title: Human fibroblast

city: Illkirch

first: Andrea

last: Riba

address: 1 rue Laurent Fries

country: France

institute: IGBMC

data_processing:
Image analysis, base calling and demultiplexing were performed using RTA 2.7.7 and Cell Ranger 3.0.1 mkfastq.
Alignment, barcode and UMI filtering and counting were performed using Cell Ranger 4.0.0 count and human reference GRCh38-2020-A (hg38 and Ensembl release 98).
Genome_build: hg38
Supplementary_files_format_and_content: Filtered (contains only detected cellular barcodes) feature-barcode matrix (each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)) in Market Exchange Format (MEX) and gzipped.
Supplementary_files_format_and_content: Gzipped tsv files with feature and barcode sequences corresponding respectively to row and column indices from the matrix.

growth_protocol: IMR90 primary human foetal lung fibroblast cells were cultured in DMEM 41966 (4,5g/l glucose) supplemented with 10% foetal calf serum, Penicilline 100 UI/ml and Streptomycine 100 µg/ml in 5% CO2 at 37°C. The cells were at passage 21 when performing the experiments.

extract_protocol:
GEMs were generated by combining barcoded gel beads, a RT master mix containing cells, and partitioning oil onto Chromium Chip G. Following full length cDNA synthesis and barcoding from poly-adenylated mRNA, GEM were broken and pooled before cDNA amplification by PCR using 11 cycles. After enzymatic fragmentation and size selection, sequencing library were constructed by adding Illumina (Paris, France) P5 and P7 primers as well as sample index via end repair, A tailing, adaptor ligation and PCR with 10 cycles. Library quantification and quality control was performed using Bioanalyzer 2100 (Agilent Technologies, Santa Clara CA).
Single cell 3 prime mRNA seq library were generated according to 10X Genomics User Guide Chromium NEXT GEM Single Cell 3' Reagent Kits v3.1 (P/N CG000204 Rev D).


title: d3-m6A-P7-rep1

status: Public on Apr 25 2022

type: SRA

city: Hangzhou

first: Jie

last: Cao

address: Zheda Road 38

department: Department of Polymer Science and Engineering

country: China

institute: Zhejiang University

library_source: transcriptomic

data_processing:
adapter, low quality reads and short reads were trimed with fastp v0.19.7 with following parameters: -f 10 -F 10 -x --detect_adapter_for_pe -l 25
clean reads were aligned with hg38 genome using hisat2 v2.1.0 with parameters: --rna-strandness RF
sam files were converted and sorted into bam files using samtools with parameters: samtools sort -@ 4 sam -o bam
bam files were counted using featureCounts
differentially expressed genes were obtained using a R package DESeq2
Assembly: hg38
Supplementary files format and content: txt file presents the counting result of bam files, csv file shows the tpm results used for heatmap,xlsx files mark the differentially expressed gene sets

molecule: total RNA

organism: Homo sapiens

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM)/high-glucose media(HyCloneSH30243.01) supplemented with 10% fetal bovine serum (FBS; Gibco 10270) , 1% 100× Pen Strep (HyClone SV30010) at 37 °C with 5 % CO2

extract_protocol:
total RNA was extracted with TRIZOL Reagent following protocol (thermofisher)
total RNA was used as input, and libraries were constructed following illumina's protocol. Briefly, polyA-RNA was first extracted using oligd(T) conjungated beads, fagmented into about 100 nt, reverse transcribed into cDNA and amplified by PCR.

treatment_protocol: 100mM d3-m6A was used as stock and added into DMEM at a final concentration of 500 μM, HeLa cells were incubated with d3-m6A containing DMEM for different time courses

tag: treatment

value: treated with d3-m6A for 168 hours

tag: cell line

value: HeLa


title: d3-m6A-P1-rep1

value: treated with d3-m6A for 24 hours


title: d3-m6A-P1-rep2


title: RNA-seq Adult Male hepatocytes 24

city: Newton

first: Ye

last: Zhang

state: MA

address: 39 Cout St, #6

country: USA

institute: NIBR

description: PPH treated with 50 nM of gimeracil w/ BSA

data_processing:
See details from Novogene official website. Briefly, 1)  Base calling with Illumina platform. 2) Reads, at QC step, with adapters, with N > 0.1% and with low qualities are removed. 3) STAR was used for mapping to ref genome. Raw count and FPKM was then generated.
Assembly: GRCh38.p12
Supplementary files format and content: Excel file include all sample raw counts at gene level

molecule: polyA RNA

source_name: Liver

extract_protocol:
Qiagen RNeasy kit according to manufacturer’s protocol
NEBnext Ultra RNA lib kit according to manufacturer’s protocol

tag: tissue

value: Liver

value: PHH

tag: cell type

value: Primary hepatocytes


title: d3-m6A-Ctrl-rep2

value: untreated


title: RNA-seq Adult Male hepatocytes 22

description: PPH treated with 0 nM of gimeracil w/ FFA


title: Tcf1/Lef1-deficient naive CD8, CTCF Cut&Run, rep2

city: washington dc

first: Shaoqi

last: Zhu

state: District of Columbia

address: 725 21st st nw

institute: The George Washington University

library_source: genomic

data_processing:
Library strategy: Cut&Run
The sequencing quality of Cut&Run libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bowtie2 (v2.2.5, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
For Cut&Run libraries, MACS2 (v2.1.1, Zhang et al., Genome Biol) was used for peaks calling. We used the criteria of a q value of < 0.05, 4 fold change at peak summit as identified binding sites.
Genome_build: mm9
Supplementary_files_format_and_content: narrowPeak

molecule: genomic DNA

organism: Mus musculus

source_name: CD8 T cells

extract_protocol:
Naïve CD8+ T cells were sort-purified from the spleen, and stimulated with IL-7 and IL-15 in vitro for 0 or 72 hrs. The live cells were permeabilized, and then incubated with CTCF antibody overnight, followed by incubation with Protein A/G-MNase, calcium-mediated MNase activation. The reaction was stopped and then genomic DNA fragments were extracted.
The DNA segments from CTCF Cut&Run were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-X platform.

tag: genotype

tag: time point

value: splenocytes

tag: cell phenotype

value: GFP+ TCRbeta+ CD62Lhi CD44lo-med CD8+


title: WT stim CD8 72h, CTCF Cut&Run, rep1

value: wild type


title: d3-m6A-Ctrl-rep1


title: RNA-seq Adult Male hepatocytes 20

description: PPH treated with 0 nM of gimeracil w/BSA


title: RNA-seq Adult Male hepatocytes 23

description: PPH treated with 50 nM of gimeracil w/ FFA


title: Tcf1/Lef1-deficient stim CD8 72h, CTCF Cut&Run, rep1


title: 4-HR_S20

city: Gothenburg

first: Ingrid

last: Wernstedt Asterholm

address: Box 432

country: Sweden

institute: University of Gothenburg

data_processing:
Quality assessment of the sequence reads was performed by generating QC statistics with FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc).
RNA-sequencing reads were filtered and trimmed with prinseq (0.20.3).
Mapping towards the mouse genome (mm10 from UCSC) was performed with the STAR aligner (2.4.0f) with default parameters.
Raw gene counts were generated with HTSeq (https://htseq.readthedocs.io/en/release_0.10.0/).
Supplementary files format and content: tab-delimited text files include counts for each sample

source_name: Control inguinal adipose tissue in HFD-fed mouse

extract_protocol:
RNA was harvested using ReliaPrep RNA Cell MiniPrep System (Promega Corporation, WI, U.S.A). The samples were enriched for RNA transcripts by depleting the ribosomal RNA (RiboMinus Technology, Thermo Fisher Scientific)
The concentrated samples were submitted to cDNA synthesis upon the adenylated 3’ ends were allowed to ligate with adapters, amplified and clustered on a chip (bridged PCR amplification).

value: inguinal adipose tissue

tag: strain

value: wildtype

value: high fat diet

tag: tumor status

value: Control inguinal adipose


title: 8-HR_S21


title: RNA-seq Adult Male hepatocytes 18

value: PPH treated with 0 nM of gimeracil w/BSA


title: RNA-seq Adult Male hepatocytes 17

description: PPH treated with 400 nM of gimeracil w/BSA


title: RNA-seq Adult Male hepatocytes 16

description: PPH treated with 200 nM of gimeracil w/ FFA


title: Tcf1/Lef1-deficient stim CD8 72h, CTCF Cut&Run, rep2


title: GO2_1

type: RNA

city: Toyoake

first: Eiji

last: Sugihara

state: Aichi

address: 1-98, Dengakugakubo, Kutsukake-cho,

country: Japan

institute: Fujita Health University

hyb_protocol: The Agilent array were hybridized and washed using the manufacturer's protocol.

scan_protocol: Agilent arrays were scanned using the Agilent Technologies Scanner G2505C.

data_processing: The data were normalized with 75 Percentile method

label_protocol: Cy3 labeled cRNA were prepared according to the standard Agilent protocol.

growth_protocol: ID8G and GO2 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 4% FBS as well as insulin (5 μg/ml), transferrin (5 μg/ml), and sodium selenite (5 ng/ml)  insulin in 5% CO2.

extract_protocol: RNA was extracted using Trizol reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions.


title: RNA-seq Adult Male hepatocytes 19

value: PPH treated with 50 nM of gimeracil w/ FFA


title: GO2_2


title: 2-HR_S18


title: RNA-seq Adult Male hepatocytes 21

description: PPH treated with 50 nM of gimeracil w/BSA


title: Tcf1/Lef1-deficient naive CD8, CTCF Cut&Run, rep1


title: ID8G_2


title: E_coli_WT_Rend_seq_MOPS_min_exp

city: Berlin

first: Lydia

last: Herzel

address: Takustr. 6

department: Biology, Chemistry and Pharmacy

country: Germany

institute: Freie Universität

data_processing:
RNA-seq and Rend-seq data processing and mapping was done as described in (Lalanne et al., Cell 2018; Parker et al., Cell Systems 2020). For 3’ end-seq in analogy to Rend-seq, 3’ end linker sequences were trimmed. To deal with non-template addition during reverse transcription, all reads were further trimmed with the fastx_trimmer of the fastxtoolkit/0.0.13 by 1nt at their 5’end and only reads of 15nt length or longer were kept for mapping with bowtie/1.2 using the options -v 0 -k 1. For further data analysis mapped data were transformed into bam-format and bedgraph-format using samtools/1.5 and bedtools/2.25.0. Coverage data include 3’ terminal single nucleotide counts per read. To identify 3’adenylated transcript ends, the unmapped reads were trimmed using cutadapt/1.16. First, 3’terminal CCAs were removed with the following settings: -a "CCA$" --minimum-length 15 -O 3 --trimmed-only. Second, A-tails of any length were trimmed (-a "A{38}" --minimum-length 15 -O 1 --trimmed-only). These trimmed reads were mapped and further converted with the same settings and code as untrimmed reads above. For total RNA 3’ end analysis mapped trimmed (i.e. A-tailed) and untrimmed 3’ end coverage profiles were summed.
Assembly: E. coli NC_000913.2, B. subtilis NC_000964.3
Supplementary files format and content: bedgraph-files, 3' most read position recorded in coverage files

organism: Escherichia coli

source_name: Bacteria

growth_protocol: E. coli cells were grown in LB, MOPS Complete or MOPS Minimal media supplemented with 0.2% Glucose. B. subtilis cells were grown in MCCG media (Parker et al., Cell Systems 2020). To harvest cells in exponential growth, cells were backdiluted from overnight cultures into the respective growth media to enable ~10 doublings at 37°C prior to harvest at an OD600 smaller or equal to 0.3 (Sezonov et al. J Bac 2007). To harvest cells in early stationary growth, cells were harvested shortly after growth had plateaued (harvest at OD600 2.8 for MOPS Complete and at OD600 2.26 for MOPS Minimal). For Kasugamycin treatment, Kasugamycin was added at a final concentration of 1mg/ml to cells at OD600 0.22 grown in MOPS Complete media. After 15 min treated and untreated cells were harvested for total RNA analysis.

extract_protocol:
Samples have been either extracted by RNAsnap (Stead et al., NAR 2012), Hot Phenol, RiboPure (ThermoFisher/Ambion), RNeasy (Qiagen) or Trizol, precipitated, Dnase treated and cleaned uo with RNA clean & concentrator columns (Zymo research).
RNA-seq for E. coli Δpnp, Δrnb, ΔpcnB and MG1655 wildtype was executed as described in (Parker et al., Cell Systems 2020). Rend-seq libraries were prepared as described in (Lalanne et al., Cell 2018) with 25s RNA fragmentation. For 3’ end sequencing the Rend-seq protocol was modified in a way that 3’ end ligation (5'_App/CTGTAGGCACCATCAAT/3ddC_3') was done preceding fragmentation for 2min. Final libraries were sequenced on Illumina HiSeq 2000 or NextSeq500 machines.
single-end RNA-seq

treatment_protocol: For total RNA analysis, 5ml of cells were transferred into 0.55ml of ice-cold stop solution (95:5 Ethanol:Phenol) in a 15ml conical tube, quickly inverted and spun at 3220g at 4°C for 5-10min. The supernatant was discarded and cell pellets flash-frozen in liquid nitrogen and stored at -80C until lysis and RNA extraction. For nascent RNA and polysome analysis, 250ml of cells were filter harvested at 37°C and scraped into liquid nitrogen (Johnson and Li, 2018). The cell paste was kept at -80°C until lysis and RNA extraction.


title: E_coli_WT_Rend_seq_MOPS_min_stat


title: E_coli_WT_Rend_seq_MOPS_comp_exp_rep2


title: RNA-seq Adult Male hepatocytes 15

description: PPH treated with 400 nM of gimeracil w/ FFA


title: E_coli_WT_Rend_seq_MOPS_comp_stat


title: RNA-seq Adult Male hepatocytes 12

value: PPH treated with 200 nM of gimeracil w/ FFA


title: ID8G_1


title: E_coli_WT_Rend_seq_MOPS_comp_exp_rep1


title: 8-HL_S15

source_name: Tumor-associated inguinal adipose tissue in HFD-fed mouse

value: Tumor-associated inguinal adipose


title: RNA-seq Adult Male hepatocytes 13

value: PPH treated with 400 nM of gimeracil w/BSA


title: 1-H-2_R_S17


title: 0-HR_S22


title: 3-HL_S13


title: E_coli_WT_3end_seq_MOPS_min_exp


title: E_coli_WT_3end_seq_MOPS_comp_stat


title: 3-H-2_R_S19


title: 4-H-2_L_S14


title: 1-HL_S11


title: RNA-seq Adult Male hepatocytes 14

description: PPH treated with 200 nM of gimeracil w/BSA


title: RNA-seq Adult Male hepatocytes 9

value: PPH treated with 50 nM of gimeracil w/BSA


title: RNA-seq Adult Male hepatocytes 8

value: Liver


title: E_coli_WT_3end_seq_MOPS_comp_exp_rep1


title: E_coli_WT_3end_seq_MOPS_min_stat


title: 2-HL_S12


title: E_coli_WT_3end_seq_MOPS_comp_exp_rep2


title: Tcf1/Lef1-deficient stim CD8+, HiC, rep2

data_processing:
The sequencing quality of Hi-C libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Hi-C libraries were mapped to mouse genome using hiclib (https://github.com/mirnylab/hiclib-legacy). UCSC genes for mouse mm9 from iGenome(http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
The resulting libraries were subject to further processing by Mirnylib (default parameters) and filterDuplicates (mode=’ram’) (https://github.com/mirnylab/hiclib-legacy) into hdf5 file.
The hdf5 files were converted into text files and then .hic files using Juicer (ref) pre function.
Genome_build: mm9
Supplementary_files_format_and_content: hic

extract_protocol:
Naïve CD8+ T cells were sort-purified from the spleen, and stimulated with IL-7 and IL-15 in vitro for 72 hrs, and then crosslinked, digested with three restriction enzymes and underwent proximity ligation.
The biotinylated DNA segments were captured, and ligated to the Illumina Paired End Adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-4000 platform.


title: E_coli_rnb_RNA_seq_MOPS_comp


title: RNA-seq Adult Male hepatocytes 10

value: PHH

value: PPH treated with 200 nM of gimeracil w/BSA


title: RNA-seq Adult Male hepatocytes 11

value: Primary hepatocytes

value: PPH treated with 400 nM of gimeracil w/ FFA


title: E_coli_rnb_3end_seq_MOPS_comp


title: 3-CR_S7

source_name: Control inguinal adipose tissue in chow-fed mouse

value: chow diet


title: E_coli_WT_Rend_seq_MOPS_comp_postKasu


title: 0-HL_S16


title: 2-CR_S6


title: RNA-seq Adult Male hepatocytes 7

value: PPH treated with 0 nM of gimeracil w/ FFA


title: E_coli_pcnB_RNA_seq_MOPS_comp

value: K-12 MG1655, pcnB::kan


title: 0-CR_S10

value: inguinal adipose tissue

value: wildtype


title: Tcf1/Lef1-deficient stim CD8+, HiC, rep1

value: splenocytes

value: GFP+ TCRbeta+ CD62Lhi CD44lo-med CD8+


title: WT stim CD8+, HiC, Rep1

value: wild type


title: E_coli_WT_RNA_seq_MOPS_comp

data_processing:
RNA-seq and Rend-seq data processing and mapping was done as described in (Lalanne et al., Cell 2018; Parker et al., Cell Systems 2020). For 3’ end-seq in analogy to Rend-seq, 3’ end linker sequences were trimmed. To deal with non-template addition during reverse transcription, all reads were further trimmed with the fastx_trimmer of the fastxtoolkit/0.0.13 by 1nt at their 5’end and only reads of 15nt length or longer were kept for mapping with bowtie/1.2 using the options -v 0 -k 1. For further data analysis mapped data were transformed into bam-format and bedgraph-format using samtools/1.5 and bedtools/2.25.0. Coverage data include 3’ terminal single nucleotide counts per read. To identify 3’adenylated transcript ends, the unmapped reads were trimmed using cutadapt/1.16. First, 3’terminal CCAs were removed with the following settings: -a "CCA$" --minimum-length 15 -O 3 --trimmed-only. Second, A-tails of any length were trimmed (-a "A{38}" --minimum-length 15 -O 1 --trimmed-only). These trimmed reads were mapped and further converted with the same settings and code as untrimmed reads above. For total RNA 3’ end analysis mapped trimmed (i.e. A-tailed) and untrimmed 3’ end coverage profiles were summed.
Genome_build: E. coli NC_000913.2, B. subtilis NC_000964.3
Supplementary_files_format_and_content: bedgraph-files

extract_protocol:
Samples have been either extracted by RNAsnap (Stead et al., NAR 2012), Hot Phenol, RiboPure (ThermoFisher/Ambion), RNeasy (Qiagen) or Trizol, precipitated, Dnase treated and cleaned uo with RNA clean & concentrator columns (Zymo research).
RNA-seq for E. coli Δpnp, Δrnb, ΔpcnB and MG1655 wildtype was executed as described in (Parker et al., Cell Systems 2020). Rend-seq libraries were prepared as described in (Lalanne et al., Cell 2018) with 25s RNA fragmentation. For 3’ end sequencing the Rend-seq protocol was modified in a way that 3’ end ligation (5'_App/CTGTAGGCACCATCAAT/3ddC_3') was done preceding fragmentation for 2min. Final libraries were sequenced on Illumina HiSeq 2000 or NextSeq500 machines.


title: 9-CR_S9

value: Control inguinal adipose


title: RNA-seq Adult Male hepatocytes 2


title: RNA-seq Adult Male hepatocytes 6

description: PPH treated with 0 nM of gimeracil w FFA


title: E_coli_pcnB_3end_seq_MOPS_comp


title: 6-CR_S8


title: RNA-seq Adult Male hepatocytes 1

description: PPH treated with 50 nM of gimeracil w FFA


title: E_coli_pnp_RNA_seq_MOPS_comp


title: RNA-seq Adult Male hepatocytes 3

value: PPH treated with 200 nM of gimeracil w/ FFA


title: RNA-seq Adult Male hepatocytes 5


title: 6-CL_S3

source_name: Tumor-associated inguinal adipose tissue in chow-fed mouse

value: Tumor-associated inguinal adipose


title: 3-CL_S2


title: RNA-seq Adult Male hepatocytes 4


title: 2-CL_S1


title: MM28_3

city: Philadelphia

first: Andrew

middle: E

last: Aplin

state: PA

address: 233 South 10th St.

institute: Thomas Jefferson University

data_processing:
De-multiplexing and data aggregation was performed using the Braod Picard Pipeline
RNA sequencing fastq files were aligned to the GRCh38 human reference genome using Star aligner (v 2.6.1a), gencode v33
RSEM was used to quantify gene and transcript level expression
transcripts per million data were calculated using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file for log normalized transcripts per million for each sample

source_name: metastatic uveal melanoma cells

growth_protocol: MM28, WM1366 and 92.1 cells were grown in RPMI 1640 medium (20% FBS, 50 IU penicillin and 50 µg/ml streptomycin).

extract_protocol:
Qiagen RNeasy mini kit
Illumina TruSeq™ Stranded mRNA Sample Preparation Kit

tag: sample type

value: uveal melanoma cell line

tag: genotype/variation

value: BAP1 mutant


title: MM28_2


title: HS7, rep2

city: Saint-Petersburg

first: Margarita

last: Sorokina

address: Akkuratova 2

country: Russia

institute: Almazov National Medical Research Centre

data_processing:
Read quality was checked for each sample using FastQC v0.11.9.
Sequenced reads were mapped to the mouse genome using mapper STAR v2.7 with rat reference genome Rnor_6.0 (Ensembl release 104) and annotation Rnor_6.0.104.chr.gtf
Aligned reads were count with featureCounts program v1.6.4.
Further analysis were made using DESeq2, fgsea и clusterProfiler R packages, as well as MSigDB and phantasus online tools.
Assembly: Genome Rnor_6.0 (Ensembl release 104)
Supplementary files format and content: tab-delimited text file includes matrix of raw counts for each of 10 Samples

organism: Rattus norvegicus

source_name: m. soleus

growth_protocol: Skeletal muscle progenitor cells were cultured in DMEM supplemented with 1% penicillin-streptomycin, 1% L-glutamine, 1% chicken fetal serum (USBiological, USA), 20% FBS (HyClone, USA), 10 % horse-serum (Gibco, USA)) on cell culture dishes covered with Geltrex (1:100 in cold DMEM, 1,5 hours at 37℃, Invitrogen, USA).

extract_protocol:
Total RNA was isolated from the cells with an Extract RNA kit (Evrogen, Russia)
Libraries were constructed using TruSeq Stranded mRNA library prep kit

treatment_protocol: Cells were isoleted and cultured to subconfluent state.

value: m. soleus

value: skeletal muscle progenitor cells

value: primary cells

value: Hindlimb suspension (HS)

tag: day


title: 9-CL_S4

value: chow diet


title: mESC 2i+LIF

data_processing:
Image analysis, base calling and demultiplexing were performed using RTA 2.7.7 and Cell Ranger 3.0.1 mkfastq.
Alignment, barcode and UMI filtering and counting were performed using Cell Ranger 3.0.1 count and mouse reference 3.0.0 (mm10 and Ensembl release 93).
Genome_build: mm10
Supplementary_files_format_and_content: Filtered (contains only detected cellular barcodes) feature-barcode matrix (each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)) in Market Exchange Format (MEX) and gzipped.
Supplementary_files_format_and_content: Gzipped tsv files with feature and barcode sequences corresponding respectively to row and column indices from the matrix.

source_name: Mouse embryonic stem cells

growth_protocol: E14Tg2a.4 mouse embryonic stem cells were cultured on 0.1% gelatin-coated culture plates in DMEM (4,5g/l glucose) supplemented with GLUTAMAX-I, 15% heat-inactivated fetal calf serum (42F5874K, ESC culture tested, GIBCO), 0.1 mM beta-mercaptoethanol, 0.1 mM non-essential amino acids 1,500 U/ml leukemia inhibitory factor (produced in house), 3 µM CHIR99021 (72054, Stem Cell Technologies) and 1 µM PD0325901 (72184, Stem Cell Technologies) in 5% CO2 at 37°C.

extract_protocol:
GEMs were generated by combining barcoded gel beads, a RT master mix containing cells, and partitioning oil onto Chromium Chip G. Following full length cDNA synthesis and barcoding from poly-adenylated mRNA, GEM were broken and pooled before cDNA amplification by PCR using 11 cycles. After enzymatic fragmentation and size selection, sequencing library were constructed by adding Illumina (Paris, France) P5 and P7 primers as well as sample index via end repair, A tailing, adaptor ligation and PCR with 10 cycles. Library quantification and quality control was performed using Bioanalyzer 2100 (Agilent Technologies, Santa Clara CA).
The single cell 3 prime mRNA seq library was generated according to 10X Genomics User Guide Chromium Single Cell 3ʹ Reagent Kits v3 (P/N CG000183 Rev A).

value: Embryonic stem cell


title: E_coli_WT_3end_seq_MOPS_comp_fraction7

description: total RNA from sucrose gradient


title: B_subtilis_WT_3end_seq_MCCG

organism: Bacillus subtilis


title: WT stim CD8+, HiC, Rep2


title: WM36_3


title: Immue cells from small intestine, cecum and colon of mouse young-4

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

description: Single cell RNA sequencing

data_processing:
The fastq files are mapped against mm10.e87 genome following by counting the UMI and removing duplicates for single cells using 'cellranger count' (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count ) with default parameters.
Genome_build: mm10.e87
Supplementary_files_format_and_content: The processed data is a seurat object saved in RDS file with assigned meta data in trascriptome matrix of intesine

source_name: Lamina Propria

growth_protocol: 4 Young (1x 8week, 2x 12week and 1x 20week) and 4 old (2x 90week, 1x 92week ,2x 108week) female wild-type C57BL6/J mice were group housed and maintained in a specific pathogen-free animal facility

extract_protocol:
Immune cells were isolated from lamina propria: tissue (cleared of crypts) was chopped finely with a scalpel and then incubated in 3ml of 1mg/ml collagenase-D (Merck, Cat. 11088866001) and 1mg/ml DNaseI in RPMI medium (ThermoFisherScientific, Cat. 21875091) in 6 well plates in an incubator shaker (80rpm) (VWR, Cat. 444-0732) for 20min at 37°C. Tissue pipetted up and down several times with a cut p1000 tip. The supernatant was passed through a 100μm strainer into 5% FBS in RPMI. Leftover tissue incubated again twice in 3ml collagenase-D/DNaseI RPMI solution in an incubator shaker (80rpm) for 30min at 37°C, collecting filtered supernatant. After the third incubation, the remaining tissue was smashed with a syringe plunger on a Falcon 40μm cell strainer (Corning, Cat. 352340) and washed with 5% FBS/RPMI to collect the maximum number of cells. The supernatant was centrifuged at 300g, 4°C for 5min. The pellet was re-suspended in 40% percoll (Sigma-Aldrich, Cat. P1644-1L) in RPMI. The cell suspension was carefully pipetted over 80% percoll in a falcon tube in order to create a gradient. The falcon tubes were centrifuged at 1600g, RT for 20min (centrifuge break disabled). The immune cells formed a white ring on the border of the two percoll concentrations: they were collected carefully and washed with FSM (2% FBS in PBS). The suspension was centrifuged at 450g, 4°C for 5min. Resulting pellet was resuspended in FSM and transferred for staining.
The 10X Single Cell 3’ v2 or v3.1 reagent kit (10X Genomics) was used for cell partitioning, cDNA amplification and library construction.

value: immune cells

tag: age

value: young


title: E_coli_WT_3end_seq_MOPS_comp_postKasu


title: E_coli_WT_3end_seq_MOPS_comp_fraction1

description: total RNA from sucrose gradient

value: wildtype


title: HS7, rep1


title: HS14, rep1


title: E_coli_WT_3end_seq_MOPS_comp_fraction3

description: total RNA from sucrose gradient


title: E_coli_pnp_3end_seq_MOPS_comp


title: Single-cell organoid

city: Nijmegen

first: Martijn

last: Broek

address: Geert Grooteplein 24, route 846

department: Molecular Biology

country: Netherlands

institute: Radboud university - RIMLS Science

data_processing:
After sequencing, Cell Ranger (v.3.1.0) was used to align the reads to the human genome GRCh38, using default settings. Next, Seurat (v.3.2.3) was used to further analyze single-cell data.
Genome_build: GRCh38 for single-cell and hf19 for bulk RNA sequencing
Supplementary_files_format_and_content: barcodes.tsv.gz = barcodes present in input data
Supplementary_files_format_and_content: features.tsv.gz = a bed file contains genes corresponding to row indices. For each gene, its gene ID and name are stored in the first and second column of the gene.tsv file, respectively
Supplementary_files_format_and_content: matrix.mtx.gz = a count matrix with Market Exchange Format (MEX). The first line contains the type code and the second line includes format and cell-ranger versions. Number of peaks, barcodes, and non-zero entries can be found in the third line.  The rest of the lines represent  nonzero entries with the first two numbers corresponding to peak and barcode indices and the last one corresponding to  the number of cut sites.
Supplementary_files_format_and_content: ReadCounts.tsv = Count matrix containing gene IDs and corresponding counts. Each column represents another sample (3x mutant (iPS134) and 3x repaired (iPS19))
Supplementary_files_format_and_content: counts.txt = Count matrix containing ENSEMBLE Ids and corresponding counts

source_name: Kidney organoid

growth_protocol: iPSCs were cultured using Essential™ 8 (E8) medium (Gibco, ThermoFisher) supplemented with E8 supplement (50X, Gibco) and 0.5% antibiotic-antimycotic (Gibco) on Geltrex-coated (ThermoFisher) cell culture plates (Greiner, Alphen aan den Rijn, the Netherlands). For experimental seeding purposes iPSCs were washed 3 times with PBS and subsequently disassociated into single cells using TrypLE Select Enzyme (ThermoFisher) for 2 minutes at 37°C. iPSCs were seeded on Geltrex-coated cell culture plates using E8 medium supplemented with E8 supplement, 0.5% (v/v) antibiotic-antimycotic and 1X RevitaCell at a density between 18,750 - 22,900 cells/cm2. Twenty-four hours after seeding, culture medium was replaced by E6 medium supplemented with 6 µM CHIR (Tocris, Bio-Techne, Abingdon, United Kingdom) to initiate differentiation (defined as day 0). From day 3 onwards, half of the wells were cultured in  E6 medium supplemented with 200 ng/mL FGF9 (RD systems) and 1 µg/ml heparin (Sigma-Aldrich) until day 7 (anterior intermediate mesoderm, AIM), whereas the other wells remained on E6 medium with CHIR until day 5 (posterior intermediate mesoderm, PIM). From day 5 onward, all cells were cultured in E6 medium with FGF9 and heparin. At day 7, cell were harvested using trypsin-EDTA and a cell suspension was made consisting of AIM and PIM cells in a 1:2 ratio. Cells aggregates, consisting of 300K cells, were transferred to Transwell™ plates (Corning) and incubated for at least 1 hour at 37⁰C, 5% (v/v) CO2, with E6 medium supplemented with 5 uM CHIR to induce self-organizing nephrogenesis. After 1 hour, medium was replaced for E6 medium supplemented with FGF9 and heparin. At day 7+5 (i.e. 5 days later), medium was changed to E6 supplemented with EGF (10 ng/ml, RD systems) and BMP7 (50 ng/ml, RD systems). Organoids were used for experiments at day 7+17 or 7+18.

extract_protocol:
D7+17 organoids were washed with PBS and digested using accutase at 37°C for 15 minutes. Accutase was inactivated by adding DMEM/F12 with 10% (v/v) FBS. The cell suspension was filtered through a 40 µm cell strainer and spun down at 1500 rpm for 5 minutes. To reduce background and obtain a single cell suspension, this step was repeated once more. Cells were then resuspended in PBS containing 0.04% (v/v) BSA and counted using a Neubauer counting chamber (Carl Roth, Karlsruhe, Germany).
Next, 1000 cells/uL per sample were loaded onto a 10x Chromium Next GEM Chip G according to the manufacturer’s instructions and processed in a Chromium controller (10X Genomics, Pleasanton, California). All single cell sequencing libraries were generated using 10x Chromium Next GEM v3.1 kits (10x Genomics) and sequencing was performed on a Novaseq6000 system (Illumina, San Diego, California), using an S2 v1.5 100 cycles flow cell (Illumina) with run settings 28-10-10-90 cycles.

value: Kidney organoid from iPS15


title: MM28_1


title: 0-CL_S5

value: inguinal adipose tissue


title: E_coli_WT_3end_seq_MOPS_comp_fraction9

description: total RNA from sucrose gradient


title: HS14, rep2


title: HS1, rep1


title: Control, rep2

value: Control


title: HS3, rep2


title: Immue cells from small intestine, cecum and colon of mouse young-5 and mouse old-5

description: Single cell RNA sequencing

value: old and young


title: Immue cells from small intestine, cecum and colon of mouse young-6 and mouse old-6

description: Single cell RNA sequencing


title: WM36_2


title: 92.1_2

value: BAP WT


title: Immue cells from small intestine, cecum and colon of mouse old-1

description: Single cell RNA sequencing

value: old


title: Control, rep1


title: HS3, rep1


title: E_coli_WT_3end_seq_MOPS_comp_input


title: 92.1_3

value: uveal melanoma cell line


title: WM36_1

value: BAP1 mutant


title: E_coli_WT_3end_seq_MOPS_comp_fraction5

description: total RNA from sucrose gradient


title: Immue cells from small intestine, cecum and colon of mouse young-3

description: Single cell RNA sequencing


title: HS1, rep2

value: m. soleus


title: E_coli_WT_3end_seq_LB_RNeasy_MicrobeExpress


title: m6A_IP_2

status: Public on Apr 24 2022

city: Rehovot

first: Ziv

last: Shulman

address: Herzl St 234

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Mars-seq: Reads were trimmed using Cutadapt
Mars-seq and m6A-IP: Reads were aligned to the genome using STAR
Mars-seq: Quantification was done using htseq-count as previously described in R. Kohen, BMC Bioinformatics, 2019.
m6A-IP: Normalization of paired libraries insert size was performed using in-house python scripts, between pairs of INPUT-IP samples. Alignment sorting and indexing were performed separately with samtools (V. 1.3.1) (Li et al. Bioinformatics, 2009).
m6A-IP: Identification of putative m6A sites was performed by assigning peak over input (POI) and peak over median (POM) scores to each site, as previously published (Schwartz et al, Cell 2014)
single-cell RNAseq: FASTQ files were aligned to the mouse mm10 reference genome using 10x Genomics Cell Ranger software v5.0.1
single-cell RNAseq: The UMI count matrix was converted to Seurat objects using R package Seurat
single-cell RNAseq: SCTransform function was used to normalize each dataset
Genome_build: Mars-seq, single-cell RNAseq: mm10, m6A-IP: mm9
Supplementary_files_format_and_content: MARS-seq: Excel file with Deseq2 output
Supplementary_files_format_and_content: m6A-IP: bam.tdf

source_name: B cells

growth_protocol: Splenic B cells were isolated and stimulated for three days in vitro with 5ug/ml LPS

extract_protocol:
Total RNA was harvested from activated cells using Trizol. Enrichment for PolyA RNA was done twice using mRNA mRNA direct kit and checked using TapeStation (Agilent). PolyA-selected RNA was barcoded and immunoprecipitated in two rounds using anti-m6A polyclonal antibody bound to magnetic protein-G beads and protein-A beads
Libraries were prepared as previously described (Garcia-Campos et al. Cell, 2019). Briefly, eluted RNA was reverse transcribed and an adapter was added using Superscript III reverse transcriptase (Thermo Fisher, 18080093). A second adaptor was added to the cDNA by ligation with T4 RNA Ligase 1 (NEB, M0437M). Following clean-up with MyOne Silane beads, the cDNA library was amplified in a PCR using KAPA HiFi HotStart ReadyMix (KAPA Biosystems KK2601).Libraries were sequenced on an Illumina NextSeq 500 machine.

value: In vitro LPS-stimulated B cells

tag: mouse strain

value: WT


title: Immue cells from small intestine, cecum and colon of mouse old-2

description: Single cell RNA sequencing


title: E_coli_WT_3end_seq_MOPS_comp


title: m6A_IP_1


title: Input_2


title: Sg_Arid1a_rep2

city: Memphis

first: Douglas

middle: R

last: Green

state: United States

address: 262 Danny Thomas Pl

department: Immunology

institute: St Jude Children's Research Hospital

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Clariom S mouse GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

label: biotin

source_name: sgRNA-transduced OT-1 cells from the dual-color transfer system at day 7.5 post-infection from spleen

label_protocol: Total RNA (1 - 20 ng) were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Specifically, OT-I cells were transduced with non-targeting control (NTC) single-guide RNA (sgNTC) labelled with GFP, or with indicated sgRNA marked by the expression of Ametrine, and then these cells were mixed at a 1:1 ratio and transferred to the same host, followed by Lm-ova  infection. Donor-derived CD8+ T cells were sorted at day 7.5 after post-infection. RNA was isolated and loaded on Clariom S mouse array platform.

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen.

value: OT-I


title: Spike_Arid1a_rep4


title: 92.1_1


title: Exp2_Ythdf3_KO_1

extract_protocol:
mRNA was extracted from sorted cells using mRNA direct kit (Invitrogen) and mRNA from each sample was barcoded during reverse transcription and pooled.
Libraries were prepared using a bulk adaptation of the previously described protocol (Keren-Shaul et al. Nat. Protoc, 2019 and Jaitin et al. Science, 2014).Following Agencourt Ampure XP bead cleanup (Beckman Coulter), the pooled samples underwent second strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT, and PCR.  Libraries were quantified by Qubit and TapeStation as well as by qPCR for the ACTB gene as previously described. Sequencing was done using a Nextseq 75 cycle high output kit (Illumina; paired end sequencing).

treatment_protocol: Splenic B cells were adoptively transferred to WT mice, which were immunized with NP-KLH for five days. FAS+ GL-7+ cells were isolated by cell sorting.

value: Activated B cells

value: B1-8hi Ythdf3-/- Tomato+


title: Exp2_Ythdf3_KO_3


title: Exp2_Ythdf1_KO_3

value: B1-8hi Ythdf1-/- GFP+


title: Sg_Smarcd2_rep1


title: Sg_Smarcd2_rep2


title: Sg_Arid1a_rep3


title: Sg_Arid1a_rep1


title: Spike_Arid1a_rep2


title: Spike_Smarcd2_rep2


title: Exp2_Ythdf1_KO_2


title: Sg_Smarcd2_rep4


title: Exp2_Ythdf1_KO_1


title: Spike_Smarcd2_rep3


title: Exp2_WT_1

value: B1-8hi Tomato+


title: Exp2_WT_4


title: Spike_Arid1a_rep3


title: Spike_Smarcd2_rep4


title: Exp1_Ythdf2_cKO_3

value: B1-8hi CD23cre Ythdf2fl/fl Tomato+


title: Exp1_Ythdf2_cKO_2


title: Sg_Arid1a_rep4


title: Spike_Smarcd2_rep1


title: Sg_Smarcd2_rep3


title: Spike_Arid1a_rep1


title: Exp2_Ythdf1_KO_4


title: Exp2_Ythdf3_KO_2


title: Exp1_WT_1


title: Ctr1_rep2_LCL_H3K27ac

city: Oxford

first: Julia

last: Truch

address: John Radcliffe Hospital, Headley Way, Headington

department: RDM - WIMM

country: United Kingdom

institute: University of Oxford

description: Genome-wide library of Immunoprecipitated fragments

data_processing:
For un-mapping reads : trimming adaptors trim_galore, combining overlapping R1-R2 reads : flash
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie2, hg19
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks
Genome_build: hg19
Genome_build: hg19
Supplementary_files_format_and_content: bigWig of filtered fragments

source_name: human lymphoblastoid cell line

growth_protocol: LCLs derived from ATR-X patients and healthy controls were incubated with RPMI medium supplemented with 15% FCS, 1% PenStrep and 1% glutamine at 37C and 5% CO2.

extract_protocol:
DNA was purified by phenol-chloroform extraction and ethanol precipitation with NaOAc, and 2 µl GlycoBlue.
For ChIP-seq, chromatin was crosslinked with 1 % formaldehyde at room temperature for 10 minutes. Crosslinking was quenched with 130 mM glycine, and cells were washed with cold PBS. Fixed material was stored at -80 C. Chromatin immunoprecipitation was performed using Agarose ChIP Assay Kit (Merck Millipore). Briefly, 10^7 cells were lysed by incubation on ice with lysis buffer for 15 minutes. Lysed cells were sonicated, insoluble material was removed by centrifugation and soluble material was diluted with dilution buffer. Immunoprecipitation was performed by incubation of diluted chromatin with antibodies for H3.3 (09-838, Millipore), H3K27ac (ab4729, Lot: GR276932-1, Abcam), H3K9me3 (ab8898, lot GR3244171-1, Abcam), H3K4me3 (ab8580, lot: GR273043-1, abcam), H3K4me1 ( ab8895, lot: GR283603-1, Abcam), H3K27me3  (ab6002, lot: GR275911-6-1, Abcam) and H3K36me3 (ab9050, lot: GR233723-2, Abcam) overnight. Chromatin binding to Protein A and or G/agarose slurry, washes and elution were performed according to the manufacturerâs instructions.
NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs).

value: human lymphoblastoid cell line

tag: phenotype

value: unaffected

tag: antibody

tag: crosslinking

value: single step cross-linking


title: Case_LCL_input

description: Genome-wide library of sonicated fragments

data_processing:
Mapping : bowtie2, hg19
For un-mapping reads : trimming adaptors trim_galore, combining overlapping R1-R2 reads : flash
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie2, hg19
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks
Genome_build: hg19
Supplementary_files_format_and_content: bigWig of filtered fragments normalised based on the coverage under peaks

extract_protocol:
Genomic DNA was extracted from 2.5 x 107 cells using 950 µL of extraction buffer (20 mM Tris HCl (pH 8.0), 10 mM EDTA, 100 mM NaCl and 0.5% SDS) followed by RNaseA/T1 (Thermo Scientific) treatment and phenol/chloroform extraction. gDNA were sonicated and diluted to 17.5 mg/mL in CAP100 buffer (12.5% glycerol, 0.1% Triton-x-100, 20mM HEPES pH 7.9 and 100mM NaCl). NeutrAvidin Agarose Resin (Thermo Scientific) was conjugated with biotinylated hKDM2B ZF-CxxC protein (kindly provided by Rob Klose). 500 mL of diluted sonicated DNA were incubated with conjugated CxxC resin for 1 hour at 4°C. Serial washes and elutions using increasing salt concentration were performed. First, two washes with 1 mL of CAP100 buffer were carried out, followed by two elutions with 50 µL of CAP300 (12.5% glycerol, 0.1% Triton-x-100, 20 mM HEPES pH 7.9 and 300 mM NaCl) and two elutions with 50 µL of CAP500 (12.5% glycerol, 0.1% Triton-x-100, 20 mM HEPES pH 7.9 and 500 mM NaCl). Subsequently, the elution process was repeated using buffers with 700 mM and 1 M NaCl sequentially. DNA purification from eluted samples were performed using QIAquick PCR purification kit (Qiagen). Samples derived from elutions using 700 mM and 1 M NaCl were used for sequencing.
NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs).

value: affected


title: Input_1


title: Ctr_LCL_input


title: Exp2_WT_3


title: Exp1_WT_2


title: Exp2_Ythdf3_KO_4


title: Case2_LCL_BioCAP

description: Genome-wide library of fragments precipitated via interactions with CxxC domain

growth_protocol: LCLs derived from ATR-X patients and healthy controls were incubated with RPMI medium supplemented with 15% FCS, 1% PenStrep and 1% glutamine at 37°C and 5% CO2.


title: IR4

city: Lanzhou

first: Pengfei

last: Wang

state: Gansu

address: No. 1 Yingmen village, Anning District

institute: Gansu Agricultural University

data_processing:
Firstly, clean reads were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A /T / G / C and low-quality reads from raw data. Simultaneously, Q20, Q30, and GC-content of the raw data were calculated. Then, we chose a certain range of length from clean reads to do all the downstream analyses. Lastly, the miRNA tags were mapped to pig reference genome (Sus scrofa 10.2) by Bowtie [18] without mismatch to analyze their expression and distribution on the reference genome.
Mapped small RNA tags were used to looking for known miRNA. miRBase 20.0 was used as reference, modified software mirdeep2 and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. The characteristics of hairpin structure of miRNA precursor can be used to predict novel miRNA. The available software miREvo and mirdeep2  were integrated to predict novel miRNA through exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the small RNA tags unannotated in the former steps.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria : Normalization formula: Normalized expression = mapped readcount/total reads*1000000. Differential expression analysis was performed using the DESeq R package. The P-values was adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 was set as the threshold for significantly differential expression by default.
Predicting the target gene of miRNA was performed by miRanda , RNAhybrid  and PITA.
GOseq software was used to analyze the GO function of differentially expressed miRNA target genes, and KOBAS software was used to analyze the KEGG signal pathway of miRNA target genes to understand the function of differentially expressed miRNA.
Genome_build: Sus scrofa 10.2
Supplementary_files_format_and_content: TPMs and readcounts

organism: Sus scrofa

source_name: Ileum

extract_protocol:
Ileum were removed, flash frozen and  total RNA was extracted from each sample using TRIzol reagent (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Y x L

tag: developmental stage

value: piglet

value: 7-day old

value: ileum

tag: infection

value: Clostridium perfringens type C

value: resistant group (IR)


title: IS5

tag: tissue

value: sensitive group (IS)


title: IR3


title: IR2


title: Ctr3_LCL_BioCAP


title: Case1_rep2_LCL_H3K27ac

tag: cell type


title: Case1_LCL_BioCAP


title: Ctr2_LCL_BioCAP


title: Exp2_WT_2

tag: genotype


title: Exp1_WT_3


title: IS3


title: IC5

value: control


title: Exp1_Ythdf2_cKO_1

value: Activated B cells


title: IC4


title: Ctr1_rep2_LCL_H3K4me3


title: IC2


title: Exp1_WT_4


title: IC1


title: IR1


title: Case3_LCL_CapC

description: DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown

data_processing:
Library strategy: NG Capture-C
Adaptor Removal: Trim Galore
Fragment reconstruction into a single read: Flash
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl)
Alignment: Bowtie 2
Processing: Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser2.pl)
Processing: Combining data from multiple replicates (custom scripts)
Processing: Removal of ploidy regions and off target capture (custom scripts)
Genome_build: hg19
Supplementary_files_format_and_content: custom format (chr start stop interactions viewpoint)

extract_protocol:
3C Libraries were generated according to the NG Capture-C protocol (Davies et al. 2016). Briefly, cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80. Cells were thawed on ice, washed in milliq dH2O and Dounce homogenised on ice (x 40 strokes). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer. The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNAse (Roche). Phenol/Chloroform extraction was then performed followed by an Ethanol precipitation and a wash with 70% Ethanol. Digestion efficiencys were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 70%. DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life technologies)
5-10ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation was performed using the NEB Next or NEB Ultra DNA sample preparation reagent kits, depending on the amount of DNA available, using the standard protocol. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. Where possible 1-2ug of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using Illumina Nextseq 500 (150 bp paired-end reads)


title: Case1_LCL_CapC


title: Case3_LCL_BioCAP


title: Case3_LCL_ATAC

description: Genome-wide library of tagmented fragments

data_processing:
Library Strategy: ATAC-seq
Mapping : bowtie2, hg19
For un-mapping reads : trimming adaptors trim_galore, combining overlapping R1-R2 reads : flash
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie2, hg19
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks
Genome_build: hg19
Supplementary_files_format_and_content: bigWig of filtered fragments

extract_protocol:
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013) on single cell suspensions. 60000-100000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen). As experimental controls, ATAC-Seq was also performed on genomic DNA (instead of isolated nuclei).
Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013.

tag: condition

value: experiment - ATAC performed on isolated nuclei


title: BMDMs cs6h_Co12h_1

city: Wuhan

first: Yan

middle: Ting

state: Hubei

address: 1277 Jiefang Avenue, Kong Hon District

department: Department of Anesthesiology, Union Hospital, Tongji Medical College

institute: Huazhong University of Science and Technology

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: BMDMs

growth_protocol: BMDMs were isolated from C57BL/6 mice.The cells were  incubated for 7 days in RPMI 1640 medium containing 10% fetal bovine serum (FBS, GIBCO, cat. no. 10100147,USA). The macrophages were incubated with macrophage colony-stimulating factor (10 ng/ml, cat. no. 416-ML-050, R&D, USA) to activate the M0 macrophages. Half the medium was replaced every two days.

extract_protocol:
RNA was extracted from macrophages treated with exosomes using RNeasy Mini Kit (cat. no. 74104, Qiagen, Germany) according to manufacturer’s protocols. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Epithelial cells were cyclically stretched for 6 h or non-cyclically stretched. BMDMs were treated with exosomes (100 μg/ml) for non-cyclical-stretched or cyclical-stretced epithelial cells for 12 h.

tag: cell line

value: BMDMs

value: macrophage

value: WT

tag: treatment

value: BMDMs were treated with exosomes cyclical-stretced epithelial cells for 12 h.


title: IS1


title: BMDMs ctrl1

value: BMDMs were treated with exosomes (100 μg/ml) for non-cyclical-stretched epithelial cells for 12 h.


title: BMDMs cs6h_Co12h_3


title: Myc binding, silvestrol-treated, replicate 1

data_processing:
Library strategy: CUT&RUN
Paired-end sequencing reads were trimmed with Trim Galore (version 0.5.0) with default parameters.
Reads were aligned to the reference mouse mm10 assembly using Bowtie 2 (version 2.3.5.1) (Langmead and Salzberg, 2012) with settings --end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700.
The BAM file was filtered with SAMtools (version 1.9), BamTools (version 2.5.1) and scripts of nf-core/chipseq6 to discard reads, mates that were unmapped, or PCR/optical duplicates, or not primary alignments, or mapped to multiple locations, or mapped to ENCODE blacklisted regions, or have more than 4 mismatches (-F 0x004 -F 0x008 -F 0x0100 -F 0x0400 -f 0x001 -q 1).
MACS (version 2.1.2) was used to call peaks from the BAM file with IgG control and recommended mappable genome size (default value for other parameters). NarrowPeak mode was used for Myc, broadPeak mode for Arid1a and Brg1.
Signal was normalized by scaling to 1 million mapped reads using BEDTools (version 2.27.1) and bedGraphToBigWig (version 377) with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files scaling tag count to 1 million mapped reads.
Supplementary_files_format_and_content: Bed files of peaks called using MACS2.

source_name: CD8+ T cells

growth_protocol: Naïve CD8 T cells were activated with anti-CD3/28 and ICAM for 36hr. First division CD 8 T cells were sorted.

extract_protocol: CUT&RUN experiments were performed as previously described (Meers et al. Improved CUT&RUN chromatin profiling tools. eLife 8, e46314 (2019)) with slight modifications.

treatment_protocol: First-division CD8+ T cells were sorted into medium with or without 200 nM Silvestrol and cultured for additional 2 h.

value: CD8+ T cells

value: Wild type


title: IR5

value: Y x L


title: Ctr1_LCL_BioCAP

value: unaffected


title: Case1_rep2_LCL_H3K4me3

value: human lymphoblastoid cell line

value: affected

value: single step cross-linking


title: Ctr3_LCL_ATAC


title: 163NL-rep2

city: Shanghai

first: Yibo

last: Lu

address: No.1678, Dongfang Road, Shanghai

department: Shanghai Children's Medical Center

institute: Shanghai Jiao Tong University

data_processing:
MGI Sub-pixel Registration used for basecalling
The quality of raw sequence datas were checked using FastQC(V0.11.9). Low quality sequences were removed with Trim Galore!(V0.6.5) and rRNA sequences were removed with SortMeRNA(V2.1).
STAR-aligner(V2.7.10) was used for aligning RNA-seq data to genomes.
Subread(V2.0.2) outputs numbers of reads assigned to features
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Cardiomyocyte (AC16 cell line)

extract_protocol:
Cell samples were lysed using Trizol reagent. DNBSEQ-T7RS reagent kit(FCL PE150 V2.0) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard DNBSEQ protocols

value: Control for knockdown of HSALNG0104472

value: Cardiomyocyte


title: BMDMs ctrl2


title: Case2_LCL_CapC


title: BMDMs ctrl3


title: IS4

value: piglet

value: 7-day old

value: ileum

value: Clostridium perfringens type C

value: sensitive group (IS)


title: IC3

value: control


title: Ctr3_LCL_CapC


title: Ctr2_LCL_CapC


title: 290NL-rep3

value: Control for overexpression of HSALNG0104472


title: Case4_LCL_ATAC

value: experiment - ATAC performed on isolated nuclei


title: Myc binding, control, replicate 1

value: CD8+ T cells


title: Ctr1_LCL_ATAC


title: IS2


title: Case2_LCL_ATAC


title: 163NL-rep3


title: circTmem241_KO

city: Beijing

first: Nian

last: LIU

address: #15 Datun Road, Chaoyang District

institute: Institute of Biophysics,CAS

data_processing:
A propriety Sub-pixel Registration algorithm developed by MGI was used for base call.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:  1) Remove the reads containing the adaptor(adaptor pollution);  2) Remove reads whose N content is greater than 5%;  3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).  The filtered "Clean Reads" are saved in FASTQ format.
Bowtie2 was used to map the clean reads to the reference gene sequence (transcriptome), and then RSEM was used to calculate the gene expression level of each sample.
The DEseq2 was used to perform differential expression analysis.DESeq2: Qvalue (Adjusted Pvalue) <= 0.05
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts and TPM values for each gene and each sample.

source_name: bone marrow

extract_protocol:
RNA was harvested using RNAprep Pure Micro Kit (Tiangen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were constructed using MGIEasy RNA Library Prep Kit V3.0 (MGI-tech) following manufacturer's protocols.

value: bone marrow

value: innate lymphoid cell progenitors

value: immune cells

value: circTmem241 knockout


title: Ctr1_LCL_CapC

value: unaffected


title: 163NL-rep1


title: BMDMs cs6h_Co12h_2

value: BMDMs

value: macrophage

value: WT

value: BMDMs were treated with exosomes cyclical-stretced epithelial cells for 12 h.


title: Case1_LCL_ATAC

value: affected


title: Ctr2_LCL_ATAC


title: Ctr4_LCL_ATAC


title: 290NL-rep1

value: Cardiomyocyte


title: circTmem241_WT

value: circTmem241 wild-type


title: 163-rep1

value: Knockdown of HSALNG0104472


title: Case1_gDNA_LCL_ATAC

value: experimental control - ATAC performed on genomic DNA


title: 163-rep2


title: Ctr3_gDNA_LCL_ATAC


title: 290-rep3

value: Overexpression of HSALNG0104472


title: Case3_gDNA_LCL_ATAC


title: 290-rep2


title: 290NL-rep2

value: Control for overexpression of HSALNG0104472


title: 163-rep3


title: 290-rep1


title: Intestinal stem cell WT (OKSM +Sen control) Rep 1

city: Singapore

first: Nicholas

last: Tolwinski

address: 16 #01-220, College Ave West

country: Singapore

institute: Yale-NUS College

data_processing:
The raw fastq files were aligned to the dm6 genome (Ensembl v97) using STAR v2.7.1a
The reads were then quantified using RSEM v1.3.1
Assembly: dm6
Supplementary files format and content: genes.results were generated using RSEM v1.3.1 and includes the quantified reads for each sample

organism: Drosophila melanogaster

source_name: Intenstinal Stem Cell

growth_protocol: Drosophila were maintained at standard humidity and temperature (25⁰C) with food containing 6g Bacto agar, 114g glucose, 56g cornmeal, 25g Brewer’s yeast and 20ml of 10% Nipagin in 1L final volume.

extract_protocol:
Adult fly midguts were dissected in 200 µl of 1x PBS in a PYREX™ Spot Plates concave glass dish (FisherScientific). The midguts were rinsed with PBS and stained with 10mg/ml Hoechst 33342 diluted 200 times in 1X PBS for 1min. Subsequently, the guts were carefully transferred onto a small droplet of 1x PBS on a 35mm glass bottom dish. Using fine forceps, the gut was repositioned to resemble its natural orientation. PBS was then removed from the area surrounding the gut, leaving a small amount of excess PBS to hold the gut in place and prevent desiccation. The 3mm glass bottom dish was then mounted onto the Zeiss LSM800 (Carl Zeiss AG, Germany) for imaging. For each construct, midguts from at least 3 flies were dissected and imaged at the 25% percentile from the anterior midgut.
The extracted RNA was quantified using Nanodrop (Thermo Fisher Scientific). Library preparation was performed using 1µg of total RNA and sequencing was performed using Illumina HiSeq 4000 System (2 × 151 bp read length, 40 million reads per sample) by NovogeneAIT Genomics (Singapore).

treatment_protocol: Transgenic flies were maintained under a white light lamp at all times.

value: intestinal stem cells

value: Control


title: Intestinal stem cell WT (OKSM +Sen control) Rep 3


title: Intestinal stem cell with OKSM & senolytic overexpression Rep 1


title: Midgut with OKSM & senolytic overexpression Rep 2

source_name: Midgut

value: midgut


title: Ctr1_LCL_H3K27ac

data_processing:
Mapping : bowtie2, hg19
For un-mapping reads : trimming adaptors trim_galore, combining overlapping R1-R2 reads : flash
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie2, hg19
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks
Genome_build: hg19
Supplementary_files_format_and_content: bigWig of filtered fragments

extract_protocol:
DNA was purified by phenol-chloroform extraction and ethanol precipitation with NaOAc, and 2 µl GlycoBlue.
NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs).

treatment_protocol: For ChIP-seq, chromatin was crosslinked with 1 % formaldehyde at room temperature for 10 minutes. Crosslinking was quenched with 130 mM glycine, and cells were washed with cold PBS. Fixed material was stored at -80 ºC. Chromatin immunoprecipitation was performed using Agarose ChIP Assay Kit (Merck Millipore). Briefly, 10^7 cells were lysed by incubation on ice with lysis buffer for 15 minutes. Lysed cells were sonicated, insoluble material was removed by centrifugation and soluble material was diluted with dilution buffer. Immunoprecipitation was performed by incubation of diluted chromatin with antibodies for H3.3 (09-838, Millipore), H3K27ac (ab4729, Lot: GR276932-1, Abcam), H3K9me3 (ab8898, lot GR3244171-1, Abcam), H3K4me3 (ab8580, lot: GR273043-1, abcam), H3K4me1 ( ab8895, lot: GR283603-1, Abcam), H3K27me3  (ab6002, lot: GR275911-6-1, Abcam) and H3K36me3 (ab9050, lot: GR233723-2, Abcam) overnight. Chromatin binding to Protein A and or G/agarose slurry, washes and elution were performed according to the manufacturer’s instructions.

value: single step cross-linking


title: Case2_LCL_H3K27ac


title: Intestinal stem cell with OKSM & senolytic overexpression Rep 2


title: Case1_LCL_H3K27ac


title: Midgut WT (OKSM +Sen control) Rep 3


title: Intestinal stem cell with OKSM overexpression Rep 2

value: OKSM


title: Ctr2_LCL_H3K27me3

value: unaffected


title: Intestinal stem cell with senolytic overepxression Rep 2

value: Senolytic


title: Midgut WT (OKSM +Sen control) Rep 2


title: Intestinal stem cell with OKSM overexpression Rep 1


title: Ctr1_gDNA_LCL_ATAC


title: Intestinal stem cell with senolytic overepxression Rep 1


title: Ctr1_LCL_H3K27me3


title: Intestinal stem cell with OKSM overexpression Rep 3


title: Midgut with OKSM overexpression Rep 3


title: Intestinal stem cell WT (OKSM +Sen control) Rep 2


title: Midgut with senolytic overepxression Rep 3


title: Ctr2_LCL_H3K27ac


title: Midgut with senolytic overepxression Rep 2


title: Case2_LCL_H33


title: Ctr3_LCL_H3K27me3


title: Case3_LCL_H33


title: Midgut with OKSM & senolytic overexpression Rep 3


title: Midgut with OKSM overexpression Rep 1


title: Case1_LCL_H33


title: Midgut with OKSM overexpression Rep 2


title: Midgut with OKSM & senolytic overexpression Rep 1


title: Ctr3_LCL_H33


title: Ctr1_LCL_H33


title: Midgut WT (OKSM +Sen control) Rep 1


title: Ctr2_LCL_H33


title: Case2_LCL_H3K36me3


title: Case1_LCL_H3K36me3


title: Ctr3_LCL_H3K36me3


title: Case3_LCL_H3K36me3


title: Ctr2_LCL_H3K36me3


title: Case3_LCL_H3K4me1


title: Ctr1_LCL_H3K36me3


title: Case1_LCL_H3K4me1


title: Case2_LCL_H3K4me1


title: LCL control, biological replicate 18

hyb_protocol: Labeled cRNA was then purified, fragmented and hybridised on arrays using a Hybridization Oven 640 (Affymetrix) following manufacturer's protocol for PrimeView™ Human Gene Expression Array Plate and following the 100 or 81/4-format 3' IVT PLUS Reagent Kit User Manual (Affymetrix).

scan_protocol: Arrays were washed and stained in a Fluidics Station 450 (Affymetrix) and scanned using a GeneChip Scanner 3000 (Affymetrix), controlled by the Affymetrix GeneChip Command Console.

data_processing: Results were analysed using Affymetrix® Transcriptome Analysis Console (TAC) and Affymetrix® Expression Console™ Softwares  (Affymetrix) and further analysed using limma (Ritchie et al., 2015), affy (Gautier et al., 2004) and genefilter (Gentleman et al., 2016) R packages

label: Biotinilated

source_name: LCL control

label_protocol: 250ng of RNA were used as the starting material for cDNA synthesis followed by the production of Biotinilated-labled cRNA following manufacturer's protocol for PrimeView™ Human Gene Expression Array Plate and following the 100 or 81/4-format 3' IVT PLUS Reagent Kit User Manual (Affymetrix).

growth_protocol: LCLs derived from ATR-X patients and healthy controls were incubated with RPMI medium supplemented with 15% FCS, 1% PenStrep and 1% glutamine at 37°C and 5% CO2

extract_protocol: RNA was extracted using RNeasy Mini kit from Qiagen. 4 x 106 cells were used as starting material. Samples were submitted to on-column DNase digestion using RNAse-Free set DNase Set and RNA quality assessed by Nanodrop and integrity was assessed using Agilent RNA ScreenTape assay system (Agilent).

value: human lymphoblastoid cell line (LCL)


title: LCL control, biological replicate 19


title: LCL control, biological replicate 14


title: Ctr3_LCL_H3K4me1


title: LCL control, biological replicate 20


title: LCL control, biological replicate 16


title: LCL control, biological replicate 17


title: Ctr2_LCL_H3K4me1


title: genomic DNA from decidua sample from artificial abortion control 2

type: genomic

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

description: decidua from AA control 2

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

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: decidua from AA control 2

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from chorionic villi and decidua samples using Qiagen DNeasy Blood & Tissue Kit according to standard instructions

tag: gender

value: Female

tag: sample type

value: clinical sample

tag: disease state

value: normal


title: genomic DNA from decidua sample from artificial abortion control 4

description: decidua from AA control 4

source_name: decidua from AA control 4


title: LCL control, biological replicate 13


title: genomic DNA from decidua sample from artificial abortion control 3

description: decidua from AA control 3

source_name: decidua from AA control 3


title: genomic DNA from chorionic villi sample from artificial abortion control 2

description: chorionic villi from AA control 2

source_name: chorionic villi from AA control 2


title: genomic DNA from chorionic villi sample from artificial abortion control 5

description: chorionic villi from AA control 5

source_name: chorionic villi from AA control 5


title: Ctr1_LCL_H3K4me1


title: LCL control, biological replicate 15


title: LCL control, biological replicate 12


title: genomic DNA from decidua sample from recurrent miscarriage patient 3

description: decidua from RM patient 3

source_name: decidua from RM patient 3

value: recurrent miscarriage


title: genomic DNA from chorionic villi sample from recurrent miscarriage patient 4

description: chorionic villi from RM patient 4

source_name: chorionic villi from RM patient 4


title: genomic DNA from chorionic villi sample from recurrent miscarriage patient 5

description: chorionic villi from RM patient 5

source_name: chorionic villi from RM patient 5


title: genomic DNA from decidua sample from recurrent miscarriage patient 2

description: decidua from RM patient 2

source_name: decidua from RM patient 2


title: genomic DNA from decidua sample from recurrent miscarriage patient 4

description: decidua from RM patient 4

source_name: decidua from RM patient 4


title: genomic DNA from chorionic villi sample from recurrent miscarriage patient 1

description: chorionic villi from RM patient 1

source_name: chorionic villi from RM patient 1


title: genomic DNA from decidua sample from recurrent miscarriage patient 1

description: decidua from RM patient 1

source_name: decidua from RM patient 1


title: LCL control, biological replicate 11


title: genomic DNA from decidua sample from artificial abortion control 5

description: decidua from AA control 5

source_name: decidua from AA control 5


title: genomic DNA from chorionic villi sample from artificial abortion control 4

description: chorionic villi from AA control 4

source_name: chorionic villi from AA control 4


title: genomic DNA from decidua sample from artificial abortion control 1

description: decidua from AA control 1

source_name: decidua from AA control 1


title: Case3_LCL_H3K4me3

source_name: human lymphoblastoid cell line

value: affected


title: genomic DNA from chorionic villi sample from artificial abortion control 3

description: chorionic villi from AA control 3

source_name: chorionic villi from AA control 3


title: genomic DNA from chorionic villi sample from recurrent miscarriage patient 2

description: chorionic villi from RM patient 2

source_name: chorionic villi from RM patient 2


title: LCL control, biological replicate 9

source_name: LCL control


title: genomic DNA from chorionic villi sample from artificial abortion control 1

description: chorionic villi from AA control 1

source_name: chorionic villi from AA control 1


title: Case2_LCL_H3K4me3


title: LCL control, biological replicate 6


title: Ctr1_LCL_H3K4me3


title: genomic DNA from chorionic villi sample from recurrent miscarriage patient 3

description: chorionic villi from RM patient 3

source_name: chorionic villi from RM patient 3


title: genomic DNA from decidua sample from recurrent miscarriage patient 5

description: decidua from RM patient 5

source_name: decidua from RM patient 5


title: Case3_LCL_SC_input


title: LCL control, biological replicate 8


title: LCL control, biological replicate 10


title: Case1_LCL_H3K4me3


title: LCL control, biological replicate 4


title: LCL control, biological replicate 2


title: LCL control, biological replicate 7


title: Ctr3_LCL_H3K4me3


title: LCL case, biological replicate 28

source_name: LCL case

value: ATR-X syndrome


title: Ctr3_LCL_SC_input


title: Ctr2_LCL_H3K4me3


title: LCL control, biological replicate 5


title: Ctr2_LCL_SC_input


title: Case2_LCL_SC_input


title: LCL control, biological replicate 3


title: LCL case, biological replicate 25


title: Case1_LCL_SC_input


title: LCL case, biological replicate 23


title: Ctr3_LCL_H3K9me3


title: LCL case, biological replicate 26


title: LCL control, biological replicate 1


title: LCL case, biological replicate 19


title: LCL case, biological replicate 17


title: LCL case, biological replicate 27


title: LCL case, biological replicate 16


title: LCL case, biological replicate 24


title: LCL case, biological replicate 21


title: LCL case, biological replicate 20


title: Ctr1_LCL_SC_input


title: LCL case, biological replicate 22


title: Ctr2_LCL_H3K9me3


title: LCL case, biological replicate 11


title: LCL case, biological replicate 18


title: LCL case, biological replicate 15


title: LCL case, biological replicate 10


title: LCL case, biological replicate 12


title: Case3_LCL_H3K9me3


title: Case2_LCL_H3K9me3


title: LCL case, biological replicate 8


title: LCL case, biological replicate 6


title: Case1_LCL_H3K9me3


title: Ctr1_rep1_LCL_Runx3

extract_protocol:
108 cells were crosslinked with 2 mM EGS for 45 minuntes and 1% FA for 20 minutes (ATRX) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (Runx3). Cells were lysed and sonicated on the Covaris to give fragments of 100-300bp. Immunoprecipitation was performed by incubation of diluted chromatin overnight.
NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs).

value: Runx3 (39301Active motif + 653604 BioLegend)

value: two steps cross-linking


title: Case1_rep2_LCL_Runx3


title: Case1_rep1_LCL_Runx3


title: LCL case, biological replicate 9


title: Ctr2_LCL_Input_DC_Abcam


title: Panc02-SIY NT replicate 3

city: Portland

first: Michael

last: Gough

state: OR

address: 4805 NW Glisan St, Suite 2N35

institute: Earle A Chiles Research Institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Data were processed using the Cell Ranger pipeline (v3.1.0) and subsequently analyzed with the Loupe Browser from 10X Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/visualization/latest/what-is-loupe-cell-browser).
BCL to fastq conversion using cellranger mkfastq with cellranger v3.1.0 and dependency bcl2fastq2 v2.20.0
cellranger count with default settings run on each sample individually to generate single cell features counts
cellranger aggr with default settings (--normalize=mapped) to aggregate all samples into a single .cloupe file for exploration in Loupe Cell Browser
Assembly: mm10
Supplementary files format and content: Processed files pertaining to each individual samples are the tab seperated values and matrix files output from running cellranger count
Supplementary files format and content: The "Allsamples" supplemental files are te tab seperated values, barcodes, and matrix files output from running cellranger aggr on all 16 samples.

source_name: Tumor

extract_protocol:
Single-cell suspensions were processed on a 10X Chromium controller using the 10X Single Cell 3’ Reagent kit  (v3.0) according to manufacturer's instructions
scRNA-seq libraries were prepared using the 10X Single Cell 3’ Reagent kit  (v3.0) according to manufacturer's instructions

value: Tumor

value: Sorted CD45+ cells

value: Untreated


title: Ctr1_LCL_H3K9me3


title: Panc02-SIY RT replicate 2

description: 10x Genomics

value: Radiation 12Gy in vivo


title: Panc02-SIY NT replicate 2

description: 10x Genomics


title: Panc02-SIY RT replicate 4

description: 10x Genomics


title: Panc02-SIY NT replicate 4

description: 10x Genomics


title: LCL case, biological replicate 13


title: Panc02-SIY RT replicate 1

description: 10x Genomics


title: Panc02-SIY NT replicate 1

description: 10x Genomics


title: Ctr3_LCL_Input_DC_Abcam


title: LCL case, biological replicate 14


title: MC38 RT replicate 4

description: 10x Genomics


title: Panc02-SIY RT replicate 3

description: 10x Genomics


title: LCL case, biological replicate 4


title: MC38 RT replicate 3

description: 10x Genomics


title: LCL case, biological replicate 7


title: LCL case, biological replicate 5


title: MC38 RT replicate 1

description: 10x Genomics


title: LCL case, biological replicate 2


title: LCL case, biological replicate 1


title: MC38 NT replicate 4

description: 10x Genomics


title: Ctr1_LCL_Input_DC_Abcam


title: LCL case, biological replicate 3


title: MC38 NT replicate 3

description: 10x Genomics


title: BRD-K98645985-treated replicate 2

data_processing:
The reads were trimmed with Trim Galore (version 0.5.0) with default parameters.
Then reads were aligned to the reference mouse mm10 assembly plus ERCC spike-in sequences using STAR (version 2.7.5a).
The resulting alignments, recorded in BAM file, were sorted, indexed, and marked for duplicates with Picard MarkDuplicates function (version 2.19.0).
Transcript quantification was calculated using RSEM.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each sample

source_name: CD8+ T cells

growth_protocol: Naïve CD8 T cells were activated with anti-CD3/28 and ICAM

extract_protocol:
Standard
RNA were isolated by using Direct-zol RNA Microprep Kits (R2061, Zymo Research)
Libraries were prepared using KAP RNA HyperPrep Kit with RiboErase (HMR) (08098131702, Roche) and purified by AMPure SPRI beads (B23318, Beckman-Coulter).

treatment_protocol: CD8 T cells were treated with DMSO or 1uM BRD-K98645985 druing activation

value: CD8+ T cells

value: Wild type


title: MC38 NT replicate 2

description: 10x Genomics


title: BRD-K98645985-treated replicate 1


title: BRD-K98645985-treated replicate 4


title: Ctr1_LCL_Input_DC_H300

value: unaffected


title: WT Control replicate 3

value: DMSO


title: MC38 RT replicate 2

description: 10x Genomics


title: WT Control replicate 4


title: Ctr3_LCL_Input_DC_H300


title: BRD-K98645985-treated replicate 3


title: Ctr3_LCL_ATRX_Abcam

value: Abcam ab97508


title: WT Control replicate 1


title: MC38 NT replicate 1

description: 10x Genomics


title: Ctr2_LCL_ATRX_Abcam


title: DMSO-treated WT ATAC-seq replicate 3

description: First division

data_processing:
Paired-end sequencing reads were trimmed with Trim Galore (version 0.5.0) with default parameters.
Reads were aligned to a hybrid genome of reference mouse mm10 assembly and drosophila Ensembl r97 using Bowtie 2 (version 2.3.5.1) with settings --end-to-end --very-sensitive -X 2000.
The BAM file was filtered with SAMtools (version 1.9), BamTools (version 2.5.1) and scripts of nf-core/chipseq to discard reads, mates that were unmapped, or PCR/optical duplicates, or not primary alignments, or mapped to multiple locations, or mapped to ENCODE blacklisted regions; only reads mapped in proper pair were kept (-F 1804 -f 2 -q 30). Reads mapped to nucleosome free regions were filter by insert size < 109.
Peaks were called using MACS (version 2.1.2) with narrowPeak setting, --extsize 200, and recommended mappable genome size (default value for other parameters).
Chromatin accessibility signal was normalized by scaling to 1 million mapped reads to spike-in using BEDTools (version 2.27.1) and bedGraphToBigWig (version 377) with default parameters.
Assembly: mm10
Supplementary files format and content: BigWig files scaling tag count to 1 million mapped reads of spike-in genome.
Supplementary files format and content: Bed files of peaks called using MACS2

growth_protocol: Naïve CD8 T cells were activated with anti-CD3/28 and ICAM.

extract_protocol: 50,000 cells were pelleted at 500 x g for 5 min at 4°C. Samples were washed in 1 ml cold PBS and resuspended in 50 ul cold cell lysis buffer (10 mM Tris pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40). Nuclei were pelleted at 1000 x g for 10 min and resuspended in 50 ml transposition reaction mixture (25 ml TD buffer, 2.5 ml TDE1, 22.5 ml ddH2O) (20034197, Illumina). Samples were incubated at 42°C for 45 min. DNA was then purified using MiniElute PCR Purification Kit (28004, Qiagen). Libraries were barcoded and amplified with Q5 High-Fidelity 2x Master Mix (M0492S, NEB).

treatment_protocol: WT CD8 T cells were treated with DMSO or 1uM BRD-K98645985 druing activation.


title: WT Control replicate 2


title: 12696T S46

city: Bethesda

first: Josh

last: Stone

state: MD

address: 9000 Rockville Pike

department: CCR

institute: National Cancer Institue

data_processing:
The sequencing quality of each sample was assessed using FastQC.
Read- and alignment-level quality were assessed using FastQ Screen, Preseq, Picard tools, RSeQC and QualiMap.
Reads were trimmed for adapter sequences and low-quality bases using Cutadapt prior to alignment against the human reference genome, hg19, using STAR in two-pass mode with GENCODE v19 annotation
Gene expression levels were quantified using RSEM.
Assembly: Hg19

source_name: lung tumor

extract_protocol:
Total RNA was extracted from frozen lung tissues using TRIzol (Invitrogen) according to the manufacturer’s protocol. Only RNA samples with RNA sufficient RNA were included for analysis.
Libraries suitable for paired-ended sequencing were generated using Illumina’s TruSeq Stranded Total RNA Library Prep Kit.

tag: batch

value: B

tag: histology

value: Lung Cancer


title: DMSO-treated WT ATAC-seq replicate 2

description: First division


title: Ctr3_LCL_ATRX_H300

extract_protocol:
10^8 cells were crosslinked with 2 mM EGS for 45 minuntes and 1% FA for 20 minutes (ATRX) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (Runx3). Cells were lysed and sonicated on the Covaris to give fragments of 100-300bp. Immunoprecipitation was performed by incubation of diluted chromatin overnight.
NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs).

tag: phenotype

value: Santa Cruz H300 sc-15408


title: Ctr1_LCL_ATRX_Abcam

tag: antibody


title: Ctr2_LCL_ATRX_H300

tag: crosslinking


title: Ctr2_LCL_Input_DC_H300


title: DMSO-treated Arid1a KO ATAC-seq replicate 2

description: First division

value: Arid1a KO


title: Ctr1_LCL_ATRX_H300


title: BRD-K98645985-treated ATAC-seq replicate 3

description: First division


title: DMSO-treated Arid1a KO ATAC-seq replicate 1

description: First division


title: BRD-K98645985-treated ATAC-seq replicate 2

description: First division


title: DMSO-treated Arid1a KO ATAC-seq replicate 3

description: First division


title: Spleen_RSV1

city: Chongqing Provence

first: Yu

last: He

address: No.136, Zhongshan 2nd Road, Yuzhong District

institute: Children's Hospital of Chongqing Medical University

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as  follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Genome_build: Mus_musculus.GRCm38 V99
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each Sample

source_name: Spleen

growth_protocol: Female BALB/c mice (6–8 weeks old) were obtained from the Experimental Animal Center of Chongqing Medical University (Chongqing, China) and maintained in a specific pathogen-free environment with a 12 h light-dark cycle at a humidity of 55% ± 5% and temperature of 25 ± 2 °C. All mice were given free access to food and water.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The BALB/c mice were infected with RSV-A2 via intranasal inoculation under 2%–5% isoflurane and at 12 h post-RSV infection, mice were anesthetized with CO2 and sacrificed by cervical dislocation.

tag: strain

value: BALB/c

tag: Sex

value: female

value: Spleen

tag: age

value: 6-8 weeks old

value: Wildtype

tag: infection status

value: RSV-infected


title: Spleen_Control1

tag: tissue

value: control


title: Spleen_RSV3

tag: genotype


title: Spleen_Control3


title: Spleen_RSV2


title: Spleen_Control2


title: DMSO-treated WT ATAC-seq replicate 1

description: First division

tag: cell type


title: Case1_Ery_scRNA

data_processing:
Sequenced data were analysed using cellranger/3.0.2
Fastq files were generated using cellranger mkfastq
single cell feature counts for a single library were generated using cellranger count
Genome_build: hg19
Supplementary_files_format_and_content: filtered_feature_bc_matrix.h5

source_name: CD34 Culture

growth_protocol: CD34+ cells were isolated from either 50mL of donor peripheral blood or leucocyte reduction filters (obtained from the NHSBT) using Ficoll-Histopaque (Sigma) density centrifugation and positive bead selection (Miltenyi).  The CD34+ fraction was cryopreserved in freezing media consisting of 90% FBS (Gibco) and 10% DMSO.  Frozen CD34+ cells were recovered into base medium (IMDM Source BioScience UK Limited) containing 3% (v/v) AB Serum, 10 μg/mL insulin, 3 U/mL heparin (all from Sigma-Aldrich, Poole, UK), 2% (v/v) fetal bovine serum (Gibco), 200 μg/mL Human holo-transferrin (R&D Systems Minneapolis, MN, USA). For the expansion phase of the three-stage erythroid culture system the media was supplemented with 3 U/mL EPO (Eprex Janssen Cilag UK), 10 ng/mL stem cell factor (SCF) and 1 ng/mL IL-3 (Peprotech, London UK). Cells were maintained at a density of 2x105 cells until day 7 when they were transferred to phase 2 differentiation media consisting of base media with 3 U/mL EPO and 10 ng/mL SCF. From this point cells were staged using cytospins and FACS using a panel of 6 flurophore-conjugated monoclonal antibodies. Staining was conducted in FACS buffer containing 10% FBS and 90% PBS (both from Gibco, UK) and samples analysed using the Attune NxT (Life Technologies, California USA). Gates were set using fluorescence-minus-one controls run for each differentiation and data analysed using FlowJo software v 10.0.8r1. Cells were collected at day 10.

extract_protocol:
scRNA-seq was performed using the 10X Genomics ChromiumTM Single Cell 3ʹ Reagent Kits v3 with 10,000 cells as starting material following the manufacturers’ instructions
3ʹ Gene Expression Library Construction using the 10X Genomics ChromiumTM Single Cell 3ʹ Reagent Kits v3  following the manufacturers’ instructions
scRNA-seq

value: affected

value: ATR-X syndrome

value: Erythroid

tag: time

value: differentiation day 10


title: Ctr3_Ery_scRNA

value: unaffected


title: Brain_RSV3

source_name: Brain

value: Brain


title: Case2_Ery_scATAC

data_processing:
sc-ATAC-seq analysis was performed using the cellranger-atac workflow
fastq files were generated using cellranger-atac mkfastq
single-cell accessibility counts for the single libraries were generated using Cellranger-atac count
Genome_build: hg19
Supplementary_files_format_and_content: csv format, singlecell.csv (Per-barcode fragment counts & metrics)
Supplementary_files_format_and_content: tsv format, fragments.tsv (Barcoded and aligned fragment file)
Supplementary_files_format_and_content: bed format, peaks.bed  (Bed file of all called peak locations)

extract_protocol:
sc-ATAC-seq was performed using the 10X Genomics ChromiumTM i7 Multiplex Kit N Set A (1000084), ChromiumTM Chip E Single Cell ATAC Kit (1000086) and ChromiumTM Single Cell ATAC Library & Gel Bead Kit (1000111) using 7000 nuclei/µl as a stock concentration following the manufacturers’ instructions
ChromiumTM Single Cell ATAC Library & Gel Bead Kit
scATAC-seq


title: Case1_Ery_scATAC


title: Ctr3_Ery_scATAC


title: Brain_RSV2


title: Brain_Control3


title: Brain_RSV1


title: Brain_Control2


title: Intestine_RSV3

source_name: Intestine

value: Intestine


title: BRD-K98645985-treated ATAC-seq replicate 1

description: First division

value: CD8+ T cells

value: Wild type

tag: treatment


title: Case1_Ery_InputSC

extract_protocol:
isolation protocol:  For ChIP-seq, chromatin was crosslinked with 1 % formaldehyde at room temperature for 10 minutes. Crosslinking was quenched with 130 mM glycine, and cells were washed with cold PBS. Fixed material was stored at -80 ºC. Chromatin immunoprecipitation was performed using Agarose ChIP Assay Kit (Merck Millipore). Briefly, 107 cells were lysed by incubation on ice with lysis buffer for 15 minutes. In samples noted as spiked in, fixed Drosophila melanogaster S2 cells  were added. Lysed cells were sonicated on the Covaris S220. Insoluble material was removed by centrifugation and soluble material was diluted with dilution buffer. Immunoprecipitation was performed by incubation of diluted chromatin with antibodies for H3.3 (09-838, Millipore), H3K27me3 (ab6002, lot: GR275911-6-1, Abcam), H3K27ac (ab4729, lot: GR276932-1, Abcam), H3K4me3 (07-473, lot: 2664283, Millipore), H3K4me1 (ab195391, lot: GR304893-2, Abcam) overnight. Chromatin binding to Protein A and or G/agarose slurry, washes and elution were performed according to the manufacturer’s instructions.
DNA was purified by phenol-chloroform extraction and ethanol precipitation with NaOAc, and 2 µl GlycoBlue.
NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs).

tag: chip antibody

value: single step cross-linking

tag: spike in

value: sample spiked in with Fixed Drosophila melanogaster S2 cells


title: Ctr3_Ery_InputSC

tag: disease state


title: Intestine_Control3

value: BALB/c

value: female


title: Intestine_Control2

value: 6-8 weeks old


title: Intestine_RSV2

value: Wildtype


title: Intestine_RSV1

value: RSV-infected


title: Ctr2_Ery_scATAC

value: control


title: Lung_Control3

source_name: Lung

value: Lung


title: Lung_RSV1


title: Intestine_Control1


title: Lung_RSV3


title: Case2_Ery_H3K27ac

value: affected

value: ATR-X syndrome


title: Ctr2_Ery_H3K27ac

value: Erythroid


title: scRNAseq_HTO

data_processing:
Mars-seq: Reads were trimmed using Cutadapt
Mars-seq and m6A-IP: Reads were aligned to the genome using STAR
Mars-seq: Quantification was done using htseq-count as previously described in R. Kohen, BMC Bioinformatics, 2019.
m6A-IP: Normalization of paired libraries insert size was performed using in-house python scripts, between pairs of INPUT-IP samples. Alignment sorting and indexing were performed separately with samtools (V. 1.3.1) (Li et al. Bioinformatics, 2009).
m6A-IP: Identification of putative m6A sites was performed by assigning peak over input (POI) and peak over median (POM) scores to each site, as previously published (Schwartz et al, Cell 2014)
single-cell RNAseq: FASTQ files were aligned to the mouse mm10 reference genome using 10x Genomics Cell Ranger software v5.0.1
single-cell RNAseq: The UMI count matrix was converted to Seurat objects using R package Seurat
single-cell RNAseq: SCTransform function was used to normalize each dataset
Genome_build: Mars-seq, single-cell RNAseq: mm10, m6A-IP: mm9
Supplementary_files_format_and_content: MARS-seq: Excel file with Deseq2 output
Supplementary_files_format_and_content: m6A-IP: bam.tdf

source_name: B cells

extract_protocol: mRNA was extracted from sorted cells using mRNA direct kit (Invitrogen) and mRNA from each sample was barcoded during reverse transcription and pooled.

treatment_protocol: Splenic B cells were adoptively transferred to WT mice, which were immunized with NP-KLH for five days. All transferred cells were isolated by cell sorting.

value: B cells isolated from immunized mice

tag: mouse strain

value: B1-8hi CD23cre Tomato+ and B1-8hi CD23-Ythdf2fl/fl Tomato+


title: Lung_Control2


title: Lung_Control1


title: Brain_Control1

value: Brain


title: Case2_Ery_InputSC


title: Ctr2_Ery_InputSC

value: unaffected


title: scRNAseq_cDNA


title: Ctr3_Ery_H3K27ac


title: WT ATAC-seq replicate 6

data_processing:
Paired-end sequencing reads were trimmed with Trim Galore (version 0.5.0) with default parameters.
Reads were aligned to a hybrid genome of reference mouse mm10 assembly and drosophila Ensembl r97 using Bowtie 2 (version 2.3.5.1) with settings --end-to-end --very-sensitive -X 2000.
The BAM file was filtered with SAMtools (version 1.9), BamTools (version 2.5.1) and scripts of nf-core/chipseq to discard reads, mates that were unmapped, or PCR/optical duplicates, or not primary alignments, or mapped to multiple locations, or mapped to ENCODE blacklisted regions; only reads mapped in proper pair were kept (-F 1804 -f 2 -q 30).
Peaks were called using MACS (version 2.1.2) with narrowPeak setting, --extsize 200, and recommended mappable genome size (default value for other parameters).
Chromatin accessibility signal was normalized by scaling to 1 million mapped reads using BEDTools (version 2.27.1) and bedGraphToBigWig (version 377) with default parameters. For Myc KO vs wild type (WT replicate 4-6), it was scaled to 1 million reads mapped to spike-in drosophila genome.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files scaling tag count to 1 million mapped reads or 1 million mapped reads of spike-in genome.
Supplementary_files_format_and_content: Bed files of peaks called using MACS2

growth_protocol: Naïve CD8 T cells were activated with anti-CD3/28 and ICAM for 36hr. First division Myc high and Myc low cells were sorted.

treatment_protocol: For c-Myc KO samples, Naïve CD8 T cells were treated with 4OHT for 24hr., and then activated by anti-CD3/28 with ICAM for 36hr. For Arid1a KO samples, Naïve CD8 T cells were activated by anti-CD3/28 with ICAM for 36hr., and then first-division CD8 T cells were sorted.

value: CD8+ T cells

value: Wild type


title: Ctr1_Ery_InputSC

value: single step cross-linking


title: WT ATAC-seq replicate 5


title: Ctr1_Ery_H3K4me1


title: 9perACSH Xylose Rep 5

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

data_processing:
For RNA-seq analysis, the paired-end FASTQ files were were trimmed using Trimmomatic version 0.3 with the default settings except for a HEADCROP of 5, LEADING of 3, TRAILING of 3,  SLIDINGWINDOW of 3:30, and MINLEN of 36. After trimming the reads were aligned to the Z. mobilis (ZM4, 8b) genome using BWA-mem version 0.7.12-r1039 with default settings. Aligned reads were mapped to gene locations using HTSeq version 0.6.0 using default settings. Raw sequencing reads were normalized using the reads per kilobase per million mapped reads (RPKM).
Assembly: GCA_003052025.1
Supplementary files format and content: Zhang_RPKM_data.txt - RPKM normalized read count values from RNA-seq, linear format
Supplementary files format and content: Zhang_RawCounts_data.txt - Raw read count values from RNA-seq, linear format

organism: Zymomonas mobilis

source_name: bacteria

growth_protocol: Z. mobilis was grown in bioreactors as described in Yang, S., et al., Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032. Biotechnol Biofuels, 2018. 11: p. 125.

extract_protocol:
RNA was extracted from cultures using a phenol-chloroform method as described in Rhodius, V.A. and C.A. Gross, Using DNA microarrays to assay part function. Methods Enzymol, 2011. 497: p. 75-113.
Illumina Low Input RNASeq w/rRNA Depletion: rRNA was removed from 100 ng of total RNA using Ribo-Zero rRNA Removal Kit (Illumina). Stranded cDNA libraries were generated using the Illumina Truseq Stranded mRNA Library Prep kit. The rRNA depleted RNA was fragmented and reversed transcribed using random hexamers and SSII (Invitrogen) followed by second strand synthesis. The fragmented cDNA was treated with end-pair, A-tailing, adapter ligation, and 10 cycles of PCR. The prepared library was quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument. The quantified library was then multiplexed with other libraries, and the pool of libraries was then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v4, and Illumina’s cBot instrument to generate a clustered flow cell for sequencing. Sequencing of the flow cell was performed on the Illumina HiSeq 2500 sequencer using HiSeq TruSeq SBS sequencing kits, v4, following a 2x100 indexed run recipe.

treatment_protocol: Samples for RNA-seq were collected by mixing 10 mL of culture with 1.25 mL ice-cold unbuffered phenol and ethanol mixture (5:95, vol/vol) as described in chwalbach, M.S., et al., Complex physiology and compound stress responses during fermentation of alkali-pretreated corn stover hydrolysate by an Escherichia coli ethanologen. Appl Environ Microbiol, 2012. 78(9): p. 3442-57.

value: Z. mobilis 2032

value: bacteria

value: 9perACSH Xylose


title: Ctr1_Ery_H3K27ac


title: Myc KO ATAC-seq replicate 2

value: Myc KO


title: Ctr1_Ery_H3K4me3


title: Myc KO ATAC-seq replicate 3


title: WT ATAC-seq replicate 4


title: Myc KO ATAC-seq replicate 1


title: Lung_RSV2

value: BALB/c

value: female

value: 6-8 weeks old

value: Wildtype

value: RSV-infected


title: 9perACSH Xylose Rep 4