title: RNA-seq_ES_JB_rep1

status: Public on Feb 05 2024

city: Clermont-Ferrand

first: franck

last: court

address: 28 Place Henri Dunant

institute: GReD CNRS

data_processing:
RNA-seq were mapped on the mouse genome (mm39 masked  for JF1 SNPs) using TopHat2 with a transcript annotation file from UCSC (refGene track).
The read count per gene was obtained with the HTseq-count script on properly paired reads and RefGene transcript annotation file.
Differential expression analysis between groups was based on read count using DESeq2 and edgeR R packages.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include count values per gene

growth_protocol: ES cell lines were maintained in gelatin-coated dishes with ESGRO complete plus medium (Millipore, SF001-500P) containing LIF, BMP4, and a GSK3-β inhibitor. ES-derived neural precursor cells were generated using in vitro corticogenesis as described in Montibus et al 2021 (PMID: 32405722).

extract_protocol:
The total RNA were extracted using the RNeasy MiniKit (Qiagen, 74104) following the manufacturer's protocol. RNA samples were quality-checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies).
TruSeq Stranded mRNA library preparation or NEBNext® Ultra™ II mRNA-Seq library preparation  and sequencing on illumina  HiSeq4000  or Illumina NovaSeq 6000 were performed by Integragen, SA (Evry, France), according to the manufacturer's protocol.

value: ES cells

value: JF1 x C57BL/6


title: RNA-seq_ES_JB_rep2

type: SRA

country: France

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: cell line

tag: cell type

tag: genotype


title: RNA-seq_ES_BJ_rep1

value: C57BL/6 x JF1


title: RNA-seq_ES_BJ_rep2


title: BM_CR_123

status: Public on Jan 11 2024

city: Heidelberg

first: Anna

last: Mathioudaki

state: None / N/A

address: Meyerhofstraße 1, 1

country: Germany

institute: EMBL Heidelberg

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Sample demultiplexing based on genotypes was performed using souporcell (https://www.nature.com/articles/s41592-020-0820-1)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: Bone marrow aspirates

extract_protocol:
Ficoll-processed primary BM samples were sorted into CD34+ and CD3+ fractions.
Library was performed according to the manufacter’s protocol CG000204 (single cell 3’ v2 protocol, 10x Genomics).

value: T cells & HSPCs

tag: tissue

value: Bone marrow aspirates

tag: patient diagnosis

value: acute myeloid leukemia

tag: disease state

value: complete remission (CR)


title: 15278_Eye_8PCW

status: Public on Nov 29 2023

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

country: United Kingdom

institute: Newcastle University

data_processing:
The BCL files were de-multiplexed using CellRanger mkfastq version 3.01 and then aligned and quan-tify them against the human reference genome GRCh38 using Cellranger count
We performed quality control checks for each sample in R for each sample and removed any cells with fewer than 1000 reads or 500 genes or greater than 10% mitochondrial reads. Any cells which expressed haemoglobin genes were also removed from the analysis. Doublets were predicted using DoubletFinder and filtered from the data.
The Seurat R package (version 4.3.0) was then used to process the data prior to integration. Firstly the raw data was normalised using the standard parameters.

source_name: Whole Eye

extract_protocol:
All samples were isolated and dissociated to single cells using a neurosphere dissociation kit (Miltenyi Biotech).
Libraries generated using the Chromium Single Cell 3’ Library & Gel Bead Kit (version 3, 10x Genomics)
Single cell RNA-Seq libraries were sequenced to 50,000 reads per cell on an Illumina NovaSeq 6000

value: Whole Eye

tag: developmental stage


title: 10PCW_232020_Retina_10PCW

source_name: Retina

value: Retina


title: 15222_Eye_7.7PCW


title: 14817_Eye_8PCW


title: 15046_Eye_7.5PCW


title: Day 59 Human Fetal Retina Paired snRNA snATAC [snRNA-seq]

status: Public on Oct 30 2023

city: Seattle

first: Thomas

last: Reh

state: Washington

address: 1959 NE Pacific Street, UW School of Medicine, Seattle, WA 98195

department: Department of Neurobiology and Biophysics

country: USA

institute: University of Washington

description:
d59_fetal_gex
10x Genomics

data_processing:
Read demutliplexing and intensity to fastq conversion done using cellranger mkfastq or cellranger-atac mkfastq
(RNA samples only): Gene by cell matricies were created using cellranger count
(Multiome samples only): Reads were alligned, peaks were called, and fragment files and peak x cell matricies were created using cellranger-atac count
(Multiome samples only): Peaks were re-called using Macs2 (through Signac) and new peak x cell matricies were created using Signac::FeatureMatrix()
Downstream processing was preformed in R using Seurat, Signac, ChromVar, and Monocle3
Assembly: GRCh38-2020-A
Supplementary files format and content: (Multiome samples only): CellRanger outputs: filtered feature bc matrices h5, fragment files, and barcode metrics
Supplementary files format and content: (RNA samples only): CellRanger outputs: filter feature bc matrices h5

molecule: nuclear RNA

source_name: retina

extract_protocol:
Tissue was dissociated with papaine and DNase (Worthington),. Cultured cells were dissociated with Accutase (Sigma). All dissociated cells spun at 300 g (4 C), then resuspended in culture medium to reach 1000 cells/uL.
10x Chromium Single Cell 3' V3.1 (scRNA-seq) and 10x Chromonium Next Gem Single Cell Multiome ATAC + Gene Expression (Multiome)

value: retina

tag: age

tag: cellranger version


title: 14849_Eye_10PCW


title: 14601.fixed_Eye_10PCW


title: 15189.2_Eye_8.5PCW


title: 14601_Eye_10PCW


title: mTeSR, rep 2

status: Public on Oct 10 2023

city: Houston

first: Aryeh

last: Warmflash

state: TX

address: 6100 Main St

institute: Rice University

data_processing:
To quantify the abundance of transcripts for each sample, Salmon v1.8.0 was used (Rob Patro et al.). To align our data, we used the human transcriptome (GRCh38) index for salmon, with salmon index using the selective alignment method (salmon_sa_index:default in http://refgenomes.databio.org/v3/genomes/splash/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4). We quantified transcripts with Salmon using the -l A flag to infer the library type (paired-end) automatically and the –validateMappings -o flag to use the mapping-based mode. The resulting datasets were then processed using the tximeta2 package in R (Love et al., 2020), and the counts matrix was exported for downstream analyses in MATLAB
Assembly: GRCh38
Supplementary files format and content: Excel file with the counts matrix for each replicate in each sample, obtained by processing the Salmon output with the tximeta2 package in R.

growth_protocol: hPSCs were grown in the chemically defined medium mTeSR1 in tissue culture dishes and kept at 370C, 5% CO2

extract_protocol:
Total RNA was collected with the Invitrogen RNAqueous-Micro Total RNA Isolation Kit. Processed RNA was stored at −80 ̊C, and RNA integrity was checked by Nanodrop, agarose gel electrophoresis, and qPCR and the Agilent 2100 system. Sequencing was performed by Novogene Co. using the Illumina paired-end 150 platform (HiSeq2500). Another biological repeat was performed using the same protocol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: hPSCs were seeded at the density 200k per well in a 12-well plate 24 hours before treatment, and were kept in mTeSR1. hPSCs were all grown in mTeSR1 for the length of the protocol with the addition of the recombinant proteins or small molecules when specified: untreated pluripotent cells grown in mTeSR1, hPSCs treated with WNT3a (300ng/ml) in mTeSR1 for 6 hours, hPSCs treated with WNT3a (300ng/ml)  in mTeSR1 for 18 hours or hPSCs treated with CHIR (8uM)  in mTeSR1 for 6 hours.

value: hPSCs

value: WT

tag: treatment


title: Pigf_KO_Day_0_clone 2_biol rep 2

status: Public on May 19 2024

city: Madrid

first: Vicente

middle: Pérez

last: García

state: Madrid

address: C/ Nicolás Cabrera 1

department: Tissue and organ homeostasis

country: Spain

institute: Centro de Biologia Molecular Severo Ochoa

data_processing:
Reads were mapped to Mus musculus GRCm38 genome  assembly using HISAT2 v2.1.0.
Read counts and normalization were performed with SeqMonk software.
Assembly: GRCm38
Supplementary files format and content: Matrix with raw counts for each sample per column

extract_protocol:
Total RNA was extracted with Trizol followed by Dnase treatment using TURBO DNA-free kit (Life Technologies AM1907).
RNA-seq libraries were generated from 500ng using TruSeq Stranded mRNA library prop (Illumina, 20020594).

value: Trophoblast stem cells

tag: time point


title: Pigf_KO_Day_0_clone 4_biol rep 4


title: 15189.1_Eye_8.5PCW


title: MuSC RNA-seq I BMP6 biol rep 2b

status: Public on Oct 01 2023

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

institute: Charite

description:
GSE159594_TPM_joined.tab: TPM_BGI_1_IP77_B
GSE159594_FPKM_joined.tab: FPKM_BGI_1_IP77_B
MuSC IP77, 100 ng/ml BMP6 (solved in 4 mM HCl containing 0.1% BSA) for 1 hour, replicate 2

data_processing:
FASTQ files were aligned to the mouse genome: GeneCode M32 (GRCm39) using STAR v2.7.11a with the following settings: --runThreadN 36 --outReadsUnmapped Fastx --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66 --seedSearchStartLmax 25 --alignSoftClipAtReferenceEnds No --outSAMattrIHstart 0 --alignEndsType EndToEnd --twopassMode Basic. The resulting *.bam file was sorted and indexed using samtools v1.17.
The sorted *.bam file was passed to StringTie v2.2.1 with the following settings: -u -p 36. The resulting *.gtf files were merged using stringtie merge and normalized read counts (TPM and FPKM) were generated using stringtie ballgown. The read counts of all experimental samples were then concatenated into a single table: output.tpm.csv and output.fpkm.csv.
Genome_build: GeneCode M32 (GRCm39)
Supplementary_files_format_and_content: Stringtie ballgown output files: *.cov.refs.ballgown.gtf => contains details of the transcripts that StringTie assembles from RNA-Seq data in the GTF format; *.gene_abund.ballgown.tab => contains gene abundance counts as normalized FPKM and TPM values as a CSV table; *.out.ballgown.gtf => This is a file listing all the transcripts in the reference annotation that are fully covered, end to end, by reads. The output format is a GTF file as described above. Each line of the GTF is corresponds to a gene or transcript in the reference annotation.
Supplementary_files_format_and_content: FPKM_joined.tab, FPKM_joined.csv, TPM_joined.tab, TPM_joined.csv => fused tables with all the samples of the experiment in CSV and EXCEL format provided as TPM and FPK values.

source_name: muscle

growth_protocol: Muscle stem cells were isolated from muscle of female 6-8-week-old mice, cultured on Matrigel® for expansion over 2 days. In order to limit the effect of BMPs in the culture medium (e.g. from serum supplements), cells were cultured prior to the BMP stimulation for 6 h in serum-free medium containing BMP soluble receptor (recombinant mouse BMPR-IA/ALK3-Fc Chimera, R&D Systems, 437-MR) in a concentration of 200 ng/ml.

extract_protocol:
Cells were lysed directly in their dish, homogenized, and stored at -80°C for subsequent RNA isolation. Lysis (RLT buffer+10% beta-ME), homogenization (QIAshredder, Qiagen), and total RNA extraction were done according to the manual of the RNeasy Micro kit (Qiagen, Hilden, Germany). The RNA concentration was measured using the NanoDrop2000 photometer and aliquots of 1-2 µg RNA were snap-frozen in liquid nitrogen and stored at -80°C.
The construction of the eukaryotic strand-specific transcriptome library was performed according to the ?SureSelect Strand-Specific RNA Library Prep for Illumina Multiplexed Sequencing Kit (Illumina). Briefly, 500 ng total RNA was enriched for polyA-carrying molecules using oligo-dT beads. The RNA was then fragmented and the first cDNA strand was synthesized using random primers. Second strand cDNA was synthesized and the resulting cDNA was subjected to end repair and 3' adenylation. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments, which were then amplified by PCR.
The library was then sequenced on a Illumina HiSeq 4000 machine as 50 bp single-end reads with an intended sequencing depth of >40 Mio reads. After removing of the sequencing adapters, the resulting FASTQ files were finally filtered for the desired length of 50 bp and for quality scores of Phred+33.

treatment_protocol: Cells were stimulated with a one-hour pulse with 100 ng/ml BMP4 or BMP6 or only with vehicle used for reconstitution of BMP in the case of controls.

value: 100 ng/ml BMP6

value: muscle stem cells

value: wildtype (C57BL/6J)

tag: biological replicate


title: MuSC RNA-seq I BMP6 biol rep 1b

description:
GSE159594_TPM_joined.tab: TPM_BGI_1_IP75_B
GSE159594_FPKM_joined.tab: FPKM_BGI_1_IP75_B
MuSC IP75, 100 ng/ml BMP6 (solved in 4 mM HCl containing 0.1% BSA) for 1 hour, replicate 1


title: 15220_Eye_8PCW


title: MuSC RNA-seq I control biol rep 1b

description:
GSE159594_TPM_joined.tab: TPM_BGI_1_IP75_A
GSE159594_FPKM_joined.tab: FPKM_BGI_1_IP75_A
MuSC IP75, Vehicle (4 mM HCl containing 0.1% BSA) for 1 hour, replicate 1

value: vehicle (control)


title: MuSC RNA-seq I control biol rep 2a

description:
GSE159594_TPM_joined.tab: TPM_BGI_1_IP54_A
GSE159594_FPKM_joined.tab: FPKM_BGI_1_IP54_A
MuSC IP54, Vehicle (4 mM HCl containing 0.1% BSA) for 1 hour, replicate 2


title: MuSC RNA-seq I BMP4 biol rep 1a

description:
GSE159594_TPM_joined.tab: TPM_BGI_1_IP48_B
GSE159594_FPKM_joined.tab: FPKM_BGI_1_IP48_B
MuSC IP48, 100 ng/ml BMP4 (solved in 4 mM HCl containing 0.1% BSA) for 1 hour, replicate 1

value: 100 ng/ml BMP4


title: MuSC RNA-seq I BMP4 biol rep 2a

description:
GSE159594_TPM_joined.tab: TPM_BGI_1_IP54_B
GSE159594_FPKM_joined.tab: FPKM_BGI_1_IP54_B
MuSC IP54, 100 ng/ml BMP4 (solved in 4 mM HCl containing 0.1% BSA) for 1 hour, replicate 2


title: BM_REL_123

description: 10x Genomics

value: relapse (REL)


title: Vector_Day_0_ clone1_biol rep 1

value: Vector


title: MuSC RNA-seq I control biol rep 1a

description:
GSE159594_TPM_joined.tab: TPM_BGI_1_IP48_A
GSE159594_FPKM_joined.tab: FPKM_BGI_1_IP48_A
MuSC IP48, Vehicle (4 mM HCl containing 0.1% BSA) for 1 hour, replicate 1


title: PC-9_OE_2

status: Public on Sep 20 2023

city: Shanghai

first: Shaohua

last: Wang

address: No 12 Middle Wulumuqi Road

country: China

institute: Department of Thoracic Surgery

data_processing:
Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Bioconductor DESeq2 (V1.6.3) used for differential analysis
Assembly: GRCh37
Supplementary files format and content: xlsx file for differential gene expression information for OE_1/2/3 vs con_1/2/3

source_name: c-Jun overexpression plasmid transfected PC-9

growth_protocol: PC-9 cells were cultured in Dulbecco's modified eagle medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS), 100 U/mL penicillin and 100 µg/mL streptomycin.

extract_protocol:
mRNA was isolated from total RNA using NEB Next poly (A) mRNA Magnetic Isolation Module (NEB, MA, USA) and rRNA was removed using RiboZero Magnetic Gold Kit (Epicentre NY, USA).
RNA library was prepared using KAPA Stranded RNA-SEQ Library Prep Kit (illumina, CA, USA) according to instruction manual prior to subject to sequencing using illumina NovaSeq 6000.

value: Lung adenocarcinoma (LUAD)

value: untreated


title: MuSC RNA-seq I control biol rep 2b

description:
GSE159594_TPM_joined.tab: TPM_BGI_1_IP77_A
GSE159594_FPKM_joined.tab: FPKM_BGI_1_IP77_A
MuSC IP77, Vehicle (4 mM HCl containing 0.1% BSA) for 1 hour, replicate 2


title: PC-9_OE_1

value: c-Jun overexpression plasmid transfected PC-9


title: PC-9_OE_3


title: PC-9_Con_1

source_name: Mock transfected PC-9

value: Mock transfected PC-9


title: PC-9_Con_2


title: UC c_UC colon

status: Public on Jun 13 2023

type: RNA

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

institute: IDIBAPS

description: UC c

hyb_protocol: NanoString® ISH probes were prepared by incubation at 95°C for 2 min and placed on ice, and the ISH probe mix (1nM 980 plex ISH probe, 10nM Attenuation probes, 1nM SMI-0006 custom, 1X Buffer R, 0.1 U/μL SUPERase•In™ [Thermo Fisher Scientific] in DEPC H2O) was pipetted into the hybridization chamber. The chamber was sealed to prevent evaporation, and hybridization was performed at 37°C overnight. Tissue sections were washed twice in 50% formamide (VWR) in 2X SSC at 37°C for 25 min, washed twice with 2X SSC for 2 min at room temperature, and blocked with 100 mM NHS-acetate in the dark for 15 min. In preparation for loading onto the CosMx SMI instrument, a custom-made flow cell was affixed to the slide.

scan_protocol: RNA target readout on the CosMx SMI instrument was performed. Briefly, the assembled flow cell was loaded onto the instrument and Reporter Wash Buffer was flowed to remove air bubbles. A preview scan of the entire flow cell was taken, and 15-25 fields of view (FoVs) were placed on the tissue to match regions of interest identified by H&E staining of an adjacent serial section. RNA readout began by flowing 100 μl of Reporter Pool 1 into the flow cell and incubation for 15 min. Reporter Wash Buffer (1 mL) was flowed to wash unbound reporter probes, and Imaging Buffer was added to the flow cell for imaging. Nine Z-stack images (0.8 μm step size) for each FoV were acquired, and photocleavable linkers on the fluorophores of the reporter probes were released by UV illumination and washed with Strip Wash buffer. The fluidic and imaging procedure was repeated for the 16 reporter pools, and the 16 rounds of reporter hybridization-imaging were repeated multiple times to increase RNA detection sensitivity. After RNA readout, the tissue samples were incubated with a 4-fluorophore-conjugated antibody cocktail against CD298/B2M (488 nm), PanCK (532 nm), CD45 (594 nm), and CD3 (647 nm) proteins and DAPI stain in the CosMxTM SMI instrument for 2 h. After unbound antibodies and DAPI stain were washed with Reporter Wash Buffer, Imaging Buffer was added to the flow cell and nine Z-stack images for the 5 channels (4 antibodies and DAPI) were captured.

data_processing:
Images were segmented to obtain cell boundaries, assign transcripts at the cell-level, and obtain a transcript by cell count matrix. Cells with an average negative control count greater than 0.5 and less than 20 detected features were filtered out. After quality control, a mean of 95,3% of cells across samples and FoVs was retained, corresponding to ~46,160 cells per sample on average.
CosMx_normalized_matrix.txt: Counts of molecules for each gene in each segmented cell.
a.csv, b.csv, c.csv: Spatial transcriptomics polygon data.

label: SMI imaging barcodes

source_name: UC colon

label_protocol: After HIER, tissue sections were digested with 3 µg/ml Proteinase K diluted in ACD Protease Plus at 40°C for 30 minutes. Tissue sections were then washed twice with diethyl pyrocarbonate (DEPC)-treated water (DEPC H2O) and incubated in 0.00075% fiducials (Bangs Laboratory) in 2X saline sodium citrate, 0.001% Tween-20 (SSCT solution) for 5 min at room temperature in the dark. Excess fiducials were rinsed from the slides with 1X PBS, then tissue sections were fixed with 10% neutral buffered formalin (NBF) for 5 min at room temperature. Fixed samples were rinsed twice with Tris-glycine buffer (0.1M glycine, 0.1M Tris-base in DEPC H2O) and once with 1X PBS for 5 min each before blocking with 100 mM N-succinimidyl (acetylthio) acetate (NHS-acetate, Thermo Fisher Scientific) in NHS-acetate buffer (0.1M NaP, 0.1% Tween pH 8 in DEPC H2O) for 15 min at room temperature. The sections were then rinsed with 2X saline sodium citrate (SSC) for 5 min and an Adhesive SecureSeal Hybridization Chamber (Grace Bio-Labs) was placed over the tissue.

extract_protocol: FFPE tissue sections were prepared for CosMxTM SMI profiling. Briefly, five-micron tissue sections mounted on VWR Superfrost Plus Micro slides (cat# 48311-703) were baked overnight at 60°C, followed by preparation for in-situ hybridization (ISH) on the Leica Bond RXm system by deparaffinization and heat-induced epitope retrieval (HIER) at 100°C for 15 minutes using ER2 epitope retrieval buffer (Leica Biosystems product, Tris/EDTA-based, pH 9.0).

treatment_protocol: Surgical samples were fixed in formalin and paraffin embedded (FFPE) for CosMxTM SMI and tissue staining (IHC IF, ISH).

value: colon

tag: gender

value: male

tag: biopsy

value: sigmoid colon

tag: disease

value: ulcerative colitis (UC)


title: UC b_UC colon

description: UC b

value: female


title: HC a_non-IBD colon

description: HC a

source_name: non-IBD colon

value: healthy (non-IBD)


title: CD a_CD colon

description: CD a

source_name: CD colon

value: Crohn's disease (CD)


title: CD c_CD colon

description: CD c

value: transverse colon


title: CD b_CD colon

description: CD b


title: PC-9_Con_3


title: SOC, replicate 4, scRNAseq

status: Public on Jun 01 2023

city: Pittsburgh

first: Lillian

last: Tran

state: Pennsylvania

address: 200 Lothrop Street

department: Surgery

institute: University of Pittsburgh

description:
10x Genomics
DCREG_SOC 004

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Filtered gene-barcode matrices generated using the 10X Genomics Cell Ranger analysis pipeline were pre-processed and analyzed with the R package Seurat version 4.0
Cells with detected gene number between 500 and 6000, mitochondrial gene percentage < 35%, and hemoglobin gene percentage < 0.5% were kept for further downstream analysis
Assembly: Hg38
Supplementary files format and content: matrix files

source_name: Liver allograft

extract_protocol:
Freshly collected 18g core biopsy of liver allograft tissue obtained 12 months post-transplant from 4 STUDY and 4 SOC living donor liver transplant patients was minced into small pieces and incubated with 1 mg/ml collagenase digestion solution at 37 °C for 8 minutes. The isolated liver cell suspensions were resuspended in 20%∆ FCS, 2mM EDTA, 1XPBS solution. Cells were washed and re-suspended in 4% Ultrapure BSA/1x DPBS
Library was performed according to the manufacter’s instructions (single cell 3’ v3 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: non-parenchymal, parenchymal

value: Liver allograft

tag: time

value: 12 months post-transplant


title: SOC, replicate 3, scRNAseq

description:
10x Genomics
DCREG_SOC 003


title: MuSC Microarray control biol rep 3

description:
Gene expression data from control treated MuSC
MuSC vehilce treated, biological rep. 3

hyb_protocol: Biotinylated cDNA was hybridized to the array at 45°C, 60 rpm for 16 h. The hybridized array was stained with streptavidin phycoerythrin conjugate using the Affymetrix GeneChip® Fluidics Station 450. Hybridization and staining steps were done with the Affymetrix GeneChip® Hybridization, Wash, and Stain Kit.

scan_protocol: The arrays were scanned with the Affymetrix GeneChip® Scanner 3000 G7.

data_processing: Microarray data were analyzed with the R packages "affy" and "oligo" of the Bioconductor suite. Data quality control was carried out by creating pseudo images for each array using the "oligo" package and visually inspecting them for the presence of artifacts. The raw count *.CEL files were normalized using Robust Multichip Averaging (RMA) with quantile normalization, background correction, and annotation (using the MG 1.0 ST Chip Description File "mogene10stv1cdf" from Bioconductor).

label: biotin

source_name: MuSC from mouse #2 treated with vehicle

label_protocol: Affymetrix GeneChip™ WT PLUS Reagent Kit was used to generate sense-strand target (ST) cDNA. Briefly, first-cycle cDNA was generated from total RNA using a reverse transcription priming method that specifically primes non-ribosomal RNA from the sample, including both poly(A) and nonpoly(A) mRNA. This was then used to generate antisense cRNA by in vitro transcription. The second-cycle ST cDNA was synthesized from cRNA using random primers resulting in a product that contained dUTP at a fixed ratio relative to dTTP. Uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1) were then used to recognize and fragment the cDNA at the unnatural dUTP residues. Fragmented cDNA was then biotinylated by terminal deoxynucleotidyl transferase (TdT). Fragmentation and biotinylation were done with the Affymetrix GeneChip® WT Terminal Labeling Kit.

growth_protocol: Muscle stem cells were isolated from muscle of female 6-8-week-old mice, cultured on Matrigel® for expansion over 2 days. In order to limit the effct of BMPs in the culture medium (e.g. from serum supplements), cells were cultured prior to the BMP stimulation for 6 h in serum-free medium containing BMP soluble receptor (recombinant mouse BMPR-IA/ALK3-Fc Chimera, R&D Systems, 437-MR) in a concentration of 200 ng/ml. Cells were then stimulated for 1 h with a pulse of of 100 ng/ml BMP4 or BMP6 or only with vehicle used for reconstitution of BMP in the case of controls.

extract_protocol: Total RNA was extracted. Cells were lysed directly in their dish, homogenized, and stored at -80 deg C for subsequent RNA isolation. Lysis (RLT buffer+10% βME), homogenization (QIAshredder, Qiagen), and total RNA extraction were done according to the manual of the RNeasy Micro kit (Qiagen).

treatment_protocol: Cells were stimulated with a pulse of 1 h duration with 100 ng/ml BMP6 or only with vehicle used for reconstitution of BMP in case of controls.

value: control

value: adult muscle stem cells

tag: mouse strain


title: UC a_UC colon

description: UC a


title: MuSC Microarray BMP6 biol rep 1

description:
Gene expression data from BMP6 treated MuSC
MuSC BMP6 treated, biological rep. 1

source_name: MuSC from mouse #1 treated with 100 ng/ml BMP6

value: BMP6 [100 ng/ml]


title: 630CMOBSuccinate_4

status: Public on May 24 2023

city: Paris

first: Marc

last: Monot

address: 28 rue du docteur roux

institute: Institut Pasteur

description: 633 C. difficile strains in MOB medium with Succinate

data_processing:
The RNA‐seq analysis was performed with the Sequana framework (Cokelaer et al, 2017 doi:10.21105/joss.00352)
Version used: RNA‐seq pipeline (v0.13.0)
Reads were trimmed from adapters using Cutadapt 2.10
Then mapped to the Clostridium difficile 630 genome using Bowtie2
Differential expression testing was conducted using DESeq2 library 1.24.0, scripts based on SARTools 1.7.0
Assembly: Clostridioides difficile 630 (NC_009089.1) complemented by the known ncRNA (PMID: 23675309)
Supplementary files format and content: Files in CSV that contains Gene_ID, log2FoldChange, pvalue

organism: Clostridioides difficile

growth_protocol: Strains were grown in anaerobic conditions (5% H2, 5% CO2, 90% N2) in MOB at 37°C with or without 120mM of Succinate

extract_protocol:
Cells were harvested at an OD of 0.6 by centrifugation for 2 min at 4°C. The cells were first broken by shaking in a Fastprep apparatus for 2 x 30 sec in the presence of one gram of 0.1-mm diameter glass Sigma beads, then treated with Trizol reagent, chloroform/ isoamylalcohol and precipitated with isopropanol. The pellet was resuspended in TE
RNA libraries were prepared for sequencing using standard Illumina protocols
Illumina stranded Total RNA prep Ligation kit with RiboZero Plus

treatment_protocol: Bacterial strains and plasmids used in this study are listed in Table S1 C. difficile strains were grown anaerobically in MOB medium

tag: strain

value: wild type


title: MuSC Microarray BMP6 biol rep 2

description:
Gene expression data from BMP6 treated MuSC
MuSC BMP6 treated, biological rep. 2

source_name: MuSC from mouse #2 treated with 100 ng/ml BMP6


title: MuSC Microarray control biol rep 2

description:
Gene expression data from control treated MuSC
MuSC vehicle treated, biological rep. 2


title: MuSC Microarray control biol rep 1

description:
Gene expression data from control treated MuSC
MuSC vehicle treated, biological rep. 1

source_name: MuSC from mouse #1 treated with vehicle


title: 630CMOBSuccinate_3

description: 632 C. difficile strains in MOB medium with Succinate


title: SOC, replicate 1, scRNAseq

description:
10x Genomics
DCREG_SOC 001

tag: cell type


title: SOC, replicate 2, scRNAseq

description:
10x Genomics
DCREG_SOC 002


title: MuSC Microarray BMP6 biol rep 3

description:
Gene expression data from BMP6 treated MuSC
MuSC BMP6 treated, biological rep. 3

source_name: MuSC from mouse #3 treated with 100 ng/ml BMP6


title: HC c_non-IBD colon

description: HC c


title: 630CMOBSuccinate_2

description: 631 C. difficile strains in MOB medium with Succinate

tag: genotype


title: 630CMOBSuccinate_1

description: 630 C. difficile strains in MOB medium with Succinate


title: 630CMOB_4

description: 630 C. difficile strains in MOB medium


title: 630CMOB_1

description: 630 C. difficile strains in MOB medium


title: 630CMOB_3

description: 630 C. difficile strains in MOB medium


title: 630CMOB_2

description: 630 C. difficile strains in MOB medium


title: 630BMOB_1

description: 630 C. difficile strains in MOB medium


title: 630BMOBSuccinate_2


title: 630BMOBSuccinate_4


title: 630BMOB_4

description: 630 C. difficile strains in MOB medium


title: 630p1687BHI_4

status: Public on Apr 19 2023

description: 630 1687 plasmid C. difficile strains with 240µM Deoxycholate in BHIG medium

data_processing:
The RNA‐seq analysis was performed with the Sequana framework (Cokelaer et al, 2017 doi:10.21105/joss.00352)
Version used: RNA‐seq pipeline (v0.13.0)
Reads were trimmed from adapters using Cutadapt 2.10
Then mapped to the Mus musculus GRCm38/mm10 genome using STAR 2.7.3a
Differential expression testing was conducted using DESeq2 library 1.24.0, scripts based on SARTools 1.7.0
Assembly: Clostridioides difficile 630 (NC_009089.1) complemented by the known ncRNA (PMID: 23675309)
Supplementary files format and content: Files in CSV that contains Gene_ID, log2FoldChange, pvalue

growth_protocol: Strains were grown aerobically in BHISG at 37°C with 240µM of Deoxycholate

treatment_protocol: Bacterial strains and plasmids used in this study are listed in Table S1 C. difficile strains were grown anaerobically in BHISG medium (BHI with 0.5% (w/v) yeast extract, 0.01 mg/mL cysteine and 100mM glucose)

value: wild type + 1687 plasmid


title: 630BMOBSuccinate_1


title: 630p1687BHI_3


title: 630BMOBSuccinate_3


title: 630pVideBHI_3

description: 630 empty plasmid C. difficile strains with 240µM Deoxycholate in BHIG medium

value: wild type + empty plasmid


title: 630pVideBHI_4


title: 630p1687BHI_2


title: 630pVideBHI_1


title: 1687BHIDOC_4

description: 630 delta 1687 C. difficile strains with 240µM Deoxycholate in BHIG medium

value: CD1687 Mutant


title: 630pVideBHI_2


title: 630p1687BHI_1


title: 1687BHIDOC_2


title: 630BMOB_3

description: 630 C. difficile strains in MOB medium


title: 630BHIDOC_4

description: 630 C. difficile strains with 240µM Deoxycholate in BHIG medium


title: 630BMOB_2

description: 630 C. difficile strains in MOB medium


title: 630BHIDOC_3


title: 1687BHIDOC_1


title: 630BHIDOC_2


title: GenolabM_A1-2

status: Public on Mar 13 2023

city: Tomsk

first: Irina

last: Larionova

state: Tomsk oblast

address: Lenin Ave, 36, Tomsk, Tomsk Oblast, Russia

country: Russia

institute: Tomsk State University

description:
Whole transcriptome probes
Instrument model used to produce the reads: GeneMind Genolab M
GenolabM_A1-2
Please note that the assigned instrument model "Illumina NovaSeq 6000" is a placeholder. The correct instrument model is: Genolab M

data_processing:
Raw sequencing reads were primary processed in the Space Ranger v.1.3 using the count command with default parameters. Raw reads were additionally assessed with FastQC quality control algorithm, and results were visualized with MultiQC tool.
After read mapping and counting, resulted feature-barcode matrix was uploaded into R environment and processed via the Seurat R package.
Normalization of the raw read counts in feature-barcode matrix was performed with the SCTransform function in the Seurat package.
Following dimension reduction and clusterization steps, the SCT normalized counts were used in Wilcoxon rank sum test to find differentially expressed genes.
Assembly: hg38
Supplementary files format and content: .h5 Filtered HDF5 Feature-Barcode Matrix
Supplementary files format and content: .json Scale factors for slide images
Supplementary files format and content: .png High resolution slide images
Supplementary files format and content: .png Low resolution slide images
Supplementary files format and content: .csv Tissue spot positions
Library strategy: Spatial Transcriptomics

source_name: Ovarian cancer

extract_protocol:
Three tumor FFPE samples obtained from patients with high-grade serous ovarian cancer were analyzed. Patients were treated in the Department of Gynecological Oncology, Cancer Research Institute of Tomsk National Research Medical Center (Tomsk, Russia). The study was carried out according to Declaration of Helsinki (from 1964, revised in 1975 and 1983) and was approved by the local committee of Medical Ethics of Tomsk Cancer Research Institute; all patients signed informed consent for the study. Shortly, FFPE tissue sections were placed on the Capture Areas of 10x Genomics Visium slides, deparaffinized, and stained by hematoxylin and eosin. Tumor tissue slides were scanned using the Leica Aperio AT2 station (Leica, Germany) and images were processed with Aperio ScanScope.
Libraries were prepared using standard protocol provided by 10x Genomics (User Guide | CG000407). The obtained cDNA libraries were analyzed following 10x Genomics sequencing recommendation for FFPE Visium libraries. Sequencing cycles comprised 28 bp (Read 1), 10 bp (Index 1 and 2) and 50 bp (Read 2). Illumina NextSeq 2000 sequencing was performed using NextSeq 1000/2000 P2 reagents (100 cycles), whereas GeneMind Genolab M used FCM reagents (150 cycles).

tag: tissue

value: Ovarian cancer

tag: patient

tag: slide

tag: area


title: GenolabM_B1-2

description:
Whole transcriptome probes
Instrument model used to produce the reads: GeneMind Genolab M
GenolabM_B1-2
Please note that the assigned instrument model "Illumina NovaSeq 6000" is a placeholder. The correct instrument model is: Genolab M

tag: disease state


title: D28 post-injury FDL, biol rep 2

status: Public on Oct 25 2022

city: Rocheser

first: Jessica

last: Ackerman

state: NY

address: 665 Elmwood Ave

institute: University of Rochester

data_processing:
Demultiplexing: spaceranger-1.3.1/spaceranger mkfastq --run=. --samplesheet=spaceRanger.csv --output-dir ./spaceRanger --nopreflight --jobmode=slurm --localcores=24 --localmem=120
Counting: spaceranger-1.3.1/spaceranger count --fastqs=./fastq_path --jobmode=slurm --maxjobs=100 --nopreflight --transcriptome=${REF} --project=${PROJECT} --id=Sample_${SAMPLEPREFIX} --sample=${SAMPLEPREFIX} --slide=${SLIDE} --area=${AREA} --image=${IMAGE}
Assembly: combined cellranger provided “refdata-gex-mm10 2020-A” and user provided tdTomato sequence
Supplementary files format and content: feature barcode matrix data (.tsv, .mtx)

source_name: murine hindpaw

extract_protocol:
Whole hindpaws from experimental mice were collected and fresh frozen prior to sectioning onto gene expression slides (10X Visium)
RNA extraction, cDNA amplification, and library construction were carried out according to the 10X Genomics Visium user guide, rev F

treatment_protocol: Experimental mice were given tamoxifen D-7 to -4 prior to complete transection and repair of the FDL tendon in the hindpaw to label resident Scx-lin+ cells and visualize their contribution

value: murine hindpaw

tag: age

value: 10-12 weeks

value: Scx-CreER; Ai9 F/+

value: Day 28


title: 630BHIDOC_1


title: D28 post-injury FDL, biol rep 1


title: D21 post-injury FDL, biol rep 2

value: Day 21


title: Uninjured FDL control, D0 biol rep 2

value: Day 0


title: D14 post-injury FDL, biol rep 2

value: Day 14


title: 4797-051-60

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description: Gene expression data from bronchial brushing 4797-051-60.

data_processing:
Demultiplexing and creation of FASTQ files were performed using BaseSpace.
Samples were aligned using hg19 and 2-pass STAR alignment (v2.5.2b). Gene-level posterior mean counts were calculated using RSEM (v1.3.0) and Ensembl Gene annotation build 75.
Posterior mean counts were filtered to exclude those that did not have more than one count per million (cpm) in at least 10% of the samples, and then corrected for sequencing batch using ComBat-seq.
Assembly: hg19
Supplementary files format and content: DECAMP_bronchial_COVID19_posterior_mean_counts.tsv: a tab-separated value (TSV) file containing the posterior mean counts as computed by RSEM
Supplementary files format and content: DECAMP_bronchial_COVID19_normalized_counts.tsv: a tab-separated value (TSV) file containing the ComBat-corrected counts for a subset of features that passed expression filtering.

source_name: Brushing of bronchial epithelium

extract_protocol:
Total RNA was isolated from nasal and bronchial brushings using the miRNeasy Mini Kit [QIAGEN].
Libraries were generated using the Illumina TruSeq Stranded Total RNA kit.

value: Brushing of bronchial epithelium

tag: subject

tag: Sex

value: Male

tag: smoking status

value: Former smoker

tag: fev1 %_predicted

tag: mp score


title: D21 post-injury FDL, biol rep 1


title: Uninjured FDL control, D0 biol rep 1


title: 4797-052-60

description: Gene expression data from bronchial brushing 4797-052-60.

value: Female


title: 4797-045-60

description: Gene expression data from bronchial brushing 4797-045-60.


title: 4797-041-60

description: Gene expression data from bronchial brushing 4797-041-60.


title: 1687BHIDOC_3


title: 4797-028-60

description: Gene expression data from bronchial brushing 4797-028-60.


title: GenolabM_A1-1

description:
Whole transcriptome probes
Instrument model used to produce the reads: GeneMind Genolab M
GenolabM_A1-1
Please note that the assigned instrument model "Illumina NovaSeq 6000" is a placeholder. The correct instrument model is: Genolab M


title: 4797-026-60

description: Gene expression data from bronchial brushing 4797-026-60.

value: Current smoker


title: 4797-033-60

description: Gene expression data from bronchial brushing 4797-033-60.


title: 4797-027-60

description: Gene expression data from bronchial brushing 4797-027-60.


title: 4797-031-60

description: Gene expression data from bronchial brushing 4797-031-60.


title: 4797-023-60

description: Gene expression data from bronchial brushing 4797-023-60.


title: 4797-025-60

description: Gene expression data from bronchial brushing 4797-025-60.


title: D14 post-injury FDL, biol rep 1


title: 4797-029-60

description: Gene expression data from bronchial brushing 4797-029-60.


title: 4797-046-60

description: Gene expression data from bronchial brushing 4797-046-60.


title: 4797-011-60

description: Gene expression data from bronchial brushing 4797-011-60.


title: 4797-014-63

description: Gene expression data from bronchial brushing 4797-014-63.


title: 4797-012-60

description: Gene expression data from bronchial brushing 4797-012-60.


title: 4797-008-60

description: Gene expression data from bronchial brushing 4797-008-60.


title: 4797-009-60

description: Gene expression data from bronchial brushing 4797-009-60.


title: 4797-007-60

description: Gene expression data from bronchial brushing 4797-007-60.


title: 4797-006-60

description: Gene expression data from bronchial brushing 4797-006-60.


title: 4797-020-60

description: Gene expression data from bronchial brushing 4797-020-60.


title: 4797-003-60

description: Gene expression data from bronchial brushing 4797-003-60.


title: 4797-010-60

description: Gene expression data from bronchial brushing 4797-010-60.


title: 4796-117-60

description: Gene expression data from bronchial brushing 4796-117-60.


title: 4797-022-60

description: Gene expression data from bronchial brushing 4797-022-60.


title: 4796-111-60

description: Gene expression data from bronchial brushing 4796-111-60.


title: 4797-043-60

description: Gene expression data from bronchial brushing 4797-043-60.


title: 4797-002-60

description: Gene expression data from bronchial brushing 4797-002-60.


title: 4796-110-60

description: Gene expression data from bronchial brushing 4796-110-60.


title: 4796-107-60

description: Gene expression data from bronchial brushing 4796-107-60.


title: 4796-108-60

description: Gene expression data from bronchial brushing 4796-108-60.


title: 4796-095-60

description: Gene expression data from bronchial brushing 4796-095-60.


title: 4796-099-60

description: Gene expression data from bronchial brushing 4796-099-60.


title: 4797-005-60

description: Gene expression data from bronchial brushing 4797-005-60.


title: 4796-091-60

description: Gene expression data from bronchial brushing 4796-091-60.


title: 4796-112-60

description: Gene expression data from bronchial brushing 4796-112-60.


title: 4796-102-60

description: Gene expression data from bronchial brushing 4796-102-60.


title: 4796-093-60

description: Gene expression data from bronchial brushing 4796-093-60.


title: 4796-103-60

description: Gene expression data from bronchial brushing 4796-103-60.


title: 4796-094-60

description: Gene expression data from bronchial brushing 4796-094-60.


title: 4796-106-60

description: Gene expression data from bronchial brushing 4796-106-60.


title: 4796-090-60

description: Gene expression data from bronchial brushing 4796-090-60.


title: 4796-084-60

description: Gene expression data from bronchial brushing 4796-084-60.


title: 4796-080-60

description: Gene expression data from bronchial brushing 4796-080-60.


title: 4796-088-60

description: Gene expression data from bronchial brushing 4796-088-60.


title: 4796-076-60

description: Gene expression data from bronchial brushing 4796-076-60.


title: 4796-073-60

description: Gene expression data from bronchial brushing 4796-073-60.


title: 4796-074-60

description: Gene expression data from bronchial brushing 4796-074-60.


title: 4796-072-60

description: Gene expression data from bronchial brushing 4796-072-60.


title: 4796-070-60

description: Gene expression data from bronchial brushing 4796-070-60.


title: 4796-069-60

description: Gene expression data from bronchial brushing 4796-069-60.


title: 4796-067-60

description: Gene expression data from bronchial brushing 4796-067-60.


title: 4796-065-60

description: Gene expression data from bronchial brushing 4796-065-60.


title: 4796-085-60

description: Gene expression data from bronchial brushing 4796-085-60.


title: 4796-060-60

description: Gene expression data from bronchial brushing 4796-060-60.


title: 4796-066-60

description: Gene expression data from bronchial brushing 4796-066-60.


title: 4796-064-60

description: Gene expression data from bronchial brushing 4796-064-60.


title: 4796-058-60

description: Gene expression data from bronchial brushing 4796-058-60.


title: 4796-057-60

description: Gene expression data from bronchial brushing 4796-057-60.


title: 4796-056-60

description: Gene expression data from bronchial brushing 4796-056-60.


title: 4796-054-60

description: Gene expression data from bronchial brushing 4796-054-60.


title: 4796-050-60

description: Gene expression data from bronchial brushing 4796-050-60.


title: 4796-059-60

description: Gene expression data from bronchial brushing 4796-059-60.


title: 4796-055-60

description: Gene expression data from bronchial brushing 4796-055-60.


title: 4796-051-60

description: Gene expression data from bronchial brushing 4796-051-60.


title: 4796-052-60

description: Gene expression data from bronchial brushing 4796-052-60.


title: 4796-046-60

description: Gene expression data from bronchial brushing 4796-046-60.


title: 4796-045-60

description: Gene expression data from bronchial brushing 4796-045-60.


title: 4796-053-60

description: Gene expression data from bronchial brushing 4796-053-60.


title: 4796-044-60

description: Gene expression data from bronchial brushing 4796-044-60.


title: 4796-047-60

description: Gene expression data from bronchial brushing 4796-047-60.


title: 4796-039-60

description: Gene expression data from bronchial brushing 4796-039-60.


title: 4796-043-60

description: Gene expression data from bronchial brushing 4796-043-60.


title: 4796-037-60

description: Gene expression data from bronchial brushing 4796-037-60.


title: 4796-035-60

description: Gene expression data from bronchial brushing 4796-035-60.


title: 4796-032-60

description: Gene expression data from bronchial brushing 4796-032-60.


title: 4796-031-60

description: Gene expression data from bronchial brushing 4796-031-60.


title: 4796-034-60

description: Gene expression data from bronchial brushing 4796-034-60.


title: 4796-033-60

description: Gene expression data from bronchial brushing 4796-033-60.


title: 4796-030-60

description: Gene expression data from bronchial brushing 4796-030-60.


title: 4796-027-60

description: Gene expression data from bronchial brushing 4796-027-60.


title: 4796-029-60

description: Gene expression data from bronchial brushing 4796-029-60.


title: 4796-024-60

description: Gene expression data from bronchial brushing 4796-024-60.


title: 4796-023-60

description: Gene expression data from bronchial brushing 4796-023-60.


title: 4796-025-60

description: Gene expression data from bronchial brushing 4796-025-60.


title: 4796-014-60

description: Gene expression data from bronchial brushing 4796-014-60.


title: 4796-008-60

description: Gene expression data from bronchial brushing 4796-008-60.


title: 4796-004-60

description: Gene expression data from bronchial brushing 4796-004-60.


title: 4796-015-60

description: Gene expression data from bronchial brushing 4796-015-60.


title: 4796-036-60

description: Gene expression data from bronchial brushing 4796-036-60.


title: 4796-041-60

description: Gene expression data from bronchial brushing 4796-041-60.


title: 4796-009-60

description: Gene expression data from bronchial brushing 4796-009-60.


title: 4796-016-60

description: Gene expression data from bronchial brushing 4796-016-60.


title: 4796-013-60

description: Gene expression data from bronchial brushing 4796-013-60.


title: 4795-144-60

description: Gene expression data from bronchial brushing 4795-144-60.


title: 4796-001-60

description: Gene expression data from bronchial brushing 4796-001-60.


title: 4795-141-60

description: Gene expression data from bronchial brushing 4795-141-60.


title: 4795-143-60

description: Gene expression data from bronchial brushing 4795-143-60.


title: 4795-124-60

description: Gene expression data from bronchial brushing 4795-124-60.


title: 4795-125-60

description: Gene expression data from bronchial brushing 4795-125-60.


title: 4795-119-60

description: Gene expression data from bronchial brushing 4795-119-60.


title: 4795-114-60

description: Gene expression data from bronchial brushing 4795-114-60.


title: 4795-123-60

description: Gene expression data from bronchial brushing 4795-123-60.


title: HC b_non-IBD colon

description: HC b

value: colon

tag: gender

value: female

tag: biopsy

value: descending colon

tag: disease

value: healthy (non-IBD)


title: 4795-120-60

description: Gene expression data from bronchial brushing 4795-120-60.


title: 4795-108-60

description: Gene expression data from bronchial brushing 4795-108-60.


title: 4795-112-60

description: Gene expression data from bronchial brushing 4795-112-60.


title: 4796-018-60

description: Gene expression data from bronchial brushing 4796-018-60.


title: 4795-110-60

description: Gene expression data from bronchial brushing 4795-110-60.


title: 4795-101-60

description: Gene expression data from bronchial brushing 4795-101-60.


title: 4795-100-60

description: Gene expression data from bronchial brushing 4795-100-60.


title: 4795-099-60

description: Gene expression data from bronchial brushing 4795-099-60.


title: 4795-098-60

description: Gene expression data from bronchial brushing 4795-098-60.


title: 4795-103-60

description: Gene expression data from bronchial brushing 4795-103-60.


title: 4795-094-60

description: Gene expression data from bronchial brushing 4795-094-60.


title: 4795-097-60

description: Gene expression data from bronchial brushing 4795-097-60.


title: 4795-096-60

description: Gene expression data from bronchial brushing 4795-096-60.


title: 4795-095-60

description: Gene expression data from bronchial brushing 4795-095-60.


title: 4795-089-60

description: Gene expression data from bronchial brushing 4795-089-60.


title: 4795-086-60

description: Gene expression data from bronchial brushing 4795-086-60.


title: 4795-092-60

description: Gene expression data from bronchial brushing 4795-092-60.


title: 4795-082-60

description: Gene expression data from bronchial brushing 4795-082-60.


title: 4795-081-60

description: Gene expression data from bronchial brushing 4795-081-60.


title: 4795-080-60

description: Gene expression data from bronchial brushing 4795-080-60.


title: 4795-074-60

description: Gene expression data from bronchial brushing 4795-074-60.


title: 4795-070-60

description: Gene expression data from bronchial brushing 4795-070-60.


title: 4795-072-60

description: Gene expression data from bronchial brushing 4795-072-60.


title: 4795-071-60

description: Gene expression data from bronchial brushing 4795-071-60.


title: 4795-069-60

description: Gene expression data from bronchial brushing 4795-069-60.


title: 4795-066-60

description: Gene expression data from bronchial brushing 4795-066-60.


title: 4795-065-60

description: Gene expression data from bronchial brushing 4795-065-60.


title: 4795-087-60

description: Gene expression data from bronchial brushing 4795-087-60.


title: 4795-064-60

description: Gene expression data from bronchial brushing 4795-064-60.


title: 4795-062-60

description: Gene expression data from bronchial brushing 4795-062-60.


title: 4795-058-60

description: Gene expression data from bronchial brushing 4795-058-60.


title: 4795-056-60

description: Gene expression data from bronchial brushing 4795-056-60.


title: 4795-059-60

description: Gene expression data from bronchial brushing 4795-059-60.


title: 4795-055-60

description: Gene expression data from bronchial brushing 4795-055-60.


title: 4795-060-60

description: Gene expression data from bronchial brushing 4795-060-60.


title: 4795-046-60

description: Gene expression data from bronchial brushing 4795-046-60.


title: 4795-054-60

description: Gene expression data from bronchial brushing 4795-054-60.


title: 4795-045-60

description: Gene expression data from bronchial brushing 4795-045-60.


title: 4795-051-60

description: Gene expression data from bronchial brushing 4795-051-60.


title: 4795-053-60

description: Gene expression data from bronchial brushing 4795-053-60.


title: 4795-042-60

description: Gene expression data from bronchial brushing 4795-042-60.


title: 4795-041-60

description: Gene expression data from bronchial brushing 4795-041-60.


title: 4795-040-60

description: Gene expression data from bronchial brushing 4795-040-60.


title: 4795-044-60

description: Gene expression data from bronchial brushing 4795-044-60.


title: 4795-036-60

description: Gene expression data from bronchial brushing 4795-036-60.


title: 4795-031-60

description: Gene expression data from bronchial brushing 4795-031-60.


title: 4795-037-60

description: Gene expression data from bronchial brushing 4795-037-60.


title: 4795-039-60

description: Gene expression data from bronchial brushing 4795-039-60.


title: 4795-035-60

description: Gene expression data from bronchial brushing 4795-035-60.


title: 4795-026-60

description: Gene expression data from bronchial brushing 4795-026-60.


title: 4795-024-60

description: Gene expression data from bronchial brushing 4795-024-60.


title: 4795-032-60

description: Gene expression data from bronchial brushing 4795-032-60.


title: 4795-023-60

description: Gene expression data from bronchial brushing 4795-023-60.


title: 4795-017-60

description: Gene expression data from bronchial brushing 4795-017-60.


title: 4795-021-60

description: Gene expression data from bronchial brushing 4795-021-60.


title: 4795-019-60

description: Gene expression data from bronchial brushing 4795-019-60.


title: 4795-013-60

description: Gene expression data from bronchial brushing 4795-013-60.


title: 4795-010-60

description: Gene expression data from bronchial brushing 4795-010-60.


title: 4795-011-60

description: Gene expression data from bronchial brushing 4795-011-60.


title: 4795-038-60

description: Gene expression data from bronchial brushing 4795-038-60.


title: 4795-014-60

description: Gene expression data from bronchial brushing 4795-014-60.


title: 4795-007-60

description: Gene expression data from bronchial brushing 4795-007-60.


title: 4795-008-60

description: Gene expression data from bronchial brushing 4795-008-60.


title: 4795-012-60

description: Gene expression data from bronchial brushing 4795-012-60.


title: 4795-004-60

description: Gene expression data from bronchial brushing 4795-004-60.


title: 4795-005-60

description: Gene expression data from bronchial brushing 4795-005-60.


title: 4795-030-60

description: Gene expression data from bronchial brushing 4795-030-60.


title: 4793-042-60

description: Gene expression data from bronchial brushing 4793-042-60.


title: 4795-018-60

description: Gene expression data from bronchial brushing 4795-018-60.


title: 4795-002-60

description: Gene expression data from bronchial brushing 4795-002-60.


title: 4793-039-60

description: Gene expression data from bronchial brushing 4793-039-60.


title: 4794-002-60

description: Gene expression data from bronchial brushing 4794-002-60.


title: 4795-091-60

description: Gene expression data from bronchial brushing 4795-091-60.


title: 4793-032-60

description: Gene expression data from bronchial brushing 4793-032-60.


title: 4793-035-60

description: Gene expression data from bronchial brushing 4793-035-60.


title: 4794-001-60

description: Gene expression data from bronchial brushing 4794-001-60.


title: 4793-028-60

description: Gene expression data from bronchial brushing 4793-028-60.


title: 4793-021-60

description: Gene expression data from bronchial brushing 4793-021-60.


title: 4793-027-60

description: Gene expression data from bronchial brushing 4793-027-60.


title: 4793-025-60

description: Gene expression data from bronchial brushing 4793-025-60.


title: 4793-017-60

description: Gene expression data from bronchial brushing 4793-017-60.


title: 4793-007-60

description: Gene expression data from bronchial brushing 4793-007-60.


title: 4793-012-60

description: Gene expression data from bronchial brushing 4793-012-60.


title: 4793-006-60

description: Gene expression data from bronchial brushing 4793-006-60.


title: 4793-015-60

description: Gene expression data from bronchial brushing 4793-015-60.


title: 4793-005-60

description: Gene expression data from bronchial brushing 4793-005-60.


title: 4793-011-60

description: Gene expression data from bronchial brushing 4793-011-60.


title: 4793-033-60

description: Gene expression data from bronchial brushing 4793-033-60.


title: 4792-024-60

description: Gene expression data from bronchial brushing 4792-024-60.


title: 4792-031-60

description: Gene expression data from bronchial brushing 4792-031-60.


title: 4793-013-60

description: Gene expression data from bronchial brushing 4793-013-60.


title: 4792-029-60

description: Gene expression data from bronchial brushing 4792-029-60.


title: 4792-015-60

description: Gene expression data from bronchial brushing 4792-015-60.


title: 4792-018-60

description: Gene expression data from bronchial brushing 4792-018-60.


title: 4792-030-60

description: Gene expression data from bronchial brushing 4792-030-60.


title: 4792-009-60

description: Gene expression data from bronchial brushing 4792-009-60.


title: 4793-016-60

description: Gene expression data from bronchial brushing 4793-016-60.


title: 4792-005-60

description: Gene expression data from bronchial brushing 4792-005-60.


title: 4791-006-60

description: Gene expression data from bronchial brushing 4791-006-60.


title: 4792-001-60

description: Gene expression data from bronchial brushing 4792-001-60.


title: 4791-002-60

description: Gene expression data from bronchial brushing 4791-002-60.


title: 4790-090-60

description: Gene expression data from bronchial brushing 4790-090-60.


title: 4790-084-60

description: Gene expression data from bronchial brushing 4790-084-60.


title: 4790-089-60

description: Gene expression data from bronchial brushing 4790-089-60.


title: 4792-020-60

description: Gene expression data from bronchial brushing 4792-020-60.


title: 4792-036-60

description: Gene expression data from bronchial brushing 4792-036-60.


title: 4792-013-60

description: Gene expression data from bronchial brushing 4792-013-60.


title: 4790-081-60

description: Gene expression data from bronchial brushing 4790-081-60.


title: 4790-078-60

description: Gene expression data from bronchial brushing 4790-078-60.


title: 4790-077-60

description: Gene expression data from bronchial brushing 4790-077-60.


title: 4790-080-60

description: Gene expression data from bronchial brushing 4790-080-60.


title: 4792-007-60

description: Gene expression data from bronchial brushing 4792-007-60.


title: 4790-076-60

description: Gene expression data from bronchial brushing 4790-076-60.


title: 4791-003-60

description: Gene expression data from bronchial brushing 4791-003-60.


title: 4791-004-60

description: Gene expression data from bronchial brushing 4791-004-60.


title: 4790-074-60

description: Gene expression data from bronchial brushing 4790-074-60.


title: 4790-070-60

description: Gene expression data from bronchial brushing 4790-070-60.


title: 4790-069-60

description: Gene expression data from bronchial brushing 4790-069-60.


title: 4792-017-60

description: Gene expression data from bronchial brushing 4792-017-60.


title: 4790-073-60

description: Gene expression data from bronchial brushing 4790-073-60.


title: 4790-072-60

description: Gene expression data from bronchial brushing 4790-072-60.


title: 4792-010-60

description: Gene expression data from bronchial brushing 4792-010-60.


title: 4790-061-60

description: Gene expression data from bronchial brushing 4790-061-60.


title: 4790-063-60

description: Gene expression data from bronchial brushing 4790-063-60.


title: 4790-057-60

description: Gene expression data from bronchial brushing 4790-057-60.


title: 4790-060-60

description: Gene expression data from bronchial brushing 4790-060-60.


title: 4790-059-60

description: Gene expression data from bronchial brushing 4790-059-60.


title: 4790-056-60

description: Gene expression data from bronchial brushing 4790-056-60.


title: 4790-054-60

description: Gene expression data from bronchial brushing 4790-054-60.


title: 4790-055-60

description: Gene expression data from bronchial brushing 4790-055-60.


title: 4790-053-60

description: Gene expression data from bronchial brushing 4790-053-60.


title: 4790-051-60

description: Gene expression data from bronchial brushing 4790-051-60.


title: 4790-052-60

description: Gene expression data from bronchial brushing 4790-052-60.


title: 4790-050-60

description: Gene expression data from bronchial brushing 4790-050-60.


title: 4790-043-60

description: Gene expression data from bronchial brushing 4790-043-60.


title: 4790-041-60

description: Gene expression data from bronchial brushing 4790-041-60.


title: 4790-037-60

description: Gene expression data from bronchial brushing 4790-037-60.


title: 4790-046-60

description: Gene expression data from bronchial brushing 4790-046-60.


title: 4790-040-60

description: Gene expression data from bronchial brushing 4790-040-60.


title: 4790-039-60

description: Gene expression data from bronchial brushing 4790-039-60.


title: 4790-045-60

description: Gene expression data from bronchial brushing 4790-045-60.


title: 4790-034-60

description: Gene expression data from bronchial brushing 4790-034-60.


title: 4790-035-60

description: Gene expression data from bronchial brushing 4790-035-60.


title: 4790-027-60

description: Gene expression data from bronchial brushing 4790-027-60.


title: 4790-029-60

description: Gene expression data from bronchial brushing 4790-029-60.


title: 4790-024-60

description: Gene expression data from bronchial brushing 4790-024-60.


title: 4790-031-60

description: Gene expression data from bronchial brushing 4790-031-60.


title: 4790-028-60

description: Gene expression data from bronchial brushing 4790-028-60.


title: 4790-025-60

description: Gene expression data from bronchial brushing 4790-025-60.


title: 4790-022-60

description: Gene expression data from bronchial brushing 4790-022-60.


title: 4790-038-60

description: Gene expression data from bronchial brushing 4790-038-60.


title: 4790-014-60

description: Gene expression data from bronchial brushing 4790-014-60.


title: 4790-044-60

description: Gene expression data from bronchial brushing 4790-044-60.


title: 4790-019-60

description: Gene expression data from bronchial brushing 4790-019-60.


title: 4790-023-60

description: Gene expression data from bronchial brushing 4790-023-60.


title: 4790-030-60

description: Gene expression data from bronchial brushing 4790-030-60.


title: 4790-021-60

description: Gene expression data from bronchial brushing 4790-021-60.


title: 4790-011-60

description: Gene expression data from bronchial brushing 4790-011-60.


title: 4790-013-60

description: Gene expression data from bronchial brushing 4790-013-60.


title: 4790-026-60

description: Gene expression data from bronchial brushing 4790-026-60.


title: 4790-006-60

description: Gene expression data from bronchial brushing 4790-006-60.


title: 4790-009-60

description: Gene expression data from bronchial brushing 4790-009-60.


title: 4790-002-60

description: Gene expression data from bronchial brushing 4790-002-60.


title: 4790-008-60

description: Gene expression data from bronchial brushing 4790-008-60.


title: 4790-005-60

description: Gene expression data from bronchial brushing 4790-005-60.


title: 4790-003-60

description: Gene expression data from bronchial brushing 4790-003-60.


title: 4790-012-60

description: Gene expression data from bronchial brushing 4790-012-60.


title: 4714-023-60

description: Gene expression data from bronchial brushing 4714-023-60.


title: 4790-016-60

description: Gene expression data from bronchial brushing 4790-016-60.


title: 4790-001-60

description: Gene expression data from bronchial brushing 4790-001-60.


title: 4714-007-60

description: Gene expression data from bronchial brushing 4714-007-60.


title: 4714-013-60

description: Gene expression data from bronchial brushing 4714-013-60.


title: 4714-008-60

description: Gene expression data from bronchial brushing 4714-008-60.


title: 4714-009-60

description: Gene expression data from bronchial brushing 4714-009-60.


title: 4714-005-60

description: Gene expression data from bronchial brushing 4714-005-60.


title: 4714-001-60

description: Gene expression data from bronchial brushing 4714-001-60.


title: 4438-076-60

description: Gene expression data from bronchial brushing 4438-076-60.


title: 4438-067-60

description: Gene expression data from bronchial brushing 4438-067-60.


title: 4438-073-60

description: Gene expression data from bronchial brushing 4438-073-60.


title: 4438-068-60

description: Gene expression data from bronchial brushing 4438-068-60.


title: 4438-066-60

description: Gene expression data from bronchial brushing 4438-066-60.


title: 4438-056-60

description: Gene expression data from bronchial brushing 4438-056-60.


title: 4714-012-60

description: Gene expression data from bronchial brushing 4714-012-60.


title: 4438-055-60

description: Gene expression data from bronchial brushing 4438-055-60.


title: 4438-054-60

description: Gene expression data from bronchial brushing 4438-054-60.


title: 4438-041-60

description: Gene expression data from bronchial brushing 4438-041-60.


title: 4438-051-60

description: Gene expression data from bronchial brushing 4438-051-60.


title: 4438-085-60

description: Gene expression data from bronchial brushing 4438-085-60.


title: 4438-036-60

description: Gene expression data from bronchial brushing 4438-036-60.


title: 4438-058-60

description: Gene expression data from bronchial brushing 4438-058-60.


title: 4438-059-60

description: Gene expression data from bronchial brushing 4438-059-60.


title: 4438-034-60

description: Gene expression data from bronchial brushing 4438-034-60.


title: 4438-052-60

description: Gene expression data from bronchial brushing 4438-052-60.


title: 4438-091-60

description: Gene expression data from bronchial brushing 4438-091-60.


title: 4438-045-60

description: Gene expression data from bronchial brushing 4438-045-60.


title: 4438-030-60

description: Gene expression data from bronchial brushing 4438-030-60.


title: 4438-031-60

description: Gene expression data from bronchial brushing 4438-031-60.


title: 4438-035-60

description: Gene expression data from bronchial brushing 4438-035-60.


title: 4438-037-60

description: Gene expression data from bronchial brushing 4438-037-60.


title: 4438-032-60

description: Gene expression data from bronchial brushing 4438-032-60.


title: 4438-028-60

description: Gene expression data from bronchial brushing 4438-028-60.


title: 4438-026-60

description: Gene expression data from bronchial brushing 4438-026-60.


title: 4438-023-60

description: Gene expression data from bronchial brushing 4438-023-60.


title: 4438-024-60

description: Gene expression data from bronchial brushing 4438-024-60.


title: 4790-032-60

description: Gene expression data from bronchial brushing 4790-032-60.


title: 4438-022-60

description: Gene expression data from bronchial brushing 4438-022-60.


title: 4438-017-60

description: Gene expression data from bronchial brushing 4438-017-60.


title: 4438-019-60

description: Gene expression data from bronchial brushing 4438-019-60.


title: 4438-021-60

description: Gene expression data from bronchial brushing 4438-021-60.


title: 4438-029-60

description: Gene expression data from bronchial brushing 4438-029-60.


title: 4438-016-60

description: Gene expression data from bronchial brushing 4438-016-60.


title: 4438-015-60

description: Gene expression data from bronchial brushing 4438-015-60.


title: 4438-005-60

description: Gene expression data from bronchial brushing 4438-005-60.


title: 4438-014-60

description: Gene expression data from bronchial brushing 4438-014-60.


title: 4438-012-60

description: Gene expression data from bronchial brushing 4438-012-60.


title: 4438-009-60

description: Gene expression data from bronchial brushing 4438-009-60.


title: 4438-025-60

description: Gene expression data from bronchial brushing 4438-025-60.


title: 4438-027-60

description: Gene expression data from bronchial brushing 4438-027-60.


title: 4438-010-60

description: Gene expression data from bronchial brushing 4438-010-60.


title: 4438-004-60

description: Gene expression data from bronchial brushing 4438-004-60.


title: 4278-003-60

description: Gene expression data from bronchial brushing 4278-003-60.


title: 4238-038-60

description: Gene expression data from bronchial brushing 4238-038-60.


title: 4278-002-60

description: Gene expression data from bronchial brushing 4278-002-60.


title: 4438-003-60

description: Gene expression data from bronchial brushing 4438-003-60.


title: 4238-030-60

description: Gene expression data from bronchial brushing 4238-030-60.


title: 4238-029-60

description: Gene expression data from bronchial brushing 4238-029-60.


title: 4438-018-60

description: Gene expression data from bronchial brushing 4438-018-60.


title: 4238-028-60

description: Gene expression data from bronchial brushing 4238-028-60.


title: 4238-022-60

description: Gene expression data from bronchial brushing 4238-022-60.


title: 4238-016-60

description: Gene expression data from bronchial brushing 4238-016-60.


title: 4238-019-60

description: Gene expression data from bronchial brushing 4238-019-60.


title: 4238-008-60

description: Gene expression data from bronchial brushing 4238-008-60.


title: 4238-012-60

description: Gene expression data from bronchial brushing 4238-012-60.


title: 4438-013-60

description: Gene expression data from bronchial brushing 4438-013-60.


title: 4238-017-60

description: Gene expression data from bronchial brushing 4238-017-60.


title: 4238-027-60

description: Gene expression data from bronchial brushing 4238-027-60.


title: 4238-018-60

description: Gene expression data from bronchial brushing 4238-018-60.


title: 4238-002-60

description: Gene expression data from bronchial brushing 4238-002-60.


title: 4238-025-60

description: Gene expression data from bronchial brushing 4238-025-60.


title: 4238-004-60

description: Gene expression data from bronchial brushing 4238-004-60.


title: 4202-021-60

description: Gene expression data from bronchial brushing 4202-021-60.


title: 4202-033-63

description: Gene expression data from bronchial brushing 4202-033-63.


title: 4202-023-60

description: Gene expression data from bronchial brushing 4202-023-60.


title: 4202-004-60

description: Gene expression data from bronchial brushing 4202-004-60.


title: 4202-025-60

description: Gene expression data from bronchial brushing 4202-025-60.


title: 4202-006-60

description: Gene expression data from bronchial brushing 4202-006-60.


title: 4202-015-60

description: Gene expression data from bronchial brushing 4202-015-60.


title: 4202-012-60

description: Gene expression data from bronchial brushing 4202-012-60.


title: 4202-022-60

description: Gene expression data from bronchial brushing 4202-022-60.


title: 4202-019-60

description: Gene expression data from bronchial brushing 4202-019-60.


title: 4202-017-60

description: Gene expression data from bronchial brushing 4202-017-60.


title: 4202-016-60

description: Gene expression data from bronchial brushing 4202-016-60.


title: 4238-037-60

description: Gene expression data from bronchial brushing 4238-037-60.


title: 4202-003-60

description: Gene expression data from bronchial brushing 4202-003-60.


title: Single-cell training high-fat diet rep1 [TH1.SM]

status: Public on Oct 13 2022

city: Piscataway

first: Jiekun

last: Yang

state: NJ

address: 145 Bevier Rd

institute: Rutgers University

data_processing:
Gene count matrices for each single-cell sample were generated by aligning reads to the mm10 genome (refdata-gex-mm10-2020-A) using 10X Genomics Cell Ranger software v4.0.0.
For each sample, we removed ambient RNA contamination using SoupX with a fixed contamination fraction of 20%.
We then excluded low-quality cells using four quality control (QC) metrics: (i) number of genes with non-zero expression fewer than 500; (ii) number of UMIs fewer than 200 or more than 6000; (iii) percentage of reads mapping to mitochondrial genes more than 10; and (iv) number of reads mapped to Mki67 more than 0.
We removed potential cell doublets using DoubletFinder with default parameters and 3.1% homotypic doublet proportion estimation based on statistics published by 10X Genomics.
Next we integrated all the 41 samples across three tissues together for an atlas, and samples belonging to a single tissue together for tissue-specific maps. Integration was done without any batch correction using Seurat v3.
Genome_build: mm10
Supplementary_files_format_and_content: Seurat object saved in R qs format for all the 204,883 cells included in the atlas

source_name: skeletal muscle (triceps)

extract_protocol:
Fresh tissues were enzymatically digested and dissociated according to tissue dissociation kit protocols (adipose tissue Cat No 130-105-808, skeletal muscle Cat No 130-098-305 by Miltenyi) using the gentleMACS™ Dissociator (Miltenyi). Dissociated tissues were filtered, centrifuged, and the isolated cells were resuspended in 0.1% BSA in PBS and immediately processed for the generation of single-cell RNA (scRNA) libraries using the droplet-based RNA sequencing technology.
Briefly, 5000-6000 cells were profiled per sample using the Chromium Single Cell 3’ RNA reagent kit v3 according to the 10X Genomics protocol.

treatment_protocol: Mice were separated into standard vs. high-fat diet groups (10% vs. 60% Kcal fat ad libitum, weeks 0-6) and each group was further separated into sedentary and training by voluntary wheel running (weeks 3-6). Tissue collection was done following a 6-hour fast and a 24-hour exercise wash-out done by locking of the wheels.

tag: strain

value: skeletal muscle (triceps)

value: 12-week old

tag: treatment

value: 6-week high-fat-diet and 3-week training interventions


title: Single-cell training high-fat diet rep4 [TH4.SM]


title: Single-cell training high-fat diet rep3 [TH3.SM]


title: Single-cell training high-fat diet rep2 [TH2.SM]


title: Single-cell sedentary high-fat diet rep1 [SH1.SM]

value: 6-week high-fat-diet and 3-week sedentary interventions


title: Single-cell sedentary high-fat diet rep3 [SH3.SM]


title: Single-cell sedentary standard (chow) diet rep3 [SC3.SM]

value: 6-week chow-diet and 3-week sedentary interventions


title: Single-cell training standard (chow) diet rep1 [TC1.SM]

value: 6-week chow-diet and 3-week training interventions


title: Single-cell sedentary standard (chow) diet rep2 [SC2.SM]


title: Bulk training high-fat diet rep4 [TH10.Tricep]

data_processing:
Six FASTQ files for each sample were concatenated for read de-duplication using unique molecular identifiers (UMIs).
We then ran Salmon 0.14.2 to quantify the number of unique reads for each transcript against Ensembl version 98 mouse transcripts.
The transcript level information was summarized to the gene-level using R package tximport.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts and log2CPM values for every gene and every sample

source_name: triceps

extract_protocol:
Total RNA was extracted at the Goodyear lab using an RNA extraction kit (Direct-zol™ RNA MiniPrep, Zymo Research). 10ng of total RNA quantified and quality assessed by Advanced Analytical Fragment Analyzer was used for library preparation on Tecan Evo150.
3′ DGE-custom primers 3V6NEXT-bmc#1-12 were added to a final concentration of 1 uM. to generate two subpools of 15 samples each. After addition of the oligonucleotides, Maxima H Minus RT was added per manufacturer’s recommendations with Template-Switching oligo 5V6NEXT followed by incubation at 42℃ for 90’ and inactivation at 80℃ for 10’. Following the template switching reaction, cDNA from 12 wells containing unique well identifiers were pooled together and cleaned using RNA Ampure beads at 1.0X. cDNA was eluted with 17 ul of water followed by digestion with Exonuclease I at 37℃ for 30 minutes, and inactivated at 80℃ for 20 minutes. Second strand synthesis and PCR amplification was done by adding the Advantage 2 Polymerase Mix (Clontech) and the SINGV6 primer directly to the exonuclease reaction. Eight cycles of PCR were performed followed by clean up using regular SPRI beads at 0.6X, and eluted with 20ul of elution buffer (Qiagen). Successful amplification of cDNA was confirmed using the Fragment Analyzer. Illumina libraries were then produced using standard Nextera tagmentation substituting P5NEXTPT5-bmc primer in place of the normal N500 primer. Final libraries were cleaned using SPRI beads at 0.7X and quantified using the Fragment Analyzer and qPCR before being loaded for sequencing using the Hiseq 2000 (Illumina, Inc) in 50bp single-end mode at the BioMicro Center at MIT.
3′ Digital Gene Expression (DGE) RNA-seq

value: triceps


title: Single-cell training standard (chow) diet rep3 [TC3.SM]


title: Single-cell training standard (chow) diet rep2 [TC2.SM]


title: 4202-002-60

description: Gene expression data from bronchial brushing 4202-002-60.


title: Single-cell training standard (chow) diet rep4 [TC4.SM]


title: Single-cell training high-fat diet rep3 [TH3.vWAT]

source_name: visceral white adipose tissue

value: visceral white adipose tissue


title: Single-cell training high-fat diet rep4 [TH4.vWAT]


title: Bulk training high-fat diet rep5 [TH17.Tricep]


title: Single-cell training high-fat diet rep1 [TH1.vWAT]


title: Bulk training high-fat diet rep3 [TH11.Tricep]


title: Single-cell sedentary high-fat diet rep2 [SH2.SM]


title: Bulk sedentary high-fat diet rep5 [SH12.Tricep]


title: Single-cell sedentary standard (chow) diet rep1 [SC1.SM]


title: Single-cell training high-fat diet rep2 [TH2.vWAT]


title: Bulk sedentary high-fat diet rep4 [SH8.Tricep]


title: Bulk training high-fat diet rep1 [TH5.Tricep]


title: Bulk training high-fat diet rep2 [TH6.Tricep]


title: Single-cell sedentary high-fat diet rep1 [SH1.vWAT]


title: Single-cell sedentary high-fat diet rep3 [SH3.vWAT]


title: Single-cell sedentary high-fat diet rep2 [SH2.vWAT]


title: Single-cell training standard (chow) diet rep4 [TC4.vWAT ]


title: Bulk training standard (chow) diet rep5 [TC18.Tricep]


title: Bulk sedentary high-fat diet rep3 [SH7.Tricep]


title: Single-cell sedentary standard (chow) diet rep2 [SC2.vWAT]


title: Bulk training standard (chow) diet rep4 [TC14.Tricep]


title: Bulk training standard (chow) diet rep2 [TC6.Tricep]


title: Single-cell training standard (chow) diet rep3 [TC3.vWAT]


title: Single-cell training high-fat diet rep4 [TH4.scWAT]

source_name: subcutaneous white adipose tissue

value: subcutaneous white adipose tissue


title: Bulk sedentary high-fat diet rep2 [SH4.Tricep]


title: Single-cell training standard (chow) diet rep2 [TC2.vWAT]


title: Bulk sedentary high-fat diet rep1 [SH3.Tricep]


title: Single-cell sedentary standard (chow) diet rep3 [SC3.vWAT]


title: Bulk sedentary standard (chow) diet rep3 [SC8.Tricep]


title: Bulk training standard (chow) diet rep3 [TC7.Tricep]


title: Single-cell sedentary high-fat diet rep3 [SH3.scWAT]


title: Single-cell training high-fat diet rep3 [TH3.scWAT]


title: Bulk sedentary standard (chow) diet rep4 [SC11.Tricep]


title: Single-cell training standard (chow) diet rep1 [TC1.vWAT]


title: Single-cell sedentary high-fat diet rep2 [SH2.scWAT]


title: Single-cell training high-fat diet rep2 [TH2.scWAT]


title: Single-cell training standard (chow) diet rep4 [TC4.scWAT]


title: Bulk training high-fat diet rep3 [TH11.vWAT]


title: Single-cell training standard (chow) diet rep3 [TC3.scWAT]


title: Single-cell sedentary high-fat diet rep1 [SH1.scWAT]


title: Bulk sedentary standard (chow) diet rep2 [SC4.Tricep]


title: Bulk training standard (chow) diet rep1 [TC1.Tricep]


title: Bulk sedentary standard (chow) diet rep1 [SC3.Tricep]


title: Single-cell training high-fat diet rep1 [TH1.scWAT]


title: Bulk training high-fat diet rep5 [TH17.vWAT]


title: Bulk sedentary standard (chow) diet rep5 [SC12.Tricep]


title: Single-cell sedentary standard (chow) diet rep1 [SC1.vWAT]


title: 4790-015-60

description: Gene expression data from bronchial brushing 4790-015-60.

value: Brushing of bronchial epithelium

value: Male


title: Bulk training high-fat diet rep1 [TH5.vWAT]


title: Bulk training high-fat diet rep2 [TH6.vWAT]


title: Bulk training high-fat diet rep4 [TH10.vWAT]


title: Single-cell training standard (chow) diet rep2 [TC2.scWAT]


title: Single-cell sedentary standard (chow) diet rep3 [SC3.scWAT]


title: Bulk sedentary high-fat diet rep5 [SH12.vWAT]


title: Bulk sedentary high-fat diet rep4 [SH8.vWAT]


title: Single-cell sedentary standard (chow) diet rep1 [SC1.scWAT]


title: Single-cell sedentary standard (chow) diet rep2 [SC2.scWAT]


title: Bulk sedentary high-fat diet rep3 [SH7.vWAT]


title: Bulk training standard (chow) diet rep4 [TC14.vWAT ]


title: Single-cell training standard (chow) diet rep1 [TC1.scWAT]


title: Bulk sedentary high-fat diet rep2 [SH4.vWAT]


title: Bulk training standard (chow) diet rep5 [TC18.vWAT]


title: Bulk training standard (chow) diet rep1 [TC1.vWAT]


title: Bulk training standard (chow) diet rep2 [TC6.vWAT]


title: Bulk sedentary standard (chow) diet rep5 [SC12.vWAT]


title: Bulk sedentary high-fat diet rep1 [SH3.vWAT]


title: Bulk sedentary standard (chow) diet rep4 [SC11.vWAT]


title: Bulk training standard (chow) diet rep3 [TC7.vWAT]


title: Bulk training high-fat diet rep2 [TH6.scWAT]


title: Bulk training high-fat diet rep4 [TH10.scWAT]


title: Bulk sedentary high-fat diet rep3 [SH7.scWAT]


title: Bulk sedentary standard (chow) diet rep2 [SC4.vWAT]


title: Bulk training high-fat diet rep5 [TH17.scWAT]


title: Bulk training high-fat diet rep3 [TH11.scWAT]


title: Bulk sedentary standard (chow) diet rep3 [SC8.vWAT]


title: Bulk sedentary high-fat diet rep4 [SH8.scWAT]


title: Bulk sedentary high-fat diet rep1 [SH3.scWAT]


title: Bulk training high-fat diet rep1 [TH5.scWAT]


title: Bulk sedentary high-fat diet rep2 [SH4.scWAT]


title: Bulk sedentary standard (chow) diet rep1 [SC3.vWAT]


title: Bulk training standard (chow) diet rep4 [TC14.scWAT]


title: Bulk training standard (chow) diet rep5 [TC18.scWAT]


title: Bulk training standard (chow) diet rep3 [TC7.scWAT]


title: Bulk training standard (chow) diet rep2 [TC6.scWAT]


title: Bulk training standard (chow) diet rep1 [TC1.scWAT]


title: Bulk sedentary standard (chow) diet rep5 [SC12.scWAT]


title: Bulk sedentary standard (chow) diet rep2 [SC4.scWAT]


title: Bulk sedentary standard (chow) diet rep1 [SC3.scWAT]


title: Bulk sedentary standard (chow) diet rep4 [SC11.scWAT]


title: MyglaSWRecB cells, PUUV, rep4

status: Public on Sep 30 2022

description:
A-PHV_vs_B-PUUV_degs_DESeq2.csv
B-PUUV_vs_C-NI_degs_DESeq2.csv
PUUV_4

data_processing:
The RNA‐seq analysis was performed with the Sequana framework (Cokelaer et al, 2017 doi:10.21105/joss.00352)
Version used: RNA‐seq pipeline (v0.13.0)
Reads were trimmed from adapters using Cutadapt 2.10
Then mapped to the Mus musculus GRCm38/mm10 genome using STAR 2.7.3a
Differential expression testing was conducted using DESeq2 library 1.24.0, scripts based on SARTools 1.7.0
Assembly: Mus musculus GRCm38/mm10 genome
Supplementary files format and content: Files in CSV that contains Gene_ID, log2FoldChange, pvalue; raw_counts.txt

organism: Myodes glareolus

source_name: MyglaSWRecB cells

growth_protocol: MyglaSWRecB cells were plated at 2.5x10e5 cells per well and infected 24h later

extract_protocol:
Cells were washed with PBS and incubated for 5 min at room temperature with 500 uL of Trizol (Tri Reagent, Sigma Aldrich) before addition of 150 uL of chloroform for 10 min and centrifugation at 4 °C for 10 min at 11000 rpm. The aqueous phase was recovered and precipitated with isopropanol. After centrifugation, the pellet is washed in 70% ethanol then suspended in 50 mL of RNAse free water.
RNA libraries were prepared for sequencing using standard Illumina protocols
Truseq stranded mRNA seq kit

treatment_protocol: Four wells were incubated either with PUUV or PHV at MOI 0.5 or left non-infected. RNA was prepared from cells at day 5 post infection.

value: kidney

tag: cell type

value: MyglaSWRecB epithelial cells

tag: infection

value: Puumala virus (PUUV)


title: MyglaSWRecB cells, PUUV, rep3

description:
A-PHV_vs_B-PUUV_degs_DESeq2.csv
B-PUUV_vs_C-NI_degs_DESeq2.csv
PUUV_3

tag: tissue


title: Bulk sedentary standard (chow) diet rep3 [SC8.scWAT]


title: MyglaSWRecB cells, PUUV, rep2

description:
A-PHV_vs_B-PUUV_degs_DESeq2.csv
B-PUUV_vs_C-NI_degs_DESeq2.csv
PUUV_2


title: Bulk sedentary high-fat diet rep5 [SH12.scWAT]


title: MyglaSWRecB cells, PUUV, rep1

description:
A-PHV_vs_B-PUUV_degs_DESeq2.csv
B-PUUV_vs_C-NI_degs_DESeq2.csv
PUUV_1


title: MyglaSWRecB cells, PHV, rep3

description:
A-PHV_vs_B-PUUV_degs_DESeq2.csv
A-PHV_vs_C-NI_degs_DESeq2.csv
PHV_3

value: Prospect Hill virus (PHV, New World)


title: MyglaSWRecB cells, PHV, rep2

description:
A-PHV_vs_B-PUUV_degs_DESeq2.csv
A-PHV_vs_C-NI_degs_DESeq2.csv
PHV_2


title: MyglaSWRecB cells, NI, rep3

description:
B-PUUV_vs_C-NI_degs_DESeq2.csv
A-PHV_vs_C-NI_degs_DESeq2.csv
NI_3

value: non infected


title: MyglaSWRecB cells, NI, rep1

description:
B-PUUV_vs_C-NI_degs_DESeq2.csv
A-PHV_vs_C-NI_degs_DESeq2.csv
NI_1


title: MyglaSWRecB cells, NI, rep4

description:
B-PUUV_vs_C-NI_degs_DESeq2.csv
A-PHV_vs_C-NI_degs_DESeq2.csv
NI_4


title: MyglaSWRecB cells, NI, rep2

description:
B-PUUV_vs_C-NI_degs_DESeq2.csv
A-PHV_vs_C-NI_degs_DESeq2.csv
NI_2


title: MΔχ3,4_Sample2

status: Public on Feb 09 2022

city: Vari

first: Dimitris

middle: L.

last: Kontoyiannis

state: Attiki

address: 34 Fleming

department: Institute for Fundamental Biomedical Research

country: Greece

institute: BSRC "Alexander Fleming"

data_processing:
Sequencing on an Agilent 2100 Bioanalyzer, version 2.6
The raw .fastq files were mapped with TopHat2 version 2.1.1 against the mm10 mouse reference genome (Mus_musculus.GRCm38.p6).
Bedtools was used to convert unmapped reads .bam files to .fastq files and unmapped reads were additionally mapped with Bowtie2 version 2.3.2
The final 3’ UTR read counts table was normalized for inherent systematic or experimental biases using the Bioconductor package DESeq2 after removing areas that had zero counts over all the Quant-Seq samples. Differential RNA abundance analysis was performed with metaseqR2 (v.1.3.14) Bioconductor package. The raw bam files, one for each RNA-Seq sample, were summarized to a 3’UTR read counts table, using the Bioconductor package GenomicRanges. Transcripts presenting any of the following were excluded from further analysis: i) transcripts with length less than 500bp (2910 genes), ii) transcripts whose average numbers of reads per 100 bp was less than the 25th quantile of the total normalized distribution of average reads per 100bp,  iii) transcripts with read counts below the median read counts of the total normalized count distribution (19325 transcripts with cutoff value 3 normalized read counts), iv) transcripts whose biotype matched the following: rRNA, IG_V_pseudogene, TR_V_pseudogene (54 transcripts), v) transcripts which in 50% of samples did not exceed 5 counts (41343 transcripts) condition-wise.
Genome_build: mm10
Supplementary_files_format_and_content: txt (tab delimited) files containing results of metaseqR2 (Bioconductor package) analysis including expression per replicate, fold changes, RPGMs (RPKs), TPMs and gene lenghts.

source_name: Mus musculus BMDM

growth_protocol: Bone Marrow Derived Macrophages from Control and MΔχ3,4 were differentiated in RPMI 1640 medium supplemented with 5% FBS, 1% penicillin/streptomycin , 1% L-glutamine  and 10% L-medium (produced by L929 cells) incubated for 10 days at 37oC with 5% CO2.

extract_protocol:
Total RNAs were extracted from cells using TRI Reagent (MRC, TR 118) according to the manufacturer’s protocol.
RNA samples were processed for library preparation using the 3’ mRNA-Seq Library Prep Kit Protocol for Ion Torrent (QuantSeq-LEXOGEN™, Vienna, Austria), according to manufacturer’s instructions.

treatment_protocol: BMDMs were activated with LPS (100ng/ml) for 4 hours.

tag: genotype

value: LysCre+hnRNPDfl/fl

value: bone marrow derived macrophages

value: LPS 4h

tag: volume

value: 25 microls


title: MΔχ3,4_Sample1


title: Control_Sample3

value: hnRNPDfl/fl


title: Control_Sample2


title: 178-A031921

status: Public on Nov 23 2021

city: Basel

first: Jasmin

last: Haslbauer

address: Schönbeinstrasse 40

country: Switzerland

institute: Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland

data_processing:
Alignment: four demultiplexed FASTQ files per well in the assay sequenced with the HTG EdgeSeq Parser (version 5.0.535.3181) see HTG EdgeSeq System User Manual (RUO).
Post sequencing quality control: POS% ≥ 28% as failure; Read depth ≤ 750,000 as failure; RSD ≤ 0.094 as failure .
Normalization: No pre-filtering is applied to the data prior to analysis. The DESeq2 (package version 1.14.1)model corrects for library size using the median ratio method from Anders and Huber (2010).
Dispersions are estimated with the Cox Reid-adjusted profile likelihood method developed by McCarthy et al. (2012).  Log2 fold change is estimated via Tikhonov/ridge regularization with a zero-centered normal prior distribution with variance calculated using the observed distribution of maximum likelihood coefficients (see DESeq2 documentation for details).
Supplementary_files_format_and_content: Excel file containing tables of raw, QC raw, log2 CPM (counts per million), and median normalized data.

source_name: Control_lymph node

extract_protocol:
HTG uses an extraction free technology that involves resuspending crude sample in Lysis Buffer.  The sample is then treated with Proteinase K and stored or used.
HTG EdgeSeq library construction is defined in the HTG EdgeSeq System User Manual (RUO)

tag: group

value: Control

value: lymph node


title: 178-A031917


title: 178-A031919

source_name: COVID-19_lymph node


title: FGF control and mutant

status: Public on Jan 27 2022

city: New York

first: Revathi

last: Balasubramanian

address: 635 West 165th street

department: Ophthalmology

institute: Columbia University

data_processing:
Approximately 11,000 cells were sequenced on the 10X platform. cDNA Libraries were sequenced on an Illumina NovaSeq 6000 sequencer. The data alignment, barcode processing and generation of cell gene matrices was performed by the Single Cell Analysis core facility at Columbia Genome Center using cellranger pipeline v2.0.0.
Count matrices were aggregated and filtered for further processing using Seurat v3.
Supplementary_files_format_and_content: There is no barcode file. The control and mutant cells are sequenced together. During processing and analysis, they can be separated based on TdTomato reporter expression. The manuscript (in preparation) details how the separate matrices were constructed using Seurat workflow in R.

source_name: Peripheral retina

extract_protocol:
E14 retinal tissue was harvested and pooled from 3 embryos each for mutant and control. Cells were dissociated using a Papain protocol. Cells were sorted according to fluorescent reporters and single cell suspension was transferred to the Columbia genome center for further processing.
Barcoded cDNA library was contructed using the 10X Genomics Chromium controller.

tag: developmental stage

value: Control:a-Cre; FgfR1 f/+ ; FgfR2 f/+  Mutant:a-Cre; FgfR1 f/f ; FgfR2 f/f; Rosa26-TdTomato

value: Mixed


title: MyglaSWRecB cells, PHV, rep4

description:
A-PHV_vs_B-PUUV_degs_DESeq2.csv
A-PHV_vs_C-NI_degs_DESeq2.csv
PHV_4


title: 178-A031915


title: 178-A031916


title: 178-A031918


title: 178-A031914


title: MyglaSWRecB cells, PHV, rep1

description:
A-PHV_vs_B-PUUV_degs_DESeq2.csv
A-PHV_vs_C-NI_degs_DESeq2.csv
PHV_1


title: 178-A031912


title: MΔχ3,4_Sample3


title: 178-A031910


title: 178-A031911


title: Control_Sample1


title: 178-A031906


title: 178-A031907


title: 178-A031909


title: 178-A031908


title: 178-A031905


title: 178-A031904


title: 178-A031903


title: 178-A031902


title: 178-A031897


title: 178-A031892


title: 178-A031898


title: 178-A031890


title: 178-A031901


title: 178-A031887


title: 178-A031889


title: 178-A031884


title: 178-A031881


title: 178-A031874


title: 178-A031878


title: 178-A031880


title: 178-A031873


title: 178-A031871


title: 178-A031882


title: 178-A031868


title: 178-A031862


title: 178-A031866


title: 178-A031885


title: 178-A031855


title: 178-A031853


title: 178-A031861


title: 178-A031852


title: 178-A031849


title: 178-A031856


title: 178-A031851


title: 178-A031869


title: 178-A031847


title: 178-A031850


title: Aorta of ApoE KO mice2, Gpnmb vaccine

status: Public on Oct 22 2021

city: Los Angeles

first: Masayoshi

last: Suda

state: CA

address: 8700 Beverly Blvd.

department: Medicine

institute: Cedars Sinai Medical Center

data_processing:
these libraries were analyzed on a NextSeq500 with a NextSeq 500/550 High Output Kit v2 (Illumina).
TopHat 2 (version 2.0.13) was used for mapping reads to the reference genome (Ensembl GRCm38/mm10) with annotation data downloaded from the Ensembl Asia website (URL https://asia.ensembl.org/).
Expression of each transcript was quantified as the number of fragments per kilobase of transcript per million fragments mapped (FPKM), and expression was compared among 3 groups by Cuffdiff (included in Cufflinks version 2.2.1).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Aorta

extract_protocol:
Total RNA was isolated from tissue samples with an RNeasy Mini Kit (Qiagen, 74104) and its quality was assessed by using the Agilent 2100 Bioanalyzer with the Agilent RNA6000 pico Kit (Agilent Technologies).
The TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) was employed to construct four libraries according to the specifications of the manufacturer.

treatment_protocol: We fed the HFD to ApoE KO mice from 4 weeks of age, administered Gpnmb vaccine or control vaccine at 8 weeks of age, and analyzed these mice at 16 weeks.

value: Aorta

tag: age

value: ApoE -/-

value: Gpnmb vaccine


title: Aorta of ApoE KO mice3, Gpnmbl vaccine


title: 178-A031872


title: Aorta of ApoE KO mice1, control vaccine

value: control vaccine


title: 178-A031858


title: Spt4-FRB_rapa_NET-seq_rep2

status: Public on Sep 27 2021

city: Oxford

first: Ulku

last: Uzun

address: South Parks Rd

department: Department of Biochemistry

institute: University of Oxford

data_processing:
Library strategy: NET-seq
Single-end FASTQ files were processed using usegalaxy.org and RStudio. Reads were groomed using FASTQ groomer for Sanger & Illumina 1.8 + (Blankenberg et al., 2010). Adapter sequence ATCTCGTATGCCGTCTTC were trimmed and reads < 15 nt were discarded using Clip function. Reads were aligned to a combined fasta file of S.cerevisiae and S.pombe genomes using Bowtie for Illumina (Langmead, 2011). SAM files were converted to BAM files using SAM-to-BAM (Li, 2011).
Using RStudio/Bioconductor packages, multiply aligned reads were filtered, and reads were narrowed to the 3’ends. For spike-in normalisation, counts table was created for S.pombe genes using RStudio/Bioconductor. The estimateSizeFactors function in the DEseq2/RStudio package was applied to calculate the relative amounts of S.pombe reads (i.e. normalisation ratio) in each sample (Love, Huber, and Anders 2014). NET-seq data were calibrated by dividing S.cerevisiae reads by the normalisation ratios.
genome build: SacCer3 (R64) and ASM294v2
processed data file: normalised bigwig file for positive strand
processed data file: normalised bigwig file for negative strand

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in YPD (30°C, 160 rpm) from OD600 0.2 to 0.65.

extract_protocol:
Cells were filtered and flash frozen in liquid nitrogen. 4 parts of the frozen S.cerevisiae pellet were spiked-in with one part of frozen S.pombe (containing a FLAG-tagged Rpb9) pellet (4:1 by weight). The combined pellet was lysed, and immunoprecipitation of the FLAG-tagged proteins was performed at 4°C as described in (Fischl et al., 2017). RNA was isolated with Qiagen miRNA kit according to the manufacturer’s instructions.
The isolated RNA was adapter ligated, fragmented, reverse transcribed, circularized, barcoded, and amplified as described in (Fischl et al., 2017).

value: BY4741 tor1-1; fpr1<delta>; RPL13-2xFKBP12; SPT4-FRB-eGFP; RPB3-3xFLAG

value: DMSO treatment 120 min prior to cell harvest

tag: extracted molecule

value: native RNA