title: Post-ischemia sample of left ventricle sample from patient 116V, surgery in morning

value: Post-ischemia


title: Heterozygous Ptn E/P deletion from F121-9, ESC status, replicate 2

status: Public on Feb 01 2026

type: SRA

city: San Diego

first: David

middle: M

last: Gilbert

state: CA

address: 3525 John Hopkins Ct., Ste. 200

country: USA

institute: San Diego BioMEd

description:
Library name: D9_ES_R2
nascent RNA

library_source: transcriptomic

data_processing:
Repli-seq and Bru-seq data processing methods have been described in PMC6546437. Basically, sequencing reads were mapped to mm10 then reads for 129 and cas alleles were parsed using SNPsplit.
Assembly: mm10
Supplementary files format and content: bedgraph files, featureCounts output for each allele (129 or cas)
Library strategy: BRU-Seq

molecule: total RNA

organism: Mus musculus

source_name: embryonic stem cell

growth_protocol: 2i media for mESC maintenance and RHB-A for NPC differentiation. Both have been described in PMC5991511.

extract_protocol:
Repli-seq and Bru-seq sample extraction methods have been described in PMC6546437.
Repli-seq and Bru-seq library preparation methods have been described in PMC6546437.

treatment_protocol: For tet promoter activation, doxycycline hyclate was added to the culture media (concentration and duration indicated in the file name or figre legends in PMC11838563).

tag: tissue

value: embryonic stem cell

tag: cell line

tag: batch

value: biol rep 2


title: Heterozygous Ptn E/P deletion from F121-9, ESC status, replicate 3

description:
Library name: D9_ES_R3
nascent RNA

value: biol rep 3


title: Post-ischemia sample of left ventricle sample from patient 80V, surgery in morning

city: Houston

first: Holger

middle: K.

last: Eltzschig

state: TX

department: Department of Anesthesiology

institute: The University of Texas Health Science Center at Houston

data_processing:
Alignment of RNA sequencing tags was restricted to those mapping to the same DNA strand as annotated in the GRCm38 reference genome, utilizing the STAR software. Quantification of transcripts was conducted by calculating the fragments per kilobase of transcript per million mapped reads (FPKM) values, along with transcript counts. In the preprocessing step of mRNA analysis, any gene identified as non-expressed, defined as having an FPKM expression level less than 1 in more than 80% of samples, was excluded. The normalized expression profiles of these mRNAs were then subjected to PCA for quality control and to evaluate sample similarity. Differential expression analysis was executed using the DESeq2 pipeline, with DEGs being identified based on a threshold of 1.5-fold change and an adjusted p-value below 0.05, as determined by the Benjamini-Hochberg method
Assembly: GRCm38
Supplementary files format and content: Gene quantification and differential expression

organism: Homo sapiens

source_name: Left ventricle

extract_protocol:
The AAR of the heart was harvested following 2h of reperfusion from the C57BL/6J mice subjected to myocardial IRI at either ZT8 or ZT20.
Total RNA was extracted using the RNeasy Mini kit (Qiagen) and employed to construct RNA-Seq libraries

value: Left ventricle

tag: cell type

value: AM

tag: treatment


title: CD4 T cells, collected at Baseline from Pt_19

city: Duarte

first: Jian

last: Ye

address: 1500 E Duarte Rd

department: Department of Medical Oncology and Therapeutics Research

institute: City of Hope National Medical Center

description: Library name: CD4E_109

data_processing:
Raw RNA-seq data were processed using  Partek Flow cloud-based bioinformatics platform.
Assembly: Reads were aligned to the hg38 human genome using STAR v2.7.8a with default parameters.
Supplementary files format and content: Gene-level quantification was performed using HTSeq with the annotation file hg38_ensembl_release110_v2_gene_level.transcripts, and duplicate reads were summed.

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagene)
RNA libraries for RNA-seq were prepared using polyA enrichement protocol by Novogene

treatment_protocol: PBMCs were thawed and resuspended in 1640 complete medium. Cells were stained with live/dead dye (L/D Blue, L23104) and TrueStain Fc blocker (1:100), followed by surface marker antibodies, including CD3 (BUV395, UCHT1, BD), CD4 (PerCP-Cy5.5, SK3, BioLegend), CD8 (FITC, SK1, BioLegend), CCR7 (BV421, G043H7, BioLegend), and CD45RA (APC-H7, HI100, BD). Staining was performed on ice for 60 minutes, followed by two washes with FACS buffer. Cells were resuspended in 300 μL FACS buffer, transferred to flow tubes. Sorting was performed on a BD Aria II, gating non-naïve CD4 and CD8 T cells and collecting sorted cells directly into 350 μL RLT buffer for downstream RNA extraction.

tag: group

tag: collection

value: Baseline

tag: patient id

tag: best response

value: PD

tag: pfs months


title: Homozygous Ptn E/P deletion from F121-9, ESC status,  replicate 3

description:
Library name: B8_ES_R3
nascent RNA


title: Pre-ischemia sample of left ventricle sample from patient 116V, surgery in morning

value: Pre-ischemia


title: CD4 T cells, collected at Baseline from Pt_1

description: Library name: CD4E_116


title: IMR32_CR31B_Rep3 (RIBOseq)

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

country: Belgium

institute: UGent

data_processing:
Adaptor sequence (TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC) were trimmed from RiboSeq reads using the cutadapt 3.2 with parameters (-j 10 -m 20 --discard-untrimmed).
rRNA-derived reads were identified and discarded by bowtie 2.3.4.1 with default settings.
The genes reads count were computed by RSEM v1.2.28 with default settings except using STAR 2.7.1a aligner for mapping. The reference transcripts were generated using hg38 as reference genome and GENCODE v37 as gene annotation.
Differential analysis was performed using the R package DESeq2 1.32.0.
Assembly: GRCh38
Supplementary files format and content: Transcripts Per Million (TPM) normalized counts
Library strategy: Ribo-Seq

source_name: Brain

growth_protocol: Cells were grown in complete RPMI 1640 medium (Fisher scientific, 52400041).

extract_protocol:
15µg of the lysates were treated with 7,5 units RNase I, purified with the Microspin S-400 columns and the Zymo RNA clean and concentrator kit (Zymo research, ZY-R1015). The eluted samples were size selected (28-30 nt) on a 15% PAGE urea gels.
Samples were 3' dephosphorylated with T4 PNK followed by library prep using the Small RNA library prep kit (Lexogen, 052.96). rRNA was blocked with LNA probes during the cDNA synthesis step of the library prep using the FastSelect H/M/R kit from Qiagen. Library amplification was done according to Lexogen small RNA kit. The PCR products were purified using Ampure XP beads. Library quality control was done on a DNA high sensitivity chip (BioAnalyzer Agilent, 5067-4626). Library concentrations were measured with qPCR according to Illumina's protocol. Libraries were sequenced on 2 NextSeq500 high output runs with 76bp single reads.

treatment_protocol: Cells treated with CR31B (silvestrol analog) and DMSO as control samples. After 6h, cells were treated with CHX before harvesting. Cell lysis of the cell pellets was performed using Mammalian Polysome buffer with CHX. The homogenized cell lysates were incubated for 10-30 min on ice before centrifugation (10 min, 18000g, 4°C). The cleared supernatant was recovered. The lysates were quantified using the Qubit RNA High sensitivity kit (Fisher scientific, 10034622).

value: Brain

value: neuroblast

tag: genotype

value: WT

tag: target

value: ribosome protected fragments


title: Lung, model group-2

city: Beijing

first: Jiahua

last: Wang

address: No. 16 South Xiaojie, Dongzhimennei, Dongcheng District,

department: Experimental Research Center

country: China

institute: China Academy of Chinese Medical Sciences

description:
Library name: Sample 2
QH_2

data_processing:
total RNA was extracted from the tissue samples. The concentration and purity of the RNA were detected by Nanodrop2000, the integrity of the RNA was detected by agarose gel electrophoresis, and the RIN value was determined by Agilent2100. A single library construction required a total amount of RNA ≥1ug, a concentration ≥35ng/μL, an OD260/280≥1.8, and an OD260/230≥1.0
The 3 'end of eukaryotic mRNA has the structure of ployA tail. By using magnetic beads with Oligo (dT) and ployA A-T base pairing, mRNA can be isolated from total RNA for transcriptome analysis. The next-generation high-throughput sequencing platform is designed to sequence short sequence fragments, and the enriched mRNA is a complete RNA sequence with an average length of several kb, so it needs to be interrupted randomly. With the addition of fragmentation buffer, the mRNA can be randomly broken, and small fragments of about 300bp can be separated by magnetic bead screening. Under the action of reverse transcriptase, random hexamers were added, and mRNA was used as a template to reverse synthesize one-strand cDNA, followed by two-strand synthesis to form a stable double-stranded structure. The double-stranded cDNA had A sticky End, which was complemented to a flat end by adding End Repair Mix, and then an "A" base was added to the 3 'end to connect the Y-shaped linker. The second generation high-throughput sequencing platform platform sequencing.
Assembly: mm39
Supplementary files format and content: tab-delimited text fle includes raw counts for each Samplecsvfles include FPKM values for each Sample

source_name: lung tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug oftotal 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.

value: lung tissue

value: MLF

value: Mouse lung fibroblasts


title: Homozygous Ptn E/P deletion from F121-9, ESC status,  replicate 2

description:
Library name: B8_ES_R2
nascent RNA

data_processing:
Repli-seq and Bru-seq data processing methods have been described in PMC6546437. Basically, sequencing reads were mapped to mm10 then reads for 129 and cas alleles were parsed using SNPsplit.
Assembly: mm10
Supplementary files format and content: bedgraph files, featureCounts output for each allele (129 or cas)


title: CD4 T cells, collected at Baseline from Pt_9

description: Library name: CD4E_106

value: PR


title: CD4 T cells, collected at Baseline from Pt_8

description: Library name: CD4E_107


title: Post-ischemia sample of left ventricle sample from patient 164V, surgery in morning

value: Post-ischemia


title: IL-15C induced Virtual memory T cells (n=3)

city: Seoul

first: Jaeil

last: Lee

address: 103 Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

description: Library name: IL-15C induced Virtual memory T cells

data_processing:
Raw paired-end reads were quality-checked using FastQC (v0.11.7) and trimmed with Trimmomatic (v0.38) to remove adapter sequences and low-quality bases. Cleaned reads were aligned to the Mus musculus reference genome (mm10) using HISAT2 (v2.1.0). The reference genome and annotation files were obtained from NCBI Genome Assembly and NCBI RefSeq.
Aligned reads were sorted and indexed using SAMtools (v1.9). Transcripts were assembled and quantified using StringTie (v2.1.3b). Expression levels were calculated as raw counts, FPKM, and TPM.
Low-expressed genes with zero read counts across all replicates in at least one condition were filtered out. Normalization was performed using the TMM (Trimmed Mean of M-values) method.
Differential expression analysis was conducted using edgeR’s exactTest function. P-values were adjusted by the Benjamini–Hochberg method to control the false discovery rate (FDR). Genes with |fold change| ≥ 2 and raw p-value < 0.05 were considered significantly differentially expressed genes (DEGs)
Hierarchical clustering (Euclidean distance, complete linkage) and PCA/MDS analyses were performed using R (v4.2.2). Gene enrichment and functional annotation for DEGs were performed using gProfiler with GO database terms. Adjusted p-values from enrichment tests were corrected using the Benjamini–Hochberg method.
Assembly: mm10
Supplementary files format and content: xlsx file includes FPKM, TPM, average, read count, etc for each sample.

source_name: spleen

extract_protocol:
Using anti-CD8 microbeads, CD8 T cells were isolated from splenocytes of wild-type and IL-15C–treated C57BL/6 mice by magnetic-activated cell sorting. Purified CD8 T cells were then sorted into naïve (CD44-CD49d-) and virtual memory (CD44hiCD49d-) subsets using a BD FACS Aria III cell sorter. Total RNA was extracted using the Isolate II RNA Mini Kit. Only RNA samples with RIN > 7.0 were used for downstream library construction.
Libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Prep Kit. Poly-A–containing mRNA molecules were purified using poly-T–attached magnetic beads and fragmented under elevated temperature. First-strand cDNA synthesis was performed using SuperScript II reverse transcriptase and random primers, followed by second-strand synthesis using DNA Polymerase I, RNase H, and dUTP. After end repair, A-tailing, and adapter ligation, products were purified and enriched by PCR to generate final cDNA libraries. Libraries were quantified using KAPA Library Quantification Kits and quality-checked using Agilent TapeStation D1000 ScreenTape. Indexed libraries were sequenced on an Illumina NovaSeqX platform to generate 2×100 bp paired-end reads.

treatment_protocol: Mice were treated with PBS (n=3) or IL-15 complex (IL-15+IL-15Ra) (n=3) 4 times per a week.

value: spleen

value: Virtual memory T cells

value: IL-15C treated (IL-15C)


title: CD4 T cells, collected at Baseline from Pt_24

description: Library name: CD4E_105

value: SD


title: Pre-ischemia sample of left ventricle sample from patient 164V, surgery in morning

value: Left ventricle

value: AM


title: Post-ischemia sample of left ventricle sample from patient 151V, surgery in morning


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 24hr then 24hr without doxycycline, replicate 1

description:
Library name: TP_REV_24H_R1
nascent RNA

value: embryonic stem cell

value: F121:R26puroR-M2rtTA;  Ptn^TRE

value: biol rep 1


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 12hr, replicate 2

description:
Library name: TP_12H_R2
nascent RNA

value: biol rep 2


title: IL-15C induced naïve T cells (n=3)

description: Library name: IL-15C induced naïve T cells

value: naive T cells


title: Lung, model group-3

description:
Library name: Sample 3
QH_3


title: Lung, model group-1

description:
Library name: Sample 1
QH_1


title: CD4 T cells, collected at Baseline from Pt_22

description: Library name: CD4E_108

value: Baseline

value: PD


title: Pre-ischemia sample of left ventricle sample from patient 151V, surgery in morning

value: Pre-ischemia


title: WT naïve T cells (n=3)

description: Library name: WT naïve T cells

value: Wild-type (WT)


title: Post-ischemia sample of left ventricle sample from patient 56V, surgery in morning


title: Pre-ischemia sample of left ventricle sample from patient 56V, surgery in morning


title: WT Virtual memory T cells (n=3)

description: Library name: WT Virtual memory T cells


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 12hr, replicate 1

description:
Library name: TP_12H_R1
nascent RNA


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 6hr, replicate 2

description:
Library name: TP_06H_R2
nascent RNA


title: CD4 T cells, collected at Baseline from Pt_10

description: Library name: CD4E_102


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 6hr, replicate 1

description:
Library name: TP_06H_R1
nascent RNA


title: CD4 T cells, collected at Baseline from Pt_17

description: Library name: CD4E_104

value: PR


title: CD4 T cells, collected at Baseline from Pt_25

description: Library name: CD4E_101


title: Post-ischemia sample of left ventricle sample from patient 108V, surgery in morning

value: Post-ischemia


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 24hr then 24hr without doxycycline, replicate 2

description:
Library name: TP_REV_24H_R2
nascent RNA


title: CD4 T cells, collected at Baseline from Pt_6

description: Library name: CD4E_103


title: RJA Group miRNA Sample 2

city: Changchun

first: Mingchuan

state: Jilin

address: No. 126, Xiantai Street

department: Department of Gastrointestinal Colorectal and Anal Surgery

institute: China-Japan Union Hospital of  Jilin University

description: RJA treatment sample

data_processing:
Quality Control: Raw data in FASTQ format was processed through custom perl and python scripts to remove poor-quality reads and adapter sequences. Q20, Q30, and GC-content were calculated. Reads Mapping: Small RNA tags were mapped to the reference genome using Bowtie without mismatch. miRNA Alignment: Known miRNA alignment was performed using modified mirdeep2 and srna-tools-cli. Custom scripts were used for miRNA counts and base bias analysis. Novel miRNA Prediction: miREvo and mirdeep2 were used to predict novel miRNAs by exploring secondary structure and minimum free energy. Annotation Summary: Small RNA annotation was summarized, giving priority to specific RNA types (known miRNA, rRNA, tRNA, etc.). miRNA Editing Analysis: Aligning sRNA tags to mature miRNA to detect potential base edits. Target Gene Prediction: Target genes of miRNAs were predicted using psRobot_tar for plants or miRanda for animals. Quantification of miRNA: miRNA expression levels were estimated by TPM. Differential Expression Analysis: Performed using DESeq or DEGseq depending on the presence of biological replicates. GO and KEGG Enrichment Analysis: Performed using GOseq and KOBAS software.
Assembly: genome
Supplementary files format and content: File: Readcount_TPM.xls Content Description: The Readcount_TPM.xls file is a comprehensive annotation file that details the features of the genome used in this study. It includes information about the locations and attributes of genes, exons, promoters, and other genomic elements. This file is essential for the alignment and annotation of small RNA sequencing data, particularly for the identification and quantification of miRNAs and their target sites. It serves as a reference for read mapping and differential expression analysis, allowing for accurate genomic localization of miRNA sequences and their corresponding genomic features. The GTF format enables compatibility with various bioinformatics tools used for sequencing data analysis, including those for read alignment (like Bowtie), miRNA prediction, and gene annotation.

source_name: Colon

extract_protocol:
miRNA was extracted using the NEB Next® Multiplex Small RNA Library Prep Set for Illumina®. The quality and integrity of the extracted RNA were assessed using an Agilent 2100 Bioanalyzer.
Briefly, 3’ and 5’ adaptors were ligated to the ends of small RNA. First strand cDNA was synthesized followed by PCR enrichment to generate the double-stranded cDNA library. After purification and size selection, libraries with insertions between 18~40 bp were prepared for Illumina sequencing with SE50.

treatment_protocol: Control Group: Mice received normal diet and water. DSS Group: Mice received normal diet and 2.5% (w/v) DSS in drinking water. RJA Group: Mice received normal diet, 2.5% (w/v) DSS in drinking water, and 0.2 mL of RJA (10 mg/kg bw) by daily gavage.

value: Colon

value: Wild-type

value: RJA Treatment


title: un-damaged cartilage5

city: Harbin

first: Yong

last: Zhou

address: 37 Yiyuan Street

institute: The Fourth Affiliated Hospital of Harbin Medical University

description:
Library name: SAMPLE10
UDC5

data_processing:
Original sequence data
Sequencing data filtering
Distribution of sequencing error rates
GC content distribution
Data Quality Summary
Assembly: Quantify the expression levels of the known transcripts and predicted Novel LncRNA, Novel mRNA, and Unclassified transcripts obtained from the above comparison, splicing, and screening
Supplementary files format and content: lnc_transcripts.FPKM.txt

source_name: cartilage

extract_protocol: Firstly, ribosomal RNA is removed from the total RNA, and then RNase R enzyme is used to break the RNA into short fragments of 250-300 bp. The fragmented RNA is used as a template, and random oligonucleotides are used as primers to synthesize the first strand of cDNA. Subsequently, RNase H is used to degrade the RNA strand, and dNTPs (dUTP, dATP, dGTP, and dCTP) are used as raw materials to synthesize the second strand of cDNA in the DNA polymerase I system. The purified double stranded cDNA was subjected to end repair, followed by the addition of an A-stail and sequencing adapter connection. The cDNA with a size of around 350-400 bp was screened using AMPure XP beads. Use USER enzyme to degrade the second strand of cDNA containing U, and finally perform PCR amplification to obtain a library.

value: cartilage


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 3hr, replicate 2

description:
Library name: TP_03H_R2
nascent RNA


title: RJA Group miRNA Sample 3

description: RJA treatment sample


title: Pre-ischemia sample of left ventricle sample from patient 108V, surgery in morning

value: Left ventricle


title: RJA Group miRNA Sample 1

description: RJA treatment sample


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 3hr, replicate 1

description:
Library name: TP_03H_R1
nascent RNA


title: Pre-ischemia sample of left ventricle sample from patient 93V, surgery in afternoon

value: PM


title: Normal Group miRNA Sample 3

description: Control sample

value: Normal Diet


title: Pre-ischemia sample of left ventricle sample from patient 73V, surgery in afternoon


title: un-damaged cartilage3

description:
Library name: SAMPLE8
UDC3


title: un-damaged cartilage4

description:
Library name: SAMPLE9
UDC4


title: Post-ischemia sample of left ventricle sample from patient 145V, surgery in morning

value: AM


title: TRE promoter upstream of Ptn gene, 16000ng/mL doxycycline, replicate 6

description:
Library name: TP_D1600_R2
nascent RNA

value: embryonic stem cell

value: F121:R26puroR-M2rtTA;  Ptn^TRE

value: biol rep 6


title: TRE promoter upstream of Ptn gene, 16000ng/mL doxycycline, replicate 5

description:
Library name: TP_D1600_R1
nascent RNA

value: biol rep 5


title: Normal Group miRNA Sample 1

description: Control sample


title: un-damaged cartilage2

description:
Library name: SAMPLE7
UDC2


title: Normal Group miRNA Sample 2

description: Control sample


title: DSS Group miRNA Sample 3

description: DSS-induced colitis sample

value: DSS Treatment


title: TRE promoter upstream of Ptn gene, 8000ng/mL doxycycline, replicate 6

description:
Library name: TP_D0800_R2
nascent RNA


title: Pre-ischemia sample of left ventricle sample from patient 145V, surgery in morning

value: Pre-ischemia


title: un-damaged cartilage1

description:
Library name: SAMPLE6
UDC1


title: TRE promoter upstream of Ptn gene, 8000ng/mL doxycycline, replicate 5

description:
Library name: TP_D0800_R1
nascent RNA


title: DSS Group miRNA Sample 2

description: DSS-induced colitis sample


title: Pre-ischemia sample of left ventricle sample from patient 156V, surgery in afternoon


title: damaged cartilage4

description:
Library name: SAMPLE4
DC4


title: DSS Group miRNA Sample 1

description: DSS-induced colitis sample


title: damaged cartilage5

description:
Library name: SAMPLE5
DC5


title: Post-ischemia sample of left ventricle sample from patient 120V, surgery in afternoon


title: damaged cartilage3

description:
Library name: SAMPLE3
DC3


title: RJA Group Sample 3

description: RJA treatment sample

data_processing:
Quality control was performed using fastp software to remove adapter sequences, reads containing N bases, and low-quality reads from the raw data, generating clean reads.  Reads were then aligned to the reference genome using Hisat2 (v2.0.5).  Gene expression levels were quantified using featureCounts (v1.5.0-p3), calculating FPKM for each gene.  Differential expression analysis was conducted using DESeq2 R package (1.20.0) or edgeR R package (3.22.5), applying thresholds of padj <= 0.05 and |log2(fold change)| >= 1 for significant differential expression.
Assembly: mm10
Supplementary files format and content: The processed data file named as "gene_fpkm.xls", containing aligned sequence reads.

extract_protocol:
Total RNA was extracted and its quantity and quality were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material.  mRNA was purified using poly-T oligo-attached magnetic beads.  Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X).  First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase.  RNA was degraded using RNaseH.  Second strand cDNA synthesis was performed using DNA Polymerase I and dNTP.  Overhangs were converted into blunt ends via exonuclease/polymerase activities.  After adenylation of 3’ ends, adaptors with hairpin loop structures were ligated.  cDNA fragments of 370~420 bp were selected using the AMPure XP system.  PCR amplification was performed, and PCR products were purified with AMPure XP beads to obtain the final library.


title: TRE promoter upstream of Ptn gene, 4000ng/mL doxycycline, replicate 3

description:
Library name: TP_D0400_R3
nascent RNA

value: biol rep 3


title: Post-ischemia sample of left ventricle sample from patient 156V, surgery in afternoon


title: damaged cartilage2

description:
Library name: SAMPLE2
DC2


title: TRE promoter upstream of Ptn gene, 4000ng/mL doxycycline, replicate 5

description:
Library name: TP_D0400_R1
nascent RNA


title: TRE promoter upstream of Ptn gene, 4000ng/mL doxycycline, replicate 6

description:
Library name: TP_D0400_R2
nascent RNA


title: Post-ischemia sample of left ventricle sample from patient 126V, surgery in afternoon


title: damaged cartilage1

description:
Library name: SAMPLE1
DC1


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline, replicate 5

description:
Library name: TP_D0200_R5
nascent RNA


title: Pre-ischemia sample of left ventricle sample from patient 126V, surgery in afternoon


title: RJA Group Sample 1

description: RJA treatment sample


title: RJA Group Sample 2

description: RJA treatment sample


title: HB4_mono_resistin_24hrs

city: Manchester

first: Kiran

last: Batta

address: The University of Manchester

country: United Kingdom

institute: University of Manchester

description: Library name: Sample 28

data_processing:
FASTQ files were quality assessed and aligned via STAR (v2.5.1b) to human GENCODE reference transcriptome (v42; GRCh38.p13/hg38). Reads quantification was performed using Salmon (v1.10.2) in alignment-based mode and gene-level abundances (TPM and raw counts) estimated with TxImport (v1.30.0). DEseq2 was used to perform differential gene expression analysis and calculate rlog (regularized log transformation) normalized read values for each gene (Love et al., 2014).
Assembly: GENCODE (v42; GRCh38.p13/hg38)
Supplementary files format and content: Processed files were saved in CSV (comma separated values) format. The "Tximport_raw_countmat.csv" file includes gene-level quantified reads obtained from TxImport following transcript-level quantification with Salmon (tximport function with type="salmon", tx2gene=tx2gene, txIn = TRUE, txOut = FALSE and countsFromAbundance = 'no'). The "Tximport_TPM_mat.csv" file contains gene-level abundance derived as per the "Tximport_raw_countmat.csv" file. The "DESeq2_rlog_normalised_countmat.csv" file are counts imported in DESeq2 (DESeqDataSetFromTximport function), filtered to remove non-informative/duplicated genes, and subsequently normalized (rlog function).

source_name: PBMNCs

growth_protocol: CD14+ cells were isolated from fresh healthy volunteer PBMCs and cultured in 12 well plates at a density of 5 x 105 cells/ml in RPMI, 10% FBS, 1% penicillin-streptomycin 10 ng/ml M-CSF for 6 and 24 hours.

extract_protocol:
RNA was isolated using RNeasy Micro Plus kit (QIAGEN, 74034), according to manufacturer’s recommendations.
Libraries were generated using the NEB Next Ultra II (pA) RNA (E7770, New England Biolabs) kit following a 10ng input workflow. Libraries (1x101bp) were sequenced using the NovaSeq 6000 sequencing system (Illumina), installed with SP type flow cells.

treatment_protocol: 250 ng/ml GFP or Resistin or 100 ng/ml LPS for 6 and 24 hours

value: PBMNCs

value: Monocytes

value: Healthy Volunteer

value: resistin

tag: time point


title: Pre-ischemia sample of left ventricle sample from patient 120V, surgery in afternoon


title: Post-ischemia sample of left ventricle sample from patient 100V, surgery in morning

value: Post-ischemia


title: Normal Group Sample 3

description: Control sample

value: Colon

value: Wild-type


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline, replicate 4

description:
Library name: TP_D0200_R4
nascent RNA

value: biol rep 4


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline, replicate 3

description:
Library name: TP_D0200_R3
nascent RNA


title: Normal Group Sample 2

description: Control sample

value: Normal Diet


title: HB4_mono_resistin_6hrs

description: Library name: Sample 27


title: HB4_mono_LPS_24hrs

description: Library name: Sample 26

value: LPS


title: Normal Group Sample 1

description: Control sample


title: HB4_mono_LPS_6hrs

description: Library name: Sample 25


title: Pre-ischemia sample of left ventricle sample from patient 74V, surgery in morning

value: Left ventricle

value: AM


title: DSS Group Sample 3

description: DSS-induced colitis sample


title: TRE promoter upstream of Ptn gene, 500ng/mL doxycycline, replicate 6

description:
Library name: TP_D0050_R6
nascent RNA

value: embryonic stem cell

value: F121:R26puroR-M2rtTA;  Ptn^TRE

value: biol rep 6


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline, replicate 1

description:
Library name: TP_D0200_R1
nascent RNA

value: biol rep 1


title: HB4_mono_control_24hrs

description: Library name: Sample 24

value: control


title: DSS Group Sample 2

description: DSS-induced colitis sample

value: DSS Treatment


title: Pre-ischemia sample of left ventricle sample from patient 100V, surgery in morning

value: Pre-ischemia


title: TRE promoter upstream of Ptn gene, 500ng/mL doxycycline, replicate 5

description:
Library name: TP_D0050_R5
nascent RNA

value: biol rep 5


title: Pre-ischemia sample of left ventricle sample from patient 152V, surgery in morning


title: HB4_mono_untreated_0hrs

description: Library name: Sample 22

value: PBMNCs

value: Monocytes

value: Healthy Volunteer

value: untreated


title: Post-ischemia sample of left ventricle sample from patient 152V, surgery in morning

value: Post-ischemia


title: DSS Group Sample 1

description: DSS-induced colitis sample

value: Colon

value: Wild-type


title: HB4_mono_control_6hrs

description: Library name: Sample 23


title: TRE promoter upstream of Ptn gene, 500ng/mL doxycycline, replicate 4

description:
Library name: TP_D0050_R4
nascent RNA

value: biol rep 4


title: Post-ischemia sample of left ventricle sample from patient 74V, surgery in morning

value: Left ventricle

value: AM


title: Post-ischemia sample of left ventricle sample from patient 114V, surgery in afternoon

value: PM


title: HB3_mono_resistin_24hrs

description: Library name: Sample 21

value: resistin


title: IBD_841565, colon

city: Chapel Hill

first: Terrence

last: Furey

state: North Carolina

address: 120 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

description: Library name: IBD_841565

data_processing:
A decoy-aware index was built using a concatenated transcriptome of GENCODE v39 and the predicted lncRNAs using salmon index (salmon v.1.6.0)
RNA-seq data was quantified using salmon quant (salmon v.1.6.0) in mapping-based mode.
Assembly: hg38; reads were assembled with GENCODE v39, concatenated with the set of predicted lncRNAs (coordinates are in supplementary GTF file)
Supplementary files format and content: Tab-delimited text file includes raw count data for each sample from Salmon quantification
Supplementary files format and content: Tab-delimited text file includes TPM-normalized count data for each sample from Salmon quantification
Supplementary files format and content: GTF file includes transcript and exon feature annotations for the predicted lncRNA set

molecule: polyA RNA

source_name: colon

extract_protocol:
Samples were collected and stored in RNA-later from macroscopically non-inflamed sections of colonic mucosa for patients undergoing colonoscopy or surgical resection. RNA was isolated using the Qiagen RNeasy Mini Kit.
Total RNA libraries were constructed with the Kapa Total RNA Stranded with Ribo Erase; PolyA libraries were constructed with the Illumina TruSeq polyA+ Sample Prep Kit

value: colon

value: C

tag: inflammation

value: uninflamed

tag: disease status

value: CD

tag: Sex

value: Female


title: TRE promoter upstream of Ptn gene, 250ng/mL doxycycline, replicate 5

description:
Library name: TP_D0025_R5
nascent RNA

value: embryonic stem cell

value: F121:R26puroR-M2rtTA;  Ptn^TRE

value: biol rep 5


title: Pre-ischemia sample of left ventricle sample from patient 114V, surgery in afternoon

value: Pre-ischemia


title: HB3_mono_resistin_6hrs

description: Library name: Sample 20

value: PBMNCs

value: Monocytes

value: Healthy Volunteer


title: IBD_696153, colon

description: Library name: IBD_696153

value: A

value: Male


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline, replicate 6

description:
Library name: TP_D0200_R6
nascent RNA

value: biol rep 6


title: IBD_826347, colon

description: Library name: IBD_826347

value: NIBD


title: IBD_154488, colon

description: Library name: IBD_154488

value: D


title: TRE promoter upstream of Ptn gene, 500ng/mL doxycycline, replicate 1

description:
Library name: TP_D0050_R1
nascent RNA

value: biol rep 1


title: Post-ischemia sample of left ventricle sample from patient 105V, surgery in morning

value: Left ventricle

value: AM

value: Post-ischemia


title: TRE promoter upstream of Ptn gene, 250ng/mL doxycycline, replicate 3

description:
Library name: TP_D0025_R3
nascent RNA

value: biol rep 3


title: HB3_mono_LPS_6hrs

description: Library name: Sample 18

value: LPS


title: HB3_mono_LPS_24hrs

description: Library name: Sample 19


title: Pre-ischemia sample of left ventricle sample from patient 84V, surgery in morning


title: IBD_282646, colon

description: Library name: IBD_282646

value: colon

value: C

value: uninflamed

value: Female


title: HB3_mono_control_24hrs

description: Library name: Sample 17

value: PBMNCs

value: Monocytes

value: control


title: Pre-ischemia sample of left ventricle sample from patient 105V, surgery in morning

value: Pre-ischemia


title: Post-ischemia sample of left ventricle sample from patient 161V, surgery in morning


title: Pre-ischemia sample of left ventricle sample from patient 161V, surgery in morning


title: TRE promoter upstream of Ptn gene, 250ng/mL doxycycline, replicate 4

description:
Library name: TP_D0025_R4
nascent RNA

value: embryonic stem cell

value: F121:R26puroR-M2rtTA;  Ptn^TRE

value: biol rep 4


title: HB3_mono_control_6hrs

description: Library name: Sample 16

value: Healthy Volunteer


title: HB3_mono_untreated_0hrs

description: Library name: Sample 15

value: untreated


title: TRE promoter upstream of Ptn gene, 250ng/mL doxycycline, replicate 1

description:
Library name: TP_D0025_R1
nascent RNA

value: biol rep 1


title: IBD_671530, colon

description: Library name: IBD_671530

value: A

value: CD


title: IBD_929366, colon

description: Library name: IBD_929366

value: B

value: NIBD


title: Post-ischemia sample of left ventricle sample from patient 31V, surgery in afternoon

value: Left ventricle

value: PM

value: Post-ischemia


title: TRE promoter upstream of Ptn gene, 500ng/mL doxycycline, replicate 3

description:
Library name: TP_D0050_R3
nascent RNA

value: biol rep 3


title: IBD_116783, colon

description: Library name: IBD_116783

value: colon

value: uninflamed

value: Female


title: DAOY_IFNa2_noninfected

city: Paris

first: Felix

last: Streicher

address: Rue du Dr. Roux 25-28

country: France

institute: Institut Pasteur

description: Library name: D_2

library_source: genomic

data_processing:
Reads were demultiplexed using quality-aware fastq demultiplexer v0.1.1.
Sequencing adapters were removed using trimmomatic v0.39.
Read mapping was performed with bowtie2 and samtools v2.0.4.
Mapping analysis and gene selection were performed using MAGeCK v0.5.9, normalizing the data with default parameters.
Assembly: hg38
Supplementary files format and content: .txt files listing sgRNA read counts
Library strategy: CRISPR Screen

molecule: genomic DNA

source_name: brain

extract_protocol:
DNA was isolated with two consecutive phenol-chloroform extractions and recovered by ethanol precipitation.
a PCR reaction using barcoded primers to allow for demultiplexing of the samples after sequencing was performed using the Herculase II Fusion DNA Polymerase (Agilent) and DNA oligos. The resultant PCR products were purified using a QIAquick PCR Purification kit (Qiagen, 28104) and subjected to a second PCR before being purified using Agencourt AMPure XP Beads (Beckman Coulter Life Sciences).

treatment_protocol: In total, 1.3 × 107 Caco2 or DAOY cells were treated with IFNλ1 (Caco2, 100 ng/mL) or IFNα2 (DAOY, 100 U/mL). After 16 h, cells were infected with TBEV-Hypr at an MOI of 1 in DMEM (2% FBS, 1% P/S). After 2h, the viral inoculum was removed, washed once with PBS, and cells were maintained in DMEM containing 10% FBS and 1% P/S for 24 h. Thereafter, cells were collected and fixed using the fixation buffer supplied with the Cytofix/Cytoperm™ fixation and permeabilization kit (BD Pharmigen). Fixed cells were washed in cold Cytoperm buffer and then incubated for 1 h at 4 °C under rotation with primary antibody (4G2, mouse, 1:1000) in the same buffer. Incubation with the secondary antibody (Alexa 488 anti-mouse, 1:10000) was performed for 45 min at 4 °C under rotation. Stained cells were resuspended in cold sorting buffer containing PBS, 2% FBS, 25 mM Hepes, and 5 mM EDTA. Cells were sorted into infected and non-infected cells using a BD FACS Aria Fusion machine. Sorted and control (non-infected, not IFN-treated) cells were then centrifuged for 20 min at 2000xg and resuspended in lysis buffer (NaCI 300 mM, SDS 0.1%, EDTA 10 mM, EGTA 20 mM, Tris 10 mM) supplemented with 1% Proteinase K (Qiagen) and 1% RNAse A/T1 (Sigma) and incubated overnight at 65 °C.

value: brain

value: DAOY

value: medulloblastoma

value: 16h IFN, 24h TBEV-Hypr


title: HB2_mono_LPS_24hrs

description: Library name: Sample 12

value: PBMNCs

value: Monocytes

value: Healthy Volunteer

value: LPS


title: TRE promoter upstream of Ptn gene, 100ng/mL doxycycline, replicate 1

description:
Library name: TP_D0010_R1
nascent RNA

value: embryonic stem cell

value: F121:R26puroR-M2rtTA;  Ptn^TRE

value: biol rep 1


title: DAOY_IFNa2_infected

description: Library name: D_1


title: HB2_mono_resistin_6hrs

description: Library name: Sample 13

value: resistin


title: IBD_870288, colon

description: Library name: IBD_870288

value: D

value: NIBD

value: Male


title: TRE promoter upstream of Ptn gene, 100ng/mL doxycycline, replicate 5

description:
Library name: TP_D0010_R5
nascent RNA

value: biol rep 5


title: TRE promoter upstream of Ptn gene, 100ng/mL doxycycline, replicate 6

description:
Library name: TP_D0010_R6
nascent RNA

value: biol rep 6


title: TRE promoter upstream of Ptn gene, 100ng/mL doxycycline, replicate 3

description:
Library name: TP_D0010_R3
nascent RNA

value: biol rep 3


title: Post-ischemia sample of left ventricle sample from patient 69V, surgery in morning

value: Left ventricle

value: AM

value: Post-ischemia


title: Pre-ischemia sample of left ventricle sample from patient 31V, surgery in afternoon

value: PM

value: Pre-ischemia


title: Caco2_mock

description: Library name: C_3

source_name: intestine

value: intestine

value: colorectal adenocarcinoma


title: TRE promoter upstream of Ptn gene, 100ng/mL doxycycline, replicate 4

description:
Library name: TP_D0010_R4
nascent RNA

value: embryonic stem cell

value: biol rep 4


title: Pre-ischemia sample of left ventricle sample from patient 69V, surgery in morning


title: Post-ischemia sample of left ventricle sample from patient 133V, surgery in afternoon


title: TRE promoter upstream of Ptn gene, no doxycycline, replicate 5

description:
Library name: TP_D0000_R5
nascent RNA

value: F121:R26puroR-M2rtTA;  Ptn^TRE


title: HB2_mono_LPS_6hrs

description: Library name: Sample 11

value: PBMNCs

value: Monocytes

value: Healthy Volunteer

value: LPS


title: TRE promoter upstream of Ptn gene, no doxycycline, replicate 6

description:
Library name: TP_D0000_R6
nascent RNA


title: Pre-ischemia sample of left ventricle sample from patient 104V, surgery in afternoon


title: Caco2_IFNl1_noninfected

description: Library name: C_2

value: 16h IFN, 24h TBEV-Hypr


title: HB2_mono_control_24hrs

description: Library name: Sample 10

value: control


title: DAOY_mock

description: Library name: D_3

value: brain

value: DAOY

value: medulloblastoma


title: TRE promoter upstream of Ptn gene, no doxycycline, replicate 1

description:
Library name: TP_D0000_R1
nascent RNA

value: biol rep 1


title: HB2_mono_untreated_0hrs

description: Library name: Sample 8

value: untreated


title: HB2_mono_resistin_24hrs

description: Library name: Sample 14

value: resistin


title: Pre-ischemia sample of left ventricle sample from patient 133V, surgery in afternoon

value: Left ventricle

value: PM

value: Pre-ischemia


title: HB1_mono_LPS_24hrs

description: Library name: Sample 5


title: HB1_mono_resistin_6hrs

description: Library name: Sample 6


title: Pre-ischemia sample of left ventricle sample from patient 139V, surgery in morning

value: AM


title: Post-ischemia sample of left ventricle sample from patient 79V, surgery in afternoon

value: Post-ischemia


title: Pre-ischemia sample of left ventricle sample from patient 79V, surgery in afternoon


title: TRE promoter upstream of Ptn gene, no doxycycline, replicate 3

description:
Library name: TP_D0000_R3
nascent RNA

value: embryonic stem cell

value: F121:R26puroR-M2rtTA;  Ptn^TRE

value: biol rep 3


title: HB1_mono_control_24hrs

description: Library name: Sample 3

value: PBMNCs

value: Monocytes

value: Healthy Volunteer


title: HB2_mono_control_6hrs

description: Library name: Sample 9

value: control


title: Pre-ischemia sample of left ventricle sample from patient 70V, surgery in afternoon


title: activated TRE promoter upstream of Ptn gene,  replicate 3

description:
Library name: TRE_Ptn_Dox_Rep3
nascent RNA

value: F121:R26puroR-M2rtTA;  Ptn^CAG


title: HB1_mono_resistin_24hrs

description: Library name: Sample 7


title: Caco2_IFNl1_infected

description: Library name: C_1

value: intestine

value: colorectal adenocarcinoma

value: 16h IFN, 24h TBEV-Hypr


title: activated TRE promoter upstream of Ptn gene,  replicate 2

description:
Library name: TRE_Ptn_Dox_Rep2
nascent RNA

value: biol rep 2


title: HPC7_Empty_ChIP_GATA2_rep3

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

institute: Weatheral Institute of Molecular Medicine

description: Library name: HPC7_Empty_rep3

data_processing:
Reads were aligned with Bowtie2 (version 2.4.1)
SAM files were converted to BAM files and PCR duplicate reads were filtered out using SAMtools (version 1.17)
Peak calling was performed using MACS2 (version 2.1.2)
Unique reads mapped to these regions were quantified using featuresCounts (version 2.0.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts for each sample

extract_protocol:
ChIP-seq based protocol
NEBNext® Ultra™ II DNA Library Prep Kit


title: HPC7_Lmo4_Input

description: Library name: HPC7_Lmo4_Input


title: Post-ischemia sample of left ventricle sample from patient 139V, surgery in morning

value: Left ventricle


title: Post-ischemia sample of left ventricle sample from patient 44V, surgery in morning


title: HPC7_Empty_Input

description: Library name: HPC7_Empty_Input


title: Pre-ischemia sample of left ventricle sample from patient 44V, surgery in morning


title: non-activated TRE promoter upstream of Ptn gene,  replicate 2

description:
Library name: TRE_Ptn_Rep2
nascent RNA


title: non-activated TRE promoter upstream of Ptn gene,  replicate 3

description:
Library name: TRE_Ptn_Rep3
nascent RNA


title: HB1_mono_LPS_6hrs

description: Library name: Sample 4

value: LPS


title: HPC7_Lmo4_ChIP_GATA2_rep3

description: Library name: HPC7_Lmo4_rep3


title: HPC7_Lmo4_ChIP_GATA2_rep2

description: Library name: HPC7_Lmo4_rep2


title: non-activated TRE promoter upstream of Ptn gene,  replicate 1

description:
Library name: TRE_Ptn_Rep1
nascent RNA

value: biol rep 1


title: HPC7_Lmo4_ChIP_GATA2_rep1

description: Library name: HPC7_Lmo4_rep1


title: Post-ischemia sample of left ventricle sample from patient 163V, surgery in afternoon

value: PM


title: mPGK promoter upstream of Ptn gene, replicate2

description:
Library name: mPGK_Ptn_Rep2
nascent RNA

value: F121:R26puroR-M2rtTA;  Ptn^mPGK


title: ME180 clone A40

city: Chicago

first: Jelena

last: Popovic

state: IL

address: 300 E Superior St. Tarry 4-770

department: Radiation Oncology

institute: Northwestern University

description: Library name: ME180 clone A40

data_processing:
Processed BAM files were cleaned, sorted, and marked for duplicates with Picard Tools (version 1.85) and further filtered using the TruSeq_Exome_TargetedRegions_v1.2.bed file. Variants were detected using bcftools mpileup4 with minimum base quality and maximum depth parameters set to 20 and 1000, respectively; VCF files were filtered for quality and depth of 20 and 10, annotated with SnpEff (version 4.3), and analyzed for mutational patterns with the MutationalPatterns package in RStudio.
Assembly: hg38
Supplementary files format and content: vcf files

source_name: CRISPR/Cas9 single cell clone

growth_protocol: ME180 cervical cancer cell line was purchased from ATCC® (HTB-33) and maintained in McCoy’s medium (Sigma-Aldrich, MO, United States) supplemented with 10% fetal bovine serum (FBS) (Gibco, United States), 1x antibiotic antimycotic (Sigma-Aldrich, MO, United States), 1x essential amino acids, 1mM glutamine.

extract_protocol:
Genomic DNA of selected clones was isolated using Pure Link genomic DNA Mini kit (Invitrogen, MA, United States), and quality and concentration were assessed using NanoDrop spectrophotometer
Libraries were constructed with 100 ng of QC-passed gDNA using the Illumina TruSeq Exome Library Prep Kit, hybridized to exome oligo probes with unique barcoding, validated with Qubit and Bioanalyzer, and sequenced on an Illumina NovaSeq NGS System to generate paired-end 150 bp reads.

value: cervical cancer


title: HB1_mono_control_6hrs

description: Library name: Sample 2


title: hPGK promoter upstream of Ptn gene, replicate 3

description:
Library name: hPGK_Ptn_Rep3
nascent RNA

value: embryonic stem cell

value: Ptn^hPGK


title: HB1_mono_untreated_0hrs

description: Library name: Sample 1

value: PBMNCs

value: untreated


title: activated TRE promoter upstream of Ptn gene,  replicate 1

description:
Library name: TRE_Ptn_Dox_Rep1
nascent RNA


title: HPC7_Empty_ChIP_GATA2_rep2

description: Library name: HPC7_Empty_rep2


title: HPC7_Empty_ChIP_GATA2_rep1

description: Library name: HPC7_Empty_rep1


title: mPGK promoter upstream of Ptn gene, replicate1

description:
Library name: mPGK_Ptn_Rep1
nascent RNA


title: ME180 clone IX44

description: Library name: ME180 clone IX44


title: IRF8KO_microglia_3mo_male_rep1

city: Bethesda

first: Keita

last: Saeki

state: Maryland

address: 6 Center Drive

institute: NIH/NICHD

description: Library name: RNASeq_Sample_4

data_processing:
Basecalls performed using bcl2fastq without the acceptance of index mismatch
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR v2.5.2b.
Sequence duplicates were removed using Picard v2.17.11. Aligned tags were counted with Subread featureCounts. All steps are packaged in CCBR/Pipeliner.
Assembly: mm10
Supplementary files format and content: tab-delimited text files consist of Read count per gene

source_name: microglia

growth_protocol: In vivo microglia from each brain were non-enzymatically isolated.

extract_protocol:
Microglia were FACS-sorted directly in TRIzol and stored until usage. Total RNA was purified by phase extraction.
The cDNA was synthesized using SMART-Seq v4 Ultra Low Input RNA Kit (Takara bio USA, CA) with 15-cycle amplification. Adaptors were added to 1ng cDNA using the Nextera XT library prep kit (Illumina, CA).

value: microglia


title: Pre-ischemia sample of left ventricle sample from patient 163V, surgery in afternoon

value: Pre-ischemia


title: Post-ischemia sample of left ventricle sample from patient 115V, surgery in morning

value: AM

value: Post-ischemia


title: ME180 clone A13

description: Library name: ME180 clone A13


title: ME180 clone II21

description: Library name: ME180 clone II21


title: IRF8KO_microglia_3mo_male_rep3

description: Library name: RNASeq_Sample_6


title: ME180 clone VII11

description: Library name: ME180 clone VII11


title: Pre-ischemia sample of left ventricle sample from patient 62V, surgery in morning


title: Post-ischemia sample of left ventricle sample from patient 62V, surgery in morning


title: hPGK promoter upstream of Ptn gene, replicate1

description:
Library name: hPGK_Ptn_Rep1
nascent RNA


title: WT_microglia_3mo_male_rep2

description: Library name: RNASeq_Sample_2

value: WT


title: CAG promoter upstream of Ptn gene, replicate 2

description:
Library name: CAG_Ptn_Rep2
nascent RNA

value: F121:R26puroR-M2rtTA;  Ptn^CAG


title: HygTK expression cassette with TRE promoter at Ptn locus, TRE not activated, nascent RNA, replicate 2

description:
Library name: TRE_HTK_Rep2
nascent RNA

value: F121:R26puroR-M2rtTA;  Ptn^TRE-Hyg-TK/+

value: biol rep 2


title: Pre-ischemia sample of left ventricle sample from patient 115V, surgery in morning

value: Left ventricle


title: ME180 wt

description: Library name: ME180 wt

source_name: wild type cell line

value: wild type


title: WT_microglia_3mo_male_rep3

description: Library name: RNASeq_Sample_3


title: hPGK promoter upstream of Ptn gene, replicate 2

description:
Library name: hPGK_Ptn_Rep2
nascent RNA


title: WT_microglia_3mo_male_rep1

description: Library name: RNASeq_Sample_1


title: CAG promoter upstream of Ptn gene, replicate 1

description:
Library name: CAG_Ptn_Rep1
nascent RNA

value: biol rep 1


title: A549 cells, si-AUH3

city: Nanjing

first: Huimin

last: Ma

address: 101 Longmian Avenue, Jiangning District, Nanjing City

department: School of Public Health

institute: nanjin medical university

description: Library name: Sample 6

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped toTrimmed sequence reads were mapped to GRCh38/hg38 using CLC genomic benchwork(parameters- mismath cost: 2 insertion cost. 3 deletion cost. 3 length fraction: 0.8 similarity fraction.0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: txt file contains FPKM values for all samples

growth_protocol: A549 cells were maintained in 1640 supplemented with 10% fetal bovineserum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was extracted using the Trizol(Ambion/Invitrogen, USA), and total RNA was used to construct a sequencing library.
The reagent kit used for library construction is NEBNext ®  Ultra ™  Directional RNA Library Prep Kit for Illumina ®.

treatment_protocol: Transfect A549 cells with siRNA targeting AUH or control siRNA. The experiment consisted of two groups: (1) control A549 cells, and (2) AUH knockdown A549 cells. Each group includes 3 biological replicates, totaling 6 samples. After transfection for 48 hours, RNA was extracted from all 6 samples and sequenced to compare the transcriptome changes induced by AUH knockdown.

value: Non-small cell lung cancer cells

value: AUH knockdown

value: Small interference transfection


title: Post-ischemia sample of left ventricle sample from patient 111V, surgery in morning


title: Mice KO claudin 10 rep 2 ST

city: Montrouge

first: Caroline

last: Andrique

address: 1 rue Maurice Arnoux

department: UFR Odontologie

institute: Université Paris Cité

description:
Library name: KO1-ST-Groupe3
NGS21-052_ensemblGRCm38r101_ST_noOutlier_deseq2_NormalizedMatrix.tsv

data_processing:
AOZAN software based on FastQC modules/version 0.11.5
STAR algorithm (version 2.5.2b)
Picard tools (version 2.8.1)
Featurecount (version Rsubread 1.24.1)
DESeq. 2 package version 1.14.1
Assembly: Ensembl release 101, Mus musculus GRCm38
Supplementary files format and content: Tab delimited text file includes raw counts for each samples
Supplementary files format and content: tsv files includes log fold change for each samples

source_name: hemi mandible

growth_protocol: Frozen Slides of hemi mandibles were immediately processed with LCM using a ArcturusXT™ Laser Capture Microdissection System (Thermo Scientific) at room temperature for a maximum of 2 h. Laser focus and energy settings were optimized for every slide to minimize damage from IR laser capturing of the tissue. Ameloblasts and stratum intermedium were separately captured in Arcturus®CapSure ® Macro LCM Caps (Life Technologies). RNA lysing was immediately performed using buffer RLT (RNeasy Micro Kit, Qiagen, Venlo, Netherlands). The lysate was stored at -80°C until further processing

extract_protocol:
RNA extractions were performed using RNeasy Micro Kit Quiagen. To construct the libraries, 1 μg of highquality total RNA sample (RIN > 8) was processed using TruSeq Stranded mRNA kit (Illumina) according to manufacturer instructions
TruSeq Stranded mRNA kit (Illumina) according to manufacturer instructions

treatment_protocol: The quality of the RNA (RNA integrity number) was determined on the Agilent 2100 Bioanalyzer

value: hemi mandible

value: Stratum intermedium

value: KO Claudin 10


title: A549 cells, si-AUH2

description: Library name: Sample 5


title: Mice KO claudin 10 rep 3 ST

description:
Library name: KO9-ST-Groupe2
NGS21-052_ensemblGRCm38r101_ST_noOutlier_deseq2_NormalizedMatrix.tsv


title: HygTK expression cassette with TRE promoter at Ptn locus, TRE activated, nascent RNA, replicate 2

description:
Library name: TRE_HTK_Dox_Rep2
nascent RNA

data_processing:
Repli-seq and Bru-seq data processing methods have been described in PMC6546437. Basically, sequencing reads were mapped to mm10 then reads for 129 and cas alleles were parsed using SNPsplit.
Assembly: mm10
Supplementary files format and content: bedgraph files, featureCounts output for each allele (129 or cas)
Library strategy: BRU-Seq

extract_protocol:
Repli-seq and Bru-seq sample extraction methods have been described in PMC6546437.
Repli-seq and Bru-seq library preparation methods have been described in PMC6546437.

value: embryonic stem cell

value: doxycycline


title: A549 cells, si-AUH1

description: Library name: Sample 4


title: Pre-ischemia sample of left ventricle sample from patient 95V, surgery in morning

data_processing:
Alignment of RNA sequencing tags was restricted to those mapping to the same DNA strand as annotated in the GRCm38 reference genome, utilizing the STAR software. Quantification of transcripts was conducted by calculating the fragments per kilobase of transcript per million mapped reads (FPKM) values, along with transcript counts. In the preprocessing step of mRNA analysis, any gene identified as non-expressed, defined as having an FPKM expression level less than 1 in more than 80% of samples, was excluded. The normalized expression profiles of these mRNAs were then subjected to PCA for quality control and to evaluate sample similarity. Differential expression analysis was executed using the DESeq2 pipeline, with DEGs being identified based on a threshold of 1.5-fold change and an adjusted p-value below 0.05, as determined by the Benjamini-Hochberg method
Assembly: GRCm38
Supplementary files format and content: Gene quantification and differential expression

extract_protocol:
The AAR of the heart was harvested following 2h of reperfusion from the C57BL/6J mice subjected to myocardial IRI at either ZT8 or ZT20.
Total RNA was extracted using the RNeasy Mini kit (Qiagen) and employed to construct RNA-Seq libraries

value: AM

value: Pre-ischemia


title: Pre-ischemia sample of left ventricle sample from patient 111V, surgery in morning


title: HygTK expression cassette with TRE promoter at Ptn locus, TRE activated, nascent RNA, replicate 1

description:
Library name: TRE_HTK_Dox_Rep1
nascent RNA


title: Pre-ischemia sample of left ventricle sample from patient 41V, surgery in morning


title: A549 cells, si-NC2

description: Library name: Sample 2

value: WT


title: Post-ischemia sample of left ventricle sample from patient 19V, surgery in morning

value: Post-ischemia


title: HygTK expression cassette with TRE promoter at Ptn locus, TRE not activated, nascent RNA, replicate 1

description:
Library name: TRE_HTK_Rep1
nascent RNA

value: F121:R26puroR-M2rtTA;  Ptn^TRE-Hyg-TK/+


title: Mice WT claudin 10 rep 2 ST

description:
Library name: Wt5-ST-Groupe1
NGS21-052_ensemblGRCm38r101_ST_noOutlier_deseq2_NormalizedMatrix.tsv


title: Mice KO claudin 10 rep 1 ST

description:
Library name: KO-3ST-Groupe1
NGS21-052_ensemblGRCm38r101_ST_noOutlier_deseq2_NormalizedMatrix.tsv


title: A549 cells, si-NC1

description: Library name: Sample 1


title: control cell line, nascent RNA, replicate 2

description:
Library name: R26_Rep2
nascent RNA

value: biol rep 2


title: Mice WT claudin 10 rep 1 ST

description:
Library name: Wt10-ST-Groupe2
NGS21-052_ensemblGRCm38r101_ST_noOutlier_deseq2_NormalizedMatrix.tsv


title: IRF8KO_microglia_3mo_male_rep2

description: Library name: RNASeq_Sample_5

value: microglia


title: Mice KO claudin 10 rep 3 ameloblast

description:
Library name: Ko3-AM-Groupe1
NGS21-052_ensemblGRCm38r101_AM_noOutlier_deseq2_NormalizedMatrix.tsv

value: Ameloblasts


title: Pre-ischemia sample of left ventricle sample from patient 19V, surgery in morning

value: Left ventricle


title: Post-ischemia sample of left ventricle sample from patient 123V, surgery in morning


title: granulosa cells, normal ovarian reserve, young, No96

city: Shanghai

first: Jiani

last: Lu

address: No.85 Wujin Rd.

institute: Shanghai General Hospital

description: Library name: NORL96

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Paired-end clean reads were aligned to mm10 using Hisat2 (v2.0.5). FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
Assembly: hg38
Supplementary files format and content: xlsx file include raw counts for each sample

source_name: ovarian follicle

extract_protocol:
The RNA was isolated using Trizol method.
Libraries were Fast RNA-seq Lib Prep Kit V2 following manufacturer's protocols

value: ovarian follicle

value: granulosa cells

tag: disease group

value: normal ovarian reserve

tag: age group


title: granulosa cells, normal ovarian reserve, young, No98

description: Library name: NORL98

tag: tissue


title: control cell line, nascent RNA, replicate 1

city: San Diego

first: David

institute: San Diego BioMEd

description:
Library name: R26_Rep1
nascent RNA

tag: cell line

tag: batch

value: biol rep 1


title: Mice KO claudin 10 rep 2 ameloblast

description:
Library name: KO9-AM-Groupe2
NGS21-052_ensemblGRCm38r101_AM_noOutlier_deseq2_NormalizedMatrix.tsv

value: hemi mandible

tag: cell type


title: granulosa cells, normal ovarian reserve, young, No93

description: Library name: NORL93


title: A549 cells, si-NC3

description: Library name: Sample 3

value: Non-small cell lung cancer cells

tag: treatment

value: Small interference transfection


title: Mice KO claudin 10 rep 1 ameloblast

description:
Library name: KO1-AM-Groupe3
NGS21-052_ensemblGRCm38r101_AM_noOutlier_deseq2_NormalizedMatrix.tsv

value: KO Claudin 10


title: HygTK expression cassette with mouse PGK promoter at Ptn locus, nascent RNA, replicate 3

description:
Library name: mPGK_HTK_Rep3
nascent RNA

value: embryonic stem cell

value: biol rep 3


title: granulosa cells, normal ovarian reserve, young, No91

description: Library name: NORL91


title: HygTK expression cassette with mouse PGK promoter at Ptn locus, nascent RNA, replicate 4

description:
Library name: mPGK_HTK_Rep4
nascent RNA

value: biol rep 4


title: Post-ischemia sample of left ventricle sample from patient 144V, surgery in morning

city: Houston

first: Holger

institute: The University of Texas Health Science Center at Houston

value: AM

value: Post-ischemia


title: HygTK expression cassette with mouse PGK promoter at Ptn locus, nascent RNA, replicate 2

description:
Library name: mPGK_HTK_Rep2
nascent RNA

value: biol rep 2


title: Pre-ischemia sample of left ventricle sample from patient 123V, surgery in morning

value: Pre-ischemia


title: Mice WT claudin 10 rep 2 ameloblast

description:
Library name: Wt5-AM-Groupe1
NGS21-052_ensemblGRCm38r101_AM_noOutlier_deseq2_NormalizedMatrix.tsv

value: Ameloblasts

value: WT


title: Mice WT claudin 10 rep 1 ameloblast

description:
Library name: Wt10-AM-Groupe2
NGS21-052_ensemblGRCm38r101_AM_noOutlier_deseq2_NormalizedMatrix.tsv


title: HygTK expression cassette with mouse PGK promoter at Ptn locus, nascent RNA, replicate 1

description:
Library name: mPGK_HTK_Rep1
nascent RNA


title: Post-ischemia sample of left ventricle sample from patient 55V, surgery in morning

value: Left ventricle


title: HygTK expression cassette with human PGK promoter at Ptn locus, nascent RNA, replicate 4

description:
Library name: hPGK_HTK_Rep4
nascent RNA


title: Pre-ischemia sample of left ventricle sample from patient 144V, surgery in morning


title: Pre-ischemia sample of left ventricle sample from patient 55V, surgery in morning


title: HBEC cells, siDDX42 replicate B

first: Daniel

middle: R

last: Larson

state: MD

address: 41 Medlar Dr.

institute: NIH

data_processing:
rRNA reads were removed by alignment with Bowtie2. Duplicate reads were removed using sambamba.
Transcript quantification was performed with Salmon. Alternative 3'SS annotation and analysis were performed with SUPPA2.
Assembly: hg38
Supplementary files format and content: Excel spreadsheet; transcript quantification: TranscriptQuantification_Salmon, alternative 3'SS: Alternative3SS_SUPPA2

source_name: HBEC

growth_protocol: Human bronchial epithelial cells (HBECs) were grown in Keratinocyte SFM media at 37C and 5% CO2

extract_protocol:
RNA extraction was performed on ~1 million Human Bronchial Eplithelial Cells (HBEC) using the Qiagen RNeasy mini kit (74106). Genomic DNA and degraded using the Turbo DNase kit (Invitrogen, AM1907)
rRNA depletion using NEBNext rRNA Depletion Kit v2 (E7400), and sequencing library preparation using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760)

value: HBEC

value: DDX42 knockdown


title: granulosa cells, normal ovarian reserve, young, No87

description: Library name: NORL87

value: ovarian follicle

value: granulosa cells

value: normal ovarian reserve


title: HygTK expression cassette with human PGK promoter at Ptn locus, nascent RNA, replicate 3

last: Gilbert

address: 3525 John Hopkins Ct., Ste. 200

description:
Library name: hPGK_HTK_Rep3
nascent RNA

source_name: embryonic stem cell


title: granulosa cells, normal ovarian reserve, young, No80

description: Library name: NORL80


title: HygTK expression cassette with human PGK promoter at Ptn locus, nascent RNA, replicate 2

description:
Library name: hPGK_HTK_Rep2
nascent RNA


title: HBEC cells, siDDX42 replicate A


title: granulosa cells, normal ovarian reserve, young, No70

description: Library name: NORL70


title: HBEC cells, siControl replicate B


title: granulosa cells, normal ovarian reserve, young, No55

description: Library name: NORL55


title: HygTK expression cassette with human PGK promoter at Ptn locus, nascent RNA, replicate 1

description:
Library name: hPGK_HTK_Rep1
nascent RNA

value: biol rep 1


title: Post-ischemia sample of left ventricle sample from patient 20V, surgery in morning

last: Eltzschig

source_name: Left ventricle


title: granulosa cells, normal ovarian reserve, young, No47

description: Library name: NORL47


title: Pre-ischemia sample of left ventricle sample from patient 20V, surgery in morning


title: HBEC cells, siControl replicate A


title: granulosa cells, normal ovarian reserve, young, No37

description: Library name: NORL37


title: IMR32_siNTC_rep4

first: Sarah-Lee

institute: UGent

data_processing:
Quality control of the FASTQ files was done using FastQC version 0.11.7.
FASTQ files were aligned and reads were counted using STAR version 2.7.2b.
Counts were normalized using edgeR version 3.36.0 and differential expression analysis was performed using Limma-Voom version 3.50.3 in R.
Assembly: GRCh38.96
Supplementary files format and content: Tab-delimited text file include STAR counts on the forward strand per sample

source_name: Brain

extract_protocol:
RNA extraction was performed practicing the manufacturer’s instructions of miRNeasy kit (Qiagen) including on-column DNase treatment and nanodrop (Thermo Scientific) was used to determine the concentration. RNA quality was determined with the Experion automated electrophoresis system (BioRad) prior to profiling.
The 3'UTR QuantSeq library kit from Lexogen was used, during library preparation 15 PCR cycles were used.  qPCR quantification of the libraries using the illumine Kapa library quantification kit (Lightcycler 480 qPCR mix Kapa. RNA-seq libraries were sequenced on the NextSeq 2000 platform (Illumina) using the NextSeq 1000/2000 P2 (100 cycles), single-end kit (Illumina).

value: Brain

value: neuroblast

value: control

value: siNTC


title: HygTK expression cassette with CAG promoter at Ptn locus, nascent RNA, replicate4

description:
Library name: CAG_HTK_Rep4
nascent RNA

value: embryonic stem cell

value: F121:R26puroR-M2rtTA;  Ptn^CAG-Hyg-TK/+

value: biol rep 4


title: Post-ischemia sample of left ventricle sample from patient 41V, surgery in morning

value: AM

value: Post-ischemia


title: granulosa cells, normal ovarian reserve, young, No361

description: Library name: NORL361


title: IMR32_siNTC_rep3


title: Hs_retina_PER_Input mRNA

city: Philadelphia

first: Dwight

middle: Edward

last: Stambolian

state: PA

address: 422 Curie Blvd.

department: Opthalmalogy

institute: University of Pennsylvania

description: All the cells were taken from the same eye donor.

data_processing:
The 10X pipeline used was Cell Ranger 2.0.0.
Seurat software was used to normalize gene counts and process the raw data
Genome_build: HG38
Supplementary_files_format_and_content: txt file (gene x cells)

source_name: Retina (spanning 11 cell types)

extract_protocol:
The human eyeball was immediately removed within 6 hours after death, and placed in cold phosphate buffered saline (PBS). The retina was carefully removed under a dissecting microscope, and the retina tissue was dissociated straightaway using the Papain dissociation system (Worthington, Lakewood, NJ, USA) following the manufacturer's instructions.
To assess cell viability, cells were stained with 0.4% trypan blue (Mediatech, Inc., Manassas, VA, USA) and counted using a hemocytometer. sc-RNA seq was carried out on the viable cells using Chromium 10x Genomics as per the manufacturer’s recommendations.

tag: donor

tag: disease state

value: healthy

tag: ethnicity

value: Caucasian

value: retina

tag: tissue region

value: Peripheral (per)

value: mixed sample (non-demultiplexed)

tag: age


title: HygTK expression cassette with CAG promoter at Ptn locus, nascent RNA, replicate3

description:
Library name: CAG_HTK_Rep3
nascent RNA

value: biol rep 3


title: Hs_retina_MAC_Input mRNA

value: Macula (mac)


title: IMR32_siNTC_rep2

city: Ghent

last: Bekaert

address: Corneel Heymanslaan 10

tag: genotype


title: granulosa cells, normal ovarian reserve, young, No350

description: Library name: NORL350

value: ovarian follicle

value: granulosa cells

value: normal ovarian reserve


title: HygTK expression cassette with CAG promoter at Ptn locus, nascent RNA, replicate2

description:
Library name: CAG_HTK_Rep2
nascent RNA

value: biol rep 2


title: Rat cecum tissues, Sepsis+Tongfu Pingchaun (D) group, sample 5

first: Limeng

last: Yang

address: No. 358 Datong Road, Pudong New Area

department: Department of Internal Medicine

institute: Shanghai Pudong New Area Hospital of Traditional Chinese Medicine

description:
Library name: Sample17
Column names in raw_gene_fpkm_D5

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Assembly: StringTie
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: FPKM values for each Sample

organism: Rattus norvegicus

source_name: cecum

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: cecum

value: Tongfu Pingchaun Decoction-oral gavage


title: OT-II_INPUT (Flag)

city: shanghai

first: xiaoxue

last: li

institute: Shanghai Jiao Tong University

description: Library name: OT-II_INPUT (Flag)

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp software (version 0.20.1). Clean data were obtained for downstream analyses by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. The clean reads were mapped to the genome using bowtie2(version 2.4.2). MACS2(version 2.2.7.1) was used to call peaks. IGV8 software was used to visualize called peaks from ChIP-seq samples. Called peaks were then annotated using R package ChIPseeker. And HOMER (http://homer.ucsd.edu/homer/download.html，v4.11.1) were used to find de novo and known motif. Differential peaks analysis was performed using R package MAnorm for experimental design without replication while using R package Diffbind for experimental design with replication.
Assembly: mm10
Supplementary files format and content: bigwig/bw files for each sample

source_name: Spleen and lymph node

extract_protocol:
1. Add final concentration of 1% Formaldehyde solution for Cross-Linking of DNA and Protein. Then stoped the cross-linking reaction by adding final concentration of 125mM glycine. 2. Extract chromatin from cross-linked cells by adding Lysis Buffer. 3. Sonicate chromatin DNA to fragments ranging from 100 to 500 bp. 4. Immunoprecipitate chromatin DNA and antibody-associated beads by incubating them overnight at 4°C.                                                                                5. Wash Dynabeads for eluting immunoprecipitated protein-DNA complexes by optimal method
The sequencing libraries of immunoprecipitated chromatin DNA were generated with varied index label by NEBNext® UltraTM DNA Library Prep Kit for Illumina (NEB, USA, cat. E7645L). Add End Repair Reaction Buffer (10X) and End Prep Enzyme Mix for end repair by the following condition: 20°C for 30min, 65°C for 30min. And then NEBNext Adaptor and Blunt/TA Ligase Master Mix was added to ligate adaptor at 20°C for 15min. USER Enzyme was added to remove base U of adaptor at 37°C for 5min. After purification with beads, products are amplified with PCR by the following conditions: initial denaturation at 98℃ for 10 sec; denaturation at 98℃ for 10 sec, annealing at 65℃ for 30 sec, and extension at 72℃ for 30 sec. The library size was selected and then purified with AMPure XP Beads. Qubit was used for library quantification and High-sensitivity DNA chip was used for test of library insert size. The libraries were sequenced on an Illumina NovaSeq 6000 platform and 150 bp paired-end reads were generated

value: Spleen and lymph node

value: CD4+T cell

value: Overexpression of flag-sub1 in OT-II cells


title: IMR32_siNTC_rep1

value: Brain

value: neuroblast

value: control

value: siNTC


title: granulosa cells, normal ovarian reserve, young, No352

description: Library name: NORL352


title: HygTK expression cassette with CAG promoter at Ptn locus, nascent RNA, replicate1

description:
Library name: CAG_HTK_Rep1
nascent RNA

value: embryonic stem cell

value: F121:R26puroR-M2rtTA;  Ptn^CAG-Hyg-TK/+

value: biol rep 1


title: Rat cecum tissues, Sepsis+Tongfu Pingchaun (D) group, sample 4

description:
Library name: Sample16
Column names in raw_gene_fpkm_D4


title: granulosa cells, normal ovarian reserve, young, No348

description: Library name: NORL348


title: IMR32_siTPX2_si45_rep4

value: knockdown TPX2


title: Rat cecum tissues, Sepsis+Tongfu Pingchaun (D) group, sample 6

description:
Library name: Sample18
Column names in raw_gene_fpkm_D6


title: IMR32_siTPX2_si45_rep3


title: KO_CD4_INPUT (Flag)

description: Library name: KO_CD4_INPUT (Flag)

value: SUB1 knockout

value: Overexpression of flag-junb in Sub1-KO CD4+ T cells


title: granulosa cells, normal ovarian reserve, young, No34

description: Library name: NORL34

value: ovarian follicle

value: granulosa cells

value: normal ovarian reserve


title: IMR32_siTPX2_si45_rep2


title: Rat cecum tissues, Sepsis+Tongfu Pingchaun (D) group, sample 1

description:
Library name: Sample13
Column names in raw_gene_fpkm_D1

value: cecum

value: Tongfu Pingchaun Decoction-oral gavage


title: IMR32_siTPX2_si45_rep1


title: Rat cecum tissues, Sepsis+Tongfu Pingchaun (D) group, sample 2

description:
Library name: Sample14
Column names in raw_gene_fpkm_D2


title: Rat cecum tissues, Sepsis+Tongfu Pingchaun (D) group, sample 3

description:
Library name: Sample15
Column names in raw_gene_fpkm_D3


title: granulosa cells, normal ovarian reserve, young, No328

description: Library name: NORL328


title: WT_CD4_INPUT (Flag)

description: Library name: WT_CD4_INPUT (Flag)

value: Spleen and lymph node

value: CD4+T cell

value: WT

value: Overexpression of flag-junb in WT CD4+ T cells


title: OT-II_CHIP (Flag)

description: Library name: OT-II_CHIP (Flag)

value: Overexpression of flag-sub1 in OT-II cells


title: Rat cecum tissues, Sepsis (M) group, sample 6

description:
Library name: Sample12
Column names in raw_gene_fpkm_M6

value: PBS-oral gavage


title: IMR32_siTPX2_si46_rep4

value: Brain

value: neuroblast


title: granulosa cells, normal ovarian reserve, young, No321

description: Library name: NORL321


title: granulosa cells, normal ovarian reserve, young, No329

description: Library name: NORL329


title: IMR32_siTPX2_si46_rep3


title: granulosa cells, normal ovarian reserve, young, No337

description: Library name: NORL337


title: Rat cecum tissues, Sepsis (M) group, sample 5

description:
Library name: Sample11
Column names in raw_gene_fpkm_M5


title: WT_CD4_CHIP (Flag)

description: Library name: WT_CD4_CHIP (Flag)


title: granulosa cells, normal ovarian reserve, young, No307

description: Library name: NORL307


title: KO_CD4_CHIP (Flag)

description: Library name: KO_CD4_CHIP (Flag)


title: KO_CD4_CHIP (H3K27ac)

description: Library name: KO_CD4_CHIP (H3K27ac)


title: KO_CD4_INPUT (H3K27ac)

description: Library name: KO_CD4_INPUT (H3K27ac)


title: granulosa cells, normal ovarian reserve, young, No291

description: Library name: NORL291


title: IMR32_siTPX2_si46_rep2


title: Rat cecum tissues, Sepsis (M) group, sample 3

description:
Library name: Sample9
Column names in raw_gene_fpkm_M3


title: IMR32_siTPX2_si46_rep1


title: WT_CD4_INPUT (H3K27ac)

description: Library name: WT_CD4_INPUT (H3K27ac)


title: Rat cecum tissues, Sepsis (M) group, sample 2

description:
Library name: Sample8
Column names in raw_gene_fpkm_M2


title: granulosa cells, normal ovarian reserve, young, No289

description: Library name: NORL289


title: IMR32_siTPX2_si47_rep4


title: Rat cecum tissues, Sepsis (M) group, sample 4

description:
Library name: Sample10
Column names in raw_gene_fpkm_M4


title: Rat cecum tissues, Sepsis (M) group, sample 1

description:
Library name: Sample7
Column names in raw_gene_fpkm_M1


title: IMR32_siTPX2_si47_rep3


title: WT_CD4_CHIP (H3K27ac)

description: Library name: WT_CD4_CHIP (H3K27ac)


title: KO_CD4_CHIP (H3K4me1)

description: Library name: KO_CD4_CHIP (H3K4me1)


title: KO_CD4_INPUT (H3K4me1)

description: Library name: KO_CD4_INPUT (H3K4me1)


title: IMR32_siTPX2_si47_rep2


title: Rat cecum tissues, Sham (S) group, sample 6

description:
Library name: Sample6
Column names in raw_gene_fpkm_S6


title: granulosa cells, normal ovarian reserve, young, No278

description: Library name: NORL278


title: granulosa cells, normal ovarian reserve, young, No276

description: Library name: NORL276


title: IMR32_siTPX2_si47_rep1


title: WT_CD4_INPUT (H3K4me1)

description: Library name: WT_CD4_INPUT (H3K4me1)


title: Rat cecum tissues, Sham (S) group, sample 5

description:
Library name: Sample5
Column names in raw_gene_fpkm_S5


title: Rat cecum tissues, Sham (S) group, sample 3

description:
Library name: Sample3
Column names in raw_gene_fpkm_S3


title: IMR32_MYCN (CUT&RUN)

data_processing:
The raw sequencing data of CUT&RUN was evaluated using FastQC and adapter trimming was done using TrimGalore (v0.6.5).
Mapping to the human reference genome (GRCh37/hg19) was done with bowtie2 (v.2.3.1)
Quality of aligned reads were filtered using min MAPQ 30 and reads with known low sequencing confidence were removed using Encode Blacklist regions. For sample with a percentage duplicated reads higher then 10%, deduplication was performed using MarkDuplicates (Picard, v4.0.11).
Peak calling was performed using MACS2 (v2.1.0) taking a q value of 0.05 as threshold and using the parameter keep-dup auto. NarrowPeak calling was used for transcription factors while broadPeak calling was used for histone marks.
Assembly: GRCh37/hg19
Supplementary files format and content: Bigwig files were generated using bamCoverage with binSize 10 and normalizeUsing RPKM.
Supplementary files format and content: Peak calling files from MACS2.
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN coupled with high-throughput DNA sequencing was performed on isolated nuclei using Cutana pA/G-MNase (Epicypher, 15-1016) according to the manufacturer’s manual.
Sequencing libraries were prepared with the NEBNext Ultra II kit (Illumina, E7645), followed by paired-end sequencing on a Nextseq2000 using the NextSeq 2000 P2 Reagents 100 Cycles v3 (Illumina, 20046811).

value: brain

tag: chip antibody

value: MYCN, Santa Cruz (sc53993)


title: granulosa cells, normal ovarian reserve, young, No265

description: Library name: NORL265


title: granulosa cells, normal ovarian reserve, young, No281

description: Library name: NORL281


title: Rat cecum tissues, Sham (S) group, sample 4

description:
Library name: Sample4
Column names in raw_gene_fpkm_S4


title: IMR32_IgG_run1 (CUT&RUN)


title: WT_CD4_CHIP (H3K4me1)

description: Library name: WT_CD4_CHIP (H3K4me1)


title: granulosa cells, normal ovarian reserve, young, No260

description: Library name: NORL260


title: granulosa cells, normal ovarian reserve, young, No272

description: Library name: NORL272


title: Rat cecum tissues, Sham (S) group, sample 1

description:
Library name: Sample1
Column names in raw_gene_fpkm_S1


title: CD4+T cells，KO-4

description: Library name: sample8

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina NovaseqTM 6000 sequence platform. Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing polyA and polyG; 3) removing reads containing more than 5% of unknown nucleotides (N); 4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
We aligned reads of all samples to the < research species > reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
Assembly: mm10
Supplementary files format and content: txt file include FPKM values for all sample

source_name: Spleen

extract_protocol:
The RNA of the total sample was separated and purified using TRIzol (thermofisher, 15596018) in accordance with the operation plan provided by the manufacturer. Then the quantity and purity of total RNA were controlled by NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and the integrity of RNA was detected by Bioanalyzer 2100 (Agilent, CA, USA). The concentration >50ng/μL, the RIN value >7.0, and the total RNA>1μg meet the requirements for downstream experiments.
The mRNA containing PolyA (polyadenylic acid) was specifically captured by two rounds of purification using oligo(dT) magnetic beads (Dynabeads Oligo (dT), cat.25-61005, Thermo Fisher, USA). The captured mRNA was fragmented under high-temperature conditions using the Magnesium RNA Fragmentation Module (NEBNextR magnesium RNA Fragmentation Module, cat.E6150S, USA) at 94 ° C for 5-7 minutes. cDNA was synthesized from fragmented RNA under the action of Invitrogen SuperScriptTM II Reverse Transcriptase (cat.1896649, CA, USA). Then, double-stranded synthesis was carried out using E. coli DNA polymerase I (NEB, cat.m0209, USA) and RNase H (NEB, cat.m0297, USA) to convert these complex double-stranded DNA and RNA into DNA double-stranded. Meanwhile, dUTP Solution (Thermo Fisher, cat.R0133, CA, USA) was incorporated into the two strands to complete the ends of the double-stranded DNA into flat ends, and then an A base was added to each end to enable it to connect with the connector with a T base at the end. And the size of the fragments was screened and purified by using magnetic beads. The two strands were digested with UDG enzyme (NEB, cat.m0280, MA, US), then subjected to PCR - pre-denaturation at 95 ° C for 3 minutes, denaturation at 98 ° C for a total of 8 cycles, each lasting 15 seconds, annealing to 60 ° C for 15 seconds, extension at 72 ° C for 30 seconds, and finally extension at 72 ° C for 5 minutes. Form a library (chain-specific library) with a fragment size of 300bp±50bp. Finally, we performed double-ended sequencing on it using illumina NovaseqTM 6000 (LC Bio Technology CO.,Ltd. Hangzhou, China) in accordance with standard operation, with the sequencing mode being PE150.

value: Spleen

value: SUB1 knockout

value: EAE model


title: CD4+T cells，KO-3

description: Library name: sample7


title: Ant1(Tg)/+_male_quadricep_muscle_4

city: Syracuse

first: Nicholas

last: Brennan

state: New York

address: 766 Irving Ave

department: Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

data_processing:
Illumina Bcl2FastQ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, using Cutadapt-1.2.1 and low-quality (q < 25) sequence
Trimmed sequences were mapped to mm10 whole genome using STAR and quantified to Ensembl 100 annotation, using strict paired-end compatibility, with requirement of junction reads to match introns, minimum feature overlap of 95%, and minimum reads of 1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized alignment counts per gene for each sample

source_name: Quadricep skeletal muscle

growth_protocol: All the experiments were performed using age-matched controls. The animals were fed with a regular chow diet ad libitum and were housed at an ambient temperature.

extract_protocol:
Total RNA was extracted using Trizol/chloroform phase separation followed by RNeasy Mini kit column purification. The quality and quantity of RNA was assessed with the Bioanalyzer. 500ng RNA was used as input to the Illumina Stranded mRNA kit for the construction of sequencing libraries.
RNA libraries were prepared using the Illumina Stranded mRNA prep kit following the manufacturers protocol.

value: Quadricep skeletal muscle

tag: strain

value: Male

value: 29 months


title: granulosa cells, normal ovarian reserve, young, No23

description: Library name: NORL23

value: ovarian follicle

value: granulosa cells

value: normal ovarian reserve


title: CD4+T cells，KO-2

description: Library name: sample6

value: CD4+T cell


title: Ant1(Tg)/+_male_quadricep_muscle_3


title: granulosa cells, normal ovarian reserve, young, No22

description: Library name: NORL22


title: 20minutes_with_opp

first: Adam

last: Rosenthal

address: 1521 East Franklin Street, Apartment C213

department: Microbiology and Immunology

institute: UNC

description:
Library name: Sample 6
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software V7.1  and using custom scripts available from the Sahand Hormoz lab (https://gitlab.com/hormozlab/bacteria_scrnaseq)
Assembly: Probe-based genome builds for E coli  are deposited alongside GTF files in the Hormoz lab github: https://gitlab.com/hormozlab/bacteria_scrnaseq
Supplementary files format and content: H5 files

molecule: cytoplasmic RNA

organism: Bacillus subtilis

source_name: Bacterial cells in suspension

growth_protocol: Freshly collected bacterial cells were fixed in 1% paraformaldehyde for 1 hour. Cells from 2 mL of cell culture were fixed using a 30-minute incubation in 1% paraformaldehyde (final concentration) at room temperature. Formaldehyde-fixed samples were washed with 0.02 % SSC (Saline Sodium Citrate - Invitrogen) by gentle centrifugation (6,000 x G) for 2.5 minutes. After the wash, cell pellets were resuspended in 1 mL MAAM (4:1 V:V dilution of methanol to glacial acetic acid). Samples were kept at -20oC for up to 2 days before further processing. For in-situ probe hybridization, 150 µL of fixed sample was centrifuged and washed once in PBS to remove methanol and acetic acid. After the wash step, cells were incubated in 200 µL PBS with 350 u/µL of lysozyme solution (Epicentre ready-lyse) for 30 minutes at room temperature. Lysozyme concentration was optimized and other enzyme combinations were tested to achieve a protocol with maximal probe signal and minimal cell lysis (see Supplementary Figure S12) After 30 minutes cells were pelleted and washed with 500 µL PBS-tween (PBS with 0.1 % Tween 20). Cells were then re-suspended with 100 µL of probe binding buffer consisting of 5x SSC, 30% formamide, 9mM citric acid (pH 6.0). 0.1% Tween 20, 50 ug/ml heparin, and 10% low MW dextran sulfate42. Cell suspensions were placed in a 50oC shaker-incubator and allowed to pre-equilibrate for 1 hour. After 1 hour 50 µL of probes, (600 ng/µL) were added to each cell suspension, and samples were left to incubate overnight. Following the overnight incubation samples were washed 5 times in pre-warmed (50oC) probe-wash solution (5 x SSC, 30% formamide, 9 mM citric acid pH 6.0, 0.1% Tween 20, and 50 ug/mL heparin).

extract_protocol:
Single cell
Library was performed according to specifications of McNulty et al bacterial scRNAseq protocols (single cell 3’ v2 protocol, 10x Genomics). Briefly, Single cell partitioning, barcoding, and cDNA library generation was achieved using the 10X Genomics Chromium Controller with the Chromium Single Cell 3’ Reagents Kit (v2 chemistry) as described by 10X Genomics (https://support.10Xgenomics.com/single cell-gene-expression/index/doc/user-guide-chromium-single cell-3-reagent-kits-user-guide-v2-chemistry). The protocol was modified to achieve bacterial scRNA-seq. For GEM generation (10X microfluidic encapsulation), a master mix containing the following reagents (per rxn, not accounting for excess volume) was prepared: 33 µL of 4X ddPCR Multiplex Supermix (BioRad), 4 µL of custom primer (10 µM), 2.4 µL additive A (10X Genomics), 26.8 µL dH2O. All other reagents specified by 10X Genomics were omitted. Prepared cell samples were washed 3X in PBS and diluted to 1000 cells/µL before loading on the microfluidic chip (“Chip A Single Cell”) with a targeted cell recovery of 10,000 cells.

treatment_protocol: When indicated OPP was added for either 2 minutes or 20 minutes to the cultures at the amount recommended by the click-it OPP kit

value: Bacterial cells in suspension

value: Bacillus subtilis 168

value: Late log with 20 minutes plus OPP


title: Rat cecum tissues, Sham (S) group, sample 2

description:
Library name: Sample2
Column names in raw_gene_fpkm_S2

value: cecum

value: PBS-oral gavage


title: 20minutes_no_OPP

description:
Library name: Sample 5
10x Genomics

value: Late log with 20 minutes no OPP


title: Ant1(Tg)/+_male_quadricep_muscle_2

value: 30 months


title: CD4+T cells，WT-4

description: Library name: sample4

value: Spleen

value: WT


title: granulosa cells, normal ovarian reserve, young, No134

description: Library name: NORL134


title: granulosa cells, normal ovarian reserve, young, No158

description: Library name: NORL158


title: CD4+T cells，KO-1

description: Library name: sample5

value: SUB1 knockout

value: EAE model


title: CD4+T cells，WT-3

description: Library name: sample3


title: Ant1(Tg)/+_male_quadricep_muscle_1

value: Quadricep skeletal muscle

value: Male

value: 27 months


title: granulosa cells, normal ovarian reserve, young, No122

description: Library name: NORL122

value: ovarian follicle

value: granulosa cells


title: granulosa cells, normal ovarian reserve, young, No111

description: Library name: NORL111

value: normal ovarian reserve


title: Main_figure_dataset_OPP_signal

description:
Library name: Sample 2
10x Genomics

library_source: other

molecule: other

value: Bacterial cells in suspension

value: Late transition phase


title: 2minutes_no_OPP

description:
Library name: Sample 3
10x Genomics

value: Bacillus subtilis 168

value: Late log with 2 minutes no OPP


title: WT_male_quadricep muscle_1

value: Wildtype


title: WT_male_quadricep muscle_3

value: 28 months


title: WT_male_quadricep muscle_2


title: 2minutes_with_opp

description:
Library name: Sample 4
10x Genomics

value: Late log with 2 minutes plus OPP


title: granulosa cells, normal ovarian reserve, old, No92

description: Library name: NORH92


title: granulosa cells, normal ovarian reserve, old, No90

description: Library name: NORH90


title: Main_figure_dataset_transcripts

description:
Library name: Sample 1
10x Genomics


title: E9.5-6mA IP

city: beijing

first: shan

last: wang

address: 2yabao road

institute: Capital Institute of Pediatrics

description:
Library name: E9-6mA IP
6mA MeDIP seq

data_processing:
After sequencing on the Illumina NovaSeq6000 sequencer, image analysis, base calling, and quality control were performed, resulting in the generation of raw reads (Raw Data). Quality control was initially conducted using Q30. Then, the cutadapt software (v1.9.2) was employed to trim adapters and remove low-quality reads, obtaining high-quality reads. Subsequently, the bowtie2 software (v2.2.4) was used to align the adapter-trimmed reads to the mouse reference genome (mm10) with default parameters. The MACS software (v1.4.2) was utilized for the identification of methylated regions (enrichment peaks) through Peak Calling. The diffReps software (1.55.4) was then applied for the identification of differentially methylated regions. Annotation of methylated regions with gene information was performed using the UCSC RefSeq database. The methylated regions were linked with gene information. Visualization of enrichment peaks was conducted using the UCSC Genome Browser.
Assembly: mouse genome (mm10)
Supplementary files format and content: Annotation of methylated regions with gene information was performed using the UCSC RefSeq database. The methylated regions were linked with gene information. Visualization of enrichment peaks was conducted using the UCSC Genome Browser.
Supplementary files format and content: related genes can be confirmed. Besides, the distribution of peak on different genome regions, such as intergenic, introns, downstream2k, upstream2k and exons) was performed.
Library strategy: 6mA MeDIP-Seq

source_name: brain

growth_protocol: Constructing a low-folate cell line. Mouse embryonic stem cells (mESCs) Sv/129 were maintained in Dulbecco’s modifed Eagle’s medium (DMEM, Gibco, USA) supplemented with 0.1  mM β-mercaptoethanol (Invitrogen, Carlsbad, USA), 0.1  mM non-essential amino acids (Invitrogen, Carls_x0002_bad, USA), 0.1  mM glutamate (Invitrogen, Carlsbad, USA), 15% fetal bovine serum (Gibco, USA), and 1000 U/ml mouse leukemia inhibitory factor (Millipore, Bill_x0002_erica, USA), cultured in culture dishes coated with 0.2% gelatin (Invitrogen, Carlsbad, USA). Constructing a low-folate cell line.After resuscitating normal mESCs, Sv129 cells were randomly split into FA4 and FA0. The FA0 group uses folate-free mESCs culture medium.Folate (Sigma) was added to the medium of FA0 as medium of the FA4 group(final concentration: 4 mg/L).  Next, two groups were added correspond medium and were cultured at 37°C with 5% CO2 in a humidified incubator and passaged every 2–3 days. The culture medium was changed daily.

extract_protocol:
The process of 6mA MeDIP-Seq is briefly described as follows: Genomic DNA is extracted using the DNeasy kit (QIAGEN Inc.) and then sonicated to fragment sizes of 100-300bp. Subsequently, the fragmented DNA undergoes end repair, dA-tailing, and adapter ligation using the GenSeq® Universal DNA Library Prep Kit (GenSeq, Inc.). A portion of the adapter-ligated DNA, around 10%, is labeled as "Input" and kept aside, while the remainder is subjected to immunoprecipitation using the GenSeq® 6mA MeDIP kit (GenSeq Inc.). The DNA that underwent immunoprecipitation and the Input DNA are then subjected to library amplification using Illumina PCR primers and GenSeq® 2× HiFi PCR Mix (GenSeq Inc.). The purified DNA library is quantified using the Qubit fluorescence method (ThermoFisher) and sequenced on Illumina's NovaSeq sequencing platform.
The DNA that underwent immunoprecipitation and the Input DNA that did not undergo immunoprecipitation were amplified into libraries using Illumina PCR primers and GenSeq® 2× HiFi PCR Mix (GenSeq Inc.).

treatment_protocol: Establishment of NTD Mouse Model: MTX is a folate antagonist. Under conditions of low folate diet in pregnant mice, we intraperitoneally injected MTX (1.5 mg/kg) at gestational day 7.5. We began observing the closure status of the neural tube in fetal mice during the neural tube closure window at E9.5-10.5. Normal mice appeared plump and round, with fully closed neural tubes, and were categorized into the normal group. Embryos from mice on low folate diet and injected with MTX exhibited varying degrees of developmental delay, smaller embryos, and primarily showed phenotypes of hindbrain malformations and spina bifida, and were categorized into the NTD group.

value: brain

value: Brain tissue

tag: medip kit

value: GenSeq® 6mA MeDIP KIT(GenSeq Inc.)

value: no


title: CD4+T cells，WT-2

description: Library name: sample2

value: Spleen

value: CD4+T cell

value: WT

value: EAE model


title: E8.5-6mA IP

description:
Library name: E8-6mA IP
6mA MeDIP seq


title: CD4+T cells，WT-1

description: Library name: sample1


title: WT_male_quadricep muscle_4

value: Quadricep skeletal muscle

tag: Sex

value: Male


title: granulosa cells, normal ovarian reserve, old, No83

description: Library name: NORH83

value: ovarian follicle

value: granulosa cells

tag: disease group

value: normal ovarian reserve


title: Ant1(Tg)/+_female_quadricep_muscle_4

value: Female

value: 2 months