

value: KO


title: wt12

city: Freising

first: Tobias

last: Fromme

address: Gregor-Mendel-Str. 2

department: Molecular Nutritional Medicine

country: Germany

institute: Technical University of Munich

data_processing:
Sequencing software: HiSeq Control Software 2.2.58 Image analysis and base calling: Real-Time Analysis (RTA) 1.18.64 fastq-file generation: CASAVA BCL2FASTQ Conversion Software 1.8.3
Sequenced reads with masked adaptor sequence were mapped to the murine genome, NCBI build 38, by the Genomatix Mapper 3.7.6 (Genomatix Mining Station, settings: 'deep', min. quality 92%).
Unique hits were subjected to expression analysis for RNA-seq (Genomatix Genome Analyzer, ElDorado version 12-2013) and provided as reads per kilobase of exon per megabase of library size (RPKM).
Genome_build: murine NCBI genome build 38
Supplementary_files_format_and_content: tab-delimited text file providing RPKM values for each sample.

source_name: wt, primary brown adipocytes

extract_protocol:
Primary brown adipocytes were washed with ice-cold PBS, placed on ice and scraped into Trisure (Bioline). Total RNA was prepared from Trisure (Bioline) and column-purified (SV Total RNA Isolation System, Promega).
Libraries were constructed from total RNA (TruSeq RNA Sample Prep kit v2 (Illumina)).

value: wildtype

tag: source organ

value: interscapular BAT

value: primary brown adipocytes


title: ko13

source_name: ko, primary brown adipocytes

tag: genotype


title: wt11


title: ChIP_INPUT_Mll2CD

description: ChIPseq experiment


title: PEGPH20 DSS

first: tatsuya

last: dokoshi

address: 9500 gilman

institute: UCSD

data_processing:
Partek Flow and Partek Genomics Suite software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Genome_build: mm10

source_name: colon

extract_protocol:
colon were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DSS group mouse were feeded 3% DSS for 7days. PEGPH group were injected every 3 days.

value: colon

tag: age

value: 8-12 weeks age

tag: genotype/variation

value: wild type

tag: treatment

value: 1mg/kg PEGPH20 (hyaluronidase) every 72 hours and fed 3% DSS for 7days


title: wt10

tag: strain


title: PEGPH20

tag: tissue

value: 1mg/kg PEGPH20 (hyaluronidase) every 72 hours


title: ko15


title: H9-Heart

value: High altitude


title: Control


title: Oct4IPLIBNeg

data_processing:
Base-calling using default Illumina software by Edinburgh Genomics
Upload to GeneProf (Halbritter et al. 2012) for processing using ChIP-seq pipeline, including:
Alignment to reference genome using Bowtie (Langmead et al. 2009)
Peak calls with SISSRs (Jothi et al. 2008)
Read counts per peak were calculated and peaks of the same IP were only called “lost” if less than 50% of its maximum observed binding was retained (normalizing differences in sequencing library depth)
Genome_build: mm9
Supplementary_files_format_and_content: BED (chromosome, start, end)

source_name: ChIP-seq for Oct4 in Esrrb-low ESCs

extract_protocol:
10^7 to 5x10^7 E14Tg2a Esrrb-2a-GFPd-IBIH ESCs were resuspended at 3.3x10^6 cells/ml in pre-warmed GMEMb/FCS/LIF and cross-linked for 10 min at RT with 1% formaldehyde (Sigma Cat # F8775-25ML) in the dark. Cross-linking was stopped by adding 0.125mM glycine (5 min, RT), cells were pelleted (5 min, 1000 rpm, 4°C), washed twice with ice-cold PBS and resuspended in PBS/FCS at 10^7 cells/ml. Keeping the samples refrigerated, Esrrb High (Top 10%), Esrrb Medium (15% of the distribution immediately above negative) and Esrrb Negative cells were purified using a FacsARIA cell sorter (Becton, Dickinson). Since gradual loss of fluorescence was observed in fixed cells after prolonged incubation, multiple batches of freshly fixed cells were sorted for a maximum of 45 minutes, a time when loss of fluorescence was not yet noticeable. After sorting, cell purity was determined using the same instrument. Cells were spun down, transferred to 1.5 ml Eppendorf tubes, washed with cold PBS, counted and resuspended at 5x10^6 cells/ml in swelling buffer (5mM Pipes pH8, 85mM KCl) freshly supplemented with 1X protease inhibitor cocktail (Roche Cat # 04 693 116 001)/0.5% NP-40. After 30 min on ice with occasional shaking, nuclei were centrifuged (600g, 5 min, 4°C), washed in TSE (0.1% SDS, 1% Triton, 2mM EDTA, 20mM Tris-HCl pH8)/150mM NaCl, freshly supplemented with 1X protease inhibitor cocktail, and resuspended in the same buffer at 107 cells/ml. Samples were sonicated in 1.5ml tubes using a Bioruptor (Diagenode) (4 x 10min cycles (each divided into 30s ON-30s OFF subcycles) at maximum power in circulating ice-cold water. Chromatin was then centrifuged (30 min, 14,000 rpm, 4°C) and the supernatant stored (-80°C) until use. 5ul was used to quantify chromatin concentration and check the DNA fragment size on a 1.5% w/v 0.5x TAE agarose gel. The typical fragment size was 100-250bp.  For each ChIP experiment a total of 5-10 ug of chromatin was used, pooling material generated from multiple sorting experiments. Chromatin was thawed and pre-cleared (90 min rotating on-wheel, 4°C) in 1 ml TSE/150mM NaCl containing 50µl of a 50% slurry of pA/pG sepharose beads (Sigma Cat # P9424-5ML, P3296-5ML), previously blocked with 500µg/ml BSA (Roche, Cat # 5931665103) and 1µg/ml of yeast tRNA (Invitrogen, Cat # AM7119). Pre-cleared chromatin was centrifuged (3000rpm, 1 min) in a benchtop microcentrifuge and the supernatant transferred into fresh tubes. 10ul of diluted chromatin was set apart for input DNA extraction and precipitation. Immunoprecipitations with anti-Nanog rabbit polyclonal (made in-house) (0.5 ug/IP) and goat polyclonal anti-Oct4 (Santa Cruz Biotechnology, Cat # SC-8628) (1 ug/IP) antibodies were performed by rotating on-wheel (4°C, overnight) in a final volume of 500µl TSE/150mM NaCl. Immunocomplexes were recovered by rotating (4h, 4°C) with 25ul of a 50% slurry of pA/pG sepharose beads (Sigma Cat # P9424-5ML, P3296-5ML) or 20µl pA/pG magnetic Dynabeads (Life Technologies Cat # 10001D, 10003D) (30 mg/ml), (blocked as above). Beads were recovered by centrifugation or magnetic separation and washed sequentially (5 min rotation, RT) with 1ml of the following buffers: TSE/150mM NaCl (3x), TSE/500mM NaCl (once), TSE/750mM NaCl (once), TSE/1000mM NaCl (once), washing buffer (10mM Tris-HCl pH8, 0.25M LiCl, 0.5% NP40, 0.5% Na-Deoxycholate, 1mM EDTA), and twice in TE (10mM Tris-HCl pH8, 1mM EDTA). After the last wash, a 2-step elution was performed by incubating beads in 150µl 1% SDS, 10mM EDTA, 50mM Tris-HCl, pH8 (15 min; 65°C) after vigorous vortexing. Eluates were collected (1 min, 14,000 rpm), a second elution performed under the same conditions and both eluates pooled. For both immunoprecipitated and input chromatin samples, crosslinking was reversed by incubation (65°C, overnight) followed by proteinase K treatment (5 ul - Invitrogen Cat # AM2546), phenol/chlorophorm extraction and ethanol precipitation using 40ug of glycogen as a carrier.
Material from three independent ChIPs was pooled, resuspended in 10ul H2O and used as a template for library preparation using a MicroPlex Library Preparation Kit (Diagenode Cat # C05010010) following the manufacturer instructions. The library preparation and synthesis steps were performed using a benchtop thermocycler (Biorad). For both Oct4 and Nanog ChIP libraries Esrrb High, Esrrb Medium and Esrrb Negative samples were labelled with indexing reagents n. 4, 6 and 12 respectively. Before library amplification, Picogreen (Life Technologies Cat # P11496) was added at working concentration (1:200 from stock) in the amplification mix. 75ul of mix for each sample was transferred to three wells of a 384 well qPCR plate (Roche) and library amplification performed using a 480 LightCycler (Roche). Amplifications were stopped before the reaction reached plateau and DNA concentration quantified. In case the total amount of DNA was below 500ng, 4 additional cycles of amplification were performed. Amplified material was purified using Agencourt AMPure® XP magnetic beads (Beckman Coulter, Cat # No. A63880) and eluted in 30ul TE. Samples were submitted to the GenePool core facilities (University of Edinburgh) for quantification and analysis of fragment size on an Agilent 2100 Bioanalyser. Fragment sizes ranged from 200-450 bp in all samples.   Equimolar amounts of Oct4 or Nanog ChIP libraries from Esrrb High, Esrrb Medium and Esrrb Negative sorted cells were pooled and sequenced on a single Illumina HiSeq 2500 flowcell.

value: embryonic stem cells

tag: sorted fraction

value: Esrrb-Negative


title: Oct4IPLIBM

source_name: ChIP-seq for Oct4 in Esrrb-medium ESCs

tag: cell line

value: Esrrb-Medium

value: goat polyclonal anti-Oct4 (Santa Cruz Biotechnology, Cat # SC-8628)


title: ko14


title: H3-Heart

value: not adapted to heat

value: Heart


title: Oct4IPLIBH

source_name: ChIP-seq for Oct4 in Esrrb-high ESCs

value: Esrrb-High


title: NanogIPLIBM

description: NanogIPLIBM

source_name: ChIP-seq for Nanog in Esrrb-medium ESCs

value: anti-Nanog rabbit polyclonal (made in-house)


title: MEF_hMeDIP_rep1

city: Paris

first: samuel

last: Collombet

address: 46 rue d'Ulm

department: Biology

country: France

institute: Ecole Normale Superieure

data_processing:
Library strategy: hMeDIP-Seq
paired-end reads were mapped onto the mm10  using STAR (outFilterMultimapNmax 1; outFilterMismatchNmax 999; outFilterMismatchNoverLmax 0.06 ; alignIntronMax 1; alignEndsType EndToEnd; alignMatesGapMax 2000).
Duplicates reads were removed using Picard (http://picard.sourceforge.net) (MarkDuplicates, REMOVE_DUPLICATES = true).
Bigwig tracks were made using DeepTools BamCoverage (1.5.9.1), keeping only fragment smaller than 100bp to exclude fragment containing nucleosomes.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig of signal in rpm

source_name: MEF

growth_protocol: Reprogrammable MEFs were homozygous for a polycistronic cassette containing  Oct4, Klf4, Sox2 and c-Myc (OKSM) in the Col1a1 locus and harbored homozygous  Rosa26-M2rtTA alleles (Stadtfeld et al., 2010). During expansion, cells were grown in  DMEM (Life Technologies) supplemented with 10% FBS (Hyclone), 1% GlutaMAX  (Life Technologies), 1% non-essential amino acids (Life Technologies), 0.1% β-  16  mercaptoethanol (Sigma-Aldrich). To induce reprogramming, cells were seeded onto  0.1% gelatin-coated plates at a density of 3000 cells/cm2 in reprogramming medium  (KO-DMEM (Life Technologies) supplemented with 15% FBS (Hyclone), 1%  GlutaMAX (Life Technologies), 1% non-essential amino acids (Life Technologies),  0.5% β-mercaptoethanol (Sigma-Aldrich), 1,000 U/ml LIF (produced in-house), and 2  μg/ml doxycycline (Sigma). Where indicated, 50 μg/ml ascorbic acid (Sigma-Aldrich)  and 3 μM GSK3 inhibitor CHIR-99021 (Tocris) were added to the culture medium.

extract_protocol:
Purified genomic DNA from MEF reprogramming samples was sonicated using  Covaris to obtain fragments of 200–600 bp. Library preparation was performed using  the NEBNext Ultra library prep kit (NEB) substituting the NEB hairpin adaptors by fulllength  barcoded TruSeq adaptors from Illumina. Fragmented DNA with compatible  adaptors were pooled together. Pooled DNA was heated for 10 minutes at 99ºC, cold  down on ice, and incubated overnight with 5hmC (1 μg Ab/μg DNA; Active Motif,  39769) antibody in IP buffer (10 mM Sodium Phosphate buffer, 140 mM NaCl, 0.05%  triton X-100). Immunocomplexes were recovered using pre-equilibrated Protein G/A  Dynabeads for 2 hr at 4ºC. After washing with IP buffer, immunocomplexes were eluted  from columns by heating at 55ºC for 30 minutes in proteinase digestion buffer (50 mM  Tris-HCl pH=8, 10 mM EDTA, 0.5% SDS, 35 mg Proteinase K) and the DNA purified  using MinElute PCR Purification kit (Quiagen).
Recovered DNA was amplified by PCR  and sequenced in Illumina HiSeq2500 using 125-bp paired-end reads with HiSeq v4  Chemistry.

value: MEF

value: untreated


title: MEF_hMeDIP_rep2


title: NanogIPLIBH

description: NanogIPLIBH

source_name: ChIP-seq for Nanog in Esrrb-high ESCs


title: MEF_AGI_OSKM_d2_hMeDIP_rep2


title: MEF_AGI_OSKM_d4_hMeDIP_rep2


title: MEF_AGI_OSKM_d2_ATACseq

data_processing:
paired-end reads were mapped onto the mm10  using STAR (outFilterMultimapNmax 1; outFilterMismatchNmax 999; outFilterMismatchNoverLmax 0.06 ; alignIntronMax 1; alignEndsType EndToEnd; alignMatesGapMax 2000).
Duplicates reads were removed using Picard (http://picard.sourceforge.net) (MarkDuplicates, REMOVE_DUPLICATES = true).
Bigwig tracks were made using DeepTools BamCoverage (1.5.9.1), keeping only fragment smaller than 100bp to exclude fragment containing nucleosomes.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig of signal in rpm

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro et al., 2013). The  standard protocol was used with the following modifications. 100.000 cells were  washed once with 100μl PBS and resuspended in 50μl lysis buffer (10mM Tris-HCl pH  7.4, 10mM NaCl, 3mM MgCl2, 0.2% IGEPAL CA-630). The suspension of nuclei was  then centrifuged for 10min at 500g at 4°C, followed by the addition of 50μl transposition  reaction mix (25μl TD buffer, 2.5μl Tn5 Transposase and 22.5μl Nuclease Free H2O)  and incubation at 37°C for 45min. DNA was isolated using MinElute Kit (Qiagen).
Library amplification was done by two sequential PCR reactions (8 and 5 cycles,  respectively). Library quality was checked on a Bioanalyzer, followed by paired-end  sequencing (2x50bp) on an Illumina HiSeq2500.


title: MEF_ATACseq


title: MEF_AGI_OSKM_d4_ATACseq


title: MEF_AGI_OSKM_d4_hMeDIP_rep1


title: MEF_AGI_OSKM_d2_hMeDIP_rep1


title: Control DSS

value: fed 3% DSS for 7days


title: HiC_CD2

description:
HiC experiment
Catalytic inactive MLL2 sample: CD
CD_interaction_matrices_50Kb.tar.gz
CD_interaction_matrices_100Kb.tar.gz

data_processing:
TADbit’s fragment based mapping module (aligning with GEM) with the default parameters was used to align reads. TADbit’s filtering module was used to filter out non-informative contacts (self-circle, dangling ends, extra-dangling ends, errors, duplicated and random breaks). PUBMED: TADbit (28723903) and GEM (26094690)
Contact matrices were obtained and poor bins (containing low counts) were filtered out using TADbit’s routines. Raw counts at 50kb and 100Kb resolution are stored as tab-separated files with chromosome in first column, coordinates of first bin as second column, and number of contacts to each bin  of the chromosome in the rest of columns.
Genome_build: mm9
Supplementary_files_format_and_content: Format
Raw interaction matrices per chromosome are included in the abc format, which has commented lines (start with a “#” character) and the actual interaction counts (one per line) as lines in the format left-bin and raw-counts to all the bins of the chromosome.
*_interaction_matrices_50Kb.tar.gz
*_interaction_matrices_100Kb.tar.gz

growth_protocol: (Conditional MLL2 KO: OH means WT and TAM means KO): The Mll2F/F:CreERT2/+ ESCs were established from blastocysts of C57Bl/6 mice as previously described (Denissov et al., Development 2014). Cells were cultured in feeder-free 0.1% gelatin-coated dishes in DMEM (SIGMA G5154) supplemented with 20% FBS (HyClone), with 0.2% β-mercaptoethanol (Gibco), 1% Pen/Strep (Gibco), 1% sodium pyruvate (Gibco), 1% non-essential amino acids (MEM NEAA, Gibco), 1% GlutaMAX™ (Gibco) and 1,000U/ml recombinant LIF (Millipore). (Catalytic inactive MLL2: WT means WT and CD means Catalytic Dead): Wild-type and catalytic dead Mll2 cells were cultured in dishes coated with 0.1% gelatin and irradiated mouse embryonic fibroblasts (MEF) feeders, in 20% FBS DMEM media containing the abovementioned supplements and LIF. To remove contaminating feeder cells, ESCs cells where trypsinized and pre-plated for two rounds for 30 minutes each plating. Supernatant containing feeder-cleared ESCs was then collected and pelleted.

extract_protocol:
Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014, PubmedID: 25497547).
Libraries were prepared according to Illumina instructions.

treatment_protocol: (Conditional MLL2 KO: Induction of Cre-recombination was achieved by treating cells with 10-6 M 4-hydroxytamoxifen during 96 hours as previously described (Glaser et al., Epigenetics Chromatin 2009).

tag: strain/background

value: Embryonic stem cells

value: catalytic dead


title: NAG6_15min_G

city: Piracicaba

first: Paulo

last: Teixeira

state: SP

address: Av. Pádua Dias, 11

country: Brazil

institute: University of São Paulo (ESALQ/USP)

data_processing:
Illumina Casava version 1.8 was used for basecalling
Quality assessment of the sequencing reads was performed using the FastQC version 0.11.5
Trimmomatic version 0.36 was used to identify and discard reads containing Illumina adapter sequences
Quality-filtered reads were mapped to 69,500 cDNA sequences of the Nicotiana tabacum K326 v4.5 reference using HiSat2 version 2.0.5
featureCounts version 1.5.2  was used to count reads that mapped to each one of the 69,500 sequences
Genome_build: K326 v4.5
Supplementary_files_format_and_content: tab-delimited text file including read counts per gene for each sample

organism: Nicotiana tabacum

source_name: cell suspension

growth_protocol: Nicotiana tabacum BY-2 cells were maintained in liquid Murashige and Skoog medium (supplemented with 30 g/L sucrose, 1 mg/L 2,4-Dichlorophenoxyacetic acid, 0.1 mg/L kinetin and 1X Gamborg’s vitamins) in the dark at 27oC and 100 rpm. Cells were subcultured weekly.

extract_protocol:
Total RNA was extracted from Nicotiana tabacum cells using the Trizol reagent protocol
poly(A) RNA was isolated from 1000 ng total RNA and used to prepare non-stranded Illumina RNA-seq libraries. Following library preparation, quality control and quantification were performed using a 2100 Bioanalyzer instrument (Agilent) and the Quant-iT PicoGreen dsDNA Reagent (Invitrogen), respectively.

treatment_protocol: Cell suspensions (3 – 5 days-old) were transferred to 12-well plates (2.5 mL/well) and kept at room temperature with gentle rocking for at least 2 h. Cells were treated with 10 nM NAG6, 100 nM MpChi, 10 nM NAG6 + 100 nM MpChi or H2O (Mock treatment). Mixtures of elicitors and proteins were kept at room temperature for at least 10 minutes before addition to plant cells. Samples were harvested immediately before the start of the experiment (Time 0, untreated cells) and at four time points after the treatment (15 min, 60 min, 120 min and 180 min). The experiment was performed in triplicate.

tag: time


title: HiC_CD1

tag: mll2 status


title: HiC_WT2

description:
HiC experiment
Catalytic inactive MLL2 sample: WT
WT_interaction_matrices_50Kb.tar.gz
WT_interaction_matrices_100Kb.tar.gz

value: WT


title: NAG6_15min_E


title: HiC_WT1


title: NAG6_15min_D


title: No-treatment_0min_B

value: No treatment


title: No-treatment_0min_C


title: NanogIPLIBNeg

description: NanogIPLIBNeg

source_name: ChIP-seq for Nanog in Esrrb-low ESCs

tag: chip antibody


title: No-treatment_0min_A


title: MpChi_180min_C

value: MpChi


title: HiC_TAM3

description:
HiC experiment
Conditional MLL2 KO sample_TAM: KO
TAM_interaction_matrices_50Kb.tar.gz
TAM_interaction_matrices_100Kb.tar.gz

value: KO


title: MpChi+NAG6_180min_C


title: MpChi_180min_A


title: HiC_TAM2


title: H2O_180min_C


title: HiC_OH4

description:
HiC experiment
Conditional MLL2 KO sample_OH: WT
OH_interaction_matrices_50Kb.tar.gz
OH_interaction_matrices_100Kb.tar.gz


title: MpChi+NAG6_180min_A


title: NAG6_180min_B


title: NAG6_180min_C


title: NAG6_180min_A


title: HiC_OH5


title: HiC_OH3


title: H2O_180min_B


title: NAG6_15min_F


title: H2O_180min_A


title: HiC_OH2


title: MpChi_120min_C


title: MpChi_120min_B


title: MpChi_120min_A


title: MpChi+NAG6_120min_C


title: HiC_OH1


title: MpChi_180min_B


title: MpChi+NAG6_120min_B


title: KO3_2

first: John

last: Chang

state: CA

address: 9500 Gilman Drive

data_processing:
fastq files were processed by kallisto with following command: "kallisto quant -b 8 -l 200 -s 20 -t 4 --single"
Genome_build: GRCm38.rel79.cdna
Supplementary_files_format_and_content: kallisto output files, with the first column as gene id, and the rest as gene length, gene effective length, estimated counts and TPM, respectively.

extract_protocol:
Treg cells were sorted by flow cytometry and RNA was extracted using Trizol. Libraries were prepared using the Illumina non-stranded TruSeq kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Treg cells

value: spleen

value: Foxp3+YFP+ talin KO


title: NAG6_120min_C


title: MpChi+NAG6_180min_B


title: KO3_1


title: MpChi+NAG6_120min_A


title: NAG6_120min_B


title: NAG6_120min_A


title: H2O_120min_C


title: H2O_120min_B


title: HiC_TAM1


title: KO2_1


title: KO2_2


title: KO1_2


title: KO1_1


title: MpChi_60min_A


title: MpChi_60min_C


title: H2O_120min_A


title: MpChi+NAG6_60min_C


title: WT4_2

value: Foxp3+YFP+ wild-type


title: MpChi+NAG6_60min_A


title: MpChi+NAG6_60min_B


title: NAG6_60min_C


title: NAG6_60min_B


title: WT4_1


title: WT3_2


title: H2O_60min_C


title: NAG6_60min_A


title: WT3_1


title: WT2_2


title: WT2_1


title: H2O_60min_A


title: Eno1_replicate2

city: Edinburgh

first: Stefan

last: Bresson

state: Scotland

address: Max Born Crescent, Swann 5.1

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

description:
crosslinked RNA
barcode: NNNCTAGC

data_processing:
Library strategy: CRAC
Data was preprocessed using the flexbar and the fastx package. All sequences are of the form:     5’AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNXXXXXX==INSERT==TGGAATTCTCGGGTGCCAAGGCCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG-3’    where NNN are random nucleotides to assess for duplicates in PCR amplification and XXXXXX is a barcode to allow for multiplexing of different libraries. The barcode used for each sample is listed in the 'Raw Data' section below.
Fastq files were split by barcode using a custom python script.
Fastq files were preprocessed using flexbar (parameters –u 3 –at 1 –ao 4 –q 30 with adapter sequence TGGAATTCTCGGGTGCCAAGGC)
Identical reads were collapsed using fastx_collapser
Reads were aligned to a custom transcriptome using Novoalign. -r None -s 1 -l 17
any reads with the same random nucleotides and with 5′ ends mapping to the same coordinates were collapsed into a single read (Tuck and Tollervey, 2013)
Reads were counted using pyReadCounters (pyCRAC). --sense
Sequences were plotted along the genome using pyGTF2bedgraph (pyCRAC)
Genome_build: EF4.74
Supplementary_files_format_and_content: bedgraph files showing the distribution of reads across the yeast transcriptome

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Yeast cells were grown in SD -TRP media containing 2% glucose overnight and inoculated into fresh media at a starting OD600 of 0.05. Cells were grown for about 7 hours (until OD600=0.5) and UV (254nm) crosslinked.

extract_protocol:
Cells were lysed, followed by stringent, denaturing, two-step affinity purification of the tagged protein. Bound RNA was partially degraded with RNase, radiolabeled, and 5’ and 3’ linkers were added. Finally, covalent RNA-protein complexes were isolated by SDS-PAGE. Following Proteinase K digestion of the bound proteins, RNA fragments were amplified by RT-PCR.
RNA libraries were prepared using the standard CRAC protocol (Tuck and Tollervey, 2013)

tag: experiment


title: MpChi_15min_C


title: H2O_60min_B


title: MpChi_15min_A


title: WT1_2

tag: cell type


title: MpChi_60min_B


title: Eno1_replicate1

description:
crosslinked RNA
barcode: NNNGCGCAGC


title: WT1_1


title: MpChi+NAG6_15min_C


title: BY_replicate1

description:
crosslinked RNA
barcode: NNNTAAGC

value: untagged control


title: MpChi+NAG6_15min_B


title: H3K14Ac_pool_3samples_normobilirubinemic_ChIPseq

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

description:
Immunoprecipitated H3K14Ac linked DNA
NJ_S1_L001

data_processing:
Reads were mapped to the Rattus norvegicus (rn4) genome using bowtie2. Duplicate reads were filtered. The quality of the sequences was evaluated using fastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Broad peaks were called using MACS2  and annotated using HOMER software
Genome_build: rn4
Supplementary_files_format_and_content: Broad peaks files on paired-end data for both single experiments (without comparison to control sample) and for the comparison of hyperbilirubinemic samples with control samples.

extract_protocol:
ChIP was performed by the Magna ChIPTM G Tissue Kit (#17-20000, Merck Millipore, Temecula, CA, USA), folowing the manufacturer procedure, on 60mg tissue homogenate (in a glass-glass potter), DNA was sheared (average size of 100-400bp, by Sonopuls HD 3100, Bandelin, Germany, sonicator;  power 50%, 15”x18 cycles, 10” pause between each cycle, on ice), cross-linked with 1% formaldehyde (5’, RT), and protein-DNA complexes immune-precipitated (5μL 07-353 Ab, Merck Millipore, Temecula, CA, USA) by G magnetic beads on the magnetic rack (LSKMAGS08 Pure ProteomeTM Magnetic Stand, Merck Millipore, Temecula, CA, USA). Protein-DNA crosslink was reversed (proteinase K, 62°C, 2h; plus 95°Cx10’), and DNA stored at -20°C until use. Efficiency and specific of the ChIP procedure was assessed both by Western blot and Real Time PCR (RTqPCR), as suggested by the manufacturer.
The samples obtained by ChIP assay were quantified using Quant-iTTM PicoGreen ® dsDNA Reagent and Kits (Thermo Fisher Scientific, Waltham, MA, USA), according to manufacturer’s instruction.   Libraries were prepared using the NEBNext® UltraTM II DNA Library Prep Kit and NEBNext Multiplex oligos for Illumina (New England BioLabs®Inc, MA, USA), following the manufacturer instructions. Briefly, 10 ng of fragmented DNA underwent to end repair and adaptor ligation. The cleanup of Adaptor-ligated DNA was performed without size selection using Agencourt AMPure XP magnetic beads (Beckman Coulter Life Sciences, CA, USA). The PCR enrichment of adaptor ligated DNA was performed as follow: 1 cycle of initial denaturation 98°Cx30 sec; 10 cycles of denaturation at 98°Cx10sec and annealing and extension at 65°Cx75min; 1 cycle of final extension at 65°Cx5min, in a Bio-Rad trermal ctycler (Bio-Rad, Richmond, CA, USA). After the PCR cleanup using Agencourt AMPure XP magnetic beads (Beckman Coulter Life Sciences, CA, USA), the libraries were quantified using the PicoGreen fluorescent dye, as reported above, and stored at -20°C until use.  Before sequencing, libraries were denatured and diluted to a final concentration of 15 pM with 10% PhiX (Illumina, New England BioLabs®Inc, MA, USA) control. Paired end sequencing was performed using the MiSeq reagent kit v3 2x150 in the Illumina® MiSeq® system (Illumina, San Diego, CA, USA).

value: Gunn rat (Hds Blue:Gunn-UDPGTj)

value: control cerebella

value: H3K14Ac, 07-353, Merck Millipore


title: NAG6_15min_B


title: H3K14Ac_pool_3samples_hyperbilirubinemic_ChIPseq

description:
Immunoprecipitated H3K14Ac linked DNA
jj_S1_L001

value: hyperbilirubinmic (jj) cerebella


title: H3K14Ac_1sample_hyperbilirubinemic_ChIPseq

description:
Immunoprecipitated H3K14Ac linked DNA
jj1_S1_L001


title: NAG6_15min_A


title: H2O_15min_C


title: BY_replicate2

description:
crosslinked RNA
barcode: NNNGTGAGC


title: MpChi_15min_B


title: H2O_15min_B


title: H2O_15min_A


title: MpChi+NAG6_15min_A


title: PP2A cKO2

city: Hangzhou

first: Xuexiao

last: Jin

address: 866 Yuhangtang Road

institute: Zhejiang University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: In vitro polarized Th17 cells

growth_protocol: For polarization experiments, naïve cells were cultured at 1×106/ml with irradiated autologous antigen presenting cells (APCs) at a ratio of 1:3. Then the cells were primed for 2 days with soluble anti-CD3 (2µg/ml) and anti-CD28 (2 µg/ml),TGFβ1 (2 ng/ml), IL-6 (20 ng/ml) in the presence of anti-IL4 antibody (10 µg/ml) and anti-IFNγ antibody (10 µg/ml).

extract_protocol:
According to the instructions of RNAeasy Plus Mini kit (Qiagen).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Cells were restimulated with 50ng/ml PMA and 500ng/ml Ionomycin for 4 hours.

tag: time of collection

value: Polarized for 2 days

tag: restimulation

value: Restimulate with PMA/Iono

value: PP2A cKO


title: PP2A WT2

value: PP2A WT


title: PP2A WT1


title: PP2A cKO1


title: Spheroid_SKOV3_3_Rep 3

city: Wuhan

first: Zongyuan

last: Yang

state: Hubei

address: Jiefang avenue 1095, Hankou,

department: Gyneconogical cancer

institute: cancer biology center

description:
Spheroid_SKOV3_3_(HTA-2_0).sst-rma-gene-full-Signal
Gene expression data from SKOV3 tumor cells that could form spheroids with CAFs after 4 h coculture in suspension.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Transcriptome Array 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: PICR scanner 3000

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

source_name: SKOV3 cells that could form spheroids with CAFs after 4 h

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using Ambion® WT Expression Kit. WT Expression Kit

extract_protocol: QIAGEN All prep DNA/RNA/protein mini kit extracted total RNA according to the manufacturer's instructions

value: tumor cells


title: Spheroid_SKOV3_2_Rep 2

description:
Spheroid_SKOV3_2_(HTA-2_0).sst-rma-gene-full-Signal
Gene expression data from SKOV3 tumor cells that could form spheroids with CAFs after 4 h coculture in suspension.


title: Spheroid_SKOV3_1_Rep 1

description:
Spheroid_SKOV3_1_(HTA-2_0).sst-rma-gene-full-Signal
Gene expression data from SKOV3 tumor cells that could form spheroids with CAFs after 4 h coculture in suspension.


title: Spheroid_SKOV3_4_Rep 4

description:
Spheroid_SKOV3_4_(HTA-2_0).sst-rma-gene-full-Signal
Gene expression data from SKOV3 tumor cells that could form spheroids with CAFs after 4 h coculture in suspension.


title: Individual__SKOV3_1_Rep 1

description:
Individual__SKOV3_1_(HTA-2_0).sst-rma-gene-full-Signal
Gene expression data from SKOV3 tumor cells that could not form spheroids with CAFs after 4 h coculture in suspension.

source_name: SKOV3 cells that could not form spheroids with CAFs after 4 h


title: C1-1_cKO_batch_1

status: Public on Sep 12 2018

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

description: single cell from heart

data_processing:
Clean reads were mapped to mouse genome (mm10) using Salmon.
TPM (Transcripts Per Kilobase Million) for genes were calculated.
1. We excluded 18 samples with the mapping rates lower than 70%, and we obtained 76 WT single cells and 76 cKO single cells
2. We included GFP and tdTomato sequences in the reference genome for mapping and expression level quantification. Among 76 cKO single cells,  7 low GFP and high tdTomato cells were considered to be WT cells that had not expressed Mesp1-Cre. In 76 WT single cells, 2 low GFP and high tdTomato cells were considered not to be WT cells. These 9 cells with abnormal reporter gene expression were excluded.  Finally we obtained 143 samples for the following data analysis, so we only uploaded gene expression  of 143 samples in the processed file E9.5_Mouse_embryonic_heart_single_cells_143_samples_tpm.txt.   File showing sample filtering: Exclusion_of_27_samples_from_170_total_samples.xlsx
Genome_build: mm10
Supplementary_files_format_and_content: Txt files of gene names and tpm values for each sample.

source_name: single cell from heart

extract_protocol:
For single cell sample preparation, Ventricular part of E9.5 heart tubes were dissected and digested into single cells by 0.04% Trypsin combined with 0.05% Collagenase IV, and then transferred into DMEM containing 10% fetal bovine serum for termination. After washed in PBS without Ca2+, the single cells were manually transferred into cell lysis buffer with a mouth pipette.
Total RNA was reverse transcribed and amplified using Smart-seq2 protocol (Picelli et al., 2014), followed by Tn5 tagmentation and PCR enrichment to generate libraries using TruePrep DNA Library Prep Kit V2 for illumina (Vazyme, TD501-503) according to the manufacturer’s suggested protocol.

value: heart

value: Mesp1Cre/+; Dgcr8-/-

value: Embryonic day 9.5


title: C10-5_cKO_batch_2

description: single cell from heart


title: C10-4_cKO_batch_2

description: single cell from heart


title: C11-2_cKO_batch_2

description: single cell from heart


title: C10-8_cKO_batch_2

description: single cell from heart


title: C10-1_cKO_batch_2

description: single cell from heart


title: C10-7_cKO_batch_2

description: single cell from heart


title: C11-1_cKO_batch_2

description: single cell from heart


title: C10-3_cKO_batch_2

description: single cell from heart


title: C10-6_cKO_batch_2

description: single cell from heart


title: Individual__SKOV3_3_Rep 3

description:
Individual__SKOV3_3_(HTA-2_0).sst-rma-gene-full-Signal
Gene expression data from SKOV3 tumor cells that could not form spheroids with CAFs after 4 h coculture in suspension.


title: C11-4_cKO_batch_2

description: single cell from heart


title: C11-6_cKO_batch_2

description: single cell from heart


title: C11-5_cKO_batch_2

description: single cell from heart


title: Individual__SKOV3_2_Rep 2

description:
Individual__SKOV3_2_(HTA-2_0).sst-rma-gene-full-Signal
Gene expression data from SKOV3 tumor cells that could not form spheroids with CAFs after 4 h coculture in suspension.


title: C11-7_cKO_batch_2

description: single cell from heart


title: C11-8_cKO_batch_2

description: single cell from heart


title: C11-3_cKO_batch_2

description: single cell from heart


title: C1-2_cKO_batch_1

description: single cell from heart


title: C12-2_cKO_batch_2

description: single cell from heart


title: C12-1_cKO_batch_2

description: single cell from heart


title: C12-6_cKO_batch_2

description: single cell from heart


title: C12-7_cKO_batch_2

description: single cell from heart


title: C12-5_cKO_batch_2

description: single cell from heart


title: C12-8_cKO_batch_2

description: single cell from heart


title: C1-3_cKO_batch_1

description: single cell from heart


title: C1-7_cKO_batch_1

description: single cell from heart


title: C1-8_cKO_batch_1

description: single cell from heart


title: C2-1_cKO_batch_1

description: single cell from heart


title: C2-2_cKO_batch_1

description: single cell from heart


title: C2-6_cKO_batch_1

description: single cell from heart


title: C2-4_cKO_batch_1

description: single cell from heart


title: C3-3_cKO_batch_1

description: single cell from heart


title: C3-2_cKO_batch_1

description: single cell from heart


title: C3-5_cKO_batch_1

description: single cell from heart


title: C4-1_cKO_batch_1

description: single cell from heart


title: C4-2_cKO_batch_1

description: single cell from heart


title: C2-3_cKO_batch_1

description: single cell from heart


title: C4-3_cKO_batch_1

description: single cell from heart


title: C3-6_cKO_batch_1

description: single cell from heart


title: C2-5_cKO_batch_1

description: single cell from heart


title: C3-4_cKO_batch_1

description: single cell from heart


title: C4-4_cKO_batch_1

description: single cell from heart


title: C3-7_cKO_batch_1

description: single cell from heart


title: C4-5_cKO_batch_1

description: single cell from heart


title: C4-6_cKO_batch_1

description: single cell from heart


title: C4-8_cKO_batch_1

description: single cell from heart


title: C5-1_cKO_batch_1

description: single cell from heart


title: C5-2_cKO_batch_1

description: single cell from heart


title: C1-6_cKO_batch_1

description: single cell from heart


title: C5-4_cKO_batch_1

description: single cell from heart


title: C2-7_cKO_batch_1

description: single cell from heart


title: C3-1_cKO_batch_1

description: single cell from heart


title: C5-5_cKO_batch_1

description: single cell from heart


title: C2-8_cKO_batch_1

description: single cell from heart


title: C5-6_cKO_batch_1

description: single cell from heart


title: C3-8_cKO_batch_1

description: single cell from heart


title: C5-7_cKO_batch_1

description: single cell from heart


title: C5-8_cKO_batch_1

description: single cell from heart


title: C6-3_cKO_batch_1

description: single cell from heart


title: C6-6_cKO_batch_1

description: single cell from heart


title: C6-2_cKO_batch_1

description: single cell from heart


title: C6-4_cKO_batch_1

description: single cell from heart


title: C4-7_cKO_batch_1

description: single cell from heart


title: C6-8_cKO_batch_1

description: single cell from heart


title: C6-7_cKO_batch_1

description: single cell from heart


title: C7-6_cKO_batch_2

description: single cell from heart


title: C8-1_cKO_batch_2

description: single cell from heart


title: C6-1_cKO_batch_1

description: single cell from heart


title: C6-5_cKO_batch_1

description: single cell from heart


title: C7-2_cKO_batch_2

description: single cell from heart


title: C7-7_cKO_batch_2

description: single cell from heart


title: C7-8_cKO_batch_2

description: single cell from heart


title: C7-5_cKO_batch_2

description: single cell from heart


title: C5-3_cKO_batch_1

description: single cell from heart


title: C8-4_cKO_batch_2

description: single cell from heart


title: C8-8_cKO_batch_2

description: single cell from heart


title: C8-6_cKO_batch_2

description: single cell from heart


title: C9-2_cKO_batch_2

description: single cell from heart


title: C9-1_cKO_batch_2

description: single cell from heart


title: C9-3_cKO_batch_2

description: single cell from heart


title: C8-5_cKO_batch_2

description: single cell from heart


title: C9-5_cKO_batch_2

description: single cell from heart


title: C7-3_cKO_batch_2

description: single cell from heart


title: C9-4_cKO_batch_2

description: single cell from heart


title: C7-1_cKO_batch_2

description: single cell from heart


title: W10-1_WT_batch_2

description: single cell from heart

value: wild type


title: C8-3_cKO_batch_2

description: single cell from heart


title: W10-2_WT_batch_2

description: single cell from heart


title: W10-4_WT_batch_2

description: single cell from heart


title: W10-6_WT_batch_2

description: single cell from heart


title: W10-3_WT_batch_2

description: single cell from heart


title: W10-7_WT_batch_2

description: single cell from heart


title: W10-5_WT_batch_2

description: single cell from heart


title: W10-8_WT_batch_2

description: single cell from heart


title: W11-2_WT_batch_2

description: single cell from heart


title: W11-4_WT_batch_2

description: single cell from heart


title: W11-6_WT_batch_2

description: single cell from heart


title: W11-5_WT_batch_2

description: single cell from heart


title: W1-1_WT_batch_1

description: single cell from heart


title: W11-1_WT_batch_2

description: single cell from heart


title: W1-2_WT_batch_1

description: single cell from heart


title: W11-7_WT_batch_2

description: single cell from heart


title: W11-8_WT_batch_2

description: single cell from heart


title: W12-6_WT_batch_2

description: single cell from heart


title: W12-5_WT_batch_2

description: single cell from heart


title: W12-2_WT_batch_2

description: single cell from heart


title: W12-3_WT_batch_2

description: single cell from heart


title: W12-7_WT_batch_2

description: single cell from heart


title: W12-8_WT_batch_2

description: single cell from heart


title: C9-6_cKO_batch_2

description: single cell from heart


title: W1-3_WT_batch_1

description: single cell from heart


title: W1-6_WT_batch_1

description: single cell from heart


title: W1-5_WT_batch_1

description: single cell from heart


title: W1-7_WT_batch_1

description: single cell from heart


title: W1-8_WT_batch_1

description: single cell from heart


title: W2-1_WT_batch_1

description: single cell from heart


title: C9-8_cKO_batch_2

description: single cell from heart


title: W2-5_WT_batch_1

description: single cell from heart


title: W2-3_WT_batch_1

description: single cell from heart


title: W2-2_WT_batch_1

description: single cell from heart


title: W2-7_WT_batch_1

description: single cell from heart


title: W2-8_WT_batch_1

description: single cell from heart


title: W2-6_WT_batch_1

description: single cell from heart


title: W3-4_WT_batch_1

description: single cell from heart


title: W3-1_WT_batch_1

description: single cell from heart


title: W3-6_WT_batch_1

description: single cell from heart


title: W3-3_WT_batch_1

description: single cell from heart


title: W3-8_WT_batch_1

description: single cell from heart


title: W3-7_WT_batch_1

description: single cell from heart


title: W3-5_WT_batch_1

description: single cell from heart


title: W4-2_WT_batch_1

description: single cell from heart


title: W4-1_WT_batch_1

description: single cell from heart


title: W4-3_WT_batch_1

description: single cell from heart