title: small_RNA_Kdm3 GLKD 3-5h progeny biol rep 2

data_processing:
A base calling pipeline proceeds to the demultiplexing prior to the generation of fast-q sequencefiles, i.e. by separating the libraries according to their indexes.
Genesupport/Fasteris developed an “in-lane” control spike in each lane of the flow-cell. These spiked control reads are mapped on the PhiX reference genome
The small RNA treatment uses the UMI-tools to detect the UMI sequence and remove bases that correspond to the standard illumina adapters.
The UMI-tools identifies the adapter and with the UMI sequence in each read. The UMIs and adapter sequence are trimmed from the read to produce “inserts”
We merged 18-30nt "inserts" for each library as a fastqsanger file (provided).
For library comparisons, read counts were normalized to one million reads
unique mapper reads were obtained using sR_Bowtie -m0 (Galaxy Version 2.1.1)
For alignments we used a cleaned version of r6.36 version of Drosophila melanogaster genome (dm6, Flybase) in which sequences corresponding to unmapped (chrU), Y chromosome (chrY) and mitochondrial chromosome (chrM) were removed (dm6_clean).
Assembly: dm6_clean
Supplementary files format and content: bigWig, DEseq2 result for biological triplicates as a tab-delimited text file

extract_protocol:
Total RNA was extracted from 100 ul of embryos using TRIzol (Life Technologies). After DNase, RNA Anti 2S treatment for small RNA gel free protocol has been performed (Fasteris.com)  Anti 2S treatment for  small RNA gel free protocol
Libraries were prepared using QIAseq-miRNA kit.
Depletion of rRNA using QIAseq FastSelect –rRNA Fly Kit


title: HK2_WT_Rep2

status: Public on Feb 11 2023

type: SRA

city: Singapore

first: Xiaosai

last: Yao

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

library_source: transcriptomic

data_processing:
RNA-seq data were mapped to hg19 (hs37d5) using STAR 25, with GENCODE annotation (gencode.v19.annotation.gtf) and recommended settings from STAR manual. Gene expression levels were quantified with STAR 26. Log fold change of differential expression genes was computed with DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Deseq2 files are in tab delimited text files, including 8 standard columns "ensembleID", "GeneSymbol", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj", then followed by columns of log2(normalized counts) and columns of raw count. There are usually 4 columns of log2(normalized counts) and 4 columns of raw count, corresponding to 2 replicates per each condition of two conditions (with and without PBRM1).

molecule: total RNA

organism: Homo sapiens

source_name: normal kidney epithelial cell line

growth_protocol: Cells were grown in RPMI-1640 medium (Sigma) supplemented with 10% fetal bovine serum (Gibco). Cells were maintained in a 5% CO2-humidified incubator at 37°C.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini kit
RNAseq libraries were prepared using Illumina Tru-Seq Stranded Total RNA kit protocol

treatment_protocol: PBRM1 was knocked out using CRISPR-Cas9 mediated gene editing in 786-O, A498 and HK-2. Wildtype PBRM1 was cloned from normal kidney tissue. cDNA was either cloned into pbabe vector or pLenti-GFP.

tag: source

value: HK2(ATCC CRL-2190)

tag: treatment

value: parental


title: HK2_KO_Rep1


title: HK2_KO_Rep2


title: small_RNA_w GLKD 3-5h progeny biol rep 1

city: PARIS

first: Antoine

last: Boivin

address: 9 quai St Bernard

department: IBPS

country: France

institute: Sorbonne Universite CNRS

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: Flies were raised at 25°C on cornmeal medium. Embryos were collected on same medium plus fresh yeast.

tag: tissue

value: embryo

tag: genotype

value: w GLKD progeny


title: 786O_KO_NTC_Rep1

data_processing:
For all cell lines other than 769-P, RNA-seq data were mapped to hg19 (hs37d5) using STAR 25, with GENCODE annotation (gencode.v19.annotation.gtf) and recommended settings from STAR manual. Gene expression levels were quantified with STAR. For 769-P, RNA-seq data were mapped to GRCh38 using GMAP. Log fold change of differential expression genes was computed with DESeq2 for all cell lines
Assembly: hg19
Supplementary files format and content: Deseq2 files are in tab delimited text files, including 8 standard columns "ensembleID", "GeneSymbol", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj", then followed by columns of log2(normalized counts) and columns of raw count. There are usually 4 columns of log2(normalized counts) and 4 columns of raw count, corresponding to 2 replicates per each condition of two conditions (with and without PBRM1).

source_name: Cancer cell line

treatment_protocol: PBRM1 was knocked out using CRISPR-Cas9 mediated gene editing in 786-O, A498, HK-2 and 769-P. Wildtype PBRM1 was cloned from normal kidney tissue. cDNA was either cloned into pbabe vector or pLenti-GFP.  ARID2 was knocked out during CRISPR-Cas9 mediated gene editing in 769-P cells. RELA was knocked down in 786-O cells using shRNA.

tag: cell line

value: Non-targeting control

tag: cell type

value: Cancer cell line


title: 786O_WT_shRELA_Rep2

value: shRNA against RELA


title: small_RNA_w GLKD 3-5h progeny biol rep 2


title: small_RNA_Kdm3 GLKD 0-2h progeny biol rep 2

value: Kdm3 GLKD progeny


title: 786O_KO_shRELA_Rep1


title: small_RNA_Kdm3 GLKD 3-5h progeny biol rep 1


title: 786O_KO_Rep2


title: 786O_KO_Rep1


title: small_RNA_Kdm3 GLKD 0-2h progeny biol rep 1


title: 786O_WT_shRELA_Rep1


title: 786O_WT_Rep2


title: HK2_WT_Rep1


title: NCC2112_EV_Rep1

value: NCC2112 (in house derived cell line)

value: plenti empty vector


title: HeLa_CTRL_3

city: Pozzuoli

first: Francesco

last: Panariello

state: Napoli

address: Via Campi Flegrei 34

country: Italy

institute: TIGEM

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw counts

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM High Glucose supplemented with 10% fetal bovine serum (FBS) heat-inactivated and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) and 250 ng of total RNA was used for the construction of sequencing libraries.
3'DGE mRNA-seq research grade sequencing service (Next Generation Diagnostic srl)

treatment_protocol: HelLa cells were infected in the presence of polybrene at MOI of 1 and 1ug of puromycin was used to select infected cells

value: HeLa

value: epithelial cell

value: WT

value: control


title: 786O_WT_NTC_Rep2


title: small_RNA_w GLKD 0-2h progeny biol rep 2


title: small_RNA_w GLKD 0-2h progeny biol rep 1


title: 786O_WT_Rep1


title: 786O_KO_NTC_Rep2


title: 786O_WT_NTC_Rep1


title: L-1236

status: Public on Feb 10 2023

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

country: Germany

institute: Charite

description: 40 Mio 100PE  reads

data_processing:
Raw FASTQ files were checked for quality using FastQC v0.11.8
Alignement to the human reference sequence (GRCh37.75) was done using STAR v2.4.0.1
Read count extraction and normalization were performed using StringTie v2.2.1
Assembly: GRCh37.75
Supplementary files format and content: tab-delimited text files include RPKM and TPM values for each sample

molecule: polyA RNA

growth_protocol: Human classical Hodgkin Lymphoma cell lines were grown in RPMI-1640 GlutaMAX (Invitrogen) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin and maintained in a 5% CO2 humidified atmosphere at 37°C.

extract_protocol:
RNA was harvested using the NucleoSpin® RNA Plus Kit (Macherey and Nagel, Düren, Germany). 1000 ng total RNA were used for library construction.
A stranded polyA+ enriched cDNA library was prepared by the BGISEQ-500 RNA-Seq library preparation kit

treatment_protocol: no treatment

value: classic Hodgkin Lymphoma (mixed cellularity) from peripheral blood

value: no treatment

tag: time

value: 5 day culture


title: HDLM-2

description: 40 Mio 100PE  reads

value: classic Hodgkin Lymphoma (nodular sclerosing) from bone marrow


title: KM-H2

description: 40 Mio 100PE  reads

value: classic Hodgkin Lymphoma (mixed cellularity) from pleural effusions


title: mRNA-seq, mPFC, Scramble shRNA #4

city: Charleston

first: Makoto

last: Taniguchi

state: SC

address: 173 Ashley ave, BSB410C

country: USA

institute: Medical University of South Carolina

data_processing:
Reads were aligned to the mouse mm10 reference genome using STAR (v2.7.1a)
Only uniquely-mapped reads were retained for further analysis
Quality control metrics were assessed by Picard tool (http://broadinstitute.github.io/picard/).
Gene level expression was calculated using Htseq (v0.9.1)
Genome_build: mm10

organism: Mus musculus

source_name: AAV-shRNA expressing mPFC

extract_protocol:
AAV-mediated shRNA expression GFP-positive mPFC tissue was removed from mice brain slices. RNA was purified using QIAGEN RNA purification kit. The library preparation and sequencing was perfromed in the BIG Genomics
RNA libraries were prepared for BGI genomics

tag: strain

value: Scramble shRNA

value: mPFC


title: mRNA-seq, mPFC, Npas4 shRNA #3

value: Npas4 shRNA


title: SUP-HD1

description: 40 Mio 100PE  reads

value: classic Hodgkin Lymphoma (nodular sclerosing) from pleural effusions


title: L-428

description: 40 Mio 100PE  reads


title: L-540

description: 40 Mio 100PE  reads


title: VwtM1

city: New York

first: Marina

last: Schernthanner

state: New York

address: 1230 York Ave.

institute: The Rockefeller University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 genome assembly using STAR version 2.5.3a
Reads falling on each gene are counted by HT-Seq

source_name: brain

extract_protocol:
TRAP
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hippocampus


title: mRNA-seq, mPFC, Scramble shRNA #1


title: mRNA-seq, mPFC, Npas4 shRNA #2


title: mRNA-seq, mPFC, Scramble shRNA #3


title: mRNA-seq, mPFC, Npas4 shRNA #1


title: C2C12, DM60h, ATAC-seq, 2

city: Wuhan

first: Mingyang

last: Hu

address: No.1,Shizishan Street, Hongshan District

country: China

institute: Huazhong Agricultural University

description:
C2C12_DM60h_ATAC_peaks.broadPeak
C2C12-DM60h-1_merge_2-ATAC.nodup.tn5.bigwig

library_source: genomic

data_processing:
ATAC-seq datasets were processed with reference to the ENCODE ATAC-seq pipeline (https://github.com/kundajelab/atac_dnase_pipelines). The ATAC‐seq reads were mapped to the mouse M11 reference genome from the GENCODE database using Bowtie2 v2.2.6. Then Pearson correlation coefficients between replicates were calculated based on read coverages of genomic regions, which were computed with a bin size of 2 kb using the multiBamSummary bins function in deepTools v2.5.2 with filtered BAM files of each replicate. Align files (bam and tn5-tagAlign file) with high Pearson correlation coefficients (R > 0.9) between replicates were merged with Samtools v1.9 and the zcat command. The merged tn5-tagAlign file was used to call broad peaks using MACS2 v2.2.7 with the --broad” parameter, and the significant broad peaks were defined as those with P  < 10-10.
Assembly: mm10
Supplementary files format and content: Broad peak bed file and  bigwig files of each time point.

molecule: genomic DNA

growth_protocol: The mouse C2C12 cell line was requested from the Cell Bank of Wuhan University. The cells were cultured in 1× DMEM basic (Gibco‐BRL) with 20% fetal bovine serum (Gibco 10099133) in 5% CO2 at 37°C. The myogenic differentiation of C2C12 myoblast cells was initiated upon cells reaching 90% confluence by switching the cells to culture in DMEM containing 3% horse serum (Hyclone SH30074.03) and then culturing for 12, 24, 48, 60, and 101 h.

extract_protocol:
About 50 000 C2C12 in the proliferation and differentiation (60 hours) were lysed in 50 μL ATAC‐seq lysis buffer (10 mmol/L Tris‐HCl, pH 7.4, 10 mmol/L NaCl, 3 mmol/L MgCl2, 0.1% NP40, 0.1% Tween‐20 and 0.01% digitonin) and incubated on ice for 5 minutes. Add 1 mL cold ATAC‐buffer (10 mmol/L Tris‐HCl, pH 7.4, 10 mmol/L NaCl, 3 mmol/L MgCl2 and 0.1% Tween‐20) was added to stop the lysis. The cells were further centrifuged at 500 RCF for 10 minutes at 4°C to collect the cell pellet after removing the supernatant. The following transposition reaction mix (25 µL Illumina Tagment DNA buffer Cat#: 15027866, 16.5 µL 1 × PBS, 0.5 µL 1% digitonin, 0.5 μL 10% Tween‐20, 2.5 μL ddH2O and 5 μL Illumina Tagment DNA enzyme (Cat#: 15027916) was added to the cell pellet and incubated at 37°C for 1 hour on thermocycler. ZYMO RESEARCH DNA Clean & Concentrator‐5 Kit (Cat#: D4013) was used to purify the transposed DNA.
Final library was electrophoresed in a 2% high‐resolution agarose gel and 100‐1000 bp fragments were cut out and sequenced by using Illumina HiSeq X Ten PE150 platform.

value: Myoblast

value: differentiation 60 hours

tag: biological replicate

value: Replicate 2


title: mRNA-seq, mPFC, Scramble shRNA #2


title: C2C12, DM60h, HiC, 3

description:
C2C12_DM60h_vs_GM_loop_juicebox.filter_50reads_filter_loop_ID.bedpe
C2C12_DM60h_40000_iced.tad.bed
C2C12_DM60h_40000_iced.tad.boundaries.bed

data_processing:
The paired-end Hi-C reads from different libraries (C2C12 myoblast and myotube cells) were mapped separately to the mouse genome (mm10), and the align bam files were transformed to validPairs files using HiC-Pro pipeline v2.9.056 with the parameters “-s mapping” and “-s proc_hic”. Then validPairs of replicates at each time point were merged to build raw inter-/intra-chromosomal contact maps (4 kb, 25 kb, and 40 kb resolution), and ICE normalization was run on contact maps using HiC-Pro pipeline v2.9.056 with parameters “-s merge_persample”, “-s build_contact_maps”, and “-s ice_norm”. The visualized contact matrices were generated at resolutions of 1 kb, 5 kb, 10 kb, 25 kb, 40 kb, 50 kb, 100 kb, and 1 Mb using juicer tools v1.8.957.
The raw matrix built by HiC-Pro pipeline v2.9.056 was normalized via the ICE method, and the ICE matrix was used to calculate the insulation score. The insulation score of the ICE matrix was calculated with the parameter “-is 480000 -ids 320000 -im iqrMean -ss 160000”.
Loops of Hi-C data were analyzed using the HiCCUPS method (https://github.com/XiaoTaoWang/HiCPeaks). The resolution parameter was set as “-r 25000”. Using the raw reads matrix (25 kb) generated by HiC-Pro, the read count profile of 25 kb loops during C2C12 differentiation was calculated and transformed to a CPM matrix by the edgeR GLM model. Then the loop was selected with reads > 50 at least in one time point.
Assembly: mm10
Supplementary files format and content: Loop bedpe file of  C2C12 GM and DM65h cells and TAD, TAD boundary bed file in each time point.

growth_protocol: The mouse C2C12 cell line was requested from the Cell Bank of Wuhan University. The cells were cultured in 1× DMEM basic (Gibco‐BRL) with 20% fetal bovine serum (Gibco 10099133) in 5% CO2 at 37°C. The myogenic differentiation of C2C12 myoblast cells was initiated upon cells reaching 90% confluence by switching the cells to culture in DMEM containing 3% horse serum (Hyclone SH30074.03) and then culturing for 12, 24, 48, 60, and 107 h.

extract_protocol:
Ten million cultured cells were collected and washed once with 1× phosphate buffered saline (PBS). The cells were re-suspended in 1% formaldehyde solution and incubated at room temperature for 10 min with rotation. The formaldehyde was quenched with glycine (final concentration 125 mM) for 5 min at room temperature. Cells were washed twice with Dulbecco’s PBS and flash frozen with liquid nitrogen. Ice-cold Hi-C lysis buffer was added to the cross-linked cells, and cells were incubated on ice for 20 min. Then cells were pelleted and incubated in 50 μL 0.5% SDS at 62℃ for 5 min. After that, a final concentration of 1% TritionX-100 was added to quench the SDS. A restriction endonuclease mix (1× CutSmart buffer, 1% TritionX-100, 1 U/μL MboI) was used to fragment DNA overnight at 37℃. DNA digestion produced a 5’ overhang, which was filled with deoxyribonucleotides containing biotin-14-dATP for 1 h at 37℃ (37.5 μL of 0.4 mM biotin-14-dATP, 1.5 μL of 10 mM dCTP, 1.5 μL of 10 mM dGTP, 1.5 μL of 10 mM dTTP, 8 μL of 5 U/μL DNA Polymerase I). The chromatin was then ligated by T4 DNA ligase at 16°C overnight. After reversing cross-links and DNA purification, biotin-labeled DNA was sheared to fragments 300–500 bp in size using a Covaris S220 ultra-sonicator.
Library preparation and quality control were performed following the instructions of the Illumina TruSeq protocol (Illumina, San Diego, CA).

value: Replicate 3


title: C2C12, DM60h, ATAC-seq, 1

growth_protocol: The mouse C2C12 cell line was requested from the Cell Bank of Wuhan University. The cells were cultured in 1× DMEM basic (Gibco‐BRL) with 20% fetal bovine serum (Gibco 10099133) in 5% CO2 at 37°C. The myogenic differentiation of C2C12 myoblast cells was initiated upon cells reaching 90% confluence by switching the cells to culture in DMEM containing 3% horse serum (Hyclone SH30074.03) and then culturing for 12, 24, 48, 60, and 100 h.

value: Replicate 1


title: C2C12, DM60h, HiC, 2

data_processing:
The paired-end Hi-C reads from different libraries (C2C12 myoblast and myotube cells) were mapped separately to the mouse genome (mm10), and the align bam files were transformed to validPairs files using HiC-Pro pipeline v2.9.056 with the parameters “-s mapping” and “-s proc_hic”. Then validPairs of replicates at each time point were merged to build raw inter-/intra-chromosomal contact maps (4 kb, 25 kb, and 40 kb resolution), and ICE normalization was run on contact maps using HiC-Pro pipeline v2.9.056 with parameters “-s merge_persample”, “-s build_contact_maps”, and “-s ice_norm”. The visualized contact matrices were generated at resolutions of 1 kb, 5 kb, 10 kb, 25 kb, 40 kb, 50 kb, 100 kb, and 1 Mb using juicer tools v1.8.957.
The raw matrix built by HiC-Pro pipeline v2.9.056 was normalized via the ICE method, and the ICE matrix was used to calculate the insulation score. The insulation score of the ICE matrix was calculated with the parameter “-is 480000 -ids 320000 -im iqrMean -ss 160000”.
Loops of Hi-C data were analyzed using the HiCCUPS method (https://github.com/XiaoTaoWang/HiCPeaks). The resolution parameter was set as “-r 25000”. Using the raw reads matrix (25 kb) generated by HiC-Pro, the read count profile of 25 kb loops during C2C12 differentiation was calculated and transformed to a CPM matrix by the edgeR GLM model. Then the loop was selected with reads > 50 at least in one time point.
Assembly: mm10
Supplementary files format and content: Loop bedpe file of  C2C12 GM and DM64h cells and TAD, TAD boundary bed file in each time point.

growth_protocol: The mouse C2C12 cell line was requested from the Cell Bank of Wuhan University. The cells were cultured in 1× DMEM basic (Gibco‐BRL) with 20% fetal bovine serum (Gibco 10099133) in 5% CO2 at 37°C. The myogenic differentiation of C2C12 myoblast cells was initiated upon cells reaching 90% confluence by switching the cells to culture in DMEM containing 3% horse serum (Hyclone SH30074.03) and then culturing for 12, 24, 48, 60, and 106 h.

value: WT


title: C2C12, DM60h, HiC, 1

data_processing:
The paired-end Hi-C reads from different libraries (C2C12 myoblast and myotube cells) were mapped separately to the mouse genome (mm10), and the align bam files were transformed to validPairs files using HiC-Pro pipeline v2.9.056 with the parameters “-s mapping” and “-s proc_hic”. Then validPairs of replicates at each time point were merged to build raw inter-/intra-chromosomal contact maps (4 kb, 25 kb, and 40 kb resolution), and ICE normalization was run on contact maps using HiC-Pro pipeline v2.9.056 with parameters “-s merge_persample”, “-s build_contact_maps”, and “-s ice_norm”. The visualized contact matrices were generated at resolutions of 1 kb, 5 kb, 10 kb, 25 kb, 40 kb, 50 kb, 100 kb, and 1 Mb using juicer tools v1.8.957.
The raw matrix built by HiC-Pro pipeline v2.9.056 was normalized via the ICE method, and the ICE matrix was used to calculate the insulation score. The insulation score of the ICE matrix was calculated with the parameter “-is 480000 -ids 320000 -im iqrMean -ss 160000”.
Loops of Hi-C data were analyzed using the HiCCUPS method (https://github.com/XiaoTaoWang/HiCPeaks). The resolution parameter was set as “-r 25000”. Using the raw reads matrix (25 kb) generated by HiC-Pro, the read count profile of 25 kb loops during C2C12 differentiation was calculated and transformed to a CPM matrix by the edgeR GLM model. Then the loop was selected with reads > 50 at least in one time point.
Assembly: mm10
Supplementary files format and content: Loop bedpe file of  C2C12 GM and DM63h cells and TAD, TAD boundary bed file in each time point.

growth_protocol: The mouse C2C12 cell line was requested from the Cell Bank of Wuhan University. The cells were cultured in 1× DMEM basic (Gibco‐BRL) with 20% fetal bovine serum (Gibco 10099133) in 5% CO2 at 37°C. The myogenic differentiation of C2C12 myoblast cells was initiated upon cells reaching 90% confluence by switching the cells to culture in DMEM containing 3% horse serum (Hyclone SH30074.03) and then culturing for 12, 24, 48, 60, and 105 h.


title: C2C12, GM, HiC, 3

description:
C2C12_DM60h_vs_GM_loop_juicebox.filter_50reads_filter_loop_ID.bedpe
C2C12_GM_40000_iced.tad.bed
C2C12_GM_40000_iced.tad.boundaries.bed

data_processing:
The paired-end Hi-C reads from different libraries (C2C12 myoblast and myotube cells) were mapped separately to the mouse genome (mm10), and the align bam files were transformed to validPairs files using HiC-Pro pipeline v2.9.056 with the parameters “-s mapping” and “-s proc_hic”. Then validPairs of replicates at each time point were merged to build raw inter-/intra-chromosomal contact maps (4 kb, 25 kb, and 40 kb resolution), and ICE normalization was run on contact maps using HiC-Pro pipeline v2.9.056 with parameters “-s merge_persample”, “-s build_contact_maps”, and “-s ice_norm”. The visualized contact matrices were generated at resolutions of 1 kb, 5 kb, 10 kb, 25 kb, 40 kb, 50 kb, 100 kb, and 1 Mb using juicer tools v1.8.957.
The raw matrix built by HiC-Pro pipeline v2.9.056 was normalized via the ICE method, and the ICE matrix was used to calculate the insulation score. The insulation score of the ICE matrix was calculated with the parameter “-is 480000 -ids 320000 -im iqrMean -ss 160000”.
Loops of Hi-C data were analyzed using the HiCCUPS method (https://github.com/XiaoTaoWang/HiCPeaks). The resolution parameter was set as “-r 25000”. Using the raw reads matrix (25 kb) generated by HiC-Pro, the read count profile of 25 kb loops during C2C12 differentiation was calculated and transformed to a CPM matrix by the edgeR GLM model. Then the loop was selected with reads > 50 at least in one time point.
Assembly: mm10
Supplementary files format and content: Loop bedpe file of  C2C12 GM and DM62h cells and TAD, TAD boundary bed file in each time point.

growth_protocol: The mouse C2C12 cell line was requested from the Cell Bank of Wuhan University. The cells were cultured in 1× DMEM basic (Gibco‐BRL) with 20% fetal bovine serum (Gibco 10099133) in 5% CO2 at 37°C. The myogenic differentiation of C2C12 myoblast cells was initiated upon cells reaching 90% confluence by switching the cells to culture in DMEM containing 3% horse serum (Hyclone SH30074.03) and then culturing for 12, 24, 48, 60, and 104 h.

value: proliferation period


title: C2C12, GM, ATAC-seq, 1

description:
C2C12_GM_ATAC_peaks.broadPeak
C2C12-GM-1_merge_2-ATAC.nodup.tn5.bigwig

growth_protocol: The mouse C2C12 cell line was requested from the Cell Bank of Wuhan University. The cells were cultured in 1× DMEM basic (Gibco‐BRL) with 20% fetal bovine serum (Gibco 10099133) in 5% CO2 at 37°C. The myogenic differentiation of C2C12 myoblast cells was initiated upon cells reaching 90% confluence by switching the cells to culture in DMEM containing 3% horse serum (Hyclone SH30074.03) and then culturing for 12, 24, 48, 60, and 98 h.


title: C2C12, GM, HiC, 2

data_processing:
The paired-end Hi-C reads from different libraries (C2C12 myoblast and myotube cells) were mapped separately to the mouse genome (mm10), and the align bam files were transformed to validPairs files using HiC-Pro pipeline v2.9.056 with the parameters “-s mapping” and “-s proc_hic”. Then validPairs of replicates at each time point were merged to build raw inter-/intra-chromosomal contact maps (4 kb, 25 kb, and 40 kb resolution), and ICE normalization was run on contact maps using HiC-Pro pipeline v2.9.056 with parameters “-s merge_persample”, “-s build_contact_maps”, and “-s ice_norm”. The visualized contact matrices were generated at resolutions of 1 kb, 5 kb, 10 kb, 25 kb, 40 kb, 50 kb, 100 kb, and 1 Mb using juicer tools v1.8.957.
The raw matrix built by HiC-Pro pipeline v2.9.056 was normalized via the ICE method, and the ICE matrix was used to calculate the insulation score. The insulation score of the ICE matrix was calculated with the parameter “-is 480000 -ids 320000 -im iqrMean -ss 160000”.
Loops of Hi-C data were analyzed using the HiCCUPS method (https://github.com/XiaoTaoWang/HiCPeaks). The resolution parameter was set as “-r 25000”. Using the raw reads matrix (25 kb) generated by HiC-Pro, the read count profile of 25 kb loops during C2C12 differentiation was calculated and transformed to a CPM matrix by the edgeR GLM model. Then the loop was selected with reads > 50 at least in one time point.
Assembly: mm10
Supplementary files format and content: Loop bedpe file of  C2C12 GM and DM61h cells and TAD, TAD boundary bed file in each time point.

growth_protocol: The mouse C2C12 cell line was requested from the Cell Bank of Wuhan University. The cells were cultured in 1× DMEM basic (Gibco‐BRL) with 20% fetal bovine serum (Gibco 10099133) in 5% CO2 at 37°C. The myogenic differentiation of C2C12 myoblast cells was initiated upon cells reaching 90% confluence by switching the cells to culture in DMEM containing 3% horse serum (Hyclone SH30074.03) and then culturing for 12, 24, 48, 60, and 103 h.


title: brain in control, biological rep1

type: RNA

city: Changchun

first: Qing

last: Yang

address: Boshuo Road

institute: Changchun University of Chinese Medicine

description: Control group

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Clariom S mouse. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Mus

source_name: mouse, 0.9% saline (i.g)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: After behavioral testing, the mice were anesthetized and sacrificed. The brain tissue was quickly removed.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The removed brain tissue was placed in a clean dish on ice and rinsed with PBS.

value: brain


title: Vehicle - rep4, RNA-seq

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description: genes.data.tsv

data_processing:
RRBS - FASTQ files were trimmed using TrimGalore-0.5.0 with parameters --illumina --rrbs
RRBS - basecalls were generated by bcl2fastq v. 2.20.0.42
RRBS - Alignments were generated  bismark v0.22.1 and bowtie2 v2-2.3.5.1
RRBS - MethylKit count files were generated using  R v 3.6.1 and methylKit v1.10.0
Assembly: MesAur1.0
RNA-seq - FASTQ files were pre-processed using fastp version 0.20.1 with parameters --cut_front --cut_front_window_size 1 --cut_front_mean_quality 3 --cut_tail --cut_tail_window_size 1 --cut_tail_mean_quality 3 --cut_right --cut_right_window_size 4 --cut_right_mean_quality 15 --length_required 36
RNA-seq - reads were aligned to the Golden Hamster genome using STAR version 2.7.4a
RNA-seq - read counts were estimated using RSEM (rsem-calculate-expression) version 1.3.1
RNA-seq - differentially expressed genes were called using DESeq2 v1.24.0 and were considered significant with a Wald test p-value cutoff of 0.05 and linear fold change of 1.5
Supplementary files format and content: RRBS data was processed into bedGraph format; RNASeq data was processed into a genes X counts matrix

organism: Mesocricetus auratus

source_name: Fetus

growth_protocol: The Syrian hamster fetal cells were plated and treated following a modified version of the SH-CTA assay at pH 6.7 (Pant, K. et al 2012. Mutat. Res.: 744:54-63).  Instead of culture on a feeder layer, cells were cultured in preconditioned media (Pant, K. et al. 2010. Mutat. Res.: 698:6-10).

extract_protocol:
Cells were rinsed with dPBS then  lifted using TryplE (Thermofisher), suspended in complete medium then washed twice by centrifugation /suspension in dPBS then divided into identical aliquots, pelleted and  frozen at -80C until use.  Genomic DNA and total RNA were isolated from cell pellets using DNEasy(Blood and Tissue) and RNEasy mini kits (Qiagen, Mississauga ON),  respectively.  DNA integrity was verified by 0.8% agarose electrophoresis.   RNA integrity was measured using Agilent's 2200 tapestation(Mississauga ON) and all RIN values exceeded 9.7
RRBS libraries were prepared from 100ng genomic DNA using the Premium RRBS kit from Diagenode (catalogue number C02030032).    RNA-seq libraries were prepared from 1µg total RNAusing Illumina's Truseq stranded mRNA kit (20020594 ) and labelled with TruSeq RNA CD Indexes (20019792)

treatment_protocol: Immortalized SHF cells were plated at 10^6 cells per 10cm plate and were grown for 24 hours before treatment.  Cells were then either left untreated (naïve) or treated with vehicle alone or with 1µM or 5µM of 5-Aza-2'-deoxycytidine (5aCdR) for 48 hours.

value: MT colony-derived culture that bypassed senescence and sustained proliferation

tag: days in culture

value: CAGGACGT

value: ACGTCCTG


title: Vehicle - rep3, RNA-seq

description: genes.data.tsv

value: CCTATCCT

value: AGGATAGG


title: C2C12, GM, HiC, 1

data_processing:
The paired-end Hi-C reads from different libraries (C2C12 myoblast and myotube cells) were mapped separately to the mouse genome (mm10), and the align bam files were transformed to validPairs files using HiC-Pro pipeline v2.9.056 with the parameters “-s mapping” and “-s proc_hic”. Then validPairs of replicates at each time point were merged to build raw inter-/intra-chromosomal contact maps (4 kb, 25 kb, and 40 kb resolution), and ICE normalization was run on contact maps using HiC-Pro pipeline v2.9.056 with parameters “-s merge_persample”, “-s build_contact_maps”, and “-s ice_norm”. The visualized contact matrices were generated at resolutions of 1 kb, 5 kb, 10 kb, 25 kb, 40 kb, 50 kb, 100 kb, and 1 Mb using juicer tools v1.8.957.
The raw matrix built by HiC-Pro pipeline v2.9.056 was normalized via the ICE method, and the ICE matrix was used to calculate the insulation score. The insulation score of the ICE matrix was calculated with the parameter “-is 480000 -ids 320000 -im iqrMean -ss 160000”.
Loops of Hi-C data were analyzed using the HiCCUPS method (https://github.com/XiaoTaoWang/HiCPeaks). The resolution parameter was set as “-r 25000”. Using the raw reads matrix (25 kb) generated by HiC-Pro, the read count profile of 25 kb loops during C2C12 differentiation was calculated and transformed to a CPM matrix by the edgeR GLM model. Then the loop was selected with reads > 50 at least in one time point.
Assembly: mm10
Supplementary files format and content: Loop bedpe file of  C2C12 GM and DM60h cells and TAD, TAD boundary bed file in each time point.

growth_protocol: The mouse C2C12 cell line was requested from the Cell Bank of Wuhan University. The cells were cultured in 1× DMEM basic (Gibco‐BRL) with 20% fetal bovine serum (Gibco 10099133) in 5% CO2 at 37°C. The myogenic differentiation of C2C12 myoblast cells was initiated upon cells reaching 90% confluence by switching the cells to culture in DMEM containing 3% horse serum (Hyclone SH30074.03) and then culturing for 12, 24, 48, 60, and 102 h.


title: C2C12, GM, ATAC-seq, 2

growth_protocol: The mouse C2C12 cell line was requested from the Cell Bank of Wuhan University. The cells were cultured in 1× DMEM basic (Gibco‐BRL) with 20% fetal bovine serum (Gibco 10099133) in 5% CO2 at 37°C. The myogenic differentiation of C2C12 myoblast cells was initiated upon cells reaching 90% confluence by switching the cells to culture in DMEM containing 3% horse serum (Hyclone SH30074.03) and then culturing for 12, 24, 48, 60, and 99 h.


title: brain in CK, biological rep1

description: CK group

source_name: mouse, 40mg/kg CK (i.g) and 2mg/kg scopoletin hydrobromide (i.p)


title: C2C12, DM96h, RNA-seq, 3

description:
C2C12_differentiation_all_samples_reads_count.txt
mmu_C2C12_DM96_merge_sortBYchrSignal.UniqueMultiple.str1.out.sort.bw
mmu_C2C12_DM96_merge_sortBYchrSignal.UniqueMultiple.str2.out.sort.bw

data_processing:
The mouse reference genome and GTF files were downloaded from the GENCODE database version M11 (https://www.gencodegenes.org/mouse/). The RNA-seq data of C2C12 cells at different time points with three replicates were used to calculate the read counts of genes in the annotation file using RSEM v1.3.055. Gene expression at different time points was calculated using the Deseq2 R package56. The bigwig file of each time point was transformed by the merged bam files of 4 replicates in the same time point with STAR.
Assembly: mm10
Supplementary files format and content:  Reads count file of all samples calculated by RSEM and bigwig files of the sense  and antisense strand  of each timepoint.

growth_protocol: The mouse C2C12 cell line was requested from the Cell Bank of Wuhan University. The cells were cultured in 1× DMEM basic (Gibco‐BRL) with 20% fetal bovine serum (Gibco 10099133) in 5% CO2 at 37°C. The myogenic differentiation of C2C12 myoblast cells was initiated upon cells reaching 90% confluence by switching the cells to culture in DMEM containing 3% horse serum (Hyclone SH30074.03) and then culturing for 12, 24, 48, 60, and 97 h.

extract_protocol:
Triplicate samples of C2C12 cells cultured in growth medium (GM) and differentiation medium for 12, 24, 48, 60, and 96 h were collected, and total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions (Thermo Scientific, 15596027).
The strand-specific RNA-seq libraries were constructed following the protocol from Illumina (Illumina, San Diego, CA). The prepared libraries were sequenced on the Illumina HiSeq X Ten (PE151) platform.

value: differentiation 96 hours


title: Vehicle - rep2, RNA-seq

description: genes.data.tsv


title: brain in model, biological rep2

description: Model group

source_name: mouse, 2mg/kg scopoletin hydrobromide (i.p)


title: Rpl3L_knockout_heart_rep1

city: Cincinnati

first: Jeffery

middle: D

last: Molkentin

state: Ohio

address: 240 Albert Sabin Way MLC 7020

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression data from Rpl3L knockout heart

hyb_protocol: 3.0 ug of fragmented cDNA were hybridized to Clariom S Arrays, Mouse (Applied Biosystems). Probe arrays were incubated at 45°C for 17 hrs in the Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Probe arrays were washed and stained using the Fluidics Station 450 (Affymetrix), utilizing the fluidics protocol FS450-0007. The Stain and Antibody solutions are produced by Applied Biosystems and contained in the Genechip Hybridization Wash and Stain Kit.

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

data_processing: The .cel were created by Command Console (Affymetrix). The .cel files were analyzed by Expression Console (Affymetrix) to create .sst-rma-gene-full.chp files.

source_name: Cardiac muscle

label_protocol: The GeneChip 3’ IVT Pico Reagent Kit is used to create biotin – labeled double -strand cDNA targets for hybridization to the Clariom S Arrays, Mouse.

extract_protocol:
Hearts were harvested from euthanized mice and flash-frozen
Trizol-based extraction of total RNA was performed according to the manufacturer's instructions.

value: Heart


title: brain in CK, biological rep2

description: CK group


title: Control_heart_rep2

description: Gene expression data from control heart


title: Vehicle - rep1, RNA-seq

description: genes.data.tsv

value: ATAGAGGC

value: GCCTCTAT


title: 5 µM 5aCdR - rep 4, RNA-seq

description: genes.data.tsv

value: 5uM 5aCdR

value: GGCTCTGA

value: TCAGAGCC


title: Control_heart_rep1

description: Gene expression data from control heart


title: 5 µM 5aCdR - rep 3, RNA-seq

description: genes.data.tsv

value: TATAGCCT

value: AGGCTATA


title: Rpl3L_knockout_heart_rep2


title: brain in control, biological rep2

description: Control group


title: C2C12, DM60h, RNA-seq, 3

description:
C2C12_differentiation_all_samples_reads_count.txt
mmu_C2C12_DM60_merge_sortBYchrSignal.UniqueMultiple.str1.out.sort.bw
mmu_C2C12_DM60_merge_sortBYchrSignal.UniqueMultiple.str2.out.sort.bw

data_processing:
The mouse reference genome and GTF files were downloaded from the GENCODE database version M11 (https://www.gencodegenes.org/mouse/). The RNA-seq data of C2C12 cells at different time points with three replicates were used to calculate the read counts of genes in the annotation file using RSEM v1.3.055. Gene expression at different time points was calculated using the Deseq2 R package56. The bigwig file of each time point was transformed by the merged bam files of 17 replicates in the same time point with STAR.
Assembly: mm10
Supplementary files format and content:  Reads count file of all samples calculated by RSEM and bigwig files of the sense  and antisense strand  of each timepoint.

growth_protocol: The mouse C2C12 cell line was requested from the Cell Bank of Wuhan University. The cells were cultured in 1× DMEM basic (Gibco‐BRL) with 20% fetal bovine serum (Gibco 10099133) in 5% CO2 at 37°C. The myogenic differentiation of C2C12 myoblast cells was initiated upon cells reaching 90% confluence by switching the cells to culture in DMEM containing 3% horse serum (Hyclone SH30074.03) and then culturing for 12, 24, 48, 60, and 110 h.

extract_protocol:
Triplicate samples of C2C12 cells cultured in growth medium (GM) and differentiation medium for 12, 24, 48, 60, and 96 h were collected, and total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions (Thermo Scientific, 15596040).
The strand-specific RNA-seq libraries were constructed following the protocol from Illumina (Illumina, San Diego, CA). The prepared libraries were sequenced on the Illumina HiSeq X Ten (PE164) platform.

value: Myoblast

value: WT

value: differentiation 60 hours

value: Replicate 3


title: C2C12, DM96h, RNA-seq, 2

data_processing:
The mouse reference genome and GTF files were downloaded from the GENCODE database version M11 (https://www.gencodegenes.org/mouse/). The RNA-seq data of C2C12 cells at different time points with three replicates were used to calculate the read counts of genes in the annotation file using RSEM v1.3.055. Gene expression at different time points was calculated using the Deseq2 R package56. The bigwig file of each time point was transformed by the merged bam files of 3 replicates in the same time point with STAR.
Assembly: mm10
Supplementary files format and content:  Reads count file of all samples calculated by RSEM and bigwig files of the sense  and antisense strand  of each timepoint.

growth_protocol: The mouse C2C12 cell line was requested from the Cell Bank of Wuhan University. The cells were cultured in 1× DMEM basic (Gibco‐BRL) with 20% fetal bovine serum (Gibco 10099133) in 5% CO2 at 37°C. The myogenic differentiation of C2C12 myoblast cells was initiated upon cells reaching 90% confluence by switching the cells to culture in DMEM containing 3% horse serum (Hyclone SH30074.03) and then culturing for 12, 24, 48, 60, and 96 h.

extract_protocol:
Triplicate samples of C2C12 cells cultured in growth medium (GM) and differentiation medium for 12, 24, 48, 60, and 96 h were collected, and total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions (Thermo Scientific, 15596026).
The strand-specific RNA-seq libraries were constructed following the protocol from Illumina (Illumina, San Diego, CA). The prepared libraries were sequenced on the Illumina HiSeq X Ten (PE150) platform.

value: Replicate 2


title: brain in model, biological rep1

description: Model group

value: brain


title: C2C12, DM60h, RNA-seq, 1

data_processing:
The mouse reference genome and GTF files were downloaded from the GENCODE database version M11 (https://www.gencodegenes.org/mouse/). The RNA-seq data of C2C12 cells at different time points with three replicates were used to calculate the read counts of genes in the annotation file using RSEM v1.3.055. Gene expression at different time points was calculated using the Deseq2 R package56. The bigwig file of each time point was transformed by the merged bam files of 15 replicates in the same time point with STAR.
Assembly: mm10
Supplementary files format and content:  Reads count file of all samples calculated by RSEM and bigwig files of the sense  and antisense strand  of each timepoint.

growth_protocol: The mouse C2C12 cell line was requested from the Cell Bank of Wuhan University. The cells were cultured in 1× DMEM basic (Gibco‐BRL) with 20% fetal bovine serum (Gibco 10099133) in 5% CO2 at 37°C. The myogenic differentiation of C2C12 myoblast cells was initiated upon cells reaching 90% confluence by switching the cells to culture in DMEM containing 3% horse serum (Hyclone SH30074.03) and then culturing for 12, 24, 48, 60, and 108 h.

extract_protocol:
Triplicate samples of C2C12 cells cultured in growth medium (GM) and differentiation medium for 12, 24, 48, 60, and 96 h were collected, and total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions (Thermo Scientific, 15596038).
The strand-specific RNA-seq libraries were constructed following the protocol from Illumina (Illumina, San Diego, CA). The prepared libraries were sequenced on the Illumina HiSeq X Ten (PE162) platform.

value: Replicate 1


title: C2C12, DM60h, RNA-seq, 2

data_processing:
The mouse reference genome and GTF files were downloaded from the GENCODE database version M11 (https://www.gencodegenes.org/mouse/). The RNA-seq data of C2C12 cells at different time points with three replicates were used to calculate the read counts of genes in the annotation file using RSEM v1.3.055. Gene expression at different time points was calculated using the Deseq2 R package56. The bigwig file of each time point was transformed by the merged bam files of 16 replicates in the same time point with STAR.
Assembly: mm10
Supplementary files format and content:  Reads count file of all samples calculated by RSEM and bigwig files of the sense  and antisense strand  of each timepoint.

growth_protocol: The mouse C2C12 cell line was requested from the Cell Bank of Wuhan University. The cells were cultured in 1× DMEM basic (Gibco‐BRL) with 20% fetal bovine serum (Gibco 10099133) in 5% CO2 at 37°C. The myogenic differentiation of C2C12 myoblast cells was initiated upon cells reaching 90% confluence by switching the cells to culture in DMEM containing 3% horse serum (Hyclone SH30074.03) and then culturing for 12, 24, 48, 60, and 109 h.

extract_protocol:
Triplicate samples of C2C12 cells cultured in growth medium (GM) and differentiation medium for 12, 24, 48, 60, and 96 h were collected, and total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions (Thermo Scientific, 15596039).
The strand-specific RNA-seq libraries were constructed following the protocol from Illumina (Illumina, San Diego, CA). The prepared libraries were sequenced on the Illumina HiSeq X Ten (PE163) platform.


title: 5 µM 5aCdR - rep 1, RNA-seq

description: genes.data.tsv

value: MT colony-derived culture that bypassed senescence and sustained proliferation


title: 5 µM 5aCdR - rep 2, RNA-seq

description: genes.data.tsv

value: TAATCTTA

value: TAAGATTA


title: 1 µM 5aCdR - rep 3, RNA-seq

description: genes.data.tsv

value: 1µM 5aCdR

value: ATAGAGGC


title: C2C12, DM48h, RNA-seq, 2

description:
C2C12_differentiation_all_samples_reads_count.txt
mmu_C2C12_DM48_merge_sortBYchrSignal.UniqueMultiple.str1.out.sort.bw
mmu_C2C12_DM48_merge_sortBYchrSignal.UniqueMultiple.str2.out.sort.bw

data_processing:
The mouse reference genome and GTF files were downloaded from the GENCODE database version M11 (https://www.gencodegenes.org/mouse/). The RNA-seq data of C2C12 cells at different time points with three replicates were used to calculate the read counts of genes in the annotation file using RSEM v1.3.055. Gene expression at different time points was calculated using the Deseq2 R package56. The bigwig file of each time point was transformed by the merged bam files of 13 replicates in the same time point with STAR.
Assembly: mm10
Supplementary files format and content:  Reads count file of all samples calculated by RSEM and bigwig files of the sense  and antisense strand  of each timepoint.

extract_protocol:
Triplicate samples of C2C12 cells cultured in growth medium (GM) and differentiation medium for 12, 24, 48, 60, and 96 h were collected, and total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions (Thermo Scientific, 15596036).
The strand-specific RNA-seq libraries were constructed following the protocol from Illumina (Illumina, San Diego, CA). The prepared libraries were sequenced on the Illumina HiSeq X Ten (PE160) platform.

value: differentiation 48 hours


title: 1 µM 5aCdR - rep 1, RNA-seq

description: genes.data.tsv

value: AGGCGAAG

value: CTTCGCCT


title: C2C12, DM48h, RNA-seq, 3

data_processing:
The mouse reference genome and GTF files were downloaded from the GENCODE database version M11 (https://www.gencodegenes.org/mouse/). The RNA-seq data of C2C12 cells at different time points with three replicates were used to calculate the read counts of genes in the annotation file using RSEM v1.3.055. Gene expression at different time points was calculated using the Deseq2 R package56. The bigwig file of each time point was transformed by the merged bam files of 14 replicates in the same time point with STAR.
Assembly: mm10
Supplementary files format and content:  Reads count file of all samples calculated by RSEM and bigwig files of the sense  and antisense strand  of each timepoint.

extract_protocol:
Triplicate samples of C2C12 cells cultured in growth medium (GM) and differentiation medium for 12, 24, 48, 60, and 96 h were collected, and total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions (Thermo Scientific, 15596037).
The strand-specific RNA-seq libraries were constructed following the protocol from Illumina (Illumina, San Diego, CA). The prepared libraries were sequenced on the Illumina HiSeq X Ten (PE161) platform.


title: 1 µM 5aCdR - rep 4, RNA-seq

description: genes.data.tsv


title: C2C12, DM24h, RNA-seq, 3

description:
C2C12_differentiation_all_samples_reads_count.txt
mmu_C2C12_DM24_merge_sortBYchrSignal.UniqueMultiple.str1.out.sort.bw
mmu_C2C12_DM24_merge_sortBYchrSignal.UniqueMultiple.str2.out.sort.bw

data_processing:
The mouse reference genome and GTF files were downloaded from the GENCODE database version M11 (https://www.gencodegenes.org/mouse/). The RNA-seq data of C2C12 cells at different time points with three replicates were used to calculate the read counts of genes in the annotation file using RSEM v1.3.055. Gene expression at different time points was calculated using the Deseq2 R package56. The bigwig file of each time point was transformed by the merged bam files of 11 replicates in the same time point with STAR.
Assembly: mm10
Supplementary files format and content:  Reads count file of all samples calculated by RSEM and bigwig files of the sense  and antisense strand  of each timepoint.

extract_protocol:
Triplicate samples of C2C12 cells cultured in growth medium (GM) and differentiation medium for 12, 24, 48, 60, and 96 h were collected, and total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions (Thermo Scientific, 15596034).
The strand-specific RNA-seq libraries were constructed following the protocol from Illumina (Illumina, San Diego, CA). The prepared libraries were sequenced on the Illumina HiSeq X Ten (PE158) platform.

value: differentiation 24 hours


title: C2C12, DM48h, RNA-seq, 1

data_processing:
The mouse reference genome and GTF files were downloaded from the GENCODE database version M11 (https://www.gencodegenes.org/mouse/). The RNA-seq data of C2C12 cells at different time points with three replicates were used to calculate the read counts of genes in the annotation file using RSEM v1.3.055. Gene expression at different time points was calculated using the Deseq2 R package56. The bigwig file of each time point was transformed by the merged bam files of 12 replicates in the same time point with STAR.
Assembly: mm10
Supplementary files format and content:  Reads count file of all samples calculated by RSEM and bigwig files of the sense  and antisense strand  of each timepoint.

extract_protocol:
Triplicate samples of C2C12 cells cultured in growth medium (GM) and differentiation medium for 12, 24, 48, 60, and 96 h were collected, and total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions (Thermo Scientific, 15596035).
The strand-specific RNA-seq libraries were constructed following the protocol from Illumina (Illumina, San Diego, CA). The prepared libraries were sequenced on the Illumina HiSeq X Ten (PE159) platform.


title: C2C12, DM12h, RNA-seq, 3

description:
C2C12_differentiation_all_samples_reads_count.txt
mmu_C2C12_DM12_merge_sortBYchrSignal.UniqueMultiple.str1.out.sort.bw
mmu_C2C12_DM12_merge_sortBYchrSignal.UniqueMultiple.str2.out.sort.bw

data_processing:
The mouse reference genome and GTF files were downloaded from the GENCODE database version M11 (https://www.gencodegenes.org/mouse/). The RNA-seq data of C2C12 cells at different time points with three replicates were used to calculate the read counts of genes in the annotation file using RSEM v1.3.055. Gene expression at different time points was calculated using the Deseq2 R package56. The bigwig file of each time point was transformed by the merged bam files of 8 replicates in the same time point with STAR.
Assembly: mm10
Supplementary files format and content:  Reads count file of all samples calculated by RSEM and bigwig files of the sense  and antisense strand  of each timepoint.

growth_protocol: The mouse C2C12 cell line was requested from the Cell Bank of Wuhan University. The cells were cultured in 1× DMEM basic (Gibco‐BRL) with 20% fetal bovine serum (Gibco 10099133) in 5% CO2 at 37°C. The myogenic differentiation of C2C12 myoblast cells was initiated upon cells reaching 90% confluence by switching the cells to culture in DMEM containing 3% horse serum (Hyclone SH30074.03) and then culturing for 12, 24, 48, 60, and 101 h.

extract_protocol:
Triplicate samples of C2C12 cells cultured in growth medium (GM) and differentiation medium for 12, 24, 48, 60, and 96 h were collected, and total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions (Thermo Scientific, 15596031).
The strand-specific RNA-seq libraries were constructed following the protocol from Illumina (Illumina, San Diego, CA). The prepared libraries were sequenced on the Illumina HiSeq X Ten (PE155) platform.

value: differentiation 12 hours


title: Naïve - rep2, RNA-seq

description: genes.data.tsv

value: untreated

value: CCTATCCT

value: AGGATAGG


title: Vehicle - rep4, RRBS

value: CTCAGA


title: C2C12, DM96h, RNA-seq, 1

data_processing:
The mouse reference genome and GTF files were downloaded from the GENCODE database version M11 (https://www.gencodegenes.org/mouse/). The RNA-seq data of C2C12 cells at different time points with three replicates were used to calculate the read counts of genes in the annotation file using RSEM v1.3.055. Gene expression at different time points was calculated using the Deseq2 R package56. The bigwig file of each time point was transformed by the merged bam files of 18 replicates in the same time point with STAR.
Assembly: mm10
Supplementary files format and content:  Reads count file of all samples calculated by RSEM and bigwig files of the sense  and antisense strand  of each timepoint.

growth_protocol: The mouse C2C12 cell line was requested from the Cell Bank of Wuhan University. The cells were cultured in 1× DMEM basic (Gibco‐BRL) with 20% fetal bovine serum (Gibco 10099133) in 5% CO2 at 37°C. The myogenic differentiation of C2C12 myoblast cells was initiated upon cells reaching 90% confluence by switching the cells to culture in DMEM containing 3% horse serum (Hyclone SH30074.03) and then culturing for 12, 24, 48, 60, and 111 h.

extract_protocol:
Triplicate samples of C2C12 cells cultured in growth medium (GM) and differentiation medium for 12, 24, 48, 60, and 96 h were collected, and total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions (Thermo Scientific, 15596041).
The strand-specific RNA-seq libraries were constructed following the protocol from Illumina (Illumina, San Diego, CA). The prepared libraries were sequenced on the Illumina HiSeq X Ten (PE165) platform.

value: Myoblast

value: WT

value: differentiation 96 hours


title: C2C12, DM24h, RNA-seq, 2

data_processing:
The mouse reference genome and GTF files were downloaded from the GENCODE database version M11 (https://www.gencodegenes.org/mouse/). The RNA-seq data of C2C12 cells at different time points with three replicates were used to calculate the read counts of genes in the annotation file using RSEM v1.3.055. Gene expression at different time points was calculated using the Deseq2 R package56. The bigwig file of each time point was transformed by the merged bam files of 10 replicates in the same time point with STAR.
Assembly: mm10
Supplementary files format and content:  Reads count file of all samples calculated by RSEM and bigwig files of the sense  and antisense strand  of each timepoint.

extract_protocol:
Triplicate samples of C2C12 cells cultured in growth medium (GM) and differentiation medium for 12, 24, 48, 60, and 96 h were collected, and total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions (Thermo Scientific, 15596033).
The strand-specific RNA-seq libraries were constructed following the protocol from Illumina (Illumina, San Diego, CA). The prepared libraries were sequenced on the Illumina HiSeq X Ten (PE157) platform.

value: Replicate 2


title: Naïve - rep4, RNA-seq

description: genes.data.tsv

value: MT colony-derived culture that bypassed senescence and sustained proliferation

value: GTACTGAC

value: GTCAGTAC


title: C2C12, DM24h, RNA-seq, 1

data_processing:
The mouse reference genome and GTF files were downloaded from the GENCODE database version M11 (https://www.gencodegenes.org/mouse/). The RNA-seq data of C2C12 cells at different time points with three replicates were used to calculate the read counts of genes in the annotation file using RSEM v1.3.055. Gene expression at different time points was calculated using the Deseq2 R package56. The bigwig file of each time point was transformed by the merged bam files of 9 replicates in the same time point with STAR.
Assembly: mm10
Supplementary files format and content:  Reads count file of all samples calculated by RSEM and bigwig files of the sense  and antisense strand  of each timepoint.

extract_protocol:
Triplicate samples of C2C12 cells cultured in growth medium (GM) and differentiation medium for 12, 24, 48, 60, and 96 h were collected, and total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions (Thermo Scientific, 15596032).
The strand-specific RNA-seq libraries were constructed following the protocol from Illumina (Illumina, San Diego, CA). The prepared libraries were sequenced on the Illumina HiSeq X Ten (PE156) platform.

value: Replicate 1


title: 1 µM 5aCdR - rep 2, RNA-seq

description: genes.data.tsv

value: 1µM 5aCdR


title: Naïve - rep3, RNA-seq

description: genes.data.tsv

value: AGGCGAAG


title: Naïve - rep1, RNA-seq

description: genes.data.tsv

value: GGCTCTGA

value: TCAGAGCC


title: C2C12, DM12h, RNA-seq, 1

data_processing:
The mouse reference genome and GTF files were downloaded from the GENCODE database version M11 (https://www.gencodegenes.org/mouse/). The RNA-seq data of C2C12 cells at different time points with three replicates were used to calculate the read counts of genes in the annotation file using RSEM v1.3.055. Gene expression at different time points was calculated using the Deseq2 R package56. The bigwig file of each time point was transformed by the merged bam files of 6 replicates in the same time point with STAR.
Assembly: mm10
Supplementary files format and content:  Reads count file of all samples calculated by RSEM and bigwig files of the sense  and antisense strand  of each timepoint.

extract_protocol:
Triplicate samples of C2C12 cells cultured in growth medium (GM) and differentiation medium for 12, 24, 48, 60, and 96 h were collected, and total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions (Thermo Scientific, 15596029).
The strand-specific RNA-seq libraries were constructed following the protocol from Illumina (Illumina, San Diego, CA). The prepared libraries were sequenced on the Illumina HiSeq X Ten (PE153) platform.

value: differentiation 12 hours


title: C2C12, DM12h, RNA-seq, 2

data_processing:
The mouse reference genome and GTF files were downloaded from the GENCODE database version M11 (https://www.gencodegenes.org/mouse/). The RNA-seq data of C2C12 cells at different time points with three replicates were used to calculate the read counts of genes in the annotation file using RSEM v1.3.055. Gene expression at different time points was calculated using the Deseq2 R package56. The bigwig file of each time point was transformed by the merged bam files of 7 replicates in the same time point with STAR.
Assembly: mm10
Supplementary files format and content:  Reads count file of all samples calculated by RSEM and bigwig files of the sense  and antisense strand  of each timepoint.

growth_protocol: The mouse C2C12 cell line was requested from the Cell Bank of Wuhan University. The cells were cultured in 1× DMEM basic (Gibco‐BRL) with 20% fetal bovine serum (Gibco 10099133) in 5% CO2 at 37°C. The myogenic differentiation of C2C12 myoblast cells was initiated upon cells reaching 90% confluence by switching the cells to culture in DMEM containing 3% horse serum (Hyclone SH30074.03) and then culturing for 12, 24, 48, 60, and 100 h.

extract_protocol:
Triplicate samples of C2C12 cells cultured in growth medium (GM) and differentiation medium for 12, 24, 48, 60, and 96 h were collected, and total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions (Thermo Scientific, 15596030).
The strand-specific RNA-seq libraries were constructed following the protocol from Illumina (Illumina, San Diego, CA). The prepared libraries were sequenced on the Illumina HiSeq X Ten (PE154) platform.


title: Vehicle - rep1, RRBS

data_processing:
RRBS - FASTQ files were trimmed using TrimGalore-0.5.0 with parameters --illumina --rrbs
RRBS - basecalls were generated by bcl2fastq v. 2.20.0.42
RRBS - Alignments were generated  bismark v0.22.1 and bowtie2 v2-2.3.5.1
RRBS - MethylKit count files were generated using  R v 3.6.1 and methylKit v1.10.0
Assembly: MesAur1.0
RNA-seq - FASTQ files were pre-processed using fastp version 0.20.1 with parameters --cut_front --cut_front_window_size 1 --cut_front_mean_quality 3 --cut_tail --cut_tail_window_size 1 --cut_tail_mean_quality 3 --cut_right --cut_right_window_size 4 --cut_right_mean_quality 15 --length_required 36
RNA-seq - reads were aligned to the Golden Hamster genome using STAR version 2.7.4a
RNA-seq - read counts were estimated using RSEM (rsem-calculate-expression) version 1.3.1
RNA-seq - differentially expressed genes were called using DESeq2 v1.24.0 and were considered significant with a Wald test p-value cutoff of 0.05 and linear fold change of 1.5
Supplementary files format and content: RRBS data was processed into bedGraph format; RNASeq data was processed into a genes X counts matrix

extract_protocol:
Cells were rinsed with dPBS then  lifted using TryplE (Thermofisher), suspended in complete medium then washed twice by centrifugation /suspension in dPBS then divided into identical aliquots, pelleted and  frozen at -80C until use.  Genomic DNA and total RNA were isolated from cell pellets using DNEasy(Blood and Tissue) and RNEasy mini kits (Qiagen, Mississauga ON),  respectively.  DNA integrity was verified by 0.8% agarose electrophoresis.   RNA integrity was measured using Agilent's 2200 tapestation(Mississauga ON) and all RIN values exceeded 9.7
RRBS libraries were prepared from 100ng genomic DNA using the Premium RRBS kit from Diagenode (catalogue number C02030032).    RNA-seq libraries were prepared from 1µg total RNAusing Illumina's Truseq stranded mRNA kit (20020594 ) and labelled with TruSeq RNA CD Indexes (20019792)

value: CGGAAT


title: C2C12, GM, RNA-seq, 2

description:
C2C12_differentiation_all_samples_reads_count.txt
mmu_C2C12_GM_merge_sortBYchrSignal.UniqueMultiple.str1.out.sort.bw
mmu_C2C12_GM_merge_sortBYchrSignal.UniqueMultiple.str2.out.sort.bw

data_processing:
The mouse reference genome and GTF files were downloaded from the GENCODE database version M11 (https://www.gencodegenes.org/mouse/). The RNA-seq data of C2C12 cells at different time points with three replicates were used to calculate the read counts of genes in the annotation file using RSEM v1.3.055. Gene expression at different time points was calculated using the Deseq2 R package56. The bigwig file of each time point was transformed by the merged bam files of 4 replicates in the same time point with STAR.
Assembly: mm10
Supplementary files format and content:  Reads count file of all samples calculated by RSEM and bigwig files of the sense  and antisense strand  of each timepoint.

extract_protocol:
Triplicate samples of C2C12 cells cultured in growth medium (GM) and differentiation medium for 12, 24, 48, 60, and 96 h were collected, and total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions (Thermo Scientific, 15596027).
The strand-specific RNA-seq libraries were constructed following the protocol from Illumina (Illumina, San Diego, CA). The prepared libraries were sequenced on the Illumina HiSeq X Ten (PE151) platform.

value: proliferation period


title: C2C12, GM, RNA-seq, 1


title: Vehicle - rep2, RRBS

value: CTAGCT


title: Vehicle - rep3, RRBS

value: CTATAC


title: 5 µM 5aCdR - rep 3, RRBS

value: 5uM 5aCdR

value: CATTTT


title: LPS_cpTLR-i_10uM_3

city: Chuncheon

first: Keunwook

last: Lee

department: Biomedical Science

country: South Korea

institute: Hallym University

data_processing:
Reads with Low quality and adapters were trimmed using Trimmomatic0.38.
Paired-end reads were equally controlled by Q30.
The percentages of Q30 bases were higher than 95%.
Trimmed reads were mapped to Mus Musculus mm10 reference genome by HISAT2 and assembled using StringTie.
Assembly: mm10
Supplementary files format and content: FPKM and TPM of each sample.xlsx

source_name: Bone marrow derived macrophages

growth_protocol: Bone marrow derived cells were cultured in the presence of 20 ng/ml M-CSF for 7 days to generate BMDMs.

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following manufacturer's protocols.

treatment_protocol: BMDMs were pretreated  with two different concentraion of the peptide followed by stimulation with LPS for 2 h.

value: Bone marrow derived macrophages

value: WT

value: LPS + cpTLRi (10uM)

value: 2 h


title: LPS_cpTLR-i_10uM_2


title: C2C12, GM, RNA-seq, 3

data_processing:
The mouse reference genome and GTF files were downloaded from the GENCODE database version M11 (https://www.gencodegenes.org/mouse/). The RNA-seq data of C2C12 cells at different time points with three replicates were used to calculate the read counts of genes in the annotation file using RSEM v1.3.055. Gene expression at different time points was calculated using the Deseq2 R package56. The bigwig file of each time point was transformed by the merged bam files of 5 replicates in the same time point with STAR.
Assembly: mm10
Supplementary files format and content:  Reads count file of all samples calculated by RSEM and bigwig files of the sense  and antisense strand  of each timepoint.

extract_protocol:
Triplicate samples of C2C12 cells cultured in growth medium (GM) and differentiation medium for 12, 24, 48, 60, and 96 h were collected, and total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions (Thermo Scientific, 15596028).
The strand-specific RNA-seq libraries were constructed following the protocol from Illumina (Illumina, San Diego, CA). The prepared libraries were sequenced on the Illumina HiSeq X Ten (PE152) platform.

value: Myoblast

value: Replicate 3


title: LPS_cpTLR-i_10uM_1


title: 5 µM 5aCdR - rep 1, RRBS

value: MT colony-derived culture that bypassed senescence and sustained proliferation

value: CAGGCG


title: 5 µM 5aCdR - rep 2, RRBS

value: CATGGC


title: LPS_cpTLR-i_1uM_3

value: LPS + cpTLRi (1uM)


title: bursa of Fabricius, IBDV-infected, 3 day, rep1

city: Guangzhou

first: Zixian

last: Chen

address: Wushan Road No.483

institute: South China Agriculture University

description:
bursa of Fabricius, very variant, 3 day, rep1
Typy

data_processing:
After image recognition and base recognition, the original reads were harvested from the Illumina Novaseq 6000 sequencer. Q30 as the quality control standard, Q30> 80% indicates good sequencing quality.
After subtracting, removing low-quality reads, length filtering, new miRNA prediction, trimmed reads were compared to the merged pre-miRNA database (miRBase pre-miRNA + newly predicted pre-miRNA) using novoalign software.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Gallus gallus

source_name: bursa of Fabricius

growth_protocol: A total of fifteen 21-day-old SPF chickens were randomly divided into 2 groups

extract_protocol:
RNA was harvested and 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Chickens in the first group (n = 5) was infected with IBDV, via the oral routes. Chickens in the second group (n = 5) were inoculated with phosphate buffered saline (PBS) as a negative control.

value: bursa of Fabricius

value: 3 day

tag: infection

value: IBDV


title: bursa of Fabricius, Normal control, 3 day, rep1

description:
bursa of Fabricius, normal control, 3 day, rep1
Nor

value: mock


title: LPS_cpTLR-i_1uM_2


title: 1 µM 5aCdR - rep 4, RRBS

value: 1µM 5aCdR

value: CACTCA


title: 1 µM 5aCdR - rep 3, RRBS

value: CACGAT


title: LPS_3

value: Bone marrow derived macrophages

value: LPS


title: 1 µM 5aCdR - rep 1, RRBS

value: CAACTA


title: LPS_cpTLR-i_1uM_1

value: WT

value: 2 h


title: 1 µM 5aCdR - rep 2, RRBS

value: CACCGG


title: Naïve - rep3, RRBS

value: MT colony-derived culture that bypassed senescence and sustained proliferation

value: untreated

value: ATGAGC


title: Naïve - rep2, RRBS

value: GGTAGC


title: 5 µM 5aCdR - rep 4, RRBS

value: 5uM 5aCdR

value: CCAACA


title: LPS_1


title: Naïve - rep1, RRBS

value: GTAGAG


title: Control_2

value: 0 h


title: Control_3


title: CA1-tissue, wildtype [C57BL/6], SCL, biol rep 4

city: Hannover

first: Maximilian

last: Lenz

address: Carl-Neuberg-Straße 1

department: Institute of Neuroanatomy and Cell Biology

institute: Hannover Medical School

data_processing:
Data analysis was performed at the Galaxy platform (usegalaxy.eu; (Galaxy, 2022)). All files contained more than 10 M high-quality reads (after mapping to the reference genome; mm10) with a phred quality of at least 30 (>90% of total reads).
RNA sequencing data were uploaded to the galaxy web platform (public server: usegalaxy.eu) and transcriptome analysis was performed using the Galaxy platform in accordance with the reference-based RNA-seq data analysis tutorial (Batut et al., 2021).
Adapter sequences, low quality, and short reads were removed via the CUTADAPT tool (Galaxy version 3.5+galaxy0).
Reads were mapped using RNA STAR (Galaxy version 2.7.8a+galaxy0) with the mm10 Full reference genome (Mus musculus).
The evidence-based annotation of the mouse genome (GRCm38), version M25 (Ensembl 100) served as gene model (GENCODE). For an initial assessment of gene expression, unstranded FEATURECOUNT (Galaxy version 2.0.1+galaxy2) analysis was performed from RNA STAR output.
Assembly: mm10
Supplementary files format and content: FEATURE COUNT output (tabular files)

source_name: Brain, organotypic entorhino-hippocampal culture, CA1 isolate

growth_protocol: Entorhino-hippocampal tissue cultures were prepared at postnatal day 4 – 5 from C57BL/6J and Thy1-eGFP-M animals of either sex as previously described. Cultivation medium contained 50 % (v/v) MEM, 25 % (v/v) basal medium eagle, 25 % (v/v) heat-inactivated normal horse serum, 25 mM HEPES buffer solution, 0.15 % (w/v) bicarbonate, 0.65 % (w/v) glucose, 0.1 mg ml-1 streptomycin, 100 U ml-1 penicillin, and 2 mM glutamax. The pH was adjusted to 7.3 and the medium was replaced three times per week. All tissue cultures were allowed to mature for at least 18 days in a humidified atmosphere with 5 % CO2 at 35 °C, since at this age a steady state in structural and functional properties of the organotypic tissue cultures is reached.

extract_protocol:
RNA library preparations for transcriptome analysis were performed using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (New England Biolabs, #E6420) according to the manufacturer's instructions. Briefly, isolation of the dentate gyrus from individual tissue cultures was performed using a scalpel. One isolated dentate gyrus was transferred to 7.5 µl lysis buffer (supplemented with murine RNase inhibitor) and homogenized using a pestill. Samples were centrifuged for 30 seconds at 10000g and 5 µl of supernatant were collected from individual samples and further processed. After cDNA synthesis, cDNA amplification was performed according to the manufacturer's protocol with 12 PCR cycles. The cDNA yield was subsequently analyzed by a High Sensitivity DNA assay on a Bioanalyzer instrument (Agilent). The amount of cDNA was adjusted to 10 ng for further downstream applications.
After fragmentation and adaptor ligation, dual index primers (New England Biolabs, #E7600S) were ligated in a library amplification step using 10 PCR cycles. Libraries were finally cleaned up with 0.8X SPRI beads following a standard bead purification protocol. Library purity and size distribution were assessed with a High Sensitivity DNA assay on a Bioanalyzer instrument (Agilent). We quantified the libraries using the NEBNext Library Quant Kit for Illumina (New England Biolabs, #E7630) based on the mean insert size provided by the Bioanalyzer. A 10 nM sequencing pool (120 µl in Tris-HCl, pH 8.5) was generated for sequencing on the NovaSeq6000 sequencing platform (Illumina; service provided by CeGaT GmbH, Tübingen, Germany). We performed a paired-end sequencing with 150 bp read length.

value: wildtype

tag: lesion

value: SCL


title: Control_1


title: Pooled colonies BAP treated - rep2 (B[A]P)

description: pooled colonies from SHE assay performed on cells from single male Fetus

data_processing:
basecalls were generated by bcl2fastq v. 2.20.0.42
fastq files were trimmed using TrimGalore-0.5.0 with parameters --illumina --rrbs
Alignments were generated  bismark v0.22.1 and bowtie2 v2-2.3.5.1
MethylKit count files were generated using  R v 3.6.1 and methylKit v1.10.0
Genome_build: MesAur1.0
Supplementary_files_format_and_content: tab delimited with columns; chrBase,chr,base,strand,coverage,freqC,freqT

source_name: colonies from Syrian Hamster Fetus - Cell Transformation Assay (SH_CTA)

growth_protocol: All samples originated from cell colonies produced by a modified “Syrian Hamster Embryo(embyo is the historical term but these are fetal cells) Cell transformation assay (SHE-CTA)” using conditioned medium in lieu of irradiated feeder cell layer (see Pickles J.C. et al. 2016. Mutat.Res.Genet.Toxicol.Environ Mutagen. 802:50-58 ). The frozen Syrian hamster fetus stocks that generated the target cell colonies were produced following this standardized protocol (see. described in OECD: "Guidance document on the in vitro Syrian hamster embryo (SHE) cell transformation assay". Series on Testing & Assessment 2015;No. 214:1-24.) Samples 1 to 8 were collected from a culture derived from a morphologically-transformed, B[a]P-treated colony sampled either on day 48 when the culture was observed in senescence or on day 94 after it had bypasses senescence. Samples 9 to 16 were taken from cultures expanded (for 19-25 days) from B[a]P-treated colonies that displayed either transformed(MT) or normal (N) morphology as indicated. Samples 17 to 24 were isolated from pools of ~60 colonies that were either treated with vehicle or B[a]P using the "SHE-CTA" procedures.

extract_protocol:
Cells were harvested using TryplE (Thermofisher), rinsed twice by resuspension in dPBS followed by centrifugation, then frozen as a cell pellet at minus 80C.  Genomic DNA was harvested following the Qiagen DNEasy kit.
Libraries were prepared from 100ng genomic DNA using Diagenode's Premiere RRBS kit (catalogue number C02030032)

treatment_protocol: Target cells were treated with 5µg/mL Benzo[A]Pyrene (B[A]P) or with vehicle alone (0.2% DMSO) as indicated following the method of Pickles et al. (2016)

value: pooled colonies

tag: sh_cta treatment

value: 5µg/mL Benzo[A]Pyrene

tag: adapter

value: TCCCGA


title: Pooled colonies BAP treated - rep4 (B[a]P)

extract_protocol:
Cells were harvested using TryplE (thermofisher), rinsed twice by resuspension in dPBS followed by centrifugation, then frozen as a cell pellet at minus 80C.  Genomic DNA was harvested following the Qiagen DNEasy kit.
Libraries were prepared from100ng genomic DNA using Diagenode's Premiere RRBS kit (catalogue number C02030032)

value: TCGGCA


title: Pooled colonies BAP treated - rep3 (B[a]P)

value: TCGAAG


title: CA1-tissue, wildtype [C57BL/6], SCL, biol rep 3

value: Brain, organotypic entorhino-hippocampal culture, CA1 isolate


title: CA1-tissue, wildtype [C57BL/6], SCL, biol rep 1


title: Naïve - rep4, RRBS

value: CAAAAG


title: Pooled colonies untreated - rep4 (DMSO)

treatment_protocol: Target cells were treated with 5µg/mL Benzo[A]Pyrene (B[A]P) or with vehicle alone (0.2% DMSO) as indicated folowing the method of Pickles et al. (2016)

value: vehicle control

value: TATAAT


title: Pooled colonies untreated - rep3 (DMSO)

value: TACAGC


title: CA1-tissue, wildtype [C57BL/6], SCL, biol rep 2


title: Pooled colonies untreated - rep1 (DMSO)

value: GCGCTA


title: Pooled colonies BAP treated - rep1 (B[a]P)

value: TCATTC


title: LPS_2

value: Bone marrow derived macrophages

value: WT

value: LPS

value: 2 h


title: Pooled colonies untreated - rep2 (DMSO)

value: TAATCG


title: Donor 3, Apex, scATAC-seq

city: Chicago

first: Sebastian

last: Pott

state: IL

address: 920 E 58th St

institute: The University of Chicago

description:
10X Genomics
instrument model: Illumina NovaSeq 6000 or NextSeq 500
SP-HE-MW200928E2-408-ATAC
HeartAtlas_ATAC_barcodes_03092023.tsv.gz
HeartAtlas_ATAC_tilenames_03092023.tsv
HeartAtlas_ATAC_counts.mtx.gz

library_source: genomic single cell

data_processing:
FastQ files from 12 sequencing experiments were individually processed using 10x Genomics CellRanger-atac 1.2.0101. We used the command cellranger-atac count to align the fastq files to human reference genome hg38, followed by marking and removing duplicate reads, and producing a fragment file containing the mapped location of each unique fragment in each nucleus.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Apex

extract_protocol: scATAC-seq libraries were prepared according to v1 of the manufacturer’s guidelines for the Chromium Next GEM Single Cell ATAC Reagent Kits (10X Genomics), with the modification that we started from nuclei that were isolated. Between 9,300 and 25,000 nuclei were tagmented using Transposition Mix (10X Genomics) at 37°C for 1 h and loaded on the Chromium controller. We targeted between 6,000 and 10,000 nuclei for library preparation. QC was performed on final ATAC-seq libraries using a Qubit Fluorometer and an Agilent 2100 Bioanalyzer.

tag: individual

value: Donor 3

value: Apex

tag: Sex

value: Male

tag: age

tag: ancestry

value: White, European


title: CA1-tissue, wildtype [C57BL/6], ECL, biol rep 4

value: wildtype

value: ECL


title: Normal colony- rep4 (Nc)

description: culture derived from N colony. SHE assay performed on cells from single male Fetus

value: colony-derived culture

value: 5µg/mL Benzo[A]Pyrene

value: CTCAGA


title: CA1-tissue, wildtype [C57BL/6], ECL, biol rep 2

value: Brain, organotypic entorhino-hippocampal culture, CA1 isolate


title: CA1-tissue, wildtype [C57BL/6], ECL, biol rep 3


title: Donor 3, LV, scATAC-seq

description:
10X Genomics
instrument model: Illumina NovaSeq 6000 or NextSeq 500
SP-HE-MW200928E2-407-ATAC
HeartAtlas_ATAC_barcodes_03092023.tsv.gz
HeartAtlas_ATAC_tilenames_03092023.tsv
HeartAtlas_ATAC_counts.mtx.gz

data_processing:
FastQ files from 12 sequencing experiments were individually processed using 10x Genomics CellRanger-atac 1.2.0101. We used the command cellranger-atac count to align the fastq files to human reference genome hg38, followed by marking and removing duplicate reads, and producing a fragment file containing the mapped location of each unique fragment in each nucleus.
Note: FastQ files in SRR23392187 and SRR23392179 were not used in the data processing.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Left ventricle

value: Left ventricle


title: CA1-tissue, wildtype [C57BL/6], ECL, biol rep 1


title: Normal colony- rep3 (Nc)

value: CTATAC


title: Donor 3, RV, scATAC-seq

description:
10X Genomics
instrument model: Illumina NovaSeq 6000 or NextSeq 500
SP-HE-MW200928E2-367-ATAC
HeartAtlas_ATAC_barcodes_03092023.tsv.gz
HeartAtlas_ATAC_tilenames_03092023.tsv
HeartAtlas_ATAC_counts.mtx.gz

source_name: Right ventricle

value: Right ventricle


title: MT colony - rep4 (MTc)

description: culture derived from MT colony. SHE assay performed on cells from single male Fetus

value: CCAACA


title: Normal colony- rep2 (Nc)

value: CTAGCT


title: CA1-tissue, wildtype [C57BL/6], control, biol rep 5

value: control


title: Donor 3, Septum, scATAC-seq

description:
10X Genomics
instrument model: Illumina NovaSeq 6000 or NextSeq 500
SP-HE-MW200928E2-175-ATAC
HeartAtlas_ATAC_barcodes_03092023.tsv.gz
HeartAtlas_ATAC_tilenames_03092023.tsv
HeartAtlas_ATAC_counts.mtx.gz

source_name: Interventricular septum

value: Interventricular septum


title: MT colony - rep3 (MTc)

value: CATTTT


title: MT colony - rep2 (MTc)

value: CATGGC


title: CA1-tissue, wildtype [C57BL/6], control, biol rep 4


title: Donor 2, Apex, scATAC-seq

description:
10X Genomics
instrument model: Illumina NovaSeq 6000 or NextSeq 500
SP-HE-HE200915-398-ATAC
HeartAtlas_ATAC_barcodes_03092023.tsv.gz
HeartAtlas_ATAC_tilenames_03092023.tsv
HeartAtlas_ATAC_counts.mtx.gz

value: Donor 2

value: Apex

value: Male


title: MT colony - rep1 (MTc)

growth_protocol: All samples originated from cell colonies produced by a modified “Syrian Hamster Embryo(embyo is the historical term but these are fetal cells) Cell transformation assay (SHE-CTA)” using conditioned medium in lieu of irradiated feeder cell layer (see Pickles J.C. et al. 2016. Mutat.Res.Genet.Toxicol.Environ Mutagen. 802:50-58 ). The frozen Syrian hamster fetus stocks that generated the target cell colonies were produced following this standardised protocol (see. described in OECD: "Guidance document on the in vitro Syrian hamster embryo (SHE) cell transformation assay". Series on Testing & Assessement 2015;No. 214:1-24.) Samples 1 to 8 were collected from a culture derived from a morphologically-transformed, B[a]P-treated colony sampled either on day 48 when the culture was observed in senescence or on day 94 after it had bypasses senescence. Samples 9 to 16 were taken from cultures expanded (for 19-25 days) from B[a]P-treated colonies that displayed either transformed(MT) or normal (N) morphology as indicated. Samples 17 to 24 were isolated from pools of ~60 colonies that were either treated with vehicle or B[a]P using the "SHE-CTA" procedures.

value: CAGGCG


title: CA1-tissue, wildtype [C57BL/6], control, biol rep 3

value: wildtype


title: Donor 2, LV, scATAC-seq

description:
10X Genomics
instrument model: Illumina NovaSeq 6000 or NextSeq 500
SP-HE-HE200915-397-ATAC
HeartAtlas_ATAC_barcodes_03092023.tsv.gz
HeartAtlas_ATAC_tilenames_03092023.tsv
HeartAtlas_ATAC_counts.mtx.gz

value: White, European


title: Normal colony- rep1 (Nc)

value: colony-derived culture

value: 5µg/mL Benzo[A]Pyrene

value: CGGAAT


title: Donor 2, RV, scATAC-seq

description:
10X Genomics
instrument model: Illumina NovaSeq 6000 or NextSeq 500
SP-HE-HE200915-360-ATAC
HeartAtlas_ATAC_barcodes_03092023.tsv.gz
HeartAtlas_ATAC_tilenames_03092023.tsv
HeartAtlas_ATAC_counts.mtx.gz


title: Senescent - rep4 (SEN)

description: senescent culture derived from MT colony typed "male" using kdm5c/d qpcr test. SHE assay performed on pooled female/male Fetuses

value: CAAAAG


title: CA1-tissue, wildtype [C57BL/6], control, biol rep 1

value: Brain, organotypic entorhino-hippocampal culture, CA1 isolate


title: Donor 2, Septum, scATAC-seq

description:
10X Genomics
instrument model: Illumina NovaSeq 6000 or NextSeq 500
SP-HE-HE200915-175-ATAC
HeartAtlas_ATAC_barcodes_03092023.tsv.gz
HeartAtlas_ATAC_tilenames_03092023.tsv
HeartAtlas_ATAC_counts.mtx.gz


title: Senescence-bypass - rep2 (SENbp)

description: senescence bypass culture derived from MT colony typed "male" using kdm5c/d qpcr test. SHE assay performed on pooled female/male Fetuses

value: CACCGG


title: Senescent - rep3 (SEN)

value: ATGAGC


title: Senescent - rep2 (SEN)


title: OVX_Pre_6

city: St. Louis

first: Joseph

last: Dougherty

state: MO

address: 660 S Euclid Ave, Campus Box 8232

department: Genetics

institute: Washington University in St. Louis

data_processing:
Barcode extraction from sample fastq - see bitbucket repository for script. Requires flanking 14 bp around barcode to be identical to design, plus a 10bp sequence to be found in between the flanks. All 10bp sequences extracted from Fastqs into text file.
Tabulation of barcode counts for each sample using table() in R. Subsequently, merging to a metadata table on designed barcodes to drop sequences that were not a perfect match to a designed barcode.
Filtering for low read counts, poor barcode representation across replicates, etc. Described at length in Supplementary Methods.
Calculation of log2(cpm RNA barcode) / log2(cpm DNA barcode) for each retained barcode in each sample.
Subtract the within-sample mean of "basal" (minimal-promoter-only) barcode expression from all other barcode expression values --> REML linear mixed model: expression ~ allele + sex + sex:allele + (1|BC), where BC is the unique barcode identifier to control for effects of barcode sequence.
Assembly: hg19-derived sequences (up to 126bp); see enclosed file "Reference-Barcode Sequences, their paired internal identifiers, and the corresponding sequence placed upstream of min promoter.txt" for each allele of each sequence and its paired reporter (RNA) barcodes
Supplementary files format and content: Tab-delimited text; barcode counts for each RNA sample and the DNA sample.

source_name: Hippocampus

growth_protocol: Ad libitum feeding in single-sex group housing on 12 hour light/dark cycle.

extract_protocol:
Hippocampus dissected away from rest of brain, homogenized with power drill in glass pestle with RNAse inhibitors and translation inhibitor cycloheximide, spun 2,000g, supernatant mixed with 10% NPC and 10% DHPC 20min on ice, 20,000g spin, part of supernatant added to trizol for "input" (total hippocampal) RNA and remainder used for immunoprecipitation of GFP+ ribosomes (i.e. TRAP). See methods in paper for full details.
Reporter-specific cDNA synthesis using a reverse-complementary primer, followed by PCR, digestion, adapter ligation, and index PCR. DNA from plasmid was prepared simultaneously, starting with the first PCR step. Each step was followed by a cleanup using size-selection beads (brands Ampure XP and Magbind).

treatment_protocol: Stereotactic delivery of AAV9 to 1 hippocampal coordinate at 2 depths per side, 2µL of AAV9 per site (4 sites/mouse) 28 days prior to tissue collection. Females received either ovariectomy surgery or sham surgery prior to AAV delivery during the same surgical session.

tag: tissue (trap fraction)

value: Total hippocampus

tag: material

value: RNA

tag: condition


title: OVX_Pre_4


title: Senescence-bypass - rep1 (SENbp)

value: CAACTA


title: Donor 1, Apex, scATAC-seq

description:
10X Genomics
instrument model: Illumina NovaSeq 6000 or NextSeq 500
SP-HE-MW200804-413-ATAC
HeartAtlas_ATAC_barcodes_03092023.tsv.gz
HeartAtlas_ATAC_tilenames_03092023.tsv
HeartAtlas_ATAC_counts.mtx.gz

value: Donor 1

tag: tissue


title: Senescence-bypass - rep4 (SENbp)

tag: cell type

value: CACTCA


title: Donor 1, LV, scATAC-seq

description:
10X Genomics
instrument model: Illumina NovaSeq 6000 or NextSeq 500
SP-HE-MW200804-D-ATAC
HeartAtlas_ATAC_barcodes_03092023.tsv.gz
HeartAtlas_ATAC_tilenames_03092023.tsv
HeartAtlas_ATAC_counts.mtx.gz

value: Left ventricle


title: Primary fetal cells - rep4

description: female fetus

source_name: Individual female SHF at 13.5 days of gestation

growth_protocol: This paragraph explains the growth of the primary fetal cells and of the MT2 cell line. Fetal primary cells were isolated at 13.5-days of gestation. Fetus were washed and transferred into sterile culture dishes containing wash solution, and the differentiated organs (head, viscera, and limbs) were discarded from each fetus.  The remainder of the fetus was minced, cells were dissociated by four rounds of enzymatic digestion (Dispase, 2 U/mL in calcium magnesium free phosphate buffered saline), washed and grown (DMEM, 15% FBS, 2% antibiotics (penicillin 5000 U/mL ; streptomycin 5000 µg/mL), pH 7.0 at 37°C, 10% CO2) for 24-48 h until 60-90% confluence. Cells were detached, counted and cryopreserved (DMEM pH 7.0, 10% FBS, 10% DMSO) until needed.  Being from fetuses, the collected cells are therefore a mixture of rapidly dividing cells at different stages of differentiation (stem, progenitor, and fully differentiated) of ectodermal (e.g. skin) and mesodermal (e.g. muscle, bone, cartilage) origin, and that grow in colonies in vitro.  The MT2 cell line used here was derived from benzo[a]pyrene induced morphologically transformed (MT) colony at Bioreliance (Dr. K Pant, Boston, MA, USA).  The cell line was then transferred to Dr. RF Newbold and Dr. JC Pickles (Brunel University London, UK.  See Pickles J.C. et al. 2016. Mutat.Res.Genet.Toxicol.Environ Mutagen. 802:50-58), who generously provided the cell line to us. Here at Health Canada (Ottawa, ON) the MT2 cell line was typed as "female" using kdm5c/d qPCR test.  It was maintained in DMEM, 20% FBS, 2% antibiotics (penicillin 5000 U/mL ; streptomycin 5000 µg/mL), pH 6.7 at 37°C, 10% CO2, until the experiment.

extract_protocol:
Cells were harvested using TryplE (thermofisher), resuspended 2x with dPBS, the frozen in cell pellet.  Genomic DNA was harvested following the Qiagen DNEasy kit.
Libraries were prepared from100ng genomic DNA using Diagenode's Premiere RRBS kit (catalogue number C02030032)

treatment_protocol: Four different stocks of female primary cells (biological replicates) were thawed and used without further culture as naïve cells for genomic DNA isolation (no treatment).  To test for effects of 5aCdR, a stock of MT2 cell line was thawed and seeded. Four plates received vehicle only (0.05% DMSO as final concentration), and four others were exposed to 5aCdR (5 uM, 48h).

value: Primary fetal cells (see growth protocol)

value: no treatment

value: < 3 days, one passage


title: OVX_Pre_5


title: OVX_Pre_3


title: Donor 1, RV, scATAC-seq

description:
10X Genomics
instrument model: Illumina NovaSeq 6000 or NextSeq 500
SP-HE-MW200804-C-ATAC
HeartAtlas_ATAC_barcodes_03092023.tsv.gz
HeartAtlas_ATAC_tilenames_03092023.tsv
HeartAtlas_ATAC_counts.mtx.gz

value: Right ventricle

value: Male

value: White, European


title: Primary fetal cells - rep3

description: female fetus


title: MT2 - 5aCdR - rep1

description: Cell line typed as "female" using kdm5c/d qpcr test.

source_name: MT2 SHF cell line originally derived from a morphologically transformed clone induced by benzo[a]pyrene (5 ug/mL)

value: Colony-derived culture that bypassed senescence

value: 48 hour treatment with 5µM 5aCdR

value: estimated at passage 28

value: CAGGCG


title: OVX_Pre_2


title: Donor 1, Septum, scATAC-seq

description:
10X Genomics
instrument model: Illumina NovaSeq 6000 or NextSeq 500
SP-HE-MW200804-A-ATAC
HeartAtlas_ATAC_barcodes_03092023.tsv.gz
HeartAtlas_ATAC_tilenames_03092023.tsv
HeartAtlas_ATAC_counts.mtx.gz

value: Interventricular septum


title: MT2 - 5aCdR - rep2

value: CATGGC


title: Senescence-bypass - rep3 (SENbp)

value: colony-derived culture

value: 5µg/mL Benzo[A]Pyrene

value: CACGAT


title: MT2 - 5aCdR - rep3

value: CATTTT


title: CA1-tissue, wildtype [C57BL/6], control, biol rep 2

value: Brain, organotypic entorhino-hippocampal culture, CA1 isolate

tag: genotype

value: wildtype

value: control


title: Senescent - rep1 (SEN)

value: GTAGAG


title: Donor 3, Apex, snRNA-seq

description:
10X Genomics
instrument model: Illumina NovaSeq 6000 or NextSeq 500
HeartAtlas_RNA_barcodes_03092023.tsv.gz
HeartAtlas_RNA_genes.tsv
HeartAtlas_RNA_counts.mtx

library_source: transcriptomic single cell

data_processing:
FastQ files were individually processed using an in-house scRNA-seq pipeline dropRunner. Briefly, dropRunner utilizes FastQC to obtain quality control metrics followed by fast and efficient alignment to human reference genome hg38 using STARsolo 2.6.197 in GeneFull mode with other parameters set to default. STARsolo performs alignment and quantification of gene expression in one package.
We quantified expression at the gene level using Gencode v29 gene annotations utilizing both intronic and exonic reads to improve clustering and downstream analyses of the snRNA-seq data. We extracted the raw gene-by-barcode expression matrices output by STARsolo for downstream analyses.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

extract_protocol:
Single nuclei isolation was performed on the heart tissue aliquots as described in Litvinukova et al. 2020 (PMID:  32971526), with some modifications. Single heart aliquots were kept on dry ice until being transferred into a precooled 2 mL dounce homogenizer (Sigma) with 2 mL homogenization buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl, 1 mM dithiothreitol (DTT), 1x protease inhibitor, 0.4 U/µl, RNaseIn, 0.2 U/µl SUPERaseIn, 0.1% Triton X-100 in nuclease-free water). Samples were dounced 25 times with pestle A (loose) and 15 times with pestle B (tight), filtered through a 40-µm cell strainer, and centrifuged (500g, 5 minutes, 4ºC). Supernatant was discarded and the nuclei pellet was suspended in nuclei resuspension buffer (1x PBS, 1% BSA, 0.2 U/µL RnaseIn) and stained with NucBlue Live ReadyProbes Reagents (ThermoFisher). Hoechst-positive nuclei were enriched using fluorescence-activated cell sorting (FACS) on the FACSAria (BD Biosciences), obtaining between 172,500 and 350,000 nuclei while targeting a maximum of 350,000. Nuclei were sorted into 0.75 ml of resuspension buffer. Flow-sorted nuclei were counted in a C-Chip Disposable Hemocytometer, Neubauer Improved (INCYTO) before commencing with library preparation.
A portion of the sorted nuclei suspension was removed and brought to a concentration of between 700 and 1,200 nuclei per microliter. An appropriate number of nuclei were loaded on the Chromium controller (10X genomics) in order to target between 6,000-8,000 nuclei, according to V3 of the manufacturer’s instructions for the Chromium Next GEM Single Cell 3ʹ Reagent Kits (10X Genomics). 3’ gene expression libraries were amplified with 15 cycles during sample index PCR. QC was performed on 3’ gene expression cDNA and final libraries using a Qubit Fluorometer (ThermoFisher) and an Agilent 2100 Bioanalyzer (Agilent).
single nucleus RNA-seq library,  3' mRNA libraries (10x Genomics)

value: Donor 3

value: Apex


title: OVX_IP_6

value: RNA


title: Embryo498_1_T

city: Madison

first: Hasan

last: Khatib

state: Wisconsin

address: 1675 Observatory Dr.

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

description:
Pooled RNA sequencing
RawGeneCounts.txt

data_processing:
The FASTQ files were demultiplexed with the bcl2fastq Conversion Software (v.2.20) and checked for reads quality with the FastQC software
To trim low-quality reads and bases and remove adapter sequences, Trimmomatic was used in each sample
The trimmed reads were then aligned to the sheep reference genome (Oar_rambouillet_v1.0) using the “--quantMode GeneCounts” option to obtain gene counts.
Assembly: Oar_rambouillet_v1.0
Supplementary files format and content: Matrix tables with gene counts for all genes and all sample

organism: Ovis aries

source_name: blastocyst

extract_protocol:
Total RNA was extracted from embryos using the RNAqueous-Micro Kit (Ambion, Austin, TX, USA). DNA removal and whole transcriptome amplification were performed using the REPLI-g WTA Single Cell Kit (Qiagen, Germantown, MD, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Embryos were grouped into 12 pools based on sire and dam information, of which six pools represent the treatment group and six pools the control group, each containing five embryos

value: blastocyst

value: inner cell mass & trophectodetm

tag: treatment

value: Methionine-treated


title: Primary fetal cells - rep2

description: female fetus

value: Primary fetal cells (see growth protocol)

value: no treatment

value: < 3 days, one passage

value: GGTAGC


title: MT2 - rep4

value: Colony-derived culture that bypassed senescence

value: 48 hour treatment with vehicle (0.05% DMSO)

value: estimated at passage 28

value: CACTCA


title: Embryo511_1_T

description:
Pooled RNA sequencing
RawGeneCounts.txt


title: Embryo444_2_C

description:
Pooled RNA sequencing
RawGeneCounts.txt

value: Control


title: Donor 3, RV, snRNA-seq

value: Right ventricle

value: Male

value: White, European


title: MT2 - rep2

value: CACCGG


title: Donor 3, Septum, snRNA-seq

value: Donor 3

value: Interventricular septum


title: OVX_IP_3

value: RNA


title: Embryo444_1_C

description:
Pooled RNA sequencing
RawGeneCounts.txt

value: blastocyst

value: inner cell mass & trophectodetm


title: OVX_IP_4


title: MT2 - rep1

value: CAACTA


title: Embryo424_4_T

description:
Pooled RNA sequencing
RawGeneCounts.txt

value: Methionine-treated


title: Donor 2, Apex, snRNA-seq

value: Donor 2

value: Apex


title: Donor 2, LV, snRNA-seq

value: Left ventricle


title: FLIT mice day 21 rep3

city: Houston

first: Ziyi

last: Li

state: TX

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

data_processing:
After qPCR and RNA sequencing, reads were mapped to the UCSC Mouse Reference Genome (mm9) using STAR (v2.7).48 Reads covering gene coding regions were counted with R/Bioconductor package GenomicRanges
Genome_build: mm9
Supplementary_files_format_and_content: csv file contains raw read counts for each gene

source_name: Mice brain cortical tissue

growth_protocol: no in vitro growth

extract_protocol:
Qiagen RNA kit
RNA libraries were prepared for sequencing using standard Illumina protocols per Admera Inc

treatment_protocol: different pain models

tag: brain region

value: cortical

value: Day 21

tag: model type

value: FLIT


title: Donor 2, RV, snRNA-seq

value: Right ventricle


title: OVX_IP_1


title: OVX_IP_2


title: OVX_Pre_1

value: Total hippocampus


title: FLIT mice day 21 rep2


title: Male_Pre_12

value: Male


title: FLIT mice day 21 rep4


title: Donor 3, LV, snRNA-seq

value: White, European


title: MT2 - rep3

value: Colony-derived culture that bypassed senescence

value: 48 hour treatment with vehicle (0.05% DMSO)

tag: days in culture

value: estimated at passage 28

value: CACGAT


title: Embryo424_1_T

description:
Pooled RNA sequencing
RawGeneCounts.txt

value: blastocyst

value: inner cell mass & trophectodetm


title: Male_Pre_11

value: RNA


title: FLIT mice day 21 rep1


title: Donor 1, Apex, snRNA-seq

value: Donor 1


title: FLIT mice day 3 rep4

value: Day 3


title: Male_Pre_10


title: Embryo423_1_C

description:
Pooled RNA sequencing
RawGeneCounts.txt

value: Control


title: FLIT mice day 3 rep3

value: cortical


title: Male_Pre_9


title: Embryo410_2_C

description:
Pooled RNA sequencing
RawGeneCounts.txt


title: Donor 1, LV, snRNA-seq

value: Left ventricle


title: Donor 1, RV, snRNA-seq