title: EKOiE_2i_Sox2_pEsrrb_mNr5a2_1

tag: esrrb

tag: replicate


title: RNA_QA01

status: Public on May 04 2021

type: SRA

city: Atlanta

first: Rafick-Pierre

last: Sekaly

state: GA

address: 1750 Haygood Drive

department: Pathology

country: USA

institute: Emory University

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

library_source: transcriptomic

data_processing:
Library strategy: PathSeq metagenome
sorted cells/plasma: Raw sequencing reads were trimmed off adapter sequence contaminants using Trimmomatic v. 0.36
sorted cells/plasma: Mapped onto the Refseq Grch38 of the human genome using the STAR RNA-Seq aligner (version 2.5.3a)
sorted cells: Gene abundance was then estimated by counting using HTSeq (version 0.9.1)
sorted cells: Transcript counts were then normalized by TMM (Trimmed Mean of M-values by correcting for the library size
plasma: Unaligned paired-end reads were then assembled into contigs using Trinity
plasma: Trinity contigs were then aligned against HG38 again to further remove host-derived sequences with BLAST+. Trinity contigs that aligned to non-reference human sequences in the NCBI nucleotide database were also removed
plasma: Remaining contigs were then aligned against the NCBI nucleotide database and quantified with Salmon
plasma: Taxonomic information was assigned for each contig and transcripts per million (TPM) values were collapsed at the species level for each sample. TPM are normalized for sequencing read depth and length for each sample, allowing for a more accurate comparisons between proportion of reads mapping to the same gene in various samples
Genome_build: Human (Refseq Grch38) and Non-human (NCBI nucleotide database and quantified with Salmon)
Supplementary_files_format_and_content: xlsx data matrix files with normalized read counts (sorted cells; sample by transcript) or TPM (plasma; sample by species abundance)

molecule: total RNA

organism: human blood metagenome

source_name: Plasma

extract_protocol:
sorted cells: RNA was extracted from sorted cells lysed in RNAzol RT (MRC Inc., OH, USA), according to the manufacturer’s instructions. Briefly, 0.4 volume of sterile water was added to each lysate to allow aqueous and organic phase separation. Total RNA was then extracted from the aqueous phase by isopropanol precipitation. RNA pellets were washed with 70% ethanol and resuspended in sterile water. Extracted RNA was stored at -80°C until preparation of mRNA libraries. RNA yield and integrity were verified by microelectrophoresis using the High Sensitivity RNA ScreenTape Kit (Agilent) on the 2200 TapeStation system (Agilent).
plasma: Circulating total RNA and DNA were isolated from frozen plasma using RNAzolBD (MRC) according to the manufacturer’s recommendations.
sorted cells: mRNA libraries were constructed as described previously (Sandler et al., 2014) using the NEBNext Ultra RNA library preparation kit. Polyadenylated transcripts were purified with oligo-dT magnetic beads, fragmented, reverse transcribed using random hexamers and incorporated into barcoded cDNA libraries based on the Illumina TruSeq platform. Libraries were validated by microelectrophoresis on a 2100 Bioanalyzer system (Agilent), quantified with Kapa Library Quantification Kits (Roche), pooled and clustered on Illumina TruSeq v2 flow cells. Clustered flow cells were sequenced in 2x75 base paired-end runs on Illumina HiSeq 2000 and HiSeq 4000.
plasma: RNA fragmentation and reverse transcription using random hexamers, the obtained transcripts, as well as the isolated plasma DNA, were individually incorporated into barcoded cDNA libraries on the basis of the Illumina TruSeq platform. Libraries were validated by microelectrophoresis on a 2100 Bioanalyzer system (Agilent), quantified using Kapa Library Quantification Kits (Roche), pooled and clustered on Illumina patterned flow cells. Clustered flow cells were sequenced on an Illumina HiSeq 4000 in 75-base paired reads. To control for contamination, four water samples were processed along with plasma samples from nucleic acids extraction through sequencing.

tag: tissue

value: Plasma

value: No

value: Uganda

tag: cd4 count

tag: cd8 count

value: cd8 t cell ratio:1.27

value: Healthy


title: YV7.18B

city: Johns Island

first: Jeanine

last: Morey

state: SC

address: 3419 Maybank Hwy, Ste B

department: Conservation Medicine

institute: National Marine Mammal Foundation

data_processing:
The Illumina BCL output files were converted to fastq-sanger file format and sequence quality triming was performed on CyVerse Discovery Environment with the HTProcess-prepare_directories-and-run_fastqc-0.1 and HTProcess_trimmomatic_0.33 apps.  The following Trimmomatic parameters were used: ILLUMINACLIP:TruSeq3-SE.fa 2:30:10; LEADING:10; TRAILING:10; SLIDINGWINDOW:4:20; HEADCROP:6; MINLEN:36.
Reads were mapped to the Tursiops truncatus genome, NIST Tru_tru v1 (GCF_001922835.1), on CyVerse Discovery Environment with the HTProcess_Tophat-2.1.1 app using Bowtie as the alignment engine. Sequences annotated as hemoglobin were masked from alignment.
Read counts as FPKM (fragments per kilobase of trnascript per million mapped reads) were generated on CyVerse Discovery Environment with the HTProcess_Cufflinks-2.2.1 app with the genome as a reference. Sequences annotated as hemoglobin were masked from analysis.
Genome_build: NIST Tur_tru v1
Supplementary_files_format_and_content: Processed data is supplied in a single file.  The first column, "locus", contains the id/location from the NIST Tur_tru v1 genome.  The remaining colums contain the FPKM values for each sample as generated by Cufflinks.

organism: Tursiops truncatus

source_name: blood

extract_protocol:
Whole blood RNA was extracted using a PAXgene Blood RNA Kit (Qiagen).
Libraries were constructed using a NEBNext ultra Directional RNA Library Prep kit for Illumina and indexed with the NEBNextMultiplex Oligos for Illumina

value: blood

tag: Sex

value: Female

tag: location

value: Barataria Bay, LA

tag: sampling date

tag: fb field id


title: A2 RNA-Seq T21 blood cells

city: Bologna

first: Allison

last: Piovesan

address: Via Belmeloro 8

department: Department of Experimental, Diagnostic and Specialty Medicine

country: Italy

institute: University of Bologna

description:
Trisomy 21
A2_T21

data_processing:
The CASAVA 1.8.2 version of the Illumina pipeline was used to processed raw data for both format conversion and de-multiplexing.
Raw sequencing data were processed with BBDuk (https://jgi.doe.gov/data-and-tools/bbtools/) in order to perform trimming and clipping. Bases with a quality score less than 25 were removed as well as reads shorten than 35 nucleotides. The quality of the reads, before and after trimming, was checked with the software FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
High-quality reads were mapped against the GRCh38 human reference genome, downloaded from Ensembl (Cunningham et al., 2019), with the software STAR (version 2.5.2b, https://github.com/alexdobin/STAR). Read summarisation was performed with featureCounts (http://subread.sourceforge.net/), only reads with a mapping quality higher than 30 were used for this scope.
The option -s 2 was used to indicate that the libraries are strand-specific. The resulting table was imported in R, and the package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html) was used to calculate fragments per kilobase million (FPKM) values.
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: Blood cells

extract_protocol:
Total RNA extraction was performed with the method of Chomczynski and Sacchi. One or if necessary two purification steps were performed using RNA Clean & Concentrator-5 Kit in order to remove possible genomic DNA contamination and to reach the minimum concentration of 50 ng/μL.
TruSeq Stranded Total RNA with Ribo-Zero Gold (Illumina, San Diego, CA) was used for library preparation following the manufacturer's instructions, starting with 200 ng of RNA as input.

treatment_protocol: Blood samples from T21 and normal control recruited donors were collected in ethylenediaminetetraacetic acid (EDTA)-coated blood collection tubes, kept at room temperature and treated within two hours from blood collection. Each sample was transferred into a new tube, and plasma fraction was isolated by centrifugation at 1200 g for 10 min, while 5 mL of denaturing solution was added to the remaining blood fraction including the red blood cells and all the buffy coat, and stored at -20°C until RNA extraction.

value: Male

value: Blood cells (buffy coat and red blood cells)

tag: age (years)

tag: disease state

value: Down syndrome


title: YV5.917B


title: EKOiE_2i_Sox2_mEsrrb_pNr5a2_1

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

country: France

institute: Institut Pasteur

library_source: genomic

data_processing:
RNA-seq: Stranded paired end RNA-seq reads were aligned to the mm10 genome using STAR and quantified by RSEMusing the RSEM-STAR pipeline, with additional options "--seed 1618 --calc-pme --calc-ci --estimate-rspd --forward-prob 0.0 --paired-end".
ChIP-seq: Paired reads were trimmed by aligning read pairs to discover regions of reverse complementarity surrounded by adapters. Alignment and trimming were performed with the BioSequences package for Julia 0.6 Reads were aligned with Bowtie2 to the mm10 genome, with options "-k 10". Reads were additionally filtered for those with a single discovered alignment (in Bowtie2 "k" mode this is mapping quality = 255) and an edit distance less than 4. Duplicate reads (those aligning with same left-right coordinate) were collapsed to one. BigWig files were generated from whole fragment piles and normalised to RPM.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: tab-delimited table with TPM for all genes
Supplementary_files_format_and_content: RNA-seq: tab-delimited table with estimated raw counts for all genes
Supplementary_files_format_and_content: ChIP-seq: bigwig files

molecule: genomic DNA

organism: Mus musculus

source_name: embryonic stem cell

growth_protocol: ES cells were cultured on 0.1% gelatine (SIGMA, Cat# G1890-100G) in DMEM + GlutaMax-I (Gibco, Cat# 31966-021), 10% FCS (Gibco, Cat# 10270-098), 100 μM 2-mercaptoethanol (Gibco, Cat# 31350-010), 1× MEM non-essential amino acids (Gibco, Cat# 1140-035) and 10 ng×ml−1 recombinant LIF (MILTENYI BIOTEC, Cat# 130-099-895) (Referred to as FCS/LIF). Cells were passaged 1:10 every 2–3 days. For experiments in  2i/LIF, medium contained 1µM PD0325901 and 3 µM CHIR99021  (Axon Medchem Bv) - 0.5× DMEM/F12 (Gibco, Cat# 31331093), 0.5×Neurobasal (Gibco, Cat# 21103049), 0.5% N2 supplement 100× (Gibco, Cat# 17502048), 1% B27 supplement 50× (Gibco, Cat# 17504044), 10µg/mL Insulin (Sigma, Cat# I1882-100MG), 2 mM L-Glutamine (Invitrogen, Cat# 91139), 0.05% BSA (Sigma, Cat# A3311-10G), 100 μM 2-mercaptoethanol (Gibco, Cat# 31350-010), 10 ng/ml recombinant LIF (MILTENYI BIOTEC, Cat# 130-099-895) (Referred to as 2i/LIF). 2 days before RNA extraction or chromatin preparation, cell were washed in PBS and replated in the presence or absence of doxycycline (Sigma, Cat# I5148).

extract_protocol:
After trypsinisation, 10 million ES cells were crosslinked in 2 ml of freshly prepared PBS-DSG 2 mM at pH 7.0 (Sigma, Cat# 80424-5 mg) for 50 min at room temperature with occasional shaking. After pelleting and washing once in PBS, cells were incubated for 10 min in 2 ml PBS 1% formaldehyde (Thermo, Cat# 28908). Crosslinking was stopped with 0.125 mM glycine for 5 min at room temperature. Cells were pelleted and washed with ice-cold PBS. Cells were resuspended in 2 ml of swelling buffer (25 mM Hepes pH 7.95, 10 mM KCl, 10 mM EDTA) freshly supplemented with 1× protease inhibitor cocktail (PIC-Roche, Cat# 04 693 116 001) and 0.5% IGEPAL. After 30 min on ice, the suspension was passed 40 times in a dounce homogenizer. Cells were then centrifuged and resuspended in 300 μl of TSE150 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH8, 150 mM NaCl) buffer, freshly supplemented with 1× PIC. Samples were sonicated in 1.5 ml tubes (Diagenode) using a Bioruptor Pico (Diagenode) for 7 cycles divided into 30 s ON–30 s OFF sub-cycles at maximum power, in circulating ice-cold water. After centrifugation (30 min, full speed, 4 °C), the supernatant was either used immediately for immunoprecipitation or stored at −80 °C until use, generally within the month. Five microliters were used to quantify the chromatin concentration and check DNA size (typically 200–350 bp). Chromatin from 107 cells was used for each ChIP-seq after pre-clearing it for 3 hours rotating on-wheel at 4 °C in 300 μl of TSE150 containing 50 μl of protein G Sepharose beads (Sigma, Cat# P3296-5 ML) 50% slurry, previously blocked with BSA (500 μg×ml−1; Roche, Cat#  5931665103) and yeast tRNA (1 μg×ml−1; Invitrogen, Cat# AM7119). Immunoprecipitations with anti-Esrrb mouse monoclonal (1µg per 2 million cells, Perseus Proteomics, Cat# H6-705-00), anti-Nanog rabbit polyclonal (0.6 μg per 2 million cells, Cosmobio, Cat#  REC-RCAB001P); anti-Oct4 rabbit polyclonal (1 μg per 2 million cells, Abcam Cat # ab19857); anti-Sox2 rabbit polyclonal (1 μl per 2 million cells – concentration not specified, Active Motif  Cat#  39844); anti-Flag mouse monoclonal (1 μg per 2 million cells Sigma Cat# F3165) antibodies, were performed overnight rotating on-wheel at 4 °C in 500 μl of TSE150. 20 μl were set apart for input DNA extraction and precipitation. 25 μl of blocked protein G beads 50% slurry was added for 4 h rotating on-wheel at 4 °C. Beads were pelleted and washed for 5 min rotating on-wheel at room temperature with 1 ml of buffer in the following order: 3 × TSE150, 1 × TSE500 (as TSE150 but 500 mM NaCl), 1× washing buffer (10 mM Tris-HCl pH8, 0.25M LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 1 mM EDTA), and 2 × TE (10 mM Tris-HCl pH8, 1 mM EDTA). Elution was performed in 100 μl of elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8) for 15 min at 65 °C after vigorous vortexing. Eluates were collected after centrifugation and beads rinsed in 150 μl of TE-SDS1%. After centrifugation, the supernatant was pooled with the corresponding first eluate. For both immunoprecipitated and input chromatin, the crosslinking was reversed overnight at 65 °C, followed by proteinase K treatment, phenol/chloroform extraction and ethanol precipitation.
SPRI Bead preparation: 1 ml Sera-Mag™ Magnetic SpeedBeads™, carboxylated, 1 µm, 3 EDAC/PA5 (GE Healthcare Life Sciences, Cat# 65152105050250) were washed 3 times with a TE-Tween solution (10 mM Tris HCl pH 8, 1 mM EDTA, 0.05% Tween 20, pH 8.0) and resuspended in TE-Tween-20% PEG 8000 solution (10 mM Tris HCl pH 8, 1 mM EDTA, 0.05% Tween 20, pH 8.0).   End repair: Precipitated DNA was resuspended in 37.5µl of water and mixed with 2µl of 10mM dNTPs, 5µl of NEB T4 ligase buffer, 2.5µl of NEB T4 polymerase (Cat# M0203L), 0.5µl of NEB Klenow polymerase (Cat# M0210L) and 2.5µl of NEB T4 PNK (Cat# M0201L). Samples were incubated 30min at 20oC in a thermocycler. DNA was purified with SPRI beads: 90µl of SPRI bead suspension and 50µl isopropanol were added and samples transferred to a 96 well plate. After incubating for 5 min, the plate was put on a 96S Super Ring Magnet (Alpaqua, Cat# A001322), beads were allowed to separate completely, and the supernatant removed without disrupting the bead pellet. Beads were washed twice with 200µl of 70% Ethanol and the supernatant completely removed. DNA was eluted in 21µl of water.   A-Tailing: 20µl of sample were mixed with 2.5µl of NEB Buffer #2, 1µl of 5mM dATP, 1.5µl of NEB Klenow 3'-5' exo minus (Cat# M0212L), and incubated at 37oC for 30min in a thermocycler. DNA was purified with SPRI beads as before, but using a volume of 45µl of beads and 25µl isopropanol. DNA was elute in 20µl of water.   Adaptor ligation: 19µl of sample were mixed with 2.5µl of NEB T4 ligase buffer, 1.25µl of a 0.2µM solution of annealed adapters, and 2.5µl of NEB concentrated T4 ligase (Cat# M0202M) and incubated overnight at 16oC. DNA was purified with SPRI beads as before, but using a volume of 35µl of beads and no isopropanol, eluting in 20 µl of water. Adaptors were designed in house based on the structure of Illumina TruSeq™ indexed and forked adapters, modified to include extended indexes. 22.5µl each of 40µM ssDNA Barcoded and Universal adaptor solutions were mixed with 5µl of NEB buffer 2, and annealed in a thermocycler.   Barcoded adaptor:  5’P-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-Index -ATCTCGTATGCCGTCTTCTGCTTG.  5’P indicates the presence of a 5’phosphate group.   Universal adapter:   AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T.   * indicates the presence of a phosphorothioate bond between the last C and T.  Library amplification: 19.5 µl of sample were mixed with 1µl of a 1:10 dilution of Quant-iT Picogreen dye (Invitrogen, Cat# P11496), 25µl of KAPA HiFi HotStart 2× master Mix (Kapa Bioscience Cat# KK2502), 1µl of 10µM PCR 1.0 and 1µl of PCR 2.0 primers (See below). The amplification mix was distributed in two wells of a LightCycler 384 plate (Roche, Cat# 4729749001) and on a LightCycler 480 II instrument (Roche, Cat# 05015243001) using the following program: 1’ at 98°C; N cycles: 10” at 98°C; 20” at 64°C; 45” at 72°C. The number of cycles N was determined on real time by monitoring the fluorescence such that the amplification was stopped during the exponential phase. Samples were removed from the plate and purified with 70 µl SPRI beads without isopropanol, and eluting in 40µl of water. 1µl was used to measure the DNA concentration with a Qubit 3 and the provided reagents (Invitrogen, Cat#Q33218). 1 ng of DNA was used to check fragment size with a D1000 High Sensitivity Screentape and appropriate reagents (Agilent, Cat# 5067-5584, Cat# 5067-5585) on an Agilent 2200 Tapestation.  Library sequencing: the libraries were sequenced (paired-end 150bp reads) by Novogene Co. Ltd.

tag: cell type

value: EKOiE

tag: culture

tag: ChIP

tag: antibody

value: Active Motif, 39844

value: m

value: p


title: RNA_049v09005476

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: USA:Cleveland, Ohio

value: Yes

value: Responder (>3yr on ART)


title: RNA_049v09005288

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: Plasma

value: No

value: cd8 t cell ratio:1.4375


title: A1 RNA-Seq T21 blood cells

description:
Trisomy 21
A1_T21


title: EKOiE_2i_Oct4_pEsrrb_mNr5a2_1

value: Abcam, ab19857


title: YR3.617B

value: blood


title: YX1.917B

value: Female


title: EKOiE_2i_Oct4_pEsrrb_pNr5a2_1


title: EKOiE_2i_Oct4_mEsrrb_mNr5a2_1


title: E36_MS118_054

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: Single cell transcriptome of amplified cDNA from cynomolgus embryo at E36

data_processing:
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-e 0.1 -q 20 -n 2 -O 1 -m 30 -a CTCGAGGGCGCGCCGGATCC -g CTCGAGGGCGCGCCGGATCC -a AAAAAAAAAAAAAAAAAAAA -a TTTTTTTTTTTTTTTTTTTT". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the mouse genome, mm10, or cynomolgus monkey genome, macFas5.0,  and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels (RPM) by cufflinks-2.2.0 using the “—compatible-hits-norm”,  “—max-mle-iterations 50000", “—no-length-correction” and “—library-type fr-secondstrand” options and GRC38.p2 reference gene annotations with extended TTSs. For the reference gene annotations used in cufflinks, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Expression levels (read counts per gene) were also estimated with HTSeq v0.9.1.
Genome_build: mm10
Genome_build: macFas5.0
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include gene name, entrez_id and read count for each Sample

organism: Macaca fascicularis

source_name: Genital ridge of female cynomolgus embryo at E36

extract_protocol: RNA preparation, cDNA synthesis and amplification from single cells were perfomed essentially as reported in [Nakamura et al., Nucleic Acids Res. 2015 43(9):e60]. Library constructions for Illumina System were performed as reported in [Ishikura et.al., Cell Rep. 2016 17(10):3789-2804].

value: Genital ridge

tag: developmental stage

value: cGPCs


title: YR1.617B

value: Barataria Bay, LA


title: RNA_049v09005127

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: Non_responder (>3yrs on ART)


title: YN9.617B


title: RNA_049v09005059

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: YN3.617B


title: YN5.617B


title: E36_MS118_055


title: RNA_049v09004922

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: E36_MS115_052


title: E36_MS117_218


title: EKOiE_2i_Nanog_pEsrrb_pNr5a2_1

value: EKOiE

value: Nanog

value: Cosmobio, REC-RCAB001P


title: EKOiE_2i_Nanog_mEsrrb_mNr5a2_1

value: m


title: EKOiE_2i_Oct4_mEsrrb_pNr5a2_1

value: p


title: E36_MS117_220


title: E36_MS118_209


title: RNA_049v09005019

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: USA:Cleveland, Ohio

value: Yes


title: YK9.617B


title: EKOiE_2i_Nanog_pEsrrb_mNr5a2_1


title: RNA_049v09004905

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: Plasma

value: Responder (>3yr on ART)


title: YJ2.18B

value: Male


title: EKOiE_2i_Nanog_mEsrrb_pNr5a2_1


title: E36_MS115_100


title: YR5.617B


title: E36_MS115_059


title: RNA_049v09004852

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: No

value: cd8 t cell ratio:0.625


title: EKOiE_2i_Input_pEsrrb_mNr5a2_1

value: Input


title: E36_MS117_222

value: Genital ridge


title: RNA_049v09005271

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: YN1.617B

value: blood

value: Female


title: EKOiE_2i_Input_mEsrrb_mNr5a2_1


title: RNA_049v09004941

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: RNA_049v09004250

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: Non_responder (>3yrs on ART)


title: YF0.917B

value: Barataria Bay, LA


title: EKOiE_2i_Input_pEsrrb_pNr5a2_1

value: EKOiE


title: YF4.917B


title: E36_MS117_221

value: cGPCs


title: RNA_049v09004094

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: YF8.18B


title: EKOiE_2i_Esrrb_pEsrrb_mNr5a2_1

value: Esrrb

value: Perseus Proteomics, H6-705-00

value: m


title: EKOiE_2i_Esrrb_mEsrrb_mNr5a2_1


title: E36_MS118_202


title: YA6.18B


title: YA6.917B


title: RNA_049v09004086

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: USA:Cleveland, Ohio

value: Yes


title: RNA_049v09004037

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: Plasma


title: RNA_049v09003939

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: cd8 t cell ratio:0.385


title: E36_MS115_063


title: E36_MS118_080


title: EKOiE_2i_Esrrb_pEsrrb_pNr5a2_1

value: p


title: RNA_049v09003873

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: No


title: YA3.14B


title: EKOiE_2i_Esrrb_mEsrrb_pNr5a2_1


title: YA3.917B


title: E36_MS107_034


title: E36_MS117_210


title: YA2.917B

value: Male


title: RNA_049v09003832

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: cd8 t cell ratio:0.6


title: E14Tg2a-FLAG-Nr5a2_FCS_Nr5a2_pEsrrb_pNr5a2_2

value: FCS/LIF

value: Flag, Sigma Aldrich, F3165


title: EKOiE_2i_Input_mEsrrb_pNr5a2_1

value: Input


title: E36_MS107_032

value: Genital ridge


title: RNA_049v09003761

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: Non_responder (>3yrs on ART)


title: YA1.14B

value: blood

value: Female

value: Barataria Bay, LA


title: RNA_049v09003712

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: E36_MS115_039

value: cGPCs


title: E14Tg2a-FLAG-Nr5a2_FCS_Input_pEsrrb_pNr5a2_2


title: Y99.917B


title: E36_MS117_209


title: Y99.14B


title: RNA_049v09003658

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: USA:Cleveland, Ohio


title: RNA_049v09003655

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: cd8 t cell ratio:0.25

value: Yes


title: E36_MS115_104


title: Y98.617B


title: E14Tg2a-FLAG-Nr5a2_FCS_Esrrb_pEsrrb_pNr5a2_2

value: Esrrb

value: Perseus Proteomics, H6-705-00


title: Y96.617B


title: RNA_049v09003559

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: Plasma

value: No


title: E36_MS117_214


title: E14Tg2a-FLAG-Nr5a2_FCS_Esrrb_pEsrrb_pNr5a2_22

value: p


title: E36_MS118_079


title: E36_MS115_030


title: E14Tg2a-FLAG-Nr5a2_FCS_Nr5a2_pEsrrb_pNr5a2_17

value: FCS/LIF


title: E14Tg2a-FLAG-Nr5a2_FCS_Input_pEsrrb_pNr5a2_22


title: Y95.14B


title: Y94.617B

value: Male


title: E36_MS107_025

value: cPGCs


title: RNA_049v09003551

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: RNA_049v09003548

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: E14Tg2a-FLAG-Nr5a2_FCS_Input_pEsrrb_pNr5a2_17

value: Input


title: Y93.18B


title: RNA_049v09003504

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: Non_responder (>3yrs on ART)


title: E14Tg2a-FLAG-Nr5a2_FCS_Esrrb_pEsrrb_pNr5a2_17


title: E14Tg2a-FLAG-Nr5a2_FCS_Nr5a2_pEsrrb_pNr5a2_22

value: Flag, Sigma Aldrich, F3165


title: Y92.617B

value: blood


title: E37 (CS18) (MS136)

description: Single cell transcriptome from cynomolgus monkey embryo at E37

data_processing:
Raw data were demultiplexed with the mkfastq command in Cell Ranger (v2.1.0) with default setting to generate fastq files. The fastq files were processed with count command in Cell Ranger with default setting to map to the reference genome for cynomolgus monkeys (MacFas5.0) and obtain the read counts.
Genome_build: MacFas5.0
Supplementary_files_format_and_content: Cell Ranger output, TSV and matrix files

source_name: Cynomolgus monkey embryo E37

extract_protocol:
For preparation of E24 (CS11) embryos, the yolk sac and amnion were first carefully trimmed with forceps and ophthalmic scissors, and then the heart (and anterior tissues above the heart) and the posterior growth zone including the PS were removed.
For E28 (CS13) and E31 (CS14) embryos, the heart (and anterior tissues above the heart), and hindlimb (and tissues beneath the hindlimb) were removed, and then the urogenital ridge containing the mesonephros, CE and a portion of the proximal mesentery were isolated. For E37 embryos (CS18), similarly to E28/31 embryos, after the anterior and posterior tissues were removed, the urogenital ridges were isolated en bloc. Subsequently, most mesonephros and mesentery were trimmed, and tissues consisting of predominantly GR with an attached portion of mesonephros, putative adrenal glands and proximal mesentery were used for downstream sample processing.
Isolated embryonic fragments were washed twice with PBS and then minced with scissors in 500 μl of 0.1% trypsin/EDTA solution, then incubated for 9 min at 37°C with gentle pipetting every 3 min. After quenching of the reaction by addition of 500 μl of STO medium, cell suspensions were strained through a 70 µm nylon cell strainer and centrifuged for 220 g for 5 min.
Fragments of cynomolgus monkey embryos at E24 (CS11), E28 (CS13), E31 (CS14) and E37 (CS18) were used for scRNA-seq with a Chromium Single Cell 3ʼ Reagent Kit (v2 chemistry).
Cell pellets were resuspended in 0.1% BSA in PBS, counted, loaded into Chromium microfluidic chips and used to generate single cell gelbead emulsions with a Chromium controller (10x Genomics) according to the manufacturer’s protocol (Chromium Single Cell 3' Reagent Kits v3)

value: embryo


title: EKOiE_2i_pEsrrb_mNr5a2_3

molecule: polyA RNA

extract_protocol:
RNA extraction was performed with 500ul TRIzol (ThermoFisher, Cat# 15596026), according to the manufacturer’s protocol. To eliminate any genomic DNA contamination, this was followed by an additional DNAse I treatment (Qiagen, Cat# 79254) for 20min at 37°C followed by phenol:chloroform purification. RNAs were resuspended in Ultrapure DNAse/RNase Free Distilled Water (Thermo, Cat# 10977035).
Stranded, poly-A selected RNA-seq libraries were prepared and sequenced (paired-end 150bp reads) by Novogene Co Ltd.

treatment_protocol: 2 x 105 EKOiE or EKOiE NrKO ES cells were plated in individual wells of 6-well plates and cultured in the presence or absence of 1µg/ml doxycycline (Sigma, Cat# I5148) for 2 days

value: EKOiE

value: m


title: Y85.14B

value: Female

value: Barataria Bay, LA


title: E31 (CS14) (MS135)

description: Single cell transcriptome from cynomolgus monkey embryo at E31

source_name: Cynomolgus monkey embryo E31


title: RNA_049v09003500

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: USA:Cleveland, Ohio

value: Yes


title: RNA_049v09003328

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: Plasma


title: RNA_049v09003555

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: No


title: E28 (CS13) (MS141)

description: Single cell transcriptome from cynomolgus monkey embryo at E28

source_name: Cynomolgus monkey embryo E28


title: EKOiE_2i_mEsrrb_pNr5a2_3

value: p


title: RNA_049v09003137

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: Y91.14B


title: EKOiE_2i_pEsrrb_pNr5a2_3


title: Y83.14B


title: Y79.18B


title: RNA_049v09002867

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: Y66.18B


title: RNA_049v09002833

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: EKOiE_2i_pEsrrb_mNr5a2_2


title: EKOiE_2i_mEsrrb_mNr5a2_2


title: Sample 1

city: Sevilla

first: Lorena

last: Buono

state: Sevilla

address: Carretera de Utrera km 1

country: Spain

institute: CABD

data_processing:
Each sample was mapped against the index genome built from both oryLat2 and danRer10 assembly using Hisat2 (Kim et al., 2015)
The aligned read SAM files were assembled into transcripts and their abundance was estimated by Cufflinks  v2.2.1(Trapnell et al., 2012)
Genome_build: danRer10
Genome_build: oryLat2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (Cufflinks output)

organism: Oryzias latipes

source_name: Total embryo

growth_protocol: Zebrafish embryos were raised in E3 medium at 28C, medaka and zebraka embryos were raised in ERM at 28C.

extract_protocol:
RNA was extracted according to the Trizol manufacture’s instructions.
poly A selection for the RNA from the NEBnext Poly A module

treatment_protocol: Blastomeres from zebrafish were transplanted into isochronic medaka blastulae.

tag: Stage

value: Embryo

tag: strain

value: Cab


title: Sample 2


title: E24 (CS11) (MS140,MS156)

description: Single cell transcriptome from cynomolgus monkey embryo at E24

source_name: Cynomolgus monkey embryo E24


title: RNA_049v09002454

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: EKOiE_2i_mEsrrb_mNr5a2_3

tag: esrrb

tag: replicate


title: E36_MS107_024

tag: tissue

value: Genital ridge

value: cPGCs


title: Y65.13B


title: Y63.13B


title: RNA_049v09002295

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

tag: cd4 count

value: Non_responder (>3yrs on ART)


title: EKOiE_2i_mEsrrb_pNr5a2_2


title: Y57.13B

tag: Sex


title: RNA_049v09002214

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

tag: cd8 count


title: EKOiE_2i_mEsrrb_mNr5a2_1


title: Y56.14B

value: Male

tag: location

tag: sampling date


title: EKOiE_2i_pEsrrb_mNr5a2_1


title: RNA_049v09002210

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: RNA_049v09002100

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: cd8 t cell ratio:0.390625


title: Y50.14B

value: blood

tag: fb field id


title: EKOiE_2i_mEsrrb_pNr5a2_1

value: EKOiE


title: SAMPLE 8_chromatin pellet of Doxorubicin-induced NB4 cell [DOX-ch-2]

type: RNA

city: Guangzhou

first: Wen-Tao

last: Wang

state: Guangdong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

country: China

institute: sun yat sen university

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: B2M, 5S RNA, Hsp90ab1.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports ch/NP (i.e., NC-ch/NC-NP)ratios.

label: SYBR Green

extract_protocol: PCR assays were performed using the NB4 cells with/without Doxorubicin and using the Arraystar SYBR® Green qPCR platform following the Manufacturer’s instructions (ABI 7900 PCR, USA). Reverse transcription was performed from 10.5 μl total RNA using the rtStar™ First-Strand Synthesis Kit (Cat# AS-FS-001, Arraystar). Quantitative real-time PCR were performed (ABI 7900 PCR, USA) with 40 cycles at 95 oC for 10 seconds and 60 oC for 60 seconds.

treatment_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

tag: cell line

value: Human acute myeloid leukemia

tag: activation agent

value: Doxorubicin

tag: time

value: 4 hours


title: SAMPLE 7_chromatin pellet of Doxorubicin-induced NB4 cell [DOX-ch-1]

tag: cell type


title: RNA_049v09002049

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: USA:Cleveland, Ohio


title: SAMPLE 6_nucleoplasmic fraction of Doxorubicin-induced NB4 cell [DOX-NP-2]


title: EKOiE_FCS_mEsrrb_mNr5a2_2

tag: culture

value: FCS/LIF

value: m


title: RNA_049v09001995

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: Plasma

value: No

value: Yes

value: Responder (>3yr on ART)


title: EKOiE_2i_pEsrrb_pNr5a2_1

value: p


title: SAMPLE 5_nucleoplasmic fraction of Doxorubicin-induced NB4 cell [DOX-NP-1]


title: Y49.13B

value: Female

value: Barataria Bay, LA


title: SAMPLE 4_chromatin pellet of NB4 cell [NC-ch-2]

source_name: chromatin pellet of NB4 cell

value: control


title: RNA_049v09001920

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: Non_responder (>3yrs on ART)


title: Y45.13B

value: blood


title: Y47.13B


title: SAMPLE 3_chromatin pellet of NB4 cell [NC-ch-1]


title: EKOiE_2i_pEsrrb_pNr5a2_2

value: EKOiE


title: Y44.13B

value: Male


title: EKOiE_FCS_pEsrrb_mNr5a2_2


title: SAMPLE 2_nucleoplasmic fraction of NB4 cell [NC-NP-2]

source_name: nucleoplasmic fraction of NB4 cell

value: Human acute myeloid leukemia


title: EKOiE_FCS_mEsrrb_pNr5a2_2


title: RNA_049v09001894

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: Y43.13B


title: SAMPLE 1_nucleoplasmic fraction of NB4 cell [NC-NP-1]

value: 4 hours


title: 3-hsfa3-NTC

city: Potsdam

first: Isabel

last: Bäurle

address: Karl-Liebknecht-Str. 24-25

department: Institut für Biochemie und Biologie

country: Germany

institute: Universität Potsdam

description: non treated control

data_processing:
Paired-end reads for each sample were mapped against the Arabidopsis thaliana reference genome (TAIR10) using STAR version 2.5.1a.
Quantification at gene level was also done using STAR, --quantMode GeneCounts option.
Genome_build: TAIR10
Supplementary_files_format_and_content: Raw gene read counts for each sample.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Plants were grown under long-day conditions (16 h light/ 8 h dark).

extract_protocol:
Total RNA was extracted with RNeasy Plant Mini kit (Qiagen) and on-column DNase digest of RNA performed with RNase-Free DNase (Qiagen).
RNA quality control, library preparation, and sequencing were performed by BGI Genomics with the DNBseq platform generating 2x150 bp paired-end sequencing reads.

treatment_protocol: For heat treatment 4 d-old seedlings were exposed to 37°C for 1 h, 23°C for 90 min and 44°C for 45 min. After the indicated recovery times (4h, 28h, 52h) samples were harvested by flash-freezing.

tag: accession

tag: genotype

tag: treatment

value: NTC


title: EKOiE_FCS_pEsrrb_pNr5a2_2

value: FCS/LIF

tag: esrrb


title: 3-hsfa3-ACC+52h

description: 52h after acclimation


title: Y41.13B


title: RNA_049v09001880

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: USA:Cleveland, Ohio


title: Y34.14B


title: 3-hsfa3-ACC+4h

description: 4h after acclimatation


title: RNA_049v09001877

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: Plasma


title: RNA_049v09001901

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: No


title: 3-hsfa3-ACC+28h

description: 28h after acclimatation


title: EKOiE_FCS_pEsrrb_mNr5a2_1

value: m

tag: replicate


title: RNA_049v09001765

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

tag: tissue

value: Yes


title: RNA_049v09001848

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

tag: cd4 count


title: 3-hsfa2-ACC+52h

description: 52h after acclimation


title: Y30.13B

tag: Sex


title: Y26.13B


title: EKOiE_FCS_mEsrrb_pNr5a2_1

value: p


title: Y26.14B


title: Y19.917B

value: Female


title: EKOiE_FCS_pEsrrb_pNr5a2_1


title: EKOiE_FCS_mEsrrb_mNr5a2_1


title: RNA_049v09001761

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

tag: cd8 count


title: RNA_049v09001681

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: 3-hsfa2-ACC+4h

description: 4h after acclimatation


title: Y06.13B

tag: location

value: Barataria Bay, LA


title: 33.16B

value: Sarasota Bay, FL

tag: sampling date


title: RNA_049v09001619

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: Non_responder (>3yrs on ART)


title: RNA_049v09001654

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: 3-hsfa2-ACC+28h

description: 28h after acclimatation


title: 3-hsfa2-NTC

description: non treated control


title: RNA_049v09001588

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: 3-hsfa2,3-ACC+52h

description: 52h after acclimation

value: hsfa2 hsfa3


title: RNA_049v09001510

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: 3-hsfa2,3-ACC+28h

description: 28h after acclimatation


title: 3-hsfa2,3-NTC

description: non treated control


title: Y15.14B

value: blood

tag: fb field id


title: 3-Col-NTC

description: non treated control

value: wild type


title: RNA_049v09001514

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: 3-hsfa2,3-ACC+4h

description: 4h after acclimatation


title: 294.16B

value: Male


title: ∆wee1 treated  with 20mM H2O2_rep2

city: Kolkata

first: Geetanjali

last: Sundaram

address: 35 Ballugunje circular road

department: Biochemistry

country: India

institute: University of Calcutta

description: MT

data_processing:
Raw FASTQ Adapter Trimming and Quality filtering were performed using cutadapt
Mapping was done to the reference genome(downloaded from ensemblgenomes)using Hisat2 to evaluate sample quality
Differential expression analysis was done using Cuffdiff
Gene Ontology Annotations were assigned using Uniprot

organism: Schizosaccharomyces pombe

source_name: whole cell extract

growth_protocol: Cells were grown to mid-log phase at 300C in yeast extract with supplements (YES) medium

extract_protocol:
TRIzol ™ Reagent (Invitrogen) was used for RNA isolation and RNA was thereafter precipitated from the aqueous layer with isopropanol
TruSeq stranded mRNA sample preparation protocol was used

treatment_protocol: Mid-log phase cells were treated with 20mM H2O2 for 15mins, keeping untreated control separately

value: unicellular, eukaryote

value: h- wee1::ura4+ leu-32 ura4-D18

value: treated with 20mM H2O2 for 15mins


title: 292.16B


title: ∆wee1 treated  with 20mM H2O2_rep1

description: MT


title: 3-Col-ACC+52h

description: 52h after acclimation


title: 284.14B


title: 276.14B


title: 3-Col-ACC+4h

description: 4h after acclimatation


title: 268.14B


title: ∆wee1control_rep2

description: MC

value: untreated


title: 3-Col-ACC+28h

description: 28h after acclimatation


title: 2-hsfa3-NTC

description: non treated control

value: NTC


title: wild-type treated with 20mM H2O2_rep2

description: WT


title: 249.14B


title: wild-type treated with 20mM H2O2_rep1

description: WT


title: 2-hsfa3-ACC+52h

description: 52h after acclimation


title: 223.16B


title: 209.16B


title: 2-hsfa3-ACC+28h

description: 28h after acclimatation


title: wild-type control_rep2

description: WC


title: wild-type control_rep1

description: WC


title: 197.14B


title: ∆wee1control_rep1

description: MC


title: Th1-3rd_ACC1KO_RNA

city: Kisarazu

first: Toshio

last: Kanno

state: Chiba

address: 2-6-7 Kazusa-kamatari

institute: KAZUSA DNA Research Institute

description: Splenic Naïve CD4_T cells were stimulated under Th1 culture conditions (15 ng/ml IL-2, 10 ng/ml IL-12) for 5 days in vitro.

data_processing:
Read sequences (50 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using Bowtie (version 0.12.8) and TopHat (version 1.3.2).
Fragments per kilobase of exon per million mapped reads (FPKM) for each gene were calculated using Cufflinks (version 2.0.2).
Genome_build: mm10
Supplementary_files_format_and_content: Text files include FPKM values for each Sample

source_name: Five-day cultured Th1 cells generated from primary splenic Naïve CD4_T cells

extract_protocol:
Total cellular RNA was extracted with TRIzol reagent (Invitrogen).
TruSeq Stranded mRNA Library Preparation Kit (Illumina) was used according to the manufacturer's protocol.

treatment_protocol: TOFA, an inhibitor of ACC1, or IFNb was treated during the last three days.

tag: sample type

tag: strain

value: ACC1 KO


title: Th1-1st_IFNb_RNA

description: Splenic Naïve CD4_T cells were stimulated under Th1 culture conditions (15 ng/ml IL-2, 10 ng/ml IL-12) for 5 days in vitro. IFNb was treated during the last 3 days.

value: IFNb-treated Th1 cells


title: 255.16B


title: 2-hsfa2-NTC

description: non treated control


title: Th1-3rd_IFNb_RNA

growth_protocol: Splenic Naïve CD4_T cells were stimulated under Th1 culture conditions (15 ng/ml IL-2, 10 ng/ml IL-12) for 5 days in vitro.


title: 196.14B


title: 2-hsfa3-ACC+4h

description: 4h after acclimatation


title: GL2

city: Changzhou

first: Yu

last: Bin

address: 16 Dingxiang Road, Changzhou City, Jiangsu Province

institute: Changzhou Maternal And Child Health Care Hospital

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: placenta

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: placenta

tag: age

tag: disease state

value: elderly group


title: 2-hsfa2-ACC+52h

description: 52h after acclimation


title: GL1


title: Th1-1st_ACC1KO_RNA


title: 188.16B


title: Th1-3rd_TOFA_RNA

description: Splenic Naïve CD4_T cells were stimulated under Th1 culture conditions (15 ng/ml IL-2, 10 ng/ml IL-12) for 5 days in vitro. TOFA, an inhibitor of ACC1, was treated during the last 3 days.

value: ACC1 inhibitor (TOFA)-treated


title: 2-hsfa2-ACC+4h

description: 4h after acclimatation


title: P2

value: PE group


title: Th1-1st_TOFA_RNA


title: 178.16B

value: Sarasota Bay, FL


title: Th1-3rd_WT_RNA

value: control


title: 175.14B

value: Female


title: 2-hsfa2-ACC+28h

description: 28h after acclimatation


title: 2-hsfa2,3-NTC

description: non treated control

value: hsfa2 hsfa3


title: G1

value: GDM group


title: G2


title: Th1-1st_WT_RNA


title: 133.14B

value: blood


title: 3-bromopyruvate-resistant UM-UC-3 bladder cancer cell line (replicate #3-1)

type: genomic

city: Brussels

first: Cyril

last: Corbet

state: Select State/Prov.

address: Avenue Hippocrate 57

department: Institut de Recherche Expérimentale et Clinique (IREC)

country: Belgium

institute: UCLouvain

description:
SAMPLE 11
genomic DNA from 3BP-R UM-UC-3 #3-1

hyb_protocol: bisulphite-converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader following standard recommended Illumina scanner settings

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

label_protocol: Standard Illumina protocol

growth_protocol: Both parental and 3-BrPA-R UM-UC-3 cancer cells were grown in DMEM medium supplemented with heat-inactivated FBS and 1% FBS.

extract_protocol: genomic DNA was extracted and purified from UM-UC-3 cancer cells using Qiagen Dneasy kit according to standard instructions

treatment_protocol: 3-BrPA-R UM-UC-3 cancer cells were established upon long-term exposure to increasing concentrations (from 10 to 100 µM) of 3-bromopyruvate until resistance occurs.

tag: tumor type

value: bladder cancer

tag: cell line

tag: phenotype


title: TNF_24h_3

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

institute: Max-Planck-Institute for biochemistry

data_processing:
libraries were sequenced using Illumina NovaSeq 6000
After sequencing raw reads were filteredto discard reads with contaminations, low quality or adapter residues
The raw file were mapped to the mouse genome build GRCm38.90 using topHat v. 2.0.12
the reads were counted per gene using the featureCounts tool from the SubRead package (v. 1.6.3)
differentail expression analysis was done using EdgeR (v. 3.28.1)
Genome_build: GRCm38.90
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: TNF 24h BMDMs

growth_protocol: In the presence of M-CSF

extract_protocol:
RNA was harvested using Trizol reagent. Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies), and then diluted to 1 ng/μl before checking insert size on an Agilent 2100 and  quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity >2 nM).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10ng/ml IL4, IL13 and/or TNF

value: bone marrow

value: 8-10 weeks old

tag: treatment

value: 10ng/ml TNF 24h

tag: genotype/variation

value: wild-type


title: 2-hsfa2,3-ACC+52h

description: 52h after acclimation

tag: accession

tag: genotype


title: 2-hsfa2,3-ACC+4h

description: 4h after acclimatation


title: P1

tag: tissue


title: C1

value: control group


title: 2-hsfa2,3-ACC+28h

description: 28h after acclimatation


title: FLAG_PFDN5_rep1

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

institute: CABIMER

description:
Replicate 1
flag_pfdn5_flag_log2_readCount_r1.bw

data_processing:
Two biological replicates of the ChIP-seq data for each condition were primarily filtered using the FASTQ Toolkit program. Data were aligned using align function from Rsubread package, to map reads to the hg19 human reference genome using type = 1, TH1 = 2 and unique = TRUE parameters.
The downstream analysis was performed on bamfiles with duplicates removed using the samtools rmdup command
Bigwig files were created on Flag-PFDN5 over Flag for each replicate using bamCompare from deeptools package (v3.1.3) with --scaleFactorsMethod readCount --operation log2 parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

growth_protocol: Human HCT166 cells were maintained in McCoy's 5A modified medium supplemented with 10 % foetal bovine serum, 60 mg/l penicillin, and 100 mg/l streptomycin

extract_protocol: Human chromatin immunoprecipitation was carried out by fixation (10 minutes, 1 % formaldehyde, 37 ºC) and quenching (5 minutes, 2 % glycine), cells were lysed in lysis buffer (50 mM Tris-HCl, 10 mM EDTA, 1% SDS, pH 8.1 and protease inhibitors). Samples were then sonicated (Bioruptor, Diagenode) with cycles of 30 seconds for 15 minutes and the extracts of 300 bp obtained were cleared by centrifugation. Sonicated chromatin were incubated with 50 µl of magnetic dynabeads protein A o G (Life technology) coupled to anti-FLAG (Sigma, F3165, ChIP) antibody-.  Immunoprecipitated material was washed with three different wash buffers (wash buffer 1: 0.1 % (w/v) SDS; 1 % (v/v) Triton-X100; 2 mM EDTA; 20 mM Tris-HCl pH 8; 150 mM NaCl. Wash buffer 2: 0.1 % (w/v) SDS; 1 % (v/v) Triton-X100; 2 mM EDTA; 20 mM Tris-HCl pH 8; 500 mM NaCl. Wash buffer 3: 0.25 M LiCl; 1 % (v/v) NP-40; 1 % (w/v) Sodium deoxicholate; 1 mM EDTA; 10 mM Tris-HCl pH 8) and TE (10 mM Tris-HCl pH 8; 1 mM EDTA). DNA was eluted using elution buffer (1 % (w/v) SDS; 0.1 M NaHCO3) and, treated with 5 µl proteinase K (20 mg/ml) for 1 hour at 37 ºC. The resultant DNA was fenol-chloroform extracted, and precipitated.

tag: expression

tag: condition

value: ChIP


title: 3-bromopyruvate-resistant UM-UC-3 bladder cancer cell line (replicate #2-2)

description:
SAMPLE 10
genomic DNA from 3BP-R UM-UC-3 #2-2


title: native UM-UC-3 bladder cancer cell line (replicate #2-2)

description:
SAMPLE 4
genomic DNA from parental (native) UM-UC-3 #2-2

source_name: parental UM-UC-3 #2-2

value: parental


title: 1-hsfa3-NTC

description: non treated control

value: NTC


title: native UM-UC-3 bladder cancer cell line (replicate #3-1)

description:
SAMPLE 5
genomic DNA from parental (native) UM-UC-3 #3-1

source_name: parental UM-UC-3 #3-1


title: IL_24h_3

source_name: IL4/IL13 24h BMDMs

value: 10ng/ml IL4/IL13 24h


title: C2

value: placenta


title: TNF_24h_1


title: 3-bromopyruvate-resistant UM-UC-3 bladder cancer cell line (replicate #2-1)

description:
SAMPLE 9
genomic DNA from 3BP-R UM-UC-3 #2-1


title: 3-bromopyruvate-resistant UM-UC-3 bladder cancer cell line (replicate #1-2)

description:
SAMPLE 8
genomic DNA from 3BP-R UM-UC-3 #1-2


title: FLAG_input_rep1

description: Replicate 1

value: Flag

value: input


title: IL_24h_2


title: native UM-UC-3 bladder cancer cell line (replicate #3-2)

description:
SAMPLE 6
genomic DNA from parental (native) UM-UC-3 #3-2

source_name: parental UM-UC-3 #3-2


title: 2-Col-ACC+52h

description: 52h after acclimation

value: wild type


title: FLAG_PFDN5_input_rep1

description: Replicate 1


title: 2-Col-NTC

description: non treated control


title: spatial_transcriptomics_Tuberculoid 1

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Libraries were sequenced on an Illumina Nova-Seq (Illumina, San Diego, CA) as 150bp paired end reads and were converted from bcl files to fastq files using bcl2fastq.
After sequencing, the reads were aligned to the human genome (hg38), and the expression matrix was extracted using the spaceranger pipeline.
Seurat was then used to analyze the expression matrix. Specifically, the SCTransform function was used to scale the data and find variable genes with default parameters. PCA was applied for dimensional reduction. The FindTransferAnchors function was used to Find a set of anchors between the spatial-seq data and scRNA-seq data, which were then transferred from the scRNA-seq to the saptial-seq data using the TransferData function.  The predicted cell type composition for each spot was then used to cluster the spots by the k-means algorithm. The clusters were annotated based the average cell type prediction score across all the spots in the cluster.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene in every spot
Supplementary_files_format_and_content: *png = H&E staining image

source_name: Tuberculoid patient skin lesion

extract_protocol:
Skin samples were frozen in OCT medium and stored at -80°C until sectioning.
Optimization of tissue permeabilization was performed on 20-μm-thick sections using Visium Spatial Tissue Optimization Reagents Kit (10X Genomics, Pleasanton, CA, USA), which established an optimal permeabilization time to be 6 minutes. Samples were mounted onto a Gene Expression slide (10X Genomics), fixed in ice-cold methanol, stained with hematoxylin and eosin, and scanned under a microscope (Keyence, Itasca, IL, USA). Tissue permeabilization was performed to release the poly-A mRNA for capture by the poly(dT) primers that are precoated on the slide and include an Illumina TruSeq Read, spatial barcode, and unique molecular identifier (UMI). Visium Spatial Gene Expression Reagent Kit (10X Genomics) was used for reverse transcription to produce spatially barcoded full-length cDNA and for second strand synthesis followed by denaturation to allow a transfer of the cDNA from the slide into a tube for amplification and library construction. Visium Spatial Single Cell 3ʹ Gene Expression libraries consisting of Illumina paired-end sequences flanked with P5/P7 were constructed after enzymatic fragmentation, size selection, end repair, A-tailing, adaptor ligation, and PCR. Dual Index Kit TT Set A (10X Genomics) was used to add unique i7 and i5 sample indexes and generate TruSeq Read 1 for sequencing the spatial barcode and UMI and TruSeq Read 2 for sequencing the cDNA insert, respectively.

value: skin lesion

tag: diagnosis

value: Tuberculoid


title: IL_TNF_24h_3

source_name: IL4/IL13+TNF 24h BMDMs

value: 10ng/ml IL4/IL13+TNF 24h


title: 2-Col-ACC+4h

description: 4h after acclimatation


title: native UM-UC-3 bladder cancer cell line (replicate #1-2)

description:
SAMPLE 2
genomic DNA from parental (native) UM-UC-3 #1-2

source_name: parental UM-UC-3 #1-2

value: bladder cancer


title: native UM-UC-3 bladder cancer cell line (replicate #1-1)

description:
SAMPLE 1
genomic DNA from parental (native) UM-UC-3 #1-1

source_name: parental UM-UC-3 #1-1


title: IL_TNF_24h_1

value: bone marrow


title: 3-bromopyruvate-resistant UM-UC-3 bladder cancer cell line (replicate #3-2)

description:
SAMPLE 12
genomic DNA from 3BP-R UM-UC-3 #3-2


title: 1-hsfa3-ACC+52h

description: 52h after acclimation


title: IL_TNF_24h_2

value: 8-10 weeks old


title: 2-Col-ACC+28h

description: 28h after acclimatation


title: spatial_transcriptomics_Reversal reaction 3

source_name: Reversal reaction patient skin lesion

value: Reversal reaction


title: 1-hsfa3-ACC+4h

description: 4h after acclimatation


title: 3-bromopyruvate-resistant UM-UC-3 bladder cancer cell line (replicate #1-1)

description:
SAMPLE 7
genomic DNA from 3BP-R UM-UC-3 #1-1


title: spatial_transcriptomics_Reversal reaction 2


title: FLAG_rep1

description: Replicate 1


title: IL_24h_1

value: wild-type


title: native UM-UC-3 bladder cancer cell line (replicate #2-1)

description:
SAMPLE 3
genomic DNA from parental (native) UM-UC-3 #2-1

source_name: parental UM-UC-3 #2-1


title: IL_TNF_6h_3

source_name: IL4/IL13+TNF 6h BMDMs

value: 10ng/ml IL4/IL13+TNF 6h


title: 3C-HCT116-siNT-Rep1

city: Dallas

first: Nicholas

middle: K

last: Conrad

state: TX

address: 6000 Harry Hines Blvd

department: Microbiology

institute: UT Southwestern Medical Center

description: PAC-seq

data_processing:
Library strategy: PAC-seq
Adaptor and poly(A) tail trimming and measurement by fastp and cutadapt
Mapping to hg19 using HISAT2.
Genome coverage calculated by bedtools
DPAC was used to identify poly(A) sites and clusters and to generate counts of clusters (Routh 2019;  PMC6553543)
DESeq2 was used for differential analysis of poly(A) clusters.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files for each sample that used as input in gene count tables for DPAC and to calculate relative gene expression; Also included are two txt files of the gene counts and poly(A) cluster counts

source_name: 116-DDI cells

growth_protocol: Cells were grown under standard cell line conditions (DMEM media supplemented with Penn-strep/L-Gln/10%FBS) at 37C/5%CO2

extract_protocol:
Trizol was used to extract RNA, which was subsequently treated with RQ1 Dnase steps and phenol:chloroform:isoamyl alcohol (25:24:1) and chloroform extracted.
Libraries were prepared by ClickSeq Technologies based on the protocol of Routh et al 2017 (PMC5499544).
PAC-seq. The general strategy is that first-strand synthesis is  primed with a dT-p7-adaptor primer. The cDNA synthesis step is doped with an azide-containing chain-terminating nucleotide that is subsequently linked to a p5 sequencing adaptor with click chemistry.

treatment_protocol: siRNAs were transfected using RNAiMax and 24 hrs later the cells were split to allow doubling over the ensuing 72hrs (96 hrs total)

tag: cell type

value: derivative colorectal cancer cell line with MAT2A detained intron (intron 8) deleted

value: Nontargeting (NT) siRNA for 96 hr

tag: biological replicate


title: TNF_6h_3

source_name: TNF 6h BMDMs

value: 10ng/ml TNF 6h


title: 1-hsfa3-ACC+28h

description: 28h after acclimatation

source_name: seedlings


title: TNF_6h_2


title: 1-hsfa2-NTC

description: non treated control

value: NTC


title: spatial_transcriptomics_Lepromatous 2

source_name: Lepromatous patient skin lesion

value: Lepromatous


title: 3D-HCT116-siNUTD21-Rep1

description: PAC-seq

value: NUDT21/CFIm25  (siNUDT21) siRNA for 96 hr


title: spatial_transcriptomics_Reversal reaction 1


title: 1-hsfa2-ACC+52h

description: 52h after acclimation


title: TNF_6h_1


title: 1-hsfa2-ACC+4h

description: 4h after acclimatation


title: 3B-HCT116-siNUTD21-Rep1

description: PAC-seq

source_name: HCT116 cells

value: colorectal cancer cell line


title: Reversal reaction 5

data_processing:
Libraries were sequenced on an Illumina Nova-Seq (Illumina, San Diego, CA) as 50bp paired end reads and were converted from bcl files to fastq files using bcl2fastq.
The alignment was performed using Drop-seq pipelines (version 1.12).
Ambient RNA contamination was removed using SoupX (Young and Behjati, 2020).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

extract_protocol:
For each sample, a 4-mm punch biopsy was obtained following local anesthesia and was placed immediately into 10 mL of RPMI on ice. Initially, skin biopsies were incubated in 5mL of a 0.4% Dispase II solution (Roche Inc.) at 37°C for 1 hour with vigorous shaking. The dermis and epidermis were then carefully separated using forceps and transferred to separate tubes for additional processing. Epidermal samples were placed in 3mL of 0.25% Trypsin and 10U/mL DNAse for 30 minutes at 37°C. Trypsin was neutralized with 3mL of fetal calf serum (FCS), and the tissue was passed through a 70-micron nylon cell strainer which was washed with 5mL of RPMI. Epidermal cells were then pelleted at 300xg for 10 minutes and counted. Dermal samples were minced with a scalpel and incubated in a solution of 0.4% collagenase type II and 10 U/mL DNAse for 2 hours at 37°C with agitation. The cell suspension was passed through a 70-micron cell strainer and washed with 5mL of RPMI. Cells were pelleted at 300xg for 10 minutes, resuspended in 1mL of RPMI and counted. MACS enrichment for CD1a+ cells was performed for epidermis from three RR patients.
Once a single-cell suspension was obtained, we utilized Seq-Well, a massively-parallel scRNA-Seq platform for clinical samples, to capture the transcriptome of single cells. Full methods on implementation of Seq-Well are available in Gierahn et al. or on the Shalek Lab website (www.shaleklab.com). Briefly, 10-15,000 cells were loaded onto a functionalized-polydimethylsiloxane (PDMS) array preloaded with uniquely-barcoded mRNA capture beads (Chemgenes; MACOSKO-2011-10). After cells had settled into wells, the array was then sealed with a hydroxylated polycarbonate membrane with pore sizes of 10 nm, facilitating buffer exchange while confining biological molecules within each well. Following membrane-sealing, subsequent buffer exchange permits cell lysis, mRNA transcript hybridization to beads, and bead removal before proceeding with reverse transcription. The obtained bead-bound cDNA product then underwent Exonuclease I treatment (New England Biolabs; M0293M) to remove excess primer before proceeding with second strand synthesis.
Single cell RNA sequencing

value: skin biopsy


title: spatial_transcriptomics_Lepromatous 1

value: skin lesion


title: Reversal reaction 3


title: 2D-HCT116-siNUTD21-Rep1

description: PAC-seq


title: 1-hsfa2-ACC+28h

description: 28h after acclimatation


title: 2C-HCT116-siNT-Rep1

description: PAC-seq


title: IL_TNF_6h_1


title: 3A-HCT116-siNT-Rep1

description: PAC-seq


title: 1-hsfa2,3-NTC

description: non treated control

value: hsfa2 hsfa3


title: 1-hsfa2,3-ACC+52h

description: 52h after acclimation


title: Reversal reaction 4


title: Reversal reaction 2


title: 1-hsfa2,3-ACC+4h

description: 4h after acclimatation


title: IL_6h_1

source_name: IL4/IL13 6h BMDMs

value: 10ng/ml IL4/IL13 6h


title: 1-hsfa2,3-ACC+28h

description: 28h after acclimatation


title: 2A-HCT116-siNT-Rep1

description: PAC-seq


title: Ctrl_0h_3

source_name: Ctrl BMDMs


title: Ctrl_0h_2


title: 2B-HCT116-siNUTD21-Rep1

description: PAC-seq


title: 1-Col-NTC

description: non treated control

value: wild type


title: TNF_24h_2

source_name: TNF 24h BMDMs

value: bone marrow

value: 10ng/ml TNF 24h


title: 1-Col-ACC+52h

description: 52h after acclimation


title: IL_6h_3

value: 8-10 weeks old


title: Ctrl_0h_1

value: wild-type


title: 1D-HCT116-siNUTD21-Rep1

description: PAC-seq


title: Lepromatous 2


title: Reversal reaction 1


title: IL_6h_2


title: IL_TNF_6h_2

value: 10ng/ml IL4/IL13+TNF 6h


title: 1-Col-ACC+28h

description: 28h after acclimatation


title: Lepromatous 1


title: AGS_T_wo_L2715

status: Public on May 03 2021

city: Dresden

first: Claudia

last: Günther

address: Fetscherstr. 74

department: Klinik und Poliklinik für Dermatologie

institute: Universitätsklinikum Carl Gustav Carus

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: text files include RPKM values for each Samples

source_name: primary cells

growth_protocol: cell culture in 6well plates (5% CO2, 37°C)

extract_protocol:
RNA isolation native and 8 hours post UV using Rneasy Mini kit (Qiagen), DNAse digestion and cDNA synthesis
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: UVC irradiation 20J/m² dosage, cell cultivation (5% CO2, 37°C)

value: fibroblasts

value: no

value: aicardi goutieres syndrome - TREX1 deficiency


title: AGS_T_UV_L2716

value: UVC


title: 1A-HCT116-siNT-Rep1

description: PAC-seq

value: Nontargeting (NT) siRNA for 96 hr


title: Lepromatous 4


title: DDC

city: Ann Arbor

first: Guizhen

last: Zhao

state: MI

address: 2800 Plymouth Rd

department: Cardiovascular Center

institute: University of Michigan

data_processing:
The Cell Ranger Single Cell Software Suite, version 5.0.1 was used to perform sample de-multiplexing, barcode ad UMI processing, and single-cell 3′ gene counting. A detailed description of the pipeline and specific instructions to run it can be found at: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger.
Cloupe files were generated using the Cell Ranger 5.0.1 version. A description of the pipeline and instructions can be found at: https://support.10xgenomics.com/single-cell-gene-expression/software/visualization/latest/cellranger
The CellRanger count command was run on the individual Fastq datasets to produce expression data
R package Seurat v4.0 was used for cell filtration, normalization, principal component analysis, variable genes finding, clustering analysis, and Uniform Manifold Approximation and Projection (UMAP) dimensional reduction.Data were then log-normalized for the subsequent analyses. Principal component analysis (PCA) was used for dimension reduction, followed by clustering analysis in principal component analysis space using a graph-based clustering approach. UMAP was then used for the two-dimensional visualization of the identified clusters. The Seurat functions Vlnplot, FeaturePlot, DotPlot and DoHeatmap were used to visualize the gene expression with violin plot, feature plot, dot plot and heatmap, respectively. Markers for a specific cluster against all remaining cells were found by using the Seurat function FindAllMarkers.
Genome_build: Data were mapped to the pre-build mouse reference genome (mm10-2020-A), and the mapping rate of the reads mapped to genome for the two samples was more than 82%.
Supplementary_files_format_and_content: UMAP was then used for the two-dimensional visualization of the identified clusters. The Seurat functions Vlnplot, FeaturePlot, DotPlot and DoHeatmap were used to visualize the gene expression with violin plot, feature plot, dot plot and heatmap, respectively

source_name: mouse endothelial cells from aorta and heart

extract_protocol:
The aorta and heart of three mice in each group were digested with enzyme solution [2mg/ml collagenase I (Worthington Biochemical Corporation, LS004196), 60 U/ml DNase I (Roche Diagnostics, 1010459001)] at 37°C for 30-45 minutes with shaking. The cell suspension was filtered through a 40 μm strainer and enriched for endothelial cells using CD31 MicroBeads (Miltenyi Biotec, 130097418) according to the manufacturer’s instructions. The CD31-enriched single cell suspension was washed with WB and stained with Viable dye eFluor 450 (Thermo Fisher Scientific, 50-112-8817). Doublets were gated out prior to FACS sorting, and the viable cells were sorted into a collecting tube with DMEM containing 20% FBS. The cell suspensions were loaded on a 10x Genomics Chromium instrument to generate single cell gel beads in emulsion (GEMs).
Libraries were prepared using the Chromium Single cell 3' Reagent Kits v3.1 (CG000204): Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (PN-1000128), Chromium Single Cell 3’ Chip Kit v2 (PN-1000127) and Single Index Kit Set A (PN-1000213). Libraries were sequenced on an Illumina NovaSeq 6000 using paired-end sequencing with approximately >90% sequencing saturation.

value: fed DDC for 12 weeks

tag: disease

value: diabetic atherosclerosis

value: Ldlr null


title: Lepromatous 5

value: skin biopsy


title: 1-Col-ACC+4h

description: 4h after acclimatation


title: LE_T_wo_L2713

value: lupus erythematodes - TREX1 deficiency


title: WT2_UV_L2712

value: WT


title: WT2_wo_L2711


title: Lepromatous 3


title: 1C-HCT116-siNT-Rep1

description: PAC-seq

value: derivative colorectal cancer cell line with MAT2A detained intron (intron 8) deleted


title: WT1_wo_L2709


title: WT1_UV_L2710


title: Bulk_Human_Donor001_Treg

city: La Jolla

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Division of Vaccine Discovery

institute: La Jolla Institute for Allergy and Immunology

description: Whole Transcriptome Amplification (Smart-seq2 - Picelli et al.2014)

data_processing:
Bulk RNA–seq data were mapped against the human hg19 reference genome using TopHat (v2.0.9 , (--library-type fr-unstranded --no-coverage-search
Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
Genome_build: hg19
Supplementary_files_format_and_content: Bulk_Human_RawCounts.txt contains raw counts of sequencing reads obtained with HTSeq-count
Supplementary_files_format_and_content: Bulk_Human_TPM.txt contains Transcript per Million normalized counts

source_name: Human cancer tissue

growth_protocol: Cell types were isolated from tissue samples and directly sorted by Flow cytometry into trizol or lysis buffer. No particular cell growth procedure was required.

extract_protocol:
RNA-seq was performed as described previously by Seumois et al 2016 and Ganesan et al 2017 using smart-seq2 method  with 0.5ng of total RNA. Total RNA was purified using a miRNAeasy kit (Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
Barcoded Illumina sequencing libraries were constructed as per the protocol described by illumina (Nextera XT library preparation kit, Illumina).
DNA sequencing - Libraries were sequenced on the HiSeq2500 Illumina platform to obtain 50-bp single end reads and on the NovaSeq6000 to obtain 50-bp paired end reads (barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina)).

tag: cell type surface markers

value: Treg

tag: donor #


title: Bulk_Human_Donor001_Tfr

value: Tfr


title: Bap1flfl_rnapol2.XInput_ChIPseq_OHT_rep4

city: Oxford

first: Nadezda

middle: A

last: Fursova

address: South Parks Rd

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

description:
33_BAP1fl_RNAPII_input_TAM_rep4_S24
processed data file:
mESC_BAP1ff_TAM_rnapol2.XInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

data_processing:
For cChIP-seq, Bowtie 2 was used to align paired-end reads to the concatenated mouse and spike-in genome sequences (mm10+dm6 for native cChIP-seq for histone modifications; mm10+hg19 for cross-linked cChIP-seq for Polycomb factors and Pol II) with the “--no-mixed” and “--no-discordant” options. Non-uniquely mapping reads were discarded, and PCR duplicates were removed with Sambamba.
For visualization of cChIP-seq, the data were internally calibrated using dm6 or hg19 spike-in as described previously (Fursova et al. 2019). Briefly, uniquely aligned mm10 reads were randomly subsampled based on the total number of spike-in (dm6 or hg19) reads in each sample. To account for variations in the spike-in cell mixing, we used the ratio of spike-in/mouse total read counts in the corresponding Input samples to correct the subsampling factors. After normalisation, read coverages across genomic regions of interest (RING1B peaks for H2AK119ub1, H3K27me3, RING1B and SUZ12 cChIP-seq, TSS ± 2.5 kb for H3K27ac, H3K4me3 and H3K4me1 cChIP-seq, or gene bodies for total Pol II, Ser5P- and Ser2P-Pol II cChIP-seq) were compared for individual biological replicates using multiBamSummary and plotCorrelation from deepTools. For each experimental condition, biological replicates correlated well (Pearson correlation coefficient > 0.9) and were merged for downstream analysis.
For comparative box plot analysis, genomic regions of interest were annotated with read counts from merged spike-in normalised replicates using multiBamSummary from deeptools ( “--outRawCounts”).
Genome_build: mm10; dm6; hg19
Supplementary_files_format_and_content: bigWig files showing the genome coverage for merged spike-in normalised biological replicates were generated using the pileup function from MACS2.
Supplementary_files_format_and_content: bed files containing genomic intervals that were defined as active promoters, active enhancers and intergenic active enhancers based on the high enrichment of ATAC-seq and H3K27ac cChIP-seq signal in untreated Bap1fl/fl cells and the overlap with a comprehensive set of gene annotations. H3K27ac-positive ATAC peaks overlapping with transcription start site (TSS) +/- 1 kb regions were considered to be active promoters, while H3K27ac-positive ATAC peaks located further than 1 kb away from TSS of genes were considered to be active enhancers. Active enhancers that didn't overlap with any gene bodies from our comprehensive set of gene annotations (intergenic active enhancers) were used for all the downstream analysis.
Supplementary_files_format_and_content: bed files containing coordinates for the mm10 genome segmentation using a 13-state ChromHMM model: *segments.bed is a BED4 file (chr, start, end, state name) used for read annotation and *dense.bed is a BED file used for visualisation in the UCSC Genome browser in the dense format (all genome annotations are shown on a single line with different states represented by different colors).

organism:
Homo sapiens
Mus musculus

source_name: mESCs with human HEK293T cells spike-in, tamoxifen-treated (96hr OHT), gDNA-seq

growth_protocol: Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor. ). Drosophila S2 (SG4) cells were grown adhesively at 25°C in Schneider’s Drosophila Medium (Life Technologies), supplemented with 1x penicillin-streptomycin solution (Life Technologies) and 10% heat-inactivated fetal bovine serum (Labtech).

extract_protocol:
For RING1B and SUZ12 cChIP-seq, 5×107 mouse ESCs (untreated and OHT-treated) were crosslinked in 10 ml 1x PBS with 2 mM DSG (Thermo Scientific) for 45 minutes at 25°C, and then with 1% formaldehyde (methanol-free, Thermo Scientific) for a further 15 minutes. Crosslinking was stopped by quenching with 125 mM glycine. Crosslinked ESCs were mixed with 2×106 human HEK293T cells, which have been similarly double-crosslinked, and incubated in lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton-X100, 1x PIC (Roche)) for 10 minutes at 4˚C. Released nuclei were washed (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x PIC (Roche)) for 5 minutes at 4˚C. Chromatin was then resuspended in 1 ml of sonication buffer (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine, 1x PIC (Roche)) and sonicated for 30 minutes using the BioRuptor Pico (Diagenode), shearing genomic DNA to an average size of 0.5 kb. Following sonication, TritonX-100 was added to a final concentration of 1%, followed by centrifugation at 20,000 g for 10 min at 4°C to collect the clear supernatant fraction. For cChIP-seq for Pol II and its phosphorylated forms, 5×107 ESCs (untreated and OHT-treated) were crosslinked in 10 ml 1x PBS with 1% formaldehyde (methanol-free, Thermo Scientific) for 10 min at 25°C and then quenched by addition of 125 mM glycine. Cross-linked ESCs were mixed with 2×106 human HEK293T cells, which have been similarly single-crosslinked, and then incubated in FA-lysis buffer (50 mM HEPES pH 7.9, 150 mM NaCl, 2 mM EDTA, 0.5 mM EGTA, 0.5% NP40, 0.1% sodium deoxycholate, 0.1% SDS, 10 mM NaF, 1 mM AEBSF, 1×PIC) for 10 min at 4˚C. Chromatin was sonicated for 30 min using the BioRuptor Pico (Diagenode), followed by centrifugation at 20,000 g for 10 min at 4°C to collect the clear supernatant fraction.  For RING1B and SUZ12 ChIP, sonicated chromatin was diluted 10-fold with ChIP dilution buffer (1% Triton-X100, 1 mM EDTA, 20 mM Tris-HCl pH 8, 150 mM NaCl, 1xPIC). For Pol II ChIP, 300 ug of chromatin per one IP was diluted in FA-lysis buffer up to a final volume of 1 ml. Diluted chromatin was pre-cleared for 1 hr using Protein A agarose beads (Repligen) that were pre-blocked with 1 mg/ml BSA and 1 mg/ml yeast tRNA. For each ChIP reaction, 1 ml of diluted and pre-cleared chromatin was incubated overnight with the appropriate antibody, anti-RING1B (CST, D22F2, 3 ul), anti-SUZ12 (CST, D39F6, 3 ul), anti-Rpb1-NTD (CST, D8L4Y, 15 μl) as a measure of total Pol II levels, anti-Rpb1-CTD-Ser5P (CST, D9N5I, 12.5 μl) and anti-Rpb1-CTD-Ser2P (CST, E1Z3G, 12.5 μl) as a measure of Pol II phosphorylation levels. To capture antibody-bound chromatin, ChIP reactions were incubated with pre-blocked protein A agarose beads (Repligen) for 2 hr (RING1B and SUZ12) or 3 hr (Pol II) at 4°C. For RING1B and SUZ12, ChIP washes were performed as described previously (Farcas et al. 2012). For Pol II, washes were performed with FA-Lysis buffer, FA-Lysis buffer containing 500 mM NaCl, DOC buffer (250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 2 mM EDTA, 10 mM Tris-HCl pH 8), followed by two washes with TE buffer (pH 8). ChIP DNA was eluted in elution buffer (1% SDS, 0.1 M NaHCO3) and cross-linking was reversed overnight at 65oC with 200 mM NaCl and 2 ul RNase A (Sigma). Matched input samples (10% of original ChIP reaction) were treated identically. The following day, ChIP samples and inputs were incubated with Proteinase K (Sigma) for at least 1.5 hr at 56°C and purified using ChIP DNA Clean and Concentrator Kit (Zymo Research).  For native cChIP-seq for H2AK119ub1, H3K27me3, H3K27ac, H3K4me3, and H3K4me1, 5×107 mouse ESCs (untreated and OHT-treated) were mixed with 2×107 Drosophila SG4 cells in 1x PBS. Mixed cells were pelleted and nuclei were released by resuspending in ice-cold lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 5 mM sodium butyrate, and 5 mM N-ethylmaleimide). Nuclei were then washed and resuspended in 1 ml of MNase digestion buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.25 M sucrose, 3 mM CaCl2, 10 mM sodium butyrate, 10 mM N-ethylmaleimide, and 1x PIC (Roche)). Each sample was incubated with 200 units of MNase (Fermentas) at 37°C for 5 min, followed by the addition of 4 mM EDTA to halt MNase digestion. Following centrifugation at 1500 g for 5 min at 4°C, the supernatant (S1) was retained. The remaining pellet was incubated with 300 µl of nucleosome release buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2 mM EDTA, 10 mM sodium butyrate, 10 mM N-ethylmaleimide, and 1x PIC (Roche)) at 4°C for 1 hr, passed five times through a 27G needle using a 1 ml syringe, and spun at 1500 g for 5 min at 4°C. The second supernatant (S2) was collected and combined with the corresponding S1 sample from above. Digestion to mostly mono-nucleosomes was confirmed by agarose gel electrophoresis of purified S1/S2 DNA.  For ChIP, S1/S2 nucleosomes were diluted 10-fold in Native ChIP incubation buffer (70 mM NaCl, 10 mM Tris pH 7.5, 2 mM MgCl2, 2 mM EDTA, 0.1% TritonX-100, 10 mM sodium butyrate (for H3K27ac and H3K4me3 ChIPs), 10 mM N-ethylmaleimide, and 1xPIC (Roche)). Each ChIP reaction, 1 ml of diluted nucleosomes was incubated overnight at 4oC with the appropriate antibody, anti-H2AK119ub1 (CST, D27C4, 5 ul), anti-H3K27me3 (in-house, 5 ul), anti-H3K27ac (CST, D5E4, 3 μl), anti-H3K4me3 (in-house, 4 ul) or anti-H3K4me1 (CST, D1A9, 5 ul). Antibody-bound nucleosomes were captured for 1 hr at 4°C using protein A agarose (Repligen) beads, pre-blocked in Native ChIP incubation buffer supplemented with 1 mg/ml BSA and 1 mg/ml yeast tRNA, and collected by centrifugation. Immunoprecipitated material was washed four times with Native ChIP wash buffer (20 mM Tris pH 7.5, 2 mM EDTA, 125 mM NaCl, 0.1% Triton-X100) and once with TE buffer (pH 8). ChIP DNA was eluted using 100 ul of elution buffer (1% SDS, 0.1 M NaHCO3) for 30 min at room temperature, and then purified using ChIP DNA Clean and Concentrator Kit (Zymo Research). For each ChIP sample, DNA from a matched input control (corresponding to 10% of original ChIP reaction) was purified in the same way.
cChIP-seq libraries for both ChIP and Input samples were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries were analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR quantification using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads in biological triplicate or quadruplicate on Illumina NextSeq 500 platform.

treatment_protocol: To induce conditional removal of BAP1, Bap1fl/fl mESCs were treated with 800 nM 4-hydroxytamoxifen (OHT) for 96 hr.

value: mouse embryonic stem cells (mESCs)

value: Bap1fl/fl; Rosa26::ERT2-Cre

tag: clone

tag: strain

tag: replicate

tag: treatment agent

value: tamoxifen (OHT)

tag: treatment time point

value: 96 hr

tag: spike-in reference organism

value: Homo sapiens

tag: spike-in cell line

tag: ChIP

tag: antibody


title: Bap1flfl_rnapol2.XInput_ChIPseq_OHT_rep3

description:
31_BAP1fl_RNAPII_input_TAM_rep3_S28
processed data file:
mESC_BAP1ff_TAM_rnapol2.XInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: cell line

tag: genotype


title: 1B-HCT116-siNUTD21-Rep1

description: PAC-seq

value: colorectal cancer cell line

tag: treatment

value: NUDT21/CFIm25  (siNUDT21) siRNA for 96 hr


title: LE_T_UV_L2714

tag: cell type

value: fibroblasts

value: UVC

tag: disease state


title: Bap1flfl_rnapol2.XInput_ChIPseq_UNT_rep2

description:
15_BAP1fl_RNAPII_input_UNT_rep2_S16
processed data file:
mESC_BAP1ff_UNT_rnapol2.XInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with human HEK293T cells spike-in, untreated control, gDNA-seq

value: 0 hr


title: Bap1flfl_rnapol2.XInput_ChIPseq_UNT_rep4

description:
32_BAP1fl_RNAPII_input_UNT_rep4_S7
processed data file:
mESC_BAP1ff_UNT_rnapol2.XInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_rnapol2.XInput_ChIPseq_UNT_rep1

description:
13_BAP1fl_RNAPII_input_UNT_rep1_S25
processed data file:
mESC_BAP1ff_UNT_rnapol2.XInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_rnapol2.XInput_ChIPseq_OHT_rep2

description:
16_BAP1fl_RNAPII_input_TAM_rep2_S3
processed data file:
mESC_BAP1ff_TAM_rnapol2.XInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Chow

value: fed Chow for 12 weeks

tag: disease

value: no diabetic atherosclerosis

value: Ldlr null


title: Bap1flfl_RNAPol2S2P_ChIPseq_OHT_rep4

description:
27_BAP1fl_RNAPII_S2P_TAM_rep4_S21
processed data file:
mESC_BAP1ff_TAM_RNAPol2S2P_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with human HEK293T cells spike-in, tamoxifen-treated (96hr OHT), RNAPol2S2P ChIP-seq

value: Cell Signaling Technology (#E1Z3G)


title: Bap1flfl_rnapol2.XInput_ChIPseq_OHT_rep1

description:
14_BAP1fl_RNAPII_input_TAM_rep1_S29
processed data file:
mESC_BAP1ff_TAM_rnapol2.XInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_rnapol2.XInput_ChIPseq_UNT_rep3

description:
29_BAP1fl_RNAPII_input_UNT_rep3_S11
processed data file:
mESC_BAP1ff_UNT_rnapol2.XInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: shLuc

city: Moscow

first: Stepan

last: Nersisyan

address: Vavilova str 7

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

data_processing:
Quality of FASTQ files was assessed with FastQC v0.11.9. Adapters were trimmed with cutadapt v2.10. MiRNA count matrix was generated by miRDeep2 v2.0.1.2 with the use of bowtie v1.1.1 read mapper and GENCODE release 34 human genome.
Genome_build: GENCODE release 34 human genome
Supplementary_files_format_and_content: Read counts matrix

source_name: shLuc

growth_protocol: MDA-MB-231 breast cancer cell line was cultured in complete cell culture medium consisting of DMEM high glucose (Gibco) supplemented with 10% vol. fetal bovine serum (Gibco), 2 mM L-glutamine (PanEco), 1% vol. pencillin-streptomycin solution (Gibco). The cells were incubated in cell culture incubator (37 °C, 5% CO2).

extract_protocol:
RNA was extracted from frozen tumor samples using the miRNeasy Micro Kit (Qiagen) as recommended by the manufacturer.
Libraries for miRNA sequencing were prepared from total RNA samples using NEBNext Multiplex Small RNA Library Prep Kit for Illumina. Each sample was sequenced on the Illumina NextSeq 550 to generate single-end 50 nucleotide reads.

tag: genotype/variation

value: shLuc


title: Bap1flfl_RNAPol2S2P_ChIPseq_OHT_rep1

description:
05_BAP1fl_RNAPII_S2P_TAM_rep1_S10
processed data file:
mESC_BAP1ff_TAM_RNAPol2S2P_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_RNAPol2S2P_ChIPseq_UNT_rep4

description:
24_BAP1fl_RNAPII_S2P_UNT_rep4_S18
processed data file:
mESC_BAP1ff_UNT_RNAPol2S2P_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with human HEK293T cells spike-in, untreated control, RNAPol2S2P ChIP-seq


title: Bap1flfl_RNAPol2S2P_ChIPseq_OHT_rep2

description:
11_BAP1fl_RNAPII_S2P_TAM_rep2_S30
processed data file:
mESC_BAP1ff_TAM_RNAPol2S2P_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_RNAPol2S2P_ChIPseq_UNT_rep3

description:
18_BAP1fl_RNAPII_S2P_UNT_rep3_S13
processed data file:
mESC_BAP1ff_UNT_RNAPol2S2P_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_RNAPol2S5P_ChIPseq_UNT_rep4

description:
25_BAP1fl_RNAPII_S5P_UNT_rep4_S17
processed data file:
mESC_BAP1ff_UNT_RNAPol2S5P_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with human HEK293T cells spike-in, untreated control, RNAPol2S5P ChIP-seq

value: Cell Signaling Technology (#D9N5I)


title: Bap1flfl_RNAPol2S5P_ChIPseq_OHT_rep1

description:
06_BAP1fl_RNAPII_S5P_TAM_rep1_S2
processed data file:
mESC_BAP1ff_TAM_RNAPol2S5P_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with human HEK293T cells spike-in, tamoxifen-treated (96hr OHT), RNAPol2S5P ChIP-seq


title: Bap1flfl_RNAPol2S2P_ChIPseq_UNT_rep1

description:
02_BAP1fl_RNAPII_S2P_UNT_rep1_S8
processed data file:
mESC_BAP1ff_UNT_RNAPol2S2P_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_RNAPol2S5P_ChIPseq_OHT_rep2

description:
12_BAP1fl_RNAPII_S5P_TAM_rep2_S26
processed data file:
mESC_BAP1ff_TAM_RNAPol2S5P_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_RNAPol2S5P_ChIPseq_OHT_rep3

description:
22_BAP1fl_RNAPII_S5P_TAM_rep3_S19
processed data file:
mESC_BAP1ff_TAM_RNAPol2S5P_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_RNAPol2S2P_ChIPseq_UNT_rep2

description:
08_BAP1fl_RNAPII_S2P_UNT_rep2_S15
processed data file:
mESC_BAP1ff_UNT_RNAPol2S2P_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_RNAPol2S2P_ChIPseq_OHT_rep3

description:
21_BAP1fl_RNAPII_S2P_TAM_rep3_S32
processed data file:
mESC_BAP1ff_TAM_RNAPol2S2P_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_RNAPol2S5P_ChIPseq_OHT_rep4

description:
28_BAP1fl_RNAPII_S5P_TAM_rep4_S12
processed data file:
mESC_BAP1ff_TAM_RNAPol2S5P_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: tp1_2

city: bad nauheim

first: Stefan

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides (Bolger et al., 2014). Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 (GRCz11.98) using STAR 2.6.1d with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% (Dobin et al., 2013).
The number of reads aligning to genes was counted with FeatureCounts tool from the Subread package 1.6.5 (Liao et al., 2014).  Only reads mapping at least partially inside exons were admitted and aggregated per gene.
Differentially expressed genes were identified using DESeq2 version 1.26.0 (Love et al., 2014).
The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Genome_build: DanRer11
Supplementary_files_format_and_content: counts.matrix.norm_anno

organism: Danio rerio

source_name: FACS sorted tp1:EGFP+/myl7:DsRed2-NLS+ zebrafish cardiomyocytes

extract_protocol:
For RNA-seq, RNA was isolated from sorted myl7:EGFP+ and tp1:EGFP+/myl7:DsRed2-NLS+ ventricular zebrafish CMs using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
RNA amount was adjusted on number of isolated cells by FACS and approximately 1-2ng of total RNA was used as input for SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Clontech) for cDNA pre-amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine (Covaris).  Final Library Preparation was performed by Low Input Library Prep Kit v2 (Takara Clontech) and NEXTflexTM Rapid Directional qRNA-Seq Kit (Bioo Scientific) following manufacturers protocol.

tag: developmental stage

value: Adult

value: Cardiomyocytes

tag: tissue

value: Heart


title: myl7_2

source_name: FACS sorted myl7:EGFP+ zebrafish cardiomyocytes


title: tp1_1


title: Bap1flfl_RNAPol2S5P_ChIPseq_UNT_rep3

description:
19_BAP1fl_RNAPII_S5P_UNT_rep3_S22
processed data file:
mESC_BAP1ff_UNT_RNAPol2S5P_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

value: mouse embryonic stem cells (mESCs)

value: Bap1fl/fl; Rosa26::ERT2-Cre

tag: clone

tag: strain


title: HCT116_HiChip replicate 2

city: Tianjin

first: Bohan

last: Chen

address: NO.94 Weijin Road

institute: Nankai University

description: HCT116_HiChip replicate 2

data_processing:
Library strategy: HiChip
Valid fragment pairs and interaction matrix was generated using the HiC-Pro.
Then the interaction loop calling was performed using the hichipper
Genome_build: hg19
Supplementary_files_format_and_content: COAD_1.intra.loop_counts.bedpe including the interaction for the replicate 1
Supplementary_files_format_and_content: COAD_2.intra.loop_counts.bedpe including the interaction for the replicate 2

source_name: HCT116_HiChip replicate 2

growth_protocol: The colorectal cancer cell line HCT116 was obtained from the ATCC. HCT116 cells were incubated at 37°C with 5% CO2 and cultured in Dulbecco’s Modified Eagle Medium (GIBCO) medium, supplemented with 10% fetal bovine serum (FBS) (BI) and 1% penicillin-streptomycin (GIBCO).

extract_protocol: Briefly, cells were crosslinked with 1% formaldehyde and lysed. Then the chromatin was digested using MboI (NEB), and the restricted ends were religated by T4 ligase (NEB). Pelleted nuclei were dissolved in nuclear lysis buffer (50 mM Tris-HCl, pH 7.5, 10 mM EDTA, 1% SDS and protease inhibitors) and were sonicated and diluted in ChIP Dilution Buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 7.5, and 167 mM NaCl). Then immunoprecipitation was performed overnight at 4 °C by incubating H3K27ac antibody (Abcam) precoated on protein A-coated magnetic beads (Thermo Fisher Scientific). Immunocomplexes were washed three times each with low-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 7.5 and 150 mM NaCl), high-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 7.5 and 500 mM NaCl), LiCl buffer (10 mM Tris-HCl, pH 7.5, 250 mM LiCl, 1% NP-40, 1% Na-Doc and 1 mM EDTA). Beads were resuspended in DNA elution Buffer (50 mM NaHCO3 and 1% SDS). After elution, ChIP sample was incubated with 10mg/mL proteinase K 4 h at 55 °C. Then DNA was purified using AMPure XP Beads (Beckman). Streptavidin C1 beads were used to capture biotinylated DNA. QIAseq FX DNA Library Kits were used to generate the sequencing library and HiChIP libraries were size-selected to 300–700 bp using AMPure XP beads (Beckman) and subjected to 2 × 50-bp paired-end sequencing on Hiseq XTen (Illumina).

value: colon cancer

tag: chip antibody

value: H3K27ac antibody (Abcam)


title: Bap1flfl_RNAPol2S5P_ChIPseq_UNT_rep1

description:
03_BAP1fl_RNAPII_S5P_UNT_rep1_S27
processed data file:
mESC_BAP1ff_UNT_RNAPol2S5P_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: replicate

tag: treatment agent

tag: treatment time point

value: Homo sapiens


title: myl7_1


title: Bap1flfl_RNAPol2S5P_ChIPseq_UNT_rep2

description:
09_BAP1fl_RNAPII_S5P_UNT_rep2_S20
processed data file:
mESC_BAP1ff_UNT_RNAPol2S5P_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: spike-in reference organism

tag: spike-in cell line

tag: ChIP


title: shELOVL5

tag: cell line


title: HCT116_HiChip replicate 1

description: HCT116_HiChip replicate 1

source_name: HCT116_HiChip replicate 1


title: Bap1flfl_RNAPol2Total_ChIPseq_OHT_rep3

description:
20_BAP1fl_RNAPII_NTD_TAM_rep3_S1
processed data file:
mESC_BAP1ff_TAM_RNAPol2NTD_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with human HEK293T cells spike-in, tamoxifen-treated (96hr OHT), RNAPol2 (NTD) ChIP-seq

tag: genotype

value: tamoxifen (OHT)

value: 96 hr

tag: antibody

value: Cell Signaling Technology (#D8L4Y )


title: Bap1flfl_RNAPol2Total_ChIPseq_OHT_rep4

description:
26_BAP1fl_RNAPII_NTD_TAM_rep4_S9
processed data file:
mESC_BAP1ff_TAM_RNAPol2NTD_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: cell type


title: Bap1flfl_RNAPol2Total_ChIPseq_OHT_rep2

description:
10_BAP1fl_RNAPII_NTD_TAM_rep2_S14
processed data file:
mESC_BAP1ff_TAM_RNAPol2NTD_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_RNAPol2Total_ChIPseq_OHT_rep1

description:
04_BAP1fl_RNAPII_NTD_TAM_rep1_S5
processed data file:
mESC_BAP1ff_TAM_RNAPol2NTD_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_RNAPol2Total_ChIPseq_UNT_rep3

description:
17_BAP1fl_RNAPII_NTD_UNT_rep3_S23
processed data file:
mESC_BAP1ff_UNT_RNAPol2NTD_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with human HEK293T cells spike-in, untreated control, RNAPol2 (NTD) ChIP-seq

value: 0 hr


title: Bap1flfl_RNAPol2Total_ChIPseq_UNT_rep4

description:
23_BAP1fl_RNAPII_NTD_UNT_rep4_S31
processed data file:
mESC_BAP1ff_UNT_RNAPol2NTD_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_RNAPol2Total_ChIPseq_UNT_rep2

description:
07_BAP1fl_RNAPII_NTD_UNT_rep2_S4
processed data file:
mESC_BAP1ff_UNT_RNAPol2NTD_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_ring1b.suz12.XInput_OHT_rep3

description:
BAP1ff_rsXInput_TAM_rep3_S18
processed data file:
mESC_BAP1ff_TAM_ring1b.suz12.XInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_RNAPol2Total_ChIPseq_UNT_rep1

description:
01_BAP1fl_RNAPII_NTD_UNT_rep1_S6
processed data file:
mESC_BAP1ff_UNT_RNAPol2NTD_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw