title: mRNA E18.5 heart Lrrc58 het Plagl1 WT rep 5

city: Cambridge

first: Daniel

last: Lin

state: MA

address: 455 Main Street

institute: Whitehead Institute

description: Library name: 28_4_Het_WT_M

data_processing:
Gene expression quantification was performed using salmon with the --gcBias and --validateMappings options to map to the mouse transcriptome (GRCm38, version 102) (Patro et al. 2017). Only reads mapping to mRNAs or lncRNAs were considered for depth normalization.
Assembly: GRCm38v102
Supplementary files format and content: raw gene counts for all samples

source_name: Heart

extract_protocol:
Embryos from crosses between Lrrc58 homozygous trigger site mutant; Plagl1 wild-type dams and Lrrc58 heterozygous trigger site mutant; Plagl1 heterozygous trigger site sires were collected at E18.5 and dissected tissue was flash frozen in liquid nitrogen. Frozen tissue was transferred to a 50 mL conical tube, 1–2 mL of TRI Reagent was added, and the tissue was homogenized using a TissueRuptor and disposable probes (Qiagen). Following resuspension and/or homogenization, samples were phase separated with 100 μL 1-bromo-3-chloropropane (Sigma).
RNA-seq libraries were prepared from total RNA using the Watchmaker RNA Library Prep Kit (Watchmaker Genomics). Ribosomal RNA depletion was performed using RiboDepletion Oligos (Qiagen) by mixing 14 μL of RNA input, 1 μL FastSelect reagent (Qiagen), and 10 μL Frag & Prime Buffer (Watchmaker Genomics) and incubating under the following conditions: 85°C 10 minutes, 75°C 2 minutes, 70°C 2 minutes, 65°C 2 minutes, 60°C 2 minutes, 55°C 2 minutes, 37°C 2 minutes, 25°C 2 minutes, 4°C. Samples were prepared from the First Strand Synthesis step of the Watchmaker RNA Library Prep Kit (Watchmaker Genomics) onward, according to the manufacturer’s instructions. Libraries were multiplexed using xGen UDI Primers (IDT) and sequenced on the Illumina NovaSeq platform with paired-end reads.

value: Heart

value: Lrrc58 het Plagl1 WT


title: mRNA E18.5 heart Lrrc58 hom Plagl1 WT rep 7

status: Public on Apr 08 2026

type: SRA

country: USA

description: Library name: 28_5_KO_WT_M

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype

value: Lrrc58 hom Plagl1 WT


title: bone marrow; mAA; 1893-A043005

city: Basel

first: Astrid

last: Beerlage

address: Hebelstrasse 10

country: Switzerland

institute: University of Basel

description: Library name: 1893-A043005

data_processing:
All processing steps were automatically performed on the HTG EdgeSeq host system by the parser version 5.3.
Assembly: Alignment is automatically performed by the host system. Under the hood it uses bowtie 2 for alignment and a targeted probe list as a genome.
Supplementary files format and content: The processed data files are Excel sheets containing the raw gene counts, as well as QC-filtered normalized counts (CPM and median-ratio). Additionally the processed data sheets contain information on the individual QC steps.

organism: Homo sapiens

source_name: bone marrow

extract_protocol:
Quantitative nuclease protection assay (qNPA) of FFPE samples, i.e. extraction free.
Library preparation was performed by HTG Molecular Diagnostics, Tucson, AZ, USA using their established protocols. Excess functional DNA nuclease protection probes flanked with universal wing sequences are hybridized to target RNAs. Non-hybridized DNA probes and RNA are digested by S1 nuclease, essentially resulting in a 1:1 ratio of DNA detection probes and initially targeted RNA. DNA protection probes are released after heat denaturalization. Barcodes and adapters were individually added using a 16-cycle PCR reaction. Individual sample purification using AMPure XP beads (Beckman Coulter, Brea, CA, USA) and quantification using  KAPA Library Quantification kit (KAPA Biosystems, Wilmington, MA, USA).

value: bone marrow


title: Control patient line 12842 replicate 2

city: Austin

first: Anna

last: Warden

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

description: Library name: Control_12842_rep2

data_processing:
FASTQ files from sequencing experiments were mapped to hg38. RNA-seq files were mapped using the alignment tool STAR (v2.7.11b).
Raw RNA-sequencing files were evaluated for quality control using FastQC (v0.1.3).
Gene expression raw counts was quantified by HOMER’s ‘analyzeRepeats’
Batch correction was performed using CombatSeq and the sva package (v3.52.0)
Differential gene expression was calculated using the HOMER command ‘getDiffExpression.pl’. Transcript per kilobase million (TPM) was quantified for all genes matching accession number to raw counts.
Quantified read counts were normalized and analyzed using DESeq2 (v1.44.0) to determine differential expression between groups, within the R statistical computing environment (v4.4.0)
Assembly: hg38
Supplementary files format and content: tab-delimited text file inclues raw counts for each Sample
Supplementary files format and content: tab-delimited text file inclues raw TPM for each Sample

source_name: iPSC-derived Microglia

extract_protocol:
To perform the mRNA sequencing, total RNA was isolated using the RNeasy Tissue kit (Qiagen, Hilden, Germany, cat. 74104) according to the manufacturer’s instructions. RNA was assessed for quality using an Agilent Tapestation 4200, and 50 ng of RNA with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries
RNA sequencing libraries using the Illumina Stranded mRNA Prep (Illumina) following manufacturer’s instructions

value: iPSC-derived Microglia

tag: cell line

value: patient line

tag: cell type

value: Microglia

value: Control


title: Gastrocnemius, KO 1

city: Melbourne

first: Tony

last: Tiganis

state: Victoria

address: 23 Innovation Walk, Monash University, Clayton

country: Australia

institute: Monash University

description:
Library name: KO 1
column KO 1 in Nox4_RNAseq_counts.csv

data_processing:
Reads were mapped using the nf-core RNAseq pipeline as implemented in Laxy. STAR feature counts outputs were used for the counts matrix.
Assembly: GRCm39
Supplementary files format and content: raw counts matrix (STAR feature counts) as .csv file

source_name: Gastrocnemius muscle

extract_protocol:
Gastrocnemius muscle from 21-month old muscle-specific Nox4 knockout mice (MckCre:Nox4 fl/fl) and age-matched Nox4 fl/fl controls. Total RNA was isolated from homogenised mouse gastrocnemius muscle tissue with RNeasy mini kits (Qiagen, Hilden, Germany) and processed for library preparation (PolyA, unstranded) and sequencing on an Illumina Novaseq PE150 by Azenta Life Sciences (Burlington, MA).
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and  add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of  Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Novaseq instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

value: Gastrocnemius muscle

value: MckCre:Nox4 fl/fl (KO)

tag: batch


title: mRNA E18.5 heart Lrrc58 hom Plagl1 mut(pat) rep 5

description: Library name: 28_3_KO_Het_F

value: Lrrc58 hom Plagl1 mut(pat)


title: Gastrocnemius, Control 4

description:
Library name: Control 4
column Control 4 in Nox4_RNAseq_counts.csv

value: Nox4 fl/fl (control)


title: bone marrow; sAA; 1893-A043004

description: Library name: 1893-A043004


title: bone marrow; mAA; 1893-A043003

description: Library name: 1893-A043003


title: Gastrocnemius, Control 3

description:
Library name: Control 3
column Control 3 in Nox4_RNAseq_counts.csv


title: mRNA E18.5 heart Lrrc58 het Plagl1 mut(pat) rep 7

description: Library name: 28_2_Het_Het_F

value: Lrrc58 het Plagl1 mut(pat)


title: mRNA E18.5 heart Lrrc58 het Plagl1 WT rep 4

description: Library name: 28_1_Het_WT_F


title: bone marrow; sAA; 1893-A043001

description: Library name: 1893-A043001


title: mRNA E18.5 heart Lrrc58 het Plagl1 mut(pat) rep 6

description: Library name: 27_6_Het_Het_M


title: Control patient line 1035 replicate 1

description: Library name: Control_1035_rep1


title: bone marrow; sAA; 1893-A043000

description: Library name: 1893-A043000


title: Control patient line LCH117 replicate 2

description: Library name: Control_LCH117_rep2


title: Input_PA2_E11.5_Hoxa2PTE-36kb-del

first: Filippo

address: Fabrikstrasse 24,

institute: FMI

description:
Library name: Sample 6
PA2 , E11.5, Hoxa2PTE-36kb-del, Input

library_source: genomic

data_processing:
Reads were aligned to the mouse GRCm38/mm10 reference genome using the QuasR package (version 1.38.0) through the qAlign function.
BigWig files were generated using the qExportWig function from the QuasR package. The files contain CPM (Counts Per Million) values with a resolution of 100 base pairs and a scaling factor of 1e6.
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig files contain cpm values
Supplementary files format and content: wig files contain cpm values

molecule: genomic DNA

extract_protocol:
Dissected tissue from E8.5 embryos (i.e. dorsal most portion of the neural plate) and from E10.5 and E11.5 embryos (i.e. FNP, Mx, Md and PA2) were micro-dissected and incubated in trypsin 0.5%/EDTA 1X at 37 °C for 10 minutes, rinsed (DMEM 1X/ FBS 10%, followed by two washes in ice-cold 1× DMEM), dissociated by pipetting, cross-linked with 1% formaldehyde in PBS 1X for 10 minutes at room temperature (RT) and quenched with glycine (final concentration 125 mM) for 5 minutes at RT. Cells were spun down (1600 rpm, 10 minutes, 4 °C) and rinsed in ice-cold PBS. CNCCs from E11.5 Wnt1::Cre;ROSARFP and Wnt1::Cre;ROSARFP;Ezh2 flox/flox (Ezh2cKO) embryos were filtered and collected by FACS. ChIP-seq experiments with anti-H3K4me2 (Millipore, Cat. #07-030), anti-H3K27me3 (Millipore, Cat. # 07-449), anti-H3K27ac (abcam, ab4729) and anti-CTCF (Cell Signaling, CST 2899) antibodies were performed as described in Minoux et al., 2017 and Kessler et al., 2023.
ChIP-seq libraries were generated using bar-coded adapters (NEB, E7335) in combination with the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, E7370) according to manufacturers’ instructions. The quality of the libraries and size distribution was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies). Sequencing was performed on an Illumina HiSeq 2500 machine (50 bp read length, single-end) or an Illumina NovaSeq 6000 machine (50 bp read length, paired-end) .

tag: developmental stage

value: Cranial neural crest cells

tag: antibody

value: Input


title: ChipSeq_FNPMxMdPA2_E11.5_Ezh2cKO_CTCF_1

description:
Library name: Sample 8
Wnt1CreRosa.mix , E11.5, Ezh2cKO, ChipSeq , CTCF

source_name: FNP, Mx, Md, PA2

value: FNP, Mx, Md, PA2

value: CTCF


title: Control patient line 12842 replicate 1

description: Library name: Control_12842_rep1


title: Control patient line LCH117 replicate 1

description: Library name: Control_LCH117_rep1


title: Gastrocnemius, Control 2

description:
Library name: Control 2
column Control 2 in Nox4_RNAseq_counts.csv


title: Gastrocnemius, Control 1

description:
Library name: Control 1
column Control 1 in Nox4_RNAseq_counts.csv


title: Control patient line LCH132 replicate 1

description: Library name: Control_LCH132_rep1


title: Mouse lung tissue, normal control, biological replicate 3

city: Huai'an

first: Xiuqin

last: Ni

address: No.4 Mei Cheng Road, Higher Education Park

country: China

institute: Jiangsu Food and Pharmaceutical Science College

description:
Library name: Con_Lung_3
Normal mouse lung tissue without OVA induction and Rg3 treatment

data_processing:
Raw sequencing data (FASTQ files) were filtered to remove low-quality reads, adapter sequences, and reads containing more than 5% N bases using Trimmomatic software to obtain clean reads.
Read counts of each gene were calculated using featureCounts software, and the gene expression matrix was generated.
Assembly: Mus musculus reference genome, GRCm39 (mm39).
Supplementary files format and content: Processed data files are in XLSX format, including the gene-level expression matrix (Expression_Gene.xlsx). Rows represent genes (with Ensembl gene ID and gene symbol), columns include gene annotation information (locus, strand, gene type) and sample expression values (e.g., Con1, OVA1, Rg3-1), recording the expression level of each gene in each sample.

source_name: Lung

growth_protocol: Wild type Mus musculus (mice) were raised under specific pathogen-free (SPF) conditions, with a 12-hour light/dark cycle, free access to food and water, and maintained at a constant temperature of 22±2℃ and humidity of 50±5% until the experimental period.

extract_protocol:
Total RNA was extracted from mouse lung tissue using Trizol reagent (Invitrogen) according to the manufacturer's instructions. The purity and integrity of RNA were detected by NanoDrop and agarose gel electrophoresis, respectively, to ensure RNA quality meets sequencing requirements (OD260/OD280 = 1.8-2.0, RNA integrity number ≥ 7.0).
RNA libraries were constructed using the TruSeq RNA Sample Preparation Kit (Illumina). Briefly, mRNA was enriched from total RNA using oligo(dT) magnetic beads, fragmented, reverse-transcribed into cDNA, and then subjected to end repair, A-tailing, adapter ligation, and PCR amplification. The constructed libraries were quantified by Qubit and qualified by agarose gel electrophoresis before sequencing.

treatment_protocol: Mice were divided into three groups: NC group (normal saline, no OVA induction, no Rg3 treatment), OVA group (OVA induction, no Rg3 treatment), and Rg3 group (OVA induction + Ginsenoside Rg3 treatment). OVA induction was performed by intraperitoneal injection and aerosol inhalation; Ginsenoside Rg3 (20 mg/kg) was administered by gavage at the corresponding dose during OVA induction.

value: Lung

value: Wild type

tag: treatment

value: Normal saline (no OVA, no Rg3)

value: Batch 1


title: mRNA E18.5 heart Lrrc58 het Plagl1 WT rep 3

description: Library name: 27_5_Het_WT_F

value: Heart

value: Lrrc58 het Plagl1 WT


title: bone marrow; sAA; 1893-A042999

description: Library name: 1893-A042999

value: bone marrow


title: Healthy spleen 6, 31016-024

city: West Lafayette

first: Andrea

last: Pires dos Santos

address: 625 Harrison St.

institute: Purdue University

description:
Library name: Spleen sample 24
Column name in miRNA_counts.raw.xlsx: 31016-024 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx

data_processing:
CLC Genomics Workbench 21.0.4
Assembly: CanFam3.1.101
Supplementary files format and content: raw counts for each sample.
Supplementary files format and content: normalized counts for each sample.

organism: Canis lupus familiaris

source_name: Spleen

extract_protocol:
miRNeasy FFPE Kit (Qiagen)
QIAseq miRNA Library Kit (QIAGEN). A total of 100ng total RNA was converted into miRNA NGS libraries.

value: Spleen

value: Control


title: Healthy spleen 5, 31016-023

description:
Library name: Spleen sample 23
Column name in miRNA_counts.raw.xlsx: 31016-023 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx


title: mRNA E18.5 heart Lrrc58 hom Plagl1 mut(pat) rep 4

description: Library name: 27_4_KO_Het_F


title: Healthy spleen 3, 31016-021

description:
Library name: Spleen sample 21
Column name in miRNA_counts.raw.xlsx: 31016-021 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx


title: bone marrow; sAA; 1893-A042998

description: Library name: 1893-A042998


title: mRNA E18.5 heart Lrrc58 hom Plagl1 WT rep 6

description: Library name: 27_3_KO_WT_F

value: Lrrc58 hom Plagl1 WT


title: BRAFV600E patient line LCH105 replicate 2

description: Library name: BRAFV600E_LCH105_rep2

value: iPSC-derived Microglia

value: patient line

value: Microglia


title: mRNA E18.5 heart Lrrc58 hom Plagl1 WT rep 5

description: Library name: 27_1_KO_WT_M


title: mRNA E18.5 heart Lrrc58 hom Plagl1 mut(pat) rep 3

description: Library name: 27_2_KO_Het_M

value: Lrrc58 hom Plagl1 mut(pat)


title: bone marrow; mAA; 1893-A042997

description: Library name: 1893-A042997


title: bone marrow; sAA; 1893-A042995

description: Library name: 1893-A042995


title: bone marrow; mAA; 1893-A042996

description: Library name: 1893-A042996


title: BRAFV600E patient line LCH105 replicate 1

description: Library name: BRAFV600E_LCH105_rep1


title: Healthy spleen 4, 31016-022

description:
Library name: Spleen sample 22
Column name in miRNA_counts.raw.xlsx: 31016-022 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx


title: BRAFV600E patient line LCH1293 replicate 2

description: Library name: BRAFV600E_LCH1293_rep2


title: Control patient line LCH132 replicate 2

description: Library name: Control_LCH132_rep2


title: Healthy spleen 1, 31016-019

description:
Library name: Spleen sample 19
Column name in miRNA_counts.raw.xlsx: 31016-019 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx


title: Healthy spleen 2, 31016-020

description:
Library name: Spleen sample 20
Column name in miRNA_counts.raw.xlsx: 31016-020 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx


title: mRNA E18.5 heart Lrrc58 het Plagl1 mut(pat) rep 5

description: Library name: 26_5_Het_Het_F

value: Lrrc58 het Plagl1 mut(pat)


title: mRNA E18.5 heart Lrrc58 het Plagl1 WT rep 2

description: Library name: 26_6_Het_WT_M


title: bone marrow; mAA; 1893-A042994

description: Library name: 1893-A042994


title: BRAFV600E patient line 12842 replicate 2

description: Library name: BRAFV600E_LCH12842_rep2


title: bone marrow; mAA; 1893-A042993

description: Library name: 1893-A042993


title: BRAFV600E patient line LCH1293 replicate 1

description: Library name: BRAFV600E_LCH1293_rep1


title: Cancer spleen 18, 31016-018

description:
Library name: Spleen sample 18
Column name in miRNA_counts.raw.xlsx: 31016-018 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx

value: Visceral hemangiosarcoma


title: bone marrow; Control; 1893-A042992

description: Library name: 1893-A042992


title: mRNA E18.5 heart Lrrc58 hom Plagl1 WT rep 4

description: Library name: 26_4_KO_WT_F


title: BRAFV600E patient line 1035 replicate 1

description: Library name: BRAFV600E_LCH1035_rep1


title: Cancer spleen 17, 31016-017

description:
Library name: Spleen sample 17
Column name in miRNA_counts.raw.xlsx: 31016-017 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx


title: mRNA E18.5 heart Lrrc58 hom Plagl1 WT rep 3

description: Library name: 26_3_KO_WT_F


title: BRAFV600E patient line 12842 replicate 1

description: Library name: BRAFV600E_LCH1284_rep1


title: BRAFV600E patient line LCH1105 replicate 2

description: Library name: BRAFV600E_LCH1105_rep2


title: bone marrow; Control; 1893-A042990

description: Library name: 1893-A042990


title: Cancer spleen 14, 31016-014

description:
Library name: Spleen sample 14
Column name in miRNA_counts.raw.xlsx: 31016-014 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx


title: Cancer spleen 16, 31016-016

description:
Library name: Spleen sample 16
Column name in miRNA_counts.raw.xlsx: 31016-016 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx


title: Cancer spleen 15, 31016-015

description:
Library name: Spleen sample 15
Column name in miRNA_counts.raw.xlsx: 31016-015 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx


title: bone marrow; Control; 1893-A042991

description: Library name: 1893-A042991


title: bone marrow; Control; 1893-A042989

description: Library name: 1893-A042989


title: mRNA E18.5 heart Lrrc58 het Plagl1 mut(pat) rep 3

description: Library name: 23_7_Het_Het_F


title: mRNA E18.5 heart Lrrc58 het Plagl1 mut(pat) rep 4

description: Library name: 26_1_Het_Het_M


title: BRAFV600E patient line LCH1106 replicate 1

description: Library name: BRAFV600E_LCH1106_rep1


title: BRAFV600E patient line LCH1105 replicate 1

description: Library name: BRAFV600E_LCH1105_rep1


title: mRNA E18.5 heart Lrrc58 hom Plagl1 WT rep 2

description: Library name: 23_6_KO_WT_F


title: bone marrow; Control; 1893-A042988

description: Library name: 1893-A042988


title: mRNA E18.5 heart Lrrc58 hom Plagl1 mut(pat) rep 2

description: Library name: 26_2_KO_Het_F


title: BRAFV600E patient line LCH1106 replicate 2

description: Library name: BRAFV600E_LCH1106_rep2


title: mRNA E18.5 heart Lrrc58 het Plagl1 mut(pat) rep 2

description: Library name: 23_5_Het_Het_M


title: H1299, LMNB2 KO, RNAseq, rep2

city: Seoul

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

country: South Korea

institute: Chung-Ang University

data_processing:
High-throughput sequencing was carried out as paired-end 101 sequencing reads using NextSeq 500 (Illumina, Inc., USA).
STAR (v.2.7.1a) was used to align mRNA-Seq reads. Indices were generated from either the genome assembly sequence or representative transcript sequences for alignment to the genome and transcriptome.
The alignment file was used to assemble transcripts, estimate their abundances, and detect gene expression differences using RSEM(v.1.3.3).
Differentially expressed transcripts were identified using EdgeR (v.3.36.0) within R version 4.1.0 (R development Core Team, 2011) using the R package.
Assembly: GRCh38.p13.103
Supplementary files format and content: tab-delimited text file include raw counts for each sample
Supplementary files format and content: xlsx file include statistical test for each group

growth_protocol: All the cell culture reagents used in the present study were purchased from Welgene (Seoul, Republic of Korea). H1299 (human non-small cell lung carcinoma) cells were purchased from the Korean Cell Line Bank (Seoul, Republic of Korea). H1299 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin at 37 °C in an incubator with 5% CO2 in a humidified atmosphere. For synchronization at G1/S, cells were cultured in the presence of 2mM thymidine (Sigma) for 18hrs, washed three times with phosphate-buffered saline (PBS) and released in fresh medium without thymidine for 9 hrs. After another 16 hrs in thymidine, cells were provided for experiments.

extract_protocol:
Total RNA was extracted using the TRIzol solution. 100 ng of total RNA from H1299 cells were extracted, and then reverse transcription was carried out using an oligo-dT primer that had an Illumina-compatible sequence at its 5' end.
RNA libraries for RNA-seq were prepared using the TruSeq mRNA Library Prep Kit (Illumina, Inc., USA) following manufacturer's instructions.

value: Epithelial

value: LMNB2 KO


title: Cancer spleen 13, 31016-013

description:
Library name: Spleen sample 13
Column name in miRNA_counts.raw.xlsx: 31016-013 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx


title: Cancer spleen 12, 31016-012

description:
Library name: Spleen sample 12
Column name in miRNA_counts.raw.xlsx: 31016-012 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx


title: H1299, LMNB2 KO, RNAseq, rep1

value: Lung


title: Cancer spleen 11, 31016-011

description:
Library name: Spleen sample 11
Column name in miRNA_counts.raw.xlsx: 31016-011 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx


title: siGGCT3

city: Harbin

first: Lijun

last: Yang

address: yikuang street

institute: Harbin Institute of Technology

description: Library name: sample6

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: hg19
Supplementary files format and content: xls file includes gene counts for each sample
Supplementary files format and content: xls file includes FPKM expression values for each sample

growth_protocol: MHCC97H was cultured in DMEM medium with high glucose (25mM), sodium pyruvate (1mM), glutamine (2mM), penicillin (100U/mL; Sigma, St. Louis, MO, USA), streptomycin (0.1 mg/mL; Sigma) and 10% (v/v) fetal bovine serum (FBS; Gibco) at 37℃ and 5% carbon dioxide.

extract_protocol:
RNA was harvested using trizol (Ambion/Invitrogen,USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system

value: GGCT knockdown


title: mRNA E18.5 heart Lrrc58 het Plagl1 mut(pat) rep 1

description: Library name: 23_4_Het_Het_F


title: mRNA E18.5 heart Lrrc58 hom Plagl1 mut(pat) rep 1

description: Library name: 23_2_KO_Het_M


title: siGGCT2

description: Library name: sample5


title: Cancer spleen 9, 31016-09

description:
Library name: Spleen sample 9
Column name in miRNA_counts.raw.xlsx: 31016-009 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx


title: NC3

description: Library name: sample3

value: WT


title: H1299, Control, RNAseq, rep2


title: siGGCT1

description: Library name: sample4


title: Cancer spleen 10, 31016-010

description:
Library name: Spleen sample 10
Column name in miRNA_counts.raw.xlsx: 31016-010 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx


title: H1299, Control, RNAseq, rep1


title: mRNA E18.5 heart Lrrc58 het Plagl1 WT rep 1

description: Library name: 23_3_Het_WT_M

value: Heart


title: H1299, LMNB1 KO, RNAseq, rep1

value: LMNB1 KO


title: H1299, LMNB1 KO, RNAseq, rep2


title: Cancer spleen 8, 31016-008

description:
Library name: Spleen sample 8
Column name in miRNA_counts.raw.xlsx: 31016-008 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx


title: mRNA E18.5 heart Lrrc58 hom Plagl1 WT rep 1

description: Library name: 23_1_KO_WT_F


title: NC2

description: Library name: sample2


title: Cancer spleen 7, 31016-007

description:
Library name: Spleen sample 7
Column name in miRNA_counts.raw.xlsx: 31016-007 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx


title: ChipSeq_FNPMxMd_E10.5_Ezh2cKO_H3K27me3_1

description:
Library name: Sample 12
FNP,Mx,Md, E10.5, Ezh2cKO, H3K27me3

source_name: FNP, Mx, Md

value: FNP, Mx, Md

value: Cranial neural crest cells


title: sRNA MEF-CRISPRi Zswim8 knockdown guide 2

description: Library name: Z8_1D9

data_processing:
Adaptor sequences (4 random nucleotides from the 5 prime end and the 3 prime adaptor (N{4}CTGTCTCTTATACACATCTCCGAGC) were trimmed from reads using cutadapt. Reads were filtered for quality using fastq_quality_filter with the parameters “–q 30 –p 100.” To assign processed sequencing reads to miRNAs, the first 19nt of each read was matched to a dictionary of miRNA sequences downloaded from TargetScan Release 8.0, requiring no mismatches between the read and the miRNA dictionary.
Assembly: TargetScan Release 8.0 (mouse)
Supplementary files format and content: raw miRNA counts for all samples

source_name: Immortalized mouse embryonic fibroblasts (MEF)

growth_protocol: MEF CRISPRi cells were cultured in DMEM supplemented with 10% FBS. Cells were grown to contact inhibition for at least 5 days before harvesting.

extract_protocol:
Cultured cell lines were scraped from culture dishes into TRI Reagent and RNA was purified according to manufacturer's instructions.
Small-RNA sequencing libraries were prepared from 5 μg total RNA. 0.5 fmoles of miR-427-5p (X. tropicalis) and 0.5 fmoles of lsy-6-3p (C. elegans) were added to each sample as spike-ins. Small RNA species were isolated by excising the gel fragment migrating between 18-nt and 32nt radiolabeled internal standards on a 15% polyacrylamide urea gel. Size selected RNA was eluted from the gel, precipitated in ethanol, and ligated to a preadenylated 3¢ adapter (AppNNNNCTGTCTCTTATACACATCTCCGAGCddC) using T4 RNA Ligase 2 KQ mutant (NEB) in a reaction supplemented with 10% polyethylene glycol (PEG 8000, NEB). The 3¢ adapter had 4 random-sequence positions at its 5¢ end to reduce ligation bias. Ligated small RNAs were isolated on a 10% polyacrylamide urea gel, precipitated in ethanol, and ligated to a 5¢ adapter (CCUACACGACGCUCUUCCGAUCUNNNN) using T4 RNA Ligase I (NEB) in a reaction supplemented with 10% PEG. The 5¢ adapter had 4 random-sequence positions at its 3¢ end to reduce ligation bias. Ligated small RNAs were isolated on an 8% polyacrylamide urea gel, precipitated in ethanol, and reverse transcribed with SuperScript III (Invitrogen). Resulting cDNA was amplified using KAPA HiFi DNA polymerase (Kapa Biosystems). Amplified DNA was purified on a 90% formamide, 8% acrylamide gel and submitted for sequencing on the Illumina NovaSeq platform. A step-by-step protocol for constructing libraries for small-RNA sequencing is available at http://bartellab.wi.mit.edu/protocols.html.

value: Zswim8 knockout


title: Cancer spleen 6, 31016-006

description:
Library name: Spleen sample 6
Column name in miRNA_counts.raw.xlsx: 31016-006 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx

value: Spleen


title: NC1

description: Library name: sample1


title: Cancer spleen 5, 31016-005

description:
Library name: Spleen sample 5
Column name in miRNA_counts.raw.xlsx: 31016-005 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx


title: sRNA MEF-CRISPRi control knockdown 2

description: Library name: NT_9A

value: Immortalized mouse embryonic fibroblasts (MEF)

value: control


title: SCAP-Exo-3

city: Shenyang

first: AoChen

last: Wang

state: Liaoning

address: School of Stomatology

institute: China Medical University,

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts.
The processed small RNA reads were used in Bowtie (Langmead et al., 2009) for read mapping to reference sequence.
Processed reads of length at 18 to 35 nt for animals or 18-30 nt for plants were then mapped to their reference genome and analyzed using the bowtie package (no mismatch).
Assembly: GRCh38.p14

source_name: Apical papilla

growth_protocol: SCAP were seeded in 10-cm culture dishes and cultured with alpha minimum essential medium (a-MEM; HyClone) supplemented with 15% foetal bovine serum (FBS; MRC BRL), 2 mM L-glutamine (Biosource/Invitrogen), 100 U/mL penicillin-streptomycin (HyClone), and 0.1 mM L-ascorbic acid 2-phosphate (WAKO, Japan) and maintained in a humidified atmosphere containing 5% CO2 at 37 ℃. SCAP at passage 5 were used for subsequent experiments.

extract_protocol:
The culture supernatants were centrifuged successively at increasing speeds: 3,000 × g for 20 min, 20,000 × g for 30 min, and 120,000 × g for 2 h (Beckman Optima L-100XP, USA) to obtain SCAP-Exo.
The small RNA libraries were prepared from a total of 2µg total RNA isolated from each sample using NEBN ex芒Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) according to the manufacturer's instruction

treatment_protocol: When the 5th passage SCAP reached 80% confluence, the supernatant was collected after 48 h of continuous culture in exosome-free serum medium (SBI, USA). The exosome purification procedure was based on differential ultracentrifugation at 4 ℃.

value: Apical papilla

value: SCAP

value: mesenchymal stem cell

value: Extraction exosomes from cells


title: sRNA MEF (15C1) Lrrc58 site deletion clone 2

description: Library name: Lrrc58_28_10

growth_protocol: MEF cells were cultured in DMEM supplemented with 10% FBS. Cells were grown to contact inhibition for at least 5 days before harvesting.

extract_protocol:
Cultured cell lines were scraped from culture dishes into TRI Reagent and RNA was purified according to manufacturer's instructions.
Small-RNA sequencing libraries were prepared from 5 μg total RNA. 0.5 fmoles of miR-427-5p (X. tropicalis) and 0.5 fmoles of lsy-6-3p (C. elegans) were added to each sample as spike-ins. Small RNA species were isolated by excising the gel fragment migrating between 18-nt and 32nt radiolabeled internal standards on a 15% polyacrylamide urea gel. Size selected RNA was eluted from the gel, precipitated in ethanol, and ligated to a preadenylated 3¢ adapter (AppNNNNCTGTCTCTTATACACATCTCCGAGCddC) using T4 RNA Ligase 2 KQ mutant (NEB) in a reaction supplemented with 10% polyethylene glycol (PEG 8000, NEB). The 3¢ adapter had 4 random-sequence positions at its 5¢ end to reduce ligation bias. Ligated small RNAs were isolated on a 10% polyacrylamide urea gel, precipitated in ethanol, and ligated to a 5¢ adapter (CCUACACGACGCUCUUCCGAUCUNNNN) using T4 RNA Ligase I (NEB) in a reaction supplemented with 10% PEG. The 5¢ adapter had 4 random-sequence positions at its 3¢ end to reduce ligation bias. Ligated small RNAs were isolated on an 8% polyacrylamide urea gel, precipitated in ethanol, and reverse transcribed with SuperScript III (Invitrogen). Resulting cDNA was amplified using KAPA HiFi DNA polymerase (Kapa Biosystems). Amplified DNA was purified on a 90% formamide, 8% acrylamide gel and submitted for sequencing on the Illumina HiSeq platform. A step-by-step protocol for constructing libraries for small-RNA sequencing is available at http://bartellab.wi.mit.edu/protocols.html.

value: Lrrc58 site deletion


title: SCAP-Exo-1


title: sRNA MEF-CRISPRi Zswim8 knockdown guide 1

description: Library name: Z8_1D5


title: sRNA MEF (15C1) control clone 2

description: Library name: WT_31_5


title: ChipSeq_FNPMxMd_E10.5_WT_H3K27me3_1

description:
Library name: Sample 11
FNP,Mx,Md, E10.5, WT, H3K27me3


title: sRNA MEF-CRISPRi Atp6v1g1/Lpar4 double knockdown guide pair 1

description: Library name: Atp6v1g1-Lpar4_11C


title: A51_A51Ceri_3

city: Sydney

first: Jingwei

last: Chen

address: High Street

institute: Children's Cancer Institute

description: TERT-rearranged

data_processing:
Single-end RNA-sequencing reads were algined to hg38 using STAR (v2.7.8a) (--outSAMunmapped Within --twopassMode Basic --outFilterType BySJout  --outSAMattributes All    --outSAMtype BAM Unsorted  --quantMode TranscriptomeSAM --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66)
Bam files were sorted and duplicates removed using picards tools (v2.27.5).
Raw gene expression counts and normalised transcripts per million (TPM) counts were quantified using RSEM (v1.3.3).
Assembly: hg38
Supplementary files format and content: tab delimited file containing raw count data for all samples
Supplementary files format and content: tab delimited file containing normalised TPM count data for all samples

source_name: CLB-GA

growth_protocol: CLB-GA neuroblastoma cells were maintained in RMPI media supplemented with 10% fetal calf serum (FCS) in humidified incubator at 5% CO2 and 37oC.

extract_protocol:
Total RNA was extracted with Invitrogen PureLink RNA Mini Kit (Cat#12183020) according to manufacturer's protocol.
RNA integrity was confirmed on the Nanodrop (ND) 1000 spectrophotometer (Thermo Fisher Scientific) and prepared using the low input SMARTer Stranded Total RNA pico input mammalian preparation.

treatment_protocol: TERT-rearranged CLB-GA neuroblastoma cells were treated with vehicle control, 62.5nM A51, 1μM Ceritinib, or combination for 12 hours.

value: CLB-GA

value: neuroblastoma cells

value: Combination treatment of A51 (62.5nM) and Certinitib (1uM)


title: SCAP-Exo-2


title: sRNA MEF (15C1) Lrrc58 site deletion clone 1

description: Library name: Lrrc58_28_9


title: A51_A51Ceri_2

description: TERT-rearranged

value: WT


title: Cancer spleen 2, 31016-002

description:
Library name: Spleen sample 2
Column name in miRNA_counts.raw.xlsx: 31016-002 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx

value: Visceral hemangiosarcoma


title: Cancer spleen 3, 31016-003

description:
Library name: Spleen sample 3
Column name in miRNA_counts.raw.xlsx: 31016-003 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx


title: sRNA MEF (15C1)  control clone 3

description: Library name: WT_31_6


title: sRNA MEF (15C1) control clone 1

description: Library name: WT_31_4


title: sRNA MEF-CRISPRi Atp6v1g1 knockdown guide 2

description: Library name: Atp6v1g1_2C3


title: sRNA MEF-CRISPRi Atp6v1g1/Lpar4 double knockdown guide pair 2

description: Library name: Atp6v1g1-Lpar4_12C


title: Cancer spleen 1, 31016-001

description:
Library name: Spleen sample 1
Column name in miRNA_counts.raw.xlsx: 31016-001 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx


title: sRNA MEF-CRISPRi control knockdown 1

description: Library name: NT_2N1


title: Cancer spleen 4, 31016-004

description:
Library name: Spleen sample 4
Column name in miRNA_counts.raw.xlsx: 31016-004 - Total counts
miRNA_counts.raw.xlsx
miRNA_counts.cpm.TMM-adjusted.xlsx


title: A51_A51Ceri_1

description: TERT-rearranged


title: sRNA MEF (15C1) Zswim8 knockout clone 3

description: Library name: Z8_30_15


title: sRNA MEF (15C1) Zswim8 knockout clone 2

description: Library name: Z8_30_14


title: sRNA MEF-CRISPRi Lpar4 knockdown guide 1

description: Library name: Lpar4_2C5

value: Atp6v1g1 site deletion


title: A51_Ceritinib_2

description: TERT-rearranged

value: Ceritinib treatment at 1uM


title: sRNA MEF-CRISPRi Atp6v1g1 knockdown guide 1

description: Library name: Atp6v1g1_2C4


title: sci-RNA-seq3_Arabidopsis_Day0_to_Day4_Biological_Replicate_2_Technical_Replicate_1

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
Library name: Arabidopsis_Day0_to_Day4_Biological_Replicate_2_Technical_Replicate_1
sci-RNA-seq3

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, and gene counting were preformed as described in https://github.com/JunyueC/sci-RNA-seq3_pipeline
Assembly: Arabidopsis TAIR10
Supplementary files format and content: Seurat object

molecule: nuclear RNA

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Plants were grown on vermiculite under well-watered conditions for 29 days, before being subject to drought stress

extract_protocol:
Frozen tissue from each time point was crushed using a bead bashing approach, and nuclei released from homogenate by resuspending in Nuclei Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). The resulting suspension was passed through a 30-um filter.
Library construction was performed following the sci-RNA-seq3 workflow

value: leaf

tag: age

value: mature rosttes


title: Arabidopsis, Columbia-0, Rep3

city: Yangling

first: Su

middle: Ying

last: Pei

state: Shaanxi

address: No. 3 Taicheng Road

department: College of Life Sciences and Institute of Future Agriculture

institute: Northwest A&F University

description: Library name: columbia R3

data_processing:
Paired-end reads were subjected to filtering and trimming using the fastp tool (version 0.23.4).
The clean reads were aligned to the TAIR 10 genome (https://www.arabidopsis.org/) using HISAT2 (VERSION 2.2.1).
Quantification was performed with Rsubread package (version 2.12.0) and normalized using TPM (Transcripts Per Kilobase of exon model per Million mapped reads).
Assembly: TAIR 10
Supplementary files format and content: Txt files include TPM values for each sample.

source_name: fresh seeds

growth_protocol: Plants were grown on soil mixture in a growth chamber under long-day conditions at ~21°C.  seeds were stratified for 4 days at 4°.

extract_protocol:
total RNA was extracted by using RNAprep Pure Polysaccharide Polyphenol Plant Total RNA Extraction Kit (TIANGEN, DP441) following the manufacturer’s instructions.
RNA-Seq libraries  were constructed by BGI company.

treatment_protocol: freshly seeds were harvested within 24 hours.

value: fresh seeds


title: Mouse PFC EAE, replicate 7

city: Rome

first: Marco

last: Pieraccioli

address: Largo Francesco Vito 1

country: Italy

institute: Catholic University of the Sacred Heart rome

description:
Library name: PFC_EAE_7
Column name in raw_counts.txt EAE_7

data_processing:
Raw pairend-ends reads fastq files were preprocessed with cutadapt v.3.1 and fastp v.0.21.0 to remove lower quality bases and adapters.
Trimmed reads were mapped to mm10 Gencode (vM25) using STAR v2.7.9a.
Statistics on strandness reads, genebody coverage, reads distribuition and insert size estimation were performed using RSeQC v.4.0.0 and picard CollectRnaSeqMetrics v.2.26.6.
The uniquely mapped reads from biological replicates were kept and counted with featureCounts v.1.6.0.
Differential gene expression on read counts matrix were performed using DESeq2 v.1.16.0
Assembly: mm10 Gencode (vM25)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

molecule: polyA RNA

source_name: Prefrontal cortex

growth_protocol: Female SJL/J mice (8–10 weeks old; The Jackson Laboratory, Bar Harbor, ME) were housed in dedicated experimental racks to allow continuous visual monitoring (24 h/day). In addition, daily checks to monitor the CSS were performed as previously described [9,86]. In accordance with current legislation, animals were group-housed with a maximum of 5 females per cage and a minimum of 2, as isolation was not required by the experimental protocol. Food and water were available ad libitum.

extract_protocol:
The PFC of control and EAE mice were isolated and maintained in RNA-later stabilization reagent (QIAGEN). Total RNA was isolated and DNase digested using the RNAeasy Mini Kit (Qiagen) according to manufacturer’s instruction.
RNA libraries for RNA-seq were prepared with Universal Plus mRNA-Seq with NuQuant (Tecan) following manufacturer's instructions and sequenced using a 150 bp paired-end format on an Illumina NovaSeq 6000.

treatment_protocol: EAE was induced in female SJL/J mice (8-10 weeks old; The Jackson Laboratory, Bar Harbor) by subcutaneously injection on day postimmunization (d.p.i.) 0 and 7 with 100 microliters of an emulsion containing 75 micrograms of PLP139-151 (PRIMM, Milan, Italy) and enriched complete Freund's adjuvant (CFA) with 8 mg/ml of killed and heat-dried Mycobacterium Tuberculosis H37RA (Sigma-Aldrich S.r.l., Milan). Intraperitoneal administration of 300 ng Bordetella Pertussis toxin (Merck, Milan, Italy) was performed on d.p.i. 0, 1, 7 and 8. Control mice were injected only with CFA. EAE mice were euthanized at the peak of the acute phase of the disease (Clinical Score and Signs =1,75-2,5; d.p.i 17 ± 2), and control mice were euthanized on the same days for comparison. Mice were perfused with sterile saline solution under deep anesthesia (87.5 mg/Kg Ketamine + 12.5 mg/Kg xylazine; 0.1 ml/20g mouse weight), the brain was removed and one hemisphere was fixed in 4% paraformaldehyde for 48h and employed for morphological analysis, while the PFC extracted from the other hemisphere was used for molecular assays and processed accordingly.

value: Prefrontal cortex

value: mouse prefrontal cortex

value: PFC, EAE, replicate 7


title: sRNA MEF-CRISPRi Lpar4 knockdown guide 2

description: Library name: Lpar4_2C6

value: Immortalized mouse embryonic fibroblasts (MEF)


title: Mouse PFC EAE, replicate 8

description:
Library name: PFC_EAE_8
Column name in raw_counts.txt EAE_8

value: PFC, EAE, replicate 8


title: sRNA MEF (15A3) Plagl1 site deletion clone 1

description: Library name: Plagl1_18_12

value: Plagl1 site deletion


title: A51_Ceritinib_1

description: TERT-rearranged


title: sRNA MEF (15A3) Plagl1 site deletion clone 3

description: Library name: Plagl1_18_4


title: A51_A51_3

description: TERT-rearranged

value: A51 treatment at 62.5nM


title: Arabidopsis, asf1a1b, Rep1

description: Library name: asf1a1b R1


title: Arabidopsis, Columbia-0, Rep1

description: Library name: columbia R1


title: Arabidopsis, asf1a1b, Rep3

description: Library name: asf1a1b R3


title: Mouse PFC EAE, replicate 9

description:
Library name: PFC_EAE_9
Column name in raw_counts.txt EAE_9

value: PFC, EAE, replicate 9


title: Arabidopsis, asf1a1b, Rep2

description: Library name: asf1a1b R2


title: A51_A51_1

description: TERT-rearranged

value: CLB-GA

value: neuroblastoma cells


title: A51_A51_2

description: TERT-rearranged

value: WT


title: sRNA MEF (15A3) Plagl1 site deletion clone 2

description: Library name: Plagl1_18_15


title: A51_Ceritinib_3

description: TERT-rearranged


title: Mouse PFC EAE, replicate 4

description:
Library name: PFC_EAE_4
Column name in raw_counts.txt EAE_4

value: PFC, EAE, replicate 4


title: sRNA MEF (15C1) Zswim8 knockout clone 1

description: Library name: Z8_30_13

value: Zswim8 knockout


title: Arabidopsis, Columbia-0, Rep2

description: Library name: columbia R2


title: sRNA MEF (15A3) control clone 3

description: Library name: NT_24_9

value: control


title: ChIP-seq of H3K9me3 in Gas5 KO mESCs

city: Shanghai

first: Jiani

address: Siping Road, Yangpu District

institute: Tongji University

description:
Library name: Gas5KO_K9me3_ChIP_L1
H3K9me3 profile in Gas5 KO mESCs

data_processing:
Raw reads were trimmed using Trim Galore (v0.6.7). Alignment: ChIP-seq and RNA-seq reads were aligned to mm9 using Bowtie2 (v2.4.4) or STAR (v2.7.11).
Peak Calling: MACS2 (v2.1.1) used for ChIP-seq and RIP-seq peak calling with parameters -g mm --nolambda --nomodel.
Normalization: BigWig files generated via deepTools (v3.5.5) with RPKM normalization. DEGs identified using DESeq2 (v1.26.0) or Cufflinks (v2.2.1).
Assembly: mm9
Supplementary files format and content: bw files (ChIP-seq): RPKM normalized signal coverage tracks (BigWig format) for ChIP-seq visualization.
Supplementary files format and content: bw files (RIP-seq): CPM normalized signal coverage tracks (BigWig format) for RIP-seq visualization.
Supplementary files format and content: tab files: Gene expression quantification files containing unique FPKM values (tab-delimited text) for RNA-seq.

source_name: mESCs

growth_protocol: Mouse embryonic stem cells (ESCs) were maintained in high-glucose DMEM supplemented with 15% FBS, 2 mM L-Glutamine, 0.1 mM NEAA, 1% nucleosides mix, 0.1 mM β-mercaptoethanol and 1000 U/mL LIF. Cells were cultured on 0.1% gelatin-coated dishes at 37 °C with 5% CO2.

extract_protocol:
ChIP: Cells cross-linked with 1% formaldehyde, quenched with 125 mM glycine, and nuclei isolated using PBS with 0.5% Igepal CA-630. RIP/RNA-seq: RNA extracted using TRIzol Reagent or RNeasy Mini Kit. Nuclear/Cytosolic fractions were isolated via differential detergent lysis.
ChIP-seq: Libraries prepared from 25 ng DNA using KAPA HyperPlus Kit (Roche). RIP-seq/RNA-seq: Prepared using KAPA Stranded RNA-Seq Kit (with RiboErase for RNA-seq), including RNA fragmentation to 200-300 bp.

treatment_protocol: For Gas5 knockout, cells were transduced with lentiCRISPR v2 carrying sgRNAs and pCW57.1 (Cas9-inducible), selected with 1 μg/mL puromycin and 50 μg/mL hygromycin for 7 days. Cas9 expression was induced with 1 μg/mL doxycycline for 12 hours. For RNase A treatment, 5 μg/mL RNase A was added during IP.

value: mESCs

value: embryonic stem cell

value: Gas5 knockout


title: Mouse PFC EAE, replicate 2

description:
Library name: PFC_EAE_2
Column name in raw_counts.txt EAE_2

value: Prefrontal cortex

value: PFC, EAE, replicate 2


title: A51_control_3

description: TERT-rearranged

value: DMSO vehicle treatment


title: sRNA MEF (15A3) Zswim8 knockout clone 3

description: Library name: Zswim8_23_5

value: Immortalized mouse embryonic fibroblasts (MEF)


title: sRNA MEF (15A3) Zswim8 knockout clone 2

description: Library name: Zswim8_23_3


title: sRNA MEF (15A3) Zswim8 knockout clone 4

description: Library name: Zswim8_23_6


title: A51_control_2

description: TERT-rearranged


title: Mouse PFC EAE, replicate 1

description:
Library name: PFC_EAE_1
Column name in raw_counts.txt EAE_1

value: mouse prefrontal cortex

value: PFC, EAE, replicate 1


title: ChIP-seq of H3K9me3 in P25A mutant mESCs

description:
Library name: P25A_K9me3_ChIP_L1
H3K9me3 profile in P25A mutant mESCs

value: SUV39H2 P25A mutant


title: Mouse PFC EAE, replicate 3

description:
Library name: PFC_EAE_3
Column name in raw_counts.txt EAE_3

value: PFC, EAE, replicate 3


title: A51_control_1

description: TERT-rearranged

value: CLB-GA


title: ChIP-seq of H3K9me3 in K333A mutant mESCs

description:
Library name: K333A_K9me3_ChIP_L1
H3K9me3 profile in K333A mutant mESCs

value: SUV39H2 K333A mutant


title: ChIP-seq of H3K9me3 in WT mESCs

description:
Library name: WT_K9me3_ChIP_L1
H3K9me3 profile in WT mESCs

value: wild type


title: M2_WGBS

city: 上海

first: Qian

last: Zhang

state: 上海市

address: 盘山路7号

institute: Naval Medical University

description: Library name: M2

data_processing:
There are three parts in the methylation pipeline: pretreatment, alignment and caculation. Here are the steps: First, we pretreat both the solexa reads and the reference, transforming C to T or G to A. Then, we use SOAP to do the alignment and choose the best reads if appearing in several alignment results. After that, we filter duplicate reads and get the infomation of former reads to judge the methylation profile.Finally, in order to caculate methylation rate and convertion rate, we gather the information of each site on each chromosome.
Assembly: hg18
Supplementary files format and content: bigwig

source_name: Bone marrow

growth_protocol: Bone marrow HSC were freshed sorted using FACS

extract_protocol:
DNA was harvested using QIAamp DNA Kit (Qiagen). Total DNA was fragmented and used for the construction of sequencing libraries.
Genomic DNA was treated by bisulfite, and prepared by standard Illumina Genome Analyzer protocol

value: Bone marrow

value: Lin-CD133+CD34+ HSC

tag: disease state

value: MDS patient2


title: sRNA MEF (15A3) control clone 2

description: Library name: NT_24_12

value: control


title: Mouse PFC control, replicate 3

description:
Library name: PFC_ctrl3
Column name in raw_counts.txt CTRL_3

value: PFC, control, replicate 3


title: M3_WGBS

description: Library name: M3

value: MDS patient3


title: Mouse PFC control, replicate 4

description:
Library name: PFC_ctrl4
Column name in raw_counts.txt CTRL_4

value: Prefrontal cortex

value: PFC, control, replicate 4


title: ChIP-seq of SUV39H2 K333A mutant mESCs

description:
Library name: K333A_SUV39H2_ChIP_L1
ChIP-seq of K333A mutant SUV39H2

value: mESCs

value: embryonic stem cell


title: sRNA MEF (15A3) Zswim8 knockout clone 1

description: Library name: Zswim8_23_1

value: Immortalized mouse embryonic fibroblasts (MEF)

value: Zswim8 knockout


title: sRNA MEF (15A3) control clone 1

description: Library name: NT_24_11


title: ChIP-seq of H3K9me3 in SUV39H2 KO mESCs

description:
Library name: SUV39H2KO_K9me3_ChIP_L1
H3K9me3 profile in SUV39H2 KO mESCs

value: SUV39H2 knockout


title: M1_WGBS

description: Library name: M1

value: MDS patient1


title: N3_WGBS

description: Library name: N3

value: healthy donor3


title: Mouse PFC control, replicate 2

description:
Library name: PFC_ctrl2
Column name in raw_counts.txt CTRL_2

value: mouse prefrontal cortex

value: PFC, control, replicate 2


title: Mouse PFC control, replicate 1

description:
Library name: PFC_ctrl1
Column name in raw_counts.txt CTRL_1

value: PFC, control, replicate 1


title: ChIP-seq of SUV39H2 P25A mutant mESCs

description:
Library name: P25A_SUV39H2_ChIP_L1
ChIP-seq of P25A mutant SUV39H2

value: SUV39H2 P25A mutant


title: sRNA MEF (15A3) Atp6v1g1 site deletion clone 2

description: Library name: Atp6v1g1_16_10

value: Atp6v1g1 site deletion


title: Pum2-/- 3

city: wuhan

first: Xuefei

state: hubei

address: tongji

institute: Huazhong University of Science and Technology Tongji Medical College Union Hospital

description: Library name: Sample6

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: tab-delimited text file includes processed counts for each Sample
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Colon

extract_protocol:
RNA was harvested using trizol 1.3 ug of total RNA was usedfor the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library PrepKit following manufacturer's protocols.

value: Colon


title: tdT-positive hepatocytes from CCl4-treated mice, REP3

city: Minato City

first: Satoshi

last: Kawakami

address: 4-6-1 Shirokanedai

department: The Institute of Medical Science

country: Japan

institute: The University of Tokyo

description:
Library name: CCl4P3
CCL4P3

data_processing:
Reads were quality-checked (fastp v0.23.2), aligned to the mm10 genome (HISAT2 v2.1.0), and TPM values were calculated with TPMcalculator (v0.0.4).
Differentially expressed genes (DEGs) were identified using DESeq2 (v1.42.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts for each sample calculated with DEseq2.

source_name: Liver

extract_protocol:
Total RNA was extracted using the Single Cell RNA Purification Kit (Norgen).
Poly-A enriched, strand-specific (Novogene)

value: Liver

value: Hepatocytes


title: RG 3

city: Clayton

first: Luis

last: Batista

state: MO

address: 6329 San Bonita Avenue

institute: Washington University in St. Louis

description: Library name: 43867_S12

library_source: other

data_processing:
The adaptor was trimmed from the raw paired-end reads using trimmomatic.  Resulting trimmed reads are joined using FLASH read joiner.  The 3' RACE adapter was then removed using cutadapt.  Resulting reads was aligned to TERC ref sequencing using bowte2.  The resulting sam files from read alignment was used as input from a custom perl script for counting 3' non-templated A tails and templated extension.
Assembly: NR_001566.1
Supplementary files format and content: tab-delimited text fie containing summarized results from the custom perl script.

molecule: other

growth_protocol: 15% FBS and 1% penicillin-streptomycin and maintained at 37°C in 5% CO₂ and 5% O₂.

extract_protocol:
RNA was extracted using TRIzol reagent following the manufacturer’s protocol.
RNA-ligase-mediated 3`- RACE was performed by ligating a 5`- adenylated and 3`- blocked RNA linker to DNase-treated RNA using T4 RNA Ligase 2 (truncated KQ). Ligated RNA was purified and subjected to reverse transcription using a universal RT primer, followed by PCR amplification with hTR-specific primers (see Supplementary Table 1). Amplified products were purified and used for library construction with the TruSeq Nano DNA LT Library Prep Kit (Illumina), following the manufacturer’s instructions.

treatment_protocol: Cells were treated with DMSO, 30 μM sinefungin, 5 μM RG7834, or a combination of both for 20 days.


title: N1_WGBS

description: Library name: N1

value: Bone marrow

value: Lin-CD133+CD34+ HSC

value: healthy donor1


title: tdT-negative hepatocytes from CCl4-treated mice, REP3

description:
Library name: CCl4N3
CCL4N3


title: tdT-positive hepatocytes from CCl4-treated mice, REP2

description:
Library name: CCl4P2
CCL4P2


title: ChIP-seq of SUV39H2 WT mESCs (with RNase A)

description:
Library name: WT_SUV39H2_ChIP_A+_L1
SUV39H2 ChIP in WT mESCs, with RNase A

value: mESCs

value: embryonic stem cell

value: wild type


title: Primary rat oligodendrocytes, dolutegravir, 24 hrs proliferation + 72 hrs differentiation, rep 4

city: Philadelphia

first: Judith

middle: B.

last: Grinspan

state: PA

address: 3615 Civic Center Blvd., Abramson Research Center, 516D

department: Neurology

institute: Children's Hospital of Philadelphia

description: Library name: 231121DEDTG

data_processing:
Image analysis and base calling were conducted by the NovaSeq Control Software (NCS).
Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.
The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: Rattus_norvegicus.Rnor_6.0_ERCC
Supplementary files format and content: txt files for each sample include hit counts

organism: Rattus norvegicus

source_name: primary rat differentiated oligodendrocytes

growth_protocol: Primary rat oligodendrocyte precursor cells were maintained in a proliferation medium consisting of neurobasal medium + B-27 supplement, l-glutamine, pen/strep, 10 ng/mL bovine fibroblast growth factor, 2 ng/mL recombinant human platelet-derived growth factor, and 1 ng/mL neurotrophin 3. Differentiation was induced by switching to a DMEM/F12 medium containing pen/strep, 2 mM l-glutamine, 50 µg/mL transferrin, 5 µg/mL putrescine, 3 ng/mL progesterone, 2.6 ng/mL selenium, 12.5 µg/mL insulin, 0.5 µg/mL thyroxine, 0.3% glucose, and 10 ng/mL biotin. All cells were grown in incubators at 37˚C/5% CO2.

extract_protocol:
RNA was isolated from cultured OPCs or OLs using the Qiagen RNeasy Mini Kit (Qiagen).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB).

treatment_protocol: Treatment of oligodendrocyte progenitor cells occurred for 24 hours in proliferation medium with either DMSO vehicle (0.04%) or 8 µM dolutegravir. Treatment of differentiating oligodendrocytes included proliferation treatment for 24 hours followed by 72 hours of treatment with either DMSO vehicle (0.04%) or 8 µM dolutegravir in differentiation medium.

value: 8 µM dolutegravir


title: SF 3

description: Library name: 43866_S11

value: Sinefungin


title: ChIP-seq of SUV39H2 Gas5 KO mESCs

description:
Library name: Gas5KO_SUV39H2_ChIP_L1
SUV39H2 ChIP in Gas5 KO mESCs

value: Gas5 knockout


title: sRNA MEF (15A3) Atp6v1g1 site deletion clone 1

city: Cambridge

first: Daniel

last: Lin

address: 455 Main Street

institute: Whitehead Institute

description: Library name: Atp6v1g1_16_1

value: Immortalized mouse embryonic fibroblasts (MEF)


title: N2_WGBS

description: Library name: N2

value: healthy donor2


title: tdT-positive hepatocytes from CCl4-treated mice, REP1

description:
Library name: CCl4P1
CCL4P1


title: Primary rat oligodendrocytes, dolutegravir, 24 hrs proliferation + 72 hrs differentiation, rep 2

description: Library name: 231031A-DEDTG

value: primary rat differentiated oligodendrocytes


title: ChIP-seq of SUV39H2 WT mESCs (without RNase A)

description:
Library name: WT_SUV39H2_ChIP_A-_L1
SUV39H2 ChIP in WT mESCs, without RNase A


title: sRNA MEF (15A3) Atp6v1g1 site deletion clone 3

description: Library name: Atp6v1g1_16_4


title: tdT-negative hepatocytes from CCl4-treated mice, REP1

description:
Library name: CCl4N1
CCL4N1


title: Pum2-/- 1

description: Library name: Sample4


title: Pum2-/- 2

description: Library name: Sample5


title: Primary rat oligodendrocytes, dolutegravir, 24 hrs proliferation + 72 hrs differentiation, rep 3

description: Library name: 231031B-DEDTG


title: tdT-negative hepatocytes from CCl4-treated mice, REP2

description:
Library name: CCl4N2
CCL4N2


title: Combo 3

description: Library name: 43868_S13

value: Sinefungin + RG7834


title: DKC1 3

description: Library name: 43865_S10

value: DMSO


title: WT3

description: Library name: Sample3

value: Colon

value: WT


title: WT 3

description: Library name: 43864_S9


title: WT2

description: Library name: Sample2


title: Primary rat oligodendrocytes, dolutegravir, 24 hrs proliferation + 72 hrs differentiation, rep 1

description: Library name: 231024DEDTG


title: tdT-positive hepatocytes from oil-treated mice, REP2

description:
Library name: OilP2
OilP2

value: Liver

value: Hepatocytes

value: Oil


title: Primary rat oligodendrocytes, DMSO, 24 hrs proliferation + 72 hrs differentiation, rep 4

description: Library name: 231121DEDMSO


title: Combo 2

description: Library name: 43528_S11


title: SF 2

description: Library name: 43526_S9


title: WT1

description: Library name: Sample1


title: Primary rat oligodendrocytes, DMSO, 24 hrs proliferation + 72 hrs differentiation, rep 3

description: Library name: 231031B-DEDMSO


title: tdT-positive hepatocytes from oil-treated mice, REP1

description:
Library name: OilP1
OilP1


title: Primary rat oligodendrocytes, DMSO, 24 hrs proliferation + 72 hrs differentiation, rep 2

description: Library name: 231031A-DEDMSO


title: tdT-positive hepatocytes from oil-treated mice, REP3

description:
Library name: OilP3
OilP3


title: Control Chow + Intermittent Fasting, Hippocampus, replicate 3

city: Pisa

first: Paola

last: Tognini

address: 33 Piazza Martiri della Libertà

department: Health Science Interdisciplinary Center

institute: Scuola Superiore Sant’Anna

description: Library name: 84619_ID2395_63-CCIF3-H

data_processing:
FastQC v0.11.9 used for raw-read quality control.
Adapter and low-quality sequence trimmed with Trimmomatic v0.39 (ILLUMINACLIP:TruSeq3-PE.fa, SLIDINGWINDOW:4:20, MINLEN:36).
Trimmed reads aligned to the mouse reference genome with TopHat v2.1.1 (Bowtie2 v2.3.5.1 backend; default parameters).
Differential expression analysed in Cyber-T (Bayesian-regularised t-test); p < 0.05 for liver, p < 0.10 for hippocampus.
Assembly: GRCm38 / mm10 (Mus musculus).
Supplementary files format and content: genes.fpkm_table.tsv – tab-delimited matrix of FPKM values (rows = Ensembl gene IDs, columns = 29 samples).

source_name: Hippocampus

extract_protocol:
Liver or hippocampus (~20 mg) was homogenised in QIAzol lysis reagent (Qiagen). After chloroform phase-separation, RNA was precipitated with isopropanol, washed in 75 % ethanol, air-dried and resuspended in RNase-free water. RNA quantity (NanoDrop 2000c) and integrity (1 % agarose gel) were confirmed before library prep.
1 µg total RNA was enriched for poly-A mRNA with oligo-dT beads and converted into strand-specific libraries using the Illumina TruSeq Stranded mRNA kit following the manufacturer’s protocol. Libraries were bar-coded, pooled and sequenced 2 × 125 bp on an Illumina HiSeq 2500.

value: Hippocampus

value: Control Chow + Intermittent Fasting


title: RG 2

description: Library name: 43527_S10


title: Control Chow + Intermittent Fasting, Hippocampus, replicate 2

description: Library name: 84618_ID2395_62-CCIF2-H


title: tdT-negative hepatocytes from oil-treated mice, REP3

description:
Library name: OilN3
OilN3


title: DKC1 2

description: Library name: 43525_S8


title: WT 2

description: Library name: 43524_S7


title: Control Chow, Hippocampus, replicate 4

description: Library name: 84616_ID2395_60-CC4-H

value: Control Chow


title: tdT-negative hepatocytes from oil-treated mice, REP1

description:
Library name: OilN1
OilN1


title: tdT-negative hepatocytes from oil-treated mice, REP2

description:
Library name: OilN2
OilN2


title: BIS_replication-I_33

type: genomic

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

country: Germany

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

hyb_protocol: The bisulfite treatment and hybridisation was carried out by Life & Brain GmbH

scan_protocol: iscan, carried out by Life & Brain GmbH

data_processing:
ChAMP package in R environment
processed value definition: combat normalised beta methylation values (linked as supplementary file on the Series record)

label: Cy3, Cy5

source_name: Blood cells

label_protocol: Labeling was carried out by Life & Brain GmbH

extract_protocol: precipitation with sodium acetate

treatment_protocol: Genomic DNA was extracted from blood cells.

tag: Sex

value: M

value: BIS

value: Blood cells


title: Control Chow, Hippocampus, replicate 3

description: Library name: 84615_ID2395_59-CC3-H


title: Control Chow + Intermittent Fasting, Hippocampus, replicate 1

description: Library name: 84617_ID2395_61-CCIF1-H


title: Control Chow, Hippocampus, replicate 1

description: Library name: 84613_ID2395_57-CC1-H


title: STL6558

city: New York

first: Alejandra

last: Borjabad

state: NY

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: Library name: Sample16

data_processing:
All data processing was performed by Novogene Co.
Assembly: Genome assembly GRCm39
Supplementary files format and content: gene fpkm

source_name: Brain

extract_protocol:
RNA was extracted from mouse brain tissue using RNAeasy Mini Plus Kit (Qiagen). Samples were sent to Novogene Co.
RNAseq libraries were prepared using the 10X Genomics protocol for RNAseq. by Novogene Co.

value: Brain

value: EcoHIV infection + SI treatment


title: Primary rat oligodendrocytes, DMSO, 24 hrs proliferation + 72 hrs differentiation, rep 1

description: Library name: 231024DEDMSO


title: Primary rat oligodendrocytes, untreated, 24 hrs proliferation + 72 hrs differentiation, rep 2

description: Library name: 231031A-DEUT

value: untreated


title: BIS_replication-I_31

value: F


title: BIS_replication-I_30


title: Primary rat oligodendrocytes, untreated, 24 hrs proliferation + 72 hrs differentiation, rep 3

description: Library name: 231031B-DEUT

value: primary rat differentiated oligodendrocytes


title: Primary rat oligodendrocytes, untreated, 24 hrs proliferation + 72 hrs differentiation, rep 4

description: Library name: 231121DEUT


title: BIS_replication-I_29


title: Primary rat oligodendrocytes, untreated, 24 hrs proliferation + 72 hrs differentiation, rep 1

description: Library name: 231024DEUT


title: STL6556

description: Library name: Sample14


title: BIS_replication-I_32


title: High-Fat Diet + Intermittent Fasting, Hippocampus, replicate 4

description: Library name: 84612_ID2395_56-HFDIF4-H

value: High-Fat Diet + Intermittent Fasting


title: Primary rat oligodendrocyte precursor cells, dolutegravir, 24 hrs proliferation, rep 3

description: Library name: 231031B-DOPCDTG

source_name: primary rat oligodendrocyte precursor cells

value: 8 µM dolutegravir


title: Control Chow, Hippocampus, replicate 2

description: Library name: 84614_ID2395_58-CC2-H


title: Primary rat oligodendrocyte precursor cells, dolutegravir, 24 hrs proliferation, rep 4

description: Library name: 231121DOPCDTG

value: primary rat oligodendrocyte precursor cells


title: High-Fat Diet + Intermittent Fasting, Hippocampus, replicate 3

description: Library name: 84611_ID2395_55-HFDIF3-H


title: BIS_replication-I_28


title: STL6547

description: Library name: Sample12

value: EcoHIV infection


title: BIR_replication-I_26

value: BIR


title: BIR_replication-I_27


title: Primary rat oligodendrocyte precursor cells, dolutegravir, 24 hrs proliferation, rep 2

description: Library name: 231031A-DOPCDTG


title: STL6557

description: Library name: Sample15


title: STL6545

description: Library name: Sample10


title: Primary rat oligodendrocyte precursor cells, dolutegravir, 24 hrs proliferation, rep 1

description: Library name: 231024DOPCDTG


title: BIR_replication-I_25


title: High-Fat Diet + Intermittent Fasting, Hippocampus, replicate 1

description: Library name: 84609_ID2395_53-HFDIF1-H


title: High-Fat Diet, Hippocampus, replicate 4

description: Library name: 84608_ID2395_52-HFD4-H

value: High-Fat Diet


title: STL6544

description: Library name: Sample9


title: STL6546

description: Library name: Sample11


title: High-Fat Diet + Intermittent Fasting, Hippocampus, replicate 2

description: Library name: 84610_ID2395_54-HFDIF2-H

value: Hippocampus


title: High-Fat Diet, Hippocampus, replicate 3

description: Library name: 84607_ID2395_51-HFD3-H


title: BIR_replication-I_24


title: Primary rat oligodendrocyte precursor cells, DMSO, 24 hrs proliferation, rep 4

description: Library name: 231121DOPCDMSO

value: DMSO


title: STL6535

description: Library name: Sample8

value: SI treatment


title: STL6555

description: Library name: Sample13


title: STL6534

description: Library name: Sample7


title: High-Fat Diet, Hippocampus, replicate 2

description: Library name: 84606_ID2395_50-HFD2-H


title: Primary rat oligodendrocyte precursor cells, DMSO, 24 hrs proliferation, rep 3

description: Library name: 231031B-DOPCDMSO


title: Primary rat oligodendrocyte precursor cells, DMSO, 24 hrs proliferation, rep 1

description: Library name: 231024DOPCDMSO


title: BIR_replication-I_21


title: STL6533

description: Library name: Sample6


title: BIR_replication-I_23


title: Primary rat oligodendrocyte precursor cells, DMSO, 24 hrs proliferation, rep 2

description: Library name: 231031A-DOPCDMSO


title: BIR_replication-I_22


title: Primary rat oligodendrocyte precursor cells, untreated, 24 hrs proliferation, rep 4

description: Library name: 231121DOPCUT


title: STL6532

description: Library name: Sample5


title: Primary rat oligodendrocyte precursor cells, untreated, 24 hrs proliferation, rep 3

description: Library name: 231031B-DOPCUT


title: Control Chow + Intermittent Fasting, Liver, replicate 4

description: Library name: 84572_ID2395_16-CCIF4-L

value: Liver

value: Control Chow + Intermittent Fasting


title: Control Chow + Intermittent Fasting, Liver, replicate 3

description: Library name: 84571_ID2395_15-CCIF3-L


title: High-Fat Diet, Hippocampus, replicate 1

description: Library name: 84605_ID2395_49-HFD1-H


title: BIR_replication-I_19

value: Blood cells


title: STL6522

description: Library name: Sample3

value: Brain

value: Control


title: Primary rat oligodendrocyte precursor cells, untreated, 24 hrs proliferation, rep 2

description: Library name: 231031A-DOPCUT

value: untreated


title: Primary rat oligodendrocyte precursor cells, untreated, 24 hrs proliferation, rep 1

description: Library name: 231024DOPCUT


title: bone,ctrl 02

city: Chengdu

first: Fanyuan

last: Yu

state: Sichuan

address: No.14, 3rd Section, Ren Min Nan Rd

department: Endodontics

institute: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology

description:
10x Genomics
Ctr04

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0 . And the reference genome Sscrofa11.1 was downloaded from the 10x website
Assembly: NCBI :ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/003/025/GCF_000003025.6_Sscrofa11.1/GCF_000003025.6_Sscrofa11.1_genomic.fna.gz
Supplementary files format and content: Tab-separated values files and matrix files

organism: Sus scrofa

source_name: Bone

extract_protocol:
For tissue digestion and single cell isolation, we used 3mg/ml typeI collagenase diluted with serum-free DMEM. Briefly, we isolated intact regenerated bone tissues and then kept them within pre-cold PBS. And then tissues were chopped into 3-5um sized pieces and then subjected to digestion under 37℃ for 1h. After digestion, all suspension were collected and erythrolysised for following experiments.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Bone

tag: strain

value: Bama mini-pigs

value: 8 months old


title: STL6523

description: Library name: Sample4


title: BIR_replication-I_18

value: M


title: STL6521

description: Library name: Sample2


title: Control Chow, Liver, replicate 4

description: Library name: 84568_ID2395_12-CC4-L

value: Control Chow


title: BIR_replication-I_17


title: BIR_replication-I_20

value: F


title: BIR_replication-I_16

value: BIR


title: Control Chow + Intermittent Fasting, Liver, replicate 1

description: Library name: 84569_ID2395_13-CCIF1-L


title: STL6520

description: Library name: Sample1


title: Control Chow, Liver, replicate 2

description: Library name: 84566_ID2395_10-CC2-L


title: bone,1797 02

description:
10x Genomics
A179702


title: Control Chow + Intermittent Fasting, Liver, replicate 2

description: Library name: 84570_ID2395_14-CCIF2-L


title: bone,ctrl 01

description:
10x Genomics
Ctr03


title: BIR_replication-I_15


title: cerebral cortex, WT, biological rep4

city: Guangzhou

first: Jinhu

last: Zou

state: Guangdong

address: No. 1023-1063, Shatai South Road, Guangzhou City, Guangdong Province, China

department: Department of Microbiology, School of Public Health

institute: Southern Medical University

description: Library name: WT_4

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality. The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence by STAR. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Picard- tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK2 software was used to perform SNP calling. Raw vcffiles were filtered with GATK standard filter method and other parameters  (clusterWindowSize: 10; MQ0 >= 4 and (MQ0/(1.0*DP)) > 0.1; QUAL < 10; QUAL < 30.0 or QD<5.0or HRun >5), and only SNPs with distance > 5 were retained. HTSeq v 0.5.4 p3 was used to count the reads numbers mapped to each gene.
Assembly: BALB_cJ_v1
Supplementary files format and content: csv files include raw counts for each Sample

source_name: cerebral cortex

extract_protocol:
RNA was extracted using the TRIzol method (Invitrogen, CA, USA) and treated with RNase-free DNase I (Takara, Kusatsu, Japan). RNA degradation and contamination was monitored on 1% agarose gels. RNA was quantified using Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA), the quality and integrity were assessed by NanoDrop spectrophotometer (Thermo Scientific, DE, USA).
A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）.First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 200-250 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The library preparations were sequenced on an Illumina Novaseq 6000 platform by the Beijing Allwegene Technology Company Limited (Beijing, China) and paired-end 150bp reads were generated.

value: cerebral cortex

value: WT


title: cerebral cortex, WT, biological rep5

description: Library name: WT_5


title: cerebral cortex, WT, biological rep3

description: Library name: WT_3


title: BIS_replication-I_14

value: BIS


title: bone,1797 01

description:
10x Genomics
A179701


title: Control Chow, Liver, replicate 1

description: Library name: 84565_ID2395_9-CC1-L


title: Control Chow, Liver, replicate 3

description: Library name: 84567_ID2395_11-CC3-L


title: cerebral cortex, WT, biological rep2

description: Library name: WT_2


title: RNA-seq of SUV39H2 K333A mutant mESCs

description:
Library name: RNAseq_K333A_L1
RNA-seq of SUV39H2 K333A mutant mESCs

value: mESCs

value: embryonic stem cell

value: SUV39H2 K333A mutant


title: High-Fat Diet + Intermittent Fasting, Liver, replicate 1

description: Library name: 84561_ID2395_5-HFDIF1-L

value: Liver

value: High-Fat Diet + Intermittent Fasting


title: cerebral cortex, gp120tg, biological rep5

description: Library name: gp120_5

value: HIV-1 gp120 transgenic


title: BIR_replication-I_13

value: Blood cells


title: RNA-seq of SUV39H2 P25A mutant mESCs

description:
Library name: RNAseq_P25A_L1
RNA-seq of SUV39H2 P25A mutant mESCs

value: SUV39H2 P25A mutant


title: BIR_replication-I_11


title: cerebral cortex, gp120tg, biological rep4

description: Library name: gp120_4


title: High-Fat Diet + Intermittent Fasting, Liver, replicate 2

description: Library name: 84562_ID2395_6-HFDIF2-L


title: RIP-seq of SUV39H2 (3xFlag-biotin tagged)

description:
Library name: RIP_FB_SUV39H2_L1
RIP-seq of 3xFlag-biotin tagged SUV39H2

value: 3xFlag-biotin tagged SUV39H2


title: cerebral cortex, WT, biological rep1

description: Library name: WT_1


title: RIP-seq of GFP (3xFlag-biotin tagged, Control)

description:
Library name: RIP_FB_GFP_L1
RIP-seq of 3xFlag-biotin tagged GFP (Control)

value: 3xFlag-biotin tagged GFP control


title: High-Fat Diet, Liver, replicate 3

description: Library name: 84559_ID2395_3-HFD3-L

value: High-Fat Diet


title: High-Fat Diet, Liver, replicate 4

description: Library name: 84560_ID2395_4-HFD4-L


title: BIR_replication-I_10


title: E3ChM24

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

description: Library name: s24

data_processing:
The reads were mapped to the mouse genome mm10, and raw gene read counts were generated using the Mayo Clinic RNA-sequencing analytic pipeline, MAP-RSeq
Conditional quantile normalization (CQN) on the raw gene counts was used to correct for GC bias and gene length differences and obtain similar quantile-by-quantile distributions of gene expression levels across samples.
Assembly: mm10
Supplementary files format and content: .tsv file with raw gene counts

source_name: cortex

growth_protocol: 5xFAD mice were acquired from the Jackson Laboratory and maintained as heterozygotes on a C57BL/6 genetic background. Intracranial injection of AAV8 viruses in neonatal mice was performed as previously described in Hu et al., 2015.

extract_protocol:
Total RNAs were extracted from the samples using TRIzol RNA Isolation Reagents (Thermo Fisher Scientific) and RNeasy Mini Kit with DNase (QIAGEN)
RNA libraries were prepared from 200 ng of total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA) according to the manufacturer’s instructions and sequenced with Illumina HiSeq 4000 at the Mayo Clinic Center for Individualized Medicine’s Medical Genome Facility.

value: cortex

value: M


title: High-Fat Diet, Liver, replicate 2

description: Library name: 84558_ID2395_2-HFD2-L


title: cerebral cortex, gp120tg, biological rep3

description: Library name: gp120_3


title: BIS_replication-I_12


title: BIR_replication-I_9

value: F

value: BIR


title: E3ChF22

description: Library name: s22


title: E3ChF23

description: Library name: s23


title: High-Fat Diet, Liver, replicate 1

description: Library name: 84557_ID2395_1-HFD1-L


title: BIR_replication-I_8


title: E3M21

description: Library name: s21


title: Endostatin-4

city: San Antonio, TX 78229

first: Christopher

last: Litwin

address: 4939 Charles Katz Dr, San Antonio, TX 78229

department: Biochemistry and Structural Biology

institute: University of Texas Health Science Center San Antonio

description:
Library name: 23
KK_21_S39_R1/2_001

data_processing:
After RNA-seq libraries were subjected to quantification process, pooled for subsequent 150bp paired end sequencing run with Illumina NovaSeq platform. After the sequencing run, demultiplexing was employed to generate the fastq file, with the average of ~42M reads per sample.
Assembly: Salmon indexing (V.1.10.2) was performed using GenCode’s GRCm39 Ensemble Release 114 reference genome utilizing Ensembl GTF files. Quantification was corrected for GC bias using the –gcbias option. Quantification was performed with the –validateMappings option to ensure alignment accuracy.
Supplementary files format and content: Raw counts, TPM from salmon indexing

source_name: epididymal white adipose tissue

extract_protocol:
Total RNA was extracted from 100 mg of eWAT which was homogenized with a mortar and pestle in liquid nitrogen and separated with 1 mL trizol (Qiagen, 73906) with repeated vortex steps to dissociate lipid phase. The lipid layer was removed from the surface of the trizol after 5 minute incubation at room temperature and a 12,000g spin for 10 minutes at 4°C. The clear homogenate was then transferred to a new tube, and 200 µL of chloroform was added. Samples were vortexed vigorously, incubated for 10 minutes at room temperature and centrifuged for 15 minutes for 12,00g at 4°C. RNA was then collected from the aqueous phase and 500 µL isopropanol was added. RNA was vortexed, incubated for 10 minutes, and then centrifuged as per the first centrifugation step. Following centrifugation, the supernatant was removed and the pellet was washed with 75% ethanol with a final centrifugation at 7500g for 5 minutes at 4°C. Once RNA was collected, cleanup was performed using the RNeasy Plus Mini Kit columns (74136) according to manufacturer’s recommendations.
Approximately 500ng Total RNA was used for Total RNA-seq library preparation by following the NEB Directional RNA library preparation guide with NEBNext rRNA depletion kit v2 (human/mouse/rat) (New England Biolabs, Ipswich, MA). The first step in the workflow involved the depletion of rRNA by hybridization of complementary DNA oligonucleotides, followed by treatment with RNase H and DNase to remove rRNA duplexed to DNA and original DNA oligonucleotides, respectively. Following rRNA removal, the left RNA was fragmented into small pieces using divalent cautions under elevated temperature and magnesium. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). The incorporation of dUTP in second strand synthesis effectively quenches the second strand during amplification, since the polymerase used in the assay will not incorporate past this nucleotide. These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final RNA-Seq library.

treatment_protocol: Two hour tail vein injection of endostatin or vehicle control.

value: epididymal white adipose tissue

value: Wild-type

value: Endostatin


title: cerebral cortex, gp120tg, biological rep2

description: Library name: gp120_2

value: cerebral cortex


title: BIR_replication-I_6


title: RNASeq_PA2_E11.5_Ezh2cKO_2

city: Basel

first: Filippo

address: Fabrikstrasse 24,

institute: FMI

description:
Library name: Sample 23
PA2 , E11.5, Ezh2cKO, RNASeq, BioRep 2

data_processing:
Reads were aligned to the mouse GRCm38/mm10 reference genome using the QuasR Bioconductor package (version 1.38.0) through the qAlign function with parameters set splicedAlignment=TRUE.
BigWig files were generated using the qExportWig function from the QuasR package. The files contain CPM (Counts Per Million) values with a resolution of 100 base pairs and a scaling factor of 1e6.
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig files

extract_protocol:
Dissected tissue (i.e. FNP, Mx, Md and PA2) from E11.5 Wnt1::Cre;ROSARFP and Ezh2cKO embryos were kept in 1× PBS on ice, then treated with 0.5% trypsin/1× EDTA at 37 °C for 10 minutes and immediately put on ice. The tissue was rinsed once in ice-cold 1× DMEM/10% FBS, followed by two washes in ice-cold 1× DMEM. Tissue was dissociated by pipetting. CNCCs were filtered and collected by FACS. After sorting, CNCCs were pelleted by centrifugation for 5 minutes, 1000 rpm at 4°C. Total RNA was extracted using the Single Cell RNA Purification Kit (NORGEN, 51800) with genomic DNA digestion using an RNase-Free DNase I Kit (NORGEN, 25710) according to the manufacturers’ protocol. For each sample, three independent biological replicates were prepared.
For sequencing of total RNA, unstranded RNA-Seq libraries were prepared using Illumina TruSeq RNA Library Prep Kit v2 according to manufacturers’ instructions. Sequencing was performed on an Illumina HiSeq 2500 machine (50 bp read length, single-end).

value: Cranial neural crest cells


title: RNASeq_PA2_E11.5_Ezh2cKO_1

description:
Library name: Sample 22
PA2 , E11.5, Ezh2cKO, RNASeq, BioRep 1


title: E3F20

description: Library name: s20


title: cerebral cortex, gp120tg, biological rep1

description: Library name: gp120_1


title: BIS_replication-I_7

value: BIS


title: Endostatin-3

description:
Library name: 21
KK_21_S39_R1/2_001


title: BIR_replication-I_5


title: RNASeq_PA2_E11.5_Ezh2cKO_3

description:
Library name: Sample 24
PA2 , E11.5, Ezh2cKO, RNASeq, BioRep 3


title: E3M19

description: Library name: s19


title: Endostatin-2

description:
Library name: 7
KK_7_S39_R1/2_001


title: BIS_replication-I_4


title: BIR_replication-I_3


title: E3ChF18

description: Library name: s18


title: Control-4

description:
Library name: 19
KK_19_S39_R1/2_001

value: PBS


title: E3ChF17

description: Library name: s17


title: Endostatin-1

description:
Library name: 6
KK_6_S39_R1/2_001


title: RNASeq_Md_E11.5_Ezh2cKO_3

description:
Library name: Sample 21
Md , E11.5, Ezh2cKO, RNASeq, BioRep 3

source_name: Md

value: Md


title: E3F16

description: Library name: s16


title: BIR_replication-I_1

value: Blood cells


title: Control-3

description:
Library name: 18
KK_18_S39_R1/2_001


title: BIR_replication-I_2


title: E3F15

description: Library name: s15


title: RNASeq_Md_E11.5_Ezh2cKO_1

description:
Library name: Sample 19
Md , E11.5, Ezh2cKO, RNASeq, BioRep 1


title: Control-2

description:
Library name: 4
KK_4_S39_R1/2_001


title: RNASeq_Mx_E11.5_Ezh2cKO_2

description:
Library name: Sample 17
Mx , E11.5, Ezh2cKO, RNASeq, BioRep 2

source_name: Mx

value: Mx


title: RNASeq_Mx_E11.5_Ezh2cKO_3

description:
Library name: Sample 18
Mx , E11.5, Ezh2cKO, RNASeq, BioRep 3


title: BIS_Discovery_167


title: RNASeq_Mx_E11.5_Ezh2cKO_1

description:
Library name: Sample 16
Mx , E11.5, Ezh2cKO, RNASeq, BioRep 1


title: Control-1

description:
Library name: 1
KK_1_S39_R1/2_001


title: RNASeq_Md_E11.5_Ezh2cKO_2

description:
Library name: Sample 20
Md , E11.5, Ezh2cKO, RNASeq, BioRep 2


title: BIR_Discovery_166


title: E3M13

description: Library name: s13


title: BIR_Discovery_165


title: E3M14

description: Library name: s14


title: E3ChM11

description: Library name: s11


title: RNASeq_FNP_E11.5_Ezh2cKO_3

description:
Library name: Sample 15
FNP , E11.5, Ezh2cKO, RNASeq, BioRep 3

source_name: FNP

value: FNP


title: RNASeq_PA2_E11.5_WT_3

description:
Library name: Sample 12
PA2 , E11.5, WT, RNASeq, BioRep 3

value: WT


title: E3F12

description: Library name: s12


title: RNASeq_FNP_E11.5_Ezh2cKO_2

description:
Library name: Sample 14
FNP , E11.5, Ezh2cKO, RNASeq, BioRep 2


title: SCC7-T21

city: ShenZhen

first: Lin

last: Ma

state: Guangdong Province

address: Lihu Campus: Xueyuan Avenue, Nanshan District, Shenzhen

department: Medical School

institute: ShenZhen University

description: Library name: Sample 21

data_processing:
The libraries were sequenced on the Illumina NovaSeq 6000 platform, generating 150 bp paired-end reads. raw reads were obtained per sample. The raw reads in FASTQ format were processed using fastp to remove low-quality reads, yielding clean reads for downstream analysis.
The clean reads were aligned to the reference genome using HISAT2. Gene expression levels were quantified as FPKM (Fragments Per Kilobase of transcript per Million mapped reads), and read counts per gene were obtained using HTSeq-count.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions. RNA purity and concentration were measured using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA), while RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The transcriptome library was constructed following the manufacturer's protocol using the VAHTS Universal V5 RNA-seq Library Prep Kit.

value: OE

tag: ID

value: NC-IR

value: I


title: SCC7-T23

description: Library name: Sample 23

value: NC+Olaparib

value: O


title: E3M10

description: Library name: s10

value: cortex

value: M


title: SCC7-T24

description: Library name: Sample 24


title: SCC7-T22

description: Library name: Sample 22


title: BIR_Discovery_163

value: F

value: BIR


title: E3F9

description: Library name: s9


title: RNASeq_FNP_E11.5_Ezh2cKO_1

description:
Library name: Sample 13
FNP , E11.5, Ezh2cKO, RNASeq, BioRep 1

value: Cranial neural crest cells


title: BIS_Discovery_164

value: BIS


title: BIS_Discovery_162


title: RNASeq_PA2_E11.5_WT_2

description:
Library name: Sample 11
PA2 , E11.5, WT, RNASeq, BioRep 2


title: BIR_Discovery_161


title: SCC7-T20

description: Library name: Sample 20


title: E3M8

description: Library name: s8


title: SCC7-T19

description: Library name: Sample 19


title: E3ChF7

description: Library name: s7


title: BIS_Discovery_160


title: RNASeq_PA2_E11.5_WT_1

description:
Library name: Sample 10
PA2 , E11.5, WT, RNASeq, BioRep 1


title: E3ChM5

description: Library name: s5


title: BIS_Discovery_157


title: BIR_Discovery_159


title: BIS_Discovery_158


title: SCC7-T18

description: Library name: Sample 18

value: NC-IR+Olaparib

value: IO


title: RNASeq_Md_E11.5_WT_2

description:
Library name: Sample 8
Md , E11.5, WT, RNASeq, BioRep 2

value: Md


title: RNASeq_Md_E11.5_WT_3

description:
Library name: Sample 9
Md , E11.5, WT, RNASeq, BioRep 3


title: E3ChF2

description: Library name: s2


title: RNASeq_Md_E11.5_WT_1

description:
Library name: Sample 7
Md , E11.5, WT, RNASeq, BioRep 1


title: SCC7-T17

description: Library name: Sample 17


title: RNASeq_Mx_E11.5_WT_3

description:
Library name: Sample 6
Mx , E11.5, WT, RNASeq, BioRep 3

value: Mx


title: SCC7-T16

description: Library name: Sample 16


title: SCC7-T14

description: Library name: Sample 14

value: NC+Sham

value: S


title: RNASeq_Mx_E11.5_WT_2

description:
Library name: Sample 5
Mx , E11.5, WT, RNASeq, BioRep 2

value: WT


title: E3ChF6

description: Library name: s6


title: SCC7-T13

description: Library name: Sample 13

value: OE


title: SCC7-T15

description: Library name: Sample 15


title: E3ChM1

description: Library name: s1


title: BIR_Discovery_151

value: Blood cells


title: SCC7-T9

description: Library name: Sample 9

value: IR

value: EI


title: SCC7-T10

description: Library name: Sample 10

value: Olaparib

value: EO


title: E3ChM3

description: Library name: s3

value: cortex

value: M


title: H3K27me3-WT_Lung_PBS_3

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

description: Library name: sample 12

data_processing:
Trim_Galore(v0.4.4) is used to quality trim 3’ reads raw reads with the cutadapt (DOI: 10.14806/ej.17.1.200) program. A quality score cutoff of Q20 is used.
Trimmed reads are mapped to the mm10(Gencode GRCm38) reference genome by bwa(v0.7.12-r1039, PMID: 19451168) and converted to a bam file(a binary version of sam file) by samtools(v1.2, PMID: 19505943).
biobambam2 (v2.0.87, DOI: 10.1186/1751-0473-9-13) was used to mark duplicated reads and non-duplicated reads were kept by samtools (parameter “-q 1 -F 1804” version 1.2). All samples have more than 5 million fragments as suggested by CUT&RUN protocol paper. We generated bigwig files using the center 80 bp of fragments smaller than 2000 bp and normalized to 10 million fragments. We confirmed the replicability between replicates.
Assembly: mm10(GRCm38)
Supplementary files format and content: bigwig
Library strategy: Cut&Run

source_name: Lung

extract_protocol:
CD4 T cells were enriched by EasySep Mouse CD4 T Cell Isolation Kit (STEMCELL) from lymph nodes and spleens (or Lung). CD4 Treg cells  (CD4+GFP+) T cells were further sorted by FACS.
Libraries were prepared with precipitated DNA using KAPA Hyper Prep Kit (Kapa Biosystems). The library DNA was enriched by size selection with AMPure XP beads.

value: Lung

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAB #9733 Cell Signaling

value: Treg

value: Foxp3Cre x Kdm6bfl/fl

value: Day 15 post Flu virus


title: BIR_Discovery_154

value: BIR


title: H3K27me3-WT_Lung_PBS_1

description: Library name: sample 10


title: H3K27me3-WT_Lung_Flu_3

description: Library name: sample 9


title: BIS_Discovery_155

value: BIS


title: H3K27me3-WT_Lung_Flu_2

description: Library name: sample 8


title: BIR_Discovery_156


title: SCC7-T12

description: Library name: Sample 12


title: RNASeq_FNP_E11.5_WT_3

description:
Library name: Sample 3
FNP , E11.5, WT, RNASeq, BioRep 3

value: FNP

value: Cranial neural crest cells


title: H3K27me3-WT_Lung_PBS_2

description: Library name: sample 11


title: SCC7-T11

description: Library name: Sample 11

value: OE


title: RNASeq_FNP_E11.5_WT_2

description:
Library name: Sample 2
FNP , E11.5, WT, RNASeq, BioRep 2

value: WT


title: BIR_Discovery_148

value: F

value: Blood cells


title: SCC7-T7

description: Library name: Sample 7

value: IR

value: EI


title: BIR_Discovery_147


title: H3K27me3-Kdm6b_Lung_PBS_3

description: Library name: sample 6

value: PBS


title: SCC7-T6

description: Library name: Sample 6

value: IR+Olaparib

value: EIO


title: RNASeq_Mx_E11.5_WT_1

description:
Library name: Sample 4
Mx , E11.5, WT, RNASeq, BioRep 1

value: Mx


title: BIR_Discovery_146

value: M


title: BIS_Discovery_152


title: RNASeq_FNP_E11.5_WT_1

description:
Library name: Sample 1
FNP , E11.5, WT, RNASeq, BioRep 1


title: BIR_Discovery_153


title: H3K27me3-Kdm6b_Lung_PBS_1

description: Library name: sample 4

value: Lung

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAB #9733 Cell Signaling

value: Treg

value: Foxp3Cre x Kdm6bfl/fl


title: BIS_Discovery_150

value: BIS