title: DSS anti-PD1 splenocyte - replicate 2

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

description: scRNA Seq processing with Chromium Next GEM Single Cell 3' Reagent Kit v3.1 (Dual Index)

data_processing:
Paired fastq files were processed with cellRanger (6.1.2) with the transcriptome index from Mouse mm10 (2020-A) downloaded from 10xgenomics website.
Assembly: mm10
Supplementary files format and content: raw h5 file including feature count per sample

source_name: Colon

extract_protocol:
Colitis tissue was digested with the Lamina Propria Dissociation Kit (Miltenyi, 130-097-410) according to manufaturer's instructions. Dead cells were removed with the Dead Cell Removal Kit (Miltenyi, 130-090-101) and CD45 positive cells were isolated using CD45 MicroBeads (Miltenyi, 130-052-301) according to manufacturer's instructions. 10,000 cells were processed into library.
10,000 cells were processed for scRNA Seq using the Chromium Next GEM Single Cell 3' Reagent Kit v3.1 (Dual Index) (10X Genomics)
Whole mRNA 3' Dual Index; scRNA Seq

treatment_protocol: C57BL/6 WT mice were left untreated (Naive) or treated with 3% DSS in drinking water for 72h and isotype or anti-PD1 i.p. to induce colitis. Treatment group was additionally transplanted with ECP treated donor cells or untreated donor splenocytes.

value: Colon

value: CD45 positive selected cells

value: DSS+antiPD1+untreated splenocytes


title: DSS anti-PD1

status: Public on Nov 27 2024

type: SRA

country: Germany

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: S-001656717

city: Boston

first: Vrushali

middle: Dipak

last: Fangal

state: MA

address: 181 Longwood Avenue

department: Brigham and Women's Hospital

country: USA

institute: Harvard Medical School

description:
Library name: S-001656717
Column name in mouse_calcitriol_th2_matrix.csv: S-001656717

library_source: transcriptomic

data_processing:
Trimmed reads were aligned to the mouse reference genome (GRCm38) using the STAR aligner (v2.7.10a). Gene expression read counts were quantified using HTSeq (v0.13.5).
Assembly: GRCm38
Supplementary files format and content: The processed data files are tab-delimited text files, containing normalized expression values (log-CPM) for each gene across all samples. Gene identifiers are based on Ensembl (GRCm38).

source_name: TH2 cells

growth_protocol: Mice were maintained in a virus- and parasite-free animal facility under a 12-hour light/dark cycle with unrestricted access to food and water. Male and female Balb/c mice (aged 6–8 weeks) were obtained from Charles River Laboratories. The mice were bred on diets with varying vitamin D3 concentrations (400 IU, 1000 IU, or 4000 IU per kg of diet) for two generations to establish vitamin D equilibrium.

extract_protocol:
At day 5 of polarization, cells were harvested and total RNA was isolated using the microRNeasy kit (Qiagen) according to the manufacturer's instructions. RNA quality and concentration were evaluated using a Nanodrop 8000 spectrophotometer.
RNA-seq libraries were prepared using the TruSeq® Stranded Total RNA Library Prep Globin Kit (Illumina) following the manufacturer’s protocols.

treatment_protocol: To assess the effects of vitamin D, calcitriol stimulation was applied to TH2 cells at a final concentration of 100 nM during the last 24 hours of culture. The vehicle control group was treated with 2% ethanol as a solvent control for calcitriol.

value: TH2 cells

value: WT

value: control


title: S-001656716

description:
Library name: S-001656716
Column name in mouse_calcitriol_th2_matrix.csv: S-001656716


title: Naive - replicate 2

value: Untreated


title: Pooled snRNAseq of WT and MEF2_T>C CMs 1

first: Seong Won

last: Kim

address: 77 Ave Louis Pasteur

department: Genetics

description:
Library name: CP6
Pooled snRNAseq

data_processing:
Fastq files were demultiplexed and aligned to hg38 using CellRanger commands. Background reads were removed using CellBender. DropletUtils package was used to convert processed files to CellRanger output format.
Assembly: hg38
Supplementary files format and content: Processed files include gene expression matrix after CellBender in the CellRanger output format. Sample deconvolution information and sample metadata are in the assignment table.

molecule: nuclear RNA

organism: Homo sapiens

growth_protocol: hiPSCs used in this study were derived from the male parent hiPSC line PGP1. The cells were cultured on Matrigel-coated plates in mTeSR1 media. The hiPSC-CMs were generated from hiPSCs using a small molecule-mediated differentiation method, which modulates the Wnt signaling pathway and cardiomyocytes were metabolically selected by glucose deprivation as previously described.

extract_protocol:
Cells were lysed, and the isolated nuclei were incubated with the commercially available lipid-oligo barcodes (3’ CellPlex Kit from 10X Genomics). Nuclei were washed, counted, and pooled at equal number. Intact single nuclei were sorted with FACS.
The standard 10X Genomics sequencing was performed according to the manufacturer’s instructions.

treatment_protocol: Cardiomyocytes were lifted with TrypLE and cells were frozen down.

tag: cell line

value: hiPSC-CM


title: S-001656715

description:
Library name: S-001656715
Column name in mouse_calcitriol_th2_matrix.csv: S-001656715


title: Naive - replicate 1


title: S-001656720

description:
Library name: S-001656720
Column name in mouse_calcitriol_th2_matrix.csv: S-001656720

value: Vitamin D


title: S-001656714

description:
Library name: S-001656714
Column name in mouse_calcitriol_th2_matrix.csv: S-001656714


title: Pooled snRNAseq of WT and MEF2_T>C CMs 2

description:
Library name: CP10
Pooled snRNAseq


title: S-001656722

description:
Library name: S-001656722
Column name in mouse_calcitriol_th2_matrix.csv: S-001656722


title: DSS anti-PD1 splenocyte - replicate 1


title: S-001656711

description:
Library name: S-001656711
Column name in mouse_calcitriol_th2_matrix.csv: S-001656711


title: DSS Isotype - replicate 2

value: DSS+Isotype


title: S-001656719

description:
Library name: S-001656719
Column name in mouse_calcitriol_th2_matrix.csv: S-001656719


title: DSS Isotype - replicate 1


title: S-001656709

description:
Library name: S-001656709
Column name in mouse_calcitriol_th2_matrix.csv: S-001656709


title: Control3,rep3

city: Qingdao

first: Changxue

last: Liu

state: Shandong

address: Qingdao, Shandong, China

country: China

institute: The Affiliated Hospital of Qingdao University

data_processing:
Basecalls performed using CASAVA version 1.8
Adapters and low-quality read ends were removed using Trimmomatic, based on quality control statistics generated by FastQC.
Quality filtered reads were then mapped to GRCh38 using Hisat2
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . StringTie was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human bladder cancer cells

value: Control


title: Control2,rep2


title: Zenbio_HBMMSC071819A

city: Detroit

first: Katherine

last: Gurdziel

state: MI

address: 275 E. Hancock

institute: Wayne State University

data_processing:
Reads were trimmed using Bbduk
Reads were aligned using STAR
Reads were tabulated with htseq-count
Assembly: hg38
Supplementary files format and content: count

molecule: polyA RNA

source_name: Mesenchymal stem cells

growth_protocol: Human mesenchymal stem cells were thawed and seeded into T25 flask. Cells were seeded in basal media (DMEM/Nutrient Mixture F-12, DMEM/F-12; Gibco No. 11320, with 10% fetal bovine serum and 1% penicillin/streptomycin). Once confluent, RNA was collected following rinsing via TRIzol protocol.

extract_protocol:
Total RNA was extreacted using Zymo Direct-zol RNA Purification Kit.
3’ mRNA-Seq libraries were prepared by the Genome Sciences Core (GSC), WSU using the Lexogen 3’ mRNA-Seq Library Prep kit FWD.

treatment_protocol: Cells were collected after culture in basal media. Differentiation was not induced and no chemical treatments were performed.

value: Mesenchymal stem cells

value: Zenbio HBMMSC-F

value: Bone marrow derived mesenchymal stem cells

value: Basal media, Day 0


title: DSS anti-PD1 ECP


title: S-001656706

description:
Library name: S-001656706
Column name in mouse_calcitriol_th2_matrix.csv: S-001656706


title: S-001656708

description:
Library name: S-001656708
Column name in mouse_calcitriol_th2_matrix.csv: S-001656708


title: dKO rep6

city: Hong Kong

first: QIANG

last: SUN

address: Ngan Shing Street

department: Department of Orthopaedics and Traumatology

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
Briefly, the adapter and low-quality sequences were trimmed from 3’ to 5’ ends by Trimmomatic and the reads shorter than 36 bp were discarded
Subsequently, the preprocessed reads were aligned to the mouse genome (mm10) using STAR. The aligned reads were then converted to bam format using samtools.
The aligned RNA-Seq reads were accepted  and assembled into a parsimonious set of transcripts.  These transcripts were then estimated the relative abundances by Cufflinks.
Assembly: mm10
Supplementary files format and content: indexed binary file for display of track dense

source_name: Muscle

extract_protocol:
Total RNAs from cells or tissues were extracted using TRIzol reagent (Invitrogen, 15596018) according to the manufacturer’s instructions.
cDNAs were synthesized under the manufacturer’s instructions of HiScript® II Reverse Transcriptase Kit with gDNA wiper (Vazyme, R223-01). Real-time PCR was performed to quantify the expression level of mRNAs by Luna® Universal qPCR Master Mix (NEB, M3003E) and LightCycler ®480 Real-Time PCR System (Roche). GAPDH (glyceraldehydes 3-phosphate dehydrogenase) or 18s RNA were used as internal controls for normalization.

value: Muscle

value: MuSC

value: YY1 dKO


title: S-001656707

description:
Library name: S-001656707
Column name in mouse_calcitriol_th2_matrix.csv: S-001656707


title: Control1,rep1


title: shNOTCH3_3,rep3


title: S-001656705

description:
Library name: S-001656705
Column name in mouse_calcitriol_th2_matrix.csv: S-001656705


title: S-001656704

description:
Library name: S-001656704
Column name in mouse_calcitriol_th2_matrix.csv: S-001656704


title: S-001656713

description:
Library name: S-001656713
Column name in mouse_calcitriol_th2_matrix.csv: S-001656713


title: dKO rep5


title: shNOTCH3_2,rep2


title: dKO rep4


title: S-001656702

description:
Library name: S-001656702
Column name in mouse_calcitriol_th2_matrix.csv: S-001656702


title: shNOTCH3_1,rep1


title: dKO rep3


title: S-001656710

description:
Library name: S-001656710
Column name in mouse_calcitriol_th2_matrix.csv: S-001656710


title: D2_Young_Neutro_Replicate 3

city: Lyon

first: Benedicte

last: Chazaud

address: 8 Avenue Rockefeller

department: Institut NeuroMyoGène

country: France

institute: Université Claude Bernard Lyon 1

description:
Replicate 3
X2.429799

data_processing:
Primary data quality control is performed during the sequencing run to ensure the optimal flow cell loading (cluster density) and check the quality metrics of the sequencing run. Sequencing data were demultiplexed and FastQ files and a fastQC report were generated by the Bcl2FastQ Demux Pipeline (UBP) (software version v2.19.1).
Data preprocessing was carried out using the nf-core pipeline rnaseq version 1.4.2 [nf-core/rnaseq]. Mouse reference genome used was GRCm38 (mm10), with the corresponding gtf file for exons junctions. Mapping was performed with STAR version 2.6.1d. Raw counts were generated via featureCounts version 1.6.4. Coverage and transcripts abundances were estimated via StringTie version 2.0. Cell types and their respective sampling timing are listed as follows (cell type (abbreviation) [Days available]): endothelial (ECs) [D0, D2, D4, D7], fibroadipogenic precursors (FAPs) [D0, D2, D4, D7], muscle stem cells (MuSCs) [D0, D2, D4, D7],neutrophils (Neutrophils) [D2], inflammatory macrophages (Inflammatory-Mac) [D2, D4] and resolving macrophages (Resolving-Mac) [D2, D4, D7]. Each sample name was defined by a unique combination age.cellType.day (for example: Old.Neutrophils.D2), comprising three biological replicates. Data visualization and analysis were performed using custom Rstudio scripts.
Gene biotype classification was performed with the BioMart package. Only protein coding genes were retained. Genes expressed in at least 3 samples with a raw count greater than 5 were kept. A hierarchical clustering was done using 𝜌 Spearman’s correlation coefficients among TPM (Transcripts per Million) normalized samples. Variance stabilizing transformation (vst) (provided by DESeq2) was calculated on raw count matrices at three levels: whole dataset matrix, specific cell type matrices, and cell type and time point specific matrices. Principal Component Analysis (PCA) was applied at each level to reveal global effects across libraries.
Assembly: mm10
Supplementary files format and content: TPMmatrix.CSV
Supplementary files format and content: FPKMmatrix.CSV

extract_protocol:
MuSCs, FAPs, ECs, neutrophils, Ly6Cpos macrophages and Ly6Cneg macrophages were isolated from regenerating muscle. Briefly, muscles were dissociated and digested in DMEM F/12 medium containing 10 mg/ml of collagenase B and 2.4 U/ml Dispase (Roche Diagnostics GmBH) at 37°C for 30 min and passed through a 3 microm cell strainer. CD45pos and CD45neg were separated using magnetic beads. CD45pos cells were incubated with anti-mouse FcgRII/III (2.4G2) and further stained with PE-Cy7-conjugated anti-CD45 (25-0451-82, eBioscience) and APC-conjugated anti-Ly6C antibody (17-5932-82, eBioscience). CD45neg cells were stained with PE-Cy7-conjugated anti-CD45, PerCP-Cy5.5- conjugated anti-Sca-1 (45-5981-82, eBioscience), Alexa Fluor 647-conjugated anti-a7-integrin (AB0000538, AB lab, University British Columbia), PE-conjugated anti-CD31 (12-0311-82, eBioscience) and FITC-conjugated anti-CD34 (11-0341-82, eBioscience) antibodies. Cells were sorted using a FACS Aria II cell sorter (BD Biosciences).
Sequencing libraries were prepared using the Ovation SoLo from NuGen. The Ovation SoLo RNA-Seq system integrates NuGen’s Insert-Dependent Adaptor Cleavage (InDA-C) technology to provide targeted depletion of unwanted transcripts (rRNA) by specific and robust enzymatic steps. The system also includes an 8pb barcode for multiplexing followed by an 8 bp randomer for identification of unique molecules (UMI) to remove PCR duplicates from the transcript counting analysis. Libraries are quantified with Picogreen (Life Technologies) and size pattern is controlled with the DNA High Sensitivity Reagent kit on a LabChip GX (Perkin Elmer). Libraries are pooled at an equimolar ratio (i.e. an equal quantity of each sample library) and clustered at a concentration of 20 pmol on paired-end sequencing flow cell CBU2FANXX (Illumina). Sequencing is performed for 2 x 125 cycles on a HiSeq 2500 (Illumina) using the SBS V4 chemistry (Sequencing by Synthesis). The samples were subdivided into 6 different sorted cell types (MuSCs, FAPs, ECs, neutrophils, Ly6Cpos macrophages and Ly6Cneg macrophages, 4 time points (D0, D2, D4, D7) and 2 age conditions (cell isolated from young or old mice). Each of these data point was run in triplicate 3 different mice. The entire experiment was run in 4 batches of 30 samples.

treatment_protocol: Tibialis anterior muscle was injected with 50 µl cardiotoxin CTX, (Latoxan, 12 µM). Mice were euthanized at various time points after the induction of injury.

value: Neutrophils

tag: strain

tag: age

value: Young

tag: time

value: Day 2


title: D0_Young_ECs_Replicate 2

description:
Replicate 2
X2.429800

value: Endothelial cells

value: WT

value: Day 0


title: D4_Young_ECs_Replicate 3

description:
Replicate 3
X2.429798

value: Day 4


title: Shrimp Allergic human, Plasma cells, Bone Marrow

city: Tarrytown

first: Joseph

middle: Cooper

last: Devlin

state: NY

address: 777 Old Saw Mill River Rd

department: Molecular Profiling and Data Science

institute: Regeneron Pharmaceuticals

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The single cell-count matrix was filtered for by calculating the ratio of the total number of annotated genes divided by the log10 of the total number of UMIs counted. Cells with a gene to UMI ratio below about 0.1 were filtered out. Cells with more than four times the interquartile range of the total number of UMIs were filtered out. Cells with more than about 80% of reads map to a mitochondrial gene were filtered out. High quality cells with a gene to UMI ratio above about 0.1, with less than about four times the interquartile range of the total number of UMIs counted, and with less than 80% of reads mapping to a mitochondrial gene were retained. The count matrices from each individual sample capture were normalized to a total count of 10,000 and batch corrected using the Harmony algorithm to generate a combined uniform manifold approximation and projection (UMAP). Unsupervised clustering by the Leiden algorithm was then used to determine cell type clusters and a Wilcox test was used to identify specific cell type and cluster marker genes.
Assembly: GRCm38, GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow

extract_protocol:
The IgE-secretion trap method and single cell preparation is described in detail in our recent work. In brief, the IgE-secretion trap was performed with an StAv-ectoFcepsilon to specifically capture IgE-secreting plasma cells. Cells were sorted and submitted for scRNA-seq gene expression. We sequenced PCs from dLN and BM of mice exposed to HDM for 15 weeks, and from BM of mice exposed to HDM for 19 weeks with the last 8 weeks with anti-IL4Ra. At the end of the experiment, bone marrow and lung draining lymph nodes were collected and processed. Draining lymph nodes were mashed on 12-well, 70-mm filter plates (Corning Costar) in RPMI 1640 media to generate single cell suspensions. For BM extraction, femurs were cut at both ends, placed in a PCR plate with holes punched at the bottom, and spun down for 3 min at 500g. RBC lysis was performed on single cell suspensions from draining lymph nodes and bone marrow. B cells and plasma cells were isolated using EasySep mouse pan-B cell isolation kit (STEMCELL, cat: 19844) by negative selection to remove unwanted cells (CD4, CD8, CD11c, CD49b, CD90.2, Ly-6C/G (Gr-1), TER119). Purified cells were processed and secretion trap was assembled as described in the previous paragraph. Secreted IgE was captured using StAv-ectoFceRIa for 1 h at 37C with shaking at 400 rpm. Following IgE secretion trap, cells were washed and stained with an antibody mix containing B220 (RA3-6B2), CD138 (281-2), IgG1 (A85-1), IgE (R35-72), DUMP (IgM (II/41), IgD (11-26c.2a), TCRb (H57-597), Ly6G (1A8-Ly6g), CD49b (DX5), and CD11b (M1/70)) along with barcoded antigens (Der p1, Der p2, Der f1, and Ole e1). Finally, cells were labeled with DAPI before they were sorted on a BD Symphony S6.
Human allergic donor BM and matching donor sera were obtained from StemCell Technologies. Allergy status of each donor sera was checked by ImmunoCAP test (Phadia, Thermo Fisher Scientific) following the manufacturer’s instructions. To obtain mononuclear cells fresh BM aspirate was diluted 7:1 with PBS and 2mM EDTA and loaded onto 15mL of Ficoll in SepMate tube (Stem Cell Technologies). Samples were spun in SepMate tubes at 1200g for 20 minutes. Top layer of cells was removed, and cells were washed twice with autoMacs rinsing solution at 300g for 8 minutes (StemCell Technologies). B and antibody secreting cells were isolated using magnetic bead depletion (EasySep Human Pan-B Cell Isolation Kit, StemCell Technologies, Inc., Vancouver, CA, Cat: 19554) from single cell suspensions of allergic BM cells according to manufacturer’s protocol.
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics). Cells captured by secretion trap were suspended in PBS with 0.04% w/v BSA and loaded onto a Chromium® Controller device (10x Genomics) at 15,000 cells per lane. Partitions of the cells in barcoded beads were formed and the cells lysed. Reverse transcription was performed followed by breakdown of the partition. RNA-seq, Feature Barcode, and V(D)J libraries were prepared using a Chromium® Next GEM Single Cell 5’ Kit, v.2 (10x Genomics). After amplification of the libraries, cDNA was split into separate RNA-seq, Feature Barcode, and V(D)J aliquots. To enrich the V(D)J aliquot for BCR sequences, the Chromium® Automated Single Cell Mouse and Human BCR Amplification & Library Construction Kit (10x Genomics) was used. Feature Barcode libraries for DNA-barcoded Antigens or DNA-barcoded cell surface proteins were prepared using a Chromium® 5’ Feature Barcode Library Construction kit (10x Genomics). Paired-end sequencing was performed on an Illumina NovaSeq® 6000 sequencing system for RNA-seq, feature barcode, and V(D)J libraries. For RNA-seq and Feature Barcode libraries, the Cell Ranger Single-Cell Software Suite, version 6.1.1 (10x Genomics) was used to perform sample de-multiplexing, alignment, filtering, and UMI counting.

value: Plasma cells

value: bone marrow


title: dKO rep2


title: D2_Young_ECs_Replicate 2

description:
Replicate 2
X2.429795


title: D7_Young_ECs_Replicate 3

description:
Replicate 3
X2.429796

value: Day 7


title: Shellfish Allergic human, Plasma cells, Bone Marrow

description: 10x Genomics


title: Cat Allergic human, Plasma cells, Bone Marrow

description: 10x Genomics


title: dKO rep1


title: D0_Young_ECs_Replicate 3

description:
Replicate 3
X2.429791


title: HSV-1-infected_and_ACV_treated_islets_3

city: Worcester

first: Elaine

last: Lim

address: 366 Plantation Street, Paul J DiMare 5-1025

institute: UMass Chan Medical School

data_processing:
FastQC
Trimmomatic v0.39
HISAT2 v2.2.1
SAMtools v1.9
StringTie2 v1.3.6
Assembly: hg38
Supplementary files format and content: .xlsx

source_name: iPSC-derived

extract_protocol:
We fixed the cells with 4% paraformaldehyde and extracted RNA using the PureLinkTM FFPE RNA Isolation Kit, followed by DNase I treatment.
RNA library preparation and sequencing was performed by Psomagen, 151-bp paired end reads.

value: iPSC-derived

value: Stem cell derived islets

value: sc-islets

value: Wildtype

value: HSV-1 infected and ACV treated


title: D2_Old_Neutro_Replicate 1

description:
Replicate 1
X2.429792

value: Muscle

value: Old


title: Ctrl rep6

value: MuSC

value: no treatment


title: Ctrl rep5


title: D4_Old_ECs_Replicate 1

description:
Replicate 1
X2.429790


title: D7_Old_ECs_Replicate 2

description:
Replicate 2
X2.429789


title: S-001656703

description:
Library name: S-001656703
Column name in mouse_calcitriol_th2_matrix.csv: S-001656703

value: TH2 cells

value: control


title: D2_Old_ECs_Replicate 1

description:
Replicate 1
X2.429788

value: Endothelial cells

value: WT

value: Day 2


title: D2_Young_ECs_Replicate 3

description:
Replicate 3
X2.429786

value: Young


title: HSV-1-infected_and_ACV_treated_islets_1


title: D7_Old_ECs_Replicate 1

description:
Replicate 1
X2.429787


title: D7_Young_ECs_Replicate 1

description:
Replicate 1
X2.429785


title: HSV-1-infected_and_ACV_treated_islets_2


title: Ctrl rep4


title: D2_Old_Neutro_Replicate 2

description:
Replicate 2
X2.429784

value: Neutrophils


title: Ctrl rep3


title: D2_Young_Neutro_Replicate 2

description:
Replicate 2
X2.429797


title: D7_Old_ECs_Replicate 3

description:
Replicate 3
X2.429783

value: Day 7


title: HSV-1-infected_islets_3

value: iPSC-derived

value: HSV-1 infected


title: Ctrl rep2


title: D0_Old_ECs_Replicate 1

description:
Replicate 1
X2.429782

value: Day 0


title: Ctrl rep1


title: D4_Old_ECs_Replicate 2

description:
Replicate 2
X2.429781

value: Day 4


title: D2_Old_ECs_Replicate 3

description:
Replicate 3
X2.429780


title: D7_Young_ECs_Replicate 2

description:
Replicate 2
X2.429779


title: HSV-1-infected_islets_1

value: Stem cell derived islets

value: sc-islets

value: Wildtype


title: D2_Young_ECs_Replicate 1

description:
Replicate 1
X2.429778

value: Muscle


title: Prefontal, angiotensin II, sham, 28d

city: Bundoora

first: David

middle: Edward

last: Wong Zhang

state: Victoria

address: Plenty Road and, Kingsbury Dr

department: Microbiology, Anatomy, Physiology & Pharmacology

country: Australia

institute: La Trobe University

data_processing:
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene, FPKM were then calculated based on gene length and reads count mapped.
DESeq2 R package (1.20.0) to determine differential expression
Supplementary files format and content: excel files (.xls) include the differentially expressed genes with the fpkm values of each sample

source_name: Brain

extract_protocol:
total RNA was extracted via Qiagen RNeasy mini kit following manufacturer’s instruction. RNA concentration and quality was assessed using a NanoDrop spectrophotometer (Thermo Fisher Scientific). Only samples with a 260/280 ration of ≥1.8 were used for sequencing.
Bulk RNA sequencing conducted by Novogene

treatment_protocol: Infused with angiotensin II (0.28 mg/kg/day) for 28 d, photothrombosis targetting the prefrontal cortex (1.5 mm anterior to bregma) 7 days after the infusion of angiotensin II, culled mice at 28 days after infusion of angiotensin II.

value: Brain

value: 3-5 months

tag: Sex

value: male

value: Angiotensin II

value: day 28


title: Uninfected_islets_3

value: Uninfected


title: Prefontal, angiotensin II, PT stroke, 28d


title: D0_Old_ECs_Replicate 3

description:
Replicate 3
X2.429777

value: Endothelial cells

value: WT

value: Old


title: Prefontal, vehicle, PT stroke, 28d

value: Saline


title: D0_Young_ECs_Replicate 1

description:
Replicate 1
X2.429775

value: Young


title: D4_Young_ECs_Replicate 2

description:
Replicate 2
X2.429776


title: Uninfected_islets_2

value: iPSC-derived


title: Uninfected_islets_1


title: D0_Old_ECs_Replicate 2

description:
Replicate 2
X2.429773

value: Day 0


title: Prefontal, vehicle, sham, 28d


title: HepG2 cells, treated with PBS for 48 hours

city: Xi'an

first: Xiao

last: Yang

state: Shaanxi

address: 157#, Xiwu Road, Xincheng District

department: The Second Affiliated Hospital

institute: Xi'an Jiaotong University

description: C

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence
Trimmed sequence reads were mapped to GrcM38
Assembly: Star, Version 2.7.9a
Supplementary files format and content: tab-delimited text files includes raw counts for all samples
Supplementary files format and content: tab-delimited text file includes FKPM counts for all samples

source_name: Liver

growth_protocol: HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37C

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

treatment_protocol: HepG2 cells were treated with 20 uM A740003, 20 uM A438079 or PBS respectively for 48 hours

value: Liver

value: Hepatocellular carcinoma

value: PBS for 48 hours


title: D2_Old_Neutro_Replicate 3

description:
Replicate 3
X2.429771

value: Muscle

value: Neutrophils

value: Day 2


title: D4_Young_ECs_Replicate 1

description:
Replicate 1
X2.429772

value: Day 4


title: DSS anti-PD1 - replicate 2

description: scRNA Seq processing with Chromium Next GEM Single Cell 3' Reagent Kit v3.1 (Dual Index)

source_name: Colitis tissue

extract_protocol:
Colitis tissue was digested with the Lamina Propria Dissociation Kit (Miltenyi, 130-097-410) according to manufaturer's instructions. Dead cells were removed with the Dead Cell Removal Kit (Miltenyi, 130-090-101) and CD45 positive cells were isolated using CD45 MicroBeads (Miltenyi, 130-052-301) according to manufacturer's instructions. 10,000 cells were processed into library.
10,000 cells were processed for scRNA Seq using the Chromium Next GEM Single Cell 3' Reagent Kit v3.1 (Dual Index) (10X genomics)
Whole mRNA 3' Dual Index

treatment_protocol: C57BL/6 WT mice were treated with 3% DSS in drinking water and anti-PD1 i.p. to induce colitis. Treatment group was additionally transplanted with ECP treated donor cells.

value: Colon

value: CD45 positive selected cells


title: HSV-1-infected_islets_2

value: Stem cell derived islets

value: sc-islets

value: Wildtype

value: HSV-1 infected


title: HepG2 cells, treated with A438079 for 48 hours

description: B

value: WT

value: 20 uM A438079 for 48 hours


title: D4_Old_ECs_Replicate 3

description:
Replicate 3
X2.429770

value: Endothelial cells

value: Old


title: D0_Young_sCs_Replicate 2

description:
Replicate 2
X2.428158

value: Muscle Stem cells

value: Young

value: Day 0


title: HepG2 cells, treated with A740003 for 48 hours

description: A

value: Liver

value: Hepatocellular carcinoma

value: 20 uM A740003 for 48 hours


title: D0_Old_sCs_Replicate 3

description:
Replicate 3
X2.428155

value: Muscle


title: D4_Young_sCs_Replicate 3

description:
Replicate 3
X2.428156

value: Day 4


title: D4_Young_sCs_Replicate 2

description:
Replicate 2
X2.428154


title: DSS anti-PD1 - replicate 1

value: Colon

value: CD45 positive selected cells


title: hMSCs, PF4618433-3

city: Sapporo

first: Ji-Won

last: Lee

state: Does Not Apply

address: N13W7, Kita-Ku

department: Graduate school of Dental Medicine

country: Japan

institute: Hokkaido University

data_processing:
The quality of the raw reads was evaluated using FastQC v0.11.9 (www.bioinformatics.babraham.ac.uk/projects/fastqc/) and the Illumina Universal Adapter detected within the reads were trimmed using TrimGalore v0.6.10 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
The reads were then aligned to the human reference genome GRCh38 using the STAR v2.7.10b RNASeq aligner (52) and HTSeq v2.0.2 (53) was used to generate raw counts for each transcript.
Assembly: GRCh38

source_name: Bone marrow

growth_protocol:
Human bone marrow-derived mesenchymal cells were purchased from Lonza. And MSCGM mesenchymal stem cell growth medium bulletKit was purchased from Lonza. Upon cells are reaching confluence, the hMSCs were then cultured in osteogenic differentiation medium (BulletKit) containing ascorbic acid and beta-glycerophosphate for a duration of 4 days.
Ascorbic acid, Beta-glycerophosphate, Dexamethasone

extract_protocol:
RNA was harvested usign Rneasy mini plus kit (Qiagen). 2 μg of total RNA was used for the construction of sequencing libraries.
Illumina NovaSeq standard mRNA sample prep kit set was used for the library preparation.

treatment_protocol: Pyk2 inhibitor (PF-4618433) was treated for 4 days. Control group was treated with as same as percentage of DMSO.

value: Bone marrow

value: mesenchymal stem cell

value: Pyk2 inhibitor


title: DSS anti-PD1 ECP - replicate 2

value: WT


title: D2_Young_Neutro_Replicate 1

description:
Replicate 1
X2.429774

value: Neutrophils

value: Day 2


title: D7_Old_sCs_Replicate 1

description:
Replicate 1
X2.428095

value: Old

value: Day 7


title: D7_Young_sCs_Replicate 3

description:
Replicate 3
X2.428153

value: Muscle Stem cells

value: Young


title: P2-CM Gant61-Rep1

city: Minneapolis

first: Bhairab

middle: N

last: Singh

state: MN

address: 312 Church St SE, 7-124 Nils Hasselmo Hall

department: Biomedical Engineering

institute: University of Minnesota

data_processing:
2 x 150bp FastQ paired-end reads from samples (n=43.6 Million average per sample) were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.
Quality control on raw sequence data for each sample was performed with FastQC. Read mapping was performed via Hisat2 (v2.1.0) using the Mus musculus genome (GRCm38 v100) as reference. Gene quantification was done via Feature Counts for raw read counts.
 Differentially expressed genes were identified using the Proportional Estimation test based on Kal’s test feature in CLCGWB (Qiagen, Redwood City, CA) using raw read counts. We filtered the generated list based on a minimum 2X Absolute Fold Change and Bonferroni corrected p < 0.05.
Assembly: Mus musculus genome (GRCm38 v100)

source_name: Primary cells

growth_protocol: Neonatal Ventricular CMs were isolated from P1/P2 pups, wash with ice-cold DPBS twice followed by mincing in calcium and bicarbonate-free Hanks-buffer with 20mM HEPES (CBFHH buffer). Tissue digestion was performed using enzyme solution containing 1.75 mg/ml of trypsin (Difco) and 20 µg/ml of DNaseII (Sigma-Aldrich). Digested cells were washed with ice-cold DPBS and CMs were isolated by magnetic negative cell sorting using CD90 antibodies to remove fibroblasts.

extract_protocol:
For RNA isolation from P1/P2 CM, cells were harvested, washed in PBS  lysed using 350ul of RLT-lysis budder as per the manufacturer’s protocol (RNAeasy Kit Qiagen). RNA isolation was performed as per the protocol, followed by on-column DNA digestion to remove any traces of DNA as per the instructions.
Libraries were created using 40 unique dual-indexed (UDI) TruSeq stranded mRNA libraries for the project.

treatment_protocol: We plated 70,000 CMs/well in a fibronectin coated 12-well plate.  After 12h, the culture medium (DMEM, 10%FBS, Vitamin B12, 1X penicillin-streptomycin) was changed, and cells were subjected to the different treatments (SAG;4µg/ml, CyA;5µg/ml and Gant61;3uM) for 48h and harvested for further analysis.

value: P1/P2 Heart Tissue

value: Neonatal Ventricular Cariomyocytes

value: Wild-type


title: hMSCs, PF4618433-1


title: D4_Old_sCs_Replicate 1

description:
Replicate 1
X2.428098

value: Muscle


title: D0_Young_sCs_Replicate 3

description:
Replicate 3
X2.428099

value: Day 0


title: D2_Young_sCs_Replicate 3

description:
Replicate 3
X2.428094


title: DSS anti-PD1 ECP - replicate 1

value: Colon


title: S-001656724

description:
Library name: S-001656724
Column name in mouse_calcitriol_th2_matrix.csv: S-001656724

value: TH2 cells

value: Vitamin D


title: hMSCs, PF4618433-2

value: Bone marrow

value: mesenchymal stem cell


title: hMSCs, Control-3

value: control


title: D7_Young_sCs_Replicate 1

description:
Replicate 1
X2.428093

value: WT


title: D2_Old_sCS_Replicate 2

description:
Replicate 2
X2.428090

value: Day 2


title: D7_Old_sCs_Replicate 3

description:
Replicate 3
X2.428091

value: Old


title: P2-CM CyA-Rep1

value: Cyclopamine


title: P2-CM Gant61-Rep2


title: D7_Old_sCs_Replicate 2

description:
Replicate 2
X2.428089

value: Muscle Stem cells

value: Day 7


title: hMSCs, Control-1


title: P2-CM Control-Rep2

value: P1/P2 Heart Tissue

value: DMSO


title: D2_Old_sCs_Replicate 1

description:
Replicate 1
X2.428088


title: D0_Old_sCs_Replicate 1

description:
Replicate 1
X2.428086


title: CHD6_CUT&Tag_HEK293_rep3

city: beijing

first: Lina

last: Bu

state: Beijing

address: xueyuanlu 38

institute: peking university

library_source: genomic

data_processing:
Adapters were removed using TrimGalore(version 0.5.0)
Reads were mapped to the human genome version hg19 using Bowtie2 version 2.4.5 with default parameter values.
PCR duplicates reads were removed using Picard
Mpped reads wrer submitted to the Dpeak function in DANPOS version 2.2.2 (https://sites.google.com/site/danposdoc/) to calculate CUT&Tag signal (read density) at each base pair of the genome, normalize read number, and define individual enrichment peaks.
The Dpeak stored the signal value at each base pair in a Wiggle format file, which we next converted to bigWig format using the tool WigToBigWig (https://www.encodeproject.org/software/wigtobigwig/)
To calculate signal value at each base pair across each gene, we used the Profile function in DANPOS version 2.2.2.
The Profile function in DANPOS 2.2.2 was also used to calculate average CUT&Tag-Seq signal at each gene group.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: Homo sapiens

extract_protocol:
Harvest HEK293 cells were grown with indicated treatments and count the cells.  Cells should be intact and in a homogenous, single-cell suspension.  Immunoprecipitated using indicated antibodies, transposition reaction and purification DNA fragments and amplify transposed DNA fragments by PCR.
DNA libraries were prepared according to NovoNGS CUT&Tag 4.0 High-Sensitivity Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired-end reads.

value: Homo sapiens

value: Human embryonic kindey

tag: chip antibody


title: P2-CM Control-Rep1

value: Neonatal Ventricular Cariomyocytes

value: Wild-type


title: D4_Old_sCs_Replicate 2

description:
Replicate 2
X2.428087

value: Muscle

value: Day 4


title: D7_Young_sCs_Replicate 2

description:
Replicate 2
X2.428085

value: Young


title: CHD6_CUT&Tag_HEK293_rep2


title: D2_Young_sCs_Replicate 2

description:
Replicate 2
X2.428152


title: D2_Young_sCs_Replicate 1

description:
Replicate 1
X2.428084


title: D0_Young_sCs_Replicate 1

description:
Replicate 1
X2.428083

value: Day 0


title: p7

city: Shijiazhuang

first: Jing

last: Wang

address: No.466 ZhongshanRoad

institute: Hebei Medical University

description:
S0512-P8
Gene_Expression3.xls

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using fastp version 0.19.5；RNA-seq reads were aligned to the hg38 genome assembly using Hisat2 version 2.1.0 .
Gene abundance measurements were generationed and normalized  using Stringtie ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using edgeR package in R program version 3.4.3
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: brain

extract_protocol:
After retrobeads injection, following brain slice preparation and recording, the recorded and retrobeads-labelled neurons were aspirated into the patch pipette and were then broken into the PCR tube containing 1 μl lysis buffer. For mRNA in individual cells, mRNA was amplified and cDNA by SMARTer Ultra Low Input RNA for Illumina Kit, which was qualified and reversely transcribed to cDNA by Qubit and Agilent Bioanalyzer 2100 electrophoresis.
After fragmentation of cDNA (300 bp) by ultrasound, sequencing libraries (end repair, addition of poly(A), and ligation of  sequencing connectors) were built using the Ovation Ultralow Library System V2. After that, the constructed libraries were sequenced using Illumina HiseqXten.

value: brain

value: neurons


title: D2_Old_sCs_Replicate 3

description:
Replicate 3
X2.428082

value: WT

value: Day 2


title: CHD6_CUT&Tag_HEK293_rep1


title: p6

description:
S0512-P3
Gene_Expression3.xls


title: P2-CM CyA-Rep2

value: Cyclopmaine


title: D0_Old_sCs_Replicate 2

description:
Replicate 2
X2.428081

value: Muscle Stem cells

value: Old


title: hMSCs, Control-2

value: Bone marrow

value: mesenchymal stem cell

value: control


title: D4_Old_sCs_Replicate 3

description:
Replicate 3
X2.428077

value: Fibroadipogenic precursors


title: IFNβ-EVs, biol rep3

city: Nanjing

first: Meng

last: Yuan

state: Jiangsu

address: 22 Hankou Road, Nanjing, Jiangsu 210093

institute: Nanjing University

data_processing:
According to miRDeep2, a software that discovering know and novel miRNAs from deep sequencing, we can get all the identified microRNA and their expression data. Differential expression analysis used the DESeq/ DESeq2 Bioconductor package, a model based on the negative binomial distribution. After adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate, P-value of microRNAs were setted <0.05 to detect differential expressed ones.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: Human umbilical cord mesenchymal stem cells (HucMSCs) were sourced from GuLou Hospital, an affiliate of Nanjing University, in accordance with the Declaration of Helsinki and approved by the Medical Ethics Committee of Gulou Hospital. These adherent cells were cultivated in low glucose DMEM supplemented with GlutaMAXTM, 4 mM L-glutamine, and 10% fetal bovine serum (FBS). Passages 2-8 were used for experiments. EVs-depleted FBS is prepared by precipitating serum EVs by ultracentrifugation at 120,000 × g for 18h at 4 °C, and the resulting supernatant is filtered through a 0.2 μm well filter. Cells are typically kept in a humidified chamber at 37°C and 5% CO2.

extract_protocol:
Conditioned media from MSC cell cultures, treated with or without IFN-β treatment, after centrifuged them for 10 minutes at 2000 × g to remove any remaining cellular debris, the cleared supernatants were gathered and put into ultracentrifuge tubes (Polyallomer Quick-Seal centrifuge tubes 25 × 89 mm Beckman Coulter) and centrifuged for 30 minutes at 10000 × g (Type Ti 45, Beckman Coulter) in an ultracentrifuge (Optima L-90 K or Optima XE-90 Ultracentrifuge, Beckman Coulter) in order to extract macrovesicles. Subsequently, after meticulously gathering the supernatants, a Type 45 Ti rotor was used to centrifuge them for two hours at 110,000 × g and 4 °C. The EVs pellet obtained from this process was reconstituted in PBS and stored at −80 °C. Total RNA was extracted from exosome pellet using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. Individual libraries were constructed using 1µg of total RNA isolated from each sample.
Each library was indexed in order to multiplex three samples per sequencing run on the Illumina Novaseq 6000 platform.

treatment_protocol: Activation of the MSCs was done through the addition of 10 ng/mL of IFN-β to the culture for 48 hours.

value: Mesenchymal stem cells

tag: fraction

value: EV

value: with IFN-β


title: IFNβ-EVs, biol rep2


title: D4_Young_sCs_Replicate 1

description:
Replicate 1
X2.428080

value: Muscle

value: Day 4


title: p5

description:
S0512-P2
Gene_Expression3.xls


title: D0_Young_FAPs_Replicate 2

description:
Replicate 2
X2.424036

value: Young

value: Day 0


title: p4

description:
S0512-P1
Gene_Expression3.xls

value: brain

value: neurons


title: D2_Young_FAPs_Replicate 2

description:
Replicate 2
X2.424032

value: WT

value: Day 2


title: Naive-EVs, biol rep3

value: without IFN-β


title: IFNβ-EVs, biol rep1


title: D7_Young_FAPs_Replicate 3

description:
Replicate 3
X2.424033

value: Day 7


title: p3

description:
S0511-P7
Gene_Expression3.xls


title: D7_Old_FAPs_Replicate 2

description:
Replicate 2
X2.424029

value: Old


title: p1

description:
S0511-P10
Gene_Expression3.xls


title: D2_Young_FAPs_Replicate 3

description:
Replicate 3
X2.424027


title: p2

description:
S0511-P11
Gene_Expression3.xls


title: Naive-EVs, biol rep2


title: D2_Old_FAPs_Replicate 1

description:
Replicate 1
X2.424028


title: D7_Old_FAPs_Replicate 1

description:
Replicate 1
X2.424025


title: D0_Young_FAPs_Replicate 3

description:
Replicate 3
X2.424024


title: Naive-EVs, biol rep1


title: b10

description:
X181014B5
gene_expression2.xls


title: b9

description:
X181014B4
gene_expression2.xls


title: DU145 cells, shMSI2-2#, miRNA

city: Shanghai

first: Jianxiu

last: Yu

address: Room 202, Building 7, 280 South of Chongqing Road

department: Department of Biochemistry and cell biology

institute: Shanghai Jiao Tong University

description: miRNA

data_processing:
For DU145 mRNA data, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions.After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).The high quality clean reads were aligned to the reference genome (UCSC hg19) with hisat2 software (v2.0.4).Guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified.
For DU145 miRNA data, total RNA of each sample as used to prepare the miRNA sequencing library, which included the following steps: 1) 3'-adaptor ligation;2) 5'-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) Size selection of ~150 bp PCR amplicons (corresponding to ~22nt miRNAs)The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow ells, amplified in situ as lusters and finally equenced for 50 cycles on Illumina NovaSeq 6000 sequencer following the manufacturer's instructions.
Assembly: hg19 for RNA-Seq, miRBase for miRNA-Seq
Supplementary files format and content: Excel file includes mRNA expression profiling
Supplementary files format and content: Excel file includes miRNA expression profiling

source_name: cell line

extract_protocol:
RNA was extracted from total cell lysates.
RNA and miRNA libraries were prepared for sequencing using standard Illumina protocols

value: cell line

value: Prostate cancer cell


title: D7_Young_FAPs_Replicate 1

description:
Replicate 1
X2.424021

value: Fibroadipogenic precursors


title: D4_Old_FAPs_Replicate 1

description:
Replicate 1
X2.424023


title: D7_Old_FAPs_Replicate 3

description:
Replicate 3
X2.424019


title: DU145 cells, shMSI2-1#, miRNA

description: miRNA


title: b8

description:
X181014B2
gene_expression2.xls


title: D0_Old_FAPs_Replicate 1

description:
Replicate 1
X2.424017


title: D4_Old_FAPs_Replicate 2

description:
Replicate 2
X2.424016


title: D0_Young_FAPs_Replicate 1

description:
Replicate 1
X2.424015


title: D2_Old_FAPs_Replicate 2

description:
Replicate 2
X2.424018


title: D4_Young_FAPs_Replicate 3

description:
Replicate 3
X2.424034


title: b6

description:
X181013B3
gene_expression2.xls


title: D0_Old_FAPs_Replicate 3

description:
Replicate 3
X2.424012


title: b7

description:
X181014B1
gene_expression2.xls


title: DU145 cells, shMSI2-2#, mRNA

description: RNA


title: DU145 cells, shMSI2-1#, mRNA

description: RNA


title: D4_Young_FAPs_Replicate 2

description:
Replicate 2
X2.424011


title: D2_Old_FAPs_Replicate 3

description:
Replicate 3
X2.424014


title: DU145 cells, shCtrl, mRNA

description: RNA


title: D0_Old_FAPs_Replicate 2

description:
Replicate 2
X2.424008


title: b4

description:
X181010B1
gene_expression2.xls


title: b5

description:
X181013B1
gene_expression2.xls


title: D4_Old_FAPs_Replicate 3

description:
Replicate 3
X2.424009


title: D7_Young_FAPs_Replicate 2

description:
Replicate 2
X2.424006


title: Pat9_Pre

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Basecalls performed using bcl2fastq2 version 2.20
Sequenced reads were mapped to GRCh38 reference GENCODE (p7) annotation (v38) using STAR (v2.7.9a)
Reads counts are obtained using featureCounts from SubRead (v1.6.4) using –fracOverlap=0.85
Assembly: GRCh38.p7 GENCODE v38
Supplementary files format and content: Comma-separated file with raw counts; first and second columns contain ENS and Symbol gene names

source_name: Breast cancer tissue

extract_protocol:
QiagenmiRNeasy Mini Kit
KAPA RNA HyperPrep Kit with RiboErase (HMR) fit following manufacturer’s instructions

value: Breast cancer tissue

tag: condition

value: PCR

tag: subject id

tag: time point

value: Pre


title: b3

description:
X181010B0
gene_expression2.xls


title: Pat9_Post

value: Post


title: D2_Young_FAPs_Replicate 1

description:
Replicate 1
X2.424005

value: Muscle


title: D4_Young_M1_Replicate 3

description:
Replicate 3
X2.422370

value: Ly6Cpos macrophages

value: Young

value: Day 4


title: b2

description:
X181006B3
gene_expression2.xls

value: brain

value: neurons


title: D2_Young_M1_Replicate 2

description:
Replicate 2
X2.422367

value: WT

value: Day 2


title: b1

description:
X181006B1
gene_expression2.xls


title: Pat8_Pre

value: NonPCR


title: D7_Old_M2_Replicate 1

description:
Replicate 1
X2.422368

value: Ly6Cneg macrophages

value: Old

value: Day 7


title: Pat8_Post


title: l13

description:
X20180922L3
gene_expression2.xls


title: DU145 cells, shCtrl, miRNA

description: miRNA

value: cell line

value: Prostate cancer cell


title: D7_Young_M2_Replicate 3

description:
Replicate 3
X2.422366


title: Pat7_Pre

value: Breast cancer tissue

value: PCR


title: D2_Old_M2_Replicate 1

description:
Replicate 1
X2.422361


title: D7_Old_M2_Replicate 2

description:
Replicate 2
X2.422362


title: D2_Young_M2_Replicate 2

description:
Replicate 2
X2.422365


title: l12

description:
X20180922L2
gene_expression2.xls


title: Pat7_Post

value: Post


title: l11

description:
X20180922L1
gene_expression2.xls


title: D2_Old_M1_Replicate 1

description:
Replicate 1
X2.422360

value: Muscle


title: D4_Young_FAPs_Replicate 1

description:
Replicate 1
X2.424007

value: Fibroadipogenic precursors


title: D2_Young_M2_Replicate 3

description:
Replicate 3
X2.422358

value: Young


title: D2_Young_M1_Replicate 3

description:
Replicate 3
X2.422359

value: Ly6Cpos macrophages


title: Pat6_Post


title: D4_Old_M2_Replicate 1

description:
Replicate 1
X2.422356

value: Day 4


title: Pat6_Pre

value: Pre


title: D4_Young_M2_Replicate 3

description:
Replicate 3
X2.422369

value: WT


title: Pat5_Pre


title: l8

description:
X181005L3
gene_expression2.xls

value: brain

value: neurons


title: l9

description:
X181005L4
gene_expression2.xls


title: D2_Old_M1_Replicate 2

description:
Replicate 2
X2.422355

value: Day 2


title: D7_Old_M2_Replicate 3

description:
Replicate 3
X2.422354

value: Ly6Cneg macrophages

value: Old


title: Pat5_Post


title: D4_Young_M2_Replicate 1

description:
Replicate 1
X2.422351


title: l7

description:
X181005L0
gene_expression2.xls


title: D4_Young_M1_Replicate 1

description:
Replicate 1
X2.422352


title: D4_Old_M1_Replicate 2

description:
Replicate 2
X2.421550


title: l6

description:
X3-25-3
gene_expression1.xls


title: Pat4_Post

value: NonPCR


title: l10

description:
X20180922L0
gene_expression2.xls


title: K562, etoposide, 36 hours, RACE_Nano_Seq, alignments

city: Xiamen

first: Lu

last: Tang

address: Jimei road

institute: HuaQiao university

data_processing:
The reads were based-called in real-time using MinKNOW (v20.10.6) and integrated with Guppy (v4.2.3).
Raw Nanopore sequencing data were initially filtered to retain sequences with an average quality score of 7 or higher.
The clean data were aligned to the Human GRCh38/hg38 reference genome using Minimap2 (v2.17-r941) in spliced alignment mode with the command: minimap2 -ax splice -ub -G400000 --end-seed-pen 30.
Supplementary and low-quality alignments were filtered out using SAMTools (v1.10) with the command: samtools view -F0x900 -q 60. High-quality alignments were then aligned to anchor exons using the “intersect” function of the BEDTools suite (v2.30.0) (PMID: 20110278).
The transcription start sites (TSSs) or transcription termination sites (TTSs) of InSETG-4 were determined from the first aligned base of 5′ RACE-Nano-Seq reads and the last aligned base of 3′ RACE-Nano-Seq reads, respectively. The normalized abundance of TSSs or TTSs was calculated using the following formula: Normalized TSSs or TTSs = (C ×1000)/T, where C represents the counts of each TSS or TTS from respectably 5′ or 3′ RACE-Nano-Seq assays, and T denotes the total number of reads in the corresponding assay.
Assembly: GRCh38/hg38
Supplementary files format and content: Processed data RACE-Nano-Seq_Etoposide_36h_InSETG-4.bed is in BED files containing coordinates of 5' and 3' RACE products of each anchor exon. The 5th column shows the RACE products identification. The 6th column shows the reads counts of each alignments.
Supplementary files format and content: Processed TSS or TTS data is in  BedGraph files containing the TSS or TTS coordinates. The 4th column of these files shows the normalized abundance.

growth_protocol: The human chronic myeloid leukemia cell line K562 was cultured in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS, Excell Bio, Uruguay) and 1% penicillin-streptomycin (Gibco), and maintained at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted using TRNzol Universal (Tiangen, DP424) and the Total RNA Kit I (Omega, R6438-02) according to the manufacturer’s instruction. PolyA+ RNA was isolated from total RNA using mRNA capture beads (VAHTS, N401).
PolyA+ RNA was subjected to 5' RACE and 3' RACE reactions for each anchor exon essentially as described in our previous publication (PMID: 38001496), targeting two anchor exons of the InSETG-4 gene. The coordinates of the two anchor exons, the exon2 and exon3 of the InSETG-4 gene, are chr20:23159772-23159868(+) and chr20:23178710-23178772(+) respectively. The 5' RACE and 3' RACE products from each reaction were mixed in equal volumes and purified with 2× volumes of VAHTS DNA Clean Beads (Vazyme) to a final volume of 50 μL. The concentrations were measured using Merinton SMA6000 spectrophotometer. The pooled 5' and 3' RACE products were used to prepare the sequencing library. The library was constructed using the Ligation Sequencing Kit (SQK-PCS109) from Oxford Nanopore Technologies Inc. Sequencing was performed on a FLO-PRO002 R10.4 flow cell using the Oxford Nanopore PromethION platform.

treatment_protocol: K562 cells were seeded in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS, Excell Bio, Uruguay) at a density of 5 × 10⁶ cells/mL and cultured for 16 hours before treatment with 90 μM etoposide (Abmole) for 36 hours.

value: lymphoblast cells

value: etoposide_36 hours


title: D4_Old_M1_Replicate 1

description:
Replicate 1
X2.422357


title: l4

description:
X3-25-1
gene_expression1.xls


title: D4_Old_M2_Replicate 2

description:
Replicate 2
X2.421549


title: Pat3_Post

value: Breast cancer tissue


title: Pat4_Pre


title: l5

description:
X3-25-2
gene_expression1.xls


title: Pat3_Pre


title: D7_Young_M2_Replicate 1

description:
Replicate 1
X2.421548

value: Day 7


title: siNEDD4L#3

city: Xinxiang

first: zhen

last: chen

state: China

address: Hongqi District

institute: Xinxiang Medical Universty

data_processing:
A cDNA library was sequenced run with Illumina Novaseq 6000 sequence platform.
Assembly: GRCh38
Supplementary files format and content: xlsx files include FPKM values for each Sample

source_name: cell  line

extract_protocol:
Tiangen RNA extraction kits were used to extract RNA,3 μg of total RNA was used for sequencing library construction.
The cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used tosynthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H(NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR.

value: cell  line

value: esophageal squamous cell carcinoma cells

value: NEDD4L knockdown


title: D2_Old_M1_Replicate 3

description:
Replicate 3
X2.421546

value: Muscle

value: Ly6Cpos macrophages


title: l3

description:
X3-14-0
gene_expression1.xls


title: D4_Young_M2_Replicate 2

description:
Replicate 2
X2.421547

value: Young

value: Day 4


title: D2_Old_M2_Replicate 2

description:
Replicate 2
X2.422353

value: WT


title: l2

description:
X3-13-2
gene_expression1.xls

value: brain

value: neurons


title: D4_Young_M1_Replicate 2

description:
Replicate 2
X2.421545


title: siNEDD4L#1


title: MCF7 shMETTL14 Rep2 input

city: Hangzhou

first: Xupeng

last: Bai

state: Zhejiang

address: No.79 Qingchun Road

department: The First Affiliated Hospital

institute: Zhejiang University

data_processing:
Raw reads were downloaded and trimmed for low-quality data using the fastp v0.23.4. Filtering criteria: 1) Remove reads containing adapters; 2) Remove reads with an N ratio＞10%; 3) Remove reads that are all A bases; 4) Remove beads with the number of low-quality bases (Q≤20) more than 50%.
Trimmed reads were aligned to the human reference genome GRCh38/hg38 using HISAT v2.2.4 with default parameters.
Peak calling and annotation were performed with MACS2 v2.1.2 (q<0.05) and exomePeak2 v1.12.0 (P<0.00001).
The read count of each sample was assembled and normalized using StringTie v1.3.1in a reference-based approach.
Assembly: hg38
Supplementary files format and content: The tab-delimited text file includes raw counts for each sample
Supplementary files format and content: bigWig

source_name: Breast

extract_protocol:
Total RNA was harvested using the EZ-press RNA Purification Kit (EZBioscience). For RNA-seq, poly(A) mRNA was purified from total RNA using the Dynabeads mRNA DIRECT Kit (Invitrogen). For MeRNA-seq, poly(A) mRNA is subjected to fragmentation with Ambion RNA Fragmentation Reagents (Invitrogen). The m6A immunoprecipitation procedure was carried out using the fragmented RNA and m6A monoclonal antibody (Proteintech) in accordance with the RIP protocol. RNA from input and m6A IP samples was cleaned by BeyoMag mRNA Purification Kit (Beyotime).
Library preparation was performed using the NEBNext Ultra RNA Library Prep Kit (NEB).

value: Breast

value: Breast cancer cell line

value: METTL14 knockdown


title: m8

description:
X20180924m3
gene_expression2.xls


title: D4_Old_M1_Replicate 3

description:
Replicate 3
X2.421544

value: Old


title: MCF7 shMETTL14 Rep2

data_processing:
Raw reads were downloaded and trimmed for low-quality data using the fastp v0.23.4. Filtering criteria: 1) Remove reads containing adapters; 2) Remove reads with an N ratio＞10%; 3) Remove reads that are all A bases; 4) Remove beads with the number of low-quality bases (Q≤20) more than 50%.
Trimmed reads were aligned to the human reference genome GRCh38/hg38 using HISAT v2.2.4 with default parameters.
Peak calling and annotation were performed with MACS2 v2.1.2 (q<0.05) and exomePeak2 v1.12.0 (P<0.00001).
The read count of each sample was assembled and normalized using StringTie v1.3.1in a reference-based approach.
Assembly: hg38
Supplementary files format and content: The tab-delimited text file includes raw counts for each sample
Supplementary files format and content: bigWig
Library strategy: MeRIP-seq


title: D4_Old_M2_Replicate 3

description:
Replicate 3
X2.421543

value: Ly6Cneg macrophages


title: m7

description:
X20180924m1
gene_expression2.xls


title: siControl#3


title: MCF7 shMETTL14 Rep1 input


title: siControl#2


title: D2_Old_M2_Replicate 3

description:
Replicate 3
X2.421542

value: Day 2


title: D2_Young_M1_Replicate 1

description:
Replicate 1
X2.421541


title: siControl#1


title: MCF7 shMETTL14 Rep1


title: MCF7 shNC Rep2 input


title: m4

description:
X3-19-3
gene_expression1.xls


title: MCF7 shNC Rep2


title: m5

description:
X20180923m4
gene_expression2.xls


title: m6

description:
X20180924m0
gene_expression2.xls


title: D7_Young_M2_Replicate 2

description:
Replicate 2
X2.421540

value: Day 7


title: BCBM3.IP

city: Liaocheng

first: Bo

last: Fu

address: 67 Dongchang West Road

institute: Liaocheng People's Hospital

data_processing:
Paired-end reads were harvested from an Illumina NovaSeq 6000 sequencer and reads with Q30 > 80% were retained.  After 3’ adaptor-trimming, low-quality reads were removed in Cutadapt version 1.9.3, and mRNA peaks were identified with DCC software
Clean reads of all libraries were then aligned in Hisat2 version 2.0.4 to the reference genome.
Methylation modifications were identified with MACS, and differentially methylated sites between the two groups of cell lines were determined using diffReps
Read abundance at specific genomic positions was visualised in the Integrative Genomics Viewer. Identified m5C peaks were subjected to motif enrichment analysis in DREME and then localised to a given mRNA sequence. High-quality reads were mapped on to a human reference genome (GENCODE Human Release 32) using Hisat2 version 2.0.4
Data were normalised and differentially expressed RNAs (fold change ≥ 2.0 and P < 0.0001) were screened using EdgeR version 3.16.5
Assembly: hg19
Supplementary files format and content: tab-delimited text file includs raw numeric values for each sample

source_name: human breast cancer brain metastasis cell

extract_protocol:
Total RNA was extracted from the cultured cells using TRIzol reagent (Invitrogen Corporation, CA, USA). Ribosomal RNA was depleted using the Ribo-Zero rRNA Removal Kit (Illumina, Inc., CA, USA). The RNA concentrations were measured using NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA)
m5C methylated RNAs were immunoprecipitated using the GenSeqTM m5C RNA IP Kit (GenSeq Inc., China). Both non-immunoprecipated input samples and m5C immunoprecipitation samples were used for RNA-seq library generation with the NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA). Library quality was evaluated by BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).
The library was sequenced on an Illumina Hiseq sequencer to obtain 150 bp paired-end reads.

value: m5C immunoprecipitation


title: siNEDD4L#2

value: cell  line

value: esophageal squamous cell carcinoma cells


title: m3

description:
X3-19-2
gene_expression1.xls


title: D2_Young_M2_Replicate 1

description:
Replicate 1
X2.421539

data_processing:
Primary data quality control is performed during the sequencing run to ensure the optimal flow cell loading (cluster density) and check the quality metrics of the sequencing run. Sequencing data were demultiplexed and FastQ files and a fastQC report were generated by the Bcl2FastQ Demux Pipeline (UBP) (software version v2.19.1).
Data preprocessing was carried out using the nf-core pipeline rnaseq version 1.4.2 [nf-core/rnaseq]. Mouse reference genome used was GRCm38 (mm10), with the corresponding gtf file for exons junctions. Mapping was performed with STAR version 2.6.1d. Raw counts were generated via featureCounts version 1.6.4. Coverage and transcripts abundances were estimated via StringTie version 2.0. Cell types and their respective sampling timing are listed as follows (cell type (abbreviation) [Days available]): endothelial (ECs) [D0, D2, D4, D7], fibroadipogenic precursors (FAPs) [D0, D2, D4, D7], muscle stem cells (MuSCs) [D0, D2, D4, D7],neutrophils (Neutrophils) [D2], inflammatory macrophages (Inflammatory-Mac) [D2, D4] and resolving macrophages (Resolving-Mac) [D2, D4, D7]. Each sample name was defined by a unique combination age.cellType.day (for example: Old.Neutrophils.D2), comprising three biological replicates. Data visualization and analysis were performed using custom Rstudio scripts.
Gene biotype classification was performed with the BioMart package. Only protein coding genes were retained. Genes expressed in at least 3 samples with a raw count greater than 5 were kept. A hierarchical clustering was done using 𝜌 Spearman’s correlation coefficients among TPM (Transcripts per Million) normalized samples. Variance stabilizing transformation (vst) (provided by DESeq2) was calculated on raw count matrices at three levels: whole dataset matrix, specific cell type matrices, and cell type and time point specific matrices. Principal Component Analysis (PCA) was applied at each level to reveal global effects across libraries.
Assembly: mm10
Supplementary files format and content: TPMmatrix.CSV
Supplementary files format and content: FPKMmatrix.CSV

extract_protocol:
MuSCs, FAPs, ECs, neutrophils, Ly6Cpos macrophages and Ly6Cneg macrophages were isolated from regenerating muscle. Briefly, muscles were dissociated and digested in DMEM F/12 medium containing 10 mg/ml of collagenase B and 2.4 U/ml Dispase (Roche Diagnostics GmBH) at 37°C for 30 min and passed through a 3 microm cell strainer. CD45pos and CD45neg were separated using magnetic beads. CD45pos cells were incubated with anti-mouse FcgRII/III (2.4G2) and further stained with PE-Cy7-conjugated anti-CD45 (25-0451-82, eBioscience) and APC-conjugated anti-Ly6C antibody (17-5932-82, eBioscience). CD45neg cells were stained with PE-Cy7-conjugated anti-CD45, PerCP-Cy5.5- conjugated anti-Sca-1 (45-5981-82, eBioscience), Alexa Fluor 647-conjugated anti-a7-integrin (AB0000538, AB lab, University British Columbia), PE-conjugated anti-CD31 (12-0311-82, eBioscience) and FITC-conjugated anti-CD34 (11-0341-82, eBioscience) antibodies. Cells were sorted using a FACS Aria II cell sorter (BD Biosciences).
Sequencing libraries were prepared using the Ovation SoLo from NuGen. The Ovation SoLo RNA-Seq system integrates NuGen’s Insert-Dependent Adaptor Cleavage (InDA-C) technology to provide targeted depletion of unwanted transcripts (rRNA) by specific and robust enzymatic steps. The system also includes an 8pb barcode for multiplexing followed by an 8 bp randomer for identification of unique molecules (UMI) to remove PCR duplicates from the transcript counting analysis. Libraries are quantified with Picogreen (Life Technologies) and size pattern is controlled with the DNA High Sensitivity Reagent kit on a LabChip GX (Perkin Elmer). Libraries are pooled at an equimolar ratio (i.e. an equal quantity of each sample library) and clustered at a concentration of 20 pmol on paired-end sequencing flow cell CBU2FANXX (Illumina). Sequencing is performed for 2 x 125 cycles on a HiSeq 2500 (Illumina) using the SBS V4 chemistry (Sequencing by Synthesis). The samples were subdivided into 6 different sorted cell types (MuSCs, FAPs, ECs, neutrophils, Ly6Cpos macrophages and Ly6Cneg macrophages, 4 time points (D0, D2, D4, D7) and 2 age conditions (cell isolated from young or old mice). Each of these data point was run in triplicate 3 different mice. The entire experiment was run in 4 batches of 30 samples.

value: Muscle


title: l1

description:
X3-13-1
gene_expression1.xls


title: MCF7 shNC Rep1 input


title: BCBM2.IP

value: human breast cancer brain metastasis cell


title: m2

description:
X3-19-1
gene_expression1.xls


title: MCF7 shNC Rep1


title: Hi-C-WT-L1

city: Bethesda

first: Michaela

last: Willi

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

data_processing:
Data were analyzed using hicpro (Servant et al., Genome Biology, 2015) with default parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: hic file was created using hicpro and script provided by hicpro.

source_name: Mammary gland

growth_protocol: Mouse mammary tissues were harvested at day one of lactation (L1).

extract_protocol:
The Hi-C protocol was adapted from published methods. Frozen-stored mammary tissues collected at L1 were ground into powder. Chromatin was fixed with formaldehyde (final 1%) for 15 min at room temperature and quenched with glycine (final 0.125 M). Pellets were lysed in lysis buffer (10 mM Tris-HCI pH 8.0, 10 mM NaCl, 0.5% Nonidet P-40) containing Phenylmethylsulfonyl fluoride (PMSF, 100 mM) and protease inhibitors, incubated on ice for 30 min, and dounced using pre-chilled glass homogenizer, followed by another 10 min incubation on ice. After removal of supernatant, nuclei pellets were re-suspended in 3.1 NEB buffer (New England Biolabs). SDS was added to a final concentration of 0.1% and samples were incubated for 1 hr at 37°C. 1% Triton X-100 was added, followed incubation for 1 hr at 37°C. Samples were incubated overnight with 400 units of the restriction enzymes DpnII (New Englnad Biolabs) at 37°C. To inactivate the enzyme, digested samples were incubated for 30 min at 65°C. DNA ends were labeled with biotin-14-dCTP (Thermo Fisher Scientific) in a Klenow end-filling reaction. T4 ligase (New England Biolabs) was added to each sample and incubated for 4 hr at 16°C. Ligated samples were treated overnight with proteinase K (20 mg/ml, Invitrogen) at 65°C and 1 hr at 37°C with RNase A (10 mg/ml, Thermo Fisher Scientific), and DNA fragments were purified by phenol-chloroform DNA precipitation. 40 μg of DNA was sheared to an average size of 400 bp, using the manufacturer's instructions (Covaris). The sheared DNA was end repaired, adenine tailed, and double size selected using AMPure XP beads to isolate DNA ranging from 250 to 500 bp in size. Ligation fragments marked by biotin were immobilized using magnetic streptavidin beads (Thermo Fisher Scientific) and ligated to paired-end adaptors (New Englnad Biolabs). The immobilized Hi-C libraries were amplified with 15 PCR amplification cycles and size selected using AMPure XP beads to remove primer dimers. Libraries were sequenced with HiSeq 2500 (Illumina).
Libraries for sequencing were prepared using standard Illumina protocols.

tag: strain/background

tag: genotype/variation

value: wild-type

tag: Stage

value: Lactation day 1

value: Mammary gland


title: m1

description:
X3-19-0
gene_expression1.xls

tag: tissue

value: brain


title: 4C_Csn-S1-4-rep2

data_processing:
Library strategy: 4C-seq
Trimmed reads were mapped to DpnII enzyme based reduced mm10 genome using Bowtie2. Mapped reads were processed with 4Cker R package to generate bedgraph files.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bedGraph files were generated by 4Cker R package.

extract_protocol:
The 4C protocol was adapted from published methods. Frozen-stored mammary tissues collected at L1 were ground into powder. Chromatin was fixed with formaldehyde (final 1%) for 15 min at room temperature, and then was quenched with glycine (final 0.125 M). Pellets were lysed in lysis buffer (10 mM Tris HCI pH 8.0, 10 mM NaCl, 0.5% Nonidet P-40) containing Phenylmethylsulfonyl fluoride (PMSF) and protease inhibitors, incubated on ice for 30 min, and dounced using pre-chilled glass homogenizer, followed by another 10 min incubation on ice. After removal of supernatant, nuclei pellets were re-suspended in NEB buffer 3.1 (New England Biolabs). SDS was added to a final concentration of 0.2% and samples was incubated for 1 hr at 37°C. 2% Triton X-100 was added, followed incubation for 1 hr at 37°C. Samples were incubated with 400 units each of restriction enzymes BamHI (New England Biolabs) and were incubated overnight at 37°C. To enzyme inactivation SDS was added (final 1%) and incubated for 30 min at 65°C, followed by SDS-sequestration with 1% Triton X-100 at 37°C for 1 hr, T4 ligase (New England Biolabs) was added to each sample and incubated for 1 hr at 16°C. Ligated samples were treated overnight with proteinase K (20 mg/mL, Invitrogen) at 65°C and 1 hr at 37°C with RNase A (10 mg/mL, Thermo Fisher Scientific), and DNA fragments were purified by phenol-chloroform method. DNA fragments from 3C were digested with NlaIII (New England Biolabs) overnight at 37°C and ligated using T4 ligase overnight at 16°C. DNA was purified by phenol/chloroform method and then amplified with site-specific primers linked to the Illumina DNA adaptors. Libraries for next-generation sequencing were prepared and sequenced with HiSeq 2500 (Illumina).
Libraries for sequencing were prepared using standard Illumina protocols.


title: BCBM1.IP

tag: cell type


title: cyccY5-3

city: New Orleans

first: Jun-yuan

last: Ji

state: LA

address: 1700 Tulane Avenue

department: Department of Biochemistry and Molecular Biology

institute: Tulane University

data_processing:
RNA-Star alignment to dme6.51 transposon or chromosome reference with default setting
Assembly: dm6
Supplementary files format and content: txt, count table

organism: Drosophila melanogaster

source_name: whole 3rd instar larvae

extract_protocol:
The total RNA from ten third-instar larvae of w1118 (as the wild-type control), cycCY5 and Cdk8K185 homozygotes at the wandering stage (triplicate for each genotype) was extracted using 1.0 ml TRIzol Regent (Invitrogen), and then purified using an RNeasy Mini Kit (Qiagen, 74104) following the manufacturer instructions.
Standard RNA-seq preparation with Illumina RNA-seq kit

value: whole 3rd instar larvae

tag: genotype


title: cyccY5-2


title: 4C_WT4


title: c7

description:
X181004C1
gene_expression2.xls

value: neurons


title: BCBM1.Input

tag: treatment

value: non-immunoprecipated input


title: 4C_Csn-S1-4-rep1


title: BCBM3.Input


title: cyccY5-1


title: c4

description:
X3-24-1
gene_expression1.xls


title: BC3.IP

source_name: human breast cancer cell

value: human breast cancer cell


title: 4C_WT1


title: BC3.Input


title: 4C_WT2


title: c5

description:
X3-24-2
gene_expression1.xls


title: Sendai Virus (SeV)-iPSC derived mesenchymal stromal cell (MSC) line 1, Paasge 3

city: Ithaca

first: Muhandiram

middle: Prasanna

last: Weeratunga

address: 121 Pleasant Grove Rd, 911 Hasbrouck Apartments

department: Baker Institute for Animal Health

institute: Cornell University

description:
Library name: Sample 3
IPSC-MSCs-1

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
The mouse-derived reads were subtracted from the dataset, and the remaining reads were mapped to the Felis catus reference genome (Felis_catus_9.0 (GCA_000181335.4)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Felis catus

source_name: (SeV)-iPSC derived MSCs

growth_protocol: iPSC cultures were maintained in iPSC medium containing KnockOut DMEM supplemented with 15% (v/v) Embryonic Stem (ES) qualified FBS, 0.1 mM NEAA, 1 mM L-glutamine, 0.1 mM β-mercaptoethanol, 1,000 IU/mL feline leukemia inhibitory factor  and 6.0 ng/mL human basic fibroblast growth factor. iPSC-derived MSCs were maintained in MSC medium that consisted of low glucose DMEM supplemented with 30% FBS, 1% penicillin/streptomycin, and 2 mM L-glutamine.

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

tag: cell line

value: (SeV)-iPSC derived MSCs

value: Mesenchymal stromal cells


title: c3

description:
X3-24-0
gene_expression1.xls


title: Sendai Virus (SeV)-derived cat iPSC cell line 2, Paasge 15

description:
Library name: Sample 2
SV-IPSCs-2

source_name: Sendai Virus (SeV)-derived iPSCs

value: Sendai Virus (SeV)-derived iPSCs

value: Induced pluripotent stem cells


title: BC2.IP

value: m5C immunoprecipitation


title: DNP2_2_T7

city: Toulouse

first: Laurence

last: Girbal

address: 135 avenue de rangueil

institute: TBI

description: T7 of kinetics  biol rep 2

data_processing:
Reads were then mapped onto the Escherichia coli genome (version NC_000913.3, GenBank) with Bowtie2.
Counting was performed with featureCounts.
To measure genome-wide RNA half-lives, 12 RNA-sequencing data ( 2 T0 samples and 10 time points after addition of rifampicin) were used. Normalization between sequencing data was performed using the first three invariant genes for the 12 sequencing data of each condition (genes with the lowest variance in rank between sequencing data, namely b2621 (ssrA), b3123 (rnpB) and b2092 (gatC)).
Assembly: NC_000913.3
Supplementary files format and content: csv file includes raw counts of each gene in each SAMPLE

organism: Escherichia coli

source_name: cells

growth_protocol: After overnight growth in M9-glucose (16.7 mM glucose), cells were washed with M9-succinate (85 mM of succinate), and used to inoculate Erlenmeyer flasks with M9-succinate at OD600nm= 0.1. At OD600nm= 0.8, rifampicin (0.5 g/L) was added, and cell samples were taken over time and rapidly frozen in liquid nitrogen.

extract_protocol:
After mechanical lysis with glass beads, total RNA was extracted using the RNeasy Mini Kit (Qiagen) at times T0, 0.4, 1, 2, 4 and 7 min for the two biological replicates. DNA contamination was removed by DNase I treatment.
Total RNA was ribodepeleted using the riboPOOLs kit (Illumina). A paired-end 150 bp sequencing strategy was performed on Illumina PE150 platform (Novogene).

treatment_protocol: Cells were treated with either 0.7 or 2 mM 2,4-dinitrophenol (DNP). Rifampicin and DNP were added simultaneously.

value: cells

value: 2mM DNP


title: BC2.Input


title: c2

description:
X3-23-1
gene_expression1.xls


title: Sendai Virus (SeV)-derived cat iPSC cell line 1, Paasge 15

description:
Library name: Sample 1
SV-IPSCs-1


title: BCBM2.Input


title: DNP2_2_T4

description: T4 of kinetics  biol rep 2


title: BC1.IP


title: c6

description:
X181004C0
gene_expression2.xls


title: 4C_WT3


title: Sendai Virus (SeV)-iPSC derived mesenchymal stromal cell (MSC) line 2, Paasge 3

description:
Library name: Sample 4
IPSC-MSCs-2


title: mDC 1009

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description: Whole Genome Bisulfite Sequencing

data_processing:
Low-quality reads and adapter sequences were filtered out by tool Trimmomatic
Given the large file size, surviving reads were further split into subfiles. Reads from each subfile were then aligned to human reference genome hg19 by bisulfite aligner bismark. Then SAMtools was applied to merge the multiple aligned subfiles back into one library and sort files based on chromosomal locations.
Picard tool (http://broadinstitute.github.io/picard/) was employed on the sorted BAM file to mark duplicates.
Methylation calling was performed by bismark methylation extractor to generate a list of chromosomal locations with corresponding methylation depth and rate.
DMR were called by R/Bioconductor package DSS, where the significant DMRs were defined by p-value (p.threshold) = 0.05, minimum region length (minlen) = 30 bps and minimum CpG sites (minCG) = 3.
Assembly: hg19
Supplementary files format and content: TXT file for methylation calling by bismark

source_name: Leukapheresis products

extract_protocol:
Leukapheresis products were obtained under an IRB-approved protocol (Institute for Transfusion Medicine, Pittsburgh, PA). Monocyte-enriched, elutriated fractions recovered from 6 normal human donor leukapheresis products were used for generation of DCregs and monophosphoryl lipid A (MPLA; TLR4 ligand low toxicity derivative of bacterial lipopolysaccharide (LPS))-matured sDC. In instances where the elutriated monocyte fraction purity was <90%, CD14-specific immunobeads (Miltenyi, San Diego, CA) were used according to the manufacturer’s protocol to increase monocyte purity to >90%. After 7 days culture, monocyte-derived DCreg and sDC were harvested. The viability of DCregs and sDCs, determined by trypan blue staining, was routinely > 95%. A portion of each DC group was snap-frozen in liquid nitrogen and stored at -80°C for Whole Genome Bisulfate Sequencing (WGBS) DNA Methylation analysis. Portions of the remaining DC were either antibody-stained for key surface molecules, HLA-DR, CD11c, T cell costimulatory and coinhibitory molecules and CD163 (clone RM3/1, Biolegend) and flow cytometry data analyzed using Flow Jo software.
DNA was extracted from frozen cell pellets and underwent bisulfite treatment. The bisulfite modified DNA-sequencing library was generated using the Accel-NGS Methyl-Seq DNA library kit (Swift Biosciences) per the manufacturer’s instructions.

value: Leukapheresis products

value: mDC


title: Senile4

city: Chengdu

first: Li

last: Chen

state: Sichuann

address: No.17, South Renmin Road

institute: Sichuan University West China Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Tree shrew genome sequence (https://useast.ensembl.org/Tupaia_belangeri/Info/Index?db=core)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Tupaia belangeri

source_name: Retina

extract_protocol:
The retina was carefully dissected out from TS with strict compliance to the ethical guidelines. In detail, the dissected tissues were washed with cold phosphate buffered saline (PBS; Invitrogen, Carlsbad, USA), quickly frozen and then stored in liquid nitrogen before use. Preceding the library construction process, the tissues were first thawed, cut into small pieces, and then transferred to 1.5 mL tube contained with 1× homogenization buffer containing 30 mmol/L CaCl2, 18 mmol/L Mg(Ac)2, 60 mmol/L Tris-HCl (pH 7.8), 320 mmol/L sucrose, 0.1% nonidet P-40, and 0.1 mmol/L ethylene diamine tetraacetic acid (Invitrogen). The tissue pieces werethen transferred to a 2 mL Dounce homogenizer and stroke on the ice with loose pestles and then with tight pestles for 15 times. The nucleus extraction was filtered with 40 mm strainer and spanned down at the speed of 500 g for 10 min at 4 ℃ to carefully discard the supernatant. The pellets were resuspended with PBS containing 0.1% bovine serum albumin (Invitrogen) and 20 U/mL RNase Inhibitor for later 10x Genomics 30 library construction (10x Genomics, Pleasanton, USA).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Retina

tag: developmental stage

value: Senile


title: dKO

city: Hong Kong

first: QIANG

last: SUN

address: Ngan Shing Street

institute: The Chinese University of Hong Kong

data_processing:
The orginal FASTQ files were processed by CellRanger 7.0.0 to produce outputs including feature-barcode matrices.
Subsequently, the processed matices were read in by Seurat 4.3.0 for following analysis.
The aligned RNA-Seq reads were accepted  and assembled into a parsimonious set of transcripts.  These transcripts were then estimated the relative abundances by Cufflinks.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: cytoplasmic RNA

source_name: hind limb muscle

extract_protocol:
Whole live muscle cells were freshly isolated by FACs sorting
Sequential crosslinking was performed with the following steps: Whole muscle cells were isolated  with an additional step of viability validation by PI staining. Red blood cells were also eliminated by ACK buffers (150M NH4Cl, 100mM KHCO3, 10mM EDTA-2Na) before sorting. After sorting, live cells were washed with 0.04% BSA in PBS for twice and resuspended in the BSA solution at an appropriate concentration (300-1200 cells/μl). Suspended cells were counted under a microscope and Typan blue was used to examine the cell viability. After the confirmation of cell number and viability, following the 10x manufacturer’s instructions for generation of Gel Bead-In Emulsions (GEMs) using the 10X Chromium system. Next GEMs were proceeded with in-GEM reverse transcription (RT) under manufacturer’s instructions. After RT, two steps of DNA cleaning up and purification were performed to obtain the purified cDNA sample for further library construction with the manufacturer's protocols. Bioanalyzer analysis and qPCR were used to measure the quality of DNA libraries including the DNA size and purity. Finally, DNA libraries were sequenced on the Illumina Illumina HiSeq X ten platform.

value: hind limb muscle

value: YY1 dKO


title: DNP2_2_T2

description: T2 of kinetics  biol rep 2


title: Ctrl

value: no treatment


title: Senile3

description: 10x Genomics


title: input

data_processing:
The raw data were first pre-processed by initial quality assessment, adapters trimming, and low-quality filtering and then mapped to the mouse reference genome (mm10) using bowtie2, and only the non-redundant reads were kept.
The protein DNA-binding peaks (sites) were identified using MACS2 with input (IgG) sample as the background. During the peak calling, candidate peaks were compared with the background, dynamic programming was used to determine λ of Poisson distribution, and the P-value cutoff was set to 0.0001 for YY1 ChIP-Seq experiment.
Assembly: mm10
Supplementary files format and content: *.bedGraph

source_name: Muscle

growth_protocol: MuSCs were cultured in Ham’s F10 medium with 20% FBS, 5ng/ml β-FGF (PHG0026, Thermo Fisher Scientific) and 1% P/S, in coverslips and cultural wells which were coated with poly-D-lysine solution (p0899, Sigma) at 37 °C for overnight and then coated with extracellular matrix (ECM) (E-1270, Sigma) at 4 °C for at least 6 h

extract_protocol:
YY1 ChIP were performed following our previously described protocol
Ten μg of antibodies against YY1 (Santa Cruz Biotechnology, sc-1703), or normal mouse IgG (Santa Cruz Biotechnology, sc-2025) was used for immunoprecipitation. Immunoprecipitated genomic DNA was resuspended in 20 μl of water. For ChIP-seq DNA library construction, a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, E7645S) was used according to the manufacturer’s instructions. Bioanalyzer analysis and qPCR were used to measure the quality of DNA libraries including the DNA size and purity. Finally, DNA libraries were sequenced on the Illumina Genome Analyzer II platform.

value: Muscle

value: MuSC

tag: antibody

value: input


title: DNP2_2_T0

description: T0 of kinetics   biol rep 2


title: mDC 1006

description: Whole Genome Bisulfite Sequencing


title: Mature5

description: 10x Genomics

value: Mature


title: mDC 1010

description: Whole Genome Bisulfite Sequencing


title: dKO_rep3

data_processing:
Adaptor sequences and poor-quality reads were removed using Trimmomatic
The filtered reads were then aligned to mouse reference genome (mm10)
All aligned reads were then merged and assigned to restriction fragment, while low quality (MAPQ<30) or multiple alignment reads were discarded
Invalid fragments including unpaired fragments (singleton), juxtaposed fragments (re-legation pairs), un-ligated fragments (dangling end), self-circularized fragments (self-cycle), and PCR duplicates were removed from each biological replicate. The remaining validate pairs from all replicates of each stage were then merged, followed by read depth normalization using HOMER (http://homer.ucsd.edu/homer/ngs/) and matrix balancing using iterative correction and eigenvector decomposition (ICE) normalization to obtain comparable interaction matrix between different stages
Assembly: mm10
Supplementary files format and content: .hic: an indexed binary format designed to permit fast random access to contact matrix heatmaps.

extract_protocol:
Libraries were prepared by on-bead reactions using the NEB Next Ultra II DNA Library Preparation Kit (NEB, E7645S).
The beads were separated on a magnetic stand, and the supernatant was discarded. After washes, the beads were resuspended in 20 μl of 10 mM tris buffer and boiled at 98°C for 10 min. The elute was amplified for 10 to 13 cycles of PCR with Phanta Master Mix (Vazyme, P511-01), and the PCR products were purified using VAHTS DNA Clean Beads (Vazyme, N411-01)

value: dKO


title: Mature3

description: 10x Genomics


title: Mature4

description: 10x Genomics


title: mDC 1016

description: Whole Genome Bisulfite Sequencing


title: DNP2_1_T7

description: T7 of kinetics   biol rep 1


title: mDC 1007

description: Whole Genome Bisulfite Sequencing


title: DNP2_1_T4

description: T4 of kinetics   biol rep 1


title: dKO_rep2


title: Infancy5

description: 10x Genomics

value: Infancy


title: c1

description:
X3-23-0
gene_expression1.xls

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using fastp version 0.19.5；RNA-seq reads were aligned to the hg38 genome assembly using Hisat2 version 2.1.0 .
Gene abundance measurements were generationed and normalized  using Stringtie ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using edgeR package in R program version 3.4.3
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
After retrobeads injection, following brain slice preparation and recording, the recorded and retrobeads-labelled neurons were aspirated into the patch pipette and were then broken into the PCR tube containing 1 μl lysis buffer. For mRNA in individual cells, mRNA was amplified and cDNA by SMARTer Ultra Low Input RNA for Illumina Kit, which was qualified and reversely transcribed to cDNA by Qubit and Agilent Bioanalyzer 2100 electrophoresis.
After fragmentation of cDNA (300 bp) by ultrasound, sequencing libraries (end repair, addition of poly(A), and ligation of  sequencing connectors) were built using the Ovation Ultralow Library System V2. After that, the constructed libraries were sequenced using Illumina HiseqXten.

value: brain

value: neurons


title: BC1.Input

value: human breast cancer cell

value: non-immunoprecipated input


title: Senile5

description: 10x Genomics


title: DNP2_1_T2

description: T2 of kinetics   biol rep 1

value: cells

value: 2mM DNP


title: dKO_rep1


title: DNP2_2_T1

description: T1 of kinetics  biol rep 2


title: Infancy4

description: 10x Genomics

value: Retina


title: DNP2_1_T1

description: T1 of kinetics   biol rep 1


title: Senile2

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Tree shrew genome sequence (https://useast.ensembl.org/Tupaia_belangeri/Info/Index?db=core)
Supplementary files format and content: Tab-separated values files and matrix files

value: Senile


title: DCreg 1010

description: Whole Genome Bisulfite Sequencing

value: Leukapheresis products

value: DCreg


title: DNP2_2_T25

description: T 25 sec of kinetics  biol rep 2


title: YY1

value: YY1 antibody


title: Ctrl_rep3

value: Muscle

value: Ctrl


title: Ctrl_rep1

value: MuSC


title: DNP2_1_T25

description: T 25 sec of kinetics  biol rep 1


title: DNP2_1_T0

description: T0 of kinetics  biol rep 1


title: DCreg 1006

description: Whole Genome Bisulfite Sequencing


title: Mature2

description: 10x Genomics

value: Mature


title: Senile1

description: 10x Genomics


title: DCreg 1016

description: Whole Genome Bisulfite Sequencing


title: DNP07_2_T7

description: T7 of kinetics  biol rep 2

value: 0.7mM DNP


title: mDC 1011

description: Whole Genome Bisulfite Sequencing

value: mDC


title: Mature1

description: 10x Genomics


title: DNP07_2_T4

description: T4 of kinetics  biol rep 2


title: DCreg 1011

description: Whole Genome Bisulfite Sequencing


title: Infancy2

description: 10x Genomics

value: Infancy


title: DCreg 1009

description: Whole Genome Bisulfite Sequencing


title: mRNA CRC-5

first: Hanchen

last: Xu

address: No.725, South Wanping Rd

institute: Institute of Digestive, Longhua Hospital, Shanghai University of Traditional Chinese Medicine

data_processing:
Bioinformatics data analysis was provided by NewCore BioTech. (Shanghai, China). Briefly, fastp software (v0.20.0) was used to trim adaptor and remove low quality reads to get high quality clean reads. hisat2 software (v2.7.9a) was used to align the high-quality clean reads to the reference genome (hg19). cufflinks software (v2.2.4) was used to calculate the FPKM values of each gene.
Assembly: hg19
Supplementary files format and content: Excel format files with FPKM

source_name: Colorectal cancer

extract_protocol:
mRNA high throughput sequencing was performed by NewCore Biotech. (Shanghai, China). Briefly, total RNA was extracted using Trizol Reagent (ThermoFisher, 15596026).  The mRNAs were purified using a NEBNext Poly(A) mRNA Magnetic Isolation Module Kit (NEB, E7490) according to the user manual.
mRNA libraries were constructed by using Illumina TrueSeq mRNA sample preparation kit (Cat. No. RS-122-2101) according to the manufacturer's instructions. Library sequencing was performed on an Illumina NovaSeq 6000 instrument with paired end mode.

value: Colorectal cancer


title: E21-5

city: Rehovot

first: Jonathan

last: Dayan

address: Herzel 229

country: Israel

institute: Faculty of Agriculture Hebrew University of Jerusalem

description: Library name: 353_E21-5

data_processing:
Poly-A/T stretches and Illumina adapters were trimmed from the reads using cut-adapt, resulting reads shorter than 30bp were discarded. Remaining reads were mapped onto 3’ UTR regions (1000 bases) of the Gallus genome according to Refseq annotations, using STAR 2.7.10a  with End-to-end option and out Filter Mismatch Nover Lmax was set to 0.05. Deduplication was carried out by flagging all reads that were mapped to the same gene and had the same UMI. Counts for each gene were quantified using HTSeq-count 2.0.2 , using the gene transfer format (GTF) above. UMI counts were corrected for saturation by considering the expected number of unique elements when sampling without replacement. Differentially expressed genes were identified using DESeq2 with the beta Prior, cooks Cutoff and independent Filtering parameters set to False. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. Pipeline was run using snake-make.
Assembly: Gallus genome
Supplementary files format and content: CSV, name: DEoutput_all, raw counts and DE comparisons
Library strategy: MARS-Seq

organism: Gallus gallus

source_name: Broiler Chicken

extract_protocol:
Total RNA was isolated from 100 mg of frozen muscle tissue using  TRI-Reagent (Sigma-Aldrich, St. Louis, MO) according to the manufacturer’s protocol
Sequencing Libraries were prepared using LIB_PREP_PROTOCOL. READ_TYPE, 75bp single reads were sequenced on NUM_LANES lane(s) of an Illumina ILLUMINA_INSTRUMENT. The output was ~16 million reads per sample.

value: Complexus Muscle

value: Embryonic day 21

tag: batch

value: single


title: E21-3

description: Library name: 351_E21-3


title: E21-6

description: Library name: 354_E21-6


title: E21-1

description: Library name: 349_E21-1


title: Ctrl_rep2


title: Infancy1

description: 10x Genomics


title: mRNA CRC-4


title: DNP07_2_T25

description: T 25 sec of kinetics  biol rep 2

value: cells


title: E20-5

description: Library name: 341_E20-5

value: Embryonic day 20


title: DCreg 1007

description: Whole Genome Bisulfite Sequencing