title: Wild-type,8h 2

status: Public on Dec 31 2022

type: SRA

city: tianjin

first: tian

last: zhao

address: tainjin nankai

country: China

institute: nankai university

library_source: transcriptomic

data_processing:
Fastp (version 0.19.7) to perform quality control of the raw reads and get clean data.
Clean data were aligned to the mouse reference genome GRCm39 using Hisat2 (version 2.2.1).
Assemble RNA-seq aligments into transcripts to get UMI values using StringTie (version 2.1.4).
Assembly: GRCm39
Supplementary files format and content: comma-delimited text files include UMI values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Mouse peritoneal macrophages

growth_protocol: Mouse peritoneal macrophages were cultured at 37°C under 5 % CO2 in DMEM supplemented with 10 % FBS, 100 U/ml penicillin and 100 µg/ml streptomycin.

extract_protocol:
RNA was harvested using RNA extraction kit (Promega). 1 ug of total RNA was used for the construction of sequencing libraries.
Total RNA was prepared with RNA extraction kit and subjected to commercial RNA-seq analyses (Novogene)

treatment_protocol: Mouse peritoneal macrophages were infected with VSV (0.1MOI) for 8 h.

tag: cell type

value: Mouse peritoneal macrophages

tag: strain background

tag: genotype

value: WT

tag: treatment

value: VSV infection


title: Wild-type,8h 1


title: Wild-type,8h 3


title: NRF1-KO,8h 3

value: KO


title: NRF1-KO,8h 1


title: PBS ZT15 S2

city: Geneva

first: Chen

last: Wang

address: 1, rue Michel Servet

country: Switzerland

institute: University of Geneva

data_processing:
Reads were aligned with STAR v.2.7.022 to the mouse mm10
quantified with HTSeq v.0.9.1
Assembly: mm10

source_name: LN

extract_protocol:
RNA was isolated using an RNeasy Plus Micro Kit (cat. #74034, Qiagen) according to the manufacturer’s instructions. RNA integrity and quantity were assessed with a Bioanalyzer (Agilent Technologies). cDNA libraries were constructed by the Genomic platform of the University of Geneva
The SMART-Seq v4 kit from Clontech was used for the reverse transcription and cDNA amplification according to the manufacturer’s specifications, starting with 1 ng of total RNA as input. 200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina. Library molarity and quality were assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled and loaded for clustering on 2 lanes of a Single-read Illumina Flow cell. Reads of 50 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 sequencer.

tag: tissue

value: LN

tag: time

value: CD11C+ MHCII high

value: PBS


title: PBS ZT15 S1


title: PBS ZT21 S1


title: PBS ZT21 S2


title: PBS ZT21 S3


title: NRF1-KO,8h 2


title: PBS ZT15 S3


title: PBS ZT9 S3


title: PBS ZT9 S1


title: PBS ZT3 S2


title: PBS ZT3 S1


title: PBS ZT9 S2


title: PBS ZT3 S3


title: KO ZT21 S1


title: KO ZT21 S3


title: KO ZT15 S1


title: KO ZT15 S2


title: KO ZT15 S3


title: KO ZT9 S3


title: KO ZT21 S2


title: KO ZT3 S3


title: KO ZT3 S2


title: KO ZT9 S2


title: KO ZT9 S1


title: KO ZT3 S1


title: WT ZT21 S4


title: WT ZT21 S5


title: WT ZT21 S1


title: WT ZT21 S3


title: WT ZT15 S3


title: WT ZT15 S4


title: WT ZT9 S5


title: WT ZT21 S2


title: WT ZT15 S1


title: WT ZT9 S4


title: WT ZT15 S2


title: WT ZT3 S5


title: WT ZT9 S3


title: WT ZT3 S2


title: WT ZT3 S3


title: WT ZT3 S1


title: DRN-BA(Pyr) Neurons [PN2]

city: Guangzhou

first: Xiao-Dan

last: Yu

address: No. 74, Zhongshaner Road

institute: SUN YAT-SEN UNIVERSITY

data_processing:
Sequencing reads were mapped using the HISAT package against the Mus musculus UCSC
The mapped reads of each sample were assembled using StringTie.
All transcriptomes from samples were then merged to reconstruct a comprehensive transcriptome using Perl script.
After the ﬁnal transcriptome was generated, StringTie and edgeR were used to estimate the expression levels of all transcripts.
StringTie was used to determine the expression levels of mRNA by calculating Fragments Per Kilobase of exon model per Million mapped fragments (FPKM).
Assembly: not provided
Supplementary files format and content: FPKM

source_name: Brain

extract_protocol:
With visual control under a Nikon Eclipse FN1 microscope (Japan), dsRed-positive neurons were slowly aspirated into a micropipette with a 70–100-μm tip diameter.
The harvested neurons are immediately transferred into a clean centrifuge tube containing 2 μl of RNAse-free lysis buffer, with total mRNA subsequently isolated.
Complementary DNA (cDNA) and indexed cDNA libraries were prepared using a SMART-Seq Stranded Kit (Cat. Nos. 634442, Takara Bio USA, Inc.), and the experiments were performed according to the manufacturer’s standard protocols.

value: Brain

tag: Sex

value: male

value: neuron

tag: strain

value: vGluT2-ires-cre (JAX Strain:028863)

value: Day 10 after virus expression


title: WT ZT9 S1


title: DRN-BA(PV) Neurons [PV1]

value: PV-ires-cre mice (JAX Strain:017320)


title: Aging mouse O3, scRNA-seq

city: Los Angeles

first: Jiya

last: Eerdeng

state: CA

address: 1425 San Pablo St

department: DSR

country: USA

institute: University of Southern California

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and were made using the Cell Ranger software v6.0
Assembly: mm10
Supplementary files format and content: HDF5 Feature-Barcode Matrix Format

source_name: Bone Marrow

extract_protocol:
FACS sorted HSPCs including myeloid progenitors [lineage (CD3, CD4, CD8, B220, Gr1, Mac1, Ter119)-/IL-7R+/Sca1-], common lymphoid progenitors [lineage (CD3, CD4, CD8, B220, Gr1, Mac1, Ter119)-/IL7R+/Flk2+], and KLS cells [lineage (CD3, CD4, CD8, B220, Gr1, Mac1, Ter119)-/ckit+/Sca1+] from aging mice that were 30 months old. Sorted cells were washed in PBS with 0.04 % bovine serum albumin (BSA)
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, Bone marrow cells 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 beads, amplified by PCR and the apropiated sized fragments were selected with SPRI select 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: Bone Marrow

tag: phenotype

value: DMOLD

tag: age

value: 30 months

value: myeloid progenitors:KLS


title: Aging mouse O2, scRNA-seq

description: 10x Genomics

value: EMOLD


title: Aging mouse O1, scRNA-seq

description: 10x Genomics


title: WT ZT15 S5

value: WT


title: Aging mouse AN27, scRNA-seq

description: 10x Genomics

value: myeloid progenitors:MPPs:HSCs


title: WT ZT9 S2


title: Aging mouse AN28, scRNA-seq

description: 10x Genomics


title: Aging mouse AN26, scRNA-seq

description: 10x Genomics


title: Aging mouse AN27b, scRNA-seq

description: 10x Genomics


title: WT ZT3 S4


title: lncRNA Capture-Seq synapse biol rep1

city: St Lucia

first: Qiongyi

last: Zhao

state: Queensland

address: Building 79, QBI, The University of Queensland

department: Queensland Brain Institute

country: Australia

institute: The University of Queensland

description: lncRNA capture sequencing

data_processing:
Cutadapt (v1.17, https://cutadapt.readthedocs.io/en/stable/) was used to trim low-quality nucleotides (Phred quality lower than 20) and Illumina adaptor sequences at the 3’ end of each read for both lncRNA capture sequencing data.
Processed reads were aligned against the ribosome RNA and PhiX reference sequences using bowtie2 (version 2.3.4.2).  Reads that can be aligned to either the ribosome RNA or the PhiX reference were removed.
Clean reads were then aligned to the mouse reference genome (mm10) using HISAT2 (v2.1.0) (Kim et al, 2015).
SAMtools (version 1.8)57 was then used to convert “SAM” files to “BAM” files, remove duplicate reads, and sort and index the “BAM” files. To avoid the artefact signals potentially introduced by misalignments, we only kept properly paired-end aligned reads with a mapping quality of at least 20 for downstream analyses.
Three rounds of StringTie (v2.1.4)58 was applied to i) perform reference-guided transcriptome assembly by supplying the GENCODE annotation file (V25) with the “-G” option for each sample, ii) generate a non-redundant set of transcripts using the StringTie merge mode, and iii) quantifying the transcript-level expression for each sample, with the option of “-e -G merged.gtf”. Known protein-coding transcripts (with the GENCODE biotype as “protein_coding”) were removed from the StringTie results. Ballgown (v2.22.0)59 was used to conduct transcript-level differential expression analysis.
Assembly: mm10
Supplementary files format and content: bigWig files were generated using the UCSC_binary_utilities: "bedGraphToBigWig"
Supplementary files format and content: bigWig files were generated using the UCSC_binary_utilities: "bedGraphToBigWig"

source_name: synaptosomes

growth_protocol: Male C57BL/6 mice (10–14 weeks old) were housed two per cage, maintained on a 12 h light/dark time schedule and allowed free access to food and water. All testing took place during the light phase in red-light-illuminated testing rooms following protocols approved by the Institutional Animal Care and Use Committee of the University of California, Irvine and by the Animal Ethics Committee of The University of Queensland. Animal experiments were carried out in accordance with the Australian Code for the Care and Use of Animals for Scientific Purposes (8th edition, revised 2013).

extract_protocol:
Preparation of synaptosomes was carried out as previously described. Briefly, tissues were homogenized in homogenizing buffer with 10-14 strokes using a Teflon-glass tissue grinder. The homogenate was centrifuged at 1000 x g for 10 mins at 4°C. The supernatant was directly applied onto a discontinuous Percoll gradient ranging from 0% up to 23% Percoll and centrifuged at 31,000 x g for 5 mins to isolate the synaptosome fraction. RNA was extracted according to the manufacturer’s instructions. The concentration of RNA was measured using a nanophotometer (IMPLEN) or Qubit fluorometer (Thermo Fisher Scientific).
Synaptosomes were collected and total RNA was isolated as described above. cDNA libraries were generated using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s protocol. A custom-designed probe panel (ROCHE) targeting 28,228 mouse lncRNAs18 was used to capture amplified cDNA. The capture procedure was performed using the SeqCap EZ Hybridization and Wash Kit (ROCHE) and SeqCap EZ Accessory kit (ROCHE) according to the manufacturer’s instructions. Captured libraries were sequenced on an Illumina HiSeq 4000 platform with 150-bp paired-end reads (GENEWIZ)
lncRNA capture sequencing

value: synaptosomes

tag: developmental stage

value: adult


title: lncRNA Capture-Seq synapse biol rep2

description: lncRNA capture sequencing


title: lncRNA Capture-Seq synapse biol rep4

description: lncRNA capture sequencing


title: lncRNA Capture-Seq synapse biol rep3

description: lncRNA capture sequencing


title: MOUSEPOOLEDNORMAL

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description: IMPACT

library_source: genomic

data_processing:
The data processing pipeline for detecting variants in Illumina HiSeq data is as follows.
First the FASTQ files are processed to remove any adapter sequences at the end of the reads using cutadapt (v1.6). The files are then mapped using the BWA mapper (bwa mem v0.7.12 ).
After mapping the SAM files are sorted and read group tags are added using the PICARD tools.
After sorting in coordinate order the BAM’s are processed with PICARD MarkDuplicates. The marked BAM files are then processed using the GATK toolkit (v 3.2) according the best practices for tumor normal pairs. They are first realigned using ABRA (v 0.92) and then the base quality values are recalibrated with the BaseQRecalibrator. Somatic variants are then called in the processed BAMs using muTect (v1.1.7) for SNV and the Haplotype caller from GATK with a custom post-processing script to call somatic indels.
The full pipeline is available here: https://github.com/soccin/BIC-variants_pipeline
Assembly: Mouse IMPACT. Ref hg19 b37 version of the genome

molecule: genomic DNA

source_name: Pooled Normal tails

extract_protocol:
For IMPACT.KPC tumor cells from 2 weeks tumor bearing liver were directly sorted into 1.5ml Eppendorf tube  bearing liver were directly sorted into 1.5ml Eppendorf tube precoated with 10% BSA. DNA samples were extracted with QIAamp DNA Micro Kit,and submitted to the Integrated Genomics Operation (IGO) at MSKCC for quality and quantity analysis, library preparation and sequencing.
For IMPACT, 89-100ng of mouse genomic DNA were used for library construction using the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) with 8 cycles of PCR. After sample barcoding, 100-110ng of each library were pooled and captured by hybridization with the mm_IMPACT (Integrated Mutation Profiling of Actionable Cancer Targets) assay, which captures all protein-coding exons and select introns of 578 cancer-related genes. Capture pools were sequenced on the HiSeq 4000, using the HiSeq 3000/4000 SBS Kit (Illumina) for PE100 reads. Following these criteria, the average coverage was 576X, with an average of 99% of the targeted sequences covered 30X.

value: Pooled Normal tails


title: IMPACT_KPC cells  rep3

description: IMPACT

source_name: KPC

tag: cell line

value: KPC

value: Pancreatic cancer cell line

value: P48CreLSL-KrasG12D/+, LSL-Trp53R172H/+


title: IMPACT_KPC cells  rep2

description: IMPACT


title: MTX 1

city: Toulouse

first: Alice

last: Davy

address: 118 route de Narbonne

department: MCD, CBI

country: France

institute: CNRS

description:
E13.5 mouse NPC are extracted from different embryos and cultured in vitro. The cells are then amplified and then divided into sample pools: IgG input, DMSO and MTX.
Read length: 50

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Assembly: mm10
Supplementary files format and content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

source_name: E13.5 NPC

growth_protocol: Dissociated neocortical cells from E13.5 cultured with growing medium (DMEM/F12 medium containing 0.6% Glucose, 5 mM HEPES, 1 mM Putrescine, 5 ng/ml FGF-2, 20 ng/ml EGF, 10 ng/ml Insulin-transferrin-sodium selenite supplement and 2% B27 supplement) in a 5% CO2 incubator at 37°C. Neural progenitor cells were cultured in a cell culture flask as free-floating neurospheres for 72 hours.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. After quenching and cell lysis, chromatin was sonicated.
ChIP samples were purified using Agencourt AMPure XP beads and quantified with the Qubit. ChIP-seq libraries were prepared from 1.5-10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

treatment_protocol: 2 µM MTX were diluted in growing medium for inhibiting DHFR activity.

value: Neural progenitor cells

value: MTX

tag: chip antibody

value: H3K4me3 (Cat#ab8580, Abcam)


title: MTX 2


title: DMSO 1

value: DMSO


title: Input DMSO


title: IMPACT_KPC KC_KO rep1

description: IMPACT

value: KPC pv.injection 2 weeks


title: IMPACT_c57bl6

description: IMPACT

source_name: C57BL/6 tail

value: C57BL/6 tail


title: IMPACT_KPC KC_KO rep3

description: IMPACT


title: IMPACT_KPC KC_KO rep4

description: IMPACT


title: IMPACT_KPC KC_WT rep3

description: IMPACT


title: IMPACT_KPC KC_KO rep2

description: IMPACT


title: IMPACT_KPC KC_WT rep4

description: IMPACT


title: IMPACT_KPC KC_WT rep2

description: IMPACT


title: Input MTX


title: DMSO 2


title: IMPACT_KPC KC_WT rep1

description: IMPACT


title: PtencKO-2

city: White Plains

first: Jian

last: Zhong

state: New York

address: 785 Mamaroneck Ave

institute: Burke Neurological Institute

data_processing:
The quality of the sequenced reads was assessed with FastQC and QoRTs (Andrews 2010, Hartley and Mullikin (2015)).
Adapters were trimmed with Trim Galore! v0.6.7.
Sequenced reads were aligned with default parameters to the mouse reference genome (GRCm38) using STAR v2.7.6a (Dobin et al. 2013).
Gene expression estimates were obtained with featureCounts v1.6.2 using composite gene models from Gencode (version M25) (Liao, Smyth, and Shi 2014, Harrow et al. (2012)).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw abundance values for each sample as obtained from featureCounts

source_name: corticospinal neurons

extract_protocol:
RNA preparation was performed as described in Heiman et al., Nature Protocols volume 9, pages 1282–1291 (2014).
RNA library preparations, sequencing reactions, and initial bioinformatic analysis were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).  RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads, then fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The quality of the sequencing libraries was validated on the Agilent TapeStation Bioanalyzer  (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).  The sequencing libraries were clustered on flowcells which were loaded on to the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

treatment_protocol: 5-6 weeks old mice were treated with tamoxifen (50 mg/1kg body weight, Sigma-Aldrich, T5648) by oral gavage for five consecutive days. One week after the last tamoxifen administration, sensorimotor cortex tissue harboring corticospinal projection neurons (20-25mg) was collected for TRAP-seq. One mouse was used for each biological replicate.

value: 129Sv and C57BL/6

value: PTEN knockout


title: PtencKO-1


title: WT-4


title: WT-5


title: ckaBraf-1

value: Braf knock-in


title: WT-3

value: WT


title: ckaBraf-3


title: IMPACT_KPC cells  rep1

description: IMPACT


title: WT-2


title: RAW264.7, FliC, 5h, rep3

city: Yangzhou

first: Li

last: Song

state: Jiangsu

address: 48 East Wenhui Road

institute: Yangzhou University

data_processing:
HTseq (v0.6.1) software and the model of UNION were used to analyze the gene expression level of each sample
DESeq (1.10.1) software was used for differential expression analysis
GOseq (Release2.12) and KOBAS (v2.0) software was used for Gene Ontology (GO) and KEGG metabolic pathway enrichment analysis
Assembly: GCA_001632525.1
Supplementary files format and content: gzip files for each Sample

growth_protocol: The murine macrophages RAW264.7 were cultured in complete DMEM medium containing 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
RNA was harvested using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer's instructions
RNA libraries for RNA-seq were prepared using NEB Next® UltraTM RNA Library Prep Kit following manufacturer's protocols

treatment_protocol: The murine macrophage cell line RAW264.7 were stimulated with 1 μg/ml flagellin (FliC) or medium for 5 h.

value: murine macrophage

value: flagellin-stimulated


title: RAW264.7, FliC, 5h, rep1


title: RAW264.7, mock, 5h, rep3

value: unstimulated


title: RAW264.7, FliC, 5h, rep2


title: WT-1


title: RAW264.7, mock, 5h, rep2


title: Blimp-1-defecient CD4 T cells-1 [CKO_1]

city: Miaoli

first: Yu-Wen

last: Liu

state: -- None selected --

address: Zhunan: 35, Keyan Road, Zhunan Town

country: Taiwan

institute: National Health Research Institutes

data_processing:
The clustering of the index-coded sample was performed on a cBot Cluster Generation System using Hiseq PE Cluster kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125bp/150bp paired-end reads were generated.
Trimming of raw reads with Trimmomatic (v.0.38) removed adapters and low-quality reads.
Generated paired-end clean reads were aligned to the reference genome using HISAT2 v2.1.0. featureCounts v1.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: M. musculus, GRCm38
Supplementary files format and content: HISAT2 v2.1.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: spleen

extract_protocol:
RNA was harvested using TRIzol RNA extraction. 3 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

value: spleen

value: CD4 T cells

value: Blimp1 knockout

value: steady-state primary CD4 T cells


title: Control CD4 T cells-2 [WT_2]


title: Blimp-1-defecient CD4 T cells-2 [CKO_2]


title: Blimp-1-overexpressed CD4 T cells-1 [Tg_2]

value: Blimp-1 overexpression


title: Control CD4 T cells-1 [WT_1]


title: RAW264.7, mock, 5h, rep1


title: Blimp-1-overexpressed CD4 T cells-1 [Tg_1]


title: colorectal cancer serum, biological rep2

city: Nanjing

first: qiu

last: chengchao

address: Moling Street

institute: Nanjing University of Aeronautics and Astronautics

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore
Trimmed sequence reads were mapped to mm10 using Hisat2
Read count extraction and normalization were performed using stringtie
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts values for each Sample

source_name: serum

extract_protocol:
RNA was harvested using TRIzol® Reagent (Invitrogen). 5ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeqTM Stranded Total RNA Library Prep Kit following manufacturer's protocols.

value: serum

tag: disease

value: colorectal cancer


title: colorectal cancer serum, biological rep1


title: normal serum, biological rep6

value: normal


title: colorectal cancer serum, biological rep6


title: colorectal cancer serum, biological rep3


title: normal serum, biological rep5


title: colorectal cancer serum, biological rep4


title: colorectal cancer serum, biological rep5


title: normal serum, biological rep3


title: normal serum, biological rep2


title: normal serum, biological rep1


title: normal serum, biological rep4


title: pancreas Model rep3

city: chengdu

first: Linbo

last: Yao

state: China

address: West China Hospital

institute: West China Hospital, Sichuan University

data_processing:
For RNA-seq data analysis, raw data were filtered and adapters were cut using Trim galore software (0.6.6) and quality control was performed using fastp (0.20.1). Then clean reads were mapped to the GRCm38 mouse reference genome using the Star program (2.7.4a). Finally, the featureCounts (2.0.1) software was used to quantify reads.
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: pancreas

growth_protocol: Mice of 4-5 weeks old were randomly assigned into CD and HFD groups, fed with normal chow or high-fat diet for 12 weeks, respectively.

extract_protocol:
Total RNA was isolated from the pancreas and adipose tissue using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The OAAP model was induced by 2 g/kg ethanol (EtOH) intraperitoneal injection in HFD mice twice for 1 h each time

value: pancreas

value: wild type

tag: condition

value: Model


title: pancreas Model rep1


title: pancreas Control rep2

value: Control


title: adipose Model rep3

source_name: adipose

value: adipose


title: pancreas Control rep1


title: adipose Model rep2


title: adipose Control rep3


title: adipose Control rep1


title: adipose Control rep2


title: tdT+ MPs E16.5 WT rep1

city: Seoul

first: Young-Woo

last: Jo

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

data_processing:
Basecalling was performed with the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to fastq file conversion was performed with bcl2fastq v2.20.0.
Single reads were mapped to the mouse genome (mm10) in R using the Rsubread package (version 4.1).
Genome_build: mm10
Supplementary_files_format_and_content: csv files with sample IDs as row, genes as columns and values in RPKM

source_name: Isolated myogenic cells

extract_protocol:
Limb muscles were mechanically dissected and dissociated in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% horse serum (Hyclone, Logan, UT, USA), collagenase type II (800 units/mL; Worthington, Lakewood, NJ, USA), and dispase (1.1 units/mL; StemCell Technologies, Vancouver, BC, Canada) at 37 °C for 30 min. Digested suspensions were subsequently triturated and washed with DMEM to harvest mononuclear cells. Mononuclear cells were stained with Sca-1-FITC (553335; BD Bioscience, Franklin Lakes, NJ, USA), CD31-APC (102510; BioLegend, San Diego, CA, USA), CD45-APC (103112; BD Biosciences), Ter119-APC (116212; BioLegend), and Vcam1-Biotin (553331; BD Biosciences). Streptavindin-PE/Cy7 (BioLegend) was used as a secondary reagent. Lin-/tdTomato+ myogenic cells were isolated using a FACS Aria III cell sorter (BD Biosciences). Total RNA was extracted from freshly isolated limb muscle or purified mononucleated cells using TRI Reagent (Invitrogen).
Total RNA libraries were generated using SMART-SeqTM v4 UltraTM Low Input RNA Kit for sequencing (Takara Bio USA, San Diego, CA, USA), according to the manufacturer’s instructions. Libraries were sequenced as paired-ends on an Illumina Hi-Seq 4000 system.

treatment_protocol: Tamoxifen (20mg/mL in corn oil) (Sigma-Aldrich, St. Louis, MO, USA) was administered orally to pregnant mother mice including Pax7CreER allele for 2 days(240mg/kg body weight) from E12.5

value: Muscle

value: tdT+ myogenic progenitors (MPs)

value: Tamoxifen


title: DMSO1_MAR1

city: San Diego

first: Yuqing

last: Hang

address: 10010 N Torrey Pines Rd

department: IGC Core

institute: Salk Institute for biological studies

data_processing:
Fastq reads were aligned using STAR and then make tag directories for each experiment using those sam or bam files. Then we quantify gene expression across all experiments using HOMER analyzeRepeats.pl. TPM.txt file is the default file that we get when we run runSTAR on the fastq files. Here is the command: analyzeRepeats.pl rna ${GENOME%.star} -d tags/* -tpm -count exons -condenseGenes -strand +  > tpm.txt. normed_fpkm.txt file is quantified using command: analyzeRepeats.pl rna mm10 -count exons -condenseGenes -strand both -d tags/* -fpkm -normMatrix 1000000 > Total_exons_normed_fpkm.txt
Using TPKM, differential expression analysis (using DESeq2) was performed.
Assembly: mm10
Supplementary files format and content: TPM

growth_protocol: YUMM1.7 cells were cultured in DMEM/F12 medium supplemented with 10% FBS and 1% NEAA

extract_protocol:
Total RNA was extracted using Rneasy plus mini kit (Qiagen). RNA was treated with Dnase I (ThermoFisher) to remove DNA contamination.
Illumina TruSeq library kit

treatment_protocol: YUMM1.7 cells were treated with DMSO, Rotenone and 3-NPA for 48 hours in 6cm dishes in duplicates.

value: Melanoma cell line

tag: genetic background

value: BrafV600E/ Pten-/-/ Cdkn2a-/-

value: DMSO


title: LDLR_KO_high_cholesterol

city: Edinburgh

first: Ian

middle: R

last: McCracken

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: University of Edinburgh

description: 10X Genomics Single cell 3' gene expression V3

data_processing:
Data processed using the 10X Cell Ranger pipeline v3.1.0 ( 10X Genomics) using default parameters.
Genome_build: mm10

molecule: polyA RNA

source_name: DAPI- cells isolated after digestion from adventitia from thoracic aorta

extract_protocol:
Enzymatic digestion of aortic adventitia using collagenase B, pronase and DNAse. Thereafter, FACS isolation of DAPI negative cells
Library construction was conducted using the Single Cell 3’  Reagent Kit (V3) (10X Genomics)

treatment_protocol: 0.25% cholesterol diet

value: aortic adventitia

tag: mouse line

value: LDLR-KO


title: Rot2_MAR4

tag: cell type

value: ETC CI inhibitor (Rotenone)


title: EPL cells - D3 #Rep3

city: Camperdown

first: Hannah

middle: J

last: Glover

state: NSW

address: 92 Parramatta Rd

department: Physiology

institute: The University of Sydney

data_processing:
All samples were aligned to mouse assembly GRCm38 using HISAT2. BAM files were generated using samtools and counts quantified using FeatureCounts. Full pipeline available at GitHub (hannahglover)
Genome_build: GRCm38 (From Ensembl)
Supplementary_files_format_and_content: compiled matrix of FeatureCounts output

source_name: EPL cells - D3

growth_protocol: Ground state mESCs maintained in DMEM/10% FBS + 1000 U/mL LIF + Pen/Strep + B-Mec + 2i. EpiSCs were generated from A2 mESCs implanted into a pseduopregnant mouse, isolated after implanation and then maininined in KO DMEM/KOSR + Activin A + bFGF + B-me

extract_protocol:
GeneElute Mammalian Total RNA MiniPrep Kit, including on-column DNA digestion (Sigma, #RTN350, #DNASE70)
Illumina TruSeq RNA Sample Prep Kit v2 (Illumina #RS122-2001)

treatment_protocol: Ground state mESCs were differentiated to naïve mESCs by removal of 2i for 4 days. Ground state mESCs were differentiated to EPL cells by culturing in DMEM/10% FBS + 330 U/mL LIF + 400 uM -L-pro + Pen/Strep + B-Mec for 4 days.

value: mESCs derived from the inner cell mass of preimplantation mouse embryos

tag: cell subtype

value: EPL cells


title: pancreas Model rep2

tag: genotype


title: DMSO2_MAR2

tag: treatment


title: LDLR_KO_chow

treatment_protocol: chow diet

tag: tissue


title: Rot1_MAR3


title: NPA1_MAR5


title: tdT+ MPs E16.5 N2 rep1

value: Notch2 cKO


title: EPL cells - D3 #Rep2


title: EPL cells - D3 #Rep1


title: tdT+ MPs E16.5 N2 rep2


title: tdT+ MPs E16.5 WT rep2


title: tdT+ MPs E16.5 N1 rep1

value: Notch1 cKO


title: NPA2_MAR6


title: Naive mESCs - D3 #Rep2

source_name: Naive mESCs - D3

value: Naive mESCs


title: Naive mESCs - D3 #Rep3


title: Naive mESCs - D3 #Rep1


title: Ground State mESCs - D3 #Rep3

source_name: Ground State mESCs - D3

value: Ground State mESCs


title: Ground State mESCs - D3 #Rep2


title: adipose Model rep1

value: wild type

value: Model


title: EpiSCs - A2 #Rep2

source_name: EpiSCs - A2

value: EpiSCs derived from the epiblast of the postimplantation mouse embryo

value: EpiSCs


title: Ground State mESCs - D3 #Rep1


title: EpiSCs - A2 #Rep3


title: EpiSCs - A2 #Rep1


title: EPL cells - A2 #Rep3

source_name: EPL cells - A2


title: EPL cells - A2 #Rep2


title: EPL cells - A2 #Rep1


title: Naive mESCs - A2 #Rep2

source_name: Naive mESCs - A2


title: Naive mESCs - A2 #Rep3


title: Naive mESCs - A2 #Rep1


title: liver, D3

city: Worcester

first: Michael

last: Czech

state: Massachusetts

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

data_processing:
DolphinNext RNASeq Pipeline Trimmomatic (v.0.11.8) step removed Illumina adapter sequences
DolphinNext RNASeq Pipeline RSEM (v.1.2.28) aligned reads with the STAR aligner and then estimated expression levels, producing rsem_gene_expected_count.tsv
DEBrowser's DESeq2 module was used to find differentially expressed genes using the RSEM levels
The enrichGO function of the clusterProfiler package found pathways associated with the differentially expressed genes
rsem -star was used to produce rsem_gene_expected_count.tsv which is a tab delimited text file. Note: this data is NOT normalized.
Genome_build: mm10
Supplementary_files_format_and_content: rsem_gene_expected_count.tsv

source_name: liver

growth_protocol: 10w old ob/ob mice fed with NASH diet for 3 weeks

extract_protocol: Trizol RNA extraction

treatment_protocol: Ten-week-old genetically obese ob/ob mice (n=4) were injected subcutaneously with either non targeting control NTC (10mg/kg) or Dgat2-1473 (10mg/kg) and provided a NASH-inducing diet (GAN diet) for 3 weeks. After 3 weeks mice were sacrificed.

value: ob/ob

value: liver

tag: diet

value: GAN

value: NASH

value: DGAT2-GalNac 1473 siRNA


title: Ground State mESCs - A2 #Rep3

source_name: Ground State mESCs - A2


title: Ground State mESCs - A2 #Rep2


title: Ground State mESCs - A2 #Rep1


title: liver, D4


title: liver, D2


title: liver, N1

value: non-targeting control siRNA


title: liver, N4


title: liver, D1


title: ND_cont_4

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

data_processing:
Paired-end reads were mapped to reference genome GRCm38/mm10 using STAR version 2.3
Mapped reads were summaried to gene level using featureCounts version 1.5 and with GENCODE GRCm38 vM10 gene annotation
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab delimited text file containing the read counts for all genes

source_name: Ear skin

extract_protocol:
Mouse ear tissues were homogenized in Trizol using a bead cells disrupter/micro homogenizing system (Tomy Micro Smash MS-100). Total RNA was isolated following the double extraction protocol: RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (TRIzol, Thermo Fisher Scientific) followed by a Qiagen RNeasy Micro clean-up procedure according to the manufacturer's protocol.
cDNA libraries were prepared from 2 ng total RNA starting material and 1 ul of a 1:50,000 dilution of ERCC RNA Spike in Controls (Ambion® Thermo Fisher Scientific) using the SMARTSeq v2 protocol with the following modifications: 1. Addition of 20 µM TSO; 2. Use of 250 pg cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA). The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip (Perkin Elmer, Waltham, MA, USA). All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina HiSeq 4000 system (Illumina) (32 samples/lane).

treatment_protocol: B6 mice were fed a high-fat diet for 8 weeks, then PMA (200 ng/ear) was applied to the ear  and the ears were collected 24 hours later.

value: Ear skin

value: Normal diet (ND)

value: non-treated


title: ND_cont_3


title: liver, N3


title: liver, N2


title: HFD_PMA_2

value: High fat diet (HFD)

value: PMA treated


title: HFD_cont_1


title: HFD_PMA_1


title: ND_PMA_4


title: ND_cont_1


title: ND_PMA_2


title: HFD_PMA_3


title: ND_cont_2


title: ND_PMA_3


title: HFD_PMA_4


title: HFD_cont_2


title: HFD_cont_3


title: ND_PMA_1


title: HFD_cont_4


title: scRNA_ESC_Ola_IFNb_6h_Rep1

city: Heidelberg

first: Markus

last: Muckenhuber

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

data_processing:
ATAC-seq bam files: Raw reads were trimmed by Trimmomatic (v0.36) and mapped using Bowtie2 (v2.3.3.1). The mapped reads were with bedtools (v2.27.1) sorted, shifted by +4/-5bp to correct for transposase intragtion bias, duplicates and reads in blacklisted reads removed. Reads with quality score below 30 were removed.
ATAC-seq bed files: The sorted and quality filtered bam files were used for peak calling by MACS2 (v2.1.2).
ATAC Norm counttables: Bam files were used to count reads around peaks of STAT1p701 and STAT2 by bedtools (v2.27.1). Reads were normalized by sequencing depth, fragment length and enrichment to control.
ChIP bed files: Raw reads were mapped with Bowtie (v1.2.2). The mapped reads were sorted, duplicates and reads in blacklisted regions removed with bedtools (v2.27.1).
ChIP Norm counttables: Bam files were used to count reads around peaks of STAT1p701 and STAT2 by bedtools (v2.27.1). Reads were normalized by sequencing depth, fragment length and enrichment to control. For histon marks H3 signal was the control. For STAT ChIPs IgG_Rb_CST.
RNA-seq raw counttable: Ribosomal RNAs were removed by SortMeRNA (v2.1). Raw reads were aligned with STAR (v2.5.3a) and Aligned.sorted.ByCoord.out.bam and Aligned.to.Transcriptome.out.bam were created. STAR counted reads per genes in ReadsPerGene.out.tab files. These files were combined and the resulting raw count-table was the input for DESeq2.
RNA-seq count table TPM and FPKM: Ribosomal RNAs were removed by SortMeRNA (v2.1). Raw reads were aligned with STAR (v2.5.3a) and Aligned.sorted.ByCoord.out.bam and Aligned.to.Transcriptome.out.bam were created. The  Aligned.to.Transcriptome.out.bam files from STAR were used as input for RSEM (v1.3.0) to create TPM and FPKM values.
RNA-seq DESeq result tables: Result tables for DESeq2 (1.24.0) for the comparisons of 1h IFNb with 0h; 6h IFNb with 0h and 6h with 1h IFNb.
scATAC-seq: Raw reads were applied to CellRanger (v1.1.0), a full automatic pipeline especially for scATAC-seq data done by the 10x Chromium.
scATAC-seq: The default output counttable for downstream analysis.
scRNA-seq: Raw reads were applied to CellRanger (v1.3.1), a full automatic pipeline especially for scRNA-seq data done by the 10x Chromium.
scRNA-seq counttable: The default output folders with the counttable for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: ATAC-seq bam files: Quality filtered mapped read files
Supplementary_files_format_and_content: ATAC-seq bed files: File containing coordinates of peaks and enrichment scores by MACS2
Supplementary_files_format_and_content: ChIP-seq bed files: File containing coordinates of peaks and enrichment scores by MACS2
Supplementary_files_format_and_content: ChIP-seq peak list for STAT1 and STAT2 by DiffBind: Peak lists for STAT1p701 and STAT2 replicates were anaylzed by DiffBind (v2.12.0) to create list of robust binding sites over replicates. Peaks at 1h and 6h of IFNb treatment were combined
Supplementary_files_format_and_content: RNA-seq raw counttable: Counttable containing ENSEMBL gene ID and the raw read counts for each gene over the replicates in ESCs, MEFs and NPCs
Supplementary_files_format_and_content: RNA-seq count table TPM and FPKM: Counttable with normalized TPM and FPKM values for each samples of ESCs, MEFs and NPCs. In addtition, the ENSEMBL gene ID, all transcript Ids and the annotated gene length.
Supplementary_files_format_and_content: RNA-seq DESeq result tables: Results table from DESeq2 of all genes for the three compariosns of 1h vs 0h, 6h vs 0h and 6h vs 1h. Each files contains the ENSEMBL gene ID, the normalized counts for all used samples, the base mean expression, the log2 fold change of the comaprison, the standard error of the log2 fold change, the Wald statistic, pvalue and adjusted pvalue.
Supplementary_files_format_and_content: scATAC: Counttable with a the coordinates of mapped fragments, the barcode of the fragment and the counts.
Supplementary_files_format_and_content: scRNA-seq: The folder contains the deault output of Cellranger. A list of detected barcodes in the sample. A List of identified genes in the sample as ENSEMBL ID and gene symbole. And a matix which is the counttable.

growth_protocol:
Embryonic stem cells: Cultured on 0.1 % gelatinized tissue flasks in ESC media. Cells were incubated at 37 °C and 5 % CO2. Media was PowerStem ESPro1 (PAN-Biotech; P04-77510K) with self-made LIF (1:1000).
Mouse embryonic fibroblasts: Cells were incubated at 37 °C and 5 % CO2. Media was DMEM (Gibco, 11880-28), 10% FCS (PAN-Biotech; P30-3602), 1x L-Glutamine (PAN-Biotech, P04-80050), 1x PenStrep (PAN-Biotech, P06-07050).
Neural progenitor cells: ESCs were differentiated into NPCs based on the Bible-protocol Bibel et al. 2007. 4-5*10^6 cultured ESCs were split onto a T75 UltraLow-BindingPlates (Corning, 3814) in 15 ml StemPAN media (PAN-biotech, P08-50500). After 4 days 5µM retinoic acid (Sigma-Aldrich, R2625) was added. On day 8, cells were platted on plates coated with 1% Matrigel (Corning, 356230) in neuronal base medium (Gibco, 211103049), G5 supplements (Gibco, 17503012), NSC supplements (Gibco, 17502048). Experiments were performed five days after neuronal plating.

extract_protocol:
ATAC-seq: . For ESCs, the cell pellet was resuspended in 200 µl ATAC lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl2, 3 mM MgCl2, 0.1 % NP-40) and incubate for at room temperature for 2 min. 20 µl ATAC reaction buffer containing 10 µl 2x transposase buffer and 2.5 µl Tn5 enzyme (Illumina) was added and samples were incubated at 37 °C for 30 min. Samples were purified. For MEFs, the lysis buffer contained additionally 1 % digitonin.
ATAC-seq: Purified samples were directly amplifed, barcoded and purified.
ChIP-seq for histone marks in ESC: Cells were crosslinked by 1 % Formaldehyde for 10 min at room temperature and stopped with 125 mM Glycine for 5 min. Samples of around 40 million cells were treated with 40 U of MNase for 15 min at 37 °C. The samples were shared for 15 min (Burst 200; Cycle 20%; Intensity 8). Replicate 1 was shared for 30 min and no MNase treatment was performed. 4µg of antibody was used per sample and incubated for 2 hours at 4 °C. Protein G-beads were added over night. Multiple low and high salt washes were performed and the samples were eluted. Samples were reverse crosslinked and stored at -20°C.
ChIP-seq for histone marks in ESCs: Libraries were made using NEBNext Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, E7645)
ChIP-seq for STATs in ESCs and MEFs: The isolation of the chromatin was done with Simple ChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology, 9003)
ChIP-seq for STATs in ESCs and MEFs: Libraries were made using NEBNext Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, E7645)
RNA-seq: Total RNA was isolated using NucleoSpin RNA Plus Kit (Macherey-Nagel, 740984.250). Depletion of rRNA was done with Ribo-Zero rRNA Removal Kit (Illumina, 15066012) for ESCs and MEFs and with NEBNext® rRNA Depletion Kit (New England Biolabs, E6350).
RNA-seq: Libraries were prepared using NEBNext Ultra II Directional  RNA Library Prep Kit for Illumina (New England Biolabs, E7760).
scATAC-seq: The experiment was performed based on the standard manufacturer’s protocol Chromium Single Cell ATAC Reagent Kits (PN-1000110).
scRNA-seq: The experiment was performed based on the standard manufacturer’s protocol of Chromium Single Cell 3’ Reagent Kits v2 (PN-120237).

treatment_protocol: All cells were treated with 500U/ml of self-made interferon beta (16.6U/µl) for 1 hour or 6 hours

value: Embryonic stem cells


title: scRNA_ESC_Ola_IFNb_0h_Rep1


title: RNA_NPC_Ola_IFNb_6h_Rep2

description: RNA_MEF_Ola_IFNb_Counttable_Raw.txt, RNA_NPC_Ola_IFNb_Counttable_TPM_FPKM.txt

value: ES-derived neural progenitor cells


title: scRNA_ESC_Ola_IFNb_1h_Rep1


title: RNA_NPC_Ola_IFNb_6h_Rep3


title: RNA_NPC_Ola_IFNb_6h_Rep4


title: RNA_NPC_Ola_IFNb_1h_Rep3


title: RNA_NPC_Ola_IFNb_6h_Rep1


title: RNA_NPC_Ola_IFNb_1h_Rep2


title: RNA_NPC_Ola_IFNb_1h_Rep4


title: RNA_NPC_Ola_IFNb_1h_Rep1


title: RNA_NPC_Ola_IFNb_0h_Rep4


title: RNA_NPC_Ola_IFNb_0h_Rep2


title: RNA_MEF_Ola_IFNb_6h_Rep2

description: RNA_MEF_Ola_IFNb_Counttable_Raw.txt, RNA_MEF_Ola_IFNb_Counttable_TPM_FPKM.txt

value: Mouse embryonic fibroblasts


title: RNA_NPC_Ola_IFNb_0h_Rep3


title: RNA_MEF_Ola_IFNb_6h_Rep1


title: ChIP_MEF_Ola_Stat2_CST_IFNb_6h_Rep2

description: Norm_count_table_MEF_Ola_ChIP_reads_at_STAT1p701_and_STAT2_peaks_at_1h_and_6h.txt


title: RNA_MEF_Ola_IFNb_1h_Rep1


title: RNA_MEF_Ola_IFNb_1h_Rep2


title: RNA_MEF_Ola_IFNb_0h_Rep2


title: ChIP_MEF_Ola_Stat2_CST_IFNb_6h_Rep1


title: RNA_MEF_Ola_IFNb_0h_Rep1


title: ChIP_MEF_Ola_Stat2_CST_IFNb_1h_Rep2


title: ChIP_MEF_Ola_Stat2_CST_IFNb_1h_Rep1


title: ChIP_MEF_Ola_Stat1_p701_CST_IFNb_6h_Rep1


title: ChIP_MEF_Ola_Stat1_p701_CST_IFNb_6h_Rep2


title: ChIP_MEF_Ola_Stat1_p701_CST_IFNb_1h_Rep2


title: ChIP_MEF_Ola_Stat2_CST_IFNb_0h_Rep2


title: ChIP_MEF_Ola_Stat2_CST_IFNb_0h_Rep1


title: ChIP_MEF_Ola_Stat1_p701_CST_IFNb_1h_Rep1


title: RNA_NPC_Ola_IFNb_0h_Rep1


title: ChIP_MEF_Ola_Input_CST_IFNb_1h_Rep2


title: ChIP_MEF_Ola_Stat1_p701_CST_IFNb_0h_Rep2


title: ChIP_MEF_Ola_Input_CST_IFNb_0h_Rep2


title: ChIP_MEF_Ola_Input_CST_IFNb_0h_Rep1


title: ChIP_MEF_Ola_Input_CST_IFNb_1h_Rep1


title: ChIP_MEF_Ola_IgG_Rb_CST_IFNb_1h_Rep1

description:
Peak calling control for ESC STAT1_p701 and STAT2 IFNb 1h Rep1
Norm_count_table_MEF_Ola_ChIP_reads_at_STAT1p701_and_STAT2_peaks_at_1h_and_6h.txt


title: ChIP_MEF_Ola_IgG_Rb_CST_IFNb_1h_Rep2

description:
Peak calling control for ESC STAT1_p701 and STAT2 IFNb 1h Rep2
Norm_count_table_MEF_Ola_ChIP_reads_at_STAT1p701_and_STAT2_peaks_at_1h_and_6h.txt


title: ChIP_MEF_Ola_Input_CST_IFNb_6h_Rep1


title: ChIP_MEF_Ola_IgG_Rb_CST_IFNb_6h_Rep1

description:
Peak calling control for ESC STAT1_p701 and STAT2 IFNb 6h Rep1
Norm_count_table_MEF_Ola_ChIP_reads_at_STAT1p701_and_STAT2_peaks_at_1h_and_6h.txt


title: ChIP_MEF_Ola_IgG_Rb_CST_IFNb_0h_Rep1

description:
Peak calling control for ESC STAT1_p701 and STAT2 IFNb 0h Rep1
Norm_count_table_MEF_Ola_ChIP_reads_at_STAT1p701_and_STAT2_peaks_at_1h_and_6h.txt


title: ChIP_MEF_Ola_IgG_Rb_CST_IFNb_6h_Rep2

description:
Peak calling control for ESC STAT1_p701 and STAT2 IFNb 6h Rep2
Norm_count_table_MEF_Ola_ChIP_reads_at_STAT1p701_and_STAT2_peaks_at_1h_and_6h.txt


title: ChIP_MEF_Ola_IgG_Rb_CST_IFNb_0h_Rep2

description:
Peak calling control for ESC STAT1_p701 and STAT2 IFNb 0h Rep2
Norm_count_table_MEF_Ola_ChIP_reads_at_STAT1p701_and_STAT2_peaks_at_1h_and_6h.txt


title: ChIP_ESC_Ola_Stat2_CST_IFNb_6h_Rep5


title: ChIP_ESC_Ola_Stat2_CST_IFNb_6h_Rep6


title: ChIP_MEF_Ola_Input_CST_IFNb_6h_Rep2


title: ChIP_MEF_Ola_Stat1_p701_CST_IFNb_0h_Rep1


title: ChIP_ESC_Ola_Stat2_CST_IFNb_1h_Rep6


title: ChIP_ESC_Ola_Stat2_CST_IFNb_6h_Rep2


title: ChIP_ESC_Ola_Stat2_CST_IFNb_1h_Rep4


title: ChIP_ESC_Ola_Stat2_CST_IFNb_1h_Rep5


title: ChIP_ESC_Ola_Stat2_CST_IFNb_6h_Rep1


title: ChIP_ESC_Ola_Stat2_CST_IFNb_0h_Rep5


title: ChIP_ESC_Ola_Stat2_CST_IFNb_0h_Rep4


title: ChIP_ESC_Ola_Stat2_CST_IFNb_1h_Rep1


title: ChIP_ESC_Ola_Stat2_CST_IFNb_0h_Rep1


title: ChIP_ESC_Ola_Stat2_CST_IFNb_0h_Rep2


title: ChIP_ESC_Ola_Stat1_p701_CST_IFNb_1h_Rep6


title: ChIP_ESC_Ola_Stat1_p701_CST_IFNb_6h_Rep1


title: ChIP_ESC_Ola_Stat2_CST_IFNb_6h_Rep4


title: ChIP_ESC_Ola_Stat1_p701_CST_IFNb_6h_Rep4


title: ChIP_ESC_Ola_Stat1_p701_CST_IFNb_6h_Rep6


title: ChIP_ESC_Ola_Stat1_p701_CST_IFNb_6h_Rep5


title: ChIP_ESC_Ola_Stat1_p701_CST_IFNb_1h_Rep1


title: ChIP_ESC_Ola_Stat1_p701_CST_IFNb_6h_Rep2


title: ChIP_ESC_Ola_Stat2_CST_IFNb_1h_Rep2


title: ChIP_ESC_Ola_Stat1_p701_CST_IFNb_1h_Rep2


title: ChIP_ESC_Ola_Stat1_p701_CST_IFNb_1h_Rep5


title: ChIP_ESC_Ola_Stat1_p701_CST_IFNb_0h_Rep4


title: ChIP_ESC_Ola_Stat1_p701_CST_IFNb_1h_Rep4


title: ChIP_ESC_Ola_Stat1_p701_CST_IFNb_0h_Rep5


title: ChIP_ESC_Ola_Stat1_p701_CST_IFNb_0h_Rep1


title: ChIP_ESC_Ola_Stat1_p701_CST_IFNb_0h_Rep2


title: ChIP_ESC_Ola_Input_CST_IFNb_6h_Rep4


title: ChIP_ESC_Ola_Input_CST_IFNb_6h_Rep5


title: ChIP_ESC_Ola_Input_CST_IFNb_6h_Rep6


title: ChIP_ESC_Ola_Input_CST_IFNb_1h_Rep6


title: ChIP_ESC_Ola_Input_CST_IFNb_6h_Rep1


title: ChIP_ESC_Ola_Input_CST_IFNb_1h_Rep4


title: ChIP_ESC_Ola_Input_CST_IFNb_1h_Rep1


title: ChIP_ESC_Ola_Input_CST_IFNb_0h_Rep5


title: ChIP_ESC_Ola_Input_CST_IFNb_1h_Rep2


title: ChIP_ESC_Ola_Input_CST_IFNb_0h_Rep4


title: ChIP_ESC_Ola_Input_CST_IFNb_0h_Rep2


title: ChIP_ESC_Ola_IgG_Rb_CST_IFNb_6h_Rep6

description: Peak calling control for ESC STAT1_p701 and STAT2 IFNb 6h Rep6


title: ChIP_ESC_Ola_IgG_Rb_CST_IFNb_6h_Rep5

description: Peak calling control for ESC STAT1_p701 and STAT2 IFNb 6h Rep5


title: ChIP_ESC_Ola_Input_CST_IFNb_0h_Rep1


title: ChIP_ESC_Ola_IgG_Rb_CST_IFNb_1h_Rep1

description: Peak calling control for ESC STAT1_p701 and STAT2 IFNb 1h Rep1


title: ChIP_ESC_Ola_Input_CST_IFNb_1h_Rep5


title: ChIP_ESC_Ola_Input_CST_IFNb_6h_Rep2


title: ATAC_ESC_Ola_IFNb_1h_Rep2

description: Resulting peak list from peak calling with MACS2 (broad peak)


title: ATAC_ESC_Ola_IFNb_0h_Rep2


title: ChIP_ESC_Ola_IgG_Rb_CST_IFNb_1h_Rep4

description: Peak calling control for ESC STAT1_p701 and STAT2 IFNb 1h Rep4


title: ChIP_ESC_Ola_IgG_Rb_CST_IFNb_1h_Rep5

description: Peak calling control for ESC STAT1_p701 and STAT2 IFNb 1h Rep5


title: ChIP_ESC_Ola_IgG_Rb_CST_IFNb_0h_Rep5

description: Peak calling control for ESC STAT1_p701 and STAT2 IFNb 0h Rep5


title: ChIP_ESC_Ola_IgG_Rb_CST_IFNb_0h_Rep2

description: Peak calling control for ESC STAT1_p701 and STAT2 IFNb 0h Rep2


title: ChIP_ESC_Ola_IgG_Rb_CST_IFNb_6h_Rep1

description: Peak calling control for ESC STAT1_p701 and STAT2 IFNb 6h Rep1


title: ChIP_ESC_Ola_IgG_Rb_CST_IFNb_1h_Rep6

description: Peak calling control for ESC STAT1_p701 and STAT2 IFNb 1h Rep6


title: ChIP_ESC_Ola_IgG_Rb_CST_IFNb_6h_Rep4

description: Peak calling control for ESC STAT1_p701 and STAT2 IFNb 6h Rep4


title: ChIP_ESC_Ola_IgG_Rb_CST_IFNb_0h_Rep4

description: Peak calling control for ESC STAT1_p701 and STAT2 IFNb 0h Rep4


title: ChIP_ESC_Ola_IgG_Rb_CST_IFNb_6h_Rep2

description: Peak calling control for ESC STAT1_p701 and STAT2 IFNb 6h Rep2


title: ChIP_ESC_Ola_IgG_Rb_CST_IFNb_1h_Rep2

description: Peak calling control for ESC STAT1_p701 and STAT2 IFNb 1h Rep2


title: ChIP_ESC_Ola_IgG_Rb_CST_IFNb_0h_Rep1

description: Peak calling control for ESC STAT1_p701 and STAT2 IFNb 0h Rep1


title: ATAC_ESC_Ola_IFNb_6h_Rep2


title: Eed Control rep3

city: Bronx

first: Deyou

last: Zheng

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

data_processing:
The paired-end RNA-seq reads were aligned to the mouse transcriptome corresponding to the Gencode annotation (vM20) using the software Kallisto (v0.42.5). The counts for protein-coding genes were collapsed and used for DESeq2 (v3.11) for differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: The text tables were DESeq2 results with normalized counts from DESeq2.

source_name: Skin epidermis

extract_protocol:
P71 adult back skins were collected and subjected to 0.25% trypsin digestion for 60 minutes at 37ºC with 80 rpm shaking. 1:200 Sca1-PerCP-Cy5.5 (Biolegend), 1:200 α6-integrin-FITC (eBiosciences), and 1:100 EpCAM-APC (Biolegend) for 30 minutes on ice and washed twice with 1x DPBS before cell sorting. Interfollicular epidermis, enriched for epidermal progenitors, was sorted as EpCAM(+), Sca1(+), and α6-integrin(high). FACS-purified cells were collected directly into RLT Plus buffer (QIAGEN), and total RNA was isolated with the RNeasy Plus Micro Kit (QIAGEN).
10ng of total RNA were reverse transcribed and amplified using the Ovation RNA-seq System V2 (NuGEN). Libraries were constructed from 100ng of sonicated cDNA (Covaris) using the Ovation Ultralow system V2 (NuGEN).  The concentration and quality of the libraries were determined using Qubit (Invitrogen) and Bioanalyzer (Agilent). Constructed RNA-seq libraries were sequenced at GENEWIZ on the Illumina HiSeq platform, obtaining 150 nucleotide paired-end reads.

treatment_protocol: For hydroxyl-tamoxifen (4OH-Tam) (Sigma-Aldrich) topical treatment, 4OH-Tam was dissolved in absolute ethanol (Sigma-Aldrich) to a final concentration of 20 mg/ml. To induce recombination, 100ul of 4OT-Tam topically applies on shaved back skin of P50 mice once per day for 4 days. mice are collected at P71.

value: Epidermal cells

value: Epidermis

value: Postnatal day 71

value: Control


title: ATAC_ESC_Ola_IFNb_6h_Rep1


title: ATAC_ESC_Ola_IFNb_1h_Rep1


title: Eed Control rep1


title: Eed; Ring1a/b 3KO_rep2

data_processing: The RNA-seq reads were aligned to the mouse transcriptomes corresponding to the Gencode annotation (vM20) using the software Kallisto (v0.42.5). The genes with an average TPM (transcripts per million reads mapped) > 1 in either control or 3KO were used for differentially gene expression analysis with the software DESeq2 at the significance level of adjust p-value < 0.05 and more than two fold changes.

extract_protocol:
Newborn P0 back skins were collected and subjected to 0.25% collagenase digestion for 60 minutes at 37ºC with 80 rpm shaking, followed by 0.25% trypsin treatment for 15 minutes at 37ºC. The cell suspension was washed twice with 1x PBS, stained with 1:200 Sca1-PerCP-Cy5.5 (Biolegend), 1:100 α6-integrin-FITC (eBiosciences), and 1:200 EpCAM-APC (Biolegend) for 30 minutes on ice, and washed twice with 1x HBSS prior to cell sorting. Interfollicular epidermis, enriched for epidermal progenitors, was sorted as EpCAM(+), Sca1(+), and α6-integrin(high). FACS-purified cells were collected directly into RLT Plus buffer (QIAGEN), and total RNA was isolated with the RNeasy Plus Micro Kit (QIAGEN).
10ng of total RNA were reverse transcribed and amplified using the Ovation RNA-seq System V2 (Nugen). Libraries were constructed from 100ng of sonicated cDNA (Covaris) using the Ovation Ultra Low DR Multiplex system (Nugen). The concentration and quality of the libraries were determined using Qubit (Invitrogen) and Bioanalyzer (Agilent). Constructed RNA-seq libraries were sequenced on the Illumina HiSeq 2500 platform, obtaining 100-nucleotide single reads.

value: Epiermal cells

value: Postnatal day 0

value: Eed -/- Ring1a-/- Ring1b-/-


title: Eed; Ring1a/b 3KO_rep3


title: ATAC_ESC_Ola_IFNb_0h_Rep1


title: Control_rep3


title: Ring1a/b 2KO rep2

value: Ring1a-/- Ring1b-/-


title: Ring1 Control rep2


title: Eed; Ring1a/b 3KO_rep1


title: Ring1a/b 2KO rep1


title: Ring1 Control rep1


title: Eed KO rep3

value: Eed -/-


title: Eed KO rep2


title: Control_rep1


title: Control_H3K27me3_2

data_processing:
The ChIP-seq reads were aligned to the mouse reference genome (mm10) and the fly genome (Dm6) using the bowtie2 software (v2.3.3.1). Uniquely aligned reads to the mouse genome were kept for downstream analysis, after duplicate reads removed by the software samtools (v1.9).  Genomic regions broadly enriched with ChIP-seq singling were determined using a sliding window approach with the input as controls. Peaks consistently called in all replicates were used as the final peaks. Data from knockout samples without expected enriched signals were not used for peak calling, as they were experimental controls.
Genome_build: mm10
Supplementary_files_format_and_content: bed

source_name: Epidermal progenitor cells

extract_protocol:
Basal layer epidermal progenitors were isolated from newborn mice. Briefly, P0 back skins were collected and incubated for 4-6 hours in 1.26U/mL dispase (Invitrogen) at 4ºC. The epidermis was gently peeled from the underlying dermis, dissociated by 0.25% Trypsin with 2.21mM EDTA (Corning Cellgro; Manassas, VA, USA) and washed twice with 1x PBS. Cells were stained with 1:200 Sca1-PerCP-Cy5.5 (Biolegend), 1:100 α6-integrin-FITC (eBiosciences), and 1:200 EpCAM-APC (Biolegend) for 30 minutes on ice, and washed twice with 1x HBSS prior to cell sorting. Interfollicular epidermis, enriched for epidermal progenitors, was sorted as EpCAM(+), Sca1(+), and α6-integrin(high). A total of 0.4 x 10^6 cells was used per ChIP.  Prior to cell sorting, cells were stained for viability using Zombie violet (Biolegend; San Diego, CA), then cross-linked using fresh solution with a final concentration of 1% formaldehyde (Thermo Fisher Scientific; Rockford, IL) for 10 minutes at room temperature. Crosslinking was stopped by the addition of Glycine (final concentration 125mM) for 5 minutes of incubation at room temperature, followed by two washes with 1x PBS. Cells were incubated in lysis buffer 1 (50mM HEPES pH=7.5, 140mM Nacl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, protease inhibitor cocktail (Roche)) for 10 min on ice, then incubated for 10 min with lysis buffer 2 (10mM Tris-HCl pH=7.5, 200mM NaCl, 1mM EDTA, 0.5mM EGTA). Before ChIP, cells were resuspended in lysis buffer 3 (10mM Tris-HCl pH=8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% N-laurylsarcosine, 1% Triton X-100) and sonicated using a Bioruptor Sonicator (Diagenode, UCD-200) according to a 25x regimen of 30 seconds of sonication followed by 90 seconds of rest at 2.7ºC.  Chromatin was incubated overnight at 4ºC with anti-H3K27me3 antibody as indicated in Table S7.  Dynal protein G magnetic beads (Invitrogen) were added the next day and incubated for 4 hours. The beads were sequentially washed with low salt, high salt, LiCl, and Tris-EDTA buffers for 10 minutes each at 4ºC. Bound chromatin was eluted and crosslinking was reversed by overnight incubation at 65ºC, followed by RNase A (Sigma-Aldrich) and proteinase K (Roche Diagnostics) treatments.  Samples were purified using ChIP DNA Clean and Concentrator kit (Zymo Research; Irvine, CA).
For high-throughput ChIP sequencing, libraries were constructed from 3ng of Purified DNA using the DNA SMART ChIP-Seq Kit (Clontech; Palo Alto, CA, USA) according to the manufacturer’s instructions. Constructed ChIP-seq libraries were sequenced on the Illumina HiSeq platform

value: Epidermal progenitor cells


title: Ring1a/b 2KO_H3K27me1_2

value: Ring1a/b 2KO


title: Control_rep2


title: Eed Control rep2


title: Eed KO rep1


title: H3K27me3 ontrol_Input


title: Ring1a/b 2KO_H2AK119ub_1

extract_protocol:
Basal layer epidermal progenitors were isolated from newborn mice. Briefly, P0 back skins were collected and incubated for 4-6 hours in 1.26U/mL dispase (Invitrogen) at 4ºC. The epidermis was gently peeled from the underlying dermis, dissociated by 0.25% Trypsin with 2.21mM EDTA (Corning Cellgro; Manassas, VA, USA) and washed twice with 1x PBS. Cells were stained with 1:200 Sca1-PerCP-Cy5.5 (Biolegend), 1:100 α6-integrin-FITC (eBiosciences), and 1:200 EpCAM-APC (Biolegend) for 30 minutes on ice, and washed twice with 1x HBSS prior to cell sorting. Interfollicular epidermis, enriched for epidermal progenitors, was sorted as EpCAM(+), Sca1(+), and α6-integrin(high). A total of 0.4 x 10^6 cells was used per ChIP.  Prior to cell sorting, cells were stained for viability using Zombie violet (Biolegend; San Diego, CA), then cross-linked using fresh solution with a final concentration of 1% formaldehyde (Thermo Fisher Scientific; Rockford, IL) for 10 minutes at room temperature. Crosslinking was stopped by the addition of Glycine (final concentration 125mM) for 5 minutes of incubation at room temperature, followed by two washes with 1x PBS. Cells were incubated in lysis buffer 1 (50mM HEPES pH=7.5, 140mM Nacl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, protease inhibitor cocktail (Roche)) for 10 min on ice, then incubated for 10 min with lysis buffer 2 (10mM Tris-HCl pH=7.5, 200mM NaCl, 1mM EDTA, 0.5mM EGTA). Before ChIP, cells were resuspended in lysis buffer 3 (10mM Tris-HCl pH=8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% N-laurylsarcosine, 1% Triton X-100) and sonicated using a Bioruptor Sonicator (Diagenode, UCD-200) according to a 25x regimen of 30 seconds of sonication followed by 90 seconds of rest at 2.7ºC.  Chromatin was incubated overnight at 4ºC with anti-H2AK119ub antibody as indicated in Table S7.  Dynal protein G magnetic beads (Invitrogen) were added the next day and incubated for 4 hours. The beads were sequentially washed with low salt, high salt, LiCl, and Tris-EDTA buffers for 10 minutes each at 4ºC. Bound chromatin was eluted and crosslinking was reversed by overnight incubation at 65ºC, followed by RNase A (Sigma-Aldrich) and proteinase K (Roche Diagnostics) treatments.  Samples were purified using ChIP DNA Clean and Concentrator kit (Zymo Research; Irvine, CA).
For high-throughput ChIP sequencing, libraries were constructed from 3ng of Purified DNA using the DNA SMART ChIP-Seq Kit (Clontech; Palo Alto, CA, USA) according to the manufacturer’s instructions. Constructed ChIP-seq libraries were sequenced on the Illumina HiSeq platform


title: H2AK119ub Ring1a/b 2KO_Input


title: H2AK119ub Eed cKO_Input

value: Eed-/-


title: Eed cKO_H2AK119ub_2


title: Eed cKO_H2AK119ub_1


title: Control_H2AK119ub_2


title: H2AK119ub Control_Input


title: Control_H2AK119ub_1


title: 30 month rep 2

city: Boston

first: Ronald

middle: L

last: Neppl

state: MA

address: 60 Fenwood Rd.

department: Orthopedic Surgery

institute: Brigham and Women's Hospital, Harvard Medical School

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic v.0.36.
Trimmed reads were mapped to Mus musculus GRCm38/mm10 using STAR aligner v.2.5.2b
Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2.
Genome_build: mm10

source_name: Gastrocnemius

extract_protocol:
Gastrocnemius muscles were removed and flash frozen. Total RNA was extracted using Trizol Reagent.
The NEBNext Ultra RNA Library Prep Kit for Illumina  was used for the construction of sequencing libraries.

value: Gastrocnemius

value: 30 months


title: 24 month rep 1

value: 24 months


title: 24 month rep 2


title: 12 month rep 1

value: 12 months


title: 12 month rep 2


title: Eed cKO_H3K27me3_1

value: Eed cKO


title: Ring1a/b 2KO_H3K27me1_1


title: 3 month rep 1

value: 3 months


title: Control_H3K27me3_1

value: Epidermis


title: WT_BMDMs_LPS_Untreated 3

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

institute: ETH/University of Zurich

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.5.4b, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_91-2018-02-26
Supplementary_files_format_and_content: tad-delimited, raw counts

growth_protocol: Isolated BM cells were seeded in 60 mm non-treated plastic dishes for 7 days at 37 oC and 5% CO2 conditions.

extract_protocol:
RNA was isolated with Qiagen RNA Isolation Kit as per the manufacturer’s protocol.
TruSeq RNA stranded protocol

treatment_protocol: Cells were activated with LPS for 6 h.

value: PRIMARY MACROPHAGE

value: LPS TREATMENT


title: 3 month rep 2


title: 30 month rep 1


title: WT_BMDMs_LPS_Untreated 1


title: WT_BMDMs_LPS_Untreated 2


title: WT_BMDMs_Untreated 2

value: NO TREATMENT


title: WT_BMDMs_Untreated 1


title: Lamin-A-KO_BMDMs_LPS_Untreated 2


title: Lamin-A-KO_BMDMs_LPS_Untreated 1


title: Lamin-A-KO_BMDMs_LPS_Untreated 3


title: Lamin-A-KO_BMDMs_Untreated 3


title: Tumor-infiltrating Ly6G+ neutrophils_3

data_processing:
Paired-end reads were mapped to reference genome using STAR version 2.5.2b
Mapped paired-end reads were summarized to gene level using featureCounts v.1.5.0 and with GENCODE GRCm38 vM7 gene annotation
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated in R_3.1.2 using edgeR_3.8.6 Bioconductor package with normalized.lib.sizes=TRUE option and log2 transformation
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text file includes gene-level log2 transformed FPKM values for all samples

source_name: Tumor

extract_protocol:
Neutrophils were sorted based on their expression of Dapi-CD45+Lin(CD3/B220/NK1.1)- Ly6G+Ly6C+ on Day 27 post-transplantation of tumor cells. RNAs were harvested using Trizol reagent and analyzed on an Agilent Bioanalyzer for quality assessment. cDNA libraries were prepared using 2 ng total RNA and 1 ul of a 1:50,000 dilution of ERCC RNA Spike in Controls (Ambion® Thermo Fisher Scientific) using the SMARTSeq v2 protocol. Samples were subjected to an indexed PE sequencing run of 2x151 cycles on an Illumina HiSeq 4000.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ly6G+ neutrophils

tag: tumor model

value: post pancreatic ductal adenocarcinoma (PDAC) orthotopic tumor transplantation


title: Lamin-A-KO_BMDMs_Untreated 2

tag: strain


title: Lamin-A-KO_BMDMs_Untreated 1


title: Bone marrow Ly6G.hi neutrophils_3

source_name: Bone marrow

value: Ly6G.hi neutrophils


title: Tumor-infiltrating Ly6G+ neutrophils_2


title: Bone marrow Ly6G.hi neutrophils_2


title: Tumor-infiltrating Ly6G+ neutrophils_1


title: Bone marrow Ly6G.hi neutrophils_1


title: GenomicDNA_Case_6181

type: genomic

city: CAMPERDOWN

first: Annie

last: Pan

address: Reagent Crescent

department: School of Life and Environmental Sciences

institute: University of Sydney

hyb_protocol: According to the service provider GeneSeek, NE, http://genomics.neogen.com/en/beadchips

data_processing:
The raw data (idat) files were provided as a service by GeneSeek (Lincoln, NE, USA). The processed file was presented in the format of ped and map files since the processed matrix could not be obtained from Geneseek (Lincoln, NE, USA), without an additional charge. The PED file is a white-space (space or tab) delimited file: the first six columns are mandatory: Family ID, Individual ID, Paternal ID, Maternal ID, Sex (1=male; 2=female; other=unknown), and phenotype. Genotypes (column 7 onwards) should also be white-space delimited; they can be any character (e.g. 1,2,3,4 or A,C,G,T or anything else) except 0 which is, by default, the missing genotype character. All markers should be biallelic. All SNPs (whether haploid or not) must have two alleles specified. Either Both alleles should be missing (i.e. 0) or neither. No header row should be given. The MAP describes a single marker and must contain exactly 4 columns: chromosome (1-22, X, Y or 0 if unplaced), snp identifier, Genetic distance (morgans), and Base-pair position (bp units). The MAP file must therefore contain as many markers as are in the PED file. The markers in the PED file do not need to be in genomic order: (i.e. the order MAP file should align with the order of the PED file markers). Note: Idat files could no longer be obtained from the service provider for 9 of the 163 healthy controls (thus, 154 healthy control samples are included in the records).
value definition: Genotype 11,12,22,or 00 (no call)

label: cy3, cy5

organism: Canis lupus familiaris

source_name: Whole blood_affected

extract_protocol: Genomic DNA was extracted from whole blood samples using the phenol-chloroform salting-out method as previously described (Miller et al. 1988), or the spin column-based nucleic acid purification method according to the manufacturer’s protocol (QIAamp; QIAGEN, Melbourne, VIC, Australia).

tag: sample group

value: Cerebellar abiotrophy (CA) case

value: Whole blood


title: WT_BMDMs_Untreated 3


title: Blood Ly6G+ neutrophils_2

source_name: Blood


title: GenomicDNA_Case_WK6368

scan_protocol: According to the service provider GeneSeek, NE, http://genomics.neogen.com/en/beadchips


title: GenomicDNA_Case_WK6363

label_protocol: According to the service provider GeneSeek, NE, http://genomics.neogen.com/en/beadchips


title: Blood Ly6G+ neutrophils_3


title: GenomicDNA_Case_AP74


title: GenomicDNA_Case_AP75


title: GenomicDNA_Case_WK6263


title: GenomicDNA_Control_WK6335

source_name: Whole blood_healthy

value: healthy control


title: Blood Ly6G+ neutrophils_1


title: GenomicDNA_Control_WK6333


title: GenomicDNA_Control_WK6331


title: GenomicDNA_Control_WK6334


title: GenomicDNA_Control_WK6342


title: GenomicDNA_Case_WK6365


title: GenomicDNA_Control_WK6327


title: ckaBraf-2

data_processing:
The quality of the sequenced reads was assessed with FastQC and QoRTs (Andrews 2010, Hartley and Mullikin (2015)).
Adapters were trimmed with Trim Galore! v0.6.7.
Sequenced reads were aligned with default parameters to the mouse reference genome (GRCm38) using STAR v2.7.6a (Dobin et al. 2013).
Gene expression estimates were obtained with featureCounts v1.6.2 using composite gene models from Gencode (version M25) (Liao, Smyth, and Shi 2014, Harrow et al. (2012)).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw abundance values for each sample as obtained from featureCounts

source_name: corticospinal neurons

extract_protocol:
RNA preparation was performed as described in Heiman et al., Nature Protocols volume 9, pages 1282–1291 (2014).
RNA library preparations, sequencing reactions, and initial bioinformatic analysis were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).  RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads, then fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The quality of the sequencing libraries was validated on the Agilent TapeStation Bioanalyzer  (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).  The sequencing libraries were clustered on flowcells which were loaded on to the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

value: 129Sv and C57BL/6

value: Braf knock-in


title: GenomicDNA_Control_WK6332


title: GenomicDNA_Case_WK6364


title: GenomicDNA_Control_WK6330


title: GenomicDNA_Control_WK6329


title: GenomicDNA_Control_WK6326


title: H3K27me3 Eed cKO_Input

value: Epidermal progenitor cells

tag: age

value: Postnatal day 0


title: GenomicDNA_Control_305


title: GenomicDNA_Control_632


title: GenomicDNA_Control_633


title: GenomicDNA_Control_WK6328


title: GenomicDNA_Control_631


title: GenomicDNA_Case_WK6205


title: GenomicDNA_Control_629


title: GenomicDNA_Control_WK6325


title: GenomicDNA_Control_619


title: GenomicDNA_Control_618


title: GenomicDNA_Control_625


title: GenomicDNA_Control_616


title: GenomicDNA_Control_626


title: GenomicDNA_Control_621


title: GenomicDNA_Control_623


title: GenomicDNA_Control_AP83


title: GenomicDNA_Control_AP84


title: GenomicDNA_Control_AP82


title: GenomicDNA_Control_AP81


title: GenomicDNA_Control_AP77


title: GenomicDNA_Control_AP78


title: GenomicDNA_Control_WK6373


title: GenomicDNA_Control_WK6372


title: GenomicDNA_Control_WK6371


title: GenomicDNA_Control_WK6367


title: GenomicDNA_Control_WK6270


title: GenomicDNA_Control_USCF1782


title: GenomicDNA_Control_USCF1781


title: GenomicDNA_Control_WK6366


title: GenomicDNA_Control_628


title: GenomicDNA_Control_USCF1778


title: GenomicDNA_Control_USCF1779


title: GenomicDNA_Control_USCF1777


title: GenomicDNA_Control_AP85


title: GenomicDNA_Control_USCF1776


title: GenomicDNA_Control_USCF1775


title: GenomicDNA_Control_USCF1767


title: GenomicDNA_Control_USCF1765


title: GenomicDNA_Control_USCF1768


title: GenomicDNA_Control_USCF1773


title: GenomicDNA_Control_USCF1772


title: GenomicDNA_Control_USCF1771


title: GenomicDNA_Control_USCF1764


title: GenomicDNA_Control_USCF1758


title: GenomicDNA_Control_USCF1769


title: GenomicDNA_Control_USCF1757


title: GenomicDNA_Control_USCF1770


title: GenomicDNA_Control_USCF1763


title: GenomicDNA_Control_USCF1774


title: GenomicDNA_Control_USCF1754


title: GenomicDNA_Control_USCF1756


title: GenomicDNA_Control_USCF1755


title: GenomicDNA_Control_USCF1766


title: GenomicDNA_Control_USCF1752


title: GenomicDNA_Control_USCF1753


title: GenomicDNA_Control_USCF1751


title: GenomicDNA_Control_USCF1749


title: GenomicDNA_Control_USCF1762


title: GenomicDNA_Control_USCF1748


title: GenomicDNA_Control_USCF1747


title: GenomicDNA_Control_USCF1745


title: GenomicDNA_Control_USCF1746


title: GenomicDNA_Control_USCF1743


title: GenomicDNA_Control_USCF1742


title: GenomicDNA_Control_USCF1739


title: GenomicDNA_Control_USCF1735


title: GenomicDNA_Control_USCF1730


title: GenomicDNA_Control_USCF1736


title: GenomicDNA_Control_USCF1731


title: GenomicDNA_Control_USCF1729


title: GenomicDNA_Control_USCF1728


title: GenomicDNA_Control_USCF1740


title: GenomicDNA_Control_USCF1750


title: GenomicDNA_Control_USCF1737


title: GenomicDNA_Control_USCF1723


title: GenomicDNA_Control_USCF1722


title: GenomicDNA_Control_USCF1725


title: GenomicDNA_Control_USCF1727


title: GenomicDNA_Control_USCF1724


title: GenomicDNA_Control_USCF1713


title: GenomicDNA_Control_USCF1721


title: GenomicDNA_Control_USCF1705


title: GenomicDNA_Control_USCF1704


title: GenomicDNA_Control_USCF1712


title: GenomicDNA_Control_USCF1726


title: GenomicDNA_Control_USCF1703


title: GenomicDNA_Control_USCF1709


title: GenomicDNA_Control_USCF1701


title: GenomicDNA_Control_USCF1710


title: GenomicDNA_Control_USCF1711


title: GenomicDNA_Control_USCF0699


title: GenomicDNA_Control_USCF1708


title: GenomicDNA_Control_USCF1707


title: GenomicDNA_Control_USCF1738


title: GenomicDNA_Control_USCF0695


title: GenomicDNA_Control_USCF0698


title: GenomicDNA_Control_USCF0694


title: GenomicDNA_Control_USCF0693


title: GenomicDNA_Control_USCF0691


title: GenomicDNA_Control_614


title: GenomicDNA_Control_USCF0692


title: GenomicDNA_Control_USCF0603


title: GenomicDNA_Control_USCF0696


title: GenomicDNA_Control_USCF0697


title: GenomicDNA_Control_USCF0602


title: GenomicDNA_Control_USCF0641


title: GenomicDNA_Control_615


title: GenomicDNA_Control_609


title: GenomicDNA_Control_607


title: GenomicDNA_Control_610


title: GenomicDNA_Control_605


title: GenomicDNA_Control_604


title: GenomicDNA_Control_601


title: GenomicDNA_Control_602


title: GenomicDNA_Control_608


title: GenomicDNA_Control_6315


title: GenomicDNA_Control_6319


title: GenomicDNA_Control_6316


title: GenomicDNA_Control_6271


title: GenomicDNA_Control_600


title: GenomicDNA_Control_6318


title: GenomicDNA_Control_6272


title: GenomicDNA_Control_6024


title: GenomicDNA_Control_6196


title: GenomicDNA_Control_6147


title: GenomicDNA_Control_6056


title: GenomicDNA_Control_6026


title: GenomicDNA_Control_6112


title: GenomicDNA_Control_6267


title: GenomicDNA_Control_6063


title: GenomicDNA_Control_6021


title: GenomicDNA_Control_6352


title: GenomicDNA_Control_6357


title: GenomicDNA_Control_6354


title: GenomicDNA_Control_6355


title: GenomicDNA_Control_6061


title: GenomicDNA_Control_613


title: GenomicDNA_Control_6350


title: GenomicDNA_Control_6142


title: GenomicDNA_Control_6348


title: GenomicDNA_Control_6143


title: GenomicDNA_Control_6347


title: GenomicDNA_Control_6268


title: Pig olfactory mucosa cells  - 12_WT

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

data_processing:
Illumina NextSeq500 software used for basescaling
Raw data were analyzed using Cell Ranger Single-cell software v6.0.0. The raw gene-barcode matrices were aligned to the Sscrofa11-1 genome.
Cell Ranger output was analyzed with the Seurat package v.4.0. using R v.4.0.2. Each individual data was filtered to keep cells with  200-7,000 genes, less than 99% of dropouts, and less than 5% of mitochondrial sequences.
Doublet cells were removed with DoubletFinder.
normalization and variance stabilization  with SCTransform, and dimensionality reduction by Principal Component Analysis was performef for each sample separetely.
Global integration was done after normalization and identification of the 4000 most variable features of each dataset.
Genome_build: Sscrofa11-1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Sus scrofa

source_name: Pig olfactory mucosa cells

extract_protocol:
In a glass dounce tissue grinder previously cooled on ice, 7 tissue slices and 1ml of citric acid-based buffer (Sucrose 0.25 M, Citric Acid 25 mM) were added. Tissue samples were homogenized with 3-5 strokes of loose pestle and incubated on ice for 5 min. After 5 more strokes using a loose pestle, samples were incubated on ice for 5 min, homogenized again with 3 strokes using the loose pestle and 5 strokes using the tight one. The suspension was filtered through a 40 µm cell strainer, and 1ml of citric acid-based buffer was used to wash the containers. After a centrifugation for 5min at 500g at 4°C, the supernatant was carefully removed and the sample was resuspended in 1ml of Wash buffer (Tris-HCl pH 7.4 10 mM, NaCl 10 mM, MgCl2 3mM, BSA 1%, Tween 20 0.1%, DTT 1 mM, RNaseIn® 0.6 U/μL, SuperaseIn® 0.2 U/μL). Sample was filtered through a 5 µm cell strainer and centrifuged for 5min at 500g at 4°C. Nuclei were resuspended in 50-100 µl of diluted nuclei buffer (Nuclei Buffer® 1X (Multiome kit, 10X Genomics), DTT 1 mM, RNaseIn® 0.6U/µl, SuperaseIn® 0.2 U/μL). Nuclei morphology and isolation were controlled with a Floid cell imaging station. After counting with a Countess II FL Automated Cell Counter, nuclei were diluted to the desired concentration (for a target capture of 10,000 nuclei).
snNucSeq was performed according to the protocol provided by 10X Genomics.
snNucSeq (10X Genomics)

treatment_protocol: Olfactory neuroepithelium from CFTR-null and control piglets were dissected included in OCT and immediately frozen on liquid N2.  300 µm sections were made using a cryostat, and kept at -80°C.

value: Olfactory neuroepithelium

value: Newborn

value: wild type piglet


title: GenomicDNA_Control_6265


title: Pig olfactory mucosa cells - 15_CFTR

value: CFTR knock out piglet


title: ko_p20

description: CFTR knock-out piglet

data_processing:
(i) Reads quality control using fastQC, (ii) mapping with STAR_2.4.0 versus Sscrofa11.2 following ENCODE RNA-seq options, (iii) features quantification using featureCounts (subread-1.5.0-p3-Linux-x86_64) with –primary -g gene_id -p -s 2 -C -T options.
The number of fragments aligned to each gene was counted using the HTSeq package, with the script htseq-count (mode intersection-nonempty).
Raw count data was normalized to account for the depth of sequencing. Size factors were calculated using DESeq2’s function estimateSizeFactorsForMatrix, and raw counts were divided by the corresponding size factor for each sample.
DESeq2 was used with standard parameters to test the differential expression.
Genome_build: Sscrofa11-2
Supplementary_files_format_and_content: STARaligner count table

source_name: Olfactory epithelium cells

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen) with on-column DNAse digestion.
mRNA was prepared for sequencing using the TruSeq RNA sample preparation kit (Illumina).

treatment_protocol: Olfactory neuroepithelium from CFTR-null and control piglets were dissected and snap frozen in liquid nitrogen. RNA was extracted using the RNeasy mini kit (Qiagen) with on-column DNAse digestion

value: Olfactory epithelium

value: CFTR knock-out piglet


title: ko_p6

description: CFTR knock-out piglet


title: ko_p18

description: CFTR knock-out piglet


title: ko_p21

description: CFTR knock-out piglet


title: GenomicDNA_Control_6029


title: wt_p23

description: Wild type piglet

value: Wild type piglet


title: TCPMOH_sample12

city: East Lansing

first: Karilyn

middle: E

last: Sant

state: MI

address: 1355 Bogue St., Life Science B440

department: Pharmacology & Toxicology

institute: Michigan State University

description: 8-10 pooled embryos exposed to 50nM TCPMOH from 24-100 hours post fertilization (hpf)

data_processing:
Imported into Galaxy, FastQC used for read quality assessment
Cutadapt used for trimming: settings for paired-end reads, a minimum filter length of 20, and a quality cutoff of 20
Alignment and annotation using Spliced Transcripts Alignment to a Reference (STAR) software, Read counts from featureCounts software
DEseq2 used to assess differential expression
Lrpath's RNA-Enrich function was used for pathway analysis (KEGG)
Genome_build: Genome build and transcription annotation files obtained from the Lawson Lab, Umass Medical School (v. 4.3.2) - https://www.umassmed.edu/lawson-lab/reagents/zebrafish-transcriptome/
Supplementary_files_format_and_content: DEseq2 results (mean, fold change, p-values)

organism: Danio rerio

source_name: Whole eleutherolarvae (100 hpf)

extract_protocol:
Thermo GeneJet RNA kits, per manufacturer instructions for tissues
Illumina Stranded mRNA Prep Kit following manufacturer instructions; RNA-seq, PE100, 25M reads, Illumina NovaSeq 6000 platform

treatment_protocol: Zebrafish embryos were exposed from 24-100 hpf to respective treatments. At 100 hpf, embryos were quickly rinsed in clean 0.3X Danieau's medium, and transferred into Eppendorf tubes in pools of 8-10 embryos. Embryos were placed into RNA later and stored at -20 degrees Celsius until RNA isolation

value: AB (wild-type)

value: 100 hpf

tag: exposure

value: TCPMOH (50 nM), waterborne

tag: chemical cas#


title: wt_p5

description: Wild type piglet


title: TCPMOH_sample14


title: TCPMOH_sample13


title: wt_p12

description: Wild type piglet


title: TCPM_sample10

description: 8-10 pooled embryos exposed to 50nM TCPM from 24-100 hours post fertilization (hpf)

value: TCPM (50 nM), waterborne


title: DMSO_sample5

description: 8-10 pooled embryos exposed to DMSO (vehicle control) from 24-100 hours post fertilization (hpf)

value: DMSO (0.01% v/v), waterborne


title: wt_p9

description: Wild type piglet


title: TCPM_sample8


title: TCPMOH_sample15


title: TCPMOH_sample11


title: DMSO_sampe4


title: TCPM_sample7


title: DMSO_sample2


title: TCPM_sample6


title: DMSO_sample1


title: Cana3

city: Turku

first: Riku

last: Kiviranta

address: Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

data_processing:
The raw reads were subjected to quality control using FastQC
The reads were aligned to the latest version of UCSC zebrafish (danRer10) using R(v.3.6.1), Bioconductor(v.3.9) and Rsubread(v.2.0.0)
Raw read counts for all the samples and genes were loaded into R version 3.6.1, Bioconductor(v.3.9) and Rsubread(v.2.0.0) for 64bit Linux x86 with RefSeq gene annotation (from same source as genome) and reversely stranded strand specificity.
Genome_build: danRer10
Supplementary_files_format_and_content: Tab-separated file of RPKM normalized read counts normalized data.csv, ROTS-tested expression comparisons ROTS_resulttable_<comparison>.csv, FC >|2| and fdr<0.05 filtered ROTS data Filtered_<comparison>.csv

source_name: Zebrafish embryo

extract_protocol:
The 27 hpf embryos (n = 5 per sample) were lysed and their total RNA was extracted with RNAeasy Mini Kit (QIAGEN, Hilden Germany) using DNAase I digestion step and eluted to 25µl aqua.
RNA-seq was performed on the NovaSeq 6000 SP platform as 50 bp paired-end reads using the Illumina TruSeq Stranded mRNA HT Kit

treatment_protocol: Healthy GFP positive, 23 hours post-fertilization (hpf) embryos were dechorionated and selected for the experiments. Selected 23 hpf embryos were treated with DMSO or the SGLT2 inhibitors empagliflozin (50 µM) and canagliflozin (50µM) (Selleckchem, Houston TX, USA).

value: Canagliflozin


title: Cana1


title: Empa2

value: Empagliflozin


title: DMSO_sample3


title: Empa4


title: Cana4


title: Control4

value: Control


title: Control3


title: Empa3


title: Control2


title: Empa1


title: TCPM_sample9


title: Cana2


title: N12

city: beijing

first: xiangying

last: yan

address: Dongzhimen Jiedao

institute: Institute of Chinese Medicine

data_processing:
Use fastp software to clean and filter the original offline data to obtain high-quality sequences (Clean Reads).
Use Hisat2 2.1.0 software to compare Clean Reads with reference genes (the reference genome version is GRnor_6.0.100).
Stringtie 1.3.3b software was used to compare the results and quantify the transcriptome expression; Normalize with TMM (trimmed mean of M values) algorithm, and finally calculate FPKM (Fragments Per Kilobase Million) value of each gene.
Differential analysis of gene expression between samples/groups using edgeR 3.30.3 software package.
Assembly: GRnor_6.0.100
Supplementary files format and content: gene_exp_add_all_diff.txt: Tab-delimited text file includes counts and FPKM values for each Sample.

organism: Rattus norvegicus

growth_protocol: All rats were housed under specific pathogens-free conditions, with a constant temperature of 24℃±1℃ in a 12-h light/12-h dark cycle room and were fed with ad libitum water and food access.

extract_protocol:
RNA was harvested using RNeasy Mini Kit (250) Qiagen #74106.
After the total RNA passes the quality inspection, it is further purified and reverse transcribed to obtain double stranded cDNA, which is used as a template for PCR amplification to construct a cDNA library.

treatment_protocol: Rats in the normal control group were fed a normal diet. DEN model, DEN+PZH low-dose and DEN+PZH high-dose groups were injected intraperitoneally with 0.01% DEN (catalog number N0756, Sigma Aldrich, St. Louis, MO, USA) weekly by the experimentalists for a period of 16 weeks.

value: liver

value: NO


title: G28

value: PZH


title: N3


title: N1


title: RCF-x432-3

city: Atlanta

middle: E.

last: Davis

address: 2015 Uppergate Dr NE

institute: Emory University

description:
Sample 18
RCFcounts.csv

data_processing:
Base calling was conducted with RTA v3.4.4 and demultiplexing was performed with bcl2fastq v2.20.0.422
Total RNA was aligned and gene counts were determined with STAR aligner in the Illumina BaseSpace app, RNA-Seq Alignment.
Genome_build: Sample 1-~18 reads aligned with rn5 reference genome; sample 19-36 reads aligned with hg19 reference genome.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Heart, left ventricular myocardium

growth_protocol: RCFs were cultured in Dulbecco’s modified Eagle’s medium (DMEM-ThermoFisher) supplemented with 10% FBS and 1% penstrep. THP-1 cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (ThermoFisher) supplemented with 10% FBS, 1% penstrep, and 1% L-glutamine.

extract_protocol:
Total RNA were isolated by using Qiagen RNeasy mini kit following manufacturer's protocol.
1 ng of RNA was used as input for library preparation with the Takaro Bio SMARTer Stranded Total RNA-Seq Kit v2 Pico Input Mammalian

treatment_protocol: To stimulate fibroblasts, RCFs were quiesced for 12 h, treated with 20 µg/mL sEVs for 12 h, and then treated with 10 ng/mL transforming growth factor beta (TGF-β; ThermoFisher) for another 12 h. THP-1 cells were then differentiated into macrophages by 24 h incubation with 150 nM phorbol 12-myristate 13-acetate (PMA; Sigma-Aldrich) followed by 24 h incubation in RPMI medium. Macrophages were then treated with 20 µg/mL sEVs for 12 h and activated with 20 ng/mL tissue necrosis factor alpha (TNF-⍺; R&D Systems, Minneapolis, MN, USA) for 12 h.

value: Cardiac fibroblast

value: Heart, left ventricular myocardium

value: miR-432-5p inhibitor for 24 hours


title: M17

source_name: liver


title: RCF-x432-2

description:
Sample 17
RCFcounts.csv


title: COL, scRNAseq

city: Guangzhou

first: Sheng

last: Zhang

state: None Selected

address: 132 Waihuan West Road, Guangzhou Science Park, Luogang District

institute: School of Materials Science and Engineering, Sun Yat-sen University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: rn6 and GRCh38 respectively for the Rattus norvegicus and Homo sapiens data
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: spinal cord

extract_protocol:
Spinal cord slice culture system: After 12 days of cultivation, the organotypic was removed from  the hydrogel, and hydrogel with cells was digested by collagenaseand  trypsin. Digestion was neutralized with DMEM supplemented with  10% FBS. After concentration (300g, 5min), The cell pellet was washed and resuspension with  PBS supplemented with 0.04% BSA. The cell numbers and viability (>75%) were confirmed  using TC20 Automated Cell Counter. In hspASC-HUVEC co-culture system: After  five days of cultivation, the approaches used for cell digestion and suspension preparation were  identical to the Spinal cord slice culture system
The cell suspension was loaded into Chromium microfluidic chips with 30  chemistry and barcoded with a 10× Chromium Controller  (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed  and sequencing libraries constructed with reagents from a Chromium Single Cell 30   reagent kit (10X Genomics) according to the  manufacturer’s instructions. Sequencing was performed with Illumina  NovaSeq 6000.

value: cells migrated out from spinal cord slice

value: spinal cord

tag: growth protocol

value: Spinal cord slices cultured on COLI

tag: model

value: organotypic model

value: Sprague Dawley

value: 3 weeks old


title: G27


title: DSCM, scRNAseq

description: 10x Genomics

value: Spinal cord slices cultured on DSCM


title: G42


title: RCF-x192-3

description:
Sample 15
RCFcounts.csv

value: miR-192-5p inhibitor for 24 hours


title: RCF-x192-1

description:
Sample 13
RCFcounts.csv


title: RCF-x432exo-2

description:
Sample 11
RCFcounts.csv

value: miR-432-5p depleted CPC sEVs for 24 hours


title: RCF-x432exo-3

description:
Sample 12
RCFcounts.csv


title: RCF-x192-2

description:
Sample 14
RCFcounts.csv


title: RCF-CTRexo-1

description:
Sample 4
RCFcounts.csv

value: CPC sEVs for 24 hours


title: Control1

value: Control


title: RCF-CTRexo-2

description:
Sample 5
RCFcounts.csv


title: RCF-x192exo-1

description:
Sample 7
RCFcounts.csv

value: miR-192-5p depleted CPC sEVs for 24 hours


title: RCF-CTRexo-3

description:
Sample 6
RCFcounts.csv


title: RCF-NT-3

description:
Sample 3
RCFcounts.csv

value: untreated


title: M13

value: liver

value: PZH


title: RCF-NT-2

description:
Sample 2
RCFcounts.csv

value: Cardiac fibroblast

value: Heart, left ventricular myocardium


title: RCF-NT-1

description:
Sample 1
RCFcounts.csv


title: RCF-x192exo-3

description:
Sample 9
RCFcounts.csv