title: Zido_4 [094_ZIDO]

city: Amsterdam

first: Georges

middle: E.

last: Janssens

address: Meibergdreef 9

department: Laboratory Genetic Metabolic Diseases

country: Netherlands

institute: Amsterdam UMC

description: H2W5YDSXY_103918-001-094_TCGTCTGA-GTCCTTGA

data_processing:
Reads were subjected to quality control FastQC, trimmed using Trimmomatic v0.32 and aligned to the C. elegans genome obtained from Ensembl (wbcel235.v91), using HISAT2 v2.1.0
Counts were obtained using HTSeq (v0.11.0, default parameters) using the corresponding GTF taking into account the directions of the reads. Statistical analyses were performed using the edgeR v3.26.8 and limma/voom v 3.40.6 R packages
All genes with more than 2 counts in at least 3 of the samples were kept. Count data were transformed to log2-counts per million (logCPM), normalized by applying the trimmed mean of M-values method and precision weighted using voom.
Genome_build: wbcel235.v91
Supplementary_files_format_and_content: csv file of CMPs (counts per million) for RNAseq data mapped to gene level for each sample

source_name: zidovudine_whole worm

growth_protocol: Gravid adult worms were age-synchronized using alkaline hypochlorite treatment, and incubated in M9 buffer overnight. Larval stage 1 worms were seeded to NGM plates and grown to larval stage 4.

extract_protocol:
For isolation of total mRNA, whole worms were homogenized with a 5 mm steel bead using a TissueLyser II (QIAGEN) for 5 min at frequency of 30 times/second. RNA was extracted according to the instructions of the RNaesy Mini Kit (QIAGEN). Contaminating genomic DNA was removed using RNase-Free DNase (QIAGEN). RNA was quantified with a NanoDrop 2000 spectrophotometer (Thermo Scientific; Breda, The Netherlands) and stored at -80°C until use.
RNA libraries were prepared and sequenced with the Illumina platform by Genome Scan (Leiden, The Netherlands). The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the sample(s). The sample preparation was performed according to the protocol "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760S/L). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp). Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used. NovaSeq control software NCS v1.6 was used.

treatment_protocol: ~1000 worms were transferred to plates containing compounds, as well as 5-fluorouracil at larval stage 4 of development. They were treated with zidovudine or DMSO control for 24 hours before harvest. At time of harvest, worms were washed in buffer and water, then snap frozen in liquid nitrogen.

tag: strain

value: day 1 adult

value: 50 μM zidovudine

value: whole worm


title: Wild Type eWAT Sample 1

status: Public on Dec 29 2022

type: SRA

city: Seoul

first: Han Geuk

last: Seo

address: 120 Neungdong-ro, Gwangjin-gu

country: South Korea

institute: Konkuk University

library_source: transcriptomic

data_processing:
Illumina NextSeq 500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to mm10 whole genome using STAR (version 2.5.4) with parameters -outFilterIntronMotifs RemoveNoncanonicalUnannotated.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by Cufflinks packages (version 2.2.1).
Differentially expressed genes were detected using Cuffdiff (version 2.2.1) against Ensemble genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Epididymal white adipose tissue

growth_protocol: Epididymal white adipose tissue (eWAT) isolated from 20-week-old male mice

extract_protocol:
Total RNA extraction was performed using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions.
The quantity and quality of the total RNA were evaluated using Agilent 2100 bioanalyzerRNA kit (Agilent). The isolated total RNA was processed for preparing mRNA sequencing library using the Illumina TruSeqStranded mRNA Sample Preparation kit (Illumina), according to the manufacturer's protocol.

tag: tissue

value: Epididymal white adipose tissue

tag: age

value: 20 wk

tag: genotype

value: Wild

tag: treatment

value: Normal Diet

tag: gender

value: male


title: Patient48Pre-treatment

type: RNA

city: Houston

first: Jin

middle: S

last: Im

state: Texas

address: 1515 Holcombe Blvd, Unit 900

country: USA

institute: The University of Texas M.D. Anderson Cancer Center

hyb_protocol: Up to 100 ng amplified RNAs were hybridized with target-specific, fluorescence-labeled 594 CodeSet and reporter probes from the nCounter Immunology panel (Human v2 – NanoString, Seattle, WA) for 20 h, and added to the robotic nCounter Prep Station for automated sample processing for the remaining steps.

scan_protocol: The cartridge was then moved to the nCounter Digital Analyzer MAX (nanoString) where the samples were scanned and fluorescent targets counted.

data_processing: The nSolver software version 4 (NanoString, Seattle, WA, USA) was used for preprocessing of raw counts, subsequent normalization, and downstream analysis.

organism: Homo sapiens

source_name: Myelodysplastic syndrome

label_protocol: RNA was further amplified using a NanoString Low Input Amplification Kit (NanoString, Seattle, WA, USA).

extract_protocol: Total RNAs were isolated from previously cryopreserved PBMC using the RNeasy Plus Micro Kit (Qiagen, Germantown, MD, USA).

tag: patient diagnosis

value: Myelodysplastic syndrome

value: Peripheral blood

value: Immunotherapy + Hypomethylating agent

tag: response

value: Response

tag: sampling time

value: Pre-treatment


title: Zido_2 [092_ZIDO]

description: H2W5YDSXY_103918-001-092_CCACAACA-GTACCACA

organism: Caenorhabditis elegans


title: Zido_3 [093_ZIDO]

description: H2W5YDSXY_103918-001-093_TTACCGAC-CGAATACG


title: ATAC CNS (donor), CD45.1+CD88+CD317+ myeloid cells, Day15

city: Dallas

first: Victor

last: Salinas

address: 5323 Harry Hines Blvd.

department: Neurology

institute: University of Texas Southwestern Medical Center

description: 10X Genomics

library_source: genomic

data_processing:
Sample demultiplexing, alignment, filtering, barcode counting, and UMI counting were conducted on CellRanger software (10X Genomics).
Assembly: mm10
Supplementary files format and content: BED-like tabular file (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/output/fragments)

molecule: genomic DNA

source_name: CNS

extract_protocol:
Bone marrow chimeric mice (BL/6) were generated by injecting CD45.1+ bone marrow cells into irradiated CD45.2+ mice. These subsequently underwent induction with active experimental autoimmune encephalopathy (EAE). At peak of disease (day 15 post induction), cell suspensions from brain and spinal cord were sorted for CD88, CD317, and either CD45.1 or CD45.2 expression. Cell populations were subjected to single cell analysis using the 10X Multiomics platform.
Library was prepared according to the manufacturer's instructions for the 10X Single Cell Multiome ATAC + Gene Expression kit

value: CNS

tag: cell type

value: Myeloid

value: EAE induction

tag: antibody


title: ZFP251 KO eWAT Sample 3

value: ZFP251 KO


title: DMSO_4 [090_CTRL]

description: H73NLDSXY_103918-001-090R_TCTCCGAT-TCGACATC

source_name: DMSO_whole worm

value: day 1 adult

value: DMSO vehicle


title: DMSO_3 [089_CTRL]

description: H2W5YDSXY_103918-001-089_GGACATCA-TACCTGCA

value: whole worm


title: DMSO_2 [088_CTRL]

description: H2W5YDSXY_103918-001-088_TGGTGAAG-CTTACAGC


title: DMSO_1 [087_CTRL]

description: H2W5YDSXY_103918-001-087_GGAATGTC-AGGAACAC


title: Wild Type eWAT Sample 3

value: Epididymal white adipose tissue


title: Zido_1 [091_ZIDO]

description: H2W5YDSXY_103918-001-091_GATAGCCA-CAACACAG

value: 50 μM zidovudine


title: CD8+--IL-10_self-product high group_rep5

city: Wuhan

first: Pingping

last: Han

state: Hubei

address: Shizishan Street, Hongshan District

country: China

institute: Huazhong Agricultural University

description: Gene expression data from blood at 35-day-old weaned pigs

hyb_protocol: Chips were washed and stained with a GeneChip Fluidics Station 450 (Affymetrix) using the standard fluidics protocol.

scan_protocol: The probe arrays were scanned using the Affymetrix® GeneChip® Scanner 3000

data_processing: Raw expression data were processed and normalized using the Robust Multichip Average (RMA) methods using Bioconductor packages in R (version=3.6.3). Differentially expressed pleiotropic genes were identified by empirical Bayes correction using LIMMA packages with the threshold of P < 0.05 and |log fold change [FC]| >1.

label: biotin

organism: Sus scrofa

source_name: CD8+--IL-10 trait pair,self-product high group

label_protocol: The RNA labelling and hybridization were conducted by a commercial Affymetrix array service (GeneTech Biotechnology Limited Company, Shang Hai, China)

growth_protocol: At the age of 35 days, all piglets were weighed.

extract_protocol: IFN-alpha and IL-10 were determined by immunological kits following the manufacturers’instructions (Beijing Shanbo, China). EPICS ALTRA flow cytometry was used to measure CD4+ and CD8+ at the Medical Laboratory Animal Centre (Hubei Medical College, China). The total RNAs were extracted from blood samples with Trizol reagent following supplier’s recommendation.

treatment_protocol: Blood samples were collected from the anterior vena cava.

value: blood


title: CD8+--IL-10_self-product high group_rep2


title: CD8+--IL-10_self-product high group_rep4


title: Palate_Day3_155

city: Chicago

first: Trevor

middle: R

last: Leonardo

state: Illinois

address: 801 South Paulina Street

department: Medicine

institute: University of Illinois at Chicago

description: 1x5mm wound, 2x5mm collection

hyb_protocol: 10ug of fragmented cRNA was hybridized to HG-U133 Plus 2.0 microarrays

scan_protocol: Affymetrix Standard protocol

data_processing: R/bioconductor, affy package, RMA normalization, Custom CDF hgu133plus2hsensgcdf_22.0.0 from BrainArray

label_protocol: Affymetrix standard eukariotic 3' labeling protocol

extract_protocol: Trizol followed by Qiagen RNeasy column-based kit purification was performed according to the manufacturer's instructions.

treatment_protocol: Participants between 18-35 years of age were screened using a survey-form, which contained information regarding demographics and general health. Individuals were ineligible for the study if they: currently used tobacco products, had an oral disease needing emergency treatment, had a known skin disease other than acne, or had a medical problem that made them a high surgical risk. Furthermore, females were ineligible for the study if they were currently pregnant, trying to become pregnant, or breast-feeding. All wounding procedures were performed by a periodontist. Wounds were placed between 10-11 a.m. to minimize variability. Individuals were asked to refrain from alcohol and non-prescription drugs for a period of 24 hours prior to the experimental sessions. One skin and one mucosal wound were placed on each subject. For oral wounds, the side of the mouth was chosen by coin toss. The wounding site was anesthetized using 2% lidocaine. A mucosal wound measuring 1x5 millimeters (mm) was placed between the first and second molars, approximately 3 mm from the marginal gingiva using a Bard Parker handle, with two blades affixed 1 mm apart to assure uniformity of the wounds. A single blade scalpel was then used to make a relatively uniform 1.5 mm deep wound, removing the biopsy tissues. The wounds were not dressed and subjects were instructed not to change their normal oral hygiene procedures, with the exception of avoiding the use of alcohol-based mouthwash. A 2x5 mm longitudinal excisional biopsy was made using a 2 mm two blade scalpel to collect oral wound biopsies. The dermal wound site was on the ventral side of the non-preferred forearm, approximately 4 centimeters below the elbow. The biopsy site was anesthetized with 2% lidocaine. Dermal wounds were created in a similar fashion to mucosal wounds, a 1x5 mm longitudinal wound approximately 1.5 mm deep. Wounds were dressed for one day with a standard adhesive bandage. Dermal and oral wounds were biopsied at 6 hours, Day 1, Day 3, and Day 7 post-wounding. Unwounded tissue (time 0) was also processed. A separate wound was used for each biopsy.

value: female

tag: subject

tag: time

value: Day 3

value: palate


title: CD8+--IL-10_self-product low group_rep3

source_name: CD8+--IL-10 trait pair,self-product low group


title: CD8+--IL-10_self-product low group_rep5


title: CD8+--IL-10_self-product high group_rep1


title: CD8+--IL-10_self-product low group_rep1


title: Palate_Day7_155

description: 1x5mm wound, 2x5mm collection

value: Day 7


title: CD8+--IL-10_self-product high group_rep3


title: CD8+--IL-10_self-product low group_rep4


title: Palate_0hours_155

description: 1x5mm wound, 2x5mm collection

value: 0 hours


title: Skin_Day7_155

description: 1x5mm wound, 2x5mm collection

value: skin


title: CD8+--IL-10_self-product low group_rep2


title: CD8+--IFN-α_self-product high group_rep5

source_name: CD8+--IFN-alpha trait pair,self-product high group


title: CD8+--IFN-α_self-product high group_rep3


title: Palate_Day7_153

description: 1x5mm wound, 2x5mm collection

value: male


title: CD8+--IFN-α_self-product high group_rep1


title: Skin_0hours_155

description: 1x5mm wound, 2x5mm collection


title: Palate_Day3_153

description: 1x5mm wound, 2x5mm collection


title: CD8+--IFN-α_self-product high group_rep2


title: CD8+--IFN-α_self-product low group_rep3

source_name: CD8+--IFN-alpha trait pair,self-product low group


title: CD8+--IFN-α_self-product low group_rep4


title: Skin_Day7_153

description: 1x5mm wound, 2x5mm collection


title: Skin_Day3_155

description: 1x5mm wound, 2x5mm collection


title: CD8+--IFN-α_self-product high group_rep4


title: CD8+--IFN-α_self-product low group_rep5


title: Palate_0hours_153

description: 1x5mm wound, 2x5mm collection


title: Skin_Day3_153

description: 1x5mm wound, 2x5mm collection


title: Skin_0hours_153

description: 1x5mm wound, 2x5mm collection


title: CD8+--IFN-α_self-product low group_rep2


title: CD4+--IL-10_self-product high group_rep5

source_name: CD4+--IL-10 trait pair,self-product high group


title: Palate_Day3_150

description: 1x5mm wound, 2x5mm collection


title: Palate_0hours_150

description: 1x5mm wound, 2x5mm collection


title: CD4+--IL-10_self-product high group_rep3


title: CD4+--IL-10_self-product low group_rep5

source_name: CD4+--IL-10 trait pair,self-product low group


title: CD4+--IL-10_self-product high group_rep1


title: CD8+--IFN-α_self-product low group_rep1


title: CD4+--IL-10_self-product low group_rep4


title: Skin_Day7_149

description: 1x5mm wound, 2x5mm collection


title: Skin_Day7_150

description: 1x5mm wound, 2x5mm collection


title: CD4+--IL-10_self-product low group_rep3


title: Palate_Day7_149

description: 1x5mm wound, 2x5mm collection


title: Palate_Day3_149

description: 1x5mm wound, 2x5mm collection


title: CD4+--IL-10_self-product high group_rep4


title: Skin_Day3_150

description: 1x5mm wound, 2x5mm collection


title: Palate_Day7_150

description: 1x5mm wound, 2x5mm collection


title: CD4+--IL-10_self-product low group_rep2


title: Palate_Day3_147

description: 1x5mm wound, 2x5mm collection


title: Skin_Day3_149

description: 1x5mm wound, 2x5mm collection


title: CD4+--IL-10_self-product low group_rep1


title: CD4+--IFN-α_self-product high group_rep4

source_name: CD4+--IFN-alpha trait pair,self-product high group


title: CD4+--IFN-α_self-product high group_rep5


title: CD4+--IL-10_self-product high group_rep2


title: Skin_Day7_147

description: 1x5mm wound, 2x5mm collection


title: CD4+--IFN-α_self-product high group_rep2


title: Skin_Day3_147

description: 1x5mm wound, 2x5mm collection


title: Skin_0hours_147

description: 1x5mm wound, 2x5mm collection


title: Palate_Day7_132

description: 1x5mm wound, 2x5mm collection


title: CD4+--IFN-α_self-product high group_rep1


title: Palate_Day7_147

description: 1x5mm wound, 2x5mm collection


title: Palate_Day3_132

description: 1x5mm wound, 2x5mm collection


title: CD4+--IFN-α_self-product low group_rep5

source_name: CD4+--IFN-alpha trait pair,self-product low group


title: CD4+--IFN-α_self-product low group_rep1


title: CD4+--IFN-α_self-product high group_rep3


title: Palate_Day1_156

description: 1x5mm wound, 2x5mm collection

value: Day 1


title: Palate_0hours_132

description: 1x5mm wound, 2x5mm collection


title: Skin_Day7_132

description: 1x5mm wound, 2x5mm collection


title: CD4+--IFN-α_self-product low group_rep4


title: CD4+--IFN-α_self-product low group_rep2


title: IL-10--W35_self-product high group_rep4

source_name: IL-10--W35 trait pair,self-product high group


title: IL-10--W35_self-product high group_rep3


title: IL-10--W35_self-product high group_rep5


title: Palate_6hours_156

description: 1x5mm wound, 2x5mm collection

value: 6 hours


title: CD4+--IFN-α_self-product low group_rep3


title: Empty_tumor_3

city: San Francisco

first: Benjamin

last: Huang

state: CA

address: 1450 3rd Street

institute: University of California San Francisco

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 using Bowtie v2
Transcript quantification was performed with RNA-seq by Expectation Maximization (RSEM) protocol
Assembly: hg38
Supplementary files format and content: Tab-separated value files including transcript abdundance (counts, TPM, and FPKM)

source_name: peripheral blood (Lymphocytes)

growth_protocol: CAR-T cells were grown in the presence of IL-7 and IL-15

extract_protocol:
RNA was harvested using Qiagen RNeasy Kit
RNA libraries for RNA-seq were prepared using BGISEQ mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: CD4/CD8 CAR-T cells were co-cultured with SEM (B-ALL cell line) for 24 hours. MACS enrichment was then used to isolate only the CAR-T cells and remove the residual B-ALL cells. For the CAR-T cells that were not exposed to B-ALL, they were not "treated."

value: peripheral blood (Lymphocytes)

tag: cell line

value: Empty vector

value: CD4 and CD8 T-cells

value: Exposed to SEM cell lines


title: Empty_tumor_2


title: Empty_tumor_1


title: IL-10--W35_self-product high group_rep2


title: IL-10--W35_self-product low group_rep3

source_name: IL-10--W35 trait pair,self-product low group


title: Palate_6hours_152

description: 1x5mm wound, 2x5mm collection


title: IL-10--W35_self-product high group_rep1


title: Empty_notumor_2

value: No tumor exposure control


title: Empty_notumor_1


title: Palate_0hours_156

description: 1x5mm wound, 2x5mm collection


title: IL-10--W35_self-product low group_rep5


title: IL-10--W35_self-product low group_rep2


title: CD72_tumor_2

value: CD72 targeted chimeric antigen receptor T-cells


title: Palate_0hours_152

description: 1x5mm wound, 2x5mm collection


title: IFN-α--W35_self-product high group_rep5

source_name: IFN-alpha--W35 trait pair,self-product high group


title: IFN-α--W35_self-product high group_rep2


title: Empty_notumor_3


title: Palate_Day1_152

description: 1x5mm wound, 2x5mm collection


title: IL-10--W35_self-product low group_rep4


title: CD72_notumor_2


title: Skin_6hours_156

description: 1x5mm wound, 2x5mm collection


title: CD72_notumor_1


title: Skin_0hours_156

description: 1x5mm wound, 2x5mm collection


title: IFN-α--W35_self-product low group_rep4

source_name: IFN-alpha--W35 trait pair,self-product low group


title: Skin_Day1_152

description: 1x5mm wound, 2x5mm collection


title: Skin_0hours_152

description: 1x5mm wound, 2x5mm collection


title: IFN-α--W35_self-product low group_rep3


title: CD8+--W35_self-product high group_rep5

source_name: CD8+--W35 trait pair,self-product high group


title: Skin_Day1_156

description: 1x5mm wound, 2x5mm collection


title: CD72_tumor_3


title: IFN-α--W35_self-product high group_rep4


title: IFN-α--W35_self-product high group_rep3


title: Palate_Day1_146

description: 1x5mm wound, 2x5mm collection


title: CD8+--W35_self-product high group_rep4


title: CD72_tumor_1


title: Palate_0hours_148

description: 1x5mm wound, 2x5mm collection


title: CD72_notumor_3


title: CD19_tumor_1

value: CD19 targeted chimeric antigen receptor T-cells


title: Skin_6hours_152

description: 1x5mm wound, 2x5mm collection


title: CD19_notumor_3


title: CD8+--W35_self-product high group_rep2

value: blood


title: IFN-α--W35_self-product low group_rep5


title: Palate_0hours_146

description: 1x5mm wound, 2x5mm collection


title: CD19_tumor_3


title: IFN-α--W35_self-product high group_rep1


title: IFN-α--W35_self-product low group_rep1


title: CD8+--W35_self-product high group_rep3


title: CD8+--W35_self-product low group_rep1

source_name: CD8+--W35 trait pair,self-product low group


title: IL-10--W35_self-product low group_rep1


title: IFN-α--W35_self-product low group_rep2


title: Palate_Day1_148

description: 1x5mm wound, 2x5mm collection


title: CD19_tumor_2


title: CD8+--W35_self-product low group_rep5


title: CD4+--W35_self-product high group_rep4

source_name: CD4+--W35 trait pair,self-product high group


title: CD8+--W35_self-product low group_rep3


title: CD4+--W35_self-product high group_rep5


title: CD8+--W35_self-product high group_rep1


title: Skin_0hours_148

description: 1x5mm wound, 2x5mm collection


title: Skin_6hours_146

description: 1x5mm wound, 2x5mm collection


title: CD8+--W35_self-product low group_rep4


title: CD19_notumor_2


title: Skin_6hours_148

description: 1x5mm wound, 2x5mm collection


title: CD19_notumor_1


title: CD4+--W35_self-product high group_rep1


title: CD4+--W35_self-product low group_rep5

source_name: CD4+--W35 trait pair,self-product low group


title: Colon fibroblast_Normal MiGS (N3)

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
For MiGS data, reads were aligned to hg19 with bowtie2 (options: -N0 -L 20). Reads with mapping quality (MAPQ) < 30 were discarded. Average coverage in non-overlapping 50bp bins was counted genome-wide using the preprocessing functions of MethylAction (Bhasin, et al., 2015). Chromosomes X and Y were excluded, because we from both sexes
For RNA-seq data, reads were aligned to human genome (Homo_sapiens.GRCh37) using STAR 2.4.0.1.  Read counts were quantified for ENSEMBL human genes using featureCounts (Liao, et al., 2014) (options: isGTFAnnotationFile=TRUE, useMetaFeatures=TRUE, isPairedEnd=TRUE, nthreads=18, minMQS=30). Only reads MAPQ ≥ 30 are used for subsequent analysis.  FPKM values were computed using edgeR (Robinson, et al., 2010). Chromosomes X and Y were excluded, because the samples are from both sexes.
Genome_build: hg19
Supplementary_files_format_and_content: For MiGS data, a text file has been provided for each sample that contains normalized read counts within the non-overlapping 50bp windows genome wide. Windows with all zero values or all values below a noise cutoff have been removed, so only windows considered to have signal remain. Each row represents one 50bp window. The genomic coordinates (hg19) are provided in the first three columns. The remaining column contains the normalized coverage of MiGS reads for the window in the sample.
Supplementary_files_format_and_content: For RNA-seq data, reads were counted for ENSEMBL transcription units using featureCounts. The provided CSV file contains one row for each gene, one column containing the raw read counts (no normalization for library size) for each sample, and one column containing the FPKM-normalized read counts for each sample.

source_name: Colon fibroblast

extract_protocol:
DNA and RNA are extracted using Qiagen AllPrep DNA/RNA kit
The MBD-Seq library was constructed by enriching for methylated DNA fragments using MiGS (MBD-isolated Genome Sequencing, Serre 2010). After enrichment, the library is prepared using NEBNext® DNA Library Prep Master Mix Set for Illumina (New England Biolabs) and Illumina Trueseq adapters are added for sequencing.
The RNA-seq library was constructed using the stranded Illumina RNA-seq library prep.

tag: disease state

value: Normal

value: normal fibroblast


title: Colon fibroblast_Normal MiGS (N2)


title: mdx, replicate 1

city: Los Angeles

first: Yerbol

middle: Z.

last: Kurmangaliyev

address: 675 Charles E. Young Drive South

institute: University of California, Los Angeles

data_processing:
RNA-Seq reads were mapped to the human reference genome (hg38) using STAR
Uniquely mapped were used to measure expression annotated genes (Ensembl v.92).
Raw gene counts were normalized to CPM (counts-per-million)
Differential expression analysis was performed using edgeR/LRT
Assembly: hg38
Supplementary files format and content: Excel file with normalized expression values and results of differential gene expression analysis for all genes

source_name: hPSC SMPC

growth_protocol: hPSC SMPCs cultured on acellular matrices

extract_protocol:
total RNA extraction
KAPA Stranded mRNA-Seq Kit

value: hPSC SMPC

value: skeletal muscle progenitor cell

value: mdx


title: mdx, replicate 2


title: wild-type, replicate 2

value: WT


title: CD8+--W35_self-product low group_rep2


title: CD4+--W35_self-product high group_rep3


title: wild-type, replicate 3


title: Skin_0hours_146

description: 1x5mm wound, 2x5mm collection

value: male

value: 0 hours

value: skin


title: Palate_0hours_147

description: 1x5mm wound, 2x5mm collection

value: female

value: palate


title: Colon fibroblast_Colitis MiGS (CO2)

value: Colitis

value: colitis fibroblast


title: CD4+--W35_self-product low group_rep4


title: Colon fibroblast_Colitis MiGS (CO1)


title: CD4+--W35_self-product high group_rep2


title: CD4+--W35_self-product low group_rep1


title: Skin_Day1_146

description: 1x5mm wound, 2x5mm collection

value: Day 1


title: Palate_6hours_143

description: 1x5mm wound, 2x5mm collection

value: 6 hours


title: CD4+--W35_self-product low group_rep3


title: Palate_0hours_143

description: 1x5mm wound, 2x5mm collection


title: CD4+--W35_self-product low group_rep2


title: Palate_Day1_143

description: 1x5mm wound, 2x5mm collection


title: Colon fibroblast_Colitis MiGS (CO5)


title: Palate_6hours_142

description: 1x5mm wound, 2x5mm collection


title: wild-type, replicate 1


title: WT2_Cer

city: Niigata

first: Nozomu

last: Yoshioka

address: 1－757, Asahimachi-dori, Chuo-ku

department: Graduate School of Medical and Dental Sciences

country: Japan

institute: Niigata university

data_processing:
alignment with OLego
to have BAM and Bed file
transcript level and alternative splicing events with Quantas
Assembly: mm10
Supplementary files format and content: .txt gene_id gene_symbol, Tag_Number, RPKM

source_name: Cerebellum

growth_protocol: Forebrain and cerebellum were dissected from wild-type mice

extract_protocol:
Total RNA was obtained from independent two replicates of brain from wild-type mice. The RNA was extracted using QIAzol followed by the generation of mRNA libraries using standard Illumina protocols for poly-A selection, fragmentation, and adaptor ligation according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using NEBNext Ultra II Directional RNA Library Prep Kit (E7760)

value: Cerebellum

value: wild type


title: Colon fibroblast_Normal MiGS (N1)

value: Normal


title: Colon fibroblast_Colitis MiGS (CO4)


title: Colon fibroblast_Cancer MiGS (CA3)

value: Cancer

value: cancer associated fibroblast


title: WT1_Cer


title: Colon fibroblast_Cancer MiGS (CA2)


title: Colon fibroblast_Normal RNA (N3)

description:
N3_RNA
Fibroblast_RNAseq_counts.csv

value: normal fibroblast


title: Colon fibroblast_Cancer MiGS (CA1)


title: Colon fibroblast_Normal RNA (N2)

description:
N2_RNA
Fibroblast_RNAseq_counts.csv


title: Colon fibroblast_Cancer MiGS (CA4)


title: WT1

source_name: Forebrain

value: Forebrain


title: Mecp2-null, replicate 2, scRNAseq

city: Shanghai

first: Huiping

last: Li

address: Wanyuan Road 399

institute: Children's hospital of Fudan university

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10xGenomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Dura mater

extract_protocol:
One-month-old mice were euthanized by Avertin (2, 2, 2-Tribromoethanol, 20 mg/ml) overdose and transcardially perfused with 20 ml ice-cold phosphate-buffered saline (PBS). The mice were decapitated posterior to the occipital bone immediately, and removed the overlying skin and muscles from the skull. The dorsal part of the skull was carefully removed for isolating the dura. After peeling from the skullcap, the dura was cut into small pieces in ice-cold RPMI 1640 medium (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) and incubated with an enzyme mix (0.25% Trypsin and 10 U ml−1 Collagenase type I) at 37 °C for 15 min. The solution was gently passed through 70 mm nylon mesh cell strainers with a sterile plastic plunger to yield a single-cell suspension. The single-cell suspension was then centrifuged at 300 g for 10 min. The supernatant was removed completely and the cell pellet was resuspended in FACS buffer (pH 7,4; 0.1 M PBS; 1 mM EDTA; 1% BSA). Magnetic separation of CD45 positive cells was performed according to the manufacturer’s instructions for CD45 MicroBeads (Miltenyi Biotec, Bergisch Gladbach, Germany).
RNA libraries were prepared with Chromiun Single cell 3' Reagent v3 Kits according to the manufacturer's protocol.

value: Dura mater

value: immune cells


title: 11.18.KO.t6

city: Philadelphia

first: David

middle: Sheng Ming

last: Lee

state: Pennsylvania

address: 1500 Chestnut St Apt 12D

department: Genetics

institute: University of Pennsylvania

data_processing:
Sequence reads trimmed with Trimmomatic v.0.36
Trimmed reads were mapped to Mus musculus GRCm38 reference genome using STAR v.2.5.2b
Unique gene hit counts were calculated using featureCounts from Subread v.1.5.2
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Stimulated

growth_protocol: bulk splenic TE cells from control (CTL) and CKO littermates were flow sorted to obtain a high purity (>99%) CD4+CD25- population

extract_protocol:
TruSeq stranded mRNA sequencing libraries were generated from 100 nanograms of total RNA (RIN range 5.0 - 8.7, median 7.4, average 7.0) (GeneWiz, South Plainfield, NJ).
Libraries were indexed, pooled and sequenced using Illumina HiSeq 2x150 bp paired end sequencing

treatment_protocol: TE cell activation ("stimulated") was achieved by incubating 1 million sorted TE cells with 3 μL CD3/CD28 mouse T-activator beads (Thermofisher, 11456D) per 1 mL T cell media for 6 hours followed immediately by pelleting then disruption and freezing in TRIzol

value: splenic T effector cells

value: Fl-Pcbp2/CD4cre (CKO)

tag: timepoint

tag: Sex

value: M


title: Colon fibroblast_Normal RNA (N1)

description:
N1_RNA
Fibroblast_RNAseq_counts.csv


title: Mecp2-null, replicate 1, scRNAseq


title: 10.28.WT.t6

value: Fl-Pcbp2 (CTL)

value: F


title: 5.6.KO.t6


title: 9.20.WT.t6


title: Colon fibroblast_Colitis RNA (CO5)

description:
CO5_RNA
Fibroblast_RNAseq_counts.csv

value: Colitis

value: colitis fibroblast


title: Palate_Day1_142

description: 1x5mm wound, 2x5mm collection

value: female

value: Day 1

value: palate


title: wt, replicate 2, scRNAseq

value: wild type


title: 5.13.WT.t6

value: 6 hours


title: Skin_0hours_143

description: 1x5mm wound, 2x5mm collection

value: male

value: 0 hours

value: skin


title: Colon fibroblast_Colitis RNA (CO4)

description:
CO4_RNA
Fibroblast_RNAseq_counts.csv


title: 8-4

first: Zongqi

last: You

address: #12, Wulumuqi M Road

institute: Huashan Hospital

data_processing:
Illumina Casava software used for basecalling
Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted ). Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both reads will be filtered if either end is low-quality). Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%).
Reads Count for each gene in each sample was counted by HISAT v2.1.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DESeq2 was designed for differential gene expression analysis between two samples with biological replicates. Genes with q≤0.05 and |log2_Foldchange|≥1 are identified as differentially expressed genes.
Assembly: Mus_musculus.GRCm38.97.chr
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: C57BL/6 mice, denervation, Day28

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: gastrocnemius muscle

value: sciatic nerve transection


title: Colon fibroblast_Cancer RNA (CA4)

description:
CA4_RNA
Fibroblast_RNAseq_counts.csv

value: Cancer

value: cancer associated fibroblast


title: Skin_6hours_142

description: 1x5mm wound, 2x5mm collection

tag: tissue


title: Skin_Day1_143

description: 1x5mm wound, 2x5mm collection


title: wt, replicate 1, scRNAseq

value: Dura mater

value: immune cells


title: Palate_0hours_142

description: 1x5mm wound, 2x5mm collection


title: 5.13.KO.t6

value: splenic T effector cells

value: Fl-Pcbp2/CD4cre (CKO)

value: M


title: Palate_6hours_140

description: 1x5mm wound, 2x5mm collection

value: female


title: Skin_Day1_142

description: 1x5mm wound, 2x5mm collection

value: Day 1


title: WT2

value: Forebrain


title: Colon fibroblast_Cancer RNA (CA3)

description:
CA3_RNA
Fibroblast_RNAseq_counts.csv


title: Skin_0hours_142

description: 1x5mm wound, 2x5mm collection


title: 8-1


title: 8-2


title: 4.24.WT.t6

value: Fl-Pcbp2 (CTL)

value: F


title: 10.28.WT.t0

source_name: Unstimulated

value: Baseline (0 hour)


title: 7-4

source_name: C57BL/6 mice, denervation, Day21


title: 8-3


title: Colon fibroblast_Colitis RNA (CO2)

description:
CO2_RNA
Fibroblast_RNAseq_counts.csv

value: Colitis

value: colitis fibroblast


title: 4.29.WT.t6

value: 6 hours


title: Skin_6hours_143

description: 1x5mm wound, 2x5mm collection

value: male

value: skin


title: 11.18.KO.t0


title: 9.20.WT.t0


title: Colon fibroblast_Cancer RNA (CA2)

description:
CA2_RNA
Fibroblast_RNAseq_counts.csv

value: Cancer

value: cancer associated fibroblast


title: Colon fibroblast_Cancer RNA (CA1)

description:
CA1_RNA
Fibroblast_RNAseq_counts.csv


title: Palate_6hours_129

description: 1x5mm wound, 2x5mm collection

value: palate


title: 7-3

value: gastrocnemius muscle

value: sciatic nerve transection


title: 9.20.KO.t0

value: splenic T effector cells

value: Fl-Pcbp2/CD4cre (CKO)

value: M


title: Palate_Day1_140

description: 1x5mm wound, 2x5mm collection

value: female

value: Day 1


title: 7-2


title: 5.6.WT.t0

value: Fl-Pcbp2 (CTL)

value: F


title: 7-1


title: 5.6.KO.t0

value: Baseline (0 hour)


title: 5.13.WT.t0


title: DU145_3

data_processing:
FASTQ files containing the raw sequence reads from polyA-seq were de-barcoded by allowing up to 2 mismatches between the first 6 bases and one of 4 barcodes. Reads with more than 2 mismatches from a barcode used in the experiment were discarded. The next 6 bases were designed to contain a random hexamer for de-duplication of PCR duplicates. This sequence was removed from the read and annotated into the read name. These de-barcoded FASTQ files, one per individual sample/replicate, are provided in this record.
Next, sequenced polyA tails were removed from the reads by detecting the first instance of 4 consecutive As with no more than 1 non-A base in the following 6 base pairs. The remaining sequences were aligned to the hg19 genome build using bowtie 2.2.5. Uniquely mapping alignments were retained by requiring a mapping quality (MAPQ) score > 20. PCR duplicates were removed by collapsing all alignments with identical random hexamer annotations and the same alignment position into a single alignment. Reads due to predicted internal priming of genomic A were removed by filtering all alignments with at least 7 of 10 or 6 consecutive downstream A bases. Processing regions were computed by merging all regions with a coverage of at least 10 reads in one experiment within 10 bp of each other into contiguous genomic ranges.
Genome_build: hg19
Supplementary_files_format_and_content: A text file is provided that contains the genomic coordinates for each processing region (PR) and the un-normalized count of the number of overlapping reads forming the PR. There is one column for each sample, named the same as the samples in this record.

molecule: polyA RNA

growth_protocol: LNCaP and DU145 were grown in RPMI 1640 (Thermo Fisher Scientific) with 10% FBS (Atlanta Biologicals) at 37°C and 5% CO2. Cells were harvested at 75-95% confluence by PBS wash, scraping into PBS, pelleting at 500g for 2 minutes, and storage of cell pellet at -80°C. PrEC cells (Lonza) were grown using PrEGM BulletKit (Lonza) at 37°C and 5% CO2 and were harvested according to manufacturer’s instructions.

extract_protocol:
Total cellular RNA was prepared from 4 x 10 cm plates of each cell type using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to manufacturer’s instructions. Poly(A)+ RNA was selected from 10 ug of total cellular RNA using oligo(dT)25 Dynabeads (Thermo Fisher Scientific) according to manufacturer’s instructions.
This poly(A) site sequencing technique was derived by modification of an existing technique for ribosome footprinting (Ingolia et al., Science, 2009, PMID: 19213877). Poly(A)+ RNA was fragmented by addition of 2X fragmentation buffer to 1X final concentration (6 mM Na2CO3, 44 mM NaHCO3, 1 mM EDTA) and incubation at 95°C for 40 minutes. Fragmentation was stopped on ice, and then RNA was precipitated with 300 mM NaOAc, pellet paint, and isopropanol. After resuspension in stop solution/PAGE loading buffer (Affymetrix), RNA fragments were separated on 15% PAGE/urea gels then 50-100 nt RNA was purified by excision and maceration of gel fragments followed by elution of RNA into diffusion buffer (20 mM Tris pH=7.5, 250 mM NaOAc, 1 mM EDTA, 0.25% SDS) at 37°C for 45 min with shaking. cDNA copies of poly(A)+ RNA fragments were made using SuperScript III (Thermo Fisher Scientific), and 1 of 4 anchored oligo(dT) primers (/5Phos/NNNNNNXXXXXXCCGCATCGTCCTCCCTCCCTATAGTGACTCGTATTA/iSp18/CACTCA/iSp18/CCGCTGGAAGTGACTGACACTTTTTTTTTTTTTTTTTTTTVN; N=degenerate bases; XXXXXX=4 different sample barcodes TGACCA, GCCAAT, CTTGTA, or AAGTGC ; V=C, G, or T) at 48°C for 30 minutes according to manufacturer’s instructions. Residual RNA was degraded by addition of NaOH to 0.1 M and incubation at 98°C for 15 minutes. 2X stop solution/PAGE loading buffer (Affymetrix) was added and cDNA was separated from unextended oligo(dT) primer on 10% PAGE/urea gels then 120-170 nt cDNA was purified by excision and maceration of gel fragments and elution of cDNA into diffusion buffer (20 mM Tris pH=7.5, 250 mM NaOAc, 1 mM EDTA, 0.25% SDS) at 50°C for 45 min with shaking. cDNA was precipitated using 300 mM NaOAc, pellet paint, and isopropanol, then circularized using CircLigase (Epicentre) according to manufacturer’s instructions. Circularization causes primer sequences for amplification to face each other, allowing cDNA libraries of poly(A) sites to be amplified for sequencing using primers that contain machine adaptors (AATGATACGGCGACCACCGACTATGGATACTTAGTCAGGGAGGACGATGCGG; CAAGCAGAAGACGGCATACGACCGCTGGAAGTGACTGACAC). PCR was carried out using Phusion DNA polymerase (Thermo Fisher Scientific) according to manufacturer’s instructions (initial denaturation 98°C 30 sec; cycle at 98°C 10 sec, 58°C 30 sec, 72°C 30 sec). Optimum cycle number was empirically determined using a small aliquot of cDNA library, then the rest of each cDNA library was amplified using this cycle number. Amplified libraries (150-200 bp) were gel purified on 2% agarose gels using a Gel Purification Kit (Qiagen), slightly altering manufacturer’s instructions. Briefly, gel slices were dissolved in buffer QG at room temperature instead of 50°C and all optional washes were carried out for 5 minutes each as recommended for sensitive applications. Final libraries were sequenced using a custom primer (CTATGGATACTTAGTCAGGGAGGACGATGCGG) on Illumina HiSeq 2000 at Genome Quebec.

tag: cancer

value: tumor


title: 6-4

source_name: C57BL/6 mice, denervation, Day14


title: DU145_1


title: DU145_4


title: DU145_2


title: 6-3


title: LNCaP_4

source_name: LNCaP


title: 5.13.KO.t0

tag: genotype


title: 6-2

tag: treatment


title: LNCaP_3


title: 6-1


title: LNCaP_2


title: Palate_0hours_140

description: 1x5mm wound, 2x5mm collection

tag: gender

value: 0 hours


title: 4.24.KO.t0


title: Palate_Day1_129

description: 1x5mm wound, 2x5mm collection


title: LNCaP_1


title: 5-4

source_name: C57BL/6 mice, denervation, Day7


title: 4.29.WT.t0


title: 5-3


title: Skin_6hours_129

description: 1x5mm wound, 2x5mm collection

value: 6 hours


title: 4.29.KO.t0


title: PrEC_3

source_name: PrEC

value: normal


title: Leaf3_input, rep3, RNA-seq

city: Xinxiang

first: Li

last: Wang

address: No.46, Jianshe East Road

department: College of Life Science

institute: Henan Normal University

data_processing:
Cutadapt software was used to remove low-quality bases, undetermined bases and reads containing adaptor contamination
Hisat2 software was applied to align reads to the reference genome of rice
Mapped reads of IP and Input libraries were provided for R package exomePeak for m6A peak identified.  HOMER were used for de novo motif identification, followed by localization of the motif with respect to peak summit
Called peaks were annotated by intersection with gene architecture by using R package ChIPseeker
StringTie was applied to determine the expression level for all mRNAs from Input libraries by calculating FPKM
Supplementary files format and content: fpkm expression, peak, fastq

organism: Oryza sativa

source_name: leaf

growth_protocol: Rice seeds were planted in the experimental field of Henan Normal University (35°19′ N, 113°54′ E) on May 2, 2019.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacture's protocol. Poly (A) mRNA was purified  using poly-T oligo attached magnetic beads (Invitrogen) and then fragmented into approximately ~100-nt-long oligonucleotides using Magnesium RNA Fragmentation Module.  Ten percent of fragmented mRNA was aliquoted as input control (Input). The remaining fragmented mRNA was used to collect  m6A-containing RNA fragments (immunoprecipitated, IP) by using m6A-specific antibody.
Both IP and Input RNA fragments were used to construct strand-specific cDNA libraries according to the dUTP method.

treatment_protocol: Panicles at booting stage (August 3, 2019) and flowering stage (August 14, 2019), flag leaves (LF) at flowering stage were collected at approximately 3:00 PM, respectively.

value: leaf

tag: Stage

value: flowering stage

value: Nipponbare


title: PrEC_4


title: Palate_0hours_129

description: 1x5mm wound, 2x5mm collection

value: palate


title: Skin_0hours_140

description: 1x5mm wound, 2x5mm collection

value: skin


title: Skin_Day1_129

description: 1x5mm wound, 2x5mm collection


title: PrEC_2


title: 5-1

value: gastrocnemius muscle

value: sciatic nerve transection


title: Leaf2_input, rep2, RNA-seq


title: 5-2


title: Skin_Day1_140

description: 1x5mm wound, 2x5mm collection


title: 4.24.WT.t0

value: splenic T effector cells


title: Palate_Day3_126

description: 1x5mm wound, 2x5mm collection

value: male

value: Day 3


title: Leaf1_input, rep1, RNA-seq


title: 4-3

source_name: C57BL/6 mice, denervation, Day5


title: PrEC_1


title: DICER_4

source_name: DICER(ex5) colon cancer cell line derived from HCT116

growth_protocol: DICER cells were grown in McCoy's 5A (Modified) Medium (Thermo Fisher Scientific) with 10% FBS (Atlanta Biologicals) at 37°C and 5% CO2. Cells were harvested at 75-95% confluence by PBS wash, scraping into PBS, pelleting at 500g for 2 minutes, and storage of cell pellet at -80°C.

tag: dicer status

value: hypomorph


title: 4-4


title: FS3_input, rep3, RNA-seq

source_name: panicle

value: panicle


title: Palate_Day1_126

description: 1x5mm wound, 2x5mm collection

value: Day 1


title: DICER_3


title: 4-2


title: Skin_0hours_129

description: 1x5mm wound, 2x5mm collection

value: female


title: FS2_input, rep2, RNA-seq


title: 4-1


title: BS3_input, rep3, RNA-seq

value: booting stage


title: Palate_Day1_117

description: 1x5mm wound, 2x5mm collection


title: Palate_Day3_117

description: 1x5mm wound, 2x5mm collection


title: Palate_0hours_126

description: 1x5mm wound, 2x5mm collection

value: 0 hours


title: Palate_0hours_117

description: 1x5mm wound, 2x5mm collection


title: Skin_Day3_126

description: 1x5mm wound, 2x5mm collection


title: FS1_input, rep1, RNA-seq


title: DICER_2


title: DICER_1


title: Wet AMD aqueous humor

city: Daegu

first: Areum

last: Jeong

address: 170 Hyunchungro, Nam-gu

department: Ophthalmology

institute: Yeungnam University College of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hsa (mirbase) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hsa
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: aqueous humor

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Multiplex Small  RNA Library Prep kit (New England BioLabs, Inc., USA) according to the manufacturer’ instructions.

value: aqueous humor


title: Skin_Day1_126

description: 1x5mm wound, 2x5mm collection


title: PCV aqueous humor


title: Skin_Day3_117

description: 1x5mm wound, 2x5mm collection


title: 3-4

source_name: C57BL/6 mice, denervation, Day3


title: BS1_input, rep1, RNA-seq


title: 3-3


title: Normal control aqueous humor


title: Leaf3_IP, rep3, m6A-seq

value: leaf


title: BS2_input, rep2, RNA-seq


title: 3-1


title: 2-4

source_name: C57BL/6 mice, denervation, Day1


title: Palate_Day3_122

description: 1x5mm wound, 2x5mm collection


title: Skin_0hours_117

description: 1x5mm wound, 2x5mm collection


title: U87 shCasp8 (shC8) 3

city: Rome

first: Matteo

last: Pallocca

address: Via Fermo Ognibene

country: Italy

institute: Italian National Cancer Institute "Regina Elena"

data_processing:
BaseSpace Illumina Cloud Environment was used for basecalling and demultiplexing.
RNA-seq was analyzed via the web pipeline RAP, which employs the Tuxedo suite for mapping (Tophat) and transcripts reconstruction (Cufflinks, Cuffdiff)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: U87 cell line

growth_protocol: DMEM with 10% FBS, 37°C, 5% CO2

extract_protocol:
total RNA was extracted from U87 cell line using Qiazol (Invitrogen), purified from genomic DNA contamination through a DNase I (Qiagen) digestion step and further enriched by Qiagen RNeasy columns for gene expression profiling (Qiagen). Quantity and integrity of the extracted RNA were assessed by NanoDrop Spectrophotometer (NanoDrop Technologies) and by Agilent 2100 Bioanalyzer (Agilent Technologies), respectively.
RNA libraries for sequencing were generated in triplicate according to the Illumina TruSeq Stranded Total RNA kit with an initial ribosomal depletion step using Ribo Zero Gold (Illumina, Inc., San Diego, CA, US). Starting material was 500ng of total RNA.

treatment_protocol: retrovirus infection to silence or not Caspase-8 expression

value: Glioblastoma cell

value: infection with the retroviral shC8 vector


title: Leaf2_IP, rep2, m6A-seq

value: flowering stage

value: Nipponbare


title: U87 shCasp8 (shC8) 2


title: Leaf1_IP, rep1, m6A-seq


title: 2-3

value: gastrocnemius muscle


title: FS3_IP, rep3, m6A-seq


title: 3-2

value: sciatic nerve transection


title: 2-1


title: FS2_IP, rep2, m6A-seq


title: 2-2


title: U87 scramble (shCTR) 3

value: infection with the retroviral scramble vector


title: Palate_0hours_122

description: 1x5mm wound, 2x5mm collection

value: palate


title: Skin_0hours_126

description: 1x5mm wound, 2x5mm collection

value: male

value: skin


title: Palate_Day3_115

description: 1x5mm wound, 2x5mm collection

value: Day 3


title: Palate_Day1_122

description: 1x5mm wound, 2x5mm collection

value: Day 1


title: U87 shCasp8 (shC8) 1


title: Palate_Day1_115

description: 1x5mm wound, 2x5mm collection


title: FS1_IP, rep1,m6A-seq

value: panicle


title: 1-4

source_name: C57BL/6 mice, denervation, Day0


title: U87 scramble (shCTR) 1


title: U87 scramble (shCTR) 2


title: 1-3


title: 1-2


title: Skin_Day1_122

description: 1x5mm wound, 2x5mm collection

value: female


title: Skin_Day3_122

description: 1x5mm wound, 2x5mm collection


title: 1-1


title: BS3_IP, rep3, m6A-seq

value: booting stage


title: Hypoxia_1

city: Helsinki

first: Päivi

last: Saavalainen

address: Haartmaninkatu 8

department: TRIMM

country: Finland

institute: University of Helsinki

description:
Drop-seq protocol
All sample metadata is included in the file Sample_information.xls

data_processing:
Sequencing in 75 cycles produced 20 bp Read 1 (bases 3-12 sample barcode, bases 13-20 UMI) and 55 bp Read 2 (sequence derived from the mRNA).
Raw sequence data was filtered to remove reads shorter than 20 bp.
The original pipeline suggested in (Macosko EZ et al. Cell 2015; https://github.com/broadinstitute/Drop-seq) for processing of drop-seq data was used. Briefly, reads were additionally filtered to remove polyA tails of length 6 or greater, then aligned to the human genome using STAR aligner, with default settings. Uniquely mapped reads were grouped according to the 1-12 barcode, and gene transcripts were counted by their Unique Molecular Identifiers (UMIs) to reduce bias emerging from the PCR amplification. Digital expression matrices (DGE) reported the number of transcripts per gene in a given sample (according to the distinct UMI sequences counted).
Supplementary_files_format_and_content: Digital Gene Expression (DGE): tab-delimited text file containing UMI read counts for each sample

source_name: JEG-3 cell line

growth_protocol: All experiments were performed using JEG-3 cells. These cells were cultured by Eagle's minimum essential medium (MEM) with non-essential amino acids, 90% sodium pyruvate, and 10% antibiotic-free Fetal bovine serum (FBS). Cells from passages 5-12 were used for experiments. All cell culture experiments were performed using a regular cell incubator (37 ºC with 5% CO2)

extract_protocol:
RNA was extracted from the JEG-3 cells incubated under different conditions using an RNeasy Mini Kit (Qiagen) following manufacturer’s guidelines. Cells were homogenized with QIAshredder columns (Qiagen). After extraction, RNA was quantified using a Qubit 2 fluorometer (Thermo Fisher Scientific) with the Qubit RNA HS Assay Kit (Thermo Fisher Scientific), and stored at -70°C.
RNA sequencing method was designed based on the Drop-seq protocol described in (Macosko EZ et al. Cell 2015). Briefly, 10 ng of RNA was mixed with Indexing Oligonucleotides. After 5 minutes of incubation the RNA was combined with RT mix (1 x Maxima RT buffer, 1 mM dNTPs, 10 U/µl Maxima H- RTase, 1 U/µl RNase inhibitor and 2.5 µM Template Switch Oligo). Samples were incubated for 30 minutes at 22°C and 90 minutes at 42°C. The constructed cDNA was amplified by PCR. The PCR products were pooled together in sets of 12 samples containing different Indexing Oligos and purified with Agencourt AMPure XP Beads according to the manufacturer’s instructions. The 3’-end cDNA fragments for sequencing were prepared using the Nextera XT (Illumina) tagmentation reaction. The reaction was performed according to manufacturer’s instruction, with the exception of the P5 SMART primer that was used instead of S5xx Nextera primer. Each set of 12 samples that was pooled after the PCR reaction was tagmented with a different Nextera N7xx index. Subsequently, the samples were PCR amplified and purified twice using Agencourt AMPure Beads. The libraries were sequenced on a Illumina NextSeq 500, with a custom primer producing read 1 of 20 bp and read 2 (paired end) of 50 bp. Sequencing was performed at the Functional Genomics Unit of the University of Helsinki, Finland.

treatment_protocol: Polypropylene containing 24 wells were coated with poly-dimethyl-siloxane (PDMS). Then, 0.5 mg/ml Myogel (50µl/well) and/or fibrin matrix were added on PDMS, while control wells were remained uncoated. For stabilizing the coating, the plates were incubated in 37 ºC with 5% CO2 for 24 hours. JEG-3 cells seeded 24 hours after coating of the plates. The cells were lysed after the first and third day for RNA analysis

value: epithelial placenta cells

value: multiplexed sample (mixture of treatments)


title: Hypoxia_2


title: GoatSkin21

status: Public on Dec 28 2022

city: BENGALURU

first: Veerasamy

last: Sejian

address: National Institute of Animal Nutrition and Physiology

country: India

data_processing:
Quality trimming using fastp
Alignment against Goat reference genome using Bismark
PCA using R
differential gene expression analysis using methyl kit
Annotation using Homer
Genome_build: goat genome GCF_001704415.1_ARS1
Supplementary_files_format_and_content: tab delimited format of methylation estimated

organism: Capra hircus

source_name: Goat Skin

extract_protocol:
Skin tissue was chopped into fine pieces and lysed by adding Buffer ATL, ProteinaseK and Buffer AL. The lysate was bound to Dneasy Mini Spin Column and the DNA was eluted in Buffer AE after subsequent washes. (Dneasy® Blood& Tissue Kit Cat.No.69506)
The purified gDNAwas bisulfite converted using Lightning Conversion Reagent and amplified with specific PreAmp primeres followed by Amplification with Library Amp Primers and Index primers. (Pico Methyl-Seq Library Prep Kit for Illumina-based sequencing; Cat.No. D5456-A)

value: Skin

value: Heat stress


title: GoatSkin19

institute: National Institute of Animal Nutrition and Physiology


title: GoatSkin16

value: Control


title: GoatSkin14


title: GoatSkin13


title: GoatSkin11


title: Skin_Day3_115

description: 1x5mm wound, 2x5mm collection


title: GoatSkin8


title: GoatSkin6


title: Palate_0hours_115

description: 1x5mm wound, 2x5mm collection

value: 0 hours


title: GoatSkin3


title: GoatSkin5


title: BS2_IP, rep2, m6A-seq

value: Nipponbare


title: 24C

tag: breed


title: 22C


title: BS1_IP, rep1, m6A-seq


title: 20C


title: 19C


title: GoatSkin20


title: 17C


title: GoatSkin10


title: 16C


title: Skin_Day1_115

description: 1x5mm wound, 2x5mm collection


title: 12C


title: 11C


title: 15C


title: 14C


title: 13C


title: 7C


title: 8C


title: 10C


title: 6C


title: 5C


title: 9C


title: 21C


title: 23C


title: 2C


title: 3C


title: 4C


title: 1D


title: 18C


title: Gastrocnemius, protein restriction sample for 3 month protein restriciton condition,bio rep1

city: Tokyo

first: Sihui

last: Ma

address: Yayoi 1-1-1

institute: The university of Tokyo

description:
Gene expression data of gastrocnemius under protein restriction condition
Low protein_3month_LP_1
LP9

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genom 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: After washing and staining, array scanning was performed using GeneChip Hybridization and Affymetrix Gene Array Scanner 3000

data_processing: The data were analyzed with R using Affymetrix default analysis settings and global scaling as normalization method.

organism: Rattus norvegicus

source_name: Gastrocnemius, 3 month protein restriciton condition

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: 3.5-week-old male Wistar rats were purchased from Charles River Japan (Kana-gawa, Japan) and kept in a room maintained at 22 ± 2°C with relative humidity at 40–60% and a 12 h light (8:00–20:00) and 12 h darkness (20:00–8:00) cycle. They were al-lowed free access to water throughout the experiment.

extract_protocol: Total RNA was isolated from homogenized gastrocnemius tissue using RNeasy Fibrous Tissue Mini Kit (Qiagen, CA, USA) according to the manufacturer’s instruc-tions. The total RNA concentration was measured with a NanoDrop® spectrophotom-eter (ND-1000, NanoDrop, DE, USA). The quality of the RNA was determined by as-sessing the A260/280, A260/230 ratio and by agarose gel electrophoresis.

treatment_protocol: In the pre-experimental period, the rats were fed a purified diet containing 15% protein from casein for 3 days. After then, rats were randomly divided into 2 groups (n=12 and 13) with same average weight, then provided with different diets: a 15% casein diet (CN, n=13) as a control diet, or a calorie-matched 8% casein diet (LP, n=12) as a low-protein diet for 4 weeks. On the 27th day, rats in each group were divided into 2 subgroups again. 6 of each group were named as CN or LP, while the other rats are named CN-R or LP-R. For CN and LP group, rats were anesthetized with isoflurane (Fujifilm Wako Pure Chemical Corp., Osaka, Japan) after 16-hour fasting. Other rats (CN-R and LP-R) are kept with the same diet they received previously, while on the 84th day, sampling was conducted after a 16-hour fasting.

value: protein restriction 3month


title: Gastrocnemius, protein restriction sample for 3 month protein restriciton condition,bio rep4

description:
Gene expression data of gastrocnemius under protein restriction condition
Low protein_3month_LP_4
LP13


title: Gastrocnemius, protein restriction sample for 3 month protein restriciton condition,bio rep2

description:
Gene expression data of gastrocnemius under protein restriction condition
Low protein_3month_LP_2
LP10


title: Gastrocnemius, control sample for 3 month protein restriciton condition,bio rep4

description:
Gene expression data of gastrocnemius under protein restriction condition
Low protein_3month_con_4
CON6


title: Gastrocnemius, protein restriction sample for 3 month protein restriciton condition,bio rep3

description:
Gene expression data of gastrocnemius under protein restriction condition
Low protein_3month_LP_3
LP11


title: Gastrocnemius, control sample for 3 month protein restriciton condition,bio rep2

description:
Gene expression data of gastrocnemius under protein restriction condition
Low protein_3month_con_2
CON3

value: control 3month


title: Gastrocnemius, protein restriction sample for 1 month protein restriciton condition,bio rep4

description:
Gene expression data of gastrocnemius under protein restriction condition
Low protein_1month_LP_4
LP12

source_name: Gastrocnemius, 1 month protein restriciton condition

value: protein restriction 1month


title: IM_rep1

type: genomic

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

country: Germany

institute: Max Planck Institute for Infection Biology

description:
non transformed human primary cells
P471-IM

hyb_protocol: Bisulfite converted DNA was further processed according to Illumina 450k Methylation standard protocol

scan_protocol: Arrays were imaged using the Illumina iScan System with recommended scanner settings

data_processing: Subset-quantile Within Array Normalization (SWAN) was performed using the R-Bioconductor/ChAMP package. Applyed filters removed probes with a detection p-value > 0.01, with a bead-count < 3, probes in which the probed CpG falls near a SNP as defined in Zhou W. et al., 2016, probes in which the probe aligns to multiple locations as defined in Nordlund *et al.*, 2013, and non-cg probes as well as probes located on sex chromosomes

label: Cy3, C5

source_name: IM organoids

label_protocol: Standard Illumina labeling protocol

growth_protocol: Organoids were cultivated as described in Schlaermann et al., 2016, Gut

extract_protocol: Genomic DNA was isolated according to the Qiagen AllPrep DNA/RNA/miRNA Universal Kit protocol.

treatment_protocol: no treatment

tag: cell type

value: IM organoids

value: stomach

tag: age


title: Gastrocnemius, protein restriction sample for 1 month protein restriciton condition,bio rep3

description:
Gene expression data of gastrocnemius under protein restriction condition
Low protein_1month_LP_3
LP11


title: Gastrocnemius, protein restriction sample for 1 month protein restriciton condition,bio rep2

description:
Gene expression data of gastrocnemius under protein restriction condition
Low protein_1month_LP_2
LP8


title: Gastrocnemius, control sample for 3 month protein restriciton condition,bio rep1

description:
Gene expression data of gastrocnemius under protein restriction condition
Low protein_3month_con_1
CON1


title: Normal_rep1

description:
non transformed human primary cells
P471-N

source_name: normal organoids

value: normal organoids


title: BCL6- ILC3_rep1

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

data_processing:
Sequence reads were obtained by BGISEQ-500
Clean reads were mapped to mouse genome mm10 using Bowtie2
Gene expression was indicated by RPKM (Reads Per Kilobases per Million reads)
The differentially expressed genes were carried out by DESeq2 using a cut-off thresh hold of log2 Fold Change >1 and adjusted p value <0.05.
Assembly: mm10
Supplementary files format and content: Txt file including FPKM values

source_name: negative A

extract_protocol:
Total RNAs were isolated with RNeasy Mini Kit (QIAGEN)
RNA-seq library was constructed by BGI Genomics.

value: Bcl6^RFP/RFP-Rorc^GFP/+ (B6 background)

value: Total Intestine LP

value: BCL6- ILC3


title: BCL6+ ILC3_rep1

source_name: positive A

value: BCL6+ ILC3


title: BCL6- ILC3_rep2

source_name: negative B


title: Atrophy_rep2

description:
non transformed human primary cells
P479-A

source_name: atrophy organoids

value: atrophy organoids

value: male


title: Gastrocnemius, control sample for 1 month protein restriciton condition,bio rep4

description:
Gene expression data of gastrocnemius under protein restriction condition
Low protein_1month_con_4
CON5

value: control 1month


title: Atrophy_rep1

description:
non transformed human primary cells
P471-A

value: female


title: Normal_rep2

description:
non transformed human primary cells
P479-N


title: IM_rep2

description:
non transformed human primary cells
P479-IM


title: Gastrocnemius, protein restriction sample for 1 month protein restriciton condition,bio rep1

description:
Gene expression data of gastrocnemius under protein restriction condition
Low protein_1month_LP_1
LP7


title: OPCs, ko2

city: SHENZHEN

first: Yixun

last: Su

state: GUANGDONG

address: 628 Zhenyuan Road

department: Research center

institute: The Seventh Affiliated Hospital, Sun Yat-sen University

data_processing:
Sub-pixel Registration software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text file includes RPKM values and read_counts for each Sample

source_name: Oligodendroglia progenitor cells

growth_protocol: Mice were divided in 2 group: wt: control group. ko: NG2-CreERTM: DISC1 exon3 fl/+ (DISC1 ∆3) mice. On postnatal day 7, mice were sacrificed to isolate OPCs by pdgfrα immunopanning.

extract_protocol:
Immediately after cell isolation, RNA was extracted by Trizol (Thermo) according to the manufacturer’s protocol.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmentedinto small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA wasgenerated using random hexamer-primed reverse transcription, followed by a second-strand cDNAsynthesis. afterwards, A-Tailing Mix and RNA Index Adapters were addedby incubating to endrepair. The cDNA fragments obtained from previous step were amplified by PCR, and productswere purified by Ampure XP Beads, then dissolved in EB solution. The product was validated onthe Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR productsfrom previous step were heated denatured and circularized by the splint oligo sequence to get thefinal library. The single strand circle DNA (ssCir DNA) was formatted as the final library. Thefinal library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: Tamoxifen was given by gavage for 4 consecutive days (p4-p7).

tag: postnatal day

value: NG2-CreERTM:DISC1 exon3 fl/+ (DISC1 {delta}3)

value: Oligodendroglia progenitor cells


title: Gastrocnemius, control sample for 1 month protein restriciton condition,bio rep3

description:
Gene expression data of gastrocnemius under protein restriction condition
Low protein_1month_con_3
CON4


title: OPCs, wt3

value: wildtype

value: Tamoxifen was given by gavage for 4 consecutive days (p4-p7)


title: OPCs, wt2


title: Veh_rep5

city: San Antonio

first: Kexin

last: Xu

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio

data_processing:
Basecalls were performed using Illumina Casava software.
Reads were aligned to hg19 genome assembly using STAR 2.5.2b. Refseq transcripts were supplied in GTF format file.
featureCounts package was used to count the uniquely mapped reads in union mode.
Differentially expressed genes were detected by DESeq2 with FDR thresold 0.05
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads counts for each Sample

source_name: 67NR tumors

growth_protocol: MCF7 cells were grown in high glucose DMEM meidum with 10% FBS and 1% P/S

extract_protocol:
total RNA was extracted by Trizol Reagent from Invitrogen (Cat no 15596026).
RNA library was prepared by the KAPA Stranded mRNA-Seq kit (KK8421), according to the manufacturer’s instructions.

treatment_protocol: MCF7 cells were transduced with shEZH2 or shControl. Or Syngeneic BALB/c mice implanted with 67NR cells were treated with EZH2 inhibitor

value: 67NR (BALB/c)

tag: transfection

value: 20% Captisol (Vehicle)


title: Gastrocnemius, control sample for 1 month protein restriciton condition,bio rep2

description:
Gene expression data of gastrocnemius under protein restriction condition
Low protein_1month_con_2
CON2


title: Veh_rep4

tag: cell line


title: OPCs, ko1


title: Corpus_undifferentiated_rep3 [methylation]

description: non transformed human primary cells

hyb_protocol: Bisulfite converted DNA was further processed according to Illumina MethylationEPIC standard protocol

data_processing: Subset-quantile Within Array Normalization (SWAN) and batch effect correction were performed using the R-Bioconductor/ChAMP package. Applyed filters removed probes with a detection p-value > 0.01, with a bead-count < 3, probes in which the probed CpG falls near a SNP as defined in Zhou W. et al., 2016, probes in which the probe aligns to multiple locations as defined in Nordlund *et al.*, 2013, and non-cg probes as well as probes located on sex chromosomes

source_name: undifferentiated corpus mucosoids

growth_protocol: Human primary gastric epithelial cells were isolated and cultivated as described in Boccellato et al., 2018, Gut

extract_protocol: Genomic DNA was isolated according to the QIAamp DNA mini kit protocol. Deviating, the cells were lysed directly on the filter with RLT lysis buffer (Qiagen) and the protocol for crude cell lysates was subsequently followed.

treatment_protocol: Differentiation was induced by removing Wnt and R-spondin from the cell culture medium for seven days


title: Antrum_undifferentiated_rep3 [methylation]

description: non transformed human primary cells

source_name: undifferentiated antrum mucosoids


title: Corpus_undifferentiated_rep1 [methylation]

description: non transformed human primary cells


title: Gastrocnemius, control sample for 1 month protein restriciton condition,bio rep1

description:
Gene expression data of gastrocnemius under protein restriction condition
Low protein_1month_con_1
CON1


title: Fundus_undifferentiated_rep2 [methylation]

description: non transformed human primary cells

source_name: undifferentiated fundus mucosoids


title: Corpus_differentiated_rep2 [methylation]

description: non transformed human primary cells

source_name: differentiated corpus mucosoids


title: Corpus_undifferentiated_rep2 [methylation]

description: non transformed human primary cells


title: Veh_rep2


title: OPCs, wt1


title: Feed with soybean meal and package 2, fish 5

city: Ås

first: Aleksei

last: Krasnov

state: Viken

address: Øreveien, 47B

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned with Agilent microarray scanner

data_processing: After removal of flagged spots, lowess normalization was performed

organism: Salmo salar

source_name: Distal intestine

label_protocol: Amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Salmon was reared as described in overall design

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

tag: diet

value: Feed with soybean meal and package 2


title: Veh_rep3


title: Fundus_undifferentiated_rep3 [methylation]

description: non transformed human primary cells

value: stomach


title: Veh_rep1


title: Antrum_differentiated_rep2 [methylation]

description: non transformed human primary cells

source_name: differentiated antrum mucosoids


title: BCL6+ ILC3_rep2

source_name: Positive B


title: Corpus_differentiated_rep1 [methylation]

description: non transformed human primary cells


title: GSK_rep4


title: GSK_rep3


title: Feed with soybean meal and package 2, fish 4


title: Feed with soybean meal and package 2, fish 1


title: GSK_rep1


title: Fundus_differentiated_rep3 [methylation]

description: non transformed human primary cells

source_name: differentiated fundus mucosoids


title: Antrum_differentiated_rep3 [methylation]

description: non transformed human primary cells


title: Feed with soybean meal and package 2, fish 3


title: OPCs, ko3


title: Fundus_differentiated_rep2 [methylation]

description: non transformed human primary cells


title: Feed with soybean meal and package 1, fish 4

value: Feed with soybean meal and package 1


title: Feed with soybean meal and package 2, fish 2


title: Antrum_differentiated_rep1 [methylation]

description: non transformed human primary cells


title: Feed with soybean meal and package 1, fish 5


title: Antrum_undifferentiated_rep1 [methylation]

description: non transformed human primary cells


title: Fundus_undifferentiated_rep1 [methylation]

description: non transformed human primary cells


title: Antrum_undifferentiated_rep2 [methylation]

description: non transformed human primary cells


title: GSK_rep2


title: Fundus_differentiated_rep1 [methylation]

description: non transformed human primary cells


title: Feed with soybean meal, fish 3

value: Feed with soybean meal


title: Feed with soybean meal and package 1, fish 1


title: Feed with soybean meal, fish 5


title: Feed with soybean meal and package 1, fish 2


title: Feed with soybean meal, fish 4


title: Corn gluten feed with package 2, fish 4

value: Corn gluten feed with package 2


title: Feed with soybean meal and package 1, fish 3


title: Corpus_differentiated_rep3 [methylation]

description: non transformed human primary cells


title: Feed with soybean meal, fish 2


title: Feed with soybean meal, fish 1


title: Corn gluten feed with package 2, fish 2


title: Corn gluten feed with package 2, fish 5


title: Corn gluten feed with package 2, fish 3


title: Corn gluten feed with package 2, fish 1


title: Corn gluten feed, fish 5

value: Corn gluten feed


title: Corn gluten feed, fish 4


title: Control feed, fish 5

value: control


title: Corn gluten feed, fish 3


title: Corn gluten feed, fish 1


title: Corn gluten feed, fish 2


title: Control feed, fish 4


title: Control feed, fish 2


title: E11.5_control, replicate 5

city: Yokohama

first: Atsuki

last: Imai

state: Japan

institute: Yokohama National University

data_processing:
Read files were mapped to the mouse reference genome (GRCm38 p6) using STAR aligner (ver.2.7.9a) (Dobin, A. et al. Bioinformatics. 2013).
Gene counts were obtained using ‘featureCounts’ function in Rsubread package (ver.2.8.2) and the genes showing log2(RPM+1) values > 4 in at least one sample were used.
Assembly: GRCm38 p6
Supplementary files format and content: A tab-delimited text file includes RPM values for all samples.

source_name: Primordial germ cells

extract_protocol:
100 PGCs were directly sorted in a lysis buffer and total RNA was used for library construction.
RNA libraries for RNA-seq were prepared according to a method called Quartz-seq and LIMprep as previously described (Sasagawa Y, et al. Genome Biology. 2013).

treatment_protocol: Single-cell suspensions were prepared from testes of control and Dnd1-cKO embryos by incubation with accutase (SF006, Merck Millipore, MA) at 37℃ for 40 min. Then, FACS was performed on a Cell Sorter (MoFlo Astrios, BeckmanCoulter, CA) to collect Nanog-EGFP positive PGCs.

value: Primordial germ cells

value: Dnd1flox/flox; Nanog-EGFP


title: Control feed, fish 1


title: E11.5_control, replicate 3


title: E11.5_control, replicate 4


title: E11.5_control, replicate 2


title: AGCT10

city: New York

first: Varshini

last: Vasudevaraja

state: NY

address: 240 E 38th street

department: Pathology

institute: NYU Langone Health

description: DNA methylation data from adult granulosa cell tumors

hyb_protocol: The DNA is bisulfite-converted using the EZ-96 DNA Methylation Kit from Zymo Research.  After bisulfite conversion, the DNA then undergoes restoration using the Illumina Infinium HD FFPE DNA Restore Kit. The DNA then undergoes a whole-genome overnight amplification.  The amplified DNA is then enzymatically fragmented using end-point fragmentation.  The DNA is then isolated and precipitated in isopropanol and re-suspended in Illumina RA1 buffer.  The re-suspended DNA is then denatured at 95⁰C, and the resulting single-stranded DNA is dispensed directly onto the Illumina Array for hybridization.  The DNA hybridizes with the array overnight in an oven at 48⁰C.  After hybridization, the BeadChips are then washed with Illumina PB1 buffer to remove any unhybridized and non-specifically hybridized DNA.

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: minfi- R package was used to analyze the data. Data was preprocessed and quantile normalized.

label: Cy5 and Cy3

source_name: Genomic DNA from ovarian adult granulosa cell tumors

label_protocol: Standard Illumina Protocol

extract_protocol: Using a Promega Maxwell 16 instrument, DNA was extracted from formalin-fixed paraffin-embedded (FFPE) specimens with the Maxwell® 16 FFPE Plus LEV DNA Purification Kit

value: ovary

value: Female


title: E11.5_control, replicate 1


title: AGCT06


title: AGCT08


title: Control feed, fish 3


title: AGCT07


title: AGCT05


title: AGCT03


title: E11.5_Dnd1-cKO, replicate 5


title: AGCT04


title: JGCT35

description: DNA methylation data from juvenile granulosa cell tumors

source_name: Genomic DNA from ovarian juvenile granulosa cell tumors


title: JGCT29


title: E11.5_Dnd1-cKO, replicate 1


title: E11.5_Dnd1-cKO, replicate 4


title: JGCT34


title: JGCT19


title: E11.5_Dnd1-cKO, replicate 3


title: JGCT09


title: RNA-seq for F480pGFPn_rep1

city: Nanjing

first: Qianghu

address: 101Longmian Avenue, Jiangning District

institute: Nanjing Medical University

data_processing:
STAR version 2.6.1b
raw reads were trimmed and then mapped to the mm10 mouse genome using STAR.
Quantification of genes was conducted using featureCounts.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: Bone marrow

extract_protocol: none provided

value: Bone marrow

value: WT

tag: replicate

value: replicate = biological replicate 1


title: OE, UdsC, microaerob, 15min IPTG, Rep 3

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

description: Rhodobacter sphaeroides UdsC overexpression (15 min IPTG) grown under microaerobic conditions, rep 3

data_processing:
All reads were trimmed for adaptor sequences using trim-galore (version 0.6.3), low-quality reads have been rejected in the same data processing step. Options were set to -q 10 --length 15 -j 8
Reads were mapped to the Rhodobacter sphaeroides 2.4.1 whole genome (NC_007493.2, NC_007494.2, NC_009007.1, NC_007488.2, NC_007489.1, NC_007490.2, and NC_009008.1) using the READemption pipeline (version 0.4.3) subcommand align with the integrated mapper segemehl (version 0.2.0)
READemption (version 0.4.3) was used for gene quantification with parameters gene_quanti --features CDS,tRNA,rRNA,tmRNA,ncRNA,sRNA
READemption (version 0.4.3) with DESeq2 (version 1.22.1) was used to perform the differential gene expression analysis, subcommand deseq
Differential gene expression was validated with baySeq (version 2.20.0)
Assembly: Genome_build: GCF_000012905.2 ASM1290v2
Supplementary files format and content: wiggle format

organism: Cereibacter sphaeroides

source_name: bacterial cell

growth_protocol: Cells were grown in malate minimal medium in presence of  low oxygen concentration of 25 µM dissolved oxygen (microaerobic)

extract_protocol:
Total RNA was isolated as published (Grützner et al., 2021, Nucleic Acids Res. 49(6), doi: 10.1093/nar/gkab146)
RNA was processed as published (Grützner et al., 2021, Nucleic Acids Res. 49(6), doi: 10.1093/nar/gkab146); NEBnext Multiplex Small RNA Library Prep Set

treatment_protocol: Cells were harvested during exponential growth phase.

value: bacterial cell

value: UdsC overexpression

value: microaerob, 15min IPTG


title: AGCT01


title: OE, UdsC, microaerob, 15min IPTG, Rep 1

description: Rhodobacter sphaeroides UdsC overexpression (15 min IPTG) grown under microaerobic conditions, rep 1


title: E11.5_Dnd1-cKO, replicate 2


title: JGCT17


title: JGCT13


title: OE, UdsC, microaerob, 15min IPTG, Rep 2

description: Rhodobacter sphaeroides UdsC overexpression (15 min IPTG) grown under microaerobic conditions, rep 2


title: JGCT37


title: OE, UdsC, microaerob, 0min IPTG, Rep 3

description: Rhodobacter sphaeroides UdsC overexpression (0 min IPTG) grown under microaerobic conditions, rep 3

value: microaerob, 0min IPTG


title: AGCT09


title: JGCT31


title: JGCT10


title: JGCT21


title: JGCT20


title: OE, UdsC, microaerob, 0min IPTG, Rep 1

description: Rhodobacter sphaeroides UdsC overexpression (0 min IPTG) grown under microaerobic conditions, rep 1


title: RNA-seq for F480pGFPn_rep3

value: replicate = biological replicate 3


title: RNA-seq for F480pGFPp_rep3


title: KO, UdsC, microaerob, Rep 2

description: Rhodobacter sphaeroides UdsC mutant grown under microaerobic conditions, rep 2

value: UdsC deletion mutant

value: microaerob


title: JGCT22


title: KO, UdsC, microaerob, Rep 1

description: Rhodobacter sphaeroides UdsC mutant grown under microaerobic conditions, rep 1


title: JGCT11


title: WT_phototroph_Rep_3

first: Tobias

last: Friedrich

address: 421 Curie Boulevard

institute: University of Pennsylvania

description: Rhodobacter sphaeroides 2.4.1 wild type grown under phototrophic conditions, rep 3

data_processing:
Alignment of FASTQ files against the Rhodobacter sphaeroides 2.4.1 genome (NC_007493.2, NC_007494.2, NC_009007.1, NC_007488.2, NC_007489.1, NC_007490.2, and NC_009008.1) was performed using READemption v.1.0.5.
Read counts per gene were calculated using the summarizedOverlaps function.
DESeq2 v.1.32 was used for the normalisation of the reads and the identification of transcriptional changes.
Additionally, bona fide RNase E cleavage sites or 5’ends enriched in the mutant were identified.
Assembly: Rhodobacter sphaeroides 2.4.1
Supplementary files format and content: Comma separated files include raw read counts per gene for each sample.

source_name: bacterial cells

growth_protocol: Cells were grown in malate minimal medium, either in presence of high oxygen concentration of 180 µM dissolved oxygen (aerobic cultures), low oxygen concentration of 25 µM dissolved oxygen (microaerobic cultures) or without oxygen but illuminated with 60 W*m-2 white light (phototrophic cultures).

tag: growth condition

value: phototrophic

value: wild type


title: HU_Flag_Dppa5a_rep1

city: Kunming

first: Ping

last: Zheng

address: Qingsong Road 21

institute: Kunming Institute of Zoology, Chinease Academy of Sciences

data_processing:
Basecalls performed using CASAVA version 2.19
Reads were mapped to mm10 genome using tophat2 (version 2.0.8) with default parameters.
For RNA-seq, fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using cufflinks version 2.1.1; Differentialy expressed genes were determined using cuffdiff (version 2.1.1).
For RIP-seq, raw counts of genes were counted using htseq software (version 0.6.1) with mouse RefSeq annotation and used for differentially expressed genes analysis using DEGseq (version 1.38.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each RNA-seq Sample
Supplementary files format and content: tab-delimited text files include counts for each RIP-seq Sample

source_name: cell line

growth_protocol: Mouse embryonic fibroblasts were cultured in DMEM supplemented with 10% FBS. Mouse embryonic stem cells (mESCs) were routinely maintained on inactivated mouse embryonic fibroblasts in the culture medium: Dulbecco’s Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) medium supplemented with 20% Knockout serum replacement,1 mM sodium pyruvate, 2 mM L-glutamine, 1% non-essential amino acids, 0.1mM β-mercaptoethanol, penicillin (100 U/mL)/streptomycin (100 μg/mL) and 1000 units/mL mouse leukemia inhibitory factor (LIF). To harvest mESCs, cells were passaged twice on gelatin coated dishes.

extract_protocol:
Total RNA or immunoprecipitated RNAs were extracted  using standard Trizol procedure.
RNA libraries were constructed by Novogene Corporation (Beijing, China). RNA-seq libraries were constructed using Illumina NEBNext® UltraTM RNA Library Prep Kit.

value: cell line

value: home made

value: Mouse embyonic stem cells

value: 3Flag-Dppa5a overexpresson

value: HU

tag: rip antibody

value: Flag (Enogene, E12-001-3)

tag: rna fraction

value: immunoprecipitated RNA


title: Flag_Dppa5a_rep2

tag: tissue

value: untreated


title: RNA-seq for F480pGFPn_rep2

value: Bone marrow

tag: genotype

value: WT

value: replicate = biological replicate 2


title: KO, UdsC, microaerob, Rep 3

description: Rhodobacter sphaeroides UdsC mutant grown under microaerobic conditions, rep 3

value: bacterial cell

tag: treatment


title: OE, UdsC, microaerob, 0min IPTG, Rep 2

description: Rhodobacter sphaeroides UdsC overexpression (0 min IPTG) grown under microaerobic conditions, rep 2

value: UdsC overexpression

value: microaerob, 0min IPTG


title: RNA-seq for F480pGFPp_rep2


title: HU_Flag_Dppa5a_rep2


title: RNA-seq for F480pGFPp_rep1

value: replicate = biological replicate 1


title: WT_phototroph_Rep_1

city: Philadelphia

description: Rhodobacter sphaeroides 2.4.1 wild type grown under phototrophic conditions, rep 1

value: phototrophic


title: IgG_rep2

value: IgG (Millipore, CS200621)


title: Flag_Dppa5a_rep1

value: cell line


title: WT_microaerob_Rep_3

description: Rhodobacter sphaeroides 2.4.1 wild type grown under microaerobic conditions, rep 3

value: microaerobic

value: wild type


title: JGCT06

value: ovary

tag: gender

value: Female


title: IgG_rep1

value: home made

value: Mouse embyonic stem cells

value: 3Flag-Dppa5a overexpresson


title: WT_microaerob_Rep_2

description: Rhodobacter sphaeroides 2.4.1 wild type grown under microaerobic conditions, rep 2


title: MEF_rep2

value: primary

value: Mouse embryonic fibroblasts

value: untreated

value: total RNA


title: WT_microaerob_Rep_1

description: Rhodobacter sphaeroides 2.4.1 wild type grown under microaerobic conditions, rep 1


title: MEF_rep1


title: WT_aerob_Rep_3

description: Rhodobacter sphaeroides 2.4.1 wild type  grown under aerobic conditions, rep 3

value: aerobic


title: mESC_rep2


title: WT_aerob_Rep_2

description: Rhodobacter sphaeroides 2.4.1 wild type grown under aerobic conditions, rep 2


title: JGCT05

description: DNA methylation data from juvenile granulosa cell tumors


title: AGCT02

description: DNA methylation data from adult granulosa cell tumors


title: JGCT04


title: WT_aerob_Rep_1

description: Rhodobacter sphaeroides 2.4.1 wild type grown under aerobic conditions, rep 1


title: JGCT08


title: JGCT07


title: rne_phototroph_Rep_3

description: Rhodobacter sphaeroides rne-ts mutant grown under phototrophic conditions, rep 3

value: RNase E mutant


title: rne_phototroph_Rep_2

description: Rhodobacter sphaeroides rne-ts mutant grown under phototrophic conditions, rep 2


title: uterus tissue, CRCs-transplanted group, day 7, #3

city: 湖北

first: Yiyi

last: Kang

address: Donghu road

institute: WuHan University

data_processing:
The index trimmed pair-end 150 base pair reads were aligned to the murine reference genome (mm38) using Hisat2 (v2.1.0).
StringTie (v2.1.1) was used to assemble and quantitative full-length transcripts representing multiple splice variants for each gene locus.
Assembly: mm38
Supplementary files format and content: Processed data files include count values for each Sample

source_name: uterus

extract_protocol:
Total RNA was extracted from uterine tissues or cells with the RNeasy Mini Kit (74104, Qiagen) according to the manufacturer's instructions.
RNA libraries were prepared using the Ribo-Zero GoldrRNA Removal (Illumina) followed by sequencing on NovaSeq6000 (Illumina).

treatment_protocol: The abdominal wall of anesthetized mice was cut longitudinally to expose the uterus. 27-gauge needle was inserted into the uterine cavity, rotated and withdrawn 10 times to cause mechanical damage. Mice were randomly divided into three groups with 3 mice in each group: sham operated group, injury group, WT CRCs-transplanted group, plus Ihh-/- CRCs-transplanted group. For cells-transplantation, 50 μL of WT or Ihh-/- CRCs (1×106 ) suspension were injected to the uterine cavity immediately after the uterine injury. The injury group received 50 μL of PBS. Mice were sacrificed on day 7 of injury/transplantation. The tissue was collected for morphology, RNA and RNA sequencing analysis.

value: uterus

value: WT

value: curretage, followed by CRCs transplantation


title: uterus tissue, CRCs-transplanted group, day 7, #2


title: uterus tissue, CRCs-transplanted group, day 7, #1


title: rne_microaerob_Rep_3

description: Rhodobacter sphaeroides rne-ts mutant grown under microaerobic conditions, rep 3


title: rne_phototroph_Rep_1

description: Rhodobacter sphaeroides rne-ts mutant grown under phototrophic conditions, rep 1

value: phototrophic


title: uterus tissue, injury group, day 7, #3

value: curretage


title: WT_phototroph_Rep_2

description: Rhodobacter sphaeroides 2.4.1 wild type grown under phototrophic conditions, rep 2

value: wild type


title: rne_microaerob_Rep_2

description: Rhodobacter sphaeroides rne-ts mutant grown under microaerobic conditions, rep 2

value: microaerobic


title: uterus tissue, injury group, day 7, #1


title: mESC_rep1

value: cell line


title: rne_microaerob_Rep_1

description: Rhodobacter sphaeroides rne-ts mutant grown under microaerobic conditions, rep 1


title: rne_aerob_Rep_3

description: Rhodobacter sphaeroides rne-ts mutant grown under aerobic conditions, rep 3


title: uterus tissue, sham operated group, day 7, #2

value: sham operation


title: uterus tissue, sham operated group, day 7, #3


title: uterus tissue, injury group, day 7, #2


title: rne_aerob_Rep_2

description: Rhodobacter sphaeroides rne-ts mutant grown under aerobic conditions, rep 2


title: uterus tissue, sham operated group, day 7, #1


title: rne_aerob_Rep_1

description: Rhodobacter sphaeroides rne-ts mutant grown under aerobic conditions, rep 1


title: JGCT01

value: ovary

value: Female


title: WT.2

data_processing:
Paired-end reads were merged using FLASH (VI.2.7,http://ccb.jhu.edu/software/FLASH/)
Quality filtering on the raw tags were performed under specific filtering conditions to obtain the  high-quality clean tag according to the QIIME(V1.9.1,  http://qiime.org/scripts/split libraries fastq.html[3]quality controlled process.
The tags were compared with the reference database (Silva database, https://www.arb-silva.de/) using UCHIME algorithm (UCHIME Algorithm,http://www.drive5.com/usearch/manual/uchime_algo.html) to detect chimera sequences, and then the chimera sequences were removed[5].Then the Effective Tags finally obtained
Supplementary files format and content: zip./excel; ASV abundance of relative different bacteria in all taxa orders
Library strategy: 16s rDNA sequencing

organism: feces metagenome

source_name: colonic feces

extract_protocol:
Total genome DNA from samples was extracted using CTAB/SDS method. DNA concentration  and purity was monitored on 1% agarose gels, DNA was diluted to l ug/μL using sterile water, and then amplified.
Sequencing libraries were generated using TruSeq® DNA PCR-Free Sample Preparation Kit  (Illumina, USA) following manufacturer's recommendations and index codes were added.

tag: mouse genotype

tag: source

value: mouse colonic feces

value: bacterial cells


title: WT.3


title: WT.4


title: KO.4

value: KO


title: WT.1


title: KO.3


title: Sublingual salivary gland, 7 days post radiation 2

city: San Francisco

first: Jianlong

last: Li

address: 513 Parnassus Avenue

department: Cell and Tissue Biology

institute: UCSF

data_processing:
Raw data (FASTQ) were processed through fasp.
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software
FeatureCounts was used to count the read numbers mapped to each gene
Differential expression analysis between two conditions was performed using DESeq2 R package
Assembly: mm10
Supplementary files format and content: comma seprated values (csv) files include raw read count values for each sample

source_name: salivary gland

extract_protocol:
RNA was isolated from 4 x 50 µm tissue sections of non-IR, 7- or 14- days post-IR sublingual glands using the RNAqueous Micro Kit (ThermoFisher Scientific) and total RNAs were treated with Dnase I (ThermoFisher Scientific).
RNA library construction was performed by Novogene

value: salivary gland

value: 10 Gy radiation


title: Sublingual salivary gland, 14 days post radiation 3


title: Sublingual salivary gland, 14 days post radiation 2


title: Sublingual salivary gland, 14 days post radiation 1


title: Sublingual salivary gland, 7 days post radiation 1


title: Sublingual salivary gland, no radiation control 3

value: No radiation


title: Sublingual salivary gland, 7 days post radiation 3


title: Sublingual salivary gland, no radiation control 2


title: KO.1


title: KO.2


title: JGCT03


title: QZ7

city: Tallahassee

first: Cynthia

last: Vied

state: Florida

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

data_processing:
Adapters were trimmed during demultiplexing by the core facility and trimmed reads were aligned to the genome using RNA-Seq Alignment version 1.1.1 (Illumina BaseSpace software application). The application uses STAR for alignment to the mouse genome (UCSC mm10) and Salmon was used to generate count tables.
Differential expression analysis of count tables was performed using the default settings of DESeq2 (Benjamini-Hochberg FDR correction).
Assembly: mm10
Supplementary files format and content: Microsoft Excel Worksheet (.xlsx), contains counts from DESeq2 used for differential expression analysis.

source_name: Cerebellum

growth_protocol: Male and female YY1-floxed and GFAP-cre mice were purchased from the Jackson Laboratory (Bar Harbor, ME). Animals were kept on a 12 hour light-dark cycle. Food and water were provided ad libitum. Mice were group housed. After delivery, YY1-floxed and YY1-cKO mice were kept up to 12 weeks prior to euthanization by rapid decapitation.

extract_protocol:
The cortex, midbrain and cerebellum were dissected and rapidly frozen in liquid nitrogen and stored at -80 degrees. Total RNA was extracted from the entire tissue from each animal using TRIZol Reagent (Life Technologies) and RNA clean and concentrator-5 with DNase I (Zymo Research) according to manufacturer’s directions. mRNA was isolated from the total RNA using an NEBNext Poly(A) mRNA Magnetic Isolation Module as per instructions (New England Biolabs).
cDNA libraries were generated from the isolated mRNA using an NEBNext Ultra RNA library prep kit for Illumina (New England Biolabs) and 8 nucleotide i7 and i5 dual-index primers (NEBNext multiplex oligos for Illumina, Dual Index Primers) were incorporated into each sample.  The library construction was done according to NEB instructions, modified for use with a Beckman Biomek 4000 at the Florida State University Biological Sciences core lab.  The unique dual-index (barcode) primers were added to each library to multiplex the forty-two libraries. The multiplexed sample was quantified with qPCR (Kapa Biosystems) specific for Illumina sequencing primers and the average fragment size was determined with a Bioanalyzer high sensitivity DNA chip (Agilent Technologies). The pooled sample was sequenced, with paired-end, 50 base reads on an Illumina NovaSeq 6000 located in the Translational Science Laboratory at the College of Medicine, Florida State University.  The pooled data were demultiplexed into individual sample data.

value: 12 weeks

tag: strain

tag: Sex

value: astrocytic Yy1-cKO


title: Sublingual salivary gland, no radiation control 1

value: WT


title: QZ4

tag: age

value: Male


title: QZ6


title: QZ5