title: Mettl3 cKO LSK GFP rep1

city: New York

first: Michael

middle: G.

last: Kharas

state: NY

address: 417 East 68th Street

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger pipeline v7.1.0 with default parameters
Reads were aligned to a custom-built reference that included the cDNA sequence from the Son Overexpression construct in addition to the mm10 reference.
Assembly: mm10
Supplementary files format and content: Tab-separated barcode, features and matrix files

source_name: primary cells

growth_protocol: WT and mettl3 cKO mice were used to harvest bone marrow. LSK (Lin-cKit+Sca1+) cells were FACS sorted and placed in SFEM media supplemented with cytokines (50 ng/ml SCF, 10 ng/ml IL-3, and 10 ng/ml IL-6, 10ng/ml TPO and 20 ng/ml FLT3L)

extract_protocol:
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.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, LSKs 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).

treatment_protocol:
Cells were infected with SON overexpressing lentivirus or empty vector. 48hr post infection,  GFP+ cells were sorted.
Sorted cells were resuspended in PBS+0.04% BSA at a concentration of 700 cells/ul. The Viability of cells were above 80%, cell doublets below 5% and no red blood cells. Target cell number is 5000.

value: mouse bone marrow

value: primary cells

tag: cell linage

value: hematopoietic stem and progenitor cell

value: Mettl3 cKO

value: empty vector


title: Jurkat cells, DMSO, 24 hours, replicate 3

status: Public on Dec 07 2023

type: SRA

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

country: USA

institute: Broad Institute

library_source: transcriptomic

data_processing:
RNA-Seq data analysis was performed in alignment with the ENCODE Consortium standards (https://www.encodeproject.org/chip-seq/).
Quality control tests for unmapped reads were performed based on the FastQC v.0.11.9 software (Babraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and summarized with multiQC v1.9.30 The human reads were mapped to hg19/gencode v19 genome  using STAR v2.7.2b31  with standard parameters  --outSAMtype BAM SortedByCoordinate --outSAMunmapped None      --outSAMattributes NH HI NM MD AS XS --outReadsUnmapped Fastx --outSAMstrandField intronMotif --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBan IndelSoftclipSingleend. Quality control for the mapped reads and for replicate reproducibility were performed using SARTools v1.7.3.32
Gene level reads were summarized by counting the reads that overlapped the hg19/gencode v19 gene exons by using the featureCounts v1.6.3 method implemented in the Subread v2.0.0 package (http://subread.sourceforge.net).33 Gene counts were normalized and used to quantify the differential genes between the experimental and control conditions using DESeq2 v1.32.0.34
Gene expression was estimated based on the log2(TPM+1) scores for normalized reads.35 The expressed genes were identified as the genes with  maximum log2(TPM+1)  expression ≥ 1 across all conditions. The gene differentiability was assessed with DESeq2 based on the robust shrunken log2 fold change scores  and  the approximate posterior estimation for GLM coefficients (apeglm v1.6)  method for effect size.34 The cutoffs for gene differentiability were |fold change expression| ≥ 1.5 and adj P-value ≤ 0.10. Heatmaps for the visualization of transcriptional changes induced by treatment were created by using the Morpheus software platform (https://software.broadinstitute.org/morpheus/).
Assembly: hg19 (gencode v19)
Supplementary files format and content: tab-delimited text files include counts and log2(TPM+1) values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Jurkat

extract_protocol:
Total RNA was harvested from 5x106 Jurkat cells either treated with 1uM Brequinar or with DMSO, over 8 hours and 24 hours, using an RNeasy-Plus Mini Kit (Qiagen).
Following RNA isolation, samples were sent to Novogene for library preparation and sequencing on Illumina NovaSeq 6000.

tag: cell line

value: Jurkat

tag: cell type

value: immortalized line of T lymphocyte cells

tag: genotype

value: WT

tag: treatment

value: DMSO

tag: time

value: 24 hours


title: LB sample 2 female

city: NEW HAVEN

first: Arie

last: Kaffman

state: CT

address: 300 GEORGE ST. SUITE 901, SUITE 901

institute: YALE UNIVERSITY

data_processing:
Reads were trimmed for quality using customized scripts with a minimum accepted length of 45 bases.  The trimmed reads were aligned to the mm10 reference genome using gencode annotation (Frankish, A., et al. Nucleic Acids Res, 2019) and the HISAT2 alignment software (Kim, D et al. Nat Methods, 2015).
The StringTie software (Kim, D et al. Nat Methods, 2015) was used to determine transcript abundance estimation (TPM).
Low expressing gene (TPM < 3 in all three groups) were removed and the remaining 13,245 genes were analyzed using DESeq2 script in R (Love et al., 2014) to identify genes that are differentially expressed between the three groups.
Genome_build: mm10
Supplementary_files_format_and_content: TPM values for all samples, Summary of differentially regulate genes of 3 comparisons (CTL-LB, CTL-UPS, LB-UPS)

organism: Mus musculus

source_name: P17, left hippocampus

extract_protocol:
RNA was isolated from the left hippocampus using the AllPrepâ DNA/RNA/Protein Mini Kit (QIAGEN, Cat# Cat# 80004) per manufacturer’s instructions and stored at -80°C.
Total RNA samples were quantified and checked for quality (all RINs>9.0) using the 2100 Bioanalyzer on a RNA 6000 Nano Assay (Agilent Technologies, Inc). Samples concentrations were normalized to 500ng total RNA and libraries were constructed using the KAPA mRNA HyperPrep Kit for Illumina Platforms (KAPA Biosystems) according to the manufacture’s protocol using 9 PCR cycles for library amplification. cDNA libraries were validated using the Bioanalyzer 2100 on a High Sensitivity DNA assay. Quantification was done using the KAPA Library Quantification Kit for Illumina Platforms on a Roche Lightcycler 480.  Sequencing was done on an Illumina NovaSeq 6000 using the S4 XP workflow 2x100 with each library using 1.25% of the S4 lane.

treatment_protocol: Pups were exposed to either control, LB or UPS conditions as described in see Johnson FK. et al. Translational psychiatry (2018). At postnatal day 17 (P17) pups anesthetized with chloral hydrate and immediately processed to collect the hippocampi. Dissected hippocampi were snap frozen in liquid nitrogen and stored at -80C.

tag: strain

value: Balb/cByj

tag: tissue

value: left hippocampus

tag: early life stress

value: LB

tag: Sex

value: Female

tag: age


title: WT LSK SON rep1

department: Molecular Pharmacology Program

molecule: polyA RNA

value: SON overexpressing


title: Morex8DAP, H3K9ac, rep2

city: Olomouc

first: Šimon

last: Pavlů

address: Šlechtitelů 31

department: Centre of Plant Structural and Functional Genomics

country: Czech Republic

institute: Institute of Experimental Botany of the Czech Academy of Sciences

library_source: genomic

data_processing:
Reads from the ChIP-seq pipeline went through qualitative trimming by Trim Galore (v. 0.6.2).
Mapping to the MorexV3 reference genome was performed using the Bowtie 2 (v. 2.4.2).
Duplicated reads were then removed using Picard tools (v. 2.9.0).
Peaks were called using the MACS2 software.
Assembly: MorexV3
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Hordeum vulgare

source_name: 8DAP embryo

extract_protocol: NEBNextUltraII library preparation kit

value: embryo

tag: developmental stage

value: morex

tag: chip antibody


title: LB sample 1 male

value: Male


title: Morex8DAP, H3K9ac, rep1


title: WT LSK GFP rep1

value: mouse bone marrow

value: primary cells


title: LB sample 1 female


title: Jurkat cells, DMSO, 24 hours, replicate 2


title: Jurkat cells, DMSO, 24 hours, replicate 1


title: Morex8DAP, H3K4me3, rep2


title: Control, sample 8 female

value: Control


title: Mettl3 cKO LSK SON rep1

value: hematopoietic stem and progenitor cell

value: Mettl3 cKO


title: Jurkat cells, 1 uM Brequinar, 8 hours, replicate 3

value: Jurkat

value: immortalized line of T lymphocyte cells

value: 1 uM Brequinar

value: 8 hours


title: Control, sample 7 male

value: Balb/cByj


title: embryo delRGG replicate1

city: Bern

first: Shohreh

last: Teimuri

address: Baltzerstrasse

country: Switzerland

institute: Bern University

description:
Total RNA_counts.txt
D7

data_processing:
The quality of the sequencing runs was assessed using the Illumina Sequencing Analysis Viewer (Illumina version 2.4.7), and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20.
The quality and quantity of reads generated from RNA-seq were evaluated. Most of the reads were from mature transcripts without introns, but we mapped them to the reference genome that includes introns using an alignment tool like Hisat2 that can handle large gaps.
The number of reads mapping to each gene was counted using featureCounts tool, which requires information about the location of each gene in the genome. This resulted in a table of read counts for each sample and gene.
To test for differential expression between two experimental groups containing three biological replicates each, we used the DESeq2 tool.
Supplementary files format and content: tab-delimited text files include count reads for each gene for each sample

organism: Drosophila melanogaster

source_name: Embryo

extract_protocol:
RNA extraction was done according to the Trizol protocol. The purified total RNA was assessed for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit RNA BR or HS Assay Kit (Thermo Fisher Scientific, Q10211 or Q32855, respectively) and an Agilent Advanced Analytical Fragment Analyzer System using a Fragment Analyzer RNA Kit (Agilent, DNF-471), respectively.
Sequencing libraries were made using a CORALL Total RNA-Seq Library Prep Kit with UDI 12nt Set A1 (Lexogen, 117.96) according to Lexogen's guidelines. The libraries were paired-end sequenced using either shared Illumina NovaSeq 6000 SP, S1, or S2 Reagent Kits (200 cycles; Illumina, 200240719, 2002831, or 20028315) on an Illumina NovaSeq 6000 instrument.

value: Embryo


title: embryo delRGG replicate3

description:
Total RNA_counts.txt
D9


title: Morex8DAP, H3K4me3, rep1


title: Jurkat cells, 1 uM Brequinar, 8 hours, replicate 2

value: WT


title: Control, sample 7 female

value: left hippocampus

value: Female


title: Morex8DAP, H3K27me3, rep1

value: embryo


title: Jurkat cells, 1 uM Brequinar, 8 hours, replicate 1


title: embryo Y332F replicate3

description:
Total RNA_counts.txt
D6


title: Morex24DAP, Input, rep1A

source_name: 24DAP embryo

value: morex


title: Control, sample 6 male

value: Male


title: Jurkat cells, DMSO, 8 hours, replicate 3

value: DMSO


title: Morex24DAP, Input, rep2


title: embryo Y332F replicate 1

description:
Total RNA_counts.txt
D4


title: Jurkat cells, DMSO, 8 hours, replicate 2


title: embryo Y332F replicate2

description:
Total RNA_counts.txt
D5


title: Control, sample 6 female


title: Morex24DAP, Input, rep1


title: Jurkat cells, DMSO, 8 hours, replicate 1


title: Morex24DAP, H3K27me3, rep2


title: embryo delRGG replicate2

description:
Total RNA_counts.txt
D8


title: Control, sample 5 female


title: embryo Top3b26 replicate3

description:
Total RNA_counts.txt
D3


title: embryo Top3b26 replicate 2

description:
Total RNA_counts.txt
D2


title: p10 PP C6 2

city: Dresden

first: Anthony

last: Gavalas

address: Fetscherstr. 105

country: Germany

institute: TU Dresden

data_processing:
bcl2fastq2:  2.20.0
alignment: Fragments were aligned to the human reference genome hg38 with support of the Ensembl 104 splice sites using the aligner gsnap (v2020-12-16) (gsnap.avx2 --db=hg38 --gunzip --format=sam --nthreads=12 -B 5 --novelsplicing=1 --npaths=1 --max-mismatches=0.6 --add-paired-nomappers --use-splicing=EnsemblGene-104.ss.hg38.iit)
gene counts: Fragments per gene and sample were obtained based on the overlap of the uniquely mapped fragments with the same Ensembl annotation using featureCounts (v2.0.1) (featureCounts -a EnsemblGene-104.hg38.TR.gtf -s 2 -p -Q 1 -T 8)
Assembly: hg38
Supplementary files format and content: This is a tab separated file. Each row is a gene with shows the number of counts assigned to samples. Each column is a sample and several columns provide gene information (e.g. gene ID, chromosome, start, end, strand, biotype)

source_name: H1 (W01) hES cell line

extract_protocol:
Qiagen RNeasy
mRNA was isolated from 400 ng total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to the manufacturer’s instructions. Samples were then directly subjected to the workflow for strand-specific RNA-Seq library preparation (Ultra II Directional RNA Library Prep, NEB). For ligation custom adaptors were used (Adaptor-Oligo 1: 5'-ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT-3', Adaptor-Oligo 2: 5'-P-GAT CGG AAG AGC ACA CGT CTG AAC TCC AGT CAC-3'). After ligation, adapters were depleted by an XP bead purification (Beckman Coulter). Unique dual indexing was done during the following PCR enrichment (12 cycles) using custom amplification primers carrying the same sequence for i7 and i5 index (Primer 1: AAT GAT ACG GCG ACC ACC GAG ATC TAC AC NNNNNNNN ACA TCT TTC CCT ACA CGA CGC TCT TCC GAT CT, Primer 2: CAA GCA GAA GAC GGC ATA CGA GAT NNNNNNNN GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T). After two more XP bead purifications (1:0.9), libraries were quantified using the Fragment Analyzer (Agilent). For Illumina flowcell production, samples were equimolarly pooled and sequenced on Illumina NovaSeq 6000 in 2 x 100 bp paired-end mode, resulting in 40 - 60 million fragments per sample.

treatment_protocol: as described in publication

value: H1 (W01) hES cell line

value: pancreas progenitors

value: wild type

tag: passage


title: Morex24DAP, H3K27me3, rep1


title: Morex24DAP, Input, rep2A


title: Control, sample 4 male

value: Control


title: embryo Top3b26 replicate 1

description:
Total RNA_counts.txt
D1


title: p10 PP C6 1


title: Control, sample 4 female


title: Morex24DAP, H3K9ac, rep2A


title: embryo wild-type replicate 3

description:
Total RNA_counts.txt
C11

value: wild-type


title: p5 PP C6 4


title: p5 PP C6 3


title: Control, sample 3 male


title: embryo wild-type replicate 2

description:
Total RNA_counts.txt
C10


title: Morex24DAP, H3K4me3, rep2


title: Control, sample 3 female


title: embryo wild-type replicate 1

description:
Total RNA_counts.txt
C9


title: p5 PP C6 2


title: Control, sample 9 female


title: Top3b::eGFP-s6

description:
RIPseq_normcounts.txt
2


title: Morex4DAG, Input, K9ac

source_name: 4DAG embryo


title: p5 PP C6 1


title: Control, sample 5 male


title: Control, sample 2 female


title: Morex4DAG, Input, rep2


title: Control, sample 1 male


title: p0 PP C6 2


title: Top3b::eGFP-s4

description:
RIPseq_normcounts.txt
IP_7


title: p0 PP C6 3


title: Top3b::eGFP-s5

description:
RIPseq_normcounts.txt
IP_8


title: Control, sample 1 female


title: Top3b::Y332F::eGFP-s3

description:
RIPseq_normcounts.txt
1


title: Morex4DAG, H3K27me3, rep2


title: Top3b::Y332F::eGFP-s2

description:
RIPseq_normcounts.txt
IP_5


title: p0 PP C6 1


title: Morex4DAG, Input, rep1


title: Morex24DAP, H3K9ac, rep1A


title: SupT1/Rec_rep3

city: Charlottesville

first: Lou

last: Hammarskjold

state: VA

address: 1340 Jefferson Park Avenue

institute: University of Virginia

data_processing:
Raw image files were transformed to sequence reads by CASAVA base calling.
Sequenced reads were trimmed for adapater sequences, then mapped to hg19 using STAR.
Differential expression was performed by DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: count data and differential expression data

source_name: SupT1_HERV-K Rec

growth_protocol: SupT1 cells were routinely passaged 2-3 times per week. Twenty-four hours prior to transductions, SupT1 cells were split 1:4.

extract_protocol:
Cytoplasmic RNA was extracted using phenol/chlorform prior to ethanol precipitation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SupT1 cells ( 10^6 cells) were transduced with each virus stock using an moi of 2.

value: T-lymphoblast cell line

value: HERV-K Rec

tag: molecule subtype

value: cytoplasmic RNA


title: Top3b::Y332F::eGFP-s1

description:
RIPseq_normcounts.txt
IP_4


title: Morex4DAG, H3K27me3, rep1


title: Morex4DAG, H3K9ac, rep2


title: Morex24DAP, H3K4me3, rep1


title: SupT1/Rec_rep2


title: treated and untreated samples

city: Munich

first: Sabine

last: Steffens

address: Pettenkoferstrasse 9b

department: Clinical Pathobiochemistry

institute: Institute for Cardiovascular Prevention-LMU Klinikum

data_processing:
The reads were demultiplexed using deML and then filtered.
The reads were mapped to the mouse genome (mm10, GRCm38), and counted using zUMIs (version 2.5.5) with STAR.
Differential gene expression analysis was performed using DESeq2.
The characterization of enriched the molecular functions or pathways of differentially expressed genes (DEGs) was performed by using Gene Ontology in clusterProfiler.
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: Bone marrow

extract_protocol:
BMDM from 6 male and 6 female donor mice were stimulated with ACEA for a duration of 24 hours. The RNeasy Mini kit (Qiagen) was utilized to extract total RNA from BMDMs, following the manufacturer's provided guidelines.
Libraries were then constructed with the NEB Next Ultra II FS kit (E6177S, NEB) using the prime-seq specifications

value: Bone marrow

value: BMDM

value: ApoE-/-

value: treated and untreated


title: Top3b::eGFP-s3

description:
RIPseq_normcounts.txt
IP6

value: Embryo


title: SupT1/Rec_rep1


title: Rumen epithelial,42-day-old,milk and concentrate starter introduction

city: Nanjing

first: Zhang

last: Kai

country: China

institute: Njau

library_source: transcriptomic single cell

data_processing:
The density and viability of the rumen cells were assessed and met the necessary criteria for reliable scRNA-seq experiments. Cellular suspensions were loaded onto a 10×Genomics GemCode Single-cell instrument that generated single-cell Gel Bead-In-EMlusion (GEMs) isolate single cells.
Libraries were then created and sequenced using the 10×Cell Ranger software (version 3.1). The sequencing procedure was conducted using the Illumina HiseqTM 2500/4000 platform by Gene Denovo Biotechnology Co., Ltd (Guangzhou, China).
Assembly: Oar v3.1 (GCA_000298735.1)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Ovis aries

source_name: Rumen epithelial

extract_protocol:
The rumen tissues were meticulously rinsed with D-Hanks solution until thoroughly clean, followed by precise cutting into pieces on ice. Subsequently, 10 ml of preheated 0.25% Trypsin-EDTA (Genview, USA) was introduced into a 37℃ water bath for digestion. During the digestion process, the trypsin-EDTA solution in the conical flask was adjusted every 6 minutes. Filtration was carried out using a 40μm cell mesh screen, and the digested solution was collected in a 50 mL centrifuge tube containing 10% FBS (GBICO, New York, USA). This filtration and digestion process was repeated four times. The filtered digestion solution was centrifuged at 1500 r/min for 5 minutes to separate the rumen cells. These cells were subsequently suspended in cold PBS to remove any residual trypsin and then subjected to the next centrifugation step at 1200 r/min for a duration of 5 to 8 minutes. After centrifugation, the rumen cells were cleaned again and resuspended in cold PBS to achieve the desired cell density and viability required for subsequent scRNA-seq analysis. The density and viability of the rumen cells were assessed and met the necessary criteria for reliable scRNA-seq experiments. Cellular suspensions were loaded onto a 10×Genomics GemCode Single-cell instrument that generated single-cell Gel Bead-In-EMlusion (GEMs) isolate single cells. Libraries were then created and sequenced using the 10×Cell Ranger software (version 3.1). The sequencing procedure was conducted using the Illumina HiseqTM 2500/4000 platform by Gene Denovo Biotechnology Co., Ltd (Guangzhou, China).
scRNA

value: Rumen epithelial

value: Hu sheep


title: Rumen epithelial,42-day-old,milk and alfalfa hay introduction


title: Top3b::eGFP-s2

description:
RIPseq_normcounts.txt
IP_2


title: Morex4DAG, H3K9ac, rep1

value: embryo

value: morex


title: SupT1/TatRev_rep3

source_name: SupT1_HIV TatRev

value: HIV TatRev


title: Rumen epithelial,42-day-old,milk only


title: Morex4DAG, H3K4me3, rep2


title: SupT1/TatRev_rep2


title: SRSF2 PAR-CLIP Seq in siNSUN2 HeLa cell rep2

city: anderlecht

first: Haili

last: Ma

address: route de lennik 808

country: Belgium

institute: ULB

data_processing:
The raw sequencing data were first analyzed using FastQC (v0.11.5, default parameters). Subsequently, reads were stripped of adaptor sequences (cutadapt v1.9.1) with parameters cutadapt -a AGATCGGAAGAG and cutadapt -m 15 -u 4 -a AAAAAAAAAA (only for libraries prepared by the SMARTer smRNA-seq kit), and then low-quality bases were removed with Trimmomatic (v0.33, parameters: LEADING:20, TRAILING:20, SLIDINGWINDOW:4:15, MINLEN:15). Processed reads more than 15 nt long were defined as clean reads. The resulting fastq data was again analyzed using FastQC to ensure no further processing was needed.
The remaining reads were mapped on hg19 genome using Bowtie (v1.1.2, parameters: -v 2 -m 10 --best --strata).
PARalyzer (v1.5) software was used to define the cluster of SRSF2 binding sites with the default parameters.
Assembly: hg19
Supplementary files format and content: csv file of SRSF2 binding clusters

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1% penicillin and streptomycin (Pen Strep, Gibco). K562 cells were cultured in IMDM (Gibco) supplemented with 10% FBS and 1% Pen Strep. For RNA interference maintenance, K562 cells were kept under selection with 1.5μg/ml puromycin. All cells were cultured at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
The cells were lysed, digested with 1 U/μl RNase T1 at 22 °C for 8 min, and immunoprecipitated with anti-Flag M2 magnetic beads (Sigma). The protein-RNA-bead complex was digested with 10 U/ μl RNase T1 again at 22°C for 8 min and incubated with 0.5 U/μl Alkaline Phosphatase Calf Intestinal (CIP, NEB) for 10 min at 37°C. The beads were washed and then incubated with 0.5 U/μl T4 Polynucleotide Kinase (NEB) for 15 min at 37°C. After washing, one-sixth of the beads were resuspended in LDS loading buffer (Invitrogen), boiled at 95°C for 10 min, and the mixture was resolved by SDS-PAGE to detect the immunoprecipitation efficiency. One-sixth of the beads were labeled with biotin using the RNA 3′ End Biotinylation kit (Thermo), following the manufacturer's instructions for PAR-CLIP-biotin chemiluminescent nucleic acid detection. The rest of the beads were also boiled and the mixture electrophoresed through a NuPAGE Bis-Tris protein gel. Parts containing target protein-RNA complexes were cut from the gel according to the protein-RNA-biotin signal. The protein-bound RNA in the gel pieces was recovered by D-Tube™ Dialyzer Midi (Merck-Millipore), digested with proteinase K (Roche), and extracted with phenol-chloroform.
Library preparation was performed using the Takara SMARTer smRNA-seq kit (PAR-CLIP in HeLa cells) or the NEBNext® Multiplex Small RNA Library Prep kit (PAR-CLIP in K562 cells) for Illumina, following the manufacturer's instructions.

treatment_protocol:
HeLa cells were co-transfected by electroporation with siRNA (control or siNSUN2 siRNA) and the pCMV-Flag-SRSF2 plasmid. Control and NSUN2-knockdown K562 cells were co-transfected with the pCMV-Flag-SRSF2 and pCMV-Myc-SRSF2 plasmids. SRSF2P95H mutant K562 cells were co-transfected with the pCMV-Flag-SRSF2P95H and pCMV-Myc-SRSF2P95H plasmids.
Transfected cells were cultured in a medium supplemented with 200 μM 4-thiouridine (4-SU) (Sigma) for 14 h and then irradiated once with 400 mJ/cm2 at 365 nm before harvest.

value: HeLa

value: human cervical cancer cell line

tag: replicates

tag: srsf2 genotype

value: Wildtype

tag: rna interference


title: Top3b::eGFP-s1

description:
RIPseq_normcounts.txt
IP_1


title: SupT1/TatRev_rep1

tag: cell line


title: Morex4DAG, H3K4me3, rep1


title: 8DAP embryo_B

data_processing:
CAGE tags were mapped to the morexV3 genome using BWA (version 0.7.17).
Unmapped reads were mapped by HISAT2 (version 2.0.5)
Regions with 90% overlap between replicates were extracted by BEDtools (version 2.12.0).
Assembly: MorexV3
Supplementary files format and content: bigWig

extract_protocol:
4DAG seedlings were germinated on wet tissue paper in the incubator for 4 days before harvesting and removing remnants of seed coat and endosperm. The 8 and 24DAG embryos were staged according to their time of fertilization, size and phenotype and dissected to isolate total RNA by Monarch® Total RNA Miniprep Kit (NEB cat#T2010S).
DNAFORM proprietary protocol


title: SupT1/Tat_rep3

source_name: SupT1_HIV Tat

tag: cell type

value: HIV Tat


title: SRSF2 PAR-CLIP Seq in siNSUN2 HeLa cell rep1


title: SRSF2 PAR-CLIP Seq in siCtrl HeLa cell rep2

value: siRNA-Ctrl


title: SupT1/Tat_rep2

value: T-lymphoblast cell line


title: 8DAP embryo_A


title: 24DAP embryo_B


title: SRSF2 PAR-CLIP Seq in siCtrl HeLa cell rep1


title: SupT1/Tat_rep1

value: cytoplasmic RNA


title: SupT1/Rev_rep3

source_name: SupT1_HIV Rev

value: HIV Rev


title: 4DAG embryo_B


title: SupT1/Rev_rep2


title: HCT116 cells, WT, Day 7, 400% biol rep 3, small-RNA-seq

city: DALLAS

first: David

middle: Reid

last: Corey

state: TX

address: 6001 Forest Park Rd

department: Pharmacology

institute: UT Southwestern Medical Center

data_processing:
Followed nf-core/smrnaseq workflow with Illumina mirTrace protocol and minimum trimmed length of 17 nt.
Assembly: /project/MRL/MRL_Core/shared/analysis_MRL/references/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa
Supplementary files format and content: Alignment files (bam)

source_name: Large intestine; Colon

growth_protocol: HCT116, colorectal cancer, cells were maintained in McCoy's 5A Media supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Trizol whole cell RNA extraction
Illumina TruSeq Small RNA library preparation kits with 1ug of total RNA
Illumina small-RNA-Seq with 3'adapter TGGAATTCTCGGGTGCCAAGG

value: Large intestine; Colon

value: epithelial

tag: genotype

value: WT

tag: disease state

value: Carcinoma; Colorectal


title: 4DAG embryo_A


title: 20M-3

type: RNA

city: Sendai

first: Kazusa

last: Miyahara

address: Seiryo-machi 2-1

country: Japan

institute: Tohoku University

description: Gene expression data from sperm of mouse at 20 months old

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on GeneChip™ cartridge array.

scan_protocol: GeneChips were scanned using GeneChip™ Scanner 3000 System.

data_processing: Transcriptome Analysis Console (TAC) was used for data processing.

label: biotin

source_name: sperm from mouse at 20 months old

label_protocol: cDNA is fragmented by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1). Then, the fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using a proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: Mice were purchased from a breeder and were raised to the specific months old.

extract_protocol: miRNAs were extracted by miNeasy Mini Kit (217004, QIAGEN).

treatment_protocol: Sperms were collected by retrograde perfusion and centrifuged on a 27% Percoll solution (2005-001 or 2001-017, NK system) into pullet. Then, the pellet was resuspended in PBS and recentrifuged (400×g for 2 min) to remove excess Percoll.

value: sperm


title: HCT116 cells, WT, Day 7, 400% biol rep 2, small-RNA-seq


title: SupT1/EV_rep3

source_name: SupT1_empty vector

tag: treatment

value: empty vector


title: HCT116 cells, WT, Day 7, 400%  biol rep 1, small-RNA-seq


title: 20M-1

tag: strain


title: SupT1/Rev_rep1


title: 20M-2

tag: tissue


title: 12M-3

description: Gene expression data from sperm of mouse at 12 months old

source_name: sperm from mouse at 12 months old


title: SupT1/EV_rep2


title: 3M-7

description: Gene expression data from sperm of mouse at 3 months old

source_name: sperm from mouse at 3 months old


title: 12M-5


title: 3M-4


title: 12M-1


title: S.islandicus.REY15A.E234.RNA-seq.replicate2

city: London

first: Finn

last: Werner

address: Gower Street

department: Institute of Structural and Molecular Biology

country: United Kingdom

institute: University College London

data_processing:
5’- and 3’- end adaptor and primer sequences in the reads were removed using cutadapt 4.1 with settings -e 5  -m 25  -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT where NNNNNN stands for barcode of the indexing primer.
Reads were aligned to theS. islandicus REY15A genome (bowtie 1.0.0 with settings --allow-contain -y  -v 2 -m 1 --strata --best) and the resulting bam files were filtered for proper read pairs using samtools
DNA fragment coverage was calculated using BEDTools v2.30.0 genomecov scaled to count per million fragments (read pairs). Bedgraph output was converted into bigwig file format.
For differential expression analysis, fragments overlapping with coding genes or CRISPR arrays were counted using featureCounts v2.0.6 with settings -s 1  -d 25 -p --countReadPairs -B -t repeat_region,CDS -g ID.
Count data were imported into R and differentially expressed genes and CRISPR arrays were called by Deseq2 v1.40.2 with a padj 0.01 cut-off
Assembly: NC_017276.1
Supplementary files format and content: Big wig file with fragment coverage per strand

organism: Saccharolobus islandicus REY15A

source_name: Sulfolobus islandicus

growth_protocol: Strains were grown in Brock medium supplemented with 0.2% sucrose, 0.2% tryptone, and 20 µg/ml uracil at 75 °C in Erlenmeyer shake flasks at 150 rpm

extract_protocol:
Cell cultures were rapidly mixed with 2 volumes  pre-cooled RNAprotect Bacteria Reagent (Qiagen) placed in an ice bath. Cells were harvested by centrifugation (5 min at 4000 x g at 4 ºC). Pellets were immediately subjected to RNA isolation using the mirVana miRNA isolation kit (Ambion) following the protocol for total RNA.
Ribosomal RNA was removed using the Pan-Archaea RNA-seq riboPool kit (siTOOLS biotech) and the RNA was subsequentially fragmented using Ambion RNA Fragmentation Reagents (Thermo Fisher) according to manufacturer's protocol. Fragments in the size range of 17-200 nt were subsequently purified using RNA Clean & Concentrator-5 kit (Zymo Research). Purified RNA fragments were treated to remove 3´ end blocking groups (in particular 2’,3’-cyclic phosphate from crRNAs) using 10 U T4 polynucleotide kinase (NEB) for 1h 30 min at 37°C in  70 mM Tris/HCl pH 6.5, 10 mM MgCl2, 1 mM DTT, 20 U SUPERaseIn RNase Inhibitor (Ambion) in 20 µl reactions. To phosphorylate the 5´-ends, additional 10 U polynucleotide kinase (NEB) in presence of 1 mM ATP, 10 U SUPERaseIn RNase Inhibitor (Ambion), 1x T4 PNK buffer (NEB) were added to the reactions in a total reaction volume of 50 μl and the reactions were incubated for 40 min at 37°C. Finally, the treated RNA fragments were ethanol-precipitated, resuspended in 6 μl of H2O and converted to Illumina sequencing libraries using NEBNext Small RNA Library Prep Set for Illumina kit (NEB) with 12 cycles of PCR-amplification.

value: Sulfolobus islandicus

value: E234 (pyrEF, lacS)


title: S.islandicus.REY15A.cbp1.RNA-seq.replicate1

value: cbp1, pyrEF, lacS


title: S.islandicus.REY15A.cbp1.RNA-seq.replicate2


title: 24DAP embryo_A

value: embryo

value: morex


title: HCT116 cells, WT, Day 5, 250%  biol rep 1, small-RNA-seq


title: HCT116 cells, WT, Day 5, 250% biol rep 2, small-RNA-seq


title: SupT1/EV_rep1


title: KI3

city: Shanghai

first: Zhiyin

last: Zhang

state: Huangpu

address: Xu Jia Hui Road.

department: Department of Endocrinology and Metabolism, Ruijin Hospital

institute: Shanghai Jiao Tong University

description: R20030046-NBC20200721-A-UIRX3-B-SVF-K13_combined

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: mm10
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: U-IRX3ov_Induced brown adipocyte

growth_protocol: The stromal vascular fractions (SVFs) were isolated from the BAT and iWAT of five-week-old U-IRX3ov and control mice.In brief, the fat pads were isolated, cut into pieces, and digested with type II collagenase (Sigma) at 37 °C for 30 min followed by quenching with DMEM/F12 supplemented with 10% FBS. The suspended samples were filtered using a 40-μm strainer (BD, USA) and then plated on culture dishes. The SVFs were grown to 100% confluence in DMEM/F12 supplemented with 10% FBS (plus 1% penicillin/streptomycin and 1 mM L-glutamine)

extract_protocol:
Total RNA was extracted from cultured cells or frozen adipose tissue using the Eastep Super Total RNA Extraction Kit (Promega (Beijing) Biotech Co., China). The absorbance ratio at 260/280 nm and the RNA concentration of each sample were detected using a NanoDrop ND2000 spectrophotometer (Thermo Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The primary preadipocytes were differentiated into brown/beige adipocytes in a cocktail containing 5 μg/mL insulin (Eli Lilly, USA), 1 μM dexamethasone, 1 μM rosiglitazone, 1 μM triiodothyronine (T3), and 0.5 mM IBMX (all Sigma–Aldrich, USA) for two days, and subsequently in medium with insulin, rosiglitazone, and T3 for another six days.

tag: strain background

tag: genotype/variation

value: 5 weeks

value: brown adipose tissue (BAT)

tag: induction time

value: 8 days


title: KI2

description: R20030046-NBC20200721-A-UIRX3-B-SVF-K12_combined

tag: age


title: S.islandicus.REY15A.E234.RNA-seq.replicate1


title: 3M-3


title: SupT1_rep3

value: T-lymphoblast cell line

value: untreated


title: HCT116 cells, WT, Day 3, 50% biol rep 3, small-RNA-seq


title: HCT116 cells, WT, Day 5, 250% biol rep 3, small-RNA-seq


title: CTRL3

description: R20030046-NBC20200721-A-UIRX3-B-SVF-Ctr13_combined

source_name: control_Induced brown adipocyte

value: control


title: Leaf Treatment R2

city: Faisalabad

first: Iqrar

middle: Ahmad

last: Rana

state: Punjab

address: Jail road

department: Center for Advanced Studies in Agriculture and Food Security

country: Pakistan

institute: University of agriculture

data_processing:
Sequence read filtering by BGI internal software
We use Trinity to performde novo assembly with clean reads
Then we perform gene family clustering with Tgicl to get final Unigenes.
We use Blastx or Diamond align Unigenes to NT, NR, KOG, KEGG and SwissProt database to do the annotation.
Assembly: Pop_tri_V3
Supplementary files format and content: Tab-delimited excel files include FPKM values and gene annotations for each sample.
Supplementary files format and content: Text  files having assembeled reads to the reference.

organism: Dalbergia sissoo

source_name: Leaf

extract_protocol:
Thermofisher plant RNA Isolation kit
The library was prepared following BGISEQ-500 transcriptome library workflow.

treatment_protocol: The Botryodiplodia theobromeae infection culture was applied on the base of the 1 year old plant.

value: Leaf

value: Botryodiplodia theobromeae


title: HCT116 cells, WT, Day 3, 50% biol rep 2, small-RNA-seq

value: Large intestine; Colon

value: epithelial

value: WT


title: Leaf Treatment R1


title: SupT1_rep2

value: cytoplasmic RNA


title: CTRL2

description: R20030046-NBC20200721-A-UIRX3-B-SVF-Ctr12_combined


title: HCT116 cells, WT, Day 3, 50%  biol rep 1, small-RNA-seq

value: Carcinoma; Colorectal


title: SupT1_rep1


title: CTRL1

description: R20030046-NBC20200721-A-UIRX3-B-SVF-Ctr11_combined


title: Leaf Control R1

value: Control


title: KARR-seq A549 RSV G1 Rep 2

status: Public on Dec 06 2023

city: Farmington

first: Youzhi

last: Cheng

state: Connecticut

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

data_processing:
KARR-seq: For paired end FASTQ formatted files, SeqPrep (commit: 575507b) was first used to merge overlapping read pairs (2 x 150 bp) into single end reads. Unmerged read pairs were discarded. The resulting single end results were then aligned to mm10, hg19 or dm3 reference genome using STAR (v2.5.2a) as well as the species' corresponding RefSeq transcripts. The pre-merging step was skipped for single-end FASTQ files, and directly aligned using STAR. The following STAR parameters were used to recover gapped and chimeric reads (--runMode alignReads --outFilterMultimapNmax 100 --outSAMattributes all --alignIntronMin 1 --scoreGapNoncan -4 --scoreGapATAC -4 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --limitOutSJcollapsed 10000000 --limitIObufferSize 1500000000). Only chimeric reads (CIGAR N gap between mapped segments of the read) were kept, spliced sites filtered and interaction pairs tabulated. Pairix was used to index the interaction pairs file.
Assembly: mm10,hg19,dm3
Supplementary files format and content: Processed files are bgzipped text files that follows the 4DN-standard pairs file format (pairix)
Library strategy: KARR-seq

organism:
Homo sapiens
Respiratory syncytial virus

source_name: human epithelial cells

growth_protocol: HEK293T and HepG2 cells were cultured in DMEM (Gibco 11995) supplemented with 10% (v/v) fetal bovine serum (Gibco), 1% penicillin and streptomycin (Gibco) at 37 ˚C with 5% CO2.

extract_protocol:
Resuspend cell pellets in 410 µL 25 mM K3BO3, with 50 µL 10% SDS, 30 µL proteinase K, 10 µL RNase inhibitor. The mixture was shaken at 55 ˚C for 2 h and was subjected to phenol-chloroform extraction and ethanol precipitation. Extracted RNA were used for enrichment, end repair, and proximity ligation.
Libraries were conctructed by using the SMARTer Stranded Total RNA-seq kit v2 – pico input mammalian.

treatment_protocol: Cells were crosslinked in 1% formaldehyde for 10 min and then quenched with 125 mM glycine for 5 min. Cells were incubated 30 min in lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630, 5 mM EDTA) supplemented with 20 mM N3-kethoxal, proteinase inhibitor, and RNase inhibitor, and was collected by centrifuging. The cell pellet was then washed and shook in lysis buffer supplemented with 12.5 µM G1-DBCO-biotin dendrimer at 1,000 rpm at 37 ˚C for 1 h. After the reaction, cells were collected and washed once as above.

value: epithelial cells

value: Cells were infected by RSV


title: KARR-seq A549 VSV G1 Rep 2

organism:
Homo sapiens
Vesicular stomatitis virus

value: Cells were infected by VSV


title: KARR-seq A549 VSV G1 Rep 1


title: KARR-seq A549 RSV G1 Rep 1


title: KI1

description: R20030046-NBC20200721-A-UIRX3-B-SVF-K11_combined

value: 5 weeks


title: L2866-LB_KAS

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

data_processing:
read alignment, ATAC-seq and KAS-seq data: Bowtie 1.0.1
bigWig file generation: custom code
read alignment, Hi-C: Juicer
Assembly: custom assembly
Supplementary files format and content: bedGraph of read coverage, normalized to RPM for bigWig files for ATAC-seq and KAS-seq; .hic file for Hi-C
Library strategy: KAS-seq

organism: Bdellovibrio bacteriovorus

growth_protocol: The strain designated as Bdellovibrio bacteriovorus ``ICPB 3264 [H-I A3.12]'' was obtained from ATCC (https://www.atcc.org/products/25637). Cells were grown in ATCC medium 526 (10.0 g Peptone, 3.0 g Yeast extract, 1.0 L distilled water, autoclaved at 121C) at 30C, except where otherwise indicated for the HEPES starvation condition (in which case cells were centrifuged down and the media was replaced with HEPES buffer supplemented with 2 mM CaCl2 and 4 mM MgCl2).

extract_protocol:
500-mM N3-kethoxal solution was brought to 37C, then added to 1 mL of culture at a final concentration of 5 uM. Cells were then incubated for 5 minutes at 30c in a ThermoMixer at 1000 RPM. Cells were then pelleted by centrifugation at 13,000 RPM for 1 minute, resuspended in 100 uL 1x PBS buffer, and DNA was immediately isolated using the Monarch Genomic DNA Purification Kit (NEB, Cat # T3010S), with the modification that elution was carried out with 87.5 uL 25 mM K3BO3 solution (pH 7.0). Biotin was clicked onto kethoxal-modified guanines by mixing 87.5 uL DNA, 2.5 uL 20 mM DBCO-PEG4-biotin (Sigma, Cat # 760749; DMSO solution), and 10 uL 10x PBS, and incubating at 37C for 90 minutes. DNA was isolated using AMPure XP beads and eluted in 130 uL 25 mM K3BO3 (pH 7.0), then sheared on a Covaris E220 for 120 seconds down to ~150-200 bp.
Libraries were built on beads using the NEBNext Ultra II DNA Library Prep kit (NEB, Cat # E7645L). Biotin pull down was initiated py pipetting 20 uL Dynabeads MyOne Streptavidin T1 beads (ThermoFisher Scientific, Cat # 65306) into DNA lo-bind tubes. Beads were separated on magnet, resuspended in 200 uL of 1x TWB buffer (Tween Washing Buffer; 5 mM Tris-HCl pH 7.5; 0.5 mM EDTA; 1 M NaCl; 0.05% Tween 20), then separated on magnet again and  resuspended in 300 uL of 2x BB (Binding Buffer; 10 mM Tris-HCl pH 7.5, 1 mM EDTA; 2 M NaCl). The DNA (130 uL) was added together with 170 uL 0.1x TE buffer, and incubated at RT on rotator for ~15 minutes. Beads were separated on magnet, resuspended in 200 uL of 1x TWB, and incubated at 55C in a Termomixer for 2 minutes with shaking at 1000 rpm. Beads were again separated on magnet and the 200-uL 55C TWB wash step was repeated. Beads were separated on magnet and resuspended in 50 uL 0.1x TE. End repair was carried out by adding 7 uL NEB End Repair Buffer and 3 uL NEB End Repair Enzyme, incubating at 20C for 30 minutes, then at 65C for 30 minutes. End repair was followed by adaptor ligation by adding 2.5 uL NEB Adaptor, 1 uL NEB Ligation Enhancer and 30 uL NEB Ligation Mix, incubating at 20C for 20 minutes, then adding 3 uL USER Enzyme and incubating at 37C for 15 minutes. Beads were separated on magnet, resuspended in 200 uL of 1X TWB, then incubated at 55C in a Thermomixer for 2 minutes with shaking at 1000 rpm. Subsequently beads were separated on magnet and resuspended in 100 uL of 0.1X TE, separated on magnet again, resuspended in 15 uL of 0.1X TE Buffer, and transfered to PCR tubes. Beads were then incubated at 98C for 10 minutes, and libraries were amplified by adding 5 uL of i5 primer, 5 uL of i7 primer and 25 uL of 2X Q5 Hot Start Polymerase Mix, using the following PCR program: 30 seconds at 98C; 15 cycles of 98C for 10 seconds, 65C for 30 seconds, and 72C for 30 seconds; and a final extension at 72C for 5 minutes. Beads were separated on magnet and the final libraries were purified from the supernatant using 50 uL AMPure XP beads, eluting in 0.1X TE buffer.

value: cells


title: L2868-LB_KAS


title: L2867-LB_KAS


title: L2858-LB_KAS


title: L2862-HEPES_KAS


title: L2859-LB_KAS


title: L2863-HEPES_KAS


title: L2865-HEPES_KAS


title: L2860-HEPES_KAS


title: L2864-HEPES_KAS


title: L2861-HEPES_KAS


title: L2857-LB_KAS


title: L2845-ATAC_LB

data_processing:
read alignment, ATAC-seq and KAS-seq data: Bowtie 1.0.1
bigWig file generation: custom code
read alignment, Hi-C: Juicer
Assembly: custom assembly
Supplementary files format and content: bedGraph of read coverage, normalized to RPM for bigWig files for ATAC-seq and KAS-seq; .hic file for Hi-C

extract_protocol:
Cells were fixed by adding 37% formaldehyde (Sigma) at a final concentration of 1% and incubating for 15 minutes at room temperature. Formaldehyde was then quenched using 2.5 M glycine at a final concentration of 0.25 M. Cells were subsequently centrifuged at 13,000 RPM for 1 minute, washed once in 1x PBS, and centrifuged again at 13,000 RPM for 1 minute. Lysis was then carried out by resuspending cells in 400 uL Permeabilization Buffer (33 mM Tris-HCl pH 8.0, 20% sucrose, 25 ug/mL lysozyme) and incubating 5 minutes at 30C in a ThermoMixer (with shaking at 1000 RPM). Cells were again pelleted at 13,000 RPM for 1 minute, resuspended in 50 uL transposition mix (25 uL 2x TD buffer, 2.5 uL Tn5, 22.5 uL ultrapure H2O), and incubated at 37C for 15 minutes. The reaction was stopped with the addition of 150 uL IP Elution Buffer (1% SDS, 0.1 M NaHCO3) and 2  uL Proteinase K (Promega, Cat # MC5005), then incubated at 65C overnight to reverse crosslinks. DNA was isolated by adding an equal volume of 25:24:1 phenol:chloroform:isoamyl solution, vortexing and centrifuging for 3 minutes at 14,000 rpm, then purifying the top aqueous phase using the MinElute PCR Purification Kit, eluting in 10 uL EB buffer.
Final library amplification was carried out by mixing the 10 uL eluate, 10 uL H2O, 2.5 uL i5 primer, 2.5 uL i7 primer, and 25 uL NEBNext High-Fidelity 2x PCR Master Mix, using the following thermocycler program: 3 minutes at 72C, 30 seconds at 98C, 10 cycles of: 98C for 10 seconds, 63C for 30 seconds, 72C for 30 seconds. Final libraries were purified using the MinElute PCR Purification Kit.


title: L2844-ATAC_LB


title: L2836-ATAC_HEPES


title: L2835-ATAC_HEPES


title: L2872-LB_Hi-C

extract_protocol:
Cells were crosslinked using 37% formaldehyde (Sigma) at a final concentration of 1% for 15 minutes at room temperature. Formaldehyde was then quenched using 2.5 M Glycine at a final concentration of 0.25 M. Cells were centrifuged at 13,000 rpm for 2 minutes, washed once in 1X PBS, and stored at -80C. Denaturation was carried out by resuspended cells in 50 uL of 0.5% SDS and incubating at 62C for 10 minutes. SDS was quenched by adding 145 uL of H2O and 25 uL of 10% Triton X-100 and incubating at 37C for 15 minutes. Restriction digestion was carried out by adding 25 uL of 10X CutSmart buffer and 100 U of the MluCI restriction enzyme (NEB # R0538) plus 100 U of the MboI enzyme (NEB # R0147), then incubating for >=2 hours at 37C in a Thermomixer at 900 rpm. The reaction was then incubated at 62C for 20 minutes in order to inactivate the restriction enzymes.  Fragment ends were filled in by adding 37.5 uL of 0.4 mM biotin-14-dATP (ThermoFisher Scientific, # 19524-016), 1.5 uL each of 10 mM dCTP, dGTP and dTTP, and 8 uL of 5U/uL DNA Polymerase I Large (Klenow) Fragment (NEB #M0210). The reaction was the incubated at 37C in a Thermomixer at 900 rpm for 45 minutes. Fragment end ligation was carried out by adding 663 uL H2O, 120 uL 10X NEB T4 DNA ligase buffer (NEB B0202), 100 uL of 10% Triton X-100, 12 uL of 10 mg/mL Bovine Serum Albumin (100X BSA, NEB), 5 uL of 400 U/uL T4 DNA Ligase (NEB #M0202), and incubating at room temperature for >=4 hours with rotation. Cells were then pelleted by centrifugation at 13,000 rpm for 5 minutes. The pellet was resuspended in 200 uL Elution Buffer (1% SDS, 0.1 M NaHCO3), Proteinase K was added, and incubated at 65C overnight to reverse crosslinks.  After addition of 600 uL 1XTE buffer, DNA was sheared using a Covaris E220 instrument. DNA was then purified using the MinElute PCR Purification Kit (Qiagen #28006), with elution in a total volume of 300 uL 1X EB buffer.
For streptavidin pulldown of biotin-labeled DNA, 150 uL of 10 mg/mL Dynabeads MyOne Streptavidin T1 beads (Life Technologies, 65602) were separated on a magnetic stand, then washed with 180 uL of 1X TWB (Tween Washing Buffer; 5 mM Tris-HCl pH 7.5; 0.5 mM EDTA; 1 M NaCl; 0.05\% Tween 20). Beads were then resuspended in 300 uL of 2X Binding Buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA; 2 M NaCl), the sonicated DNA was added, and beads were incubated for >=15 minutes at room temperature on a rotator. After separation on a magnetic stand, the beads were twice washed with 180 uL of 1X TWB, and heated at 55C in a Thermomixer with shaking for 2 minutes. Final libraries were prepared on beads using the NEBNext Ultra II DNA Library Prep Kit (NEB #E7645). End repair was carried out by resuspending beads in 50 uL 1X EB buffer, and adding 3 uL NEB Ultra End Repair Enzyme and 7 uL NEB Ultra End Repair Enzyme, followed by incubation at 20C for 30 minutes and then at 65C for 30 minutes. Adapters were ligated to DNA fragments by adding 30 uL Blunt Ligation mix, 1 uL Ligation Enhancer and 2.5 uL NEB Adapter, incubating at 20C for 20 minutes, adding 3 uL USER enzyme, and incubating at 37C for 15 minutes. Beads were then separated on a magnetic stand, and washed with 180 uL TWB for 2 minutes at 55C at 1000 rpm in a Thermomixer. After separation on a magnetic stand, beads were washed in 100 uL 0.1X TE buffer, then resuspended in 16 uL 0.1X TE buffer, and heated at 98C for 10 minutes. For PCR, 5 uL of each of the i5 and i7 NEB Next sequencing adapters were added together with 25 uL 2X NEB Ultra PCR Mater Mix. PCR was carried out with a 98C incubation for 30 seconds and 12 cycles of 98C for 10 seconds, 65C for 30 seconds, and 72C for 1 minute, followed by incubation at 72C for 5 minutes. Beads were separated on a magnetic stand, and the supernatant was cleaned up using 1.8X AMPure XP beads.


title: L2871-LB_Hi-C


title: L2876-LB_Hi-C


title: L2870-HEPES_Hi-C


title: L2873-HEPES_Hi-C


title: L2874-HEPES_Hi-C


title: L2869-HEPES_Hi-C


title: 80B_14954_24W_PBMC

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description: Δvpr

data_processing:
The sequencing data was demultiplexed using Illumina bcl2fastq v2.20.0.422.
The quality of raw reads was assessed with FastQC v0.11.8.
Reads were mapped to the Rhesus macaque (MacaM v7) genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the htseq-count algorithm.
Assembly: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf,https://www.unmc.edu/rhesusgenechip/index.htm#Rhesus)
Supplementary files format and content: tab delimited text file containing raw read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: Peripheral blood mononuclear cells

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kits with DNase digest and QIAcube automation stations. RNA was quantified on NanoDrop 2000 spectrophotometer and the quality was assessed by Bioanalyzer analysis.
Set A samples: Libraries were prepared using the Illumina TruSeq mRNA stranded kit, as per manufacturer’s instructions, with 400 ng of total RNA as input. The amplified libraries were validated by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were normalized, pooled and sequenced on the Illumina HiSeq 3000 system employing a single-end 101 cycles run at average read depths of 16 million reads/sample.
Set B samples: 10 ng of total RNA was used as input for cDNA amplification using 5’ template-switch PCR with the Clontech SMART-Seq v4 Ultra Low Input RNA kit. Amplified cDNA was fragmented and appended with dual indexed bar codes using Illumina NexteraXT DNA Library Prep kits. The amplified libraries were validated by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were normalized, pooled and sequenced on the Illumina HiSeq 3000 system employing a single-end 101 cycles run at average read depths of 25 million reads/sample.

value: Peripheral blood mononuclear cells

tag: set

value: B

tag: subjectid

tag: sivgenotype

value: {delta}vpr

tag: infection status

tag: timepoint (weeks)


title: 79B_2772_24W_PBMC

description: Δvpr


title: L2786-gDNA

data_processing:
read alignment, ATAC-seq and KAS-seq data: Bowtie 1.0.1
bigWig file generation: custom code
read alignment, Hi-C: Juicer
Assembly: custom assembly
Supplementary files format and content: bedGraph of read coverage, normalized to RPM for bigWig files for ATAC-seq and KAS-seq; .hic file for Hi-C
Library strategy: gDNA transposition

extract_protocol:
Genomic DNA (gDNA) was isolated using the NEB Monarch Genomic DNA Purification Kit (Cat \# T3010).
Genomic DNA libraries were generated using Tn5 transposition. Briefly, ~200 ng DNA gDNA were used, with the volume increased to 22.5 uL using ultrapure H2O. Transposition was carried out with 22.5 uL gDNA, 25 uL 2xTD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide), and 2.5 uL Tn5, incubating at 37C for 15 minutes. Transposed DNA was immediately purified using the Qiagen MinElute PCR Purification Kit (Cat # 28004), with the reaction stopped with 250 uL PB buffer, and elution in 10 uL EB buffer. Final library amplification was carried out by mixing the 10 uL eluate, 10 uL H2O, 2.5 uL i5 primer, 2.5 uL i7 primer, and 25 uL NEBNext High-Fidelity 2x PCR Master Mix, using the following thermocycler program: 3 minutes at 72C, 30 seconds at 98C, 10 cycles of: 98C for 10 seconds, 63C for 30 seconds, 72C for 30 seconds. Final libraries were purified using the MinElute PCR Purification Kit.


title: 75B_15934_24W_PBMC

description: wt

value: wt


title: L2846-ATAC_LB


title: 74B_15925_24W_PBMC

description: wt


title: 81B_15933_24W_PBMC

description: Δvpr


title: 45B_15933_2W_PBMC

description: Δvpr


title: 43B_2772_2W_PBMC

description: Δvpr


title: 18B_15933_minus4W_PBMC

description: Δvpr

value: uninfected


title: 44B_14954_2W_PBMC

description: Δvpr


title: L2837-ATAC_HEPES


title: 38B_15925_2W_PBMC [re-analysis]

description:
wt
GSM4209969


title: 37B_2729_2W_PBMC [re-analysis]

description:
wt
GSM4209968


title: 39B_15934_2W_PBMC [re-analysis]

description:
wt
GSM4209970


title: 17B_14954_minus4W_PBMC

description: Δvpr


title: 11B_15925_minus4W_PBMC [re-analysis]

description:
wt
GSM4209960


title: 12B_15934_minus4W_PBMC [re-analysis]

description:
wt
GSM4209961


title: L2875-LB_Hi-C


title: 10B_2729_minus4W_PBMC [re-analysis]

description:
wt
GSM4209959


title: 8B_14954_minus8W_PBMC

description: Δvpr


title: 3B_15934_minus8W_PBMC

description: wt


title: 1B_2729_minus8W_PBMC

description: wt


title: 99A_7406_27W_PBMC [re-analysis]

description:
ctl
GSM4209958

value: A

value: ctl


title: 73B_2729_24W_PBMC

description: wt


title: 98A_14954_27W_PBMC [re-analysis]

description:
ctl
GSM4209957


title: 16B_2772_minus4W_PBMC

description: Δvpr


title: 2B_15925_minus8W_PBMC

description: wt


title: 97A_2612_27W_PBMC [re-analysis]

description:
ctl
GSM4209956


title: 96A_2564_27W_PBMC [re-analysis]

description:
ctl
GSM4209955


title: 67A_15216_2W_PBMC

description: Δvpr


title: 90A_14847_24W_PBMC

description: Δvpr


title: 95A_2522_27W_PBMC [re-analysis]

description:
ctl
GSM4209954


title: 91A_15216_24W_PBMC

description: Δvpr


title: 66A_14847_2W_PBMC

description: Δvpr


title: 52A_2146_27W_PBMC [re-analysis]

description:
ctl
GSM4209950


title: 9B_15933_minus8W_PBMC

description: Δvpr


title: 65A_2617_2W_PBMC

description: Δvpr


title: 54A_2363_27W_PBMC [re-analysis]

description:
ctl
GSM4209952


title: 55A_2447_27W_PBMC [re-analysis]

description:
ctl
GSM4209953


title: 53A_2232_27W_PBMC [re-analysis]

description:
ctl
GSM4209951


title: 41A_14892_24W_PBMC

description: wt


title: 51A_2136_27W_PBMC [re-analysis]

description:
ctl
GSM4209949


title: 43A_15226_24W_PBMC

description: wt


title: 7B_2772_minus8W_PBMC

description: Δvpr


title: 13A_15226_2W_PBMC [re-analysis]

description:
wt
GSM4209967


title: 12A_14893_2W_PBMC [re-analysis]

description:
wt
GSM4209966


title: 11A_14892_2W_PBMC [re-analysis]

description:
wt
GSM4209965


title: 89A_2617_24W_PBMC

description: Δvpr


title: 42A_14893_24W_PBMC

description: wt


title: GD1969_Male_XY_16_S10

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Reads were aligned to mouse genome (mm10) with subread-align version 2.0.1 (PMID: 23558742)
Read counts were calculated with the featureCounts function from Rsubread version 2.0.1 (PMID: 24227677) against RefSeq gene annotation
Gene expression level from RNA-Seq is measured by rpkm (PMID: 18516045) with an in-house script.
Assembly: mm10
Supplementary files format and content: tab-delimited text file incudes: entriz ID, gene symbols, RPKM (log2) value for each sample

source_name: splenocytes

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus kit (Qiagen).  1.3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit following manufacturer's protocols

value: splenocytes

value: XYM

value: HKSP Immunized


title: GD1970_Male_XY_9_S6


title: GD1967_Male_XY_13_S8


title: GD1965-Fanko_Male_XX_8_S5

value: XXM


title: GD1962-Fanko_Male_XX_5_S2


title: GD1968_Male_XY_15_S9


title: GD1963-Fanko_Male_XX_6_S3


title: GD1964-Fanko_Male_XX_7_S4


title: KARR-seq K562 + S2 G1 Rep 2

data_processing:
library strategy: KARR-seq
KARR-seq: For paired end FASTQ formatted files, SeqPrep (commit: 575507b) was first used to merge overlapping read pairs (2 x 150 bp) into single end reads. Unmerged read pairs were discarded. The resulting single end results were then aligned to mm10, hg19 or dm3 reference genome using STAR (v2.5.2a) as well as the species' corresponding RefSeq transcripts. The pre-merging step was skipped for single-end FASTQ files, and directly aligned using STAR. The following STAR parameters were used to recover gapped and chimeric reads (--runMode alignReads --outFilterMultimapNmax 100 --outSAMattributes all --alignIntronMin 1 --scoreGapNoncan -4 --scoreGapATAC -4 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --limitOutSJcollapsed 10000000 --limitIObufferSize 1500000000). Only chimeric reads (CIGAR N gap between mapped segments of the read) were kept, spliced sites filtered and interaction pairs tabulated. Pairix was used to index the interaction pairs file.
Genome_build: mm10,hg19,dm3
Supplementary_files_format_and_content: Processed files are bgzipped text files that follows the 4DN-standard pairs file format (pairix)

organism:
Drosophila melanogaster
Homo sapiens

source_name: KARR-seq K562 + S2 G1

value: bone marrow cells


title: KARR-seq K562 + S2 G1 Rep 1


title: Serum_58w_rep3

city: Hirosaki

first: Mitsuru

last: Chiba

state: Aomori

address: 66-1 Hon-cho

department: Graduate School of Health Sciences

institute: Hirosaki University

description: gene expression in serum of 58-week-old mouse

hyb_protocol: SurePrint G3 mouse miRNA microarray slides (8 × 60 K, Ver.21.0) were hybridized with the Cy3-labeled miRNA in a hybridization solution prepared with a Gene Expression Hybridization Kit (Agilent Technologies) for 20 hours at 55°C in a rotating hybridization oven (Agilent Technologies), according to the manufacturer’s instructions. After hybridization, microarray slides were washed for 5 min at room temperature with GE Wash Buffer 1 (Agilent Technologies) and for 5 min at 37°C with GE Wash buffer 2 (Agilent Technologies), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the SureScan Microarray Scanner (G4900DA) (Agilent Technologies) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 2 μm high sensitivity, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5 (Agilent Technologies) using default parameters (Protocol name: miRNA_1105_Oct12 and Grid name: 070155_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Serum

label_protocol: Cyanine 3(Cy3)-labeled miRNAs were synthesized from each 1.0 ng of serum RNA in 4-week-old, 8-week-old, 36-week-old, or 58-week-old mice using a miRNA Complete Labeling Reagent and Hyb kit (Agilent Technologies), according to the manufacturer’s instructions.

extract_protocol: Total RNAs from serum were extracted using the Isogen II reagent and ethachinmate (Nippongene,) according to the manufacturer’s instructions. RNA concentration of serum and feces was measured using a Qubit 4 Fluorometer (ThermoFisher Scientific) and Qubit™ microRNA Assay kits (ThermoFisher Scientific) according to manufacturer’s instructions. The quality of total RNAs was confirmed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Pico kit (both Agilent Technologies), according to the manufacturer’s instructions.

treatment_protocol: Blood obtained from the heart was collected in BD Microtainer tubes with serum separator additive BD Microgard closure (Becton Dickinson Biosciences). Blood was then centrifuged at 6000 × G at room temperature for 3 min, and serum was collected.

value: Serum

tag: gender

value: male

value: 58 weeks


title: Serum_36w_rep2

description: gene expression in serum of 36-week-old mouse

value: 36 weeks


title: Serum_58w_rep4


title: GD1960_Female_XY_F9_S19

value: XYF


title: Serum_8w_rep2

description: gene expression in serum of 8-week-old mouse

value: 8 weeks


title: Serum_4w_rep1

description: gene expression in serum of 4-week-old mouse

value: 4 weeks


title: Serum_4w_rep2


title: Serum_36w_rep4


title: Serum_8w_rep1


title: GD1959_Female_XY_F8_S18


title: GD1966_Male_XY_12_S7


title: Serum_8w_rep4


title: Serum_58w_rep1


title: GD1958_Female_XY_F7_S17


title: GD1955_Female_XX_F4_S14

value: XXF


title: GD1956_Female_XX_F5_S15


title: Serum_36w_rep1


title: Serum_4w_rep4


title: Serum_8w_rep3


title: Serum_36w_rep3


title: Serum_4w_rep3


title: Serum_58w_rep2


title: GD1952_Female_XX_F1_S11


title: GD1953_Female_XX_F2_S12


title: GD1954_Female_XX_F3_S13


title: GD1961-Fanko_Male_XX_2_S1


title: control healty sample - rep 9

city: Caserta

first: Gilda

last: Cobellis

address: Viale Abramo Lincoln

country: Italy

institute: University of Campania "Luigi Vanvitelli"

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence by using cutadapt software (version 2.5).
The tool sRNAbench was used to obtain the miRNA expression profiling respect to miRBase database (version22 - GRCh38 - GCA_000001405.15).
Reads that had a sum read count less than 10 were excluded, in all samples used.
the DESeq2 (version 1.36.0) algorithm was used to detected the differentially expressed miRNA.
Assembly: HG38-miRbase 22
Supplementary files format and content: Matrix table with raw miRNA counts for every sample
Supplementary files format and content: tab-delimited text files include normalized values (median of ratio of miRNA counts) for each Sample.

source_name: Extracellular vesicles from serum

growth_protocol: not applicable

extract_protocol:
Total RNA extraction was performed using TRIzol reagent (TRIzol Reagent, Invitrogen Life Technologies, Carlsbad, CA, USA), according to the manufacturer’s instructions.
Total RNA was used for sequencing library preparation using NEXTFLEX Small RNA-Seq Kit v3 (Perki-nElmer) according to the manufacturer’s instructions. Libraries were quantified using the TapeStation 4200 (Agilent Technologies) and Qubit fluorometer (Invitrogen Co.), then pooled such that each index-tagged sample was present in equimolar amounts. The pooled samples were subject to cluster generation and sequencing using an Illumina NextSeq 550 Dx System (Illumina) in a 1x75 single-end format.

treatment_protocol: not applicable

value: Extracellular vesicles from serum

value: control healthy samples


title: control healty sample - rep 8


title: control healty sample - rep 7


title: control healty sample - rep 6


title: control healty sample - rep 4


title: control healty sample - rep 5


title: sample37_Healthy

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then mapped to GRCh38 whole genome using Hisat2 v2.2.1
Read summarization was performed by the program featureCounts v2.0.1 as part of the SubRead package.
Counts Per Million (CPM) values were generated through the edgeR Library v3.32.1 in R
Assembly: GRCh38
Supplementary files format and content: rawCounts.csv: counts as generated by featureCounts, rows are gene features, columns are samples
Supplementary files format and content: normalizedCounts.csv:remove counts that were all zeroes (across the full set); Perform TMM normalization ; export log2(n+3) CPM

source_name: Peripheral CD8

growth_protocol: in vivo

extract_protocol:
After surgical resection, tumor specimens were washed with antibiotic-containing media and minced with crossed scalpels under sterile conditions. Tissue was dissociated via enzymatic digestion using 1,500 U/ml collagenase IV (Gibco/Life Technologies), 1,000 U/ml hyaluronidase (Sigma), and 0.05 mU/ml DNase IV (Gibco) in RPMI for 1 h at 37°C followed by mechanical agitation. Centrifugation over Ficoll-Hypaque gradient was used to separate debris from the single cell suspension. Finally, cells were cryopreserved in 10% DMSO + bovine serum. RNA was then purified from cells using RNeasy Micro Kits (Qiagen).
RNA libraries were prepared for sequencing using the SMART-Seq v4 for CDNA and the Nextera XT kit for library creation on a NextSeq 550 instrument

value: Healthy

tag: sample number

value: Peripheral CD8


title: sample38_Melanoma

source_name: TIL

value: Melanoma

tag: cell type

value: TIL


title: GD1957_Female_XY_F6_S16

value: splenocytes

tag: genotype

value: HKSP Immunized


title: sample39_Melanoma

tag: disease state


title: sample35_Healthy


title: sample36_Healthy


title: sample33_Melanoma


title: sample32_Squamous Cell Carcinoma

value: Squamous Cell Carcinoma


title: sample34_Melanoma


title: sample31_Squamous Cell Carcinoma


title: sample30_Squamous Cell Carcinoma


title: sample21_Melanoma


title: sample23_Healthy


title: sample29_Squamous Cell Carcinoma


title: sample24_Healthy


title: sample25_Melanoma


title: sample27_Melanoma


title: sample26_Melanoma


title: sample19_Melanoma


title: sample28_Squamous Cell Carcinoma


title: sample14_Healthy


title: sample17_Melanoma


title: sample15_Squamous Cell Carcinoma


title: sample22_Melanoma


title: sample18_Squamous Cell Carcinoma


title: sample13_Healthy


title: sample12_Healthy


title: sample6_Melanoma


title: sample9_Melanoma


title: sample7_Melanoma


title: sample8_Melanoma


title: sample16_Squamous Cell Carcinoma


title: sample5_Melanoma


title: sample4_Melanoma


title: sample2_Melanoma


title: sample3_Melanoma


title: sample20_Melanoma


title: EBS01

city: Padova

first: Mattia

last: Forcato

address: Via Ugo Bassi, 58/B

institute: University of Padova

description: 10x Genomics

data_processing:
Fastq generation, alignment to the human genome and gene quantification were performed with 10x Cell Ranger v3.1.0.
The UMI count matrix was used for downstream analysis with Seurat v3.1.5 R package.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: epidermis

extract_protocol:
cell detached after trypsinization from in vitro cultivated human primary keratinocyte
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: epidermis

tag: cell line

value: human primary keratinocytes

value: keratinocyte

value: c.475/495del21 mutation in KRT14 exon1

tag: treatment

value: not treated


title: sample10_Melanoma


title: sample11_Melanoma


title: sample1_Melanoma


title: eEBS01

description: 10x Genomics

tag: tissue

value: edited (c.475/495del21 mutation in KRT14 exon1)

value: edited


title: Pituitary_CR_30 [GC34624]

city: Castanet-Tolosan

first: Laurence

last: Liaubet

address: 24 chemin de Borde Rouge

department: Animal genetics

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE microarray (8X60K, Design 028005) enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min), Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_2012). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 45667 rows each corresponding to a unique ProbeName (provided as data Matrix) and 33 columns (individuals).

organism: Sus scrofa

source_name: Pituitary gland

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy purification (QIAGEN). Dye incorporation and cRNA yield were checked with the Biospec nano spectrophotometer (Shimadzu).

growth_protocol: The animals were raised at the French Experimental Unit PTEA, INRAE, Petit-Bourg in Guadeloupe. Pituitary glands were obtained in an experiment involving 36 pigs from 3 breeds slaughtered before (n=18) or after a 5-days exposure to 32°C (n=18). 33 samples were available for the following steps.

extract_protocol: Pituitary samples were disrupted, homogenized and ground to a fine powder by rapid agitation for 1 min in a liquid-nitrogen cooled grinder with stainless steel beads. An aliquot of 60-80 mg of the fine powder was then processed for total RNA isolation and purification using Trizol (Invitrogen, France) and the Nucleospin RNA II kit (Macherey-Nagel, France) according to the manufacturer’s instructions. The method included a DNase digestion step to remove contaminating DNA. The extracted total RNA was eluted in 40 or 60 μl of RNase-free water and stored at -80°C.

treatment_protocol: Pituitary samples were conserved at -80°C until extraction.

tag: breed

value: Creole

tag: temperature

value: castrated


title: Pituitary_CR_24 [GC34626]


title: Pituitary_F1_24 [GC34614]


title: Pituitary_LW_30 [GC34601]

value: Large White


title: Pituitary_CR_24 [GC34625]


title: Pituitary_F1_30 [GC34619]


title: Pituitary_F1_24 [GC34613]


title: Pituitary_LW_30 [GC34599]


title: Pituitary_LW_24 [GC34611]


title: Pituitary_LW_24 [GC34610]


title: Pituitary_F1_30 [GC34621]


title: Pituitary_F1_30 [GC34609]


title: Pituitary_CR_30 [GC34631]


title: Pituitary_LW_30 [GC34600]


title: Pituitary_LW_30 [GC34604]


title: Pituitary_CR_30 [GC34630]


title: Pituitary_F1_24 [GC34616]


title: Pituitary_LW_24 [GC34602]


title: Pituitary_LW_30 [GC34606]


title: Pituitary_LW_24 [GC34608]


title: Pituitary_F1_24 [GC34617]


title: Pituitary_CR_24 [GC34633]


title: Pituitary_CR_30 [GC34629]


title: Pituitary_F1_24 [GC34618]


title: Pituitary_CR_24 [GC34622]


title: Pituitary_F1_24 [GC34620]


title: Pituitary_CR_30 [GC34623]


title: Pituitary_LW_30 [GC34607]


title: Pituitary_LW_24 [GC34603]


title: Pituitary_F1_30 [GC34612]


title: LD_muscle_LW_24 [GC34504]

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_2012). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 40649 rows each corresponding to a unique ProbeName (provided as data Matrix) and 61 columns (individuals).

source_name: Longissimus dorsi muscle

growth_protocol: The animals were raised at the French Experimental Unit PTEA, INRAE, Petit-Bourg in Guadeloupe. Longissimus dorsi muscle were obtained in an experiment involving 36 pigs from 3 breeds slaughtered before (n=18) or after a 5-days exposure to 32°C (n=18). 35 samples were available for the following steps.

extract_protocol: Muscle samples were disrupted, homogenized and ground to a fine powder by rapid agitation for 1 min in a liquid-nitrogen cooled grinder with stainless steel beads. An aliquot of 100 mg of the fine powder was then processed for total RNA isolation and purification using Trizol (Invitrogen, France) and the Nucleospin RNA II kit (Macherey-Nagel, France) according to the manufacturer’s instructions. The method included a DNase digestion step to remove contaminating DNA. The extracted total RNA was eluted in 40 μ l of RNase-free water and stored at -80°C.

treatment_protocol: Muscle samples were conserved at -80°C until extraction.


title: Pituitary_CR_30 [GC34627]


title: Pituitary_CR_24 [GC34628]


title: LD_muscle_F1_24 [GC34513]


title: Pituitary_F1_30 [GC34615]


title: LD_muscle_F1_24 [GC34511]


title: LD_muscle_F1_30 [GC34512]


title: LD_muscle_F1_24 [GC34510]


title: LD_muscle_CR_30 [GC34522]


title: LD_muscle_CR_30 [GC34524]


title: LD_muscle_CR_24 [GC34526]


title: LD_muscle_F1_24 [GC34509]


title: LD_muscle_F1_30 [GC34505]


title: LD_muscle_CR_30 [GC34523]


title: LD_muscle_LW_24 [GC34500]


title: LD_muscle_LW_30 [GC34498]


title: LD_muscle_LW_30 [GC34493]


title: LD_muscle_LW_30 [GC34496]


title: LD_muscle_LW_24 [GC34495]


title: LD_muscle_CR_24 [GC34521]


title: LD_muscle_CR_24 [GC34525]


title: LD_muscle_LW_24 [GC34503]


title: LD_muscle_LW_30 [GC34499]


title: LD_muscle_LW_24 [GC34497]


title: LD_muscle_F1_24 [GC34506]


title: LD_muscle_CR_30 [GC34520]


title: LD_muscle_F1_30 [GC34508]


title: LD_muscle_F1_24 [GC34507]


title: LD_muscle_CR_30 [GC34517]


title: LD_muscle_LW_30 [GC34491]


title: LD_muscle_LW_30 [GC34492]


title: LD_muscle_LW_24 [GC34494]


title: Liver_F1_24 [GC45148]

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_2012). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 42051 rows each corresponding to a unique ProbeName (provided as data Matrix) and 36 columns (individuals).

source_name: Liver

growth_protocol: The animals were raised at the French Experimental Unit PTEA, INRAE, Petit-Bourg in Guadeloupe. Samples from liver were obtained in an experiment involving 36 pigs from 3 breeds slaughtered before (n=18) or after a 5-days exposure to 32°C (n=18).

extract_protocol: Liver samples were disrupted, homogenized and ground to a fine powder by rapid agitation for 1 min in a liquid-nitrogen cooled grinder with stainless steel beads. An aliquot of 70-90 mg of the fine powder was then processed for total RNA isolation and purification using Trizol (Invitrogen, France) and the Nucleospin RNA II kit (Macherey-Nagel, France) according to the manufacturer’s instructions. The method included a DNase digestion step to remove contaminating DNA. The extracted total RNA was eluted in 100 μl of RNase-free water and stored at -80°C.

treatment_protocol: Liver samples were conserved at -80°C until extraction.


title: LD_muscle_CR_24 [GC34519]


title: LD_muscle_CR_24 [GC34518]


title: Liver_F1_30 [GC45156]


title: LD_muscle_F1_30 [GC34502]


title: LD_muscle_CR_24 [GC34515]


title: LD_muscle_F1_30 [GC34501]


title: Liver_LW_24 [GC45145]


title: LD_muscle_CR_30 [GC34516]


title: Liver_CR_30 [GC45166]


title: Liver_LW_30 [GC45141]


title: Liver_CR_30 [GC45165]


title: Liver_LW_30 [GC45140]


title: Liver_CR_24 [GC45157]


title: Liver_LW_30 [GC45133]


title: Liver_F1_24 [GC45153]


title: Liver_F1_30 [GC45154]


title: Liver_F1_24 [GC45152]


title: Liver_CR_30 [GC45164]


title: Liver_CR_24 [GC45168]


title: Liver_CR_24 [GC45167]


title: Liver_LW_24 [GC45139]


title: Liver_LW_24 [GC45142]


title: Liver_F1_24 [GC45155]


title: Liver_LW_30 [GC45138]


title: Liver_F1_24 [GC45151]


title: Liver_F1_30 [GC45150]


title: Liver_LW_30 [GC45135]


title: Liver_CR_24 [GC45163]


title: Liver_CR_30 [GC45162]


title: Liver_LW_24 [GC45136]


title: Liver_F1_30 [GC45147]


title: Liver_LW_30 [GC45134]


title: Liver_F1_24 [GC45149]


title: Liver_LW_24 [GC45137]


title: Liver_F1_30 [GC45144]


title: Liver_CR_24 [GC45161]


title: Liver_CR_30 [GC45159]


title: Liver_CR_30 [GC45158]


title: Liver_CR_24 [GC45160]


title: Liver_LW_24 [GC45146]


title: Liver_F1_30 [GC45143]


title: SCAT_F1_24 [GC45184]

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_2012). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 44104 rows each corresponding to a unique ProbeName (provided as data Matrix) and 26 columns (individuals).

source_name: Sub-Cutaneous Adipose Tissue

growth_protocol: The animals were raised at the French Experimental Unit PTEA, INRAE, Petit-Bourg in Guadeloupe. Sub-Cutaneous Adipose Tissue (SCAT) were obtained in an experiment involving 36 pigs from 3 breeds slaughtered before (n=18) or after a 5-days exposure to 32°C (n=18). 26 samples were available for the following steps.

extract_protocol: SCAT samples were disrupted, homogenized and ground to a fine powder by rapid agitation for 1 min in a liquid-nitrogen cooled grinder with stainless steel beads. An aliquot of 100 mg of the fine powder was then processed for total RNA isolation and purification using Trizol (Invitrogen, France) and the Nucleospin RNA II kit (Macherey-Nagel, France) according to the manufacturer’s instructions. The method included a DNase digestion step to remove contaminating DNA. The extracted total RNA was eluted in 40 μ l of RNase-free water and stored at -80°C.

treatment_protocol: SCAT samples were conserved at -80°C until extraction.

value: 24 degreeC


title: SCAT_LW_30 [GC45169]

value: 30 degreeC


title: SCAT_CR_30 [GC45194]


title: SCAT_F1_30 [GC45180]


title: SCAT_CR_30 [GC45195]


title: SCAT_CR_24 [GC45196]


title: SCAT_LW_24 [GC45172]


title: SCAT_CR_30 [GC45202]


title: SCAT_F1_30 [GC45179]


title: SCAT_LW_30 [GC45170]


title: SCAT_LW_24 [GC45173]


title: SCAT_F1_24 [GC45191]


title: SCAT_LW_24 [GC45181]


title: SCAT_LW_24 [GC45182]


title: SCAT_F1_30 [GC45192]


title: SCAT_CR_24 [GC45193]


title: SCAT_LW_30 [GC45176]


title: Thyroid_F1_30 [GC34574]

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_2012). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 46097 rows each corresponding to a unique ProbeName (provided as data Matrix) and 36 columns (individuals).

source_name: Thyroid gland

growth_protocol: The animals were raised at the French Experimental Unit PTEA, INRAE, Petit-Bourg in Guadeloupe. Thyroid glands were obtained in an experiment involving 36 pigs from 3 breeds slaughtered before (n=18) or after a 5-days exposure to 32°C (n=18). 36 samples were available for the following steps.

extract_protocol: Thyroid samples were disrupted, homogenized and ground to a fine powder by rapid agitation for 1 min in a liquid-nitrogen cooled grinder with stainless steel beads. An aliquot of 80-100 mg of the fine powder was then processed for total RNA isolation and purification using Trizol (Invitrogen, France) and the Nucleospin RNA II kit (Macherey-Nagel, France) according to the manufacturer’s instructions. The method included a DNase digestion step to remove contaminating DNA. The extracted total RNA was eluted in 60 μl of RNase-free water and stored at -80°C.

treatment_protocol: Thyroid samples were conserved at -80°C until extraction.


title: SCAT_CR_30 [GC45198]


title: Thyroid_CR_30 [GC34589]


title: SCAT_LW_30 [GC45174]


title: SCAT_F1_24 [GC45187]


title: SCAT_LW_30 [GC45177]


title: Thyroid_F1_24 [GC34578]


title: SCAT_F1_30 [GC45186]


title: Thyroid_LW_24 [GC34567]


title: SCAT_F1_24 [GC45188]


title: Thyroid_F1_30 [GC34573]


title: Thyroid_LW_24 [GC34576]


title: SCAT_CR_24 [GC45203]


title: Thyroid_CR_30 [GC34588]


title: Thyroid_LW_24 [GC34566]


title: Thyroid_CR_30 [GC34596]


title: Thyroid_LW_30 [GC34564]


title: Thyroid_LW_30 [GC34571]


title: SCAT_F1_30 [GC45183]


title: Thyroid_CR_24 [GC34590]


title: SCAT_CR_30 [GC45200]


title: Thyroid_CR_24 [GC34587]


title: Thyroid_F1_24 [GC34585]


title: Thyroid_F1_24 [GC34579]


title: Thyroid_LW_30 [GC34563]


title: Thyroid_LW_24 [GC34575]


title: Thyroid_F1_30 [GC34586]


title: Thyroid_LW_30 [GC34570]


title: Thyroid_F1_24 [GC34583]


title: Thyroid_CR_24 [GC34597]


title: Thyroid_CR_30 [GC34595]


title: Thyroid_F1_30 [GC34580]


title: Thyroid_LW_30 [GC34568]


title: Thyroid_F1_24 [GC34581]


title: Thyroid_CR_30 [GC34594]


title: Thyroid_F1_24 [GC34582]


title: Thyroid_F1_30 [GC34577]


title: Adrenals_CR_24 [GC34551]

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_2012). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 45348 rows each corresponding to a unique ProbeName (provided as data Matrix) and 36 columns (individuals).

source_name: Adrenal glands

growth_protocol: The animals were raised at the French Experimental Unit PTEA, INRAE, Petit-Bourg in Guadeloupe. Adrenals glands were obtained in an experiment involving 36 pigs from 3 breeds slaughtered before (n=18) or after a 5-days exposure to 32°C (n=18). 36 samples were available for the following steps.

extract_protocol: Adrenal samples were disrupted, homogenized and ground to a fine powder by rapid agitation for 1 min in a liquid-nitrogen cooled grinder with stainless steel beads. An aliquot of 80-100 mg of the fine powder was then processed for total RNA isolation and purification using Trizol (Invitrogen, France) and the Nucleospin RNA II kit (Macherey-Nagel, France) according to the manufacturer’s instructions. The method included a DNase digestion step to remove contaminating DNA. The extracted total RNA was eluted in 60 μl of RNase-free water and stored at -80°C.

treatment_protocol: Adrenal samples were conserved at -80°C until extraction.


title: Adrenals_F1_24 [GC34542]


title: Thyroid_F1_30 [GC34584]


title: Thyroid_LW_30 [GC34565]


title: Thyroid_CR_24 [GC34593]


title: Thyroid_LW_24 [GC34569]


title: Thyroid_CR_30 [GC34592]


title: Thyroid_LW_24 [GC34572]


title: Thyroid_CR_24 [GC34591]


title: Adrenals_F1_30 [GC34550]


title: Adrenals_CR_30 [GC34560]


title: Adrenals_LW_30 [GC34527]


title: Adrenals_LW_24 [GC34539]


title: Adrenals_LW_30 [GC34535]


title: Adrenals_CR_30 [GC34559]


title: Adrenals_CR_30 [GC34558]


title: Adrenals_F1_24 [GC34547]


title: Adrenals_LW_24 [GC34536]


title: Adrenals_F1_30 [GC34548]


title: Adrenals_F1_24 [GC34549]


title: Adrenals_CR_24 [GC34562]


title: Adrenals_CR_24 [GC34561]


title: Adrenals_LW_30 [GC34534]


title: Adrenals_F1_30 [GC34541]


title: Adrenals_F1_24 [GC34545]


title: Adrenals_F1_30 [GC34544]


title: Adrenals_CR_30 [GC34556]


title: Adrenals_F1_24 [GC34546]


title: Adrenals_LW_30 [GC34528]


title: Adrenals_LW_24 [GC34531]


title: Adrenals_CR_30 [GC34553]


title: Adrenals_LW_30 [GC34529]


title: Adrenals_LW_30 [GC34532]


title: Adrenals_CR_24 [GC34557]


title: Adrenals_F1_24 [GC34543]


title: Adrenals_LW_24 [GC34530]


title: Adrenals_LW_24 [GC34540]


title: Adrenals_F1_30 [GC34537]


title: Adrenals_CR_24 [GC34555]


title: Adrenals_CR_30 [GC34552]


title: Adrenals_LW_24 [GC34533]


title: blood_LW_24 [GC32022]

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_2012). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 39072 rows each corresponding to a unique ProbeName (provided as data Matrix) and 35 columns (individuals).

source_name: whole blood

growth_protocol: The animals were raised at the French Experimental Unit PTEA, INRAE, Petit-Bourg in Guadeloupe. Blood were collected in an experiment involving 36 pigs from 3 breeds slaughtered before (n=18) or after a 5-days exposure to 32°C (n=18). 35 samples were available for the following steps.

extract_protocol: Total RNA was extracted according to the manufacturer's recommendations (PAXgene Blood RNA Kit, Qiagen) and the extracted total RNA was eluted in 40 µl of buffer BR5 and stored at -80°C. Quantification was performed using a Nanodrop to determine the concentration of each purification and the 260/230, 260/280 ratios. Quality was checked by electrophoresis on 0,8% agarose gel. RNA Integrity Numbers (RINs) were determined using a 2100 Bioanalyzer Instrument (Agilent). Then, RNAs were diluted at 135 and 400ng/µL in RNAse-free water for transcriptomic experiments on GeT-TRiX platform.

treatment_protocol: Whole blood RNA were collected on PAXgene Blood RNA Tubes (PreAnalytiX) and were conserved at -80°C until extraction.


title: blood_F1_30 [GC32009]


title: blood_CR_30 [GC31993]


title: Thyroid_CR_24 [GC34598]


title: blood_CR_30 [GC31992]


title: Adrenals_F1_30 [GC34538]


title: blood_LW_24 [GC32002]


title: Adrenals_CR_24 [GC34554]


title: blood_LW_24 [GC32011]


title: blood_F1_30 [GC32007]


title: blood_F1_24 [GC32005]


title: blood_F1_24 [GC32006]


title: blood_CR_24 [GC32019]


title: blood_LW_30 [GC32001]


title: blood_F1_30 [GC32021]


title: blood_CR_24 [GC31998]


title: blood_F1_24 [GC32004]


title: blood_LW_30 [GC32013]


title: blood_F1_24 [GC31999]


title: blood_LW_30 [GC32026]


title: blood_CR_30 [GC32016]


title: blood_LW_30 [GC32025]


title: blood_F1_30 [GC32000]


title: blood_LW_30 [GC32024]


title: blood_F1_24 [GC32020]


title: blood_CR_30 [GC31991]


title: blood_LW_24 [GC32012]


title: blood_LW_30 [GC32023]


title: blood_F1_30 [GC32008]


title: blood_CR_30 [GC32003]


title: blood_CR_24 [GC32017]


title: WT_DKK1_rep3

city: Richmond

first: Eun-Ah

last: Sung

address: 401 College Street

institute: Virginia Common Wealth University

data_processing:
The quality of RNA-seq reads was assessed with FastQC v0.11.9
The reads were aligned using STAR aligner v2.7.6a to mouse reference genome GRCm39
Raw gene counts of mapped reads were aggregated using featurCounts
The differential gene expression analysis was performed
with Bioconductor package DESeq2 v1.30.0 using the normalized and filtered counts per gene from the RNAseq analysis
Differentially expressed genes with adjusted p value < 0.05 were subject to further downstream bioinformatics analysis

source_name: bone marrow-derived macrophages

growth_protocol: 1x106 BMDMs/well were plated in 6-well tissue culture-treated dishes and placed in a 5% CO2 37 °C incubator for 24 hours

extract_protocol:
RNA was isolated using the Trizol and RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

treatment_protocol: BMDMs were either left unstimulated, or stimulated with DKK1 (30 ng/ml), IL-13 (2 ng/ml) or DKK1 and IL-13  for 24 hrs.

value: bone marrow-derived macrophages

tag: background strain

value: wild-type

value: DKK1 stimulation for 24 hr


title: WT_IL-13+DKK1_rep3

value: IL-13+DKK1 stimulation for 24 hr


title: WT_IL-13+DKK1_rep2


title: WT_DKK1_rep2


title: WT_IL-13+DKK1_rep1


title: blood_LW_24 [GC31996]


title: blood_F1_24 [GC31995]


title: WT_IL-13_rep1

value: IL-13 stimulation for 24 hr


title: WT_IL-13_rep2


title: WT_unstim_rep3

value: untreated


title: WT_DKK1_rep1


title: WT_unstim_rep1


title: OVERLOAD, replicate 1, scRNA-seq

city: Lexington

first: Ahmed

last: Ismaeel

state: Kentucky

address: 900 S Limestone St

department: Physiology

institute: University of Kentucky

description: 10x Genomics

data_processing:
Read sequences in fastq format were aligned to the mouse genome (mm10 build 2020-A, Ensembl release 98) using Cell Ranger v6.0.0 (10X Genomics). The filtered count matrices from Cell Ranger, including gene symbols and cell barcodes, were imported into R v4.0.2 programming environment using Seurat v4.0.2 and normalized using SCTransform
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Plantaris Muscle

growth_protocol: Mice housed in a humidity- and temperature-controlled facility, maintained on a 14:10 hour light-dark cycle with food and water ad libitum. A 6-month-old Pax7rtTA; TRE-H2B-GFP mouse was administered doxycycline (2.0 mg/mL) in drinking water supplemented with 2% sucrose for 2 weeks.

extract_protocol:
To generate a single-cell suspension, fresh plantaris muscle was first digested using collagenase II, followed by collagenase and dispase treatment. The cell suspension was serially passed through a 70 µm and 40 µm filter and incubated with antibodies against VCAM, CD31, CD45, and Sca1 at 4°C. A biotinylated secondary antibody was used for VCAM, while all other antibodies were PE-Cy7-conjugated. Immediately following the incubation, cells were pelleted (500 x g for 5 minutes), re-suspended in FACS sorting buffer, and sorted using an iCyt FACS machine (Sony Biotechnology, Champaign, IL, USA).
Cells were then loaded into the 10X Chromium Controller using the Single Cell 3' reagent kit according to the manufacturer’s protocol. RNA sequencing libraries were prepared and were sequenced on the Illumina NextSeq 500 platform, achieving a minimum of 40,000 reads per sample.

treatment_protocol: The synergist ablation surgery places a mechanical overload (MOV) on the plantaris muscle of the lower hind limb that induces a growth response associated with robust MuSC activation, proliferation and myofiber fusion. Mice were anesthetized (3% isoflurane with 1.5L of O2 per minute), placed in sternal recumbence, where a small incision was made on the dorsal aspect of the lower hind limb, with the distal portion of the gastrocnemius muscle tendon and approximately half of the soleus muscle carefully excised. No apparent damage was observed to the neural and/or vascular supply of the plantaris muscle following the surgery. At the designated time point post-surgery, mice were euthanized via CO2 inhalation followed by cervical dislocation with muscle collected and prepared accordingly for downstream analyses. The sham surgery consisted of performing the incision and carefully probing the plantaris tendon, without removing the tendon or muscle.

value: Muscle Stem Cells

value: Plantaris Muscle

tag: strain

value: Pax7rtTA; TRE-H2B-GFP

tag: age

value: 26 weeks old

value: Overload


title: SHAM, replicate 1, scRNA-seq

description: 10x Genomics

value: Sham


title: blood_LW_24 [GC32014]


title: Mammary epithelium basal cells, wildtype, bio rep 3

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Sequencing was undertaken on an Illumina NextSeq 500 to produce 81bp pair-end reads.
Read alignment was performed with the align function of the Rsubread package version 2.6.1.
Genewise read counts were obtained with the featureCounts function of the Rsubread package and Rsubread's inbuilt mm10 annotation.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files with columns for Entrez Gene ID, gene length (number of bases in union of all exons), and the number of reads. The supplementary file GenewiseCounts.txt.gz gives read counts for all samples in one file.

source_name: Mammary epithelium

extract_protocol:
miRNeasy micro kit (Qiagen Cat#217084) following manufacturer's protocol.
Illumina TruSeq RNA v2 protocol (Illumina #RS-122-2001, RS-122-2002).

value: MMTVcre Brca2(fl/fl) Trp53(fl/+)

value: Mammary epithelium

value: Basal

value: WT