title: Duodenum, SBR, Vehicle 1

status: Public on Jan 18 2026

city: Saint Louis

first: Gwendalyn

middle: J

last: Randolph

state: Missouri

address: 425 S. Euclid

institute: Washington University in St.Louis

description: Library name: Sample12

data_processing:
Fragments were sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases. Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04.
Assembly: Mouse Ensembl GRCm38.101
Supplementary files format and content: The TPM files were directly loaded into R for further analysis. Gene names were standardized, and duplicate entries were removed to retain unique gene features. Genes with zero TPM values across all samples were excluded. To reduce the impact of extreme values and facilitate comparisons, the TPM data were log2-transformed. Batch effects between experimental groups were corrected using the ComBat function from the sva R package. Normalized data were visualized with boxplots to confirm consistent sample distributions, ensuring comparability across datasets

organism: Mus musculus

source_name: Duodenum

extract_protocol:
Total RNA was extracted from the duodenum, the ileum, and the liver using Direct-zol RNA Miniprep Kits (Zymo Research). Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.
Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

treatment_protocol: The 8-week-old C57BL/6 male mice underwent either 50-60% small bowel resection or sham surgeries. Three weeks after the operation, the mice received daily treatments of WUSTL0717 (30 mg/kg) or vehicle for 7 weeks.

value: Duodenum

tag: strain

tag: genotype

value: Wild type

value: Male

value: Small bowel resection

value: Vehicle

tag: batch

value: Batch 1


title: cSCC tumor 2 scRNA-seq

status: Public on Jan 14 2026

type: SRA

city: Nanjing

first: Yuancheng

last: Li

state: JiangSu

address: No. 12 Jiangwangmiao Street

department: Institute of Dermatology

country: China

institute: Chinese Academy of Medicine Sciences and Peking Union Medical College

description: 10× Genomics

library_source: transcriptomic single cell

data_processing:
The scRNA-seq data demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The bulk RNA-seq data were processed  using the recommended CEL-Seq2 pipeline (https://github.com/yanailab/celseq2)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Homo sapiens

source_name: skin

extract_protocol:
For bulk RNA-seq, RNA of sorted NK cells were extracted by trizol reagent
scRNA-seq libraries were constructed by 10 x genomics 3' kit, bulk RNA-seq libraries were constructed by CEL-Seq2 protocol

tag: tissue

value: skin

tag: cell line

value: skin cell

tag: cell type

value: enriched CD45+ cells

tag: tissue type

value: cSCC tumor


title: aMM peri-tumor 3 scRNA-seq

description: 10× Genomics

value: aMM peri-tumor


title: BCC tumor 3 scRNA-seq

description: 10× Genomics

value: BCC tumor


title: aMM peri-tumor 2 scRNA-seq

description: 10× Genomics


title: NK control rep 1 bulk RNA-seq

description: 10× Genomics

library_source: transcriptomic

source_name: blood

value: blood

value: PBMC

value: sorted CD56dim NK cell

tag: treatment

value: NK control


title: NK dex rep 1 bulk RNA-seq

description: 10× Genomics

value: NK dex


title: cSCC tumor 3 scRNA-seq

description: 10× Genomics


title: cSCC peri-tumor 1 scRNA-seq

description: 10× Genomics

value: cSCC peri-tumor


title: BCC tumor 2 scRNA-seq

description: 10× Genomics


title: BCC peri-tumor 3 scRNA-seq

description: 10× Genomics

value: BCC peri-tumor


title: iMGL TREM2 KO SEMA6D treat rep 3

city: St Louis

first: Ricardo

last: D'Oliveira Albanus

state: MO

address: 4370 Duncan Avenue, Suite 6306D, Jeffrey T. Fort Neuroscience Bdg.

department: Neurology

country: USA

institute: Washington University School of Medicine

data_processing:
Human mRNA sequencing and bioinformatics analysis were performed by Novogene.
Raw fastq files were mapped to the GRCh38 reference genome using HISAT2 (v. 2.0.5) and the corresponding GRCh38 index files (http://daehwankimlab.github.io/hisat2/download)
Assembly: GRCh38
Supplementary files format and content: Tab-delimited processed file include number of reads mapped to each gene for each sample.

molecule: total RNA

source_name: iPSC-derived microglia

growth_protocol: Human iPSCs were maintained feeder-free on matrigel-coated plates in StemFlex medium (Gibco) in a humidified incubator (5% CO2, 37 °C). Cells were passaged as aggregates using ReLeSR (StemCell Technologies), and media was changed daily. iPSC-microglia were generated as described in McQuade et al., 2018. Briefly, iPSCs were directed down a hematopoietic lineage using the STEMdiff Hematopoietic kit (STEMCELL Technologies). After 12 days in culture, hematopoietic progenitor cells (HPCs) were transferred into a microglia differentiation medium containing DMEM/F12, 2× insulin-transferrin-selenite, 2× B27, 0.5× N2, 1× GlutaMAX, 1× nonessential amino acids, 400  μM monothioglycerol, and 5  μg/mL human insulin. Media was added to cultures every other day and supplemented with 100  ng/mL IL-34, 50  ng/mL TGF-β1, and 25 ng/mL M-CSF (PeproTech) for 28 days. In the final three days of differentiation, 100 ng/mL CD200 (Novoprotein) and 100  ng/mL CX3CL1 (PeproTech) were added to the culture.

extract_protocol:
mRNA was extracted from iMGL using RNeasy Mini kit (Qiagen) following the manufacturer's instructions.
mRNA libraries generation, sequencing, and bioinformatics analysis were performed by Novogene.

treatment_protocol: WT or TREM2 KO iMGL were treated with 10 μM SEMA6D for 24 hrs.

value: iPSC-derived microglia

value: TREM2 KO


title: cSCC peri-tumor 2 scRNA-seq

description: 10× Genomics


title: iMGL TREM2 KO SEMA6D treat rep 2


title: cSCC peri-tumor 3 scRNA-seq

description: 10× Genomics


title: aMM peri-tumor 1 scRNA-seq

description: 10× Genomics


title: BCC peri-tumor 1 scRNA-seq

description: 10× Genomics


title: iMGL TREM2 KO no treat rep 2

value: No treatment


title: EMPD tumor 2 scRNA-seq

description: 10× Genomics

value: EMPD tumor


title: iMGL TREM2 KO no treat rep 1


title: BCC peri-tumor 2 scRNA-seq

description: 10× Genomics

value: skin


title: iMGL WT SEMA6D treat rep 2

value: WT


title: BCC tumor 1 scRNA-seq

description: 10× Genomics

value: skin cell

value: enriched CD45+ cells


title: iMGL WT no treat rep 2


title: iMGL WT no treat rep 1


title: iMGL WT SEMA6D treat rep 1


title: aMM tumor 2 scRNA-seq

description: 10× Genomics

value: aMM tumor


title: aMM tumor 1 scRNA-seq

description: 10× Genomics


title: PSC27-BLEO

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

description: PE150 high throughout data

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38/hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata. Sequencing reads were aligned, processed, and iteratively corrected, using the hiclib library for Python (commit b9a7db9, https://bitbucket.org/mirnylab/hiclib).
To produce the normalized Hi-C interaction matrices, each matrix was divided by the mean row sum constant such that the sum of each row was equal to one.
Hi-C interaction heatmaps were produced using the normalized contact probabilities for each condition. Differential Hi-C interaction maps were calculated in a manner similar to Zuin et al. 2014. PNAS (PMID: 24335803), subtracting the second condition from the first (using the 200-kb normalized interaction matrices).
A/B compartment calling was performed as described by Imakaev et al. 2012. Nat. Methods (PMID: 22941365) on the normalized interaction matrices. The hiclib package was used to calculate the eigenvector decomposition of the 40-kb interaction matrix, considering only intra-arm interactions.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Matrix files generated with differential bin values such as 20000, 40000, 150000, 500000 and 1000000.
Supplementary_files_format_and_content: The first eigenvector (PC1) was used to compute the A and B compartments. Bins with PC1 values >0 were designated as A, and bins with values <0 were designated as B.

molecule: genomic DNA

source_name: Prostate stromal cell

growth_protocol: Normal human prostate-derived stromal cells (PSC27) were routinely cultured in stromal complete media supplemented with 10% FBS.

extract_protocol:
Hi-C experiment were conducted using DpnII, according to the protocol published by Belton JM. Et al. Methods 2012 (PMID: 22652625) except for using 2% formaldehyde.
Genomic DNA libraries were prepared for sequencing using standard Illumina protocols. One library was generated from each individual sample per treatment group.
DNA libraries were prepared during Hi-C protocol according to experimental procedures described in Belton JM. Et al. Methods 2012 (PMID: 22652625).

treatment_protocol: PSC27 cells were maintained at 37 C as either consecutively proliferating cells (CTRL), subject to treatment by the chemotherapeutic drug bleomycin (BLEO) at 5 ug/ml or ionizing radiation (RAD) at a 10 Gy dose.

value: Normal human prostate derived primary stromal cells

tag: protocol

value: chemotherapeutic agent bleomycin


title: iMGL TREM2 KO SEMA6D treat rep 1


title: PSC27-RAD (2)

description: PE150 high throughout data

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38/hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata. Sequencing reads were aligned, processed, and iteratively corrected, using the hiclib library for Python (commit b9a7db9, https://bitbucket.org/mirnylab/hiclib).
To produce the normalized Hi-C interaction matrices, each matrix was divided by the mean row sum constant such that the sum of each row was equal to one.
Hi-C interaction heatmaps were produced using the normalized contact probabilities for each condition. Differential Hi-C interaction maps were calculated in a manner similar to Zuin et al. 2014. PNAS (PMID: 24335803), subtracting the second condition from the first (using the 200-kb normalized interaction matrices).
A/B compartment calling was performed as described by Imakaev et al. 2012. Nat. Methods (PMID: 22941365) on the normalized interaction matrices. The hiclib package was used to calculate the eigenvector decomposition of the 40-kb interaction matrix, considering only intra-arm interactions.
Assembly: GRCh38/hg38
Supplementary files format and content: Matrix files generated with differential bin values such as 20000, 40000, 150000, 500000 and 1000000.
Supplementary files format and content: The first eigenvector (PC1) was used to compute the A and B compartments. Bins with PC1 values >0 were designated as A, and bins with values <0 were designated as B.

extract_protocol:
Starting material cells were harvested under 3 different biological conditions: proliferating (CTRL), chemotherapeutically treated (BLEO) and radiation-treated (RAD). Hi-C assays were conducted using DpnII, with minor changes to improve the final yield according to the protocol published by Belton et al. 2012. Methods. (PMID: 22652625) except for using 2% formaldehyde.
Genomic DNA libraries were prepared for sequencing using standard Illumina protocols. One library was generated from each individual sample per treatment group.

treatment_protocol: PSC27 cells were maintained at 37 C as either consecutively proliferating cells (CTRL), subject to treatment by the chemotherapeutic drug bleomycin (BLEO) at 50 μg/ml or ionizing radiation (RAD) at a 10 Gy dose.

tag: passage


title: iMGL WT no treat rep 3


title: PSC27-RAD

description: PE150 high throughout data

value: damaged by ionizing radiation


title: iMGL TREM2 KO no treat rep 3


title: H. armigera_FWD, scRNA-seq

first: Qiancheng

last: Xiao

address: Building 25, No. 1188, LIANHANG Road, Pujiang Town, Minhang District, Shanghai

institute: Shanghai OE Biotech Co., Ltd

description: Collected larvae were dissected to prepare intact wing disc samples

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics 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: HaSCD2
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Helicoverpa armigera

source_name: wing disc

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: wing disc

value: wing disc cells

tag: age

value: Day 3 fifth-instar


title: PSC27-CTRL (2)

description: PE150 high throughout data


title: Day15_KO_2

first: Feizhen

last: Wu

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

institute: Fudan Univ, Shanghai, China

description:
Library name: Sample 17
10x Genomics

data_processing:
Demultiplexing, barcode processing, gene counting, and data aggregation  were performed using Cell Ranger software (v9.0.0; 10x Genomics).
Assembly: hg38
Supplementary files format and content: Matrix,Features, Bardoces

source_name: WT-iPSC

growth_protocol: the hiPSCs were dissociated using Accutase and were cultured on Matrigel-coated plates in mTeSRTM Plus medium.

extract_protocol:
Differentiated cells collected on days 2, 5, and 15 were dissociated using Accutase and neutralized with fetal bovine serum in DMEM. For each time point, three biological replicates were obtained from both WT and KO groups. After centrifugation at 1,000 g for 5 min, cell pellets were resuspended in DPBS containing 0.04% bovine serum albumin and immediately submitted for scRNA-seq.
Single-cell libraries were generated using the Chromium GEM-X Single Cell 3′ Kit v4 (10x Genomics) according to the manufacturer’s instructions, and sequenced on an Illumina nova X to a mean depth of at least 20K reads per cell.

treatment_protocol: the hiPSCs Upon reaching approximately 80% confluence, the cells were split at a ratio of 1:5 using Accutase (Sigma, A6964). We utilized a previously established protocol involving WNT activation and inhibition to differentiate hiPSCs into cardiomyocytes. Briefly, hiPSCs were seeded and, at 80% confluence, treated with B27 minus insulin (Thermo, A1895601)/RPMI1640 (Thermo, 11875119) plus 7μM CHIR-99021 (Selleck, S1263). Following two days of CHIR99021 treatment, the medium was switched to B27 minus insulin/RPMI1640. After 24 hours, the medium was replaced with B27 minus insulin/RPMI1640 containing 5 μM IWR1 (Selleck, S7086) for two days. Subsequently, IWR1 was removed, and differentiation continued in CDM3 medium containing RPMI640, 50mg/ml BSA (Sigma, A1933), and 213mg/ml ascorbic acid (Sigma, A4544).

value: WT-iPSC

value: hiPSCs-derived cardiomyocytes

tag: time

value: NONO-KO


title: Day15_KO_1

description:
Library name: Sample 16
10x Genomics


title: Day15_WT_3

description:
Library name: Sample 15
10x Genomics


title: H. armigera_HWD, scRNA-seq


title: PSC27-CTRL

description: PE150 high throughout data

value: proliferating


title: Day15_WT_2

description:
Library name: Sample 14
10x Genomics


title: PSC27-BLEO (2)

description: PE150 high throughout data


title: Day15_KO_3

description:
Library name: Sample 18
10x Genomics


title: Day5_KO_2

description:
Library name: Sample 11
10x Genomics


title: Day15_WT_1

description:
Library name: Sample 13
10x Genomics


title: Day2_KO_3

description:
Library name: Sample 6
10x Genomics


title: Day5_WT_2

description:
Library name: Sample 8
10x Genomics


title: Day2_WT_2

description:
Library name: Sample 2
10x Genomics


title: Day2_WT_1

description:
Library name: Sample 1
10x Genomics


title: Day2_KO_1

description:
Library name: Sample 4
10x Genomics


title: Day5_KO_3

description:
Library name: Sample 12
10x Genomics


title: P1269

city: La Jolla

first: Mariko

last: Horii

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

description:
Library name: sample4
column name in raw_counts.csv:P1269

data_processing:
Quality control was performed using multiQC (v1.17). Strand specificity analysis using RSeQC confirmed that the RNA-seq libraries were stranded, with the majority of reads aligning to the antisense strand. Adapter trimming and quality filtering were performed using BBDuk (BBMap suite) with the following parameters: ktrim=r, k=16, mink=11, hdist=1, tpe, tbo, qtrim=rl, and trimq=20, using a custom adapter reference file. Reads were mapped to the human genome (GRCh38, GENCODE release with ERCC spike-in sequences added) using STAR (v.2.7.11) with the following parameters: --runMode alignReads, --outSAMtype BAM SortedByCoordinate, --outSAMunmapped Within, and --quantMode GeneCounts. Feature quantification was performed using featureCounts (subread v.2.0.1)28 with parameters -p --countReadPairs -t exon -T 13 -g gene_id. Only Ensembl genes with ≥10 counts in at least 25% of samples were retained for downstream analysis. Normalization and differential expression analysis were performed using the R (v. 4.4.1) package DESeq2 (v. 1.44.0). BiomaRt (v. 2.60.1) was used to convert Ensembl gene IDs to HUGO gene names, and gene set enrichment analysis was done using the R (v. 4.4.1) package FGSEA (v. 1.30.0).
Assembly: GRCh38, GENCODE release 44
Supplementary files format and content: txt file for raw counts
Supplementary files format and content: txt file for vst data

source_name: Placenta

extract_protocol:
Total RNA was isolated using mirVana RNA Isolation Kit (ThermoFisher). RNA concentration was measured using Qubit RNA BR assay kit (ThermoFisher). RNA integrity was checked using RNA 6000 Nano chip read by Aligent 2100 bioanalyzer.
RNA-seq libraries were prepared using either the TruSeq Stranded Total RNA Sample preparation kit with Ribo-Zero Gold (Illumina) by IGM Genomics Center at UC San Diego, or the KAPA RNA HyperPrep Kit with RiboErase (Roche).

value: Placenta

tag: gestational age_(week)

tag: Sex

value: female

tag: condition

value: PE-nonSGA


title: Day5_KO_1

description:
Library name: Sample 10
10x Genomics


title: P3217

description: Library name: sample169

data_processing:
Quality control was performed using multiQC (v1.17). Strand specificity analysis using RSeQC confirmed that the RNA-seq libraries were stranded, with the majority of reads aligning to the antisense strand. Adapter trimming and quality filtering were performed using BBDuk (BBMap suite) with the following parameters: ktrim=r, k=16, mink=11, hdist=1, tpe, tbo, qtrim=rl, and trimq=20, using a custom adapter reference file. Reads were mapped to the human genome (GRCh38, GENCODE release with ERCC spike-in sequences added) using STAR (v.2.7.11) with the following parameters: --runMode alignReads, --outSAMtype BAM SortedByCoordinate, --outSAMunmapped Within, and --quantMode GeneCounts. Feature quantification was performed using featureCounts (subread v.2.0.1)28 with parameters -p --countReadPairs -t exon -T 13 -g gene_id. Only Ensembl genes with ≥10 counts in at least 25% of samples were retained for downstream analysis. Normalization and differential expression analysis were performed using the R (v. 4.4.1) package DESeq2 (v. 1.44.0). BiomaRt (v. 2.60.1) was used to convert Ensembl gene IDs to HUGO gene names, and gene set enrichment analysis was done using the R (v. 4.4.1) package FGSEA (v. 1.30.0) and gene set variation analysis was done using GSVA (v. 1.4.4). Gene ontology analysis was done through Enrichr.
Assembly: GRCh38, GENCODE release 44
Supplementary files format and content: txt file for raw counts
Supplementary files format and content: txt file for vst data

tag: disease

value: gHTN

tag: gestational age_(weeks)

tag: placental pathology

value: MVM


title: P2948

description: Library name: sample168

value: Normal

value: male

value: nonMVM


title: P2918

description: Library name: sample164


title: Day5_WT_1

description:
Library name: Sample 7
10x Genomics

tag: genotype

value: WT


title: P2888

description: Library name: sample161

value: cHTN

tag: batch


title: Day5_WT_3

description:
Library name: Sample 9
10x Genomics


title: Day2_KO_2

description:
Library name: Sample 5
10x Genomics


title: P3287

description: Library name: sample170

tag: tissue


title: iMGL WT SEMA6D treat rep 3

value: iPSC-derived microglia


title: P2891

description: Library name: sample162

value: siPE


title: P2887

description: Library name: sample160


title: Day2_WT_3

description:
Library name: Sample 3
10x Genomics

tag: cell line


title: P2773

description: Library name: sample156


title: P2885

description: Library name: sample159

value: PE


title: P2893

description: Library name: sample163


title: P3318

description: Library name: sample171


title: P2925

description: Library name: sample165


title: P2928

description: Library name: sample166


title: P2831

description: Library name: sample157


title: P2719

description: Library name: sample153


title: P2941

description: Library name: sample167


title: Colonic biopsy: CM60

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description:
Library name: CM60
Colonic biopsy: CM60

data_processing:
Raw reads data were converted into FASTQ format and quality control was performed using the FASTQC software (Babraham Bioinformatics).
After trimming for adapters using trim_galore (Babraham Bioinformatics), mapping of the reads were obtained using the STAR program against human genome (hg38) and the quantification of genes were done using Partek Flow (v7.0.1) software using GENCODE V26 database
Assembly: Homo Sapiens genome hg38
Supplementary files format and content: read counts

source_name: Colonic biopsy

extract_protocol:
During endoscopy, at least two biopsies were collected from several segments of the colon (including sigmoid colon), fixed and routinely processed for histopathological assessment to confirm the diagnosis of MC and to exclude pathological alterations in control groups.
Sequencing libraries were prepared following the protocol included with the kit TruSeq Stranded mRNA Sample Preparation Guide (Part #15031047 Rev. E)

value: Colonic biopsy

value: H


title: P2662

description: Library name: sample152


title: P2637

description: Library name: sample149


title: P2547

description: Library name: sample146


title: P2878

description: Library name: sample158


title: P2739

description: Library name: sample155


title: P2506

description: Library name: sample145


title: P2644

description: Library name: sample150


title: P2724

description: Library name: sample154


title: P2434

description: Library name: sample141


title: P2297

description: Library name: sample136


title: P2657

description: Library name: sample151


title: P2412

description: Library name: sample140


title: P2478

description: Library name: sample143


title: P2611

description: Library name: sample148


title: P2287

description: Library name: sample135


title: P2276

description: Library name: sample134


title: P2475

description: Library name: sample142


title: P2241

description: Library name: sample132


title: P2502

description: Library name: sample144


title: P2334

description: Library name: sample137


title: B. mandarina_FWD, scRNA-seq

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics 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: Bmori_2016v1.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Bombyx mandarina

value: wing disc

tag: cell type

value: wing disc cells

value: Day 6 fifth-instar


title: P2580

description: Library name: sample147

value: Placenta

value: female


title: P2145

description: Library name: sample130


title: B. mandarina_HWD, scRNA-seq


title: P2405

description: Library name: sample139


title: P2273

description: Library name: sample133


title: P2086

description: Library name: sample129


title: P2354

description: Library name: sample138


title: B. mori_FWD, stRNA-seq

data_processing:
*library strategy: Spatial transcriptome seq
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Assembly: Bmori_2016v1.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every spot

organism: Bombyx mori

extract_protocol:
The tissue was then embedded in optimal cutting temperature (OCT) compound and snap frozen at -80 °C. The cryosections were sliced at a thickness of 10 µm and then placed onto ST arrays
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatail Gene Expression Slides & Reagent kit according to manufacturer's construction


title: P2219

description: Library name: sample131


title: P2025

description: Library name: sample127


title: P1953

description: Library name: sample125


title: P2084

description: Library name: sample128


title: P2018

description: Library name: sample126


title: P1947

description: Library name: sample124


title: TCR sequencing of Mus musculus: adult male spleen; LNP-GS Group rep3

city: Hangzhou

first: Shaolong

last: Zhang

address: Wenyixi Road 1369

institute: liangzhu Laboratory

description:
Library name: LNP-GS3-TCR
LNP-GS3

data_processing:
After library preparation, rigorous quality control (QC) was performed, evaluating total library yield (>30 ng), fragment size distribution (main peak: 300-600 bp), large fragment contamination (900-5,000 bp fragments <20%), and residual small fragments (<300 bp fragments <20%). Libraries meeting these criteria were subjected to paired-end sequencing on the Illumina NovaSeq 6000 platform.
TCR sequences were extracted with the CeleScope AccuraCode pipeline (v1.2.0; Singleron) aligned to the mouse reference genome. To suppress CDR3 diversity introduced by sequencing error, CDR3 amino-acid sequences were collapsed if hamming_distance(low_umi_cdr3, high_umi_cdr3) == 1 and，low_count / high_count < percent, merge low to high. Reads mapping to the constant regions of TRA and TRB (≥95 % coverage, IgBLAST-n v2.20) were retained; 150 bp of 5’ soft-clipped sequence was used for clonotype calling.
Assembly: mm10
Supplementary files format and content: RNA_UMI_counts_matrix.tsv: A tab-separated values file representing the raw UMI count matrix for gene expression. Rows correspond to genes, columns correspond to samples.
Supplementary files format and content: TCR_rearrangement.csv: A comma-separated values file containing annotated T-cell receptor (TCR) rearrangement data for clonality and diversity analysis. Key columns include barcode (sample identifier), chain (TRA or TRB), v_gene, j_gene, c_gene, cdr3 (amino acid sequence), reads, and umis.
Library strategy: TCR-Seq

source_name: spleen

extract_protocol:
The cDNA library was constructed from urine-derived cellular RNA (stored at −80 °C) using the Singleron AccuraCode HTP OneStep RNA-seq Kit (Singleron, Nanjing, China), following the manufacturer’s instructions.
Raw sequencing reads were processed using Celescope (v2.0.7) with default settings to generate gene expression profiles. Briefly, barcodes and unique molecular identifiers (UMIs) were extracted from R1 reads and subjected to error correction. Adapter sequences and poly-A tails were trimmed from R2 reads using Cutadapt (v3.7). The cleaned R2 reads were then aligned to the Mus musculus GRCm38 (mm10) reference genome using STAR (v2.7.11a). Uniquely mapped reads were assigned to genes using featureCounts (v2.0.1). Finally, reads with identical barcodes, UMIs, and gene annotations were aggregated to construct the gene expression matrix for downstream analysis.

value: spleen


title: TCR sequencing of Mus musculus: adult male spleen; LNP-GS Group rep2

description:
Library name: LNP-GS2-TCR
LNP-GS2


title: Healthy Subjects

type: RNA

city: Turin

first: Martina

last: Schiavello

address: Via Genova 3

country: Italy

institute: University of Turin

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://apps.thermofisher.com/apps/spa/beta/#/dashboard
To ensure the optimal quality of the data, we first analyzed spike-in miRNA templates to monitor the uniformity of the RNA extraction procedure and the efficiency of qRT-PCRs. miRNAs with threshold cycles (Ct) > 33 were considered undetectable, and excluded from the analysis. Relative quantification (Rq) was then performed using the 2–ΔΔCt method, normalizing to Cel-miR-39 expression levels.

label: TaqMan

source_name: Plasma

label_protocol: A spike-in exogenous control, Cel-miR-39-3p , lacking sequence homology to human miRNAs, was added to each sample as an external reference miRNA (4.8 × 108 copies/sample). After silica-membrane-based purification on RNeasy UCP MinElute spin column, high-quality RNAs, primarily miRNAs and other small non-coding RNAs, were eluted into 20 μL of RNase-free water and stored at -80°C. An equal amount (2 µL) of each RNA extract was processed using the TaqMan Advanced miRNA cDNA synthesis kit (Applied Biosystems, Thermo Fisher Scientific), according to the manufacturer’s instructions. For the diagnostic and prognostic screening phase, four pooled samples composed of one pool obtained from HS (n=8) and three pools obtained from COVID-19 patients, each one from 8 patients, were processed by using TaqMan™ Advanced miRNA Human Cards A and B (Applied Biosystems, Thermo Fisher Scientific).

extract_protocol: Total RNA was extracted with the miRNeasy Serum/Plasma Advanced Kit

tag: group

value: Control

tag: disease state

value: Healthy

value: Plasma

tag: inclusion criteria age

value: adult patients (age>18 years)


title: P1903

description: Library name: sample122

value: nonMVM


title: TCR sequencing of Mus musculus: adult male spleen; LNP-G Group rep2

description:
Library name: LNP-G2-TCR
LNP-G2


title: COVID-19 patients for prognostic value (poor prognosis)

value: Test


title: TCR sequencing of Mus musculus: adult male spleen; PBS Group rep3

description:
Library name: PBS3-TCR
PBS3


title: B. mandarina_FWD, stRNA-seq


title: COVID-19 patients for prognostic value (good prognosis)


title: B. mandarina_HWD, stRNA-seq


title: TCR sequencing of Mus musculus: adult male spleen; LNP-GS Group rep1

description:
Library name: LNP-GS1-TCR
LNP-GS1


title: P1905

description: Library name: sample123

value: Normal

value: male


title: P1836

description: Library name: sample120


title: TCR sequencing of Mus musculus: adult male spleen; PBS Group rep2

description:
Library name: PBS2-TCR
PBS2


title: COVID-19 patients for diagnostic value


title: P1717

description: Library name: sample116

value: siPE

value: MVM


title: P1867

description: Library name: sample121


title: TCR sequencing of Mus musculus: adult male spleen; LNP-G Group rep3

description:
Library name: LNP-G3-TCR
LNP-G3


title: P1707

description: Library name: sample114


title: Liver_G4_310, Female

city: Bethesda

first: Huaitian

last: Liu

state: MD

address: Building 37, Room 3050

department: CCR

institute: NCI

description: Library name: Liver_G4_310

data_processing:
Cutadapt was used to trim adapters and low-quality bases from raw reads.
Trimmed reads were aligned using STAR to the mm10 reference genome (GENCODE M2 annotation), with the reference index augmented to include transgene sequences (human TP53 (Δ133p53α) and EGFP).
Mapping statistics were calculated using Picard.
Gene-level expression quantification was performed using STAR/RSEM to generate gene-by-sample raw and normalized count matrices.
Assembly: GRCm38 (mm10), GENCODE M2
Supplementary files format and content: tab-delimited text file contains a gene-by-sample matrix of  read counts for all samples.
Supplementary files format and content: tab-delimited text file contains a isoforms-by-sample matrix of reads counts for all samples

source_name: Liver

growth_protocol: Tissues (heart, kidney, liver and skeletal muscle) were collected from 9–10-month-old mice across five groups (wild-type and Groups 1–4; n = 5 per tissue per group) and snap-frozen for RNA isolation.

extract_protocol:
Total RNA was isolated using the RNeasy Plus Micro Kit (QIAGEN, 74034) according to the manufacturer’s instructions. Snap-frozen tissues were homogenized in the lysis buffer provided in the kit using a bead-based tissue homogenizer. RNA quality was assessed on an Agilent TapeStation at the CCR Genomics Core, National Cancer Institute.
RNA-seq libraries were prepared from total RNA using Illumina Stranded mRNA Prep and sequenced on an Illumina NovaSeq X Plus platform using paired-end sequencing at the Frederick Sequencing and Genomics Core.

treatment_protocol: Tamoxifen was administered by intraperitoneal injection on five consecutive days at 5–6 weeks of age to activate CreERT2 and induce recombination of the Cre/loxP-inducible Δ133p53α transgene in the designated groups, as described in the associated manuscript.

value: Liver

tag: treatment

value: without tamoxifen


title: P1789

description: Library name: sample117

value: PE


title: Liver_G4_282, Male

description: Library name: Liver_G4_282


title: P1807

description: Library name: sample119

value: cHTN


title: P1791

description: Library name: sample118

value: Placenta


title: P1679

description: Library name: sample112


title: Foxp3YFP-CreKmt2d+/+, replicate 1, scRNAseq

city: Zhengzhou

first: Peng

last: Wang

address: Science Avenue

institute: Zhengzhou University

description:
Library name: Sample 1
10x Genomics

data_processing:
scRNA-seq data analysis was conduceted by NovelBio Co., Ltd. with NovelBrain Cloud Analysis Platform (www.novelbrain.com). We employed fastp with default parameters to filter adaptor sequences and remove low-quality reads, resulting in clean data. Feature-barcode matrices were generated by aligning reads to the mouse genome (mm10 Ensemble: version 100) using CellRanger v7.1.0. Down-sampling analysis was performed based on the among the mapped barcoded reads per cell of each sample, culminating in an aggregated matrix. Cells with over 200 expressed genes and a mitochondrial UMI rate below 20% passed quality filtering, and mitochondrial genes were subsequently removed from the expression table. The Seurat package (version: 4.1.1, https://satijalab.org/seurat/) was utilized for cell normalization and regression based on UMI counts and mitochondrial percentage, yielding scaled data.
Assembly: GRCm38
Supplementary files format and content: matrix

source_name: Spleen

extract_protocol:
Spleen CD4+FoxP3+ Treg cells from Foxp3YFP-CreKmt2d+/+ and Foxp3YFP-CreKmt2dfl/fl mice were sorted. The sorted Treg cells from three Foxp3YFP-CreKmt2d+/+ mice were pooled into one sample, while Treg cells from three Foxp3YFP-CreKmt2dfl/fl mice were combined into a separate sample for scRNA-seq.
Library preparation and sequencing: The scRNA-seq libraries were prepared using the 10x Genomics Chromium Controller and Chromium Single Cell 3’ V3.1 Reagent Kits (10x Genomics). Cells were concentrated to approximately 1,000 cells/uL and loaded into each channel to generate single-cell Gel Bead-In-Emulsions (GEMs). Following the reverse transcription step, GEMs were disrupted, and the barcoded cDNA was purified and amplified. The amplified cDNA was fragmented, A-tailed, ligated with adaptors and subjected to index PCR amplification. The final libraries were quantified using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific), and their size distribution was assessed using a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent). All libraries were sequenced on an Illumina sequencer using a 150 bp paired-end run.

value: Spleen

value: Treg cells


title: TCR sequencing of Mus musculus: adult male spleen; PBS Group rep1

description:
Library name: PBS1-TCR
PBS1

value: spleen


title: Foxp3YFP-CreKmt2dfl/fl, replicate 1, scRNAseq

description:
Library name: Sample 2
10x Genomics


title: P1682

description: Library name: sample113

value: female


title: P1711

description: Library name: sample115


title: P1662

description: Library name: sample111


title: TCR sequencing of Mus musculus: adult male spleen; LNP-G Group rep1

description:
Library name: LNP-G1-TCR
LNP-G1


title: Liver_G3_404, Male

description: Library name: Liver_G3_404

value: with tamoxifen


title: P1651

description: Library name: sample110


title: P936

description: Library name: sample108


title: P937

description: Library name: sample109


title: Liver_G4_275, Female

description: Library name: Liver_G4_275


title: Liver_G3_309, Female

description: Library name: Liver_G3_309


title: Liver_G3_385, Male

description: Library name: Liver_G3_385


title: Liver_G4_277, Male

description: Library name: Liver_G4_277


title: Liver_G3_273, Female

description: Library name: Liver_G3_273


title: P892

description: Library name: sample105


title: P916

description: Library name: sample106


title: Liver_G2_312, Female

description: Library name: Liver_G2_312


title: P917

description: Library name: sample107


title: Liver_G3_130, Female

description: Library name: Liver_G3_130


title: P880

description: Library name: sample103


title: B. mori_HWD, stRNA-seq

value: wing disc

value: wing disc cells

tag: age

value: Day 6 fifth-instar


title: Liver_G2_281, Female

description: Library name: Liver_G2_281


title: P813

description: Library name: sample102

value: Normal

value: nonMVM


title: Liver_G4_172, Female

description: Library name: Liver_G4_172


title: P770

description: Library name: sample101

value: male


title: Liver_G2_279, Male

description: Library name: Liver_G2_279


title: P739

description: Library name: sample100


title: Liver_G2_278, Male

description: Library name: Liver_G2_278


title: P632

description: Library name: sample99


title: P887

description: Library name: sample104


title: MLiver_G1_272, Male

description: Library name: Liver_G1_272


title: Liver_G2_169, Female

description: Library name: Liver_G2_169


title: P2816

description: Library name: sample96

value: MVM


title: P2770

description: Library name: sample94

value: siPE


title: P3306

description: Library name: sample98


title: P2995

description: Library name: sample97


title: Liver_WT_653, Male

description: Library name: Liver_WT_653

value: Liver

value: without tamoxifen


title: P2765

description: Library name: sample93


title: Liver_WT_545, Male

description: Library name: Liver_WT_545


title: Liver_G1_311, Female

description: Library name: Liver_G1_311


title: Liver_WT_528, Female

description: Library name: Liver_WT_528


title: P2690

description: Library name: sample92


title: P2653

description: Library name: sample91


title: P2487

description: Library name: sample89


title: P2515

description: Library name: sample90


title: Liver_G1_129, Female

description: Library name: Liver_G1_129


title: Liver_G1_269, Male

description: Library name: Liver_G1_269


title: Liver_WT_173, Female

description: Library name: Liver_WT_173


title: Liver_G1_267, Female

description: Library name: Liver_G1_267


title: Muscle_G4_277, Male

description: Library name: Muscle_G4_277

source_name: Muscle

value: Muscle


title: P2804

description: Library name: sample95

value: Placenta


title: Muscle_G4_282, Male

description: Library name: Muscle_G4_282


title: P2422

description: Library name: sample87


title: Liver_WT_355, Female

description: Library name: Liver_WT_355


title: P2121

description: Library name: sample85


title: P2235

description: Library name: sample86


title: P2470

description: Library name: sample88


title: Muscle_G4_310, Female

description: Library name: Muscle_G4_310


title: Muscle_G4_275, Female

description: Library name: Muscle_G4_275


title: Muscle_G3_385, Male

description: Library name: Muscle_G3_385


title: Muscle_G3_309, Female

description: Library name: Muscle_G3_309


title: P2104

description: Library name: sample84


title: Muscle_G3_404, Male

description: Library name: Muscle_G3_404


title: Muscle_G4_172, Female

description: Library name: Muscle_G4_172


title: P1714

description: Library name: sample83


title: P1658

description: Library name: sample82


title: P1648

description: Library name: sample81


title: P1628

description: Library name: sample79


title: Muscle_G2_312, Female

description: Library name: Muscle_G2_312


title: Muscle_G2_281, Female

description: Library name: Muscle_G2_281


title: P1598

description: Library name: sample77


title: Muscle_G3_273, Female

description: Library name: Muscle_G3_273


title: Muscle_G1_311, Female

description: Library name: Muscle_G1_311


title: Muscle_G1_269, Male

description: Library name: Muscle_G1_269


title: Muscle_G1_129, Female

description: Library name: Muscle_G1_129


title: P1486

description: Library name: sample70


title: Muscle_WT_653, Male

description: Library name: Muscle_WT_653


title: P1542

description: Library name: sample73

value: gHTN


title: Muscle_WT_545, Male

description: Library name: Muscle_WT_545


title: P1613

description: Library name: sample78

value: PE


title: P1575

description: Library name: sample76


title: P1399

description: Library name: sample68


title: Muscle_WT_528, Female

description: Library name: Muscle_WT_528


title: Muscle_WT_355, Female

description: Library name: Muscle_WT_355


title: P1344

description: Library name: sample66


title: Muscle_G2_279, Male

description: Library name: Muscle_G2_279


title: Muscle_G2_278, Male

description: Library name: Muscle_G2_278


title: Muscle_G1_267, Female

description: Library name: Muscle_G1_267


title: P1646

description: Library name: sample80


title: P1325

description: Library name: sample64


title: P1521

description: Library name: sample72


title: P1319

description: Library name: sample63


title: Kidney_G4_275, Female

description: Library name: Kidney_G4_275

source_name: Kidney

value: Kidney


title: Muscle_G3_130, Female

description: Library name: Muscle_G3_130


title: Muscle_G1_272, Male

description: Library name: Muscle_G1_272


title: P1569

description: Library name: sample75


title: P1299

description: Library name: sample60

value: female


title: Kidney_G4_172, Female

description: Library name: Kidney_G4_172


title: P1267

description: Library name: sample58

value: cHTN


title: P1293

description: Library name: sample59


title: Kidney_G3_385, Male

description: Library name: Kidney_G3_385

value: with tamoxifen


title: Muscle_G2_169, Female

description: Library name: Muscle_G2_169


title: P1553

description: Library name: sample74


title: Kidney_G3_309, Female

description: Library name: Kidney_G3_309


title: Kidney_G4_282, Male

description: Library name: Kidney_G4_282


title: Kidney_G3_130, Female

description: Library name: Kidney_G3_130


title: P1265

description: Library name: sample57


title: P1373

description: Library name: sample67


title: P1248

description: Library name: sample55


title: P1220

description: Library name: sample54


title: P1327

description: Library name: sample65


title: Muscle_WT_173, Female

description: Library name: Muscle_WT_173


title: Kidney_G3_404, Male

description: Library name: Kidney_G3_404


title: P1188

description: Library name: sample51


title: Kidney_G4_310, Female

description: Library name: Kidney_G4_310


title: Kidney_G2_169, Female

description: Library name: Kidney_G2_169


title: P1182

description: Library name: sample50


title: P1255

description: Library name: sample56


title: Kidney_G4_277, Male

description: Library name: Kidney_G4_277


title: P1142

description: Library name: sample47


title: P1316

description: Library name: sample62


title: P1445

description: Library name: sample69


title: Kidney_G1_269, Male

description: Library name: Kidney_G1_269


title: P1488

description: Library name: sample71


title: P1145

description: Library name: sample48


title: P1312

description: Library name: sample61


title: P1219

description: Library name: sample53


title: Kidney_G2_312, Female

description: Library name: Kidney_G2_312


title: P1090

description: Library name: sample45


title: Kidney_G1_129, Female

description: Library name: Kidney_G1_129


title: Kidney_G2_278, Male

description: Library name: Kidney_G2_278


title: Kidney_WT_545, Male

description: Library name: Kidney_WT_545


title: P1216

description: Library name: sample52


title: P1074

description: Library name: sample43


title: Kidney_G2_279, Male

description: Library name: Kidney_G2_279


title: Kidney_G3_273, Female

description: Library name: Kidney_G3_273


title: Heart_G4_310, Female

description: Library name: Heart_G4_310

source_name: Heart

value: Heart


title: Kidney_G2_281, Female

description: Library name: Kidney_G2_281


title: P1161

description: Library name: sample49


title: HeLa cells, Control, rep 3

city: Porto

first: Bruno

last: Sousa

address: R. Alfredo Allen 208

country: Portugal

institute: Instituto de Investigaçã́o e Inovação em Saúde (i3S)

description: Library name: Unknown_CH585-001T0005

data_processing:
fastp v0.20.1; HISAT2 v2.2.1; htseq-count v1.99.2; DESeq2 v1.46.0
Sequence reads were trimmed for adapter sequences/low-quality sequence using fastp with default parameters.
Trimmed sequences were mapped to hg38 using the HISAT2 splice-aware aligner with default parameters.
Gene-level read count extraction was carried out with htseq-count with default parameters using the hg38 ncbirefseq GTF file.
After read count extraction, DESeq2 was used for differential gene expression. Correction for batch effects (2 batches) was applied in the final analysis.
Assembly: hg38
Supplementary files format and content: htseq text files with raw counts for each sample

source_name: HeLa

extract_protocol:
RNA was harvested using trizol.
Library construction carried out by Biomarker Technologies (BMKGENE).

value: HeLa

value: siNTC

value: batch 1


title: Heart_G4_282, Male

description: Library name: Heart_G4_282


title: HeLa cells, Control, rep 5

description: Library name: Unknown_CK005-001T0003

value: batch 2


title: Kidney_WT_173, Female

description: Library name: Kidney_WT_173


title: HeLa cells, Control, rep 1

description: Library name: Unknown_CH585-001T0001


title: HeLa cells, PTBP1 Knockdown, rep5

description: Library name: Unknown_CK005-001T0004


title: Kidney_G1_311, Female

description: Library name: Kidney_G1_311


title: HeLa cells, Control, rep 4

description: Library name: Unknown_CK005-001T0001


title: Kidney_WT_528, Female

description: Library name: Kidney_WT_528


title: P1084

description: Library name: sample44

value: nonMVM


title: Kidney_G1_267, Female

description: Library name: Kidney_G1_267


title: WE Rapa-U18, Biol rep 3

city: Santiago

first: Benjamín

last: Szenfeld

state: Las Condes

address: Av Plaza 680

department: Genetics and Genomics

country: Chile

institute: Institute of Science and Innovation in Medicine

description: Library name: Sample 24

data_processing:
Galaxy Europe was used to upload the RNA-seq FASTQ files and generate paired datasets for each sample (forward and reverse reads). Then, the Salmon tool was employed to map the sequences to the reference transcriptome and obtain expression quantifications per sample in the form of TPMs and counts.
Assembly: sacCer3
Supplementary files format and content: Tabular files include, for each gene, the raw counts, TPM, Length, and EffectiveLength.

organism: Saccharomyces cerevisiae

source_name: DBVPG6765 (Wine/European, "WE")

growth_protocol: Yeast taken from patches on YPD plates were grown in triplicates at 28 °C.

extract_protocol:
Cells were centrifuged and treated with 2U zymolyase for 30 minutes at 37°C. RNA was extracted using the E.Z.N.A. Total RNA Kit I (OMEGA), according to the manufacturer's instructions. Subsequently, the samples were treated with DNase I (Promega) to eliminate genomic DNA contamination. RNA integrity was confirmed using a Fragment Analyzer (Agilent).
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA protocol following the manufacturer’s instructions.

treatment_protocol: Treated with U18 (5 mL of YNB medium containing 200 mg/mL U18666A) and Rapa-U18 (5 mL of YNB medium containing 0.25 nM Rapamycin and 200 ug/mL U18666A)

value: DBVPG6765 (Wine/European, "WE")

value: WT (ho::NatMX, ura3::KanMX)

value: 0.25 nM Rapamycin and 200 ug/mL U18666A


title: P1132

description: Library name: sample46

value: Normal


title: Kidney_WT_653, Male

description: Library name: Kidney_WT_653

value: without tamoxifen


title: WE Rapa-U18, Biol rep 2

description: Library name: Sample 23


title: Heart_G4_277, Male

description: Library name: Heart_G4_277


title: P1007

description: Library name: sample42

value: Placenta

value: MVM


title: HeLa cells, Control, rep 2

description: Library name: Unknown_CH585-001T0003


title: Heart_G4_275, Female

description: Library name: Heart_G4_275


title: HeLa cells, PTBP1 Knockdown, rep2

description: Library name: Unknown_CH585-001T0004


title: HeLa cells, PTBP1 Knockdown, rep4

description: Library name: Unknown_CK005-001T0002


title: Kidney_WT_355, Female

description: Library name: Kidney_WT_355

value: Kidney


title: Heart_G4_172, Female

description: Library name: Heart_G4_172


title: NA Rapa-U18, Biol rep 1

description: Library name: Sample 19

source_name: YPS128 (North American, "NA")

value: YPS128 (North American, "NA")


title: SA Rapa-U18, Biol rep 3

description: Library name: Sample 18

source_name: Y12 (Sake, "SA")

value: Y12 (Sake, "SA")


title: Heart_G3_404, Male

description: Library name: Heart_G3_404

value: with tamoxifen


title: Heart_G3_130, Female

description: Library name: Heart_G3_130

value: Heart


title: NA Rapa-U18, Biol rep 3

description: Library name: Sample 21


title: HeLa cells, PTBP1 Knockdown, rep3

description: Library name: Unknown_CH585-001T0006

value: HeLa


title: WA Rapa-U18, Biol rep 3

description: Library name: Sample 15

source_name: DBVPG6044 (West African, "WA")

value: DBVPG6044 (West African, "WA")


title: Heart_G3_385, Male

description: Library name: Heart_G3_385


title: SA Rapa-U18, Biol rep 2

description: Library name: Sample 17


title: Subject 36, post treatment of Placebo group

city: Solna

first: Nageswara Rao

last: Boggavarapu

state: stockholm

address: Visionsgatan 4

department: Women and Children health

country: Sweden

institute: Karolinska Institutet

description:
Library name: 36B
Placebo_DeSeq2_Counts.txt

data_processing:
Bioinformatic analyses were performed using Partek Flow Genomic Analysis Software (Partek, St. Louis, Missouri, USA), And R
Sequenced raw FASTQ files were trimmed for Nextera transposase adapters.
Trimmed reads were mapped to the reference genome HG38 using STAR aligner.
Mapped reads were further filtered and quantified to transcripts and genes using Hg38 assembly and Ensembl Transcripts release 100.
Assembly: hg38
Supplementary files format and content: raw counts, deseq2 normalised values for each sample

source_name: Breast Tissue

extract_protocol:
RNA extraction from tissues was performed using the Zymo quick DNA/RNA-microprep kit (Zymo Research, Cat.R1501) according to the manufacturer's instructions.
cDNA library was constructed using well established Smart-seq2 protocol (Picelli et al. 2013, Picelli et al. 2014)

value: Breast Tissue

tag: subject id

value: Subject 36

tag: treatment/time point

value: post treatment of Placebo


title: Heart_G2_312, Female

description: Library name: Heart_G2_312


title: Subject 30, post treatment of Placebo group

description:
Library name: 30B
Placebo_DeSeq2_Counts.txt

value: Subject 30


title: Heart_G3_273, Female

description: Library name: Heart_G3_273


title: HeLa cells, PTBP1 Knockdown, rep1

description: Library name: Unknown_CH585-001T0002

value: batch 1


title: WA Rapa-U18, Biol rep 1

description: Library name: Sample 13

value: WT (ho::NatMX, ura3::KanMX)

value: 0.25 nM Rapamycin and 200 ug/mL U18666A


title: WE Rapa-U18, Biol rep 1

description: Library name: Sample 22

value: DBVPG6765 (Wine/European, "WE")


title: WE Rapa, Biol rep 3

description: Library name: Sample 12

value: 0.25 nM Rapamycin


title: WE Rapa, Biol rep 2

description: Library name: Sample 11


title: SA Rapa-U18, Biol rep 1

description: Library name: Sample 16


title: Heart_G2_279, Male

description: Library name: Heart_G2_279

value: without tamoxifen


title: NA Rapa-U18, Biol rep 2

description: Library name: Sample 20


title: WE Rapa, Biol rep 1

description: Library name: Sample 10


title: NA Rapa, Biol rep 2

description: Library name: Sample 8


title: Subject 30, pre treatment of Placebo group

description:
Library name: 30A
Placebo_DeSeq2_Counts.txt

value: pre treatment of Placebo


title: NA Rapa, Biol rep 3

description: Library name: Sample 9

value: YPS128 (North American, "NA")


title: Heart_G2_278, Male

description: Library name: Heart_G2_278


title: NA Rapa, Biol rep 1

description: Library name: Sample 7


title: Subject 36, pre treatment of Placebo group

description:
Library name: 36A
Placebo_DeSeq2_Counts.txt


title: Heart_G3_309, Female

description: Library name: Heart_G3_309


title: Subject 24, post treatment of Placebo group

description:
Library name: 24B
Placebo_DeSeq2_Counts.txt

value: Subject 24


title: Subject 22, post treatment of Placebo group

description:
Library name: 22B
Placebo_DeSeq2_Counts.txt

value: Subject 22


title: Heart_G2_169, Female

description: Library name: Heart_G2_169

value: Heart


title: SA Rapa, Biol rep 3

description: Library name: Sample 6

value: Y12 (Sake, "SA")


title: Heart_G1_311, Female

description: Library name: Heart_G1_311

value: with tamoxifen


title: Heart_G1_272, Male

description: Library name: Heart_G1_272


title: Subject 24, pre treatment of Placebo group

description:
Library name: 24A
Placebo_DeSeq2_Counts.txt

value: Breast Tissue


title: SA Rapa, Biol rep 2

description: Library name: Sample 5


title: Heart_G2_281, Female

description: Library name: Heart_G2_281


title: WA Rapa, Biol rep 3

description: Library name: Sample 3

value: DBVPG6044 (West African, "WA")


title: WA Rapa, Biol rep 2

description: Library name: Sample 2


title: Subject 3, pre treatment of Placebo group

description:
Library name: 3A
Placebo_DeSeq2_Counts.txt

value: Subject 3


title: WA Rapa-U18, Biol rep 2

description: Library name: Sample 14


title: HCC1806-HM3,shMSLN-3

city: Chongqing

first: boxuan

last: wang

address: 重庆市渝中区医学院路1号

institute: 重庆医科大学

description:
Library name: Sample6
SH3

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter
Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format
Assembly: Homo_sapiens_9606.NCBI.GCF_000001405.39_GRCh38.p13.v2201
Supplementary files format and content: FPKM,txt
Supplementary files format and content: readcount,txt

growth_protocol: HCC1806-HM3 cell lines were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidifired atmosphere  in a 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from tissues using TRIzol (Invitrogen, Carlsbad, California, USA) according to manual instruction
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). A certain amount of RNA are denatured at suitable temperature to open the secondary structure, and mRNA is enriched by oligo (dT) attached magnetic beads. After reacting at a suitable temperature for a fixed time period, RNAs are fragmented with fragmentation reagents. Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). A certain amount of RNA are denatured at suitable temperature to open the secondary structure, and mRNA is enriched by oligo (dT) attached magnetic beads. After reacting at a suitable temperature for a fixed time period, RNAs are fragmented with fragmentation reagents. Next, the single-stranded library products are produced via denaturation. The reaction system for circularization is set up to get the single-stranded cyclized DNA products. Any uncyclized single stranded linear DNA molecules will be digested. The final single strand circularized library is amplified with phi29 and rolling circle amplification (RCA) to make DNA nanoball (DNB) which carries more than 300 copies of the initial single stranded circularized library molecule

value: Human breast squamous cell carcinoma cells

value: MSLN knockdown


title: SA Rapa, Biol rep 1

description: Library name: Sample 4

value: WT (ho::NatMX, ura3::KanMX)


title: Heart_G1_129, Female

description: Library name: Heart_G1_129


title: Heart_G1_269, Male

description: Library name: Heart_G1_269


title: Subject 22, pre treatment of Placebo group

description:
Library name: 22A
Placebo_DeSeq2_Counts.txt


title: NSCs

city: Guangzhou

first: yuanfei

last: wu

address: No. 1 Xinzao Road, Xinzao Town, Panyu District

institute: Guangzhou Medical University

description:
Library name: sample1
NSCs

data_processing:
Cut off low-quality reads, and use a sliding window mode, with 4 bases as a window. If the average base mass value of the window is lower than 15, cut off reads from there, and the parameter selection is: sliding window: 4: 15;
Truncate the reads whose head and tail mass are less than 3 or contain N(N means that the base information cannot be determined), and select the parameters: LEADING:3, trailing: 3;
Cut off the polluted reads of the linker, and use two modes to remove the linker: 1. Simple alignment mode: the comparison score between seed and linker sequence reaches 7 (about 12 bp); 2.palindrome mode: when read1 and read2 overlap.When the base score of the region is greater than 30, part of the seed sequence is truncated. Parameter selection: illuminaclip: adapter.fa: 2: 30: 7: 1: true;
Discard the pruned reads； shorter than 36nt;
Discard the reads that cannot form a pair.
Assembly: BWA(Burrows Wheeler Aligner) software was used to compare clean reads to the reference genome.
Supplementary files format and content: The Raw Data obtained by high-throughput sequencing are stored in FASTQ (fq for short) file format.

organism: Rattus norvegicus

extract_protocol:
Genomic DNA was isolated using phenol-chloroform-isoamyl alcohol extraction with overnight RNase A treatment, followed by ethanol precipitation. Isolated genomic DNA was diluted to 100-200 ng/uL using TE buffer, and sonicated in 130 uL scale to 200-400 bp using Covaris Focused-ultrasonicator according to the machine settings. End repair was performed using ∼5 ug of sonicated DNA in 100 uL, followed by 3′-adenylation and adaptor ligation according to Illumina TruSeq DNA sample preparation procedures. The ligated DNA was purified using low melting point agarose gel, and cut with a size selection between 200-400 bp. DNA was recovered by gel purification kit (QIAGEN) with a yield of ∼1 ug, diluted in Tris-EDTA buffer (400 uL, 1 mM Tris, pH 8.0, 0.1 mM EDTA), denatured at 95°C for 10 min, and chilled on ice for 10 min.
A portion of 10 uL of DNA was saved as input. The rest of DNA was combined with 3 ug of anti-6mA antibody (Synaptic Systems, dissolved as 0.5 ug/uL) in 500 uL of 1 × IP buffer; 5 × IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% vol/vol IGEPAL CA-630) was prepared as a stock solution), and incubated at 4°C for 6 hr. At the same time, 40 uL of Protein A magnetic beads (Invitrogen) was washed twice in 0.5 ml of 1 × IP buffer, and pre-blocked in 0.5 ml of 1 × IP buffer containing 20 ug/uL of Bovine Serum Album (Sigma-Aldrich) at 4°C for 6 hr. The Protein A beads were washed twice with 0.5 ml of 1 × IP buffer, added to the DNA-6mA antibody mixture, and incubated at 4°C with gentle rotation overnight. The beads were then washed 4 times with 0.5 ml of 1 × IP buffer for 10 min. Methylated DNA was eluted twice by 100 uL of elution buffer containing 6mA monophosphate at 4°C for 1 hr (to prepare for a 450 uL elution buffer solution, mix 90 μl (5 × stock) of IP buffer, 150 μl (20 mM stock) of N6-methyladenosine, 5′-monophosphate sodium salt (Sigma-Aldrich), and 210 μl of water). The two elution solutions were combined, to which 20 uL of NaOAc (3 M, pH 5.3), 500 uL of EtOH, and 0.5 uL of glycogen at 20 ng/uL were added. The solution was frozen at −80°C overnight, and centrifuged at 14,000 × g for 20 min at 4°C. The precipitated DNA was dissolved in 7 uL of ddH2O, PCR amplified for 15 to 18 cycles, purified by Agencourt AMPure XP (Beckman Coulter), and suspended in 16 uL of resuspension buffer to yield the sequencing library.


title: WA Rapa, Biol rep 1

description: Library name: Sample 1


title: Neurons

description:
Library name: sample2
Neurons

source_name: Neurons

value: Neurons


title: Subject 4, pre treatment of Placebo group

description:
Library name: 4A
Placebo_DeSeq2_Counts.txt

value: Subject 4


title: Subject 35, post treatment of Mifepristone treatment group

description:
Library name: 35B
Treatment_DeSeq2_Counts.txt

value: Subject 35


title: HCC1806-HM3,shMSLN-2

address: 重庆市渝中区医学院路1号

description:
Library name: Sample5
SH2


title: HCC1806-HM3,shNC-3

address: 重庆市渝中区医学院路1号

description:
Library name: Sample3
NC3

value: Control


title: Subject 3, post treatment of Placebo group

description:
Library name: 3B
Placebo_DeSeq2_Counts.txt

value: post treatment of Placebo


title: Heart_WT_545, Male

description: Library name: Heart_WT_545

value: without tamoxifen


title: HCC1806-HM3,shMSLN-1

address: 重庆市渝中区医学院路1号

description:
Library name: Sample4
SH1


title: Subject 4, post treatment of Placebo group

description:
Library name: 4B
Placebo_DeSeq2_Counts.txt


title: HCC1806-HM3,shNC-2

address: 重庆市渝中区医学院路1号

description:
Library name: Sample2
NC2


title: Subject 35, pre treatment of Mifepristone treatment group

description:
Library name: 35A
Treatment_DeSeq2_Counts.txt

value: pre treatment of Mifepristone treatment


title: HCC1806-HM3,shNC-1

address: 重庆市渝中区医学院路1号

description:
Library name: Sample1
NC1


title: NSCs-input

description:
Library name: sample4
NSCs-input


title: Heart_WT_355, Female

description: Library name: Heart_WT_355


title: Heart_WT_653, Male

description: Library name: Heart_WT_653


title: Neurons-input

description:
Library name: sample5
Neurons-input


title: Heart_WT_528, Female

description: Library name: Heart_WT_528


title: Heart_G1_267, Female

description: Library name: Heart_G1_267


title: Subject 21, pre treatment of Mifepristone treatment group

description:
Library name: 21A
Treatment_DeSeq2_Counts.txt

value: Subject 21


title: Subject 21, post treatment of Mifepristone treatment group

description:
Library name: 21B
Treatment_DeSeq2_Counts.txt


title: Meg01, day3, EV#4

city: Amsterdam

first: Emile

last: van den Akker

address: Plesmanlaan 125

country: Netherlands

institute: Sanquin Research Amsterdam

description:
Library name: sample 12
EV_4

data_processing:
In the trimming, Illumina adapter and poly-A sequences were removed from the reads
The trimmed reads were then aligned using HISAT2 (Kim et al, 2019)
After the HISAT2 alignment, SAMTools (Li et al, 2009) was used to sort and merge the alignments from multiple flow cells.
Quantification was performed using HT-seq count (Anders et al, 2015) after first sorting the alignments on readname using SAMTools.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: hematopoietic

extract_protocol:
RNA was isolated using TRIzol RNA isolation reagents (ThermoFisher Scientific)
RNA-Seq library was prepared for analysis according to the Illumina TruSeq stranded mRNA protocol (www.illumina.com).

value: hematopoietic

value: leukemic

value: WT

value: EV


title: Meg01, day3, FLI1Met100*#4

description:
Library name: sample 8
M_4


title: Meg01, day3, FLI1Met100*#1

description:
Library name: sample 5
M_1


title: Meg01, day3, FLI1Met100*#3

description:
Library name: sample 7
M_3


title: Meg01, day3, EV#3

description:
Library name: sample 11
EV_3


title: Meg01, day3, FLI1-WT#3

description:
Library name: sample 3
WT_3


title: K_IRT_3

first: Shun

address: 1665, Kongjiang Road, Yangpu

department: Urology

institute: Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University

description: Library name: Sample12

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: GRCm39
Supplementary files format and content: xls file includes raw count for each sample

source_name: KPC

growth_protocol: MB49 and KPC cells were cultured in complete Dulbecco's Modified Eagle Medium (DMEM) containing 10% fetal bovine serum and 1% penicillin/streptomycin at 37℃ with 5% CO2 atmosphere.

extract_protocol:
The cells were collected for total RNA extraction using TRIzol® Reagent. Genomic DNA was removed by DNase I, and the 1% agarose gels were used to monitor the RNA degradation and contamination. Next, RNA quality was identified by 2100 Bioanalyser (Agilent Technologies) and quantified by ND-2000 (NanoDrop Technologies). RNA sample with high-quality was utilized to establish sequencing library (OD260/280 = 1.8 ~ 2.2, OD260/230 ≥ 2.0, RIN ≥ 8.0, 28 S:18 S ≥ 1.0 and ≥ 1 μg).
The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA.

treatment_protocol: Senescent or none-senescent tumor cells (MB49 cell, sMB49 cells, KPC cells, and sKPC cells) were treated with 8 Gy-RT and cultured for 48 h.Then the cells were collected for total RNA sequence.

value: KPC

value: mouse pancreatic ductal adenocarcinoma cell

value: 8 Gy-RT


title: Meg01, day3, EV#2

description:
Library name: sample 10
EV_2


title: Subject 15, post treatment of Mifepristone treatment group

description:
Library name: 15B
Treatment_DeSeq2_Counts.txt

value: Breast Tissue

value: Subject 15


title: Subject 15, pre treatment of Mifepristone treatment group

description:
Library name: 15A
Treatment_DeSeq2_Counts.txt


title: K_IRT_1

description: Library name: Sample10


title: Subject 14, post treatment of Mifepristone treatment group

description:
Library name: 14B
Treatment_DeSeq2_Counts.txt

value: Subject 14


title: Meg01, day3, EV#1

description:
Library name: sample 9
EV_1


title: Meg01, day3, FLI1-WT#2

description:
Library name: sample 2
WT_2


title: Subject 14, pre treatment of Mifepristone treatment group

description:
Library name: 14A
Treatment_DeSeq2_Counts.txt


title: K_IRT_2

description: Library name: Sample11


title: K_CON_2

description: Library name: Sample8


title: SVGp12 cells, siH1.0_2

first: Songjoon

last: Baek

address: 41 Library Drive

institute: NCI / NIH

data_processing:
The samples have 119 to 177 million pass filter reads with more than 93% of bases above the quality score of Q30.
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (hg38) and the annotated transcripts using STAR.
Assembly: hg38
Supplementary files format and content: The gene expression quantification analysis was performed for all samples using STAR/RSEM tools.

source_name: SVGp12 cells, H1.0 Smartpool knockdown

growth_protocol: SVGp12 cells were seeded 24hrs in fresh EMEM supplemented with 10% FBS and Pen-strep. Cells were subjected to histone H1 subtype knockdown using siH1.5/siH1.0/siScramble smartpool  oligos. The cells were allowed to grow in a 37C and 5%CO2 humidity controlled  incubator.

extract_protocol:
After 72hours , cells were harvested for RNA- extraction using Trizol reagent. Total RNA was extracted and subjected to DNAse treatment. Collected RNA was used for library prep for paired end reads.
Total RNA libraries were prepared using Illumina TruSeq Stranded Total RNA Library Prep Kit (RS-122-2201)
Libraries were multiplexed and sequenced on one lane of an Illumina HiSeq2500 instrument using TruSeq V4.0 chemistry and sequenced for 126 cycles in paired-end mode.

treatment_protocol: Cells were subjected to histone H1 subtype knockdown using siH1.5/siH1.0/siScramble smartpool  oligos using standard manufacturer's protocol for lipofectamine RNAiMax.  Cells were grown for 72 hours and then harvested for RNA extraction

value: Fetal glial cells

value: H1.0 knockdown

value: siRNA


title: Heart_WT_173, Female

description: Library name: Heart_WT_173

value: Heart


title: Subject 10, post treatment of Mifepristone treatment group

description:
Library name: 10B
Treatment_DeSeq2_Counts.txt

value: Subject 10


title: Meg01, day3, FLI1-WT#4

description:
Library name: sample 4
WT_4


title: SVGp12 cells, siH1.5_2

source_name: SVGp12 cells, H1.5 smartpool knockdown

value: H1.5 knockdown


title: K_CON_1

description: Library name: Sample7

value: Control


title: Meg01, day3, FLI1Met100*#2

description:
Library name: sample 6
M_2

value: hematopoietic


title: Meg01, day3, FLI1-WT#1

description:
Library name: sample 1
WT_1

value: leukemic


title: SVGp12 cells, siH1.0_1


title: K_CON_3

description: Library name: Sample9

value: WT


title: SVGp12 cells, siScramble_1

source_name: SVGp12 cells, Control sample

value: Control sample


title: M_IRT_3

description: Library name: Sample6

value: mouse bladder cancer cell


title: Subject 10, pre treatment of Mifepristone treatment group

description:
Library name: 10A
Treatment_DeSeq2_Counts.txt

value: pre treatment of Mifepristone treatment


title: Subject 9, pre treatment of Mifepristone treatment group

description:
Library name: 9A
Treatment_DeSeq2_Counts.txt

value: Subject 9


title: XA0048160-847-1051_TCAGCTCT-CCAGCATT_S35,  ED

city: Chapel Hill

first: Sarah

last: Linnstaedt

state: NC

address: 109 Mason Farm Road

description: Library name: XA0048160-847-1051_TCAGCTCT-CCAGCATT_S35

data_processing:
Sequencing reads aligned using the STAR(v2.7.6a) against the hg38 reference genome, with GENCODEV47 annotation file. Salmon (v1.4.0) was used to quantify aligned transcript-level expression from the aligned reads.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw count for each sample

source_name: Whole Blood

extract_protocol:
Blood samples were collected at the time of enrollment using PAXgene RNA tubes. Total RNA was isolated using the PAXgene blood miRNA kit (QIAGEN) and RNA was stored at −80˚C until use. RNA concentration and purity were measured using a NanoDrop One (Nanodrop Technologies, Wilmington, DE), and RNA integrity was measured using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Template libraries for total RNA sequencing were produced from 600 ng total RNA using Ovation Human Blood RNA-Seq Library Systems kit (NuGen, San Carlos, CA) according to manufacturer's specifications. Libraries were multiplexed in groups of six and sequenced on a HiSeq 4000 (Illumnia) at the University of North Carolina at Chapel Hill High Throughput Sequencing Facility.

value: whole blood

value: mixed

tag: Sex

value: Female

value: NorthEast

tag: monocytes

value: Black


title: XA0053980-847-1075_CCTACCTA-ACCACAAC_S90,  ED

institute: University of North Carolina at Chapel Hill

description: Library name: XA0053980-847-1075_CCTACCTA-ACCACAAC_S90


title: M_IRT_1

description: Library name: Sample4

value: 8 Gy-RT


title: Subject 8, pre treatment of Mifepristone treatment group

description:
Library name: 8A
Treatment_DeSeq2_Counts.txt

value: Breast Tissue

value: Subject 8


title: Subject 9, post treatment of Mifepristone treatment group

description:
Library name: 9B
Treatment_DeSeq2_Counts.txt


title: SVGp12 cells, siH1.5_1

value: Fetal glial cells

value: H1.5 knockdown

value: siRNA


title: XA0053211-847-1078_CTGAACAC-ATGAAGCC_S68,  ED

description: Library name: XA0053211-847-1078_CTGAACAC-ATGAAGCC_S68


title: M_CON_2

description: Library name: Sample2

value: Control


title: XA0047642-847-1057_TAGGAAGC-GACAATGC_S26,  ED

description: Library name: XA0047642-847-1057_TAGGAAGC-GACAATGC_S26


title: XA0046977-847-1021_ATGGAACG-CATTGCAC_S16,  ED

description: Library name: XA0046977-847-1021_ATGGAACG-CATTGCAC_S16


title: SVGp12 cells, siScramble_2


title: M_IRT_2

description: Library name: Sample5

value: WT


title: XA0053993-847-1074_CTATGTCG-CGCATATG_S92,  ED

description: Library name: XA0053993-847-1074_CTATGTCG-CGCATATG_S92


title: XA0046971-847-1003_AGATTCGC-ACACACGT_S15,  ED

description: Library name: XA0046971-847-1003_AGATTCGC-ACACACGT_S15


title: XA0046961-847-1011_GTGCCTAA-CACTCACT_S14,  ED

description: Library name: XA0046961-847-1011_GTGCCTAA-CACTCACT_S14


title: RUNX1 FB-KO Rep3

city: Milwaukee

first: Anooj

last: Arkatkar

state: WI

address: 8701 W Watertown Plank Rd.

department: Cell Biology, Neurobiology, and Anatomy

institute: Medical College of Wisconsin

description: Library name: S6352

data_processing:
Reads were processed using salmon (v1.5.2) with a pre-computed index of the mm10 mouse transcriptome obtained from refgenie (refgenie server 0.7.0)
Transcripts were quantified using the salmon-quant function with the --validateMappings and --gcBias flags enabled. Alignment quality was confirmed by mutliQC (v1.18).
Quantification files were loaded into DESeq2 (v1.44.0) using tximport (v1.32.0).
Differential expression was calculated using DESeq2 with default parameters.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file is the quantification file output from salmon. Columns correspond to transcript ID, transcript length (bp), estimated effective transcript length (bp), transcript abundance (transcripts per million or TPM), and transcript counts.

extract_protocol:
RNA was extracted from ventricular tissue below the ligature using Trizol reagent per manufacturer's protocol (Thermo, #15596-026) and dissolved in RNAse-free water.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification (Novogene)

treatment_protocol: Myocardial infarction by LAD ligation. Tamoxifen diet began immediately following surgery and was maintained until collection.

value: Heart

value: Postn CreER+/-; Runx1 fl

value: myocardial infarction

value: F


title: H. fasciatum grown with 1 mM Met as the sulfur source - rep C

city: Columbus

first: Justin

last: North

address: 484 W 12th Ave

department: Department of Microbiology

institute: Ohio State University

description: Library name: 05C

data_processing:
The Illumina indexes were trimmed off using the Trimmomatic v0.38 tool.
The sequnences were aligned using Bowtie2 v2.5.1
Duplicated sequences were marked using Samtools v1.17 and filtered out using picard v3.0.0
Reads were summarized by mapping them to genes from the reference genome using subread
Assembly: GCF_004341395.1
Supplementary files format and content: The processed data file is the .txt featurecounts output which assigns genes in the Heliophilum fasciatum genome with read counts from each replicate of each condition

organism: Heliophilum fasciatum

source_name: Strain

growth_protocol: Heliophilum fasciatum cultures were grown in defined minimal media consisting of 20 mM mM sodium pyruvate, 0.034 mM EDTA-disodium salt, 0.36 mM MgCl2·2H2O, 0.5 mM CaCl2·2H2O, 20 mM NH4Cl, 5.2 mM K2HPO4, 4.4 mM KH2PO4, 20 µM chelated FeCl3·6H2O solution, 15 µg/L Biotin, 20 µg/L Vitamin B12, 12.5 nM Na2SeO3, 50 µg/L para(4)-benzoic acid, and 1 ml/L trace elements (per L: 10 g EDTA-disodium salt, 0.8 g MnCl2·4 H2O, 0.4 g H3BO3, 0.4 g NaMoO4·2H2O, 0.2 g ZnCl2, 0.2 g NiSO4·6H2O, 0.08 g CoCl2·6H2O, 0.02 g CuCl2·2H2O, 0.02 g VOSO4·2H2O, 0.02 g Na2WO4·2H2O).

extract_protocol:
10 ml of RNAprotect Bacteria Reagent (Qiagen) was added to 5 ml of culture prior to cell pelleting and RNA isolation using the RNeasy Mini Kit (Qiagen).
The Illumina stranded total RNA library preparation kit at 80% of the reagent volume was used to construct the libraries

treatment_protocol: Individual sulfur sources were added separately to tubes of medium from anaerobic stocks to the following final concentrations: 5 µM sulfate, 1 mM sulfate, 5 µM thiosulfate, 1 mM thiosulfate, or 1 mM methionine

value: Strain

value: Heliophilum fasciatum

value: 1 mM Met as the sulfur source


title: Subject 6, post treatment of Mifepristone treatment group

description:
Library name: 6B
Treatment_DeSeq2_Counts.txt

value: Subject 6


title: XA0053954-847-1072_TCGATACC-CAGTACTG_S88,  ED

description: Library name: XA0053954-847-1072_TCGATACC-CAGTACTG_S88

value: whole blood

value: mixed

value: Male

value: NorthEast

value: Black


title: XA0046990-847-1020_AACTTCGC-GATGTTCG_S19,  ED

description: Library name: XA0046990-847-1020_AACTTCGC-GATGTTCG_S19

value: Female

value: Other


title: XA0047010-847-1012_CCATCTAC-CGACACTA_S20,  ED

description: Library name: XA0047010-847-1012_CCATCTAC-CGACACTA_S20


title: M_CON_3

description: Library name: Sample3

value: mouse bladder cancer cell

value: Control


title: H. fasciatum grown with 1 mM Met as the sulfur source - rep B

description: Library name: 05B


title: M_CON_1

description: Library name: Sample1

value: WT


title: XA0047611-847-1043_ATCGAGTC-TTCTGTGC_S24,  ED

description: Library name: XA0047611-847-1043_ATCGAGTC-TTCTGTGC_S24


title: XA0047635-847-1044_TGCTGTCT-AGGTCATC_S25,  ED

description: Library name: XA0047635-847-1044_TGCTGTCT-AGGTCATC_S25


title: Subject 6, pre treatment of Mifepristone treatment group

description:
Library name: 6A
Treatment_DeSeq2_Counts.txt

value: Breast Tissue

value: pre treatment of Mifepristone treatment


title: XA0054349-847-1077_GACATGAG-CAGAGAGT_S108,  ED

description: Library name: XA0054349-847-1077_GACATGAG-CAGAGAGT_S108


title: Subject 8, post treatment of Mifepristone treatment group

description:
Library name: 8B
Treatment_DeSeq2_Counts.txt

value: Subject 8


title: XA0048147-847-1038_ATCGACGT-CAGATACG_S34,  ED

description: Library name: XA0048147-847-1038_ATCGACGT-CAGATACG_S34


title: RUNX1 FB-KO Rep2

description: Library name: S6351

value: Heart

value: Postn CreER+/-; Runx1 fl

value: myocardial infarction

value: F


title: H. fasciatum grown with 1 mM Met as the sulfur source - rep A

description: Library name: 05A

value: Strain

value: Heliophilum fasciatum

value: 1 mM Met as the sulfur source


title: H. fasciatum grown with 1 mM S2O3 as the sulfur source - rep B

description: Library name: 04B

value: 1 mM S2O3 as the sulfur source


title: XA0055329-846-1112_GACAGCTT-GATACGTG_S125,  ED

description: Library name: XA0055329-846-1112_GACAGCTT-GATACGTG_S125

value: whole blood

value: mixed

value: Male

value: NorthEast

value: White


title: RUNX1 FB-KO Rep1

description: Library name: S6283

value: M


title: XA0055307-846-1103_CAATTGGC-TCTGTCCA_S123,  ED

description: Library name: XA0055307-846-1103_CAATTGGC-TCTGTCCA_S123

value: Black


title: CTL Rep2

description: Library name: S6286

value: Postn CreER+/-; Runx1 WT


title: XA0050538-833-1102_GAAGGATC-AGGCTCTT_S50,  ED

description: Library name: XA0050538-833-1102_GAAGGATC-AGGCTCTT_S50

value: Female

value: Midwest


title: CTL Rep3

description: Library name: S6287

value: Heart


title: H. fasciatum grown with 1 mM S2O3 as the sulfur source - rep C

description: Library name: 04C


title: H. fasciatum grown with 1 mM S2O3 as the sulfur source - rep A

description: Library name: 04A


title: XA0054192-846-1102_CAACCTAG-ATGACCGA_S100,  ED

description: Library name: XA0054192-846-1102_CAACCTAG-ATGACCGA_S100


title: XA0053202-846-1101_ACCGGATT-TGGCATGA_S67,  ED

description: Library name: XA0053202-846-1101_ACCGGATT-TGGCATGA_S67


title: XA0055238-846-1111_CACAACGT-GATCGTAC_S120,  ED

description: Library name: XA0055238-846-1111_CACAACGT-GATCGTAC_S120


title: XA0054276-846-1091_GTTACACC-AGAAGTGC_S104,  ED

description: Library name: XA0054276-846-1091_GTTACACC-AGAAGTGC_S104


title: CTL Rep1

description: Library name: S6228

value: myocardial infarction


title: XA0054228-846-1094_TGAGACAG-CTGGTATC_S101,  ED

description: Library name: XA0054228-846-1094_TGAGACAG-CTGGTATC_S101


title: XA0053495-842-1268_TAGGAAGC-GACAATGC_S92,  ED

description: Library name: XA0053495-842-1268_TAGGAAGC-GACAATGC_S92


title: XA0050903-842-1207_TACGTTCC-GATGTGGA_S76,  ED

description: Library name: XA0050903-842-1207_TACGTTCC-GATGTGGA_S76


title: HLC19 cell line transfected with PRG4 vector treated with DMSO_replicate 4

city: Castellana Grotte (BA)

first: Grazia

last: Serino

address: Via Turi, 27

institute: National Institute of Gastroenterology “S. de Bellis”, Research Hospital

description: Library name: HLC19_PRG4 vector_DMSO_rep4

data_processing:
Basecalling (Ion Torrent S5)
Alignment (Torrent mapping alignment program)
Quantification (Ion Torrent Ampliseq RNA plugin, unique mapping mode)
Count Normalizition (Transcriptome Analysis Console)
Assembly: hg19_Ampliseq transcriptome
Supplementary files format and content: Count Normalized in reads per million

growth_protocol: HCC cell spheroids were generated by seeding 1×10³ cells per well of HLC19 and HLF HCC cell lines stably transduced with an empty control vector (EV) or a PRG4 expressing vector (PV) in a 96-well ultra-low attachment round bottom plate. Once they assumed a characteristic spheroid shape (after 4 days), spheroids were embedded in Matrigel® and allowed to settle for 3 days before starting the treatment.

extract_protocol:
Medium overlaying matrigel-embedded spheroids was removed, and 1 ml of QIAzol reagent (Qiagen, USA) was added to dissolve matrigel and contained cells. From this moment on, the RNA extraction protocol has been carried out as per the manufacturer's instructions. RNA was then assyed for concentration and purity, and DNAse treatment was then carried out using the Turbo DNA-free kit (Ambion, Thermo Fisher Scientific, USA).
Libraries were templated with the Ion Chef and sequenced using a 540 chip on the Ion GeneStudio S5 Prime system (Thermo Fisher Scientific,Waltham, MA, USA).

treatment_protocol: Spheroids were treated with either DMSO as control (vehicle) or Regorafenib (5 µM) for four days (t = 96 h), with a medium and treatment renewal after 48 h.

tag: vector

value: PRG4 vector

value: Hepatocellular carcinoma (HCC)

value: Dimethyl sulfoxide


title: HLC19 cell line transfected with PRG4 vector treated with Regorafenib_replicate 4

description: Library name: HLC19_PRG4 vector_Regorafenib_rep4

value: Regorafenib (5 µM)


title: H. fasciatum grown with 5 uM S2O3 as the sulfur source - rep B

description: Library name: 03B

value: Strain

value: Heliophilum fasciatum

value: 5 uM S2O3 as the sulfur source


title: XA0047846-842-1127_CATCACTC-GAACAGCA_S36,  ED

description: Library name: XA0047846-842-1127_CATCACTC-GAACAGCA_S36

value: whole blood

value: mixed


title: XA0050953-842-1213_AAGGATCG-AAGTCGCA_S78,  ED

description: Library name: XA0050953-842-1213_AAGGATCG-AAGTCGCA_S78

value: Male


title: H. fasciatum grown with 5 uM S2O3 as the sulfur source - rep C

description: Library name: 03C


title: H. fasciatum grown with 5 uM S2O3 as the sulfur source - rep A

description: Library name: 03A


title: H. fasciatum grown with 1 mM SO4 as the sulfur source - rep C

description: Library name: 02C

value: 1 mM SO4 as the sulfur source


title: XA0047288-842-1013_TAGCACCA-CTAGCCTA_S32,  ED

description: Library name: XA0047288-842-1013_TAGCACCA-CTAGCCTA_S32

value: Black


title: XA0047612-865-1011_ACTCGACA-GCACAAGA_S15,  ED

description: Library name: XA0047612-865-1011_ACTCGACA-GCACAAGA_S15

value: NorthEast


title: HLC19 cell line transfected with Empty control vector treated with Regorafenib_replicate 4

description: Library name: HLC19_Empty vector_Regorafenib_rep4

value: Empty vector


title: XA0046911-846-1013_TCTTCGAC-TACTGCTC_S22,  ED

description: Library name: XA0046911-846-1013_TCTTCGAC-TACTGCTC_S22

value: Female

value: Other


title: HLC19 cell line transfected with Empty control vector treated with DMSO_replicate 4

description: Library name: HLC19_Empty vector_DMSO_rep4


title: XA0049459-841-1045_GTACACCT-GAGACCAA_S41,  ED

description: Library name: XA0049459-841-1045_GTACACCT-GAGACCAA_S41

value: SouthEast

value: White


title: HLC19 cell line transfected with PRG4 vector treated with Regorafenib_replicate 3

description: Library name: HLC19_PRG4 vector_Regorafenib_rep3

value: PRG4 vector

value: Hepatocellular carcinoma (HCC)


title: H. fasciatum grown with 1 mM SO4 as the sulfur source - rep A

description: Library name: 02A


title: HLC19 cell line transfected with PRG4 vector treated with DMSO_replicate 3

description: Library name: HLC19_PRG4 vector_DMSO_rep3

value: Dimethyl sulfoxide


title: XA0047335-841-1018_CCACAACA-CATCCAAG_S33,  ED

description: Library name: XA0047335-841-1018_CCACAACA-CATCCAAG_S33


title: XA0047387-841-1012_CAAGCCAA-GAACGAAG_S34,  ED

description: Library name: XA0047387-841-1012_CAAGCCAA-GAACGAAG_S34


title: Heliophilum fasciatum grown with 5 uM SO4 as the sulfur source - rep C

description: Library name: 01C

value: Strain

value: 5 uM SO4 as the sulfur source


title: H. fasciatum grown with 1 mM SO4 as the sulfur source - rep B

description: Library name: 02B

value: Heliophilum fasciatum


title: AA34070_SG2C

city: Brisbane

first: Juliet

last: French

address: 300 Herston Rd

country: Australia

institute: QIMRB

description: Library name: AA34070_SG2C

data_processing:
The quality of sequencing data was confirmed with FastQC both before and after trimming.
Paired-end reads were independently trimmed with Trimmomatic and aligned to the human reference genome (hg38) using STAR.
SAMtools and NovoSort were respectively used to filter reads with proper mapping and sort the read pairs by name.
RSEM was used to estimate read counts per transcript and generate transcript per million (TPM) counts.
Assembly: hg38
Supplementary files format and content: FPKM counts extracted from RSEM output

source_name: Breast

extract_protocol:
Total RNA was extracted from T47D cells using the RNeasy Plus mini kit (Qiagen).
Libraries were prepared using the TruSeq stranded mRNA library prep kit (Illumina) as per the manufacturer’s protocol.

value: Breast

value: Mammary epithelial

value: knockdown of  BHLHE40 using gapmer RNAs


title: XA0054407-833-1114_GCACTACA-GAAGCACA_S111,  ED

description: Library name: XA0054407-833-1114_GCACTACA-GAAGCACA_S111

value: whole blood

value: mixed

value: Male

value: Midwest


title: XA0054313-833-1119_ACGTGACT-ACTCGTTC_S106,  ED

description: Library name: XA0054313-833-1119_ACGTGACT-ACTCGTTC_S106

value: Female


title: HLC19 cell line transfected with Empty control vector treated with DMSO_replicate 3

description: Library name: HLC19_Empty vector_DMSO_rep3

value: Empty vector


title: AA34069_SG2B

description: Library name: AA34069_SG2B


title: HLC19 cell line transfected with Empty control vector treated with Regorafenib_replicate 3

description: Library name: HLC19_Empty vector_Regorafenib_rep3

value: Regorafenib (5 µM)


title: Heliophilum fasciatum grown with 5 uM SO4 as the sulfur source - rep A

description: Library name: 01A


title: AA34068_SG2A

description: Library name: AA34068_SG2A


title: AA34067_SG1C

description: Library name: AA34067_SG1C


title: HLC19 cell line transfected with PRG4 vector treated with Regorafenib_replicate 2

description: Library name: HLC19_PRG4 vector_Regorafenib_rep2


title: XA0054429-833-1113_ATCCTGTC-ACGAGATG_S112,  ED

description: Library name: XA0054429-833-1113_ATCCTGTC-ACGAGATG_S112

value: White


title: Heliophilum fasciatum grown with 5 uM SO4 as the sulfur source - rep B

description: Library name: 01B


title: XA0053945-833-1099_AGCAGCAA-GTAGAAGC_S86,  ED

description: Library name: XA0053945-833-1099_AGCAGCAA-GTAGAAGC_S86


title: HLC19 cell line transfected with Empty control vector treated with Regorafenib_replicate 2

description: Library name: HLC19_Empty vector_Regorafenib_rep2


title: AA34066_SG1B

description: Library name: AA34066_SG1B


title: H3K18La_2

city: Tsingdao

first: Longfei

last: Li

address: yushan road no.5

institute: Ocean university of China

description: Library name: H3K18La_2

data_processing:
Base calling was performed by the Illumina sequencing platform, and raw data were generated in FASTQ format.
Adapter sequences and low-quality reads were removed using fastp.
Clean reads were aligned to the reference genome using Bowtie2.
Mapped reads were processed to generate normalized genome-wide coverage tracks.
Enriched regions (peaks) were identified using MACS2.
Assembly: GCA_964237555.1
Supplementary files format and content: bigWig files containing normalized genome-wide signal tracks.
Library strategy: CUT&Tag

organism: Oryctolagus cuniculus

source_name: corneal-limbal

extract_protocol:
Genomic DNA was extracted following the CUT&Tag procedure using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, TD904). Briefly, cells or nuclei were immobilized on concanavalin A–coated magnetic beads and incubated with primary and secondary antibodies. A protein A/G–Tn5 transposase complex was then applied to tagment chromatin at antibody-bound sites. DNA fragments were released by SDS treatment and purified using magnetic beads, followed by PCR amplification to generate sequencing libraries.
Sequencing libraries were constructed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, TD904). Following H3K18la antibody-guided in situ tagmentation by protein A/G–Tn5 transposase, DNA fragments containing sequencing adapters were directly PCR-amplified using Illumina-compatible index primers. Amplified libraries were purified with magnetic beads and quality-checked prior to sequencing.

value: corneal-limbal

value: Limbal stem cells

value: WT

tag: cut&tag andibody


title: XA0054361-833-1118_AACAGTCC-CTTCTCAG_S110,  ED

description: Library name: XA0054361-833-1118_AACAGTCC-CTTCTCAG_S110


title: AA34062_CTRL

description: Library name: AA34062_CTRL


title: AA34064_SG1A

description: Library name: AA34064_SG1A


title: AA34061_CTRL

description: Library name: AA34061_CTRL


title: HLC19 cell line transfected with PRG4 vector treated with Regorafenib_replicate 1

description: Library name: HLC19_PRG4 vector_Regorafenib_rep1

value: PRG4 vector

value: Hepatocellular carcinoma (HCC)


title: HLC19 cell line transfected with PRG4 vector treated with DMSO_replicate 2

description: Library name: HLC19_PRG4 vector_DMSO_rep2

value: Dimethyl sulfoxide


title: XA0049607-865-1031_GACAGCTT-GATACGTG_S30,  ED

description: Library name: XA0049607-865-1031_GACAGCTT-GATACGTG_S30

value: NorthEast

value: Black


title: XA0048251-833-1068_AATCCAGC-GCATCCTA_S54,  ED

description: Library name: XA0048251-833-1068_AATCCAGC-GCATCCTA_S54


title: XA0048239-833-1085_CGTCTAAC-CAACGAGT_S53,  ED

description: Library name: XA0048239-833-1085_CGTCTAAC-CAACGAGT_S53


title: CRISPR screen -RGS18-RT_high

city: Taipei

first: Hsueh-Chi

middle: S

last: Yen

address: No. 128, Sec. 2, Academia Rd.

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description:
Library name: RGS18-RT_high
CRISPR screen -RGS18-RT_high

library_source: other

data_processing:
Amplicon sequences were first translated into amino acid seqeunce. Amino acid sequences that perfectly matched the designed sequences would be counted.
Supplementary files format and content: Tab-delimited text file includes raw data counts in each sample

molecule: other

growth_protocol: HEK293T cells (ATCC® CRL-3216) were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (Hyclone), 100 μg/ml streptomycin, and 100 U/ml penicillin (Gibco). Cells were maintained at 37 °C in a humidified incubator with 6% CO₂.

extract_protocol:
Genomic DNA from each bin of cells was extracted by phenocloroform.
Genomic DNA from each bin was extracted and used for PCR amplification of the integrated oligos using TaKaRa Ex Taq® DNA Polymerase Hot-Start Version (Takara Bio). PCR products were purified using the MinElute PCR Purification Kit (QIAGEN) and quantified using Qubit™ fluorometric quantification (Thermo Fisher Scientific). A second PCR was performed to add Illumina indices.

value: Human embryonic kidney cells


title: HLC19 cell line transfected with Empty control vector treated with DMSO_replicate 2

description: Library name: HLC19_Empty vector_DMSO_rep2


title: XA0050049-865-1030_CCTTGTAC-CTCCTACA_S39,  ED

description: Library name: XA0050049-865-1030_CCTTGTAC-CTCCTACA_S39

value: whole blood


title: AA20594_SG2A

description: Library name: S7_AA20594

value: Breast

value: Mammary epithelial

value: knockdown of BRRIAR lncRNA using gapmer RNAs


title: HLC19 cell line transfected with Empty control vector treated with Regorafenib_replicate 1

description: Library name: HLC19_Empty vector_Regorafenib_rep1


title: CRISPR screen -RGS15-RT_total

description:
Library name: RGS18-RT_total
CRISPR screen -RGS15-RT_total


title: CRISPR screen -UBA5-RT_total

description:
Library name: UBA5-RT_total
CRISPR screen -UBA5-RT_total


title: Astrocytes

description:
Library name: sample3
Astrocytes

source_name: Astrocytes

value: Astrocytes


title: H3K18La

description: Library name: H3K18La


title: AA20856_SG2C

description: Library name: S9_AA20856


title: IgG

description: Library name: IgG

value: IgG


title: HLC19 cell line transfected with PRG4 vector treated with DMSO_replicate 1

description: Library name: HLC19_PRG4 vector_DMSO_rep1


title: CRISPR screen -RAB18-RT_total

description:
Library name: RAB18-RT_total
CRISPR screen -RAB18-RT_total


title: HLC19 cell line transfected with Empty control vector treated with DMSO_replicate 1

description: Library name: HLC19_Empty vector_DMSO_rep1

value: Empty vector


title: XA0050051-831-1036_AACTTCGC-GATGTTCG_S63,  ED

description: Library name: XA0050051-831-1036_AACTTCGC-GATGTTCG_S63

value: mixed

value: Female

value: SouthEast


title: XA0049599-865-1037_ATCGAGTC-TTCTGTGC_S73,  ED

description: Library name: XA0049599-865-1037_ATCGAGTC-TTCTGTGC_S73


title: R-TR3

city: Hefei

last: Jiao

address: No. 130, Changjiang West Road, Hefei, Anhui Province, Anhui Agricultural University

institute: Anhui Agricultural University College of Animal Science and Technology

description:
Library name: Sample 6
Hu sheep

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Oar_v4.0 whole genome.
Transcript per Kilobase per Million mapped reads (TPM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments 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.
Assembly: Oar_v4.0
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Ovis aries

source_name: rumen

growth_protocol: Ewes at 115 days of gestation.

extract_protocol:
RNA was harvested using  Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext UltraTM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Restricted feeding.

value: rumen

value: Not available

value: WT

value: Restricted feeding


title: XA0046415-843-1002_CTGTACTC-CTAGATGC_S21,  ED

description: Library name: XA0046415-843-1002_CTGTACTC-CTAGATGC_S21


title: CRISPR screen -RAB18-RT_high

description:
Library name: RAB18-RT_high
CRISPR screen -RAB18-RT_high


title: GPS-peptidomic screen replicate 2 Bin 8

description:
Library name: Bin8_rep2
GPS-peptidomic screen replicate 2 Bin 8


title: XA0047951-831-1033_CCATCTAC-CGACACTA_S37,  ED

description: Library name: XA0047951-831-1033_CCATCTAC-CGACACTA_S37

value: Male

value: White