title: BMDM, WT-1

data_processing:
The libraries were sequenced on an DNBSEQ-T7 platform and 150 bp paired-end reads were generated. About 50M raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads.
Then about 49M clean reads for each sample were retained for subsequent analyses.
The clean reads were mapped to the reference genome using HISAT22. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: grcm38
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample

source_name: bone marrow

growth_protocol: The femur and tibia were collected from mice , and bone marrow cells were ﬂushed with complete DMEM containing 50 mg/ml streptomycin and 10% FBS. Erythrocytes were removed via treatment with red blood cell lysis buffer, and the cell suspensions were ﬁltered through a 40-μm cell strainer for the removal of any cell clumps. The single-cell suspensions were then cultured for 1 h at 37 °C, and non-adherent cells were collected and re-plated in complete DMEM with 25% medium conditioned by recombinant mouse M-CSF (carrier-free, 50 ng/ml). For full differentiation of BMDMs, the cells were cultured for an additional 8 days with replacement of the medium every 2 days.

treatment_protocol: The Escherichia coli (E. coli), Staphylococcus aureus (S. aureus) and Candida albicans (C. albicans) were obtained from the China General Microbiological Culture Collection Center (CGMCC) (Beijing, China). Bacteria were cultured overnight in indicated medium and washed twice with PBS. Followed by treatment with LPS (10mg/kg) or infected with E. coli (MOI, 50), S. aureus (MOI, 50), C. albicans (MOI, 30) for wild-type BMDMs at 12 hours

value: bone marrow

value: Macrophage

value: None (Control)


title: HeLa_noAb_rep1

status: Public on Jan 14 2026

type: SRA

city: Chicago

first: Chuan

last: He

state: Illinois

address: 929 E 57th St., GCIS E319

country: USA

institute: The University of Chicago

description: Library name: HeLa_noAb_rep1

library_source: transcriptomic

data_processing:
The FASTQ file was trimmed using Cutadapt (v4.6) and aligned to ribosomal RNA (rRNA) sequences with Bowtie2 (v2.4.2) to filter out rRNA reads. The remaining non-rRNA reads were aligned to the reference genome using STAR (v2.7.3a), and PCR duplicates were removed with UMI-tools (v1.1.1).
Assembly: GRCh38.p13, GENCODE Release 39; GRCm38.p6, GENCODE Release M25
Supplementary files format and content: bigWig files

molecule: total RNA

organism: Homo sapiens

source_name: Cervical cancer

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and  100 U/mL penicillin-streptomycin (Gibco). Mouse embryonic stem cells were cultured in DMEM (Invitrogen) supplemented with 20% FBS (GeminiBio), 1 mmol/L L-glutamine (Gibco), 1% nonessential amino acid (Gibco), 100 U/mL penicillin-streptomycin (Gibco), 1,000 U/mL leukemia inhibitory factor (LIF, Millipore), 0.1 mmol/L 2-mercaptoethanol (Sigma), 3 μmol/L CHIR99021 (Stemcell), 1 μmol/L PD0325901 (Stemcell), and 1% EmbryoMax nucleosides (100×, Millipore). All cell lines were cultured in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Cells were fixed with 1.5% paraformaldehyde for 10 minutes, quenched with 125 mM glycine at room temperature for 5 minutes, and permeabilized with 0.5% Triton X-100 on ice for 10 minutes. Samples were then blocked with 1 mg/ml BSA, followed by sequential staining with a primary antibody, a secondary antibody, and protein A/G-reverse transcriptase. In situ reverse transcription was performed at 37°C for 1 h. Subsequently, cells were digested with proteinase K at 37°C for 2 h. Total nucleic acids were extracted using phenol-chloroform and concentrated by ethanol precipitation.
Biotinylated cDNA was enriched using streptavidin beads. A 3' cDNA adapter (5′Phos-NNNNNNNNAGATCGGAAGAGCGTCGTGT-3′SpC3) was ligated using T4 RNA ligase 1 by incubating at 25°C for 16 h. The cDNA was then recovered from the beads. The library was prepared through PCR amplification using NGS sequencing primers, followed by gel purification to isolate fragments between 180 bp and 400 bp.

tag: tissue

value: Cervical cancer

tag: cell line

value: HeLa

tag: cell type

value: Cervical cancer cells

tag: genotype

value: WT

tag: treatment

tag: antibody


title: Cortex, CAG-Cre Pos, RVAff, rep2

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

description: Library name: 834

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.101
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

organism: Mus musculus

source_name: cortex

extract_protocol:
Purified RNA extracted from homogenized coritcal tissue using PureLink RNA extraction kit. 5-10 ug of total RNA was used for construction of sequencing libraries
RNA libraries were created using Poly-A selection

value: cortex

value: CAG-Cre.pos; Reverb.Alpha.fl/fl

value: Tamoxifen 4mg/day x 5 days at 2 months


title: CTRL071

city: Houston

first: Warapen

last: Treekitkarnmongkol

state: TX

address: 2130 W. Holcombe Blvd.,  Unit 2951

department: Translational Molecular Pathology

institute: UT MD Anderson Cancer Center

description: Control

library_source: other

data_processing:
Raw FASTQ file of each sample was parsed, normalized into count per million and transformed to log2CPM using HTG EdgeSeq Parser and HTG EdgeSeq Reveal software.
Assembly: The miRNA probe list is based on miRBase version 20.
Supplementary files format and content: Raw FASTQ file of each sample was parsed, normalized into count per million and transformed to log2CPM using HTG EdgeSeq Parser and HTG EdgeSeq Reveal software.

molecule: other

source_name: Plasma

extract_protocol:
15 uL of plasma was profiled for miRNAs by the extraction-free method using the HTG edge miRNA whole transcriptome assay kit (HTG Molecular, Tuscon, AZ, Cat# 916-001-024) according to the recommended vendor’s protocol.
Probes hybrized to target miRNAs were retrieved and added sequencing adapters as well as sample barcodes via PCR for preparing library. The libraries were quantified by quantitative PCR (qPCR) using KAPA Library Quantification kit (Roche, Cat# KK4824) and loaded onto the MiSeq (Illumina) together with the MiSeq Reagent Kit v3 (150 cycles) (Illumina, Cat# MS-102-3001).

value: Plasma

tag: cohort

value: Diagnostic cohort

tag: disease

value: Control


title: BMDM, S. aureus-2

city: Xi'an

first: Jing

last: Geng

address: No.30 Huangcheng West Road, Xiwu Av (Administration, Teaching, Residential area

department: The Second Affiliated Hospital

country: China

institute: Xi’an Jiaotong University

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Staphylococcus aureus


title: Cortex, CAG-Cre Neg RVAff, rep4

description: Library name: 843

value: CAG-Cre.neg; Reverb.Alpha.fl/fl


title: Cortex, CAG-Cre Neg RVAff, rep2

description: Library name: 831


title: HeLa_noAb_rep2

description: Library name: HeLa_noAb_rep2


title: HeLa_m6A_pRT13_rep1

description: Library name: HeLa_m6A_pRT13_rep1

value: m6A antibody (CST,Cat #56593)


title: CTRL068

description: Control


title: BMDM, S. aureus-1


title: BMDM, WT-2


title: Raw264.7, OE-Calhm6fl-1

description:
C6FL-1
overexpression of full-length Calhm6

data_processing:
The libraries were sequenced on an DNBSEQ-T7 platform and 150 bp paired-end reads were generated. About 49M raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads.
Then about 48M clean reads for each sample were retained for subsequent analyses.
The clean reads were mapped to the reference genome using HISAT22. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: grcm38
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample

growth_protocol: RAW264.7 cell lines were obtained from the National Collection of Authenticated Cell Cultures (Shanghai, China), tested for mycoplasma contamination and were found to be negative, then were cultured in DMEM supplemented with 10% FBS and 1× penicillin-streptomycin (Invitrogen).

value: macrophage


title: Cortex, CAG-Cre Neg RVAff RVBff, rep6

description: Library name: 692

value: CAG-Cre.neg; Reverb.Alpha.fl/fl ; Reverb.Beta.fl/fl


title: HeLa_IgG_rep2

description: Library name: HeLa_IgG_rep2

value: IgG


title: Cortex, CAG-Cre Pos, RVAff, rep3

description: Library name: 835


title: CTRL067

description: Control


title: HeLa_m6A_pRT13_rep2

description: Library name: HeLa_m6A_pRT13_rep2


title: Raw264.7, OE-Calhm6fl-2

description:
C6FL-2
overexpression of full-length Calhm6


title: Raw264.7, OE-Calhm6iso-1

description:
C6iso3-1
overexpression of Calhm6 isoform


title: HeLa_m6A_pRT30_rep2

description: Library name: HeLa_m6A_pRT30_rep2


title: CTRL063

description: Control


title: BMDM, E. coli-2

value: bone marrow

value: Macrophage

value: Escherichia coli


title: Cortex, CAG-Cre Neg RVAff, rep1

description: Library name: 829


title: CTRL061

description: Control


title: Cortex, CAG-Cre Pos RVAff RVBff, rep5

description: Library name: 684

value: CAG-Cre.pos; Reverb.Alpha.fl/fl ; Reverb.Beta.fl/fl


title: CTRL062

description: Control


title: Cortex, CAG-Cre Pos, RVAff, rep1

description: Library name: 842


title: HeLa_m6A_no2Ab_pRT30_rep2

description: Library name: HeLa_m6A_no2Ab_pRT30_rep2

value: Cervical cancer

value: HeLa

value: Cervical cancer cells

value: WT

value: without the secondary antibody


title: HeLa_CSTm6A_rep1

description: Library name: HeLa_CSTm6A_rep1


title: BMDM, C. albicans-2

value: Candida albicans


title: CTRL066

description: Control

value: Plasma

value: Diagnostic cohort

value: Control


title: CTRL065

description: Control


title: CTRL060

description: Control


title: BMDM, LPS_IFNγ-2

value: LPS, IFNγ


title: HeLa_m6A_no2Ab_pRT30_rep1

description: Library name: HeLa_m6A_no2Ab_pRT30_rep1

value: m6A antibody (CST,Cat #56593)


title: HeLa_m6A_pRT3_rep2

description: Library name: HeLa_m6A_pRT3_rep2


title: Cortex, CAG-Cre Neg RVAff RVBff, rep3

description: Library name: 680

value: cortex

value: CAG-Cre.neg; Reverb.Alpha.fl/fl ; Reverb.Beta.fl/fl

value: Tamoxifen 4mg/day x 5 days at 2 months


title: CTRL058

description: Control


title: BMDM, LPS_IFNγ-1

value: bone marrow

value: Macrophage


title: HeLa_noAb_pRT30_rep1

description: Library name: HeLa_noAb_pRT30_rep1


title: Cortex, CAG-Cre Neg RVAff RVBff, rep5

description: Library name: 686


title: HeLa_m6A_pRT3_rep1

description: Library name: HeLa_m6A_pRT3_rep1


title: HeLa_noAb_pRT30_rep2

description: Library name: HeLa_noAb_pRT30_rep2


title: CTRL057

description: Control


title: AHJF-EFWT-noIAV-2

type: RNA

city: Baltimore

first: Adonis

last: D'Mello

state: Maryland

address: Health Science Facility III, 670 W Baltimore St 3rd floor

institute: IGS- University of Maryland Baltimore

description: Bacterial infection

data_processing: Data were processed using the NanoString nSolver software v4.0 comparing EF3030 mutants to wildtype, and pH1N1+EF3030 infections EF3030 infections (including initial QC, negative control count thresholding negative control count thresholding value of 30, positive control normalization using geometric mean with default settings but excluding housekeeping genes that were found to vary in expression in our assays, and calculation of expression ratios).

source_name: Human Lung

growth_protocol: HBECs were isolated from donated human lung tissue that was not viable for transplant provided by International Institute for the Advancement of Medicine (IIAM) and collected as previously described [PMID:15492373]. Isolated cells were initially grown on 10 cm collagen coated dishes (Advanced Biomatrix) in BronchiaLife Complete Growth Media (LifeLine Cell Technologies) at 37°C with 5% CO2. After reaching 80% confluence, cells were passaged to 6.5 mm permeable supports with a 4um pore size (Costar) coated with FNC coating mix (AthenaES) and maintained in the same media. Once cells reached 100% confluency, growth media was removed from the apical surface and the cells were differentiated with PneumaCult-ALI basal medium (StemCell technologies). Basal media was replaced every day for seven days, and then three times weekly until the cell surface was 70% ciliated, usually occurring at approximately 18-21 days on air. During growth, cells were washed three times per week with PBS (Gibco) to remove excess mucus. All protocols using human tissue were reviewed by the UAB IRB as exempt as deidentified tissue procured through the IIAM.

extract_protocol: RNeasy mini kit (Qiagen Protocol).

treatment_protocol: Mature HBECs were washed, basally fed with PneumaCult-ALI basal medium and infected with 100,000 plaque forming units of A/California/07/2009 (H1N1). H1N1 was obtained from the Center for Disease Control and Prevention. After 72 hours of infection, HBECs were infected with 1,000 colony forming units of Spn in 20 uL of physiological saline. Spn was grown in beef heart infusion broth (Becton, Dickson and Company) supplemented with 10% catalase (Worthington) and 10% horse serum for 10-12 hours at 37°C with 5% CO2 before quantification by OD600 reading and dilution in physiological saline. After 6 hours of Spn infection, the apical surface was washed with 110uL of 10mM Tris HCl and 0.1mM EDTA. 10 uL of this wash was removed for quantification of Spn by growth on sheep’s blood agar plates (Remel). 2.5 uL of 10% SDS and 2uL of 10% sodium deoxycholate was add to the remaining 100 uL of wash and incubated on the cell surface for 20 minutes at room temperature to ensure complete lysis of the HBECs and Spn. HBECs were scraped and collected in 600uL buffer RLT from the RNeasy mini kit (Qiagen) and RNA was extracted per kit protocol.

tag: infection

value: Streptococcus pneumoniae EF3030

value: Infected human broncial epithelium

tag: replicate


title: Cortex, CAG-Cre Pos RVAff RVBff, rep2

description: Library name: 669

value: CAG-Cre.pos; Reverb.Alpha.fl/fl ; Reverb.Beta.fl/fl


title: Cortex, CAG-Cre Neg RVAff RVBff, rep4

description: Library name: 685


title: AHJF-EFWT-noIAV-3

description: Bacterial infection


title: HeLa_m6A_pRT30_rep1

description: Library name: HeLa_m6A_pRT30_rep1

value: Cervical cancer

value: HeLa

value: Cervical cancer cells


title: CTRL059

description: Control


title: CTRL064

description: Control


title: Cortex, CAG-Cre Neg RVAff RVBff, rep2

description: Library name: 671


title: HeLa_m6A_deepseq_rep1

description: Library name: HeLa_m6A_deepseq_rep1

value: WT


title: BMDM, C. albicans-1

value: Candida albicans


title: BMDM, E. coli-1

value: Escherichia coli


title: Cortex, CAG-Cre Pos RVAff RVBff, rep1

description: Library name: 668


title: HeLa_noAb_deepseq_rep2

description: Library name: HeLa_noAb_deepseq_rep2


title: CTRL056

description: Control

value: Plasma

value: Diagnostic cohort

value: Control


title: CTRL054

description: Control


title: Cortex, CAG-Cre Pos RVAff RVBff, rep3

description: Library name: 670

value: cortex


title: Cortex, CAG-Cre Pos RVAff RVBff, rep4

description: Library name: 681


title: HeLa_noAb_deepseq_rep1

description: Library name: HeLa_noAb_deepseq_rep1


title: HeLa_m6A_deepseq_rep2

description: Library name: HeLa_m6A_deepseq_rep2

value: m6A antibody (CST,Cat #56593)


title: CTRL053

description: Control


title: Cortex, CAG-Cre Neg DBDff, rep4

description: Library name: 4053

value: CAG-Cre.neg; Reverb.Alpha.-DBDfl/fl

value: Tamoxifen 4mg/day x 5 days at 2 months


title: CTRL055

description: Control


title: AHJF-EFWT-IAV-3

description: Influenza + Bacterial infection

tag: agent

value: Influenza A pH1N1


title: AHJF-EFWT-IAV-1

description: Influenza + Bacterial infection

value: Streptococcus pneumoniae EF3030


title: Ruch2, L122R, H3K27ac, R1

city: Charlestown

first: Luis Antonio

last: Corchete

institute: Krantz Family Center for Cancer Research

description: Ruch2, L122R, H3K27ac, R1

library_source: genomic

data_processing:
Reads were trimmed for quality and adapters were removed using trimgalore (v.0.4.3)
Alignment against the human genome (version hg38, Ensembl) was carried out using the BWA-MEM algorithm (v. 0.7.15) and the resulting SAM files were transformed to BAM, sorted by coordinates and indexed using the samtools tool (v.1.4.1). Samtools was also used for the removal of the mitochondrial chromosome and unscaffolded regions. The cDNA-detector (v. 0.1.0) program was used to remove possible cDNA contamination in the BAM files. Duplicate marking was carried out as the sambamba tool (v. 1.0.1). Low-quality reads were removed with the FilterBAM tool (v. 2) by setting a Phred score of 30 as the minimum alignment quality.
Determination of the ChIP-seq peaks for each of the histone markers was carried out with the macs2 (v. 2.0.10) program using the “callpeak” option and input samples as a control. Blacklisted regions were obtained from ENCODE (version GRCh38)and removed using the “subtract” command of bedtools (v. 2.30.0)
Bigwig files were generated using the “bamCoverage” option of the deeptools tool (v.3.1.2), with a bin size of 10 bp and applying a counts per million (CPM)-like normalization along with the “–centerReads” and “–ignoreDuplicates” options. The scores for each genomic region were calculated using the “computeMatrix” option also from deeptools, using an upstream to downstream distance of 1,500 bp from the center of the interval.
Assembly: GRCh38
Supplementary files format and content: bigWig, encodePeak (except for input samples)

molecule: genomic DNA

growth_protocol: RD and Ruch2 cells with or without treatment were cultured in DMEM supplemented with 10% FBS, PenStrep, and collected before confluency for ChIP-seq experiments.

extract_protocol:
Cells were crosslinked with a 1% formaldehyde final concentration, then resuspended and digested with Micrococcal nuclease. Digested DNA fragments between 150-900 base pairs were sonicated using a Branson 250 sonicator, with pulse amplitude of 32%, pulsing for 0.7 seconds with 1.3 seconds in between for a total pulse period of 5 minutes on ice. Chromatin was diluted 10x and incubated with 3-5 ug of antibodies overnight at 4°C with agitation. Histone complexes were precipitated by Protein G Magnetic Beads, then washed 3x with a low salt solution and 1x with a high salt solution. Chromatin was eluted and cross-linking was reversed with 5M NaCl and then treated with Proteinase K. DNA was purified using DNA wash Buffer and then eluted with Elution Buffer.
ChIP libraries were built by starting from ChIP DNA (5ng), followed by end preparation, adaptor ligation and amplification, indexed with Dual Index 7 Primers and 5 Primers from Multiplex Oligos (CST# 47538) compatible with Illumina. AMPure XP and SPRI Select beads were used to clean up amplified DNA.

treatment_protocol: RD and Ruch2 cells with the dox-inducible contruct, were seeded, and then treated with doxycycline, for 72 hours, before collection for chromatine immunoprecipitation.

tag: myod1 status

tag: chip antibody


title: Cortex, CAG-Cre Pos DBDff, rep3

description: Library name: 4055

value: CAG-Cre.pos; Reverb.Alpha.-DBDfl/fl


title: Ruch2, L122R, Input, R1

description: Ruch2, L122R, Input, R1


title: Cortex, CAG-Cre Pos DBDff, rep2

description: Library name: 4051


title: AHJF-EFWT-IAV-2

description: Influenza + Bacterial infection

value: Infected human broncial epithelium


title: Cortex, CAG-Cre Neg RVAff RVBff, rep1

description: Library name: 667

value: CAG-Cre.neg; Reverb.Alpha.fl/fl ; Reverb.Beta.fl/fl


title: AHJF-EFd7920d7890-noIAV-2

description: Bacterial infection


title: Ruch2, L122R, H3K4me3, R1

description: Ruch2, L122R, H3K4me3, R1


title: CTRL049

description: Control


title: AHJF-EFWT-noIAV-1

description: Bacterial infection


title: Ruch2, MYOD1, H3K4me3, R1

description: Ruch2, MYOD1, H3K4me3, R1

value: Wild type


title: CTRL048

description: Control


title: Cortex, CAG-Cre Neg DBDff, rep1

description: Library name: 4046


title: CTRL052

description: Control


title: CTRL051

description: Control


title: Ruch2, L122R, L122R, R1

description: Ruch2, L122R, L122R, R1

value: Flag


title: CTRL047

description: Control


title: AHJF-EFd7920d7890-IAV-1

description: Influenza + Bacterial infection


title: AHJF-EFd7920d7890-noIAV-3

description: Bacterial infection


title: Cortex, CAG-Cre Neg DBDff, rep3

description: Library name: 4052


title: CTRL050

description: Control


title: TG2A.NG.PB.S2iL rep1

city: Guangzhou

first: Man

last: Zhang

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Research

institute: Guangzhou Laboratory

description:
Library name: TG2A.NG.PB.S2iL rep1
TG2A.NG.PB.S2iL rep1

data_processing:
The raw RNA-seq reads were processed using TrimGalore to remove adapter sequences and low-quality bases. The cleaned reads were then aligned to mm10 with STAR (V2.7.6a). Gene expression values were normalized across samples using the variance modeling tool DESeq2
Assembly: mm10
Supplementary files format and content: Tab-separated values files

molecule: polyA RNA

extract_protocol:
Cellular total RNA was collected using a Trizol extraction method
RNA libraries were constructed using the Illumina Ribo-Zero plus rRNA Depletion kit (20037135, Illumina)

value: ESC

value: wild-type

value: ESC culture(+lif, 2i)


title: CTRL046

description: Control

value: Plasma


title: CTRL045

description: Control

value: Diagnostic cohort


title: AHJF-EFd7920d7890-noIAV-1

description: Bacterial infection


title: AHJF-EFd7920d7890-IAV-3

description: Influenza + Bacterial infection


title: Cortex, Aldh1l1-Cre RVAff RVBff Neg control, rep2

description: Library name: 49_aldh1l1_rvab

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.7.9a
Gene counts quantitated with Subread:featureCount 2.0.3 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.101
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

value: Aldh1l1-Cre.neg; Reverb.Alpha.fl/fl ; Reverb.Beta.fl/fl

value: Tamoxifen 4mg/day x 5 days at 2 months old via gavage


title: Cortex, CAG-Cre Neg DBDff, rep2

description: Library name: 4048

value: cortex


title: Ruch2, MYOD1, H3K27ac, R1

description: Ruch2, MYOD1, H3K27ac, R1


title: AHJF-EFd7920d7890-IAV-2

description: Influenza + Bacterial infection


title: EZH2KO.10S2iL rep2

description:
Library name: EZH2KO.10S2iL rep2
EZH2KO.10S2iL rep2


title: RD, L122R, H3K27ac, R2

description: RD, L122R, H3K27ac, R2

source_name: RD

value: RD


title: CTRL043

description: Control

value: Control


title: CTRL044

description: Control


title: AEIC-EFWT-noIAV-1

description: Bacterial infection


title: Ruch2, MYOD1, MYOD1, R1

description: Ruch2, MYOD1, MYOD1, R1


title: EZH2KO.10S2iL rep1

description:
Library name: EZH2KO.10S2iL rep1
EZH2KO.10S2iL rep1


title: Cortex, CAG-Cre Pos DBDff, rep1

description: Library name: 4050

value: Tamoxifen 4mg/day x 5 days at 2 months


title: EZH2KO.10SL.rescued rep2

description:
Library name: EZH2KO.10SL.rescued rep2
EZH2KO.10SL.rescued rep2

value: ESC culture(+lif)


title: Ruch2, MYOD1, Input, R1

description: Ruch2, MYOD1, Input, R1


title: CTRL042

description: Control


title: TG2A.NG.PB.S2iL rep2

description:
Library name: TG2A.NG.PB.S2iL rep2
TG2A.NG.PB.S2iL rep2


title: AEIC-EFWT-noIAV-3

description: Bacterial infection

value: Streptococcus pneumoniae EF3030


title: EZH2KO.10SL.rescued rep1

description:
Library name: EZH2KO.10SL.rescued rep1
EZH2KO.10SL.rescued rep1


title: AEIC-EFWT-IAV-2

description: Influenza + Bacterial infection

value: Influenza A pH1N1

value: Infected human broncial epithelium


title: RD, L122R, H3K4me3, R1

description: RD, L122R, H3K4me3, R1


title: AEIC-EFd7920d7890-noIAV-3

description: Bacterial infection


title: CTRL040

description: Control


title: AEIC-EFWT-noIAV-2

description: Bacterial infection


title: CTRL069

description: Control


title: CTRL039

description: Control


title: RD, L122R, L122R, R1

description: RD, L122R, L122R, R1


title: RD, L122R, H3K27ac, R1

description: RD, L122R, H3K27ac, R1


title: RD, L122R, H3K4me3, R2

description: RD, L122R, H3K4me3, R2


title: EZH2KO.10SL rep3

description:
Library name: EZH2KO.10SL rep3
EZH2KO.10SL rep3


title: ESC.rep3

description:
Library name: ESC.rep3
ESC.rep3


title: RD, L122R, Input, R2

description: RD, L122R, Input, R2


title: RD, L122R, L122R, R2

description: RD, L122R, L122R, R2


title: RD, L122R, Input, R1

description: RD, L122R, Input, R1


title: CTRL041

description: Control


title: RD, MYOD1, H3K4me3, R2

description: RD, MYOD1, H3K4me3, R2

value: Wild type


title: AEIC-EFd7920d7890-IAV-3

description: Influenza + Bacterial infection


title: ESC rep2

description:
Library name: ESC rep2
ESC rep2


title: AEIC-EFd7920d7890-IAV-1

description: Influenza + Bacterial infection


title: CTRL035

description: Control


title: Beefy_S_2

city: 江苏省南京市

first: 浩

last: 路

address: 江苏省南京市南京农业大学滨江校区

institute: 南京农业大学郭仁朋课题组

description: Library name: Sample 14

data_processing:
Raw sequencing data were generated using Illumina platforms, and base calling was performed with Illumina CASAVA software. Raw reads were subjected to quality control to remove adapter sequences, reads containing poly-N, and low-quality reads, resulting in high-quality clean reads. All downstream analyses were conducted based on these clean reads.
Assembly: Clean reads were aligned to the Bos taurus reference genome (genome assembly ARS-UCD2.0) using HISAT2 (v2.2.1). The reference genome index was built with HISAT2, and gene model annotation files corresponding to ARS-UCD2.0 were obtained from the official genome database.
Supplementary files format and content: GProcessed data files format and content: Gene-level read counts were generated using featureCounts (v1.5.0-p3). Gene expression levels were quantified as FPKM based on gene length and mapped read counts. Differentially expressed genes were identified using the DESeq2 R package. Functional enrichment analyses, including GO and KEGG pathway analyses, were performed using the clusterProfiler package.

organism: Bos taurus

source_name: bovine muscle stem cells

growth_protocol: BMuSCs were cultured at 37 °C in a humidified atmosphere containing 5% CO₂. For serum-containing culture, culture dishes were pre-coated with collagen Ⅰ (Gibco), and cells were maintained in DMEM/F12 (Gibco) supplemented with 15% FBS (Gibco), 5 ng/mL basic fibroblast growth factor (bFGF, GenScript), penicillin (100 U/mL), and streptomycin (100 µg/mL). For serum-free culture, culture dishes were pre-coated with vitronectin (Gibco) at 1 µg/cm², and cells were cultured in DMEM/F12 (Gibco) supplemented with 200 µg/mL L-ascorbic acid 2-phosphate trisodium salt (Gibco), 20 µg/mL insulin (Abmole), 20 µg/mL transferrin (Sigma), 20 ng/mL sodium selenite (Sigma), 40 ng/mL bFGF (GenScript), 0.1 ng/mL transforming growth factor-β3 (TGF-β3, GenScript) and neuregulin 1 (NRG1, GenScript), 800 µg/mL recombinant albumin (Sigma), as well as penicillin (100 U/mL) and streptomycin (100 µg/mL). In addition, small molecules were supplemented with 500 nM forskolin (Selleck) and/or 1 µM SB202190 (Selleck).

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: Following standard subculturing procedures, at least 1×10⁶ cells were harvested, transferred into a 1.5 mL microcentrifuge tube, and resuspended in 500 μL of PBS. Cells were centrifuged at 12,000 rpm for 2 min, after which the supernatant was discarded. The resulting cell pellet was immediately flash-frozen in liquid nitrogen for 2 min and subsequently stored at −80 °C. All frozen samples were shipped on dry ice to Novogene Corporation for RNA sequencing analysis.

value: bovine muscle stem cells


title: CTRL034

description: Control


title: AEIC-EFd7920d7890-noIAV-2

description: Bacterial infection


title: EZH2KO.10SL rep2

description:
Library name: EZH2KO.10SL rep2
EZH2KO.10SL rep2

value: ESC


title: EZH2KO.10SL rep1

description:
Library name: EZH2KO.10SL rep1
EZH2KO.10SL rep1


title: CTRL037

description: Control


title: AEIC-EFd7920d7890-noIAV-1

description: Bacterial infection


title: CTRL038

description: Control


title: CTRL036

description: Control


title: RD, MYOD1, MYOD1, R2

description: RD, MYOD1, MYOD1, R2

value: Flag


title: AEIC-EFWT-IAV-1

description: Influenza + Bacterial infection


title: Beefy_S_3

address: 江苏省南京市南京农业大学滨江校区

institute: 南京农业大学郭仁朋课题组

description: Library name: Sample 15


title: CTRL033

description: Control


title: ESC rep1

description:
Library name: ESC rep1
ESC rep1

value: wild-type


title: Beefy_S_1

address: 江苏省南京市南京农业大学滨江校区

institute: 南京农业大学郭仁朋课题组

description: Library name: Sample 13


title: AEIC-EFd7920d7890-IAV-2

description: Influenza + Bacterial infection


title: TG2A.NG.PB.ESC rep1

description:
Library name: TG2A.NG.PB.ESC rep1
TG2A.NG.PB.ESC rep1


title: Beefy_FS_3

address: 江苏省南京市南京农业大学滨江校区

institute: 南京农业大学郭仁朋课题组

description: Library name: Sample 12


title: RD, MYOD1, H3K27ac, R1

description: RD, MYOD1, H3K27ac, R1


title: RD, MYOD1, H3K27ac, R2

description: RD, MYOD1, H3K27ac, R2


title: TG2A.NG.PB.ESC rep2

description:
Library name: TG2A.NG.PB.ESC rep2
TG2A.NG.PB.ESC rep2


title: RD, MYOD1, Input, R2

description: RD, MYOD1, Input, R2


title: CTRL032

description: Control

value: Plasma


title: CTRL031

description: Control

value: Diagnostic cohort


title: Beefy_FS_2

address: 江苏省南京市南京农业大学滨江校区

institute: 南京农业大学郭仁朋课题组

description: Library name: Sample 11


title: EPZ.iPrE2 rep2

description:
Library name: EPZ.iPrE2 rep2
EPZ.iPrE2 rep2

value: PrESC

value: PrESC culture


title: EPZ.iPrE2 rep1

description:
Library name: EPZ.iPrE2 rep1
EPZ.iPrE2 rep1


title: RD, MYOD1, H3K4me3, R1

description: RD, MYOD1, H3K4me3, R1


title: RD, MYOD1, Input, R1

description: RD, MYOD1, Input, R1


title: Beefy_FS_1

address: 江苏省南京市南京农业大学滨江校区

institute: 南京农业大学郭仁朋课题组

description: Library name: Sample 10


title: C57.PrESC rep2

description:
Library name: C57.PrESC rep2
C57.PrESC rep2


title: EPZ.iPrE1 rep2

description:
Library name: EPZ.iPrE1 rep2
EPZ.iPrE1 rep2


title: CTRL028

description: Control


title: RD, MYOD1, MYOD1, R1

description: RD, MYOD1, MYOD1, R1


title: Beefy_F_2

address: 江苏省南京市南京农业大学滨江校区

institute: 南京农业大学郭仁朋课题组

description: Library name: Sample 8


title: CTRL029

description: Control


title: Beefy_F_3

address: 江苏省南京市南京农业大学滨江校区

institute: 南京农业大学郭仁朋课题组

description: Library name: Sample 9


title: Ruch2_Plain_B6_S18

description:
Raw_Counts_Ruch2_all_samples.txt
Normalized_Counts_Ruch2_all_samples.txt
Normalized_counts_RUCHoe_vs_PLAIN.txt
B06_Plain

data_processing:
Raw reads were trimmed based on quality and the presence of adapters using the trimmomatic tool (v. 0.39). Thus, for the  elimination of the sequences of the adapters, the palindromic mode was used, considering a maximum mismatch of two nucleotides with a palindrome clip score threshold of 30 and a simple clip score threshold of 10. Additionally, quality trimming was performed using a window of 4 bp and an average quality score of 20. Very low-quality bases (Phred < 3) were also removed from the beginning and the end of the reads. Reads with a length of less than 18 nucleotides were discarded.
Surviving paired reads were aligned with the STAR aligner (v.2.7.10b) against the human genome (GRCh38 version, Ensembl) using as gene reference a Gene transfer format (gtf) file from Ensembl (v. 107).
Read counting at the gene level was carried out using the htseq tool (v. 1.99.2) in its union mode for a reverse-stranded sequencing protocol
Counting data were normalized using the DESeq2 (v. 1.38.3) package using the size factor method. Genes with low expression were preliminarily removed in all analyses
Assembly: GRCh38
Supplementary files format and content: Raw_counts_RDoe.txt: raw counts from htseq-count
Supplementary files format and content: Normalized_Counts_Ruch2_all_samples.txt: Normalized DESeq2 counts for the L122R +Dox vs. WT +Dox contrast, adjusted for sequencing batch effects
Supplementary files format and content: Normalized_counts_RUCHoe_vs_PLAIN.txt: DESeq2 normalized counts for L122R  +Dox vs. WT (Plain) and  WT +Dox vs. WT (Plain)  contrast

growth_protocol: Ruch2 cells with or without treatment were cultured in DMEM supplemented with 10% FBS, PenStrep, and collected before confluency for RNA-seq experiments.

extract_protocol:
RNA-seq samples were collected using TriZol to lyse cells, then extracted from cells usingQIAGEN RNA Extraction kit.
Genomic DNA was removed using DNase I. TruSeq Stranded mRNA Library Prep kit (96 samples) was used to build mRNA libraries (Illumina # 20020595). Qubit DNA assay was used to determine DNA concentration. samples. Agilent 2100 Electrophoresis Bioanalyzer was used to check mRNA library size (~260bp for RNA libraries and ~150-900bp) and quality before the sequencing run. NextSeq 2000, along with P3 reagents (100 cycles) was used for the sequencing run (Illumina # 20040559). On average, >20M reads per sample were acquired, covering 75bp from both ends

treatment_protocol: Ruch2 cells with the dox-inducible contruct, were seeded, and then treated with doxycycline, for 72 hours, before collection for RNA-extraction, control group without dox treatment.

tag: doxycycline induction

value: -Dox

tag: peptide

value: Plain

value: WT

tag: batch


title: C57.PrESC rep1

description:
Library name: C57.PrESC rep1
C57.PrESC rep1


title: EPZ.iPrE1 rep1

description:
Library name: EPZ.iPrE1 rep1
EPZ.iPrE1 rep1


title: Ruch2_Plain_B1_S13

description:
Raw_Counts_Ruch2_all_samples.txt
Normalized_Counts_Ruch2_all_samples.txt
Normalized_counts_RUCHoe_vs_PLAIN.txt
B01_Plain


title: C57.ESC rep2

description:
Library name: C57.ESC rep2
C57.ESC rep2


title: CTRL030

description: Control

value: Control


title: CTRL026

description: Control


title: Beefy_9_3

address: 江苏省南京市南京农业大学滨江校区

institute: 南京农业大学郭仁朋课题组

description: Library name: Sample 6


title: Ruch2_-Dox_MYOD1_B12_S24

description:
Raw_Counts_Ruch2_all_samples.txt
Normalized_Counts_Ruch2_all_samples.txt
B12_MYOD1_DOXneg


title: C57.ESC rep1

description:
Library name: C57.ESC rep1
C57.ESC rep1

value: ESC culture(+lif)


title: CTRL025

description: Control


title: CTRL027

description: Control


title: Beefy_9_2

address: 江苏省南京市南京农业大学滨江校区

institute: 南京农业大学郭仁朋课题组

description: Library name: Sample 5


title: Ruch2_-Dox_MYOD1_B7_S19

description:
Raw_Counts_Ruch2_all_samples.txt
Normalized_Counts_Ruch2_all_samples.txt
B07_MYOD1_DOXneg


title: Beefy_9_1

address: 江苏省南京市南京农业大学滨江校区

institute: 南京农业大学郭仁朋课题组

description: Library name: Sample 4


title: Ruch2_Plain_B11_S23

description:
Raw_Counts_Ruch2_all_samples.txt
Normalized_Counts_Ruch2_all_samples.txt
Normalized_counts_RUCHoe_vs_PLAIN.txt
B11_Plain


title: CTRL024

description: Control


title: Ruch2_-Dox_L122R_C2_S26

description:
Raw_Counts_Ruch2_all_samples.txt
Normalized_Counts_Ruch2_all_samples.txt
C02_L122R_DOXneg


title: Beefy_F_1

address: 江苏省南京市南京农业大学滨江校区

institute: 南京农业大学郭仁朋课题组

description: Library name: Sample 7


title: CTRL023

description: Control


title: EZH2-10-rescued-H3K27me3 rep2

description:
Library name: EZH2-10-rescued-H3K27me3_rep2
EZH2-10-rescued-H3K27me3 rep2

data_processing:
The raw reads were processed using TrimGalore to remove adapter sequences and low-quality bases. The cleaned reads were aligned to the mouse mm10 genome using bowtie2 To analyze repetitive sequences, the multi-mapped reads were kept but only the best alignment was reported; if more than one equivalent best alignment was found, then one random alignment was reported. Broad peaks were called uing Sicer2 with default paramaters. Alignment bam files were transformed into read coverage files (bigwig format) using deepTools with the RPKM  normalization method.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

extract_protocol:
Cells were collected for CUT&TAG libraries construction without extraction.
CUT&TAG libraries were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme Biotech, #TD904). Briefly, 1 × 105 cells were washed with 500 μl wash buffer and centrifuged at 200×g for 5 min at room temperature. Cell pellets were resuspended with 100 μl wash buffer. A total of 10 μl concanavalin A-coated magnetic beads were washed twice with 100 μl binding buffer and then added to the cell tubes and incubated at room temperature for 10 min. After removing the supernatant, the bead-bound cells were resuspended with 50 μl antibody buffer containing primary antibody (Dilute according to instructions). After incubation overnight at 4°C, the primary antibody was carefully discarded and anti-rabbit IgG (Vazyme, Ab207, 1:100) diluted with 50 μl Dig-wash buffer was added to the cells. The cells were then incubated with rotation at room temperature for 1 h. The cells were then washed gently with 200 μl Dig-wash buffer three times, and 2 μl pA/G–Tnp together with 98 μl Dig-300 buffer was added to the samples. After incubating at room temperature for 1 h, the samples were washed gently with 200 μl Dig-300 buffer three times. Then, 10 μl 5 × TTBL mixed with 40 μl Dig-300 buffer was added to each sample and the samples were incubated at 37 °C for 1 h. The interactions were quenched by adding 2 μl 10% SDS and incubating the samples at 55°C for 10 min. The supernatant was transfered to a new tube, and added 50 μl DNA Extract beads to  purify the DNA. For library amplification, 15 μl of purified DNA was mixed with 25 μl of 2× CAM, along with 5 μl of uniquely barcoded i5 and i7 primers from the TruePrep Index Kit V2 for Illumina (Vazyme Biotech, # TD202). A total volume of 50 μl of sample was placed in a BioRAD cycler (BIO-RAD, #T100) using the following program: 72 °C for 3 min; 98 °C for 3 min; 12 cycles of 98 °C for 10 s, 60 °C for 5 s, and 72°C for 1 min; and holding at 14 °C. To purify the PCR products, 100 μl volumes of VAHTS DNA Clean Beads (Vazyme Biotech, #N411) were added and incubated at room temperature for 5 min. The beads were washed twice with 200 μl fresh 80% ethanol and eluted in 25 μl elution buffer. All CUT&Tag libraries were sequenced by BerryBenomics using the Illumina NovaSeq 6000 platform in PE150 mode (BerryBenomics, Beijing, China).

value: mouse embryonic stem cells


title: Ruch2_-Dox_L122R_B9_S21

description:
Raw_Counts_Ruch2_all_samples.txt
Normalized_Counts_Ruch2_all_samples.txt
B09_L122R_DOXneg


title: CTRL022

description: Control


title: EZH2KO-12-H3K27me3 rep2

description:
Library name: EZH2KO-12-H3K27me3_rep2
EZH2KO-12-H3K27me3 rep2


title: FBS_1

address: 江苏省南京市南京农业大学滨江校区

institute: 南京农业大学郭仁朋课题组

description: Library name: Sample 1


title: CTRL021

description: Control


title: CTRL020

description: Control


title: EZH2-12-rescued-H3K27me3 rep1

description:
Library name: EZH2-12-rescued-H3K27me3_rep1
EZH2-12-rescued-H3K27me3 rep1


title: FBS_2

address: 江苏省南京市南京农业大学滨江校区

institute: 南京农业大学郭仁朋课题组

description: Library name: Sample 2


title: Ruch2_OE_MYOD1_r2_B8_S20

description:
Raw_Counts_Ruch2_all_samples.txt
Normalized_Counts_Ruch2_all_samples.txt
Normalized_counts_RUCHoe_vs_PLAIN.txt
B08_MYOD1_DOXpos

value: +Dox


title: Ruch2_OE_MYOD1_r3_C1_S25

description:
Raw_Counts_Ruch2_all_samples.txt
Normalized_Counts_Ruch2_all_samples.txt
Normalized_counts_RUCHoe_vs_PLAIN.txt
C01_MYOD1_DOXpos


title: EZH2-12-rescued-H3K27me3 rep2

description:
Library name: EZH2-12-rescued-H3K27me3_rep2
EZH2-12-rescued-H3K27me3 rep2


title: Rhino8_PB_R1

city: Escondido

first: Elena

last: Ruggeri

state: CA

address: 15600 San Paqual Valley Rd.

institute: San Diego Zoo Wildlife Alliance

description: Library name: Rhino8_PB_R1

data_processing:
Galaxy Web Platform
Assembly: CerSimCot 1.0
Supplementary files format and content: tab-delimited text files include count values for each Sample

organism: Ceratotherium simum simum

source_name: In vivo cells

extract_protocol:
Total RNA was isolate using the Picopure RNA isolation kit
Illumina TruSeq Stranded Total RNA Prep with Ribo-Zero Plus

value: In vivo cells

value: Granulosa Cell

value: in vivo


title: EZH2-10-rescued-H3K27me3 rep1

description:
Library name: EZH2-10-rescued-H3K27me3_rep1
EZH2-10-rescued-H3K27me3 rep1


title: EZH2KO-10-H3K27me3 rep2

description:
Library name: EZH2KO-10-H3K27me3_rep2
EZH2KO-10-H3K27me3 rep2


title: EZH2KO-12-H3K27me3 rep1

description:
Library name: EZH2KO-12-H3K27me3_rep1
EZH2KO-12-H3K27me3 rep1


title: Ruch2_-Dox_MYOD1_B2_S14

description:
Raw_Counts_Ruch2_all_samples.txt
Normalized_Counts_Ruch2_all_samples.txt
B02_MYOD1_DOXneg


title: CTRL019

description: Control


title: CTRL017

description: Control


title: Rhino7_PB_R1

description: Library name: Rhino7_PB_R1


title: FBS_3

address: 江苏省南京市南京农业大学滨江校区

institute: 南京农业大学郭仁朋课题组

description: Library name: Sample 3

value: bovine muscle stem cells


title: Ruch2_OE_MYOD1_r1_B3_S15

description:
Raw_Counts_Ruch2_all_samples.txt
Normalized_Counts_Ruch2_all_samples.txt
Normalized_counts_RUCHoe_vs_PLAIN.txt
B03_MYOD1_DOXpos


title: Ruch2_-Dox_L122R_B4_S16

description:
Raw_Counts_Ruch2_all_samples.txt
Normalized_Counts_Ruch2_all_samples.txt
B04_L122R_DOXneg


title: Rhino4_noPB_R1

description: Library name: Rhino4_noPB


title: PrESC-H3K27me3 rep2

description:
Library name: PrESC-H3K27me3_rep2
PrESC-H3K27me3 rep2

value: Primitive endoderm stem cells


title: Rhino3_noPB_R1

description: Library name: Rhino3_noPB


title: CTRL016

description: Control


title: EZH2KO-10-H3K27me3 rep1

description:
Library name: EZH2KO-10-H3K27me3_rep1
EZH2KO-10-H3K27me3 rep1


title: Rhino6_noPB_R1

description: Library name: Rhino6_noPB_R1


title: CTRL014

description: Control


title: Ruch2_OE_L122R_r3_C3_S27

description:
Raw_Counts_Ruch2_all_samples.txt
Normalized_Counts_Ruch2_all_samples.txt
Normalized_counts_RUCHoe_vs_PLAIN.txt
C03_L122R_DOXpos


title: PrESC-H3K27me3 rep1

description:
Library name: PrESC-H3K27me3_rep1
PrESC-H3K27me3 rep1

value: wild-type


title: ESCH3K27me3 rep1

description:
Library name: ESCH3K27me3_rep1
ESCH3K27me3 rep1


title: Ruch2_OE_L122R_r2_B10_S22

description:
Raw_Counts_Ruch2_all_samples.txt
Normalized_Counts_Ruch2_all_samples.txt
Normalized_counts_RUCHoe_vs_PLAIN.txt
B10_L122R_DOXpos


title: ESCH3K27me3 rep2

description:
Library name: ESCH3K27me3_rep2
ESCH3K27me3 rep2


title: Ruch2_OE_L122R_r1_B5_S17

description:
Raw_Counts_Ruch2_all_samples.txt
Normalized_Counts_Ruch2_all_samples.txt
Normalized_counts_RUCHoe_vs_PLAIN.txt
B05_L122R_DOXpos


title: CTRL015

description: Control

value: Plasma


title: mm_atac_spreb_Jk3-RSS_only.5

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description: Library name: mm_atac_spreb_Jk3-RSS_only.5

data_processing:
Raw data were aligned to reference genome mm9 using BWA MEM. Read alignments were adjusted to account for TAC transposon binding: +4bp for + strand alignments, -5bp for - strand alignments. Peaks were called using Macs2 with --nomodel set and no background provided, and peaks with score >5 were retained. Nucleosome positioning signal was computed by first binning properly paired read pairs into nucleosome-free or nucleosome-containing bins, based on their fragment size. Fragments <=100bp were considered nucleosome free (background) and converted to a single read covering the length of the fragment. Fragments 180-247bp were considered single-nucleosome-containing and converted to a single read the length of the fragment; similarly, fragments 315-473bp or 558-615bp were considered two- or three-nucleosome containing, and split into 2 or 3 reads covering half or 1/3 of the total fragment length. Single-, two-, and three- nucleosome reads were combined into the nucleosome signal read set. Nucleosome positioning analysis was run using danpos (Chen et al., 2013) with command dpos and parameters -m 1 -a 10 -jd 20 --clonalcut 0, and contrasting nucleosome signal to nucleosome background for each sample. Wig tracks from danpos were re-normalized to counts per billion bases using the sum of alignment lengths over 1 billion from the original BAM file, and converted to bigWig using UCSC tool wigToBigWig (Kent et al., 2010).
Assembly: mm9
Supplementary files format and content: *.bw: bigWig
Supplementary files format and content: *.bed: bed (tab-delimited text)

source_name: Small pre-B cells

extract_protocol:
Cells were washed with PBS, then lysed with ATAC lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Resulting nuclei were then incubated with tagmentation enzyme (Illumina).
Libraries from purified samples were made with the Nextera Indexing kit (Illumina).

treatment_protocol: Small pre-B cells were flow sorted as B220+CD19+CD43-IgM-FSClo.

value: Small pre-B cells

value: Jk3-RSS repair

value: Cells were isolated from bone marrow


title: Rhino2_PB_R1

description: Library name: Rhino2_PB


title: Rhino5_noPB_R1

description: Library name: Rhino5_noPB_R1


title: RD_Plain_r1_C04

description:
Raw_counts_RDoe_All_Samples.txt
Normalized_counts_RDoe_vs_PLAIN.txt

data_processing:
Raw reads were trimmed based on quality and the presence of adapters using the trimmomatic tool (v. 0.39). Thus, for the  elimination of the sequences of the adapters, the palindromic mode was used, considering a maximum mismatch of two nucleotides with a palindrome clip score threshold of 30 and a simple clip score threshold of 10. Additionally, quality trimming was performed using a window of 4 bp and an average quality score of 20. Very low-quality bases (Phred < 3) were also removed from the beginning and the end of the reads. Reads with a length of less than 18 nucleotides were discarded.
Surviving paired reads were aligned with the STAR aligner (v.2.7.10b) against the human genome (GRCh38 version, Ensembl) using as gene reference a Gene transfer format (gtf) file from Ensembl (v. 107).
Read counting at the gene level was carried out using the htseq tool (v. 1.99.2) in its union mode for a reverse-stranded sequencing protocol
Counting data were normalized using the DESeq2 (v. 1.38.3) package using the size factor method. Genes with low expression were preliminarily removed in all analyses
Assembly: GRCh38
Supplementary files format and content: Raw_counts_RDoe.txt: raw counts from htseq-count
Supplementary files format and content: Normalized_counts_RDoe.txt: Normalized DESeq2 counts for the L122R +Dox vs. WT +Dox contrast, adjusted for peptide type and sequencing batch effects
Supplementary files format and content: Normalized_counts_RDoe_vs_PLAIN.txt: DESeq2 normalized counts for L122R  +Dox vs. WT (Plain) and  WT +Dox vs. WT (Plain)  contrast

growth_protocol: RD cells with or without treatment were cultured in DMEM supplemented with 10% FBS, PenStrep, and collected before confluency for RNA-seq experiments.

treatment_protocol: RD cells with the dox-inducible contruct, were seeded, and then treated with doxycycline, for 72 hours, before collection for RNA-extraction, control group without dox treatment.

value: RD

value: No Dox


title: Rhino1_PB_R1

description: Library name: Rhino1_PB

value: WT


title: CTRL013

description: Control

value: Diagnostic cohort

value: Control


title: RD_Plain_r2_D01

value: Plain


title: iPax3 re-isolated, N3OE, rep3

city: Minneapolis

first: Aline Miyoko

last: Sakaguchi Yamashita

state: Minnesota

address: 2231 6th St SE

department: Department of Medicine

institute: University of Minnesota

description: Library name: iPax3NICD3_in_vivo3

data_processing:
Data alignment and comparison of gene expression was analyzed using the CHURP pipeline at the UMGC. 2 x 150bp FASTQ paired-end reads for a total of 26 biological samples (22.8 million reads average per sample) were trimmed using Trimmomatic (v0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30. Quality control on raw sequence data for each sample was performed with FastQC. Read mapping was performed via HISAT241 (v2.1.0) using the mouse genome (GRCh39.106) as reference. Gene quantification was done via Feature Counts for raw read counts. Differentially expressed genes were identified using the EdgeR (negative binomial, R programming) feature in CLCGWB (Qiagen, Redwood City, CA) using raw read counts. We filtered the generated list based on a minimum 2x absolute fold change and FDR-corrected p < 0.05.
Assembly: mm10
Supplementary files format and content: Raw sequencing data for each sample (.FASTQ)

source_name: re-isolated satellite cells

extract_protocol:
RNA isolation: samples with low input of RNA (in vivo cells, re-isolated donor-derived satellite cells), RNA was extracted using Buffer RLT (QIAGEN) and nucleic acid beads.
For library contruction: samples with low input (in vivo cells, re-isolated donor-derived satellite cells). The cDNA was synthesized using the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification kit (New England Biolabs) and the libraries were generated with the Nextera XT DNA Library Preparation Kit (Illumina).

value: re-isolated satellite cells

value: iPAX3 cells

value: donor-derived satellite cells

value: NICD3 overexpression


title: mm_atac_spreb_Jk3-RSS_only.3

description: Library name: mm_atac_spreb_Jk3-RSS_only.3


title: CTRL010

description: Control


title: CTRL012

description: Control


title: iPax3 re-isolated, N3OE, rep1

description: Library name: iPax3NICD3_in_vivo1


title: iPax3 re-isolated, N3OE, rep4

description: Library name: iPax3NICD3_in_vivo4


title: RD_OE_MYOD1_RDMyoD-2_S7

description:
Raw_counts_RDoe_All_Samples.txt
Normalized_counts_RDoe.txt
Normalized_counts_RDoe_vs_PLAIN.txt

value: +Dox


title: mm_atac_spreb_Jk3-RSS_only.4

description: Library name: mm_atac_spreb_Jk3-RSS_only.4


title: CTRL008

description: Control


title: iPax3 re-isolated, N3OE, rep2

description: Library name: iPax3NICD3_in_vivo2


title: RD_OE_L122R_RDL122R-1_S3


title: RD_OE_MYOD1_RDMyoD1-1_S2


title: RD_Plain_r3_D10


title: mm_atac_spreb_Jk3-GAGArepair.4

description: Library name: mm_atac_spreb_Jk3-GAGArepair.4


title: Mutant Dnmt3a/Npm1/Kras

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description: C57BL/6J (Stock 000664) and B6.SJL-Ptprca Pepcb/BoyJ (Stock 002014) were obtained from The Jackson Laboratory. B6(Cg)-Dnmt3atm1Trow/J (Stock 032289) and B6.Cg-Tg(Mx1-cre)1Cgn/J (Stock 003556) were bred and used as previously described(5). C57BL/6-Npm1tm1Trow/J (Stock 033164) and B6N.129S6(Cg)-Gt(ROSA)26Sortm3(CAG-flpo/ERT2)Alj/J (Stock 019016) were bred and used as previously described(5). The 4-allele cross of these strains was also bred and used as previously described(5). For induction of Mx1-Cre, mice were injected five times (once every other day) via intraperitoneal injection with 15mg/kg high molecular weight polyinosinic-polycytidylic acid (polyI:C) (InvivoGen). For induction of FlpoER, mice were administered 125mg/kg tamoxifen three times (on consecutive days) via oral gavage. After polyI:C or tamoxifen administration, genomic DNA was extracted from PB cells to confirm allele recombination. The Jackson Laboratory’s Institutional Animal Care and Use Committee (IACUC) approved all experiments.

library_source: transcriptomic single cell

data_processing:
The scRNA-Seq fastq files were processed in Cell Ranger v.5.0.1, using the 10x Genomics provided murine transcriptome reference mm10-2.1.0. Downstream analysis steps were performed on the filtered_matrix.h5 files following ambient RNA correction with SoupX assuming a contamination fraction of 15%. Gene expression was scaled in AltAnalyze v.2.14 to log2 adjusted counts per 10,000 reads (CPTT), with outlier cells removed in the AltAnalyze ICGS2 module (default QC thresholds).
Assembly: mm10
Supplementary files format and content: h5

molecule: cytoplasmic RNA

source_name: spleen

extract_protocol:
CD117+ hematopoietic cells were enriched from healthy or malignant mouse spleens using magnetic-activated cell sorting (MACS). In each experiment, cells were washed on Laminar Wash MINI or HT2000 System (Curiox Biosystems Inc) with the following settings: 25 cycles, flow rate of 10uL/s, initial volume of 55uL.
Pooled cells were captured by 10X Chromium X 3’ version 3.1 kit (1000268, 10X Genomics).

value: spleen

value: cKit+ progenitors

value: Mutant Dnmt3a, Npm1, Hdac1, Idh1, Kras, Arid1a, Hist1h2be, Hist1h2bk, Crbn, Cic


title: CTRL009

description: Control

value: Plasma


title: Wild-type spleen

value: wild-type


title: RD_OE_L122R_RDL122R-2_S8


title: mm_atac_spreb_WT.17

description: Library name: mm_atac_spreb_WT.17

value: Small pre-B cells

value: Cells were isolated from bone marrow


title: mm_atac_spreb_Jk3-GAGArepair.3

description: Library name: mm_atac_spreb_Jk3-GAGArepair.3


title: mm_atac_spreb_Jk3-GAGArepair.5

description: Library name: mm_atac_spreb_Jk3-GAGArepair.5


title: CTRL007

description: Control


title: RD_OE_MYOD1_HA_r1_C6_S30

value: RD


title: CTRL011

description: Control


title: RD_OE_MYOD1_HA_r2_D3_S39

value: WT


title: Mutant Dnmt3a/Npm1/Nras

value: Mutant Dnmt3a, Npm1, Nras, Xpo1, Spen, Elf3, Flcn, Arid1b


title: RD_OE_MYOD1_FLAG_r2_D7_S43

value: FLAG


title: CTRL018

description: Control

value: Diagnostic cohort

value: Control


title: CTRL005

description: Control


title: Mutant Dnmt3a/Npm1

value: Mutant Dnmt3a, Npm1


title: RD_OE_MYOD1_FLAG_r1_C10_S34


title: mm_atac_spreb_WT.16

description: Library name: mm_atac_spreb_WT.16


title: mm_atac_spreb_WT.15

description: Library name: mm_atac_spreb_WT.15


title: Liver, Tmem55b knockdown, rep4

city: Oakland

first: Marisa

last: Medina

address: 5700 Martin Luther King Jr. Way

department: Pediatrics

institute: UCSF

data_processing:
STAR 2-pass alignment
feature counts
DEseq2
Assembly: GRCm39
Supplementary files format and content: comma-separated variable (csv) file with raw counts for each sample

source_name: Liver

extract_protocol:
RNA was extracted using Qiagen Rneasy mini kit. 1µg of total RNA was used for the construction of sequencing libraries.
poly-A selected, strand-specific, paired end

value: Liver

tag: Sex

value: Male

tag: age

value: 10-11 weeks

tag: strain

tag: diet

value: 4 wks Western diet

value: Tmem55b ASO


title: RD_OE_L122R_HA_r2_D5_S41

tag: cell line

value: +Dox


title: CTRL004

description: Control

tag: tissue

value: Plasma


title: Liver, Non-targeting control, rep4

tag: treatment

value: NTC ASO


title: CTRL002

description: Control

tag: cohort


title: C57BL/6J, CD8+ T cells, hCD19 CAR and pMIG vectors_2

city: Seoul

first: Hyungseok

last: Seo

address: Gwanak ro 1

department: College of Pharmacy

country: South Korea

institute: Seoul National University

description: Library name: pMIG_NT__2

data_processing:
Raw FASTQ files were first quality–checked with FastQC v0.11.7. Adapter sequences and low-quality bases (SLIDINGWINDOW:4:15, LEADING:3, TRAILING:3, MINLEN:36) were removed using Trimmomatic v0.38.
Trimmed reads were then aligned to the Mus musculus mm10 reference genome (NCBI_108) with HISAT2 v2.1.0 (default settings), achieving >97% mapping rate per sample.
Transcript assembly and quantification were performed using StringTie v2.1.3b (–e –G), yielding raw read counts, FPKM, and TPM values for each gene.
Count matrices were imported into edgeR (Bioconductor) for differential expression analysis: counts were normalized by TMM, dispersion was estimated, and exactTest was applied to identify DE genes (|FC| ≥ 2, raw p-value < 0.05).
Assembly: mm10
Supplementary files format and content: All processed expression and differential‐expression results are provided in a single comma‐separated values file, data2.csv, containing 16,945 rows (one per gene) and the following columns: Gene_ID, Transcript_ID, Gene_Symbol, Description, gene_biotype, Protein_ID, MGI, IMGT/GENE-DB, FPKM, TPM, Fold-change(fc), logCPM, raw.pval, bh.pval, mean, TMM, readcount and log10raw.pval
Supplementary files format and content: Sample names in column headers exactly match those in the raw FASTQ filenames. (e.g. LbOE_NT__1) included in the sample description field

growth_protocol: CD8⁺ T cells isolated from C57BL/6J mice spleens were cultured in RPMI-based T cell medium (10% fetal bovine, 1% penicillin-streptomycin, 100X HEPES, 100X MEM Essential Vitamins, 100X Nonessential amino acids, 100X Na pyruvate, 100x GlutaMax in RPMI 1640 Medium) containing 100 IU/mL human IL-2 in humidified 5% CO2 atmosphere at 37℃

extract_protocol:
Total RNA was extracted from cells using RNeasy Mini kit(74106, Qiagen) according to the manufacturer’s instructions and the total RNA concentration was analyzed by a UV-Vis Spectrophotometer.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following TruSeq Stranded mRNA Reference Guide # 1000000040498 v00.

value: spleen

tag: cell type

value: CD8+ T cells

tag: genotype


title: Liver, Tmem55b knockdown, rep3


title: CTRL003

description: Control

tag: disease


title: RD_OE_L122R_HA_r1_C8_S32

value: RD


title: RD_OE_L122R_FLAG_r1_C12_S36


title: Liver, Tmem55b knockdown, rep2


title: C57BL/6J, CD8+ T cells, hCD19 CAR and LXRβ Overexpression vectors_2

description: Library name: LbOE_NT__2

value: LXRbeta overexpression


title: CTRL001

description: Control


title: C57BL/6J, CD8+ T cells, hCD19 CAR and pMIG vectors_1

description: Library name: pMIG_NT__1

value: WT


title: C57BL/6J, CD8+ T cells, hCD19 CAR and LXRβ Overexpression vectors_1

description: Library name: LbOE_NT__1


title: Liver, Non-targeting control, rep3


title: Mutant Dnmt3a/Npm1/Flt3

value: cKit+ progenitors

value: Mutant Dnmt3a, Npm1, Nf1, Flt3 (p.M579T), Flt3 (p.D842G), Arid1a, Cux1, Pik3cd, Kmt2d, Setd1a


title: CTL2

city: montreal

first: Gilbert

last: Bernier

state: Quebec

address: 5415 Assomption Blvd

country: Canada

institute: Hopital Maisonneuve-Rosemont Research center

description: Library name: CTL2

data_processing:
Peaks calling with MACS2 with the significance cut-off q-value = 0.05
Assembly: hg38
Supplementary files format and content: bigWig

source_name: DIV60 neurons

growth_protocol: Neurons were grown for 16 days in DDM/B27/LN media followed DDM/B27 media  for a total of 60 days

extract_protocol:
Cells lysis was performed followed by nuclei extraction. Those steps were followed by tagmentation and DNA purification (Diagenode protocol)
cDNA was prepared according to the manufacturer's instruction (Diagenode #C01080001) and sequenced using the illumina platform

value: DIV60 neurons

value: Neurons

value: CTL


title: CTRL006

description: Control

data_processing:
Raw FASTQ file of each sample was parsed, normalized into count per million and transformed to log2CPM using HTG EdgeSeq Parser and HTG EdgeSeq Reveal software.
Assembly: The miRNA probe list is based on miRBase version 20.
Supplementary files format and content: Raw FASTQ file of each sample was parsed, normalized into count per million and transformed to log2CPM using HTG EdgeSeq Parser and HTG EdgeSeq Reveal software.

value: Diagnostic cohort

value: Control


title: AD2

description: Library name: AD2

value: AD


title: Liver, Non-targeting control, rep2

value: Liver

value: Male

value: 10-11 weeks

value: 4 wks Western diet


title: RD_OE_L122R_FLAG_r2_D9_S45

value: +Dox

value: FLAG


title: 4f-SAMMY-seq heterochromatin fraction from murine neurons, Mecp2 OE, biol rep 2

city: Milan

first: Michal

last: Kubacki

address: Via Olgettina 58

country: Italy

institute: San Raffaele Scientific Institute

description:
Library name: Neu_M2_rep2_S3
Heterochromatin (DNase-resistant, S3) fraction from Mecp2-overexpressing neurons.

data_processing:
Quality Control and Trimming: Raw sequencing reads from all experiments underwent quality control using FastQC. Adapters and low-quality bases were removed using Trim Galore or Trimmomatic.
Reads were aligned to mm10 using BWA-mem. Post-alignment filtering removed PCR duplicates and low-quality mapped reads.
Normalized signal tracks (bigWig format) were generated using deepTools bamCoverage. Log2 ratio of S2S/S3 coverage was calculated to define chromatin accessibility.
Fifferential chromatin regions were identified by comparing log2(S2S/S3) ratios between conditions. Statistical significance was determined using FDR < 0.05.
Annotation and Functional Analysis: CUT&Tag peaks were annotated to genomic features using the ChIPseeker R package. Gene Ontology (GO) functional enrichment analysis was performed on gene lists derived from all experiments using clusterProfiler.
Assembly: mm10
Supplementary files format and content: Normalized chromatin accessibility signal as log2(S2S/S3) ratios in bigWig format. Genomic regions defined as euchromatin or heterochromatin in BED format. Tables of differentially accessible genomic regions.

source_name: embryonic brain

growth_protocol: Murine Neural Progenitor Cells (NPCs): Derived from the telencephalic cortex of E13.5 mouse embryos, NPCs were cultured in adhesion on flasks coated with 1:100 Matrigel. The culture medium was Neural Inducing Medium (NIM) composed of DMEM/F12, Hormon Mix, penicillin/streptomycin, glutamine, glucose, Heparin, 10 ng/ml bFGF, and 10 ng/ml EGF. Murine Primary Neurons (Ns): Prepared from E18.5 wild-type mouse embryos, neurons were maintained in Neurobasal medium supplemented with glucose, penicillin/streptomycin, L-glutamine, and 1% B27.Human iPSC-derived Neurons (hNs): Wild-type human NPCs were differentiated into cortical neurons. Differentiation was induced in DMEM/F1 with N2 and B27 supplements, SU5402, PD0325901, and DAPT. Following dissociation, cells were plated on Poly-L-Lysine/Laminin/Fibronectin coated plates in neuronal maturation medium (Neurobasal A with B-27, Glutamine, BDNF, Ascorbic acid, Laminin, DAPT, and dbcAMP) for at least 3 weeks before experiments.

extract_protocol:
For RNA-seq: Total RNA was isolated from primary murine NPCs, Ns, and human-derived Ns using Trizol (Sigma-Aldrich) according to the manufacturer's protocol. For CUT&Tag: Nuclei from 100,000 cells were isolated and immobilized on Concanavalin A-coated beads. They were then incubated overnight at 4°C with primary antibodies (anti-MeCP2, anti-V5, or anti-Smarcb1). Following incubation with a secondary antibody, pA-Tn5 transposase was applied to fragment and tag antibody-bound DNA sites. For 4f-SAMMY-seq: 200,000 cells were subjected to DNase I treatment to fragment DNA based on chromatin accessibility. DNA was then fractionated to separate the DNase-sensitive euchromatin fraction (S2S) from the DNase-resistant heterochromatin fraction (S3).
Libraries from S2S and S3 fractions were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina and Unique Dual Index NEBNextMultiplex Oligos. Libraries were pooled and sequenced on an Illumina NextSeq 2000 instrument.

treatment_protocol: Lentiviral particles (LV) were produced in 293T cells and concentrated by ultracentrifugation. Murine NPCs and Ns: Cells were transduced one day after seeding. NPCs were transduced with LV-Mecp2 or LV-EGFP at a Multiplicity of Infection (MOI) of 10. Ns were transduced at an MOI of 5. Cells were harvested for analysis 5 days post-transduction. Human iPSC-derived Neurons: Neurons cultured for 4 weeks were transduced with LV-MECP2 or LV-EGFP at an MOI of 10. Cells were harvested 5 days after infection.

value: embryonic brain

value: primary neurons

value: wild-type

value: lentiviral transduction with Mecp2


title: Liver, Tmem55b knockdown, rep1

value: Tmem55b ASO


title: P7, intravenous (P5), PBS, replicate 3

city: Paris

first: Andrée

last: Delahaye-Duriez

address: 48, boulevard serurier

country: France

institute: INSERM

description: Library name: p7ivp5-pbs-3

data_processing:
Analyses were performed using the Eoulsan pipeline, including read filtering, mapping, alignment filtering, read quantile normalisation, and differential analysis. In the Eoulsan pipeline, reads were aligned against the rnor6 genome from Ensembl version 96 using STAR (version 2.7.2d).
Then, alignments from reads matching more than once on the reference genome were removed using samtools (Java version). We used the rnor6 GTF genome annotation version 96 from the Ensembl database to compute gene expression. All overlapping regions between alignments and referenced exons were counted and aggregated by genes using HTSeq-count 0.5.3. Finally, normalisation of sample counts, statistical treatments and differential analyses were performed using DESeq2 1.8.1
We used the rnor6 GTF genome annotation version 96 from the Ensembl database to compute gene expression. All overlapping regions between alignments and referenced exons were counted and aggregated by genes using HTSeq-count 0.5.3. Finally, normalisation of sample counts, statistical treatments and differential analyses were performed using DESeq2 1.8.1
Normalisation of sample counts, statistical treatments and differential analyses were performed using DESeq2 1.8.1
Assembly: rnor6 genome from Ensembl version 96
Supplementary files format and content: processed_raw_counts.csv contains raw count for all samples with gene annotations

organism: Rattus norvegicus

source_name: brain

growth_protocol: Wistar Han strain rats were intraperitoneally (i.p) injected twice daily from the post-natal day (P)1 to P4 and once in the morning of P5 with 10 uL recombinant mouse IL-1β (Miltenyi Biotec, Bergisch Gladbach, Germany) diluted in 1X PBS (0.12 M) to a final dose of 20 μg/kg, or the same volume of 1X PBS. Separation from the dam was no more than five minute per injection. Sex determination was performed at birth and confirmed at tissue collection. Male pups were used, as only males develop a consistent hypomyelination phenotype in this paradigm reflecting the clinical scenario of a male bias to injury. All litters were culled to 12 pups from P1 by random selection after sex determination.

extract_protocol:
RNA was extracted using the NucleoSpin RNA XS Plus kit (Macherey-Nagel, Dueren, Germany) according to the manufacturer’s recommendations and eluted in 16 μL of RNase-free water. Each protocol had N=3 replicates. RNA quality was assessed using an Agilent fragment analyser (5300 Fragment Analyzer System), and all samples were >7 cutoff.
Messenger (polyA+) RNAs were purified from 100 ng of total RNA using oligo(dT). Libraries were prepared using the strand-specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina). Libraries were multiplexed by 15 on six flow cell lanes. A 75 bp single read sequencing was performed on a NextSeq 500 device (Illumina). An average of 27 ± 7 M reads passing the Illumina quality filter was obtained for each sample.

treatment_protocol: Rats were anesthetised 48 hours after HuMSCs administration with an i.p injection of pentobarbital sodium and phenytoin sodium (150 mg/kg, Euthasol, Virbac AH, Inc., Fort Worth, U.S.A) and intracardially perfused with 0.9% sodium chloride. The olfactory bulbs and cerebellum were removed, and remaining tissues dissociated using the Miltenyi Biotec Neural Tissue Dissociation kit (for P7 brains) or Adult Brain Dissociation kit (P12 and P22 brains), on the gentleMACS Octo Dissociator with heaters as per the manufacturers' instructions. From the resulting brain homogenate, microglia were enriched using anti-CD11b/c antibody-coupled microbeads (Miltenyi Biotec). After collection of the CD11b/c positive cell fraction, the isolated cells were centrifuged, and cell pellets were conserved at -80°C until messenger RNA (mRNA) extraction.

value: brain

value: male

value: isolated CD11b/c positive microglia

tag: developmental stage

value: PBS

value: run 409


title: RD_HDR_WT_WT_C9r1_A01_S01

description:
Raw_counts_HDR.txt
Normalized_counts_HDR.txt

data_processing:
Raw reads were trimmed based on quality and the presence of adapters using the trimmomatic tool (v. 0.39). Thus, for the  elimination of the sequences of the adapters, the palindromic mode was used, considering a maximum mismatch of two nucleotides with a palindrome clip score threshold of 30 and a simple clip score threshold of 10. Additionally, quality trimming was performed using a window of 4 bp and an average quality score of 20. Very low-quality bases (Phred < 3) were also removed from the beginning and the end of the reads. Reads with a length of less than 18 nucleotides were discarded.
Surviving paired reads were aligned with the STAR aligner (v.2.7.10b) against the human genome (GRCh38 version, Ensembl) using as gene reference a Gene transfer format (gtf) file from Ensembl (v. 107).
Read counting at the gene level was carried out using the htseq tool (v. 1.99.2) in its union mode for a reverse-stranded sequencing protocol
Counting data were normalized using the DESeq2 (v. 1.38.3) package using the size factor method. Genes with low expression were preliminarily removed in all analyses
Assembly: GRCh38
Supplementary files format and content: Raw_counts_HDR.txt: raw counts from htseq-count
Supplementary files format and content: Normalized_counts_HDR.txt: DESeq2 normalized counts after batch effect adjustment

growth_protocol: RD cells were cultured in DMEM supplemented with 10% FBS, PenStrep, and collected before confluency for RNA-seq experiments.

value: RD

tag: assay

value: HDR

tag: myod1 status

value: WT/WT


title: P7, intravenous (P5), PBS, replicate 2

description: Library name: p7ivp5-pbs-2


title: 4f-SAMMY-seq euchromatin fraction from murine neurons, Mecp2 OE, biol rep 2

description:
Library name: Neu_M2_rep2_S2S
Euchromatin (DNase-sensitive, S2S) fraction from Mecp2-overexpressing neurons.


title: RD_HDR_WT_WT_C60r1_A02_S02


title: 4f-SAMMY-seq heterochromatin fraction from murine neurons, Mecp2 OE, biol rep 3

description:
Library name: Neu_M2_rep3_S3
Heterochromatin (DNase-resistant, S3) fraction from Mecp2-overexpressing neurons.


title: RD_HDR_WT_WT_C60r2_A08_S08


title: P7, intravenous (P5), PBS, replicate 1

description: Library name: p7ivp5-pbs-1


title: Liver, Non-targeting control, rep1

value: Liver

value: Male

value: 10-11 weeks

value: NTC ASO


title: 4f-SAMMY-seq heterochromatin fraction from murine neurons, EGFP control, biol rep 3

description:
Library name: Neu_GFP_rep3_S3
Heterochromatin (DNase-resistant, S3) fraction from neurons transduced with EGFP.

value: embryonic brain

value: lentiviral transduction with EGFP


title: P7, intravenous (P5), IL1-beta, HuMSCs (125M cells/kg), replicate 3

description: Library name: p7ivp5-il1-dose3-3

value: IL1-beta, HuMSCs (125M cells/kg)


title: 4f-SAMMY-seq heterochromatin fraction from murine neurons, Mecp2 OE, biol rep 1

description:
Library name: Neu_M2_rep1_S3
Heterochromatin (DNase-resistant, S3) fraction from Mecp2-overexpressing neurons.

value: primary neurons

value: wild-type

value: lentiviral transduction with Mecp2


title: 4f-SAMMY-seq heterochromatin fraction from murine neurons, EGFP control, biol rep 2

description:
Library name: Neu_GFP_rep2_S3
Heterochromatin (DNase-resistant, S3) fraction from neurons transduced with EGFP.


title: RD_HDR_L122R_WT_C93r1_A04_S04


title: RD_HDR_WT_WT_C9r2_A07_S07


title: RD_HDR_L122R_WT_C11r2_A09_S09


title: P7, intravenous (P5), IL1-beta, HuMSCs (125M cells/kg), replicate 2

description: Library name: p7ivp5-il1-dose3-2

value: brain

value: male


title: RD_HDR_L122R_WT_C93r2_A10_S10


title: WTCHG_merged_70575033

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

data_processing:
RNA-Seq reads were quality trimmed using trimgalore  v0.6.5 and were mapped to the mouse genome ( mm10, Genome Reference Consortium GRCm38)  using using STAR 2.7.0f
Number of reads aligned to the exonic region of each gene were counted using rsem based on the Ensembl annotation.
Assembly: mm10
Supplementary files format and content: tab-delimited text files contain rsem counts for each sample

source_name: tumour

extract_protocol:
Total RNA was extracted from frozen murine tumors. The samples were transferred into RNAlater and homogenized with Miltenyi GentleMACS in RLT buffer and further processed using Qiagen RNeasy Mini kit with on-column DNAse digestion.
Library preparation and RNASeq were performed by the Wellcome Trust Oxford Genomics Centre (Oxford, UK) using RiboZero to deplete rRNA species.

value: tumour

value: FVB


title: WTCHG_merged_70545030


title: WTCHG_merged_70555031


title: WTCHG_merged_70565032


title: WTCHG_merged_70585034


title: 4f-SAMMY-seq euchromatin fraction from murine neurons, EGFP control, biol rep 3

description:
Library name: Neu_GFP_rep3_S2S
Euchromatin (DNase-sensitive, S2S) fraction from neurons transduced with EGFP.


title: RD_HDR_L122R_WT_C11r1_A03_S03

value: RD


title: 4f-SAMMY-seq heterochromatin fraction from murine neurons, EGFP control, biol rep 1

description:
Library name: Neu_GFP_rep1_S3
Heterochromatin (DNase-resistant, S3) fraction from neurons transduced with EGFP.


title: 4f-SAMMY-seq euchromatin fraction from murine neurons, EGFP control, biol rep 2

description:
Library name: Neu_GFP_rep2_S2S
Euchromatin (DNase-sensitive, S2S) fraction from neurons transduced with EGFP.


title: RD_HDR_Ctrl_RD-60_S12

value: HDR


title: P7, intravenous (P5), IL1-beta, HuMSCs (50M cells/kg), replicate 3

description: Library name: p7ivp5-il1-dose2-3

value: isolated CD11b/c positive microglia

value: IL1-beta, HuMSCs (50M cells/kg)

value: run 409


title: WTCHG_merged_70535029


title: P7, intravenous (P5), IL1-beta, HuMSCs (125M cells/kg), replicate 1

description: Library name: p7ivp5-il1-dose3-1


title: P7, intravenous (P5), IL1-beta, HuMSCs (50M cells/kg), replicate 1

description: Library name: p7ivp5-il1-dose2-1


title: RD_HDR_L122R_WT_RD-11_S13


title: 4f-SAMMY-seq heterochromatin fraction from murine NPCs, Mecp2 OE, biol rep 3

description:
Library name: NPC_M2_rep3_S3
Heterochromatin (DNase-resistant, S3) fraction from Mecp2-overexpressing NPCs.

source_name: telencephalon

value: telencephalon

value: primary neuronal progenitor cells


title: 4f-SAMMY-seq euchromatin fraction from murine NPCs, Mecp2 OE, biol rep 3

description:
Library name: NPC_M2_rep3_S2S
Euchromatin (DNase-sensitive, S2S) fraction from Mecp2-overexpressing NPCs.


title: P7, intravenous (P5), IL1-beta, HuMSCs (50M cells/kg), replicate 2

description: Library name: p7ivp5-il1-dose2-2


title: 4f-SAMMY-seq euchromatin fraction from murine NPCs, Mecp2 OE, biol rep 2

description:
Library name: NPC_M2_rep2_S2S
Euchromatin (DNase-sensitive, S2S) fraction from Mecp2-overexpressing NPCs.


title: P7, intravenous (P5), IL1-beta, HuMSCs (20M cells/kg), replicate 2

description: Library name: p7ivp5-il1-dose1-2

value: IL1-beta, HuMSCs (20M cells/kg)


title: P7, intravenous (P5), IL1-beta, HuMSCs (20M cells/kg), replicate 3

description: Library name: p7ivp5-il1-dose1-3


title: RD_HDR_L122R_WT_RD-93_S14


title: OTI611-3

city: Chongqing

first: Pusheng

last: Hui

address: No.1 Youyi Road, Yuzhong District

institute: The First Affiliated Hospital of Chongqing Medical University

description: Library name: Sample6

data_processing:
After basecalling with Illumina Casava 1.7, the libraries (150-bp paired-end reads, Illumina HiSeq 2000) were processed as follows: raw reads were quality-checked with FastQC, then aligned to the reference genome (mm10) using TopHat v2.0.9. Gene expression was quantified as FPKM values with Cufflinks v2.1.1, and read counts were also obtained with HTSeq. The allSample.expr.txt file was generated by combining the FPKM values of all annotated genes across samples into a single expression matrix.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted with miRNeasy Kit (QIAGEN).
The mRNA was reverse-transcribed and amplified according to the method Geo-seq, then the library was constructed using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) according to the manufacturer’s instruction.

treatment_protocol: DU145 cells were treated with vehicle (DMSO) or OTI-611 (5 μM) for 24 h. The cells were collected for RNA-seq analysis

value: OTI-611 (5 μM) for 24 h


title: WTCHG_merged_70515027


title: P7, intravenous (P5), IL1-beta, HuMSCs (20M cells/kg), replicate 1

description: Library name: p7ivp5-il1-dose1-1


title: WTCHG_merged_70525028


title: WTCHG_merged_70495025


title: P7, intravenous (P5), IL1-beta, replicate 3

description: Library name: p7ivp5-il1-3


title: WTCHG_merged_70485024


title: 4f-SAMMY-seq heterochromatin fraction from murine NPCs, EGFP control, biol rep 3

description:
Library name: NPC_GFP_rep3_S3
Heterochromatin (DNase-resistant, S3) fraction from NPCs transduced with EGFP.

value: lentiviral transduction with EGFP


title: WTCHG_merged_70505026


title: 4f-SAMMY-seq heterochromatin fraction from murine NPCs, EGFP control, biol rep 2

description:
Library name: NPC_GFP_rep2_S3
Heterochromatin (DNase-resistant, S3) fraction from NPCs transduced with EGFP.


title: P7, intravenous (P5), IL1-beta, replicate 2

description: Library name: p7ivp5-il1-2


title: 4f-SAMMY-seq euchromatin fraction from murine NPCs, EGFP control, biol rep 2

description:
Library name: NPC_GFP_rep2_S2S
Euchromatin (DNase-sensitive, S2S) fraction from NPCs transduced with EGFP.


title: OTI611-1

description: Library name: Sample4


title: OTI611-2

description: Library name: Sample5


title: DMSO-2

description: Library name: Sample2

value: DMSO for 24hr


title: P7, intranasal (P5), PBS, replicate 3

description: Library name: p7-inasp5-pbs-3

value: PBS

value: run 404


title: WTCHG_merged_70475023


title: WTCHG_merged_70455021


title: DMSO-3

description: Library name: Sample3


title: triple_blood_2

city: Westmead

first: Brian

middle: S

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

country: Australia

institute: Westmead Institute of Medical Research

description:
Library name: triple_blood_2
HIVE seq

data_processing:
Raw sequencing reads for brain and blood samples were processed using the Illumina BCL Convert 4.1.5 pipeline where FastQ files were generated.
FastQ files were analysed using BeeNet (v1.1.3) software, mapped to the reference Mus musculus genome (mm10.104)
Assembly: mm10,104
Supplementary files format and content: tab separated values and qc files

source_name: blood

extract_protocol:
Once single-cells suspensions were generated for each sample condition, approximately 30,000 cells were loaded directly into a designated HIVE CLX collector (HIVE Collector, Honeycomb Biotechnologies, Inc. USA) in 1% FBS in DPBS. Single-cells settled into picowells of the CLX collector containing mRNA-capture beads. Media was removed from the collector and 2 mL of CLX sample wash solution was added. Then 1 mL of cell preservation solution was added. HIVE CLX collectors corresponding to each sample and group condition were stored at -80°C until transferred to the Australian Genome Research Facility Ltd. (AGRF, Melbourne, Australia) for single-cell NGS library processing and transcriptome recovery as per manufacturer’s instructions.
For transcriptome recovery, HIVE CLX collectors were sealed with a semi-permeable membrane, allowing for the addition of strong lysis solution and hybridization solution. Capture beads with transcripts were extracted from the collector by centrifugation. Remaining library preparation steps were performed in a 96-well format. Library size and assessment was performed using TapeStation software and the High Sensitivity D5000 ScreenTape assay (Agilent Technologies, CA, USA). Final pooled libraries were determined by qPCR. HIVE scRNA-sequencing libraries were sequenced using primers contained in the kit

treatment_protocol: peripheral blood leukocytes and total forebrain tissue were analysed from male offspring for HF+/SIS+/PIC+ and HF-/SIS-/PIC-. Mice were deeply anesthetised with isoflurane (5% induction, 2.5% maintenance) (IsoFlo®, Abbott Laboratories, Botany, NSW, Australia). Up to 1 mL of peripheral whole blood was collected via cardiac puncture and placed into a 1.5 mL collection tube containing anticoagulant (10% blood volume) (Heparin, Sigma, H3393) on ice. The mouse was then perfused with PBS and the whole brain was dissected. The cerebellum and olfactory bulbs were excised along the anterior to posterior axis from approximately +1.50 mm to -3.50 mm - leaving total forebrain tissue. Regions left intact included cerebral cortices, thalamus, hypothalamus, striatum and midbrain. The tissue was weighed and recorded before tissue homogenisation (gentleMACS Octo Dissociator with Heaters, Miltenyi Biotec, 130-096-427). A single-cell suspension was prepared using the Adult Brain Dissociation kit as per manufacturer’s instructions (Miltenyi Biotec, 130-107-677). To isolate peripheral leukocytes from whole blood, red blood cell lysis was performed using ammonium chloride solution (StemCell Technologies, 07850) at a volume:volume ratio of 9:1. The solution incubated at 4°C for 10-minutes, then cells were washed in Dulbecco’s phosphate-buffered saline containing Ca2+, Mg2+, glucose and pyruvate (DPBS, ThermoFisher, 14287080) by centrifugation at 250 x g for 6-minutes at 4°C.

value: blood


title: WTCHG_merged_70445020


title: WTCHG_merged_70465022


title: TOR10 cells, -sTom-p27K- med expression 2

city: Utrecht

first: Niek

last: Peters

address: Heidelberglaan 100

country: Netherlands

institute: UMC Utrecht

description: Library name: TOR10.sTom.p27K.med.RNA2

data_processing:
Illumina NextSeq500 High Output: 1x 75 bp. Quality control on the sequence reads from the raw FASTQ files was done with FastQC (v0.11.4)
Reads were aligned to the reference genome fasta (Homo_sapiens.GRCh37) using star (v2.4.2a) aligner
Readgroup were added using Picard (v1.141)
Readcounts were generated using the HTSeq-count (v0.6.1) with the Homo_sapiens.GRCh37.74.gtf gtf file as annotation
Normalization was done using R-packages DeSeq (v1.18.0) and edgeR (v3.8.6)
Assembly: Homo_sapiens.GRCh37
Supplementary files format and content: tab-delimited text files include raw reads count for each sample
Supplementary files format and content: tab-delimited text file with size factor normalized (DESeq) read counts of all samples

source_name: organoids

extract_protocol:
RNA was extracted using the RNeasy Mini RNA extraction kit (Qiagen, Cat. No. 74106) according to the manufacturer’s instructions with DNaseI treatment. RNA yield and quality were evaluated using spectrometry (Nanodrop 2000/200c, Thermo Fisher) and the BioAnalyzer (2100)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: organoids


title: P7, intranasal (P5), PBS, replicate 1

description: Library name: p7-inasp5-pbs-1

value: brain

value: male


title: P7, intranasal (P5), PBS, replicate 2

description: Library name: p7-inasp5-pbs-2


title: TOR10 cells, -sTom-p27K- med expression 1

description: Library name: TOR10.sTom.p27K.med.RNA1


title: triple_brain_2

description:
Library name: triple_brain_2
HIVE seq


title: WTCHG_merged_70435019

value: tumour

value: FVB


title: int_brain_3

description:
Library name: int_brain_3
HIVE seq


title: DMSO-1

description: Library name: Sample1


title: P7, intravenous (P5), IL1-beta, replicate 1

description: Library name: p7ivp5-il1-1

value: isolated CD11b/c positive microglia


title: WTCHG_merged_70425018


title: triple_brain_1

description:
Library name: triple_brain_1
HIVE seq


title: P7, intranasal (P5), IL1-beta, HuMSCs (125M cells/kg), replicate 3

description: Library name: p7-inasp5-il1-dose3-3

value: IL1-beta, HuMSCs (125M cells/kg)


title: P7, intranasal (P5), IL1-beta, HuMSCs (125M cells/kg), replicate 2

description: Library name: p7-inasp5-il1-dose3-2


title: WTCHG_merged_70415017


title: 4f-SAMMY-seq euchromatin fraction from murine NPCs, EGFP control, biol rep 3

description:
Library name: NPC_GFP_rep3_S2S
Euchromatin (DNase-sensitive, S2S) fraction from NPCs transduced with EGFP.

value: wild-type


title: P7, intranasal (P5), IL1-beta, HuMSCs (125M cells/kg), replicate 1

description: Library name: p7-inasp5-il1-dose3-1


title: TOR10 cells, -sTom-p27K- low expression 2

description: Library name: TOR10.sTom.p27K.low.RNA2


title: triple_blood_1

description:
Library name: triple_blood_1
HIVE seq


title: control_brain_2

description:
Library name: control_brain_2
HIVE seq


title: control_blood_2

description:
Library name: control_blood_2
HIVE seq


title: WTCHG_merged_70395015


title: control_brain_1

description:
Library name: control_brain_1
HIVE seq


title: P7, intranasal (P5), IL1-beta, HuMSCs (50M cells/kg), replicate 2

description: Library name: p7-inasp5-il1-dose2-2

value: IL1-beta, HuMSCs (50M cells/kg)


title: HUB098 cells, -sTom-p27K- med expression 1

description: Library name: HUB098.sTom.p27K.med.RNA1


title: HUB098 cells, -sTom-p27K- med expression 2

description: Library name: HUB098.sTom.p27K.med.RNA2


title: TOR10 cells, -sTom-p27K- low expression 1

description: Library name: TOR10.sTom.p27K.low.RNA1


title: P7, intranasal (P5), IL1-beta, HuMSCs (50M cells/kg), replicate 3

description: Library name: p7-inasp5-il1-dose2-3


title: control_blood_1

description:
Library name: control_blood_1
HIVE seq


title: int_brain_1

description:
Library name: int_brain_1
HIVE seq


title: int_brain_2

description:
Library name: int_brain_2
HIVE seq


title: P7, intranasal (P5), IL1-beta, HuMSCs (20M cells/kg), replicate 2

description: Library name: p7-inasp5-il1-dose1-2


title: P7, intranasal (P5), IL1-beta, HuMSCs (20M cells/kg), replicate 1

description: Library name: p7-inasp5-il1-dose1-1


title: HUB098 cells, -sTom-p27K- low expression 1

description: Library name: HUB098.sTom.p27K.low.RNA1


title: WTCHG_merged_70345010


title: WTCHG_merged_70365012


title: HUB098 cells, -sTom-p27K- low expression 3

description: Library name: HUB098.sTom.p27K.low.RNA3


title: P7, intranasal (P5), IL1-beta, replicate 3

description: Library name: p7-inasp5-il1-3


title: TOR10 cells, -sTom-p27K- high expression 1

description: Library name: TOR10.sTom.p27K.high.RNA1


title: HUB098 cells, -sTom-p27K- low expression 2

description: Library name: HUB098.sTom.p27K.low.RNA2


title: P7, intranasal (P5), IL1-beta, HuMSCs (20M cells/kg), replicate 3

description: Library name: p7-inasp5-il1-dose1-3


title: WTCHG_merged_70405016


title: P7, intranasal (P5), IL1-beta, HuMSCs (50M cells/kg), replicate 1

description: Library name: p7-inasp5-il1-dose2-1


title: HUB098 cells, -sTom-p27K- med expression 3

description: Library name: HUB098.sTom.p27K.med.RNA3


title: WTCHG_merged_70355011


title: mm_atac_spreb_Jk3-RSSrepair.1

city: Chicago

description: Library name: mm_atac_spreb_Jk3-RSSrepair.1

data_processing:
Raw data were aligned to reference genome mm9 using BWA MEM. Read alignments were adjusted to account for TAC transposon binding: +4bp for + strand alignments, -5bp for - strand alignments. Peaks were called using Macs2 with --nomodel set and no background provided, and peaks with score >5 were retained. Nucleosome positioning signal was computed by first binning properly paired read pairs into nucleosome-free or nucleosome-containing bins, based on their fragment size. Fragments <=100bp were considered nucleosome free (background) and converted to a single read covering the length of the fragment. Fragments 180-247bp were considered single-nucleosome-containing and converted to a single read the length of the fragment; similarly, fragments 315-473bp or 558-615bp were considered two- or three-nucleosome containing, and split into 2 or 3 reads covering half or 1/3 of the total fragment length. Single-, two-, and three- nucleosome reads were combined into the nucleosome signal read set. Nucleosome positioning analysis was run using danpos (Chen et al., 2013) with command dpos and parameters -m 1 -a 10 -jd 20 --clonalcut 0, and contrasting nucleosome signal to nucleosome background for each sample. Wig tracks from danpos were re-normalized to counts per billion bases using the sum of alignment lengths over 1 billion from the original BAM file, and converted to bigWig using UCSC tool wigToBigWig (Kent et al., 2010).
Assembly: mm9
Supplementary files format and content: *.bw: bigWig
Supplementary files format and content: bed (tab-delimited text)

value: Small pre-B cells

value: Jk3-RSS repair

value: Cells were isolated from bone marrow


title: HUB098 cells, -sTom-p27K- high expression 1

description: Library name: HUB098.sTom.p27K.high.RNA1


title: mm_atac_spreb_Jk3-RSSrepair.2

description: Library name: mm_atac_spreb_Jk3-RSSrepair.2


title: HUB098 cells, -sTom-p27K- high expression 2

description: Library name: HUB098.sTom.p27K.high.RNA2


title: WTCHG_merged_70385014


title: WTCHG_merged_70335009


title: mm_atac_spreb_Jk3-RSS_only.2

description: Library name: mm_atac_spreb_Jk3-RSS_only.2


title: mm_atac_spreb_Jk3-RepairM.1

description: Library name: mm_atac_spreb_Jk3-RepairM.1

value: Jk3-GAGA/RSS repair


title: CRC29 cells, -sTom-p27K- medium expression 2

description: Library name: CRC29.sTom.p27K.med.RNA2


title: WTCHG_merged_70305006


title: WTCHG_merged_70375013


title: WTCHG_merged_70315007


title: WTCHG_merged_70325008


title: mm_atac_spreb_Jk3-RSS_only.1

description: Library name: mm_atac_spreb_Jk3-RSS_only.1


title: CRC29 cells, -sTom-p27K- medium expression 3

description: Library name: CRC29.sTom.p27K.med.RNA3


title: P22, intravenous (P20), PBS, replicate 2

description: Library name: p22ivp20-pbs-2

value: run 416


title: P7, intranasal (P5), IL1-beta, replicate 1

description: Library name: p7-inasp5-il1-1


title: P7, intranasal (P5), IL1-beta, replicate 2

description: Library name: p7-inasp5-il1-2


title: P22, intravenous (P20), PBS, replicate 3

description: Library name: p22ivp20-pbs-3

value: PBS


title: mm_atac_spreb_Jk3-GAGArepair.2

description: Library name: mm_atac_spreb_Jk3-GAGArepair.2


title: CRC29 cells, -sTom-p27K- low expression 3

description: Library name: CRC29.sTom.p27K.low.RNA3


title: WTCHG_merged_70295005


title: mm_atac_spreb_Jk3-RepairF.1

description: Library name: mm_atac_spreb_Jk3-RepairF.1


title: CRC29 cells, -sTom-p27K- medium expression 1

description: Library name: CRC29.sTom.p27K.med.RNA1


title: P22, intravenous (P20), IL1-beta, HuMSCs (125M cells/kg), replicate 3

description: Library name: p22ivp20-il1-dose3-3


title: WTCHG_merged_70285004


title: CRC29 cells, -sTom-p27K- low expression 1

description: Library name: CRC29.sTom.p27K.low.RNA1


title: P22, intravenous (P20), PBS, replicate 1

description: Library name: p22ivp20-pbs-1


title: mm_atac_spreb_Jk3-GAGArepair.1

description: Library name: mm_atac_spreb_Jk3-GAGArepair.1


title: CRC29 cells, -sTom-p27K- low expression 2

description: Library name: CRC29.sTom.p27K.low.RNA2


title: WTCHG_merged_70275003


title: WTCHG_merged_70265002


title: P22, intravenous (P20), IL1-beta, HuMSCs (125M cells/kg), replicate 2

description: Library name: p22ivp20-il1-dose3-2


title: mm_atac_spreb_Jk1-GAGAmut.2

description: Library name: mm_atac_spreb_Jk1-GAGAmut.2


title: mm_atac_spreb_Jk1-GAGAmut.1

description: Library name: mm_atac_spreb_Jk1-GAGAmut.1


title: CRC29 cells, -sTom-p27K- high expression 2

description: Library name: CRC29.sTom.p27K.high.RNA2


title: P22, intravenous (P20), IL1-beta, HuMSCs (125M cells/kg), replicate 1

description: Library name: p22ivp20-il1-dose3-1


title: P22, intravenous (P20), IL1-beta, HuMSCs (50M cells/kg), replicate 2

description: Library name: p22ivp20-il1-dose2-2


title: P22, intravenous (P20), IL1-beta, HuMSCs (50M cells/kg), replicate 3

description: Library name: p22ivp20-il1-dose2-3


title: CRC29 cells, -sTom-p27K- high expression 3

description: Library name: CRC29.sTom.p27K.high.RNA3


title: mm_atac_spreb.8

description: Library name: mm_atac_spreb.8

value: WT


title: WTCHG_merged_70255001


title: mm_atac_spreb.7

description: Library name: mm_atac_spreb.7


title: P22, intravenous (P20), IL1-beta, HuMSCs (50M cells/kg), replicate 1

description: Library name: p22ivp20-il1-dose2-1


title: mm_rna_spreb_Jk1GAGAmut.2

description: Library name: mm_rna_spreb_Jk1GAGAmut.2

data_processing:
Raw reads were trimmed to remove Truseq adapters and bases from the 3’ end with quality scores less than 20 using cutadapt; trimmed reads shorter than 40bp were discarded. Trimmed reads were aligned to the reference genome using the STAR. UCSC gene annotations were quantified using FeatureCounts.
Assembly: mm9
Supplementary files format and content: tab-delimited text

extract_protocol:
Total RNA was prepared with Rneasy mini kit (Qiagen).
Libraries were prepared by the University of Chicago Genomics Facility before sequencing.

value: Cells were isolateed from bone marrow


title: CRC29 cells, -sTom-p27K- high expression 1

description: Library name: CRC29.sTom.p27K.high.RNA1

value: organoids


title: HSC,KO,rep4

city: Tianjin

first: Jianwei

last: Wang

address: 10 Yuexin Street, Binhai New Area

institute: HAIHE LABORATORY OF CELL ECOSYSTEM

description:
HSC,KO,rep4
GeneCounts_matrix_normalized.txt

data_processing:
First,Trim_galore (version0.6.6http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used for quality control and adaptor trimming.
Then, Processed reads were mapped to GRCm38 using STAR (2.7.9a)
Gene expressions were counted by  RSEM (v1.3.1 ).
Finally,  DEseq2 were performed to normalize the reads count.
Assembly: GRCm38
Supplementary files format and content: a tab-delimited text file includes normalized read counts for all samples
Supplementary files format and content: tab-delimited text files include read count, tpm and fpkm for each sample

source_name: Bone marrow

growth_protocol: hematopoietic stem cells were sorted from bone marrow

extract_protocol:
Freshly isolated HSC(Lineage- Sca1+cKit+ CD34-Flt3-) were subjected for RNA-seq
RNA libraries for RNA-seq were  prepared using the method of Smart-seq2

value: Bone marrow

value: Hematopoietic stem cell

value: Alyref-/-


title: P22, intravenous (P20), IL1-beta, HuMSCs (20M cells/kg), replicate 2

description: Library name: p22ivp20-il1-dose1-2

value: brain

value: male

value: IL1-beta, HuMSCs (20M cells/kg)


title: mm_rna_spreb_Jk1GAGAmut.3

description: Library name: mm_rna_spreb_Jk1GAGAmut.3


title: NK_CD56+CD16-_Rep 2

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

description:
Library name: NK_CD56+CD16-_Rep 2
Column name in NKrepro.cnts.txt.gz: CD56CD16_rep2

data_processing:
For analysis, paired-end reads were mapped to the human genome (Ensembl, release 93) using STAR v2.5.3a
Assembly: hg38
Supplementary files format and content: count table (.txt)

source_name: NK cell

growth_protocol: After transduction with lentivirus, HEFs were cultured in gelatin-coated plates in DMEM+10%FBS.

extract_protocol:
Total RNA from 3,000–7,000 FACS-sorted HEF or reprogrammed cells was extracted using TRIzol (ThermoFischer Scientific) following the manufacturer’s protocol. Total RNA from 10,000 natural cells (CD56+ CD16- and CD56dim CD16+ PBMC-NK cells) was used for comparison. cDNA was transcribed with SMARTSeq v4 Ultra-low input RNA kit (TakaraBio), amplified with 8 PCR cycles, and purified with AMPure XP beads (Beckman). cDNA was quantified using High sensitivity DNA kit on Bioanalyzer 2100 (Agilent).
Library preparation was performed using the Nextera XT DNA library preparation kit (Illumina) or SMART-Seq® v4 PLUS Kit (Takara) according to manufacturer’s protocol. Libraries were normalized with beads, pooled, and sequenced on Illumina NextSeq 500 platform.

treatment_protocol: Cells were sorted by FACS.

value: NK cell

value: CD56+CD16- Natural killer cells

value: wildtype

tag: transduction

tag: time

tag: sorted cells

value: live(DAPI-) and CD56+CD16-


title: NK_CD56+CD16-_Rep 3

description:
Library name: NK_CD56+CD16-_Rep 3
Column name in NKrepro.cnts.txt.gz: CD56CD16_rep3


title: HSC,Het,rep4

description:
HSC,Het,rep4
GeneCounts_matrix_normalized.txt

value: Alyref+/-


title: mm_rna_spreb.8

description: Library name: mm_rna_spreb.8

value: Small pre-B cells


title: P22, intravenous (P20), IL1-beta, HuMSCs (20M cells/kg), replicate 3

description: Library name: p22ivp20-il1-dose1-3

tag: Sex

value: isolated CD11b/c positive microglia

tag: batch

value: run 416


title: mm_rna_spreb_Jk1GAGAmut.1

description: Library name: mm_rna_spreb_Jk1GAGAmut.1


title: HSC,KO,rep2

description:
HSC,KO,rep2
GeneCounts_matrix_normalized.txt


title: HSC,KO,rep1

description:
HSC,KO,rep1
GeneCounts_matrix_normalized.txt


title: NK_CD56dimCD16+_Rep 4

description:
Library name: NK_CD56dimCD16+_Rep 4
Column name in NKrepro.cnts.txt.gz: CD56dimCD16_rep4

value: CD56dimCD16+ Natural killer cells

value: live(DAPI-) and CD56dimCD16+


title: HSC,KO,rep3

description:
HSC,KO,rep3
GeneCounts_matrix_normalized.txt


title: NK_CD56+CD16-_Rep 1

description:
Library name: NK_CD56+CD16-_Rep 1
Column name in NKrepro.cnts.txt.gz: CD56CD16_rep1


title: P22, intravenous (P20), IL1-beta, HuMSCs (20M cells/kg), replicate 1

description: Library name: p22ivp20-il1-dose1-1


title: HSC,WT,rep4

description:
HSC,WT,rep4
GeneCounts_matrix_normalized.txt

value: WT