title: Daprodustat_rep 4 (SSC28)

city: Callaghan

first: Tessa

last: Lord

state: NSW

address: University Dr

country: Australia

institute: University of Newcastle

data_processing:
For each sample, 20-30 million reads of 150 base pairs in length were generated and aligned to the mus musculus genome (mm39) using STAR aligner.
Raw gene counts were calculated, and transcripts were assembled with the StringTie tool (v 2.1.4).
EdgeR (v 3.38.4) was used to perform differential expression analysis.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include log2 counts per million (CPM) values for each sample.

source_name: Primary cultures of undifferentiated spermatogonia

growth_protocol: Primary cultures of spermatogonia were dislodged from their STO feeder layer and placed in a 24 well plate at a concentration of 100,000-200,000 cells.ml. Cells were incubated at 37C, 5% CO2, 10% O2 for 24 hours.

extract_protocol:
RNA was isolated using a Direct-zol RNA Microprep kit (Zymo Research) and processed as per manufacturer’s instructions.
cDNA libraries were generated using Illumina poly(A) enrichment, and sequencing was performed using an Illumina NovaSeq 6000

treatment_protocol: Spermatogonia were either treated with 250µM of Daprodustat or vehicle (DMSO) for 24 hours

tag: background strain

value: Id4-eGfp, Rosa26-LacZ

value: 250uM Daprodustat


title: MEF, 6h IFNb, 10xTn5

status: Public on Nov 08 2023

type: SRA

city: Heidelberg

first: Isabelle

last: Seufert

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

description: 10x Genomics

library_source: genomic

data_processing:
Demultiplexing, barcode processing, genome mapping and aggregation were conducted using the Cell Ranger ATAC software v2.0.0 (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac).
Assembly: mm10-2020-A
Supplementary files format and content: h5 single cell peak count matrix, tab-separated fragment file, comma-separated single cell info file

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse embryonic fibroblasts

growth_protocol: MEFs 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).

extract_protocol: Libraries were prepared according to the Chromium single-cell ATAC v1.1 protocol (10x Genomics) using the provided Tn5 (10xTn5), an in-house loaded Tn5 at high concentration (Tn5hc) or a dilution of Tn5hc to 30 % activity (Tn5hc 30 %).

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

tag: cell type

value: Mouse embryonic fibroblasts

tag: treatment

tag: strain


title: PREV45_Day1

city: Farmington

first: Duygu

last: Ucar

state: CT

address: 10 Discovery Dr

country: USA

institute: The Jackson laboratory for Genomic Medicine

library_source: transcriptomic

data_processing:
Raw BCL files generated by the sequencer were converted to FASTQ files. CASAVA was used to generate FASTQ files for RNAseq data. Trimmomatic (version 0.33) was used to remove adapters, leading and trailing low-quality bases.  Reads less than 36 bases long were dropped. Reads with more than 50% low-quality bases overall were filtered out. The remaining high-quality reads were then used for expression estimation. Alignment estimation of gene expression levels using the EM algorithm for paired-end read data was performed using RSEM (package version 1.2.12); default settings were used for alignment. RSEM uses bowtie2 as aligner to align the mapped reads against the hg38 reference genome. Data quality control was performed using Picard (version 1.95) and bamtools to obtain general alignment statistics from the bam file.
Gene expression values from PBMC RNA-seq data were converted into count-per-million (cpm) using edgeR R package (version 3.28.1)113. Genes with cpm values less than 0.5 across all samples were filtered out from the rest of the analyses. Differential gene expression analyses were conducted using generalized linear models (as implemented in the edgeR package) using the default TMM normalization.
Assembly: hg38
Supplementary files format and content: tab delimited text file includes raw counts for each sample
Supplementary files format and content: tab delimited text file includes counts per million (in log2) for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Total RNA was isolated from PBMCs using the Qiagen RNeasy Mini Kit (Qiagen) or  Arcturus PicoPure (Life Technologies) kits following manufacturer’s protocols.
RNA-seq libraries were prepared with KAPA mRNA HyperPrep kit (Roche) according to manufacturer’s instruction.

tag: figureid

tag: tissue

value: Blood

value: PBMCs

tag: time

value: Prevnar -13

tag: Sex

value: Female

tag: age (in years)


title: PVAX16_Day60

value: Pneumovax -23

value: Male


title: PREV17_Baseline

value: Baseline


title: PREV17_Day60


title: PREV89_Day60


title: MEF, 6h IFNb, Tn5hc (30 %)

description: 10x Genomics


title: Daprodustat_rep 1 (SSC16)

value: Primary cultures of undifferentiated spermatogonia

tag: genotype


title: PVAX87_Day1


title: Daprodustat_rep 3 (SSC27)


title: Control_rep 4 (SSC28)

value: vehicle (DMSO)


title: PREV17_Day1


title: PVAX85_Day10


title: Control_rep 2 (SSC25)


title: Control_rep 3 (SSC27)


title: PVAX85_Day60


title: Control_rep 1 (SSC16)


title: PREV23_Day1


title: Testis cells, EPAS1-cKO

description: scRNAseq data from mouse testis cells (enriched for undifferentiated spermatogonia). Two biological replicates were pooled to create a single EPAS-cKO sample for scRNAseq.

library_source: transcriptomic single cell

data_processing:
Raw base call files were demultiplexed using the RNA STARsolo pipeline and aligned to the mouse mm10 transcriptome.
A total of 2 transcriptomes (control and EPAS1-cKO) were merged in R using Seurat
Low quality cell transcriptomes and doublets were assessed within each library and excluded using the following criteria: cells with unique feature counts below 200 or above 8000 were excluded from further analysis. Filtering based on percent mitochondrial genes detected was conservatively set at <25% for all libraries based on visual inspection of overall distribution and the variability of mitochondrial gene content that occurs based on cell type and proliferation status.
Germ cells (undifferentiated spermatogonia and spermatids) were selected for downstream analysis based on the expression of known markers (e.g. Ddx4 and Zbtb16 for spermatogonia, and Acr, Acrv11, Prm1 and Gapdhs for spermatids). Germ cell populations were scaled (“vars.to.regress”), and dimensionally reduced using Seurat.
Assembly: Mus musculus mm10
Supplementary files format and content: Gene-Cell Matrix filled with Raw Read/Expression Values

source_name: Adult mouse testis cell population (spermatogonia enriched)

extract_protocol:
Single cell suspensions of control and EPAS1-cKO testis cells were created from n=2 mice each. The undifferentiated spermatogonia population was enriched using α6-integrin MACS beads. n equal number of cells from each of the biological replicates was combined in a single 'control' or 'EPAS1-cKO' tube.Live cells were loaded into a Chromium Controller (10X Genomics, Inc.).
Single-cell cDNA libraries were generated using v3 chemistry according to the manufacturer’s protocol (10X Genomics, Inc.).

treatment_protocol: Control and EPAS1-cKO mice were (6 weeks old) were treated with 20mg/kg busulfan, 14 days prior to testis cell collection.

value: EPAS1-cKO (Ddx4-Cre, Epasfl/-)

value: 20mg/kg busulfan, 14 days prior to analysis

value: testes


title: PREV31_Baseline


title: PVAX61_Day1


title: Testis cells, Control

description: scRNAseq data from mouse testis cells (enriched for undifferentiated spermatogonia). Two biological replicates were pooled to create a single control sample for scRNAseq.

value: Wild-type


title: Daprodustat_rep 2 (SSC25)


title: PREV66_Day60


title: PREV17_Day10


title: PREV45_Baseline


title: EPCR+ cells, mRNA-derived cDNA

city: Lund

first: Qinyu

last: Zhang

address: Box 188

department: Department of Molecular Hematology

country: Sweden

institute: Lund University

data_processing:
Post-sequencing libraries were processed using Cell Ranger ARC v2.0.0, also done at the Center for Translational Genomics, Lund University. The FASTQ files were aligned to the mouse reference genome (mm10).
Further data processing was done with e.g. Seurat v4.3.0 and SAILERX (commit 1b904bf3b984e5f4db088288db1ae1498f9a4b32 ). All code is provided (see below), for reference to exact procedures.
All code, software versions (conda/mamba environment specifications) etc needed to reproduce this analysis is hosted at [https://github.com/razofz/DB_QZ_multiome]
Assembly: mm10
Supplementary files format and content: Rdata with a Seurat (R package) object for the Diverse (Whole culture) sample.
Supplementary files format and content: Rdata with a Seurat (R package) object for the Immature (EPCR+) sample.
Supplementary files format and content: Tab-separated values files and Matrix Market files, all gzipped. Count matrices, output from Cell Ranger.
Supplementary files format and content: Hdf5 file with filtered count matrix
Library strategy: sc-Multiome sequencing

molecule: polyA RNA

source_name: Bone marrow

extract_protocol:
Bone marrow HSCs were isolated and cultured ex vivo for 21 days. Then 40,000 viable cells (Diverse sample) or EPCR+ viable cells (Immature sample) were sorted out via BD AriaIII and subjected to nuclei isolation.
Libraries were generated following the user guide fo the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics). Preparation of libraries and sequencing were done at the Center for Translational Genomics, Lund University.

value: Bone marrow

tag: cell line

value: Hematopoietic Stem and Progenitor Cells

value: Hematopoietic stem cells

value: wild type


title: PREV45_Day10

value: Blood


title: EPCR+ cells, transposed DNA


title: Whole culture, transposed DNA


title: PVAX75_Day10

value: PBMCs


title: Whole culture, mRNA-derived cDNA


title: IR3_KO2 rep2

city: WuHan

first: Yu

last: Fan

address: luojiashan

department: college of life science

country: China

institute: Wuhan university

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10（ensembl_mus_musculus_grcm38_p6_gca_000001635_8） whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: ensembl_mus_musculus_grcm38_p6_gca_000001635_8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: kidney

growth_protocol: Animals were housed in ventilated microisolator cages with free access to water and food under a 12:12 h light/dark cycle in a temperature-controlled room (22 ± 2°C).

extract_protocol:
Total RNA from each sample was extracted using RNAiso Plus (Takara Biotech), and concentration was measured using an ND-1000 NanoDrop (Thermo Scientific, Wilmington, DE).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). Firststrand cDNA wassynthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Mice were anesthetized and underwent midline abdominal incisions with left renal pedicle bluntly clamped for 45 min (unilateral renal occlusion). Reperfusion was recovered by removing the clamps. Wounds in abdomens were sutured. Mice were euthanized at day 3 to harvest blood, injured kidney and non-injured kidney.

value: kidney

value: Tet1  knockout

value: I/R 3D

tag: treatment 2

value: ischemia 45 min repercussion 3 days

value: C57BL/6 x 129S4/SvJae

value: female


title: PREV36_Day60

value: Prevnar -13

value: Female


title: PVAX75_Day1

value: Pneumovax -23

value: Male


title: IR3_WT2 rep2

value: WT


title: IR3_KO1 rep1


title: PVAX85_Day1


title: NI_KO2 rep2

value: Non-injury


title: PREV23_Baseline

value: Baseline


title: PVAX16_Day1


title: NI_WT1 rep1


title: NI_WT2 rep2


title: NI_KO1 rep1


title: PVAX61_Day10


title: PVAX87_Baseline


title: CAFs_4KC_mice

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

description: 10xGenomics 3’scRNAseq protocol

data_processing:
Illumina bcl files were basecalled, demultiplexed and aligned to the mouse mm10 genome using the cellranger software (version 3.1.0, 10xGenomics)
Raw counts were imported into R and single cell data was analyzed with the 'Seurat' package v.3.2.2
After filtering for library size and mitochondrial gene expression, pre-processing was performed using Seurat functions for counts normalization (SCT), dimension reduction with principal component analysis (PCA) (RunPCA with default parameters), construction of a Shared Nearest Neighbor (SNN) graph and clustering.
Assembly: mm10
Supplementary files format and content: csv files containing normalized expression matrices. Suggested cell identities have been added to the first row (rowname = “Identity”)
filtered feature matrices (output of cellranger count on the raw fastq files)

source_name: 4KC cells

extract_protocol:
Cancer associated fibroblasts (CAFs) and ductal cells from KC and 4KC mice were sorted with a BD FACS ARIA (BD Biosciences) and collected in Dulbecco’s Modified Eagle Medium (DMEM) containing 20% FCS. A pool of 5 mice were used for each condition.
Cell encapsulation, barcoding, and library preparation followed the standard scRNAseq protocol comprising reverse transcription, amplification, and indexing (10xGenomics).
Sequencing was performed using a NovaSeq Illumina device (Illumina).

treatment_protocol: Previously established LSL-KrasG12D/+;Ptf1a-Cre mice (termed KC mice) [ref: PMID: 14706336]. Acvr1bflox/flox;LSL-KrasG12D/+;Ptf1a-Cre mice (termed 4KC mice) were generated by crossing Acvr1bflox/flox mice with KC mice [ref: PMID: 23109354].

value: CAF


title: Ductal_4KC_mice

description: 10xGenomics 3’scRNAseq protocol

value: ductal tumor cells


title: PVAX75_Day60

value: Blood


title: Ductal_KC_mice

description: 10xGenomics 3’scRNAseq protocol

source_name: KC cells


title: PREV36_Day10

value: PBMCs


title: PREV10_Day10


title: PREV23_Day10


title: QO23119_Male_RoomAir

city: Philadelphia

first: Abiud

last: Cantu

state: Pennsylvania

address: 3615 Civic Center Blvd

department: Neonatology

institute: Children's Hospital of Philadelphia

data_processing:
Quantification was performed using Salmon 1.5.2
Assembly: mm10
Supplementary files format and content: Quantification file. This file is a plain-text, tab-separated file with a single header line (which names all of the columns). Includes TPM and Number of reads per transcript.

source_name: Lung

extract_protocol:
Total RNA from sorted endothelial cells was isolated using the Zymo micro kit (Zymo Research, Irvine, CA). Sample concentration and quality checks were done using the Agilent Bioanalyzer.
The libraries were prepped using the Takara SMARTer Total RNA Pico kit v3. The first 8 nt of Read 2 were UMIs followed by 3 nucleotides derived from the Pico v3 SMART UMI Adapter, both of which were trimmed.

value: Lung

tag: age

value: PND 14

value: Endothelial

value: Room Air


title: IR3_WT1 rep1

value: kidney

value: I/R 3D

value: ischemia 45 min repercussion 3 days

value: C57BL/6 x 129S4/SvJae


title: PREV10_Day60

value: Prevnar -13


title: CAFs_KC_mice

description: 10xGenomics 3’scRNAseq protocol


title: PVAX38_Day60

value: Pneumovax -23

value: Female


title: PVAX61_Day60

value: Male


title: QO23118_Male_RoomAir


title: QO23115_Female_Oxygen

value: Hyperoxia


title: PREV23_Day60


title: QO23114_Female_Oxygen


title: QO23112_Male_Oxygen


title: PREV36_Day1


title: PREV66_Day10


title: QO23110_Male_Oxygen


title: PVAX44_Day10


title: PREV31_Day60


title: PUER cells, GCSF, no OHT, +24h, rep2

city: Grand Forks

first: Manu

last: Manu

state: ND

address: 10 Cornell Street, Stop 9019

department: Biology

institute: University of North Dakota

description: ATAC-Seq of PUER cells 72h after replacing IL3 with GCSF. No OHT induction.

data_processing:
Reads were trimmed to remove adaptor sequences and filtered to have a minimum phred score of 33 and a minimum length of 20bp using Trimmomatic (v 0.39). Trimmomatic was run with the command-line options -PE -phred33 ILLUMINACLIP:<Trimmomatic-HOME>/adapters/NexteraPE-PE.fa:2:30:10:3:TRUE MINLEN:20, where <Trimmomatic-HOME> is the path to the Trimmomatic directory.
Reads were aligned to the mm10 genome, allowing for inserts up to 2kb in length, using Hisat2 (v. 2.2.0). Hisat2 was run with the command-line options -x --no-spliced-alignment -I 10 -X 2000.
Duplicates were marked using the MarkDuplicates tool of Picard (v. 2.23.1) package.
BedGraph files were created using the callpeak function in the MACS2 package. Callpeak was run using the command-line options -t -f BAMPE -B --SPMR -q 0.05.
BigWig files were created using the bedGraphToBigWig UCSC Genome Browser utility.
Assembly: mm10
Supplementary files format and content: BigWig

source_name: PUER

growth_protocol: PUER cells were routinely maintained in complete Iscove’s Modified Dulbecco’s Glutamax medium (IMDM; Gibco, 12440061) supplemented with 10% FBS, 50μM β-mercaptoethanol, 5ng/ml IL3 (Peprotech, 213-13).

extract_protocol:
50,000 cells/sample were collected and centrifuged at 500g for 5 minutes at 4°C. The supernatant was removed and the resulting pellet was resuspended in a 50μL transposition mixture consisting of 25μL 2x TD buffer, 2.5μL TDE1 (Illumina, FC-121-1030), 0.5μL 1% digitonin (Promega, G9441), and 22μL nuclease-free water. The resuspended cells were then incubated at 37°C with shaking at 300 rpm for 30 minutes. DNA was purified using a Qiagen MinElute Reaction Cleanup Kit (Qiagen, 28204) and eluted in 10μL of elution buffer (10mM Tris-HCl, pH 8).
The transposed DNA library was amplified for a limited number of cycles. First, 10μL of transposed DNA was amplified in a 50μL PCR reaction using NEBNext High-Fidelity 2x PCR Master Mix (New England BioLabs, M0541S) for 5 cycles after a 5 min elongation step. Primers included adaptors for sequencing and were barcoded according to Illumina guidelines for pooling. The PCR reaction was held at 4°C while 5μL of its product was amplified in a 15μL qPCR reaction with NEBNext High-Fidelity Master Mix and SYBR Green I (Invitrogen, S7563) at a final concentration of 0.5x. The number of PCR cycles needed to reach 1/4 of the maximum fluorescence was determined and the 50μL PCR reaction was continued for as many additional cycles. The PCR product was purified using a Qiagen MinElute PCR Purification Kit and eluted in 20μL elution buffer (10mM Tris-HCl, pH 8).

treatment_protocol: PUER cells were differentiated into macrophages by adding 200nM 4-hydroxy-tamoxifen (OHT; Sigma, H7904-5MG). Cells were differentiated into neutrophils by replacing IL3 with 10ng/ml Granulocyte Colony Stimulating Factor (GCSF; Peprotech, 300-23) and inducing with 100nM OHT after 48 hours.

value: PUER

value: bone marrow-derived progenitors

value: IL3 replaced with GCSF at -48h.


title: PUER cells, GCSF, no OHT, +24h, rep1


title: PVAX44_Day1

value: Blood

value: PBMCs


title: PUER cells, IL3, OHT, +96h, rep1

description: ATAC-Seq of PUER cells 96h after OHT induction in IL3.

value: Tamoxifen (OHT) added at 0h.


title: PUER cells, IL3, OHT, +96h, rep2


title: PUER cells, IL3, OHT, +24h, rep2

description: ATAC-Seq of PUER cells 24h after OHT induction in IL3.


title: PVAX76_Day10


title: PREV66_Baseline

value: Baseline


title: PVAX90_Baseline


title: PUER cells, IL3, OHT, +24h, rep1


title: PREV10_Baseline


title: PREV45_Day60


title: PVAX83_Baseline


title: PUER cells, GCSF, OHT, +24h, rep2

description: ATAC-Seq of PUER cells 48h after replacing IL3 with GCSF and 24h after OHT induction.

value: IL3 replaced with GCSF at -48h. Tamoxifen (OHT) added at 0h.


title: PVAX95_Day1


title: PUER cells, GCSF, OHT, +24h, rep1


title: PUER cells, GCSF, no OHT, 0h, rep2

description: ATAC-Seq of PUER cells 48h after replacing IL3 with GCSF.


title: PREV21_Baseline


title: PUER cells, GCSF, no OHT, 0h, rep1


title: PVAX83_Day60


title: PVAX95_Day60


title: PUER cells, GCSF, no OHT, -24h, rep1

description: ATAC-Seq of PUER cells 24h after replacing IL3 with GCSF.


title: PUER cells, GCSF, no OHT, -24h, rep2


title: PUER cells, IL3, no OHT, 0h, rep2

description: ATAC-Seq of undifferentiated PUER cells.

value: None.


title: PREV50_Day1


title: PVAX59_Day10


title: Ovarian Follicle, Large, Biol Rep1

city: Guwahati

first: Jaya

last: Bharati

state: ASSAM

address: ICAR-NRC on Pig, Rani

department: Animal Physiology

country: India

institute: ICAR-National Research Centre on Pig, Guwahati, Assam

data_processing:
Illumina libraries were loaded onto NovaSeq6000 for cluster generation and sequencing using 2 X 150 bp chemistry.
The raw data was subjected to data QC and data filtering using FastQC (v.0.11.4) and subsequently Trimmomatic v.0.38.
The filtered sequenced reads were then used for reference based read mapping to the reference genome of Sus scrofa (pig) using HISAT2 v2.0.5 with –dta --phred33 and the mapped transcripts were assembled using StringTie v1.3.3  with default parameters.
Gene quantification was carried out by the FeatureCounts v1.5.0-p3 using default parameters which calculates the number of mapped reads. From each follicular stage, fragments per kilobase of exon per million fragments mapped (FPKM) was used to estimate the gene expression levels.
Assembly: Sscrofa11.1, INSDC AssemblyGCA_000003025.6
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Sus scrofa

source_name: Ovarian Follicle

extract_protocol:
Total RNA was isolated from porcine ovarian follicles using TRIzol method (TRIzolTM Reagent, Invitrogen)
The QC passed RNA samples were used for preparing RNA-Seq paired end sequencing libraries using Illumina TruSeq Stranded mRNA sample Prep kitfollowing manufacturer protocol.

tag: breed

value: Indian Ghoongroo

value: Ovarian Follicle

value: Large follicle


title: Ovarian Follicle, Large, Biol Rep2


title: Ovarian Follicle, Small, Biol Rep1

value: Small Follicle


title: Ovarian Follicle, Small, Biol Rep2


title: PUER cells, IL3, no OHT, 0h, rep1


title: Ovarian Follicle, Large, Biol Rep3


title: PUER cells, GCSF, OHT, +96h, rep1

description: ATAC-Seq of PUER cells 48h after replacing IL3 with GCSF and 96h after OHT induction.


title: PUER cells, GCSF, OHT, +96h, rep2


title: K27ac_rWT_M_791-1

city: St. Louis

first: Diana

middle: Christian

last: Beard

state: Missouri

address: 660 S. Euclid Ave.

department: Neuroscience

institute: Washington University in St. Louis

data_processing:
ChIP-seq reads were mapped to the mm9 genome using bowtie2 alignment and reads were extended based on library sizes and deduplicated.
Bedtools coverage -counts parameter was used to quantify ChIP signal
Assembly: mm9
Supplementary files format and content: bed

source_name: Cortex

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using the S220 Ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) and complemented with the Accel-NGS 2S Set A adapters. Up to 4ng of DNA was used as starting material. Libraries were amplified using 11-14 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent DNA D1000 Screentape Assay Kit.

value: Cortex

tag: chip antibody

value: H3K27ac:Abcam ab4729


title: M9FH9

city: MADISON

first: Hadjer

last: Namous

state: WI

address: 1675 Observatory Dr

department: Animal and Dairy Sciences

institute: University of Wisconsin Madison

description: : Illumina - NextSeq 500 v2 High-Output - SR 75 Cycle

data_processing:
Raw and trimmed reads were provided by the sequencing facility. Each file was checked for sequencing quality using Fastq
STAR was used for mapping and generating raw counts for each sample
DESeq2 was used for differential gene expression
Supplementary files format and content: CSV file contains raw counts for each sample
Supplementary files format and content: CSV file contains normalized reads for each sample

source_name: Plasma

extract_protocol:
Cell-free RNA (cf-RNA) was extracted from plasma samples using Quick-cfRNA Serum & Plasma Kit (Zymo Search, CA, USA).
Library type: Illumina - Small RNA (microRNA); - Library prep kit: RealSeq-Biofluids. Sequencing was performed by RealSeq Biosciences
Biofluids small RNA sequencing

value: Plasma

value: Familial Hypercholesterolemia (LDLR mutation)

value: Month 9


title: K27ac_R878H_M_791-3

value: Male


title: M9FH8


title: PREV72_Day60

value: Prevnar -13


title: PREV62_Day1

value: Blood

value: Female


title: M9FH7


title: PVAX40_Day60

value: PBMCs

value: Pneumovax -23


title: M9WT8

value: Normal


title: M9WT9

description:
Illumina - NextSeq 500 v2 High-Output - SR 75 Cycle
it has a low mapping percentage of < 1% for miRNA sequencing. Hence, no reads are present in processed data files.


title: K27ac_pWT_M_753-2


title: M9WT7


title: PREV72_Day1


title: M9FH6


title: K27ac_P900L_M_796-1


title: M9FH5


title: PVAX32_Day60


title: M9FH4


title: K27ac_P900L_M_753-1


title: M9WT4


title: PVAX43_Day1


title: M9WT5


title: PVAX40_Baseline

value: Baseline


title: M9FH3


title: M9FH2


title: M9FH1


title: PVAX32_Baseline


title: K27ac_pWT_F_705-4


title: PVAX95_Day10


title: PREV62_Day10


title: K27ac_R878H_F_708-1


title: M9WT6


title: PREV62_Day60


title: M6FH8

value: Month 6


title: K27ac_P900L_F_602-5


title: K27ac_pWT_F_602-6


title: M9WT1


title: K27ac_rWT_F_708-2


title: M6FH9


title: M9WT2


title: M6FH7


title: M6WT9


title: PREV50_Day10


title: K27ac_P900L_F_705-5


title: K27ac_pWT_M_796-2


title: M6WT8


title: WT_BM_MR

city: Shimotsuke

first: Yasuhiro

last: Omata

state: Tochigi

address: 3311-1 Yakushiji

department: Department of Medicine

country: Japan

institute: Jichi Medical University

data_processing:
Real-Time analysis (RTA)
Sequence reads were processed to remove adaptor sequences with Trim Galore. Sequence quality was confirmed using FastQC.
Trimmed sequence reads were mapped to UCSC mm10 using HISTAT2.
Mapping data were ordered according to genomic location by SAMtools.
Transcripts Per Kilobase Million (TPM) was obtained using Stringtie.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include TPM values for each sample.

source_name: bone marrow cells

growth_protocol: Bone marrow cells were cultured in alpha-minimum essential medium containing fetal bovine serum and penicillin-streptmycin.

extract_protocol:
Total RNA was extracted using RNeasy micro kit (QIAGEN).
Sequencing library was constructed from 1 microgram of purified total RNA with NEB Next Ultra RNA LP Kit (NEB).

treatment_protocol: Osteoclast differentiation was induced by M-CSF and RANKL. Bone marrow cells were cultured with M-CSF for two days. For the next two days M-CSF and RANKL were added.

value: bone marrow cells

value: WT

value: M-CSF, RANKL


title: M9WT3


title: PVAX43_Day10


title: M6WT7


title: PVAX40_Day1


title: M6FH5


title: M6FH4


title: WT_BM_M

value: M-CSF


title: PREV21_Day1


title: M6WT6


title: PREV72_Day10


title: Liver, high PAM, Rep 2

city: Toronto

first: Mackenzie

middle: E

last: Smith

state: Ontario

address: 1 King's College Circle

department: Nutritional Sciences

country: Canada

institute: University of Toronto

data_processing:
Quality of the initial sequenced data was assessed using FastQC 0.11.9
Adaptors and low-quality ends were trimmed using Trim Galore 0.5.0, and quality of trimmed reads was reassessed with FastQC.
The libraries were screened for the presence of rRNA and mtRNA sequences using FastQ Screen 0.10.0.
Trimmed reads were aligned to mouse reference genome using STAR aligner 2.6.0c and GENCODE release m27.
RSeQC package 2.6.2 was used to assess read distribution, positional read duplication and to confirm the strandedness of alignments. Raw gene counts were obtained using HTSeq 0.6.1p2, while FPKM (fragments per kilobase per million mapped fragments) counts were generated using DESeq2 version 1.22.2 in R 4.1.1.
Assembly: m27
Supplementary files format and content: .csv files for both brain and liver tissue contain both FPKM and raw gene counts for each sample

source_name: Liver

extract_protocol:
Total RNA was isolated from day 35 pulverized pup left brain hemispheres (≤ 100mg starting material) and livers (≤ 5 mg starting material) using the RNeasy Lipid Tissue Mini Kit (Qiagen; item no. 74804) and the RNeasy Micro Kit (Qiagen; item no. 74004), respectively, according to manufacturer instructions. For liver RNA, extraction was followed by a 3M sodium acetate (Sigma; item no. 567422) re-purification step to remove contamination.
Libraries were prepared following the NEB NEBNext Ultra II Directional RNA Library Preparation protocol to generate stranded data. Briefly, 400 ng of total RNA was used as input material and enriched for poly-A mRNA using magnetic oligo d(T) beads, fragmented into the 200-300-bases range for 10 minutes at 94oC and converted to double stranded cDNA. Next, cDNA proceeded to library preparation and dual-index Illumina adapters were added through PCR.

treatment_protocol: diets low (<2%), medium (47%), or high (>95%) in palmitic acid fed from birth to mice

value: Liver

value: BALB/c

value: High PAM diet

value: 35 days old


title: PVAX59_Day60


title: Liver, high PAM, Rep 5

value: Male


title: Liver, high PAM, Rep 4


title: Liver, high PAM, Rep 3


title: Liver, high PAM, Rep 1


title: M6WT5

value: Plasma


title: M6WT3


title: M6WT2


title: M6WT1


title: M6WT4


title: PVAX83_Day10

value: Blood


title: M3FH9

value: Familial Hypercholesterolemia (LDLR mutation)

value: Month 3


title: Liver, medium PAM, Rep 5

value: Medium PAM diet


title: M3FH8


title: M6FH6


title: M3WT9

value: Normal


title: M6FH3


title: PREV72_Baseline

value: PBMCs

value: Baseline

value: Prevnar -13


title: M6FH2

value: Month 6


title: Liver, medium PAM, Rep 4


title: PVAX40_Day10

value: Pneumovax -23

value: Female


title: Liver, medium PAM, Rep 3

value: Liver


title: M3WT8


title: PVAX59_Baseline


title: Liver, medium PAM, Rep 2

value: BALB/c


title: M3WT7


title: PREV50_Baseline


title: M3FH7


title: PREV50_Day60


title: M6FH1


title: M3WT6


title: PREV62_Baseline


title: Liver, low PAM, Rep 5

value: Low PAM diet


title: M3FH6


title: M3FH4


title: Liver, medium PAM, Rep 1

value: 35 days old


title: PVAX32_Day10


title: PVAX83_Day1


title: M3WT5


title: Patient 23 GIST

type: RNA

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Department of Tumor Biology

country: Norway

institute: Oslo University Hospital

description: RNA isolation: Qiagen AllPrep DNA/RNA/miRNA Universal kit

scan_protocol: Data was collected using a nanoString nCounter Sprint profiler following recomendations for the assay

data_processing: Quality control and pre-processing were performed using nSolver software from nanoString. miRNA with a median expression value bellow 45 in both in metastatic and non metastatic groups were filtered. This value was chosen based on the negative controls of the assay. Normalisation and differentially expressed gene analysis were performed using NanostringDiff R package.

label: Nanostring

source_name: GIST

label_protocol: Samples were processed using the nanoString Human V3 miRNA assay

extract_protocol: RNA was isolated using Qiagen AllPrep DNA/RNA/miRNA Universal kit following the manufacturer’s instructions

treatment_protocol: Untreated tumour samples

value: primary GIST

tag: tumour stage

value: High-risk

tag: developed metastases or not

value: non-metastatic

value: female

tag: somatic mutation

value: KIT exon 11


title: PVAX32_Day1

value: Blood

tag: cell type


title: Liver, low PAM, Rep 3

tag: treatment

value: Male


title: PVAX95_Baseline

value: PBMCs


title: M3WT4

value: Plasma

value: Normal

value: Month 3


title: Patient 24 GIST

value: metastatic

value: male


title: Patient 21 GIST


title: Liver, low PAM, Rep 2

value: Liver

tag: strain


title: M3FH5

value: Familial Hypercholesterolemia (LDLR mutation)


title: PVAX59_Day1

tag: figureid

value: Pneumovax -23

value: Female


title: M3WT3

tag: tissue


title: PVAX43_Day60

tag: time


title: Patient 20 GIST

value: primary GIST

tag: Sex


title: PVAX43_Baseline

value: Baseline

tag: age (in years)


title: M3FH3

tag: genotype


title: Patient 22 GIST

value: High-risk

value: non-metastatic

value: PDGFRA exon 18


title: M3FH2


title: Patient 19 GIST

value: KIT exon 11


title: Patient 18 GIST

value: female


title: Brain, high PAM, Rep 4

source_name: Brain

value: Brain

value: BALB/c

value: High PAM diet

value: 35 days old

value: Male


title: Brain, high PAM, Rep 5


title: Liver, low PAM, Rep 1

value: Low PAM diet


title: Patient 17 GIST

value: male


title: Patient 16 GIST


title: Liver, low PAM, Rep 4

value: Liver


title: M3WT2

value: Plasma

value: Normal

value: Month 3


title: Brain, high PAM, Rep 3


title: PREV21_Day60

value: Blood

value: PBMCs

value: Prevnar -13


title: PREV21_Day10


title: Brain, high PAM, Rep 2


title: M3WT1


title: Patient 15 GIST

value: primary GIST

value: High-risk

value: non-metastatic

value: PDGFRA exon 18


title: Patient 14 GIST

value: female

value: KIT exon 11


title: scSeq_CAR1_Seq1

city: München

first: Jessica

last: Pauli

state: Bayern

address: Biedersteiner Str. 29

department: Molecular Vascular Medicine

institute: TUM Universitätsklinikum (Klinikum rechts der Isar)

data_processing:
The demultiplexing, alignment and gene counting were made using the Cell Ranger software v3.1.0 (for sample CAR1), v5.0.0 (for sample CAR2-4) and v6.0.1 (for sample CAR 5-10) (10x Genomics), using GRCh 38 and Gencode annotation v33
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: carotid artery

extract_protocol:
Human carotid arteries were harvested during carotid endarterectomy or open repair in our Department of Vascular and Endovascular Surgery. The tissue was transported in PBS on ice to our laboratory. The two distinct pieces of each tissues (except CAR1) were minced and digested using the Multi Tissue Dissociation Kit 2 (Miltenyi Biotech, 130-110-203), GentleMACS Dissociator (Miltenyi Biotech, 130-093-235), GentleMACS C tubes (Miltenyi Biotech, 130-096-334) and the 37C_Mulit_G program, all according to the manufacturer´s instructions. The cell suspension was strained (70 µm, 40 µm) and Dead Cell Removal (Miltenyi Biotech, 130-090-101) using MS Columns (Miltenyi Biotech, 130-042-201) was performed. Cells were resuspended in PBS + 0,04% BSA.
Cells were loaded into a 10x Genomics microfluidics Chip G and encapsulated with barcoded oligo-dT-containing gel beads using the 10x Genomics Chromium Controller. Gel Beads-in-emulsion (GEM) cleanup, cDNA Amplification and 3´Gene Expression Dual Index Library Construction was performed according to the manufacturer´s instructions (CG000315 Rev C). Libraries from individual samples were multiplexed into one lane before sequencing on an Illumina NovaSeq6000 instrument
Chromium next GEM Single Cell 3´ Reagent Kit v2 (CAR 1), v3.1 (CAR 2, CAR 3, CAR 4), v3.1 Dual Index (CAR 5, CAR 6, CAR 7, CAR 8, CAR 9, CAR 10)

value: carotid artery

tag: cell line

value: primary cells

value: all cells from tissue


title: Brain, medium PAM, Rep 5

value: Brain

value: BALB/c

value: Medium PAM diet

value: 35 days old

value: Male


title: Patient 13 GIST

value: male


title: non-CF subject 4, 72 hours post-infection

city: Iowa City

first: Alejandro

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

department: Department of Internal Medicine

institute: Universty of Iowa

data_processing:
Raw fastq files were pseudoaligned to human genome assembly GRCh38.p14 using kallisto software version 0.45.0
Assembly: GRCh38.p14
Supplementary files format and content: Tab-separated text file containing length, estimated counts, and transcripts per million (TPM) for each gene isoform

source_name: lung

extract_protocol:
RNA was extracted using SV 96 Total RNA Isolation System catalog #Z3500
mRNA libraries were prepared using Illumina TruSeq stranded mRNA sample preparation kit (Illumina #RS-122-2101).

treatment_protocol: CF and Non-CF human airway epithelial cell cultures were infected apically with RSV expressing GFP at MOI = 1

value: lung

tag: subject

tag: disease state

value: non-CF

tag: infection

value: 72 hours post-infection with RSV


title: Brain, medium PAM, Rep 4


title: scSeq_CAR10_Seq2


title: scSeq_CAR10_Seq1


title: Brain, medium PAM, Rep 3


title: Patient 12 GIST

value: primary GIST

value: High-risk

value: metastatic


title: non-CF subject 4, 12 hours post-infection

value: 12 hours post-infection with RSV


title: Brain, medium PAM, Rep 2


title: scSeq_CAR9_Seq2


title: non-CF subject 4, 24 hours post-infection

value: 24 hours post-infection with RSV


title: non-CF subject 4, 120 hours post-infection

value: 120 hours post-infection with RSV


title: Patient 11 GIST

value: PDGFRA exon 18


title: non-CF subject 4, 48 hours post-infection

value: 48 hours post-infection with RSV


title: Patient 10 GIST

value: KIT exon 11


title: M3FH1

value: Plasma

value: Familial Hypercholesterolemia (LDLR mutation)

value: Month 3


title: Patient 8 GIST


title: scSeq_CAR8_Seq2

value: carotid artery

value: primary cells

value: all cells from tissue


title: Brain, high PAM, Rep 1

value: Brain

value: BALB/c

value: High PAM diet

value: 35 days old

value: Male


title: Patient 7 GIST

value: primary GIST

value: High-risk

value: metastatic

value: male


title: Brain, low PAM, Rep 5

value: Low PAM diet


title: scSeq_CAR8_Seq1


title: non-CF subject 3, 72 hours post-infection

value: lung

value: non-CF

value: 72 hours post-infection with RSV


title: Brain, low PAM, Rep 4


title: Patient 6 GIST

value: KIT exon 11


title: scSeq_CAR7_Seq2

value: carotid artery


title: non-CF subject 3, 48 hours post-infection

value: 48 hours post-infection with RSV


title: Brain, medium PAM, Rep 1

value: Medium PAM diet


title: scSeq_CAR9_Seq1

value: primary cells

value: all cells from tissue


title: Patient 5 GIST


title: scSeq_CAR7_Seq1


title: scSeq_CAR6_Seq1


title: Brain, low PAM, Rep 2

value: Brain

value: BALB/c


title: non-CF subject 3, 12 hours post-infection

value: 12 hours post-infection with RSV


title: Patient 3 GIST

value: primary GIST

value: female


title: Brain, low PAM, Rep 1

value: 35 days old

value: Male


title: non-CF subject 3, 120 hours post-infection

value: 120 hours post-infection with RSV


title: HEV-3f infected  (SAMPLE 7)

city: Maisons-Alfort

first: Virginie

last: Doceul

address: 7 avenue du Général de Gaulle

institute: UMR VIROLOGIE INRAE-ANSES-ENVA

description: Test 2

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package "GeneGlobe Data Analysis Center" : https://geneglobe.qiagen.com/fr/analyze
For the normalization it uses the average of four housekeeping genes: ACTG, GAPDH, PGK1 and RPL13A
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ave Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control (i.e., HEV-3f/Mock) ratios.

label: SYBR Green

label_protocol: PCR assays were performed using the  (Qiagen) following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (Qiagen). Quantitative real-time PCR were performed (Light Cycler 96, Roche) with 45 cycles at 95 oC for 15 seconds and 60 oC for 30 seconds.

extract_protocol: 25 mg of liver was added to RLT buffer (Qiagen) supplemented with 1% β-mercaptoethanol and lysed using a Fast Prep 24 System (MP Biomedicals, Illkirch, France) in Lysis Matrix D tubes (MPBiomedicals, Illkirch, France). Total RNA was then extracted using the RNeasy minikit (Qiagen) including a digestion step on column with DNase I (Qiagen) according to the supplier’s protocol.

treatment_protocol: Eight-week-old specific pathogen free Large-White piglets were infected intravenously with 10^6 copies of HEV RNA or mock-infected with PBS. At the peak of excretion (8 days post-infection), liver tissues were snap-frozen in liquid nitrogen. Samples from 2 control pigs, 3 pigs infected with HEV-3c and 3 pigs infected with HEV-3f were analyzed in this study.

value: Liver tissue

value: 8 days post-infection

tag: moi

value: 10^6 copies HEV RNA


title: non-CF subject 4, uninfected

value: lung

value: non-CF

value: no virus


title: HEV-3f infected  (SAMPLE 8)

description: Test 2


title: HEV-3f infected  (SAMPLE 6)

description: Test 2


title: non-CF subject 3, uninfected


title: scSeq_CAR5_Seq2

value: carotid artery


title: scSeq_CAR5_Seq1

value: primary cells


title: WGBS_rWT_M_696-2

description: R878Hhypo.bed, R878Hhyper.bed

data_processing:
Reads were adaptor trimmed and mapped to the mm9 genome using bowtie2 alignment and subsequently deduplicated.
Reads were called for methylation using BS-seeker2
Methylation levels across regions were assessed using bedtools map -o sum, summing the number of reads mapping to Cs(supporting mC) and the number of reads mapping to Cs + Ts (supporting C) in the region, then dividing those two numbers (% mC/C in region)
Regions were adjusted for nonconversion rate by substracting % methylation in Lambda spike-ins per-sample from the calculated %mC/C value
Bsmooth was used to call differential CpG methylated regions. Sites were then filtered requiring >2x genomic coverage in all replicates, DMRs were called using t-stat>2.0, length >100bp, and biological replicate consistency.
Assembly: mm9
Supplementary files format and content: bed

extract_protocol:
DNA was extracted using the Allprep DNA/RNA Mini Kit (Qiagen).
50ng of DNA was sonicated using the S220 Ultrasonicator (Covaris) and subsequently bisulfite converted using the EZ DNA Methylation-Direct Kit (Zymo Research Corporation). WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit (Swift) and complemented with Methyl-Seq Combinatorial Dual Indexing Kit (Swift). Libraries were amplified using 10 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using SPRISelect beads from Beckman Coulter. Libraries were validated using the Agilent DNA D1000 Screntape Assay Kit.

value: Cortex

tag: age


title: non-CF subject 2, 72 hours post-infection

value: 72 hours post-infection with RSV


title: WGBS_rWT_F_697-3

description: R878Hhypo.bed, R878Hhyper.bed

value: Female


title: scSeq_CAR4_Seq2

value: all cells from tissue


title: HEV-3c infected  (SAMPLE 5)

description: Test 1


title: Brain, low PAM, Rep 3

value: Brain

value: BALB/c

value: Low PAM diet


title: non-CF subject 2, 48 hours post-infection

value: 48 hours post-infection with RSV


title: HEV-3c infected  (SAMPLE 4)

description: Test 1


title: non-CF subject 3, 24 hours post-infection

value: 24 hours post-infection with RSV


title: WGBS_rWT_F_697-2

description: R878Hhypo.bed, R878Hhyper.bed


title: scSeq_CAR6_Seq2


title: Patient 1 GIST

value: primary GIST

tag: tumour stage

value: High-risk

tag: developed metastases or not

value: metastatic

value: female

value: KIT exon 11


title: scSeq_CAR4_Seq1

tag: cell type


title: WGBS_R878H_M_698-4

description: R878Hhypo.bed, R878Hhyper.bed

value: Male


title: non-CF subject 2, 12 hours post-infection

value: lung

value: non-CF

value: 12 hours post-infection with RSV


title: scSeq_CAR3_Seq2

value: carotid artery

value: primary cells


title: WGBS_rWT_M_698-3

description: R878Hhypo.bed, R878Hhyper.bed

value: Cortex


title: non-CF subject 2, 24 hours post-infection


title: HEV-3c infected  (SAMPLE 3)

description: Test 1

value: Liver tissue

tag: treatment

value: 8 days post-infection

value: 10^6 copies HEV RNA


title: WGBS_R878H_M_696-1

description: R878Hhypo.bed, R878Hhyper.bed

tag: strain


title: Mock  (SAMPLE 2)

description: Control

value: Mock


title: Mock  (SAMPLE 1)

description: Control


title: non-CF subject 2, 120 hours post-infection

value: 120 hours post-infection with RSV


title: WGBS_R878H_F_697-4

description: R878Hhypo.bed, R878Hhyper.bed

value: Female


title: scSeq_CAR3_Seq1

value: all cells from tissue


title: HEV-infected HepaRG (SAMPLE 12), D100 plaque 2

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package "GeneGlobe Data Analysis Center" : https://geneglobe.qiagen.com/fr/analyze
For the normalization it uses the average of four housekeeping genes: ACTB, GAPDH, HSP90AB1 and GUSB
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ave Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control (i.e., HEV-3f/Mock) ratios.

source_name: HepaRG

label_protocol: PCR assays were performed using the Human Type I Interferon Response PCR array (Qiagen) following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (Qiagen). Quantitative real-time PCR were performed (Light Cycler 96, Roche) with 45 cycles at 95 oC for 15 seconds and 60 oC for 30 seconds.

growth_protocol: HepaRG were seeded into 6- well plates and cultured in proliferation medium for 2 weeks. Medium was then replaced for 2 extra weeks by “differentiation medium” supplemented with 1.2% DMSO (Sigma-Aldrich).

extract_protocol: Total RNA was extracted with RNeasy Mini Kit including a DNase I treatment step.

treatment_protocol: Two days before infection, differentiation medium was replaced by proliferation medium. Cells were infected overnight with an HEV-3f inoculum diluted in proliferation medium to a final volume of 1ml. The viral suspension was then removed and cells were washed three times in PBS before adding 2 ml of proliferation medium. Every 2 to 3 days, one-half (1 ml) of the culture medium was replaced with fresh growth medium and infection maintained for 100 days. A HEV-3f strain originating from a French patient suffering from acute autochthonous hepatitis E was used (GenBank under accession number JN906974)

value: HepaRG

value: 100 days

value: MOI 100

tag: experiment


title: WGBS_R878H_F_697-1

description: R878Hhypo.bed, R878Hhyper.bed

tag: tissue


title: scSeq_CAR2_Seq2


title: scSeq_CAR2_Seq1


title: non-CF subject 1, 72 hours post-infection

value: 72 hours post-infection with RSV


title: WGBS_pWT_M_753-2

description: P900Lhypo.bed, P900Lhyper.bed

value: Male


title: WGBS_pWT_M_706-6

description: P900Lhypo.bed, P900Lhyper.bed


title: non-CF subject 1, 48 hours post-infection

value: lung

value: non-CF

value: 48 hours post-infection with RSV


title: HEV-infected HepaRG (SAMPLE 11), D100 plaque 2

description: Test

tag: time


title: HEV-infected HepaRG (SAMPLE 10), D100 plaque 2

description: Test


title: non-CF subject 1, 24 hours post-infection

value: 24 hours post-infection with RSV


title: hTSC-CT30 scRNAseq

city: Beijing

first: Hongmei

last: Wang

address: 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

description: 10X Genomics

data_processing:
We applied  Cellranger v7.0.1 with gene annotation gencode.v32 to process scRNA-seq and snRNA-seq raw data. We turned the parameter '-intron' off for scRNA-seq. We used the resulting filtered_feature_bc_matrix directory for downstream analysis.
For snRNA-seq datasets, we firstly analyzed and annotated two datasets of snRNA-seq obtained from hTSCs-BL and hTSCs-CT30 using Seurat algorithm, similar to the analysis we performed on placenta samples in early pregnancy. We employed Seurat CCA algorithm to identify anchor genes and integrated two snRNA-seq datasets from hTSCs-BL and hTSCs-CT30 with snRNA-seq datasets from placental villus in early pregnancy. Subsequently, we jointly annotated the clusters using marker genes and aligned them along the differentiation trajectory using Monocle2.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: The culture of human trophoblast stem cells was performed as previously described. Briefly, the plate was coated with 5 μg/ml Collagen I (Cat#354233, Corning) at 37℃ at least for 1 h. hTSCs were cultured in hTSCs medium (DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.2% FBS, 0.5% Penicillin-Streptomycin, 0.3% BSA, 1% ITS-X supplement, 1.5 μg/ml L-ascorbic acid, 50 ng/ml EGF, 2 μM CHIR99021, 0.5 μM A83-01, 1 μM SB431542, 0.8 mM VPA and 5 μM Y27632). hTSCs were dissociated with TrypLE for 8 min at 37℃ and the cells were passaged to a new Collagen I-coated plate. hTSCs were routinely passaged every 4-5 days at a 1: 4-1: 6 ratio.

extract_protocol:
For STB-BL and STB-CT30 cell lines snRNA-seq sample extraction, cells were harvested and dissociated with TrypLE for 8 min at 37℃ and washed with phosphate buffer solution. Ice cold Nuclei EZ lysis buffer was added to resuspend the cells and grinded with a dounce tissue grinder. The lysates were bathed in ice and lysed twice. After washing with PBS, the nuclei were filtered through a 40 μm sieve to proceed RNA-seq. For hTSC-BL and hTSC-CT30 cell lines scRNA-seq sample extraction, cells were dissociated with TrypLE for 8 min at 37℃ and washed with phosphate buffer solution.
For Single-nucleus RNA sequencing, Single Cell B Chip Kit (10x Genomics, 1000074) and the nucleus suspension (600 nuclei per microliter determined by CountStar) were loaded onto the Chromium single cell controller (10x Genomics) to generate single-nucleus gel beads in the emulsion (GEMs) according to the manufacturer’s protocol. In brief, single nuclei were suspended in PBS containing 0.04% Bovine serum albumin (BSA). About 16,000 nuclei were added to each channel, with 8,000 target nuclei estimated to be recovered. Captured nuclei were lysed, and the released RNA was barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on an S1000TM Touch Thermal Cycler (Bio-Rad) at 53°C for 45 min, followed by 85°C for 5 min and held at 4°C. The cDNA was generated and then amplified, and quality was assessed using an Agilent 4200 (performed by CapitalBio Technology, Beijing). Next, single-nucleus RNA-Seq library was constructed using Single Cell 3’ Library and Gel Bead Kit V3.1 according to the manufacturer’s introduction. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per nuclei with a pair-end 150bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing). For Single-cell RNA Sequencing, the construction of transcriptome libraries was performed following the Chromium Single Cell 3’ v2 Protocol. Briefly, the cDNA was purified after GEM generation, barcode addition, GEM-RT reaction and bead cleanup. The GEX libraries were generated following the 10 x Genomics Chromium Single Cell 3’ Reagent Kits (v3) Protocol. Qubit 3.0 Fluorometer and Agilent 2100 High Sensitivity DNA Assay Kit were used to determine the library concentration and the distribution of library product fragments, respectively. Libraries were sequenced on the Illumina Novaseq 6000 platform with paired-end sequencing.

treatment_protocol: hTSCs were grown to 80% confluence in the hTSCs medium and dissociated with TrypLE for 8 min at 37°C. For the induction of STB, hTSCs were seeded in a 6-well plate pre-coated with 2.5 μg/ml Collagen I at a density of 1 × 105 cells per well and cultured in STB medium (DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.5% Penicillin-Streptomycin, 0.3% BSA, 1% ITS-X supplement, 2.5 μM Y27632, 2 μM forskolin, and 4% KSR). The medium was replaced every 2 days and analyzed on day 6.

value: human trophoblast stem cell


title: STB-BL snRNAseq

description: 10X Genomics

source_name: STB-BL

value: STB-BL

value: hTSC derived syncytiotrophoblast cell


title: non-CF subject 1, 12 hours post-infection

value: 12 hours post-infection with RSV


title: STB-CT30 snRNAseq

description: 10X Genomics


title: Non-treated HepaRG (SAMPLE 9), D100 plaque 2

description: Control

value: Mock


title: WGBS_pWT_F_306-4

description: P900Lhypo.bed, P900Lhyper.bed

value: Cortex

tag: Sex


title: Non-treated HepaRG (SAMPLE 7), D100 plaque 2

description: Control


title: hTSC-BL scRNAseq

description: 10X Genomics

source_name: hTSC-BL

value: hTSC-BL


title: WGBS_P900L_M_753-1

description: P900Lhypo.bed, P900Lhyper.bed


title: WGBS_P900L_M_706-5

description: P900Lhypo.bed, P900Lhyper.bed


title: HEV-infected HepaRG (SAMPLE 6), D100 plaque 2

description: Test


title: placenta villi, late pregnancy snATAC, donor6 [term-atac-6]

description: 10X Genomics

library_source: genomic single cell

data_processing:
We applied Cellranger v3.0.0 with gene annotation ensembl version 93 or Cellranger v7.0.1 with gene annotation gencode.v32 to process snRNA-seq raw data. For snATAC-seq raw data, we applied Cellranger-atac v1.1.0 or Cellranger-atac v1.2.0 to process the raw data. We used the resulting filtered_feature_bc_matrix directory from snRNA-seq data process step and fragments.tsv files from snATAC-seq data process step for next analysis.
We used the Seurat v3.2.3 package for standard snRNA-seq upstream analysis and SnapATAC v1.0.0 or SnapATAC v2.2.0 for standard snATAC-seq upstream analysis.
We used Harmony v1.0 for batch effect removal and DoubletFinder v2.0.3 (snRNA-seq), Scrublet v0.2.3 (snATAC-seq) for doublet removal.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: healthy placenta

extract_protocol:
The villi were separated from the early or term placenta and cut up after removing the blood with phosphate buffer solution (PBS). Ice cold Nuclei EZ lysis buffer (Sigma-Aldrich, NUC-101) containing RNAase inhibitor (TaKaRa, 2313B) and protease inhibitor (Sigma-Aldrich, P8340) were added to resuspend the tissue and grinded with a dounce tissue grinder (Sigma-Aldrich, D8938). The lysates were bathed in ice and lysed twice. After washing with PBS, the nuclei were splited in half and filtered through a 40 μm sieve to proceed ATAC-seq and RNA-seq, respectively.
Single-nucleus RNA Sequencing. Single Cell B Chip Kit (10x Genomics, 1000074) and the nucleus suspension (600 nuclei per microliter determined by CountStar) were loaded onto the Chromium single cell controller (10x Genomics) to generate single-nucleus gel beads in the emulsion (GEMs) according to the manufacturer’s protocol. In brief, single nuclei were suspended in PBS containing 0.04% Bovine serum albumin (BSA). About 16,000 nuclei were added to each channel, with 8,000 target nuclei estimated to be recovered. Captured nuclei were lysed, and the released RNA was barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on an S1000TM Touch Thermal Cycler (Bio-Rad) at 53°C for 45 min, followed by 85°C for 5 min and held at 4°C. The cDNA was generated and then amplified, and quality was assessed using an Agilent 4200 (performed by CapitalBio Technology, Beijing). Next, single-nucleus RNA-Seq library was constructed using Single Cell 3’ Library and Gel Bead Kit V3.1 according to the manufacturer’s introduction. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per nuclei with a pair-end 150bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).   Single-nucleus ATAC Sequencing. Following the 10x Genomics single cell ATAC solution, by using Chromium Chip E Single Cell Kit (Product Code 1000156) and Chromium Single Cell ATAC Library & Gel Bead Kit (Product Code 1000110), the nuclei in a bulk sample were partitioned into nanoliter-scale Gel Beads-in-emulsion (GEMs), a pool of ~750,000 10x Barcodes was sampled to separately and uniquely index the transposed DNA of each nucleus. Libraries were then generated (performed by CapitalBio Technology, Beijing). The libraries were sequenced using an Illumina Novaseq sequencer with a sequencing depth of at least 25k read pairs per nuclei with a pair-end 50bp (PE50) reading strategy.

value: healthy placenta

tag: time point

value: late pregnancy


title: non-CF subject 1, 120 hours post-infection

value: 120 hours post-infection with RSV


title: WGBS_P900L_F_306-3

description: P900Lhypo.bed, P900Lhyper.bed

tag: genotype

value: Female


title: non-CF subject 2, uninfected

value: no virus


title: non-CF subject 1, uninfected


title: CF subject 4, 72 hours post-infection

value: CF

value: 72 hours post-infection with RSV


title: placenta villi, late pregnancy snATAC, donor5 [term-atac-5]

description: 10X Genomics


title: HEV-infected HepaRG (SAMPLE 5), D100 plaque 2

description: Test

tag: cell line

value: HepaRG

value: 100 days

value: MOI 100


title: placenta villi, late pregnancy snATAC, donor4 [term-atac-4]

description: 10X Genomics


title: HEV-infected HepaRG (SAMPLE 4), D100 plaque 2

description: Test


title: WGBS_P900L_F_306-2

description: P900Lhypo.bed, P900Lhyper.bed


title: placenta villi, late pregnancy snATAC, donor3 [term-atac-3]

description: 10X Genomics


title: CF subject 4, 48 hours post-infection

value: lung

tag: subject

value: 48 hours post-infection with RSV


title: WGBS_pWT_F_306-1

description: P900Lhypo.bed, P900Lhyper.bed


title: CF subject 4, 24 hours post-infection

tag: disease state

value: 24 hours post-infection with RSV


title: Non-treated HepaRG (SAMPLE 8), D100 plaque 2

description: Control


title: OGTKO_NPC2

city: Kansas City

first: Dakota

last: Robarts

state: KS

address: 3901 Rainbow Blvd

institute: University of Kansas Medical Center

description: 10x Genomics Chromium Single Cell Gene Expression data

data_processing:
Data was analyzed using the 10x Genomics cell ranger (version 6.0.2) software suite
The demultiplexing and conversion of Illumina base call files (BCL) to raw FASTQ files was done using "cellranger mkfastq" with default parameters.
The sequencing reads were aligned to the mouse reference (GRCm38: refdata-cellranger-GRCm38-3.0.0) and analyzed using "cellranger count".
Assembly: mm10
Supplementary files format and content: cellranger generated unfilterted feature-barcode matrix file

extract_protocol:
Single cell suspension was generated using collagenase perfusion method. Cell viability and concentration were calculated by Countess II FL Automated cell counter
The RT reaction to generate 10X barcoded single stranded cDNA, in the single cell containing GEMs, is performed using an Eppendorf MasterCycler Pro thermal cycler. Post GEM-RT Cleanup is conducted by breaking the GEMS with 10X Recovery Agent to separate the aqueous phase from the Recovery Agent and Partitioning oil. A cleanup of the sscDNA containing aqueous phase is completed using Dynabeads MyOne Silane beads (Life Technologies 37002D). The second strand cDNA amplification is performed using the cDNA Amplification Mix on the Eppendorf MasterCycler Pro. The 3’ gene expression library construction is initiated with fragmentation, end repair and A-tailing of the dscDNA followed by adapter ligation and a sample index PCR using the Illumina compatible indexed adapters in the Chromium i7 Multiplex kit (10X Genomics 120262). Validation of the single cell library is conducted using the Agilent Tapestation 4200 ScreenTape assay (Agilent 5067-5576).

treatment_protocol: 5 Week OGT hepatocyte specific deletion or control

value: Nonparenchymal Cells

value: Liver

value: OGT-Floxed Mice

tag: virus

value: OGT-KO


title: Non-treated HepaRG (SAMPLE 2), D100 plaque 2

description: Control

value: Mock

tag: moi


title: Non-treated HepaRG (SAMPLE 3), D100 plaque 2

description: Control


title: placenta villi, late pregnancy snATAC, donor2 [term-atac-2]

description: 10X Genomics

value: healthy placenta

value: late pregnancy


title: OGTKO_NPC1


title: CF subject 4, 120 hours post-infection

tag: infection

value: 120 hours post-infection with RSV


title: placenta villi, late pregnancy snATAC, donor1 [term-atac-1]

description: 10X Genomics


title: CF subject 4, 12 hours post-infection

value: 12 hours post-infection with RSV


title: Non-treated HepaRG (SAMPLE 1), D100 plaque 2

description: Control


title: CF subject 4, uninfected

value: CF

value: no virus


title: CF subject 3, 72 hours post-infection

value: 72 hours post-infection with RSV


title: F4/80 Brain Cells, WNV B6J 3

city: Seattle

first: Joshua

middle: M

last: Ames

state: WA

address: 750 Republican st

institute: University of Washington

description:
lib88161
Norris_2023_RawGeneCounts.csv
Norris_2023_FilteredNormGeneCounts.csv

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads.
The FASTQs were aligned to the GRCm38 mouse reference genome, using STAR v.2.4.2a and gene counts were generated using htseq-count.
QC and metrics analysis was performed using the Picard family of tools (v1.134).
Assembly: GRCm38
Supplementary files format and content: 230104-P501-1_RawGeneCounts.csv
Supplementary files format and content: 230104-P501-1_FilteredNormGeneCounts.csv

source_name: brain

extract_protocol:
After MACs isolation, brain macrophages were washed in PBS and cell pellets prepared using the RNAqueous Micro kit (Ambion) per manufacturer’s instruction.
Total RNA was concentrated by evaporation using an Eppendorf Vacufuge system and was then added to lysis buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara).  Reverse transcription was performed followed by 20 cycles of PCR amplification to generate full length amplified cDNA.  Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.

tag: mouse strain

value: WNV

value: brain

value: F4/80 Brain Cells


title: F4/80 Brain Cells, WNV B6J 4

description:
lib88162
Norris_2023_RawGeneCounts.csv
Norris_2023_FilteredNormGeneCounts.csv


title: Control_NPC1

value: Control


title: CF subject 3, 48 hours post-infection

value: lung

value: 48 hours post-infection with RSV


title: placenta villi, late pregnancy snRNA, donor4 [term-rna-4]

description: 10X Genomics


title: Control_Hep

value: Hepatocytes

value: Liver


title: CF subject 3, 24 hours post-infection

value: 24 hours post-infection with RSV


title: F4/80 Brain Cells, HBSS B6J 4

description:
lib88159
Norris_2023_RawGeneCounts.csv
Norris_2023_FilteredNormGeneCounts.csv

value: HBSS


title: placenta villi, late pregnancy snRNA, donor3 [term-rna-3]

description: 10X Genomics

value: healthy placenta


title: F4/80 Brain Cells, WNV B6J 2

description:
lib88160
Norris_2023_RawGeneCounts.csv
Norris_2023_FilteredNormGeneCounts.csv


title: placenta villi, late pregnancy snRNA, donor2 [term-rna-2]

description: 10X Genomics

value: late pregnancy


title: ChIP-seq_p14_rhom_input2

city: Saint Louis

first: Shiming

last: Chen

address: 517 South Euclid Avenue

department: Department of Ophthalmology & Visual Sciences

institute: Washington University in St Louis

data_processing:
For each sample, reads from two sequencing lanes were first concatenated and trimmed with Trim Galore (v0.6.1).
The trimmed reads were then mapped to the mm10 genome using Bowtie2 (v 2.3.4.1) with parameters -X 2000 --very-sensitive.
Only uniquely mapped and properly paired reads were retained with samtools (v1.9) with parameters -f 0x2 -q 30.
Mitochondria reads were removed with samtools (v1.9). Duplicated reads were marked and removed with Picard (v2.21.4).
Last, reads mapped to the mm10 blacklist regions were removed by bedtools (v2.27.1) by intersect -v.
Assembly: mm10
Supplementary files format and content: bigWig files generated with deeptools (v3.0.0). Scores represent CPM values at 10bp binsize.
Supplementary files format and content: narrowPeak files generated by MACS2 (v2.1.1.20160309) callpeak with default parameters

source_name: Retina

extract_protocol:
Pooled nuclear extracts from 6 retinae were cross-linked with formaldehyde prior to immunoprecipitation with anti-CRX antibody. Input controls were generated with normal rabbit IgG. The libraries were prepared following the standard ChIP-seq protocol (Schmidt et al., 2014)
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.

value: Retina

tag: developmental stage

value: Post-natal day 14

tag: chip antibody


title: CF subject 3, 12 hours post-infection

value: CF

value: 12 hours post-infection with RSV


title: ChIP-seq_p14_rhom_ip2

value: anti-CRX


title: OGTKO_Hep

tag: cell type

value: OGT-Floxed Mice

value: OGT-KO


title: CF subject 3, 120 hours post-infection

value: 120 hours post-infection with RSV


title: F4/80 Brain Cells, HBSS B6J 2

description:
lib88157
Norris_2023_RawGeneCounts.csv
Norris_2023_FilteredNormGeneCounts.csv

value: brain

value: F4/80 Brain Cells


title: Control_NPC2

value: Nonparenchymal Cells

tag: strain

value: Control


title: placenta villi, late pregnancy snRNA, donor6 [term-rna-6]

description: 10X Genomics


title: F4/80 Brain Cells, HBSS B6J 3

description:
lib88158
Norris_2023_RawGeneCounts.csv
Norris_2023_FilteredNormGeneCounts.csv


title: CF subject 3, uninfected

value: lung

value: no virus


title: ChIP-seq_p14_rhom_ip1


title: placenta villi, late pregnancy snRNA, donor1 [term-rna-1]

description: 10X Genomics


title: placenta villi, early pregnancy snATAC, donor6 [8w-atac-6]

description: 10X Genomics

value: early pregnancy


title: ChIP-seq_p14_rhom_input1


title: F4/80 Brain Cells, WNV IL33KO 4

description:
lib88154
Norris_2023_RawGeneCounts.csv
Norris_2023_FilteredNormGeneCounts.csv

value: IL33 KO

value: WNV


title: placenta villi, early pregnancy snATAC, donor5 [8w-atac-5]

description: 10X Genomics

value: healthy placenta


title: F4/80 Brain Cells, WNV IL33KO 3

description:
lib88153
Norris_2023_RawGeneCounts.csv
Norris_2023_FilteredNormGeneCounts.csv


title: placenta villi, early pregnancy snATAC, donor4 [8w-atac-4]

description: 10X Genomics


title: CF subject 2, 72 hours post-infection

value: 72 hours post-infection with RSV


title: ChIP-seq_p14_khom_input2

value: Retina

value: Post-natal day 14


title: CF subject 2, 48 hours post-infection

value: CF

value: 48 hours post-infection with RSV


title: ChIP-seq_p14_khom_ip2

value: anti-CRX


title: F4/80 Brain Cells, WNV IL33KO 2

description:
lib88152
Norris_2023_RawGeneCounts.csv
Norris_2023_FilteredNormGeneCounts.csv


title: placenta villi, late pregnancy snRNA, donor5 [term-rna-5]

description: 10X Genomics

value: late pregnancy


title: placenta villi, early pregnancy snATAC, donor3 [8w-atac-3]

description: 10X Genomics


title: CF subject 2, 24 hours post-infection

value: 24 hours post-infection with RSV


title: ChIP-seq_p14_khom_input1


title: F4/80 Brain Cells, HBSS IL33KO 3

description:
lib88151
Norris_2023_RawGeneCounts.csv
Norris_2023_FilteredNormGeneCounts.csv

value: HBSS

value: brain

value: F4/80 Brain Cells


title: CF subject 2, 12 hours post-infection

value: lung

value: 12 hours post-infection with RSV


title: placenta villi, early pregnancy snATAC, donor2 [8w-atac-2]

description: 10X Genomics

value: early pregnancy


title: CF subject 2, 120 hours post-infection

value: 120 hours post-infection with RSV


title: ChIP-seq_p14_ehom_input2


title: placenta villi, early pregnancy snATAC, donor1 [8w-atac-1]

description: 10X Genomics


title: F4/80 Brain Cells, HBSS IL33KO 2

description:
lib88150
Norris_2023_RawGeneCounts.csv
Norris_2023_FilteredNormGeneCounts.csv

value: IL33 KO


title: ChIP-seq_p14_ehom_ip2


title: placenta villi, early pregnancy snRNA, donor6 [8w-rna-6]

description: 10X Genomics

value: healthy placenta


title: ChIP-seq_p14_ehom_input1


title: CF subject 2, uninfected

value: no virus


title: CF subject 1, 72 hours post-infection

value: 72 hours post-infection with RSV


title: placenta villi, early pregnancy snRNA, donor4 [8w-rna-4]

description: 10X Genomics


title: ChIP-seq_p14_ehom_ip1

value: Retina

value: Post-natal day 14


title: CF subject 1, 48 hours post-infection

value: CF

value: 48 hours post-infection with RSV


title: ChIP-seq_p14_wt_input2

value: WT


title: CF subject 1, 24 hours post-infection

value: 24 hours post-infection with RSV


title: placenta villi, early pregnancy snRNA, donor3 [8w-rna-3]

description: 10X Genomics


title: E11.5 -/-_MR

description: Gene expression data from KO hematopoietic progenitor cells cultured with M-CSF and RANKL

hyb_protocol: Fragmented and labeled ss cDNA was hybrydized with the array for 16 hours at 45 oC in a GeneChip Hybrydization Oven 645. The array was washed with GeneChip Fluidics Station 450.

scan_protocol: The array was stained, and scanned with GeneChip Scanner 3000 7G.

data_processing: Data was processed through GeneChip Command Console 4.0. Expression data from CEL files were normalised by RMA method with R packages.

label: Biotin

source_name: Hematopoietic progenitor cells from E11.5

label_protocol: Briefly, 250 ng of total RNA was lebeled using GeneChip WT Plus Reagent Kit. Both of poly (A) and non-poly (A) mRNA were reverse-transcribed for unbiased transcript coverage. cDNA was amplified by DNA ploymerase, followed by in vitro transcription by T7 RNA polymerase. Next, single strand cDNA was synthesized by reverse transcription of cRNA. Template RNA was removed by RNaseH, which was labled with biotin.

growth_protocol: Fetal liver and AGM were disected from Nfatc1 ex1 KO mice at E11.5, and then dissociated into cells. At first, the suspension was cultured for 20 days on fibronectin-coated 48 well plates. Next, prolifeating cells were collected, and seeded in a new 48 well plate for osteoclast differentiation.

extract_protocol: The total RNA was extracted on day 27 using RNeasy Micro Kit.

treatment_protocol: Hematopoietic progenitor cells were cultured in serum-free HemEx Type-9A medium supplemented with SCF and TPO. Then, the cells were cultured in a-minimum essential medium containing 10% fetal bovine serum, M-CSF, abd RANKL.

value: Nfatc1 ex1 -/-

tag: Stage

tag: cells

value: Hematopoietic progenitor cells

tag: treatment

value: M-CSF, RANKL


title: placenta villi, early pregnancy snRNA, donor2 [8w-rna-2]

description: 10X Genomics

tag: tissue


title: CF subject 1, 12 hours post-infection

value: lung


title: E11.5 +/+_MR

description: Gene expression data from WT hematopoietic progenitor cells cultured with M-CSF and RANKL

value: Nfatc1 ex1 +/+


title: ChIP-seq_p14_wt_ip2

value: anti-CRX


title: placenta villi, early pregnancy snRNA, donor1 [8w-rna-1]

description: 10X Genomics

tag: time point

value: early pregnancy


title: E11.5 -/-_M

description: Gene expression data from KO hematopoietic progenitor cells cultured with M-CSF

tag: genotype

value: M-CSF


title: ChIP-seq_p14_khom_ip1


title: ChIP-seq_p14_wt_input1


title: placenta villi, early pregnancy snRNA, donor5 [8w-rna-5]

description: 10X Genomics

value: healthy placenta


title: CF subject 1, 120 hours post-infection

value: 120 hours post-infection with RSV


title: CF subject 1, uninfected

value: no virus


title: E11.5 +/+_M

description: Gene expression data from WT hematopoietic progenitor cells cultured with M-CSF


title: ChIP-seq_p14_wt_ip1

value: Retina


title: STB-FOSL2-IgG, CUT&TAG, control

data_processing:
We used FastQC v0.11.9 to estimate the quality of fastq files and trim_galore v0.6.7 to filter low quality reads if necessary.
We applied bowtie2 (v2.4.2) with default parameters for raw fastq reads mapping to human (hg38) reference genome and used MACS2 to call peaks for CUT&Tag and ChIP-seq datasets. We used the ‘reduce’ function from the R package GenomicRanges for merge of peaks of each replications. Then we intersected and counted overlap peaks from CUT&Tag and previous eGRN  peaks which were assigned to nearby gene by peak to gene links. We quantitatively summarized the validation result by overlap percentage of these two peak sets. Finally we visualized the regulatory events with CUT&Tag, ChIPseq tracks and eGRN TF target peaks tracks for two genes (FLT1 and EGLN3) within the eGRN target gene list.
Assembly: hg38
Supplementary files format and content: narrowPeak (except for IgG and input)
Library strategy: CUT&TAG

growth_protocol: The culture of human trophoblast stem cell lines was performed as previously described. Briefly, the plate was coated with 5 μg/ml Collagen I (Cat#354233, Corning) at 37℃ at least for 1 h. hTSCs were cultured in hTSCs medium (DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.2% FBS, 0.5% Penicillin-Streptomycin, 0.3% BSA, 1% ITS-X supplement, 1.5 μg/ml L-ascorbic acid, 50 ng/ml EGF, 2 μM CHIR99021, 0.5 μM A83-01, 1 μM SB431542, 0.8 mM VPA and 5 μM Y27632). hTSCs were dissociated with TrypLE for 8 min at 37℃ and the cells were passaged to a new Collagen I-coated plate. hTSCs were routinely passaged every 4-5 days at a 1: 4-1: 6 ratio.

extract_protocol:
For ChIP-seq sample extraction, hTSCs-BL and STB-BL cells were dissociated with TrypLE for 8 min at 37℃ and washed with phosphate buffer solution for 3 times. About 5 × 106 cells were used for cross-linking by 1% formaldehyde. After rotating at room temperature for 10 min, the crosslinking was quenched by 125 mM Glycine and rotated for 10 min at room temperature. The crosslinked cells were quick-froze with liquid N2.
For CUT&Tag sample extraction, STB-BL cells were dissociated with TrypLE for 8 min at 37℃ and washed with phosphate buffer solution. About 5 × 104 cells were resuspend with wash buffer.
The experiment of ChIP-seq was performed as previously described (A selective WDR5 degrader inhibits acute myeloid leukemia in patient-derived mouse models). Briefly, about 5 × 106 hTSCs-BL and STB-BL were used for cross-linking by 1% formaldehyde and quenched by 125 mM glycine. Cells were lysed and nuclei were sonicated and diluted to a final concentration of 0.1% by SDS. Protein A/G magnetic beads were added and incubated at 4°C for 1 h. Pre-cleared chromatin was incubated with CEBPB antibody (Cat#23431-1-AP, Proteintech) or monoclonal rabbit isotype control (Cat#ab172730, Abcam) overnight at 4°C. Then Protein A/G magnetic beads were added to capture the specific chromatin complexes. The supernatants were collected with 500 mM NaCl and incubated at 65 °C overnight for reverse crosslinking. Sample was incubated at 37°C for 1 h with RNase A, and was incubated at 50°C for 1 h with proteinase-K. The released DNA was purified by the QIAquick PCR purification Kit and processed to sequencing library preparation. Multiplexed ChIP-seq libraries were prepared by NEBNext Ultra II DNA Library Prep Kit (Cat#E7645S, NEB). The final libraries and multiplexed libraries were subjected to Illumina Sequencing 2500 platforms.For CUT&Tag,the experiment was conducted according to the instructions provided by Vazyme (Cat#TD904). In brief, approximately 5 × 104 cells were harvested and counted, then mixed with activated ConA Beads and incubated overnight with primary antibodies (CEBPB, Cat#23431-1-AP, Proteintech and FOSL2, Cat#351814, USBiological). The secondary antibody (Cat#Ab207, Vazyme) was incubated at room temperature (RT) with rotation for 1 hour. After removing the supernatant, pA/G-Tnp Pro and TTBL were separately incubated with rotation at RT and 37℃ for 1 hour. The supernatant was then mixed with DNA Extract Beads Pro to dissolve DNA with ddH2O and used directly for PCR amplification. Subsequently, VAHTS DNA Clean Beads were added to purify the DNA, which was then subjected to next-generation sequencing using the Illumina NovaSeq 6000 platform.

tag: cell line

value: STB-BL

value: hTSC derived syncytiotrophoblast cell


title: STB-FOSL2, CUT&TAG, rep3


title: RNA-seq_p21_rhom_rep3

data_processing:
Sequencing reads were first run through Trim Galore (v0.6.1) to remove adapter sequences.
Trimmed reads were then mapped to the mm10 genome and quantified with kallisto (v0.46.2).
Kallisto output transcript-level abundance matrices were then imported and summarized into gene-level matrices with R package tximport (v1.18.0).
Assembly: mm10
Supplementary files format and content: Tsv file with raw counts by gene

extract_protocol:
For each genotype, three biological replicates, two retinas per replicate from one male and one female mouse were harvested and flash frozen in Trizol reagent. All retinas were processed for RNA simultaneously using TRIzol™ Reagent following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Post-natal day 21


title: RNAseq data for shMed30-3 in GSC3565, replicate #3

city: La Jolla

first: Guofeng

last: Zhao

address: 9500 Gilman Dr.

department: Medicine

institute: UCSD

data_processing: Following sequencing, quality control with FastQC and trimming of adaptor sequence and poly-A tails with Trim Galore, reads were mapped and assigned to the human transcripts using HISAT2. The counts file was generated by “featureCounts” on Galaxy (usegalaxy.org) with build-in genome hg38. Differential expression gene (DEG) analysis was performed using the DESeq2 package in Galaxy.

extract_protocol: RNA was extracted by Trizol (Life Technologies) RNA concentration and quality was quantified by Qubit and Agilent 2100 Bioanalyzer system, respectively. Libraries were generated using NEBNext Ultra II RNA Kits (NEB) and sequenced on the NovaSeq 6000 with 100 bp paired-end reads.


title: STB-FOSL2, CUT&TAG, rep2


title: RNAseq data for shMed30-3 in GSC3565, replicate #2


title: RNAseq data for shMed30-3 in GSC3565, replicate #1


title: 04_6F4_Scr_3

city: Regensburg

first: Uwe

last: Schwartz

address: Universitätstraße 32

department: NGS Analysis Center

institute: University of Regensburg

description: Ago2 IP scrambled LNA

hyb_protocol: 2.5 to 3.8 µg fragmented and labeled ss cDNA were hybridized to Affymetrix Clariom S mouse arrays for 16 h at 45° C and 60 rpm in a GeneChip hybridization oven 640.

scan_protocol: Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G.

data_processing: Microarray analysis was conducted using the oligo package. Briefly, probe intensities were normalized using the RMA function and only probes exhibiting intensities greater than 5 in at least two IP samples, were kept for further analysis.

label: biotin

source_name: Mus musculus septum Ago2 IP scrambled

label_protocol: Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.

growth_protocol: Male CD1 or male OXT receptor-Cre mice, both 8-9 weeks of age at the start of the experiment, were group-housed under standard temperature- and humidity-controlled conditions with tap water and standard laboratory diet ad libitum.

extract_protocol: Septal Ago2 was pulled down by means of Argonaute-co-immunoprecipitation (6F4 hybridoma, anti-mAGO2 antibody) using protein G beads.

treatment_protocol: To determine a target of miR-132-3p, miR-132-3p inhibitor or scrambled LNA was infused into the septum of male mice and tissue was punched 2 days thereafter.

value: Septum

tag: Sex

value: Male

tag: lna

value: Scrambled

tag: antibody

value: 6F4 hybridoma, anti-mAGO2


title: 06_6F4_Inh_3

description: Ago2 IP miR132-3p Inhibitor

source_name: Mus musculus septum Ago2 IP inhibitor

value: miR132-3p Inhibitor


title: STB-FOSL2, CUT&TAG, rep1


title: 02_N_Inh_3

description: Input miR132-3p Inhibitor

source_name: Mus musculus septum Input inhibitor


title: 05_6F4_Inh_2

description: Ago2 IP miR132-3p Inhibitor


title: 03_6F4_Scr_1

description: Ago2 IP scrambled LNA


title: RNA-seq_p21_rhom_rep1


title: STB-CEBPB-IgG, CUT&TAG, control


title: RNAseq data for shMed30-1 in GSC3565, replicate #3


title: STB-CEBPB, CUT&TAG, rep3


title: CB15 CbK_tgrL overexpression (replicate #1)

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
Paired reads were mapped to CP001340.1 genome with CLC Genomics Workbench 20.
Read count extraction and normalization were performed using CLC Genomic Workbench
Assembly: CP001340.1 (Caulobacter crescentus)
Supplementary files format and content: csv

organism: Caulobacter vibrioides CB15

growth_protocol: Strains grown at 30°C in PYE

extract_protocol:
Cell pellets were resuspended in 1ml TRIzol, then stored at -80°C. Samples were heated at 65°C for 10 min. 0.2 ml chloroform was mixed into samples and incubated for 5 min. Samples pelleted at 17,000xg for 15 min at 4°C. Aqueous layer transferred to fresh tube. 450 µl isopropanol was added and stored at -80°C overnight. Thawed samples were pelleted at 4°C for 30 min, then supernatant was removed. Pellets were washed in 1 ml 70% ethanol, dried, and resuspended in 100 µl RNase-free H2O. Samples were cleaned up with RNeasy Mini Kit (QIAGEN).
Samples were DNAse treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices. Sequencing was done on a NextSeq2000 giving 2x51bp reads. Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v3.9.3)

treatment_protocol: Cultures were induced with 50 µM cumate and harvested at 0.18-0.26 OD660

value: Caulobacter vibrioides CB15

value: CB15 xylX::pMM020 (pPTM057-CbK_tgrL)

value: Expression induced with 50 µM cumate


title: RNAseq data for shMed30-1 in GSC3565, replicate #1


title: CB15  empty vector (replicate #3)

value: CB15 xylX::pPTM057 (EV)


title: RNA-seq_p21_khom_rep2


title: STB-CEBPB, CUT&TAG, rep2


title: CB15 CbK_tgrL overexpression (replicate #2)


title: RNA-seq_p21_khom_rep3


title: 01_N_Scr_1

description: Input scrambled LNA

source_name: Mus musculus septum Input scrambled


title: STB-CEBPB, CUT&TAG, rep1


title: CB15  empty vector (replicate #2)


title: RNAseq data for shMed30-1 in GSC3565, replicate #2


title: RNA-seq_p21_khom_rep1


title: RNA-seq_p21_rhom_rep2


title: RNA-seq_p21_khet_rep2


title: RNAseq data for shctrl in GSC3565, replicate #3


title: RNA-seq_p21_khet_rep3


title: CB15  empty vector (replicate #1)


title: RNA-seq_p21_khet_rep1


title: CB15 CbK_tgrL overexpression (replicate #3)


title: RNAseq data for shctrl in GSC3565, replicate #1


title: BT-549-Spheroid_MUC1.kd

city: Buffalo

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: BT-549 TNBC cells

extract_protocol:
Freshly collected Spheroids were dissociated and subject to scRNA-seq
Library was performed according to the manufacter’s instructions (Single Cell 5' R2-only v2 protocol, 10x Genomics).

value: BT-549 TNBC cells

tag: condition


title: BT-549-Spheroid_CTL

description: 10x Genomics

value: CTL


title: SPA-3

city: Montréal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 0 mismatch in the index for paired-end samples, and 0 mismatch for the single read samples.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 26 (based on Ensembl 88)
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned

source_name: cell line

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

value: cell line

value: acute myeloid leukemia


title: 4SA-TAZ_rep2

city: Worcester

first: Jennifer

last: Benanti

state: MA

address: 364 Plantation St. LRB525

department: Molecular, Cell & Cancer Biology

institute: UMass Medical School

data_processing:
RNA-seq reads were aligned to the human reference genome GRCh38/hg19 by using Tophat2 (version 2.1.1) with minimal and maximal intron length set as 20 bp and 100 kb, respectively.
The resulting BAM files were sorted by name using samtools (1.4.1) and processed by using MMR to assign multi-mapper reads to their most likely genomic locations.
The BAM files output by MMR were input to featureCounts (version 1.5.3) to generated a gene-level count summary table with the following explicit option settings –d 35 –t exon –M and the GTF file for the reference genome GRCh38.89 as the genome annotation file.
Genome_build: hg38
Supplementary_files_format_and_content: raw count table in a matrix format: column 1 is the GeneID; the others are raw count per gene generated by featureCounts.

growth_protocol: Cells were cultured  in DMEM/F12 supplemented with insulin, Transferrin, Sodium Selenite, Estradiol, Hydrocortisone, Prolactin and EGF.

extract_protocol:
RNA was extracted using RNA isolation kit.
Library for RNA-Seq was prepared according to KAPA Stranded mRNA-Seq  poly(A) selected kit with 300bp insert size (KAPA Biosystems, Wilmington, MA) using 250 ng total RNAs as input.
Final library quality and quantity was analyzed by Agilent Bioanalyzer 2100 and Life Technologies Qubit3.0 Fluorometer. 150 bp paired end reads were sequenced on Illumina HighSeq 4000 (Illumnia Inc., San Diego, CA).

treatment_protocol: Cells  were transfected with vector or 4SA-TAZ and stable population was selcted using puromycin for 4 days.

value: Epithelial-like, non-tumorigenic human Mammary cells

tag: transfected with


title: Vector _rep2

value: vector


title: 4SA-TAZ_rep1


title: SPA-2


title: RNA-seq_p21_ehom_rep1

value: Retina


title: Vector_rep1


title: RNA-seq_p21_ehet_rep3

value: Post-natal day 21


title: SPA-1


title: RNA-seq_p21_ehet_rep1


title: CT-2

value: 0.1% DMSO


title: RNA-seq_p21_wt_rep2

value: WT


title: CT-1


title: RNA-seq_p21_wt_rep3


title: AZA-3

value: AZA +0.1% DMSO


title: RNA-seq_p21_ehom_rep3


title: AZA-2


title: RNA-seq_p21_wt_rep1


title: RNA-seq_p10_rhom_rep3

value: Post-natal day 10


title: RNA-seq_p21_ehom_rep2


title: cardiomyocytes, irisin knockout 2

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from the myocardium of an irisin knockout animal.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.61.0), using R version 3.6.0 and the Brainarray mogene20stmmentrezgcdf R package (version 17.0.0).

source_name: cardiomyocytes

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Transgenic knockout mice and their litter mate controls were bred and maintained at Rhode Island Hospital of Brown University.  Mice were fed with standard chow (10% fat, 70% carbohydrate and 20% protein, New Brunswick, NJ) for 24 weeks. All animals had as needed access to chow and water and were housed in a temperature-controlled room (22°C) on a 12-h light-dark cycle.

extract_protocol: Total RNA was extracted with TRIzol reagent (Life Technologies, Grand Island, NY).

treatment_protocol: CRISPR/Cas9 irisin knockout mice were generated from the transgenic core of Harvard University (Boston, MA). Zygotes were injected with a mixture of Cas9 mRNA (20 ng/ml) and five sgRNAs (5 ng/ml each). Microinjections were carried out in the cytoplasm of zygotes using a Nikon microinjection system under standard conditions. FVB mice were used as oocyte donors. Superovulated female FVB mice (6 weeks old) were mated to FVB stud males, and superovulated female homozygote FVB (12-18 grams) were then mated to hemizygote FVB stud males. Zygotes were harvested and kept in M16 medium (Brinster’s medium for ovum culture with 100 U/ml penicillin and 50 mg/ml streptomycin) at 37oC for 1 hour. Zygotes were transferred to M2 medium (M16 medium and 20 mM HEPES). The mixture of Cas9 mRNA and sgRNAs was injected into the pronucleus and cytoplasm. Injected zygotes were cultured in M16 medium for 1 hour at 37oC and then transferred into the oviducts of pseudopregnant FVB female mice.

value: FVB

value: cardiomyocytes

value: irisin knockout


title: AZA-1


title: RNA-seq_p10_rhom_rep2


title: Ribo-Seq KDM5 Knockdown Input 2

city: Bronx

first: Matanel

last: Yheskel

address: 1300 Morris Park

department: Genetics

institute: Albert Einstein College of Medicine

data_processing:
R
Reads were trimmed using fastp
Reads were aligned using Rsubread (RNA-Seq) or RNA-STAR (Ribo-Seq)
Counts were obtained using featureCounts (RNA-Seq) or ORFik (Ribo-Seq)
Differential expression analysis was performed with DESeq2
Assembly: dm6
Supplementary files format and content: RNA-Seq comma separated values (csv) of raw counts
Supplementary files format and content: Ribo-Seq differential expression analyses using the R package ORFik.
Library strategy: Ribo-Seq

organism: Drosophila melanogaster

source_name: heads

growth_protocol: Flies were kept at 25℃ with a 12-hour light/dark cycle and 50% humidity. All flies were collected or harvested 1-5 days after eclosion from 9AM-12PM

extract_protocol:
Trizol/chloroform followed by precipitation using isopropanol
TruSeq Stranded mRNA Library Preparation Kit.

value: heads

value: neurons


title: A_S-3


title: RNA-seq_p21_ehet_rep2


title: Ribo-Seq KDM5 Knockdown Input 3


title: RNA-seq_p10_rhom_rep1


title: cardiomyocytes, irisin knockout 1


title: CT-3


title: A_S-2


title: cardiomyocytes, irisin knockout 3


title: cardiomyocytes, wild type 3

description: Gene expression data from the myocardium of a wild type animal.

value: wild type


title: Ribo-Seq KDM5 Knockdown Input 1


title: cardiomyocytes, wild type 2


title: RNA-seq_p10_khom_rep3


title: A_S-1


title: Ribo-Seq KDM5 Knockdown IP 3


title: Ribo-Seq KDM5 Knockdown IP 2


title: RNA-seq_p10_khom_rep2


title: 3_THP1_CT

value: Untreated


title: 3_THP1_AZA

value: cell line

value: AZA


title: RNA-seq_p10_khet_rep3


title: Ribo-Seq Ctl Input 3


title: 3_SKM1_CT

value: acute myeloid leukemia


title: cardiomyocytes, wild type 1


title: Ribo-Seq Ctl Input 2


title: RNA-seq_p10_khet_rep1


title: RNA-seq_p10_ehom_rep3


title: Ribo-Seq Ctl Input 1


title: 3_OCIAML3_AZA


title: RNA-seq_p10_ehom_rep1


title: 3_OCIAML3_CT


title: RNA-seq_p10_ehom_rep2


title: 3_SKM1_AZA


title: Ribo-Seq Ctl IP 2


title: RNA-seq_p10_khom_rep1


title: Ribo-Seq KDM5 Knockdown IP 1


title: 3_MOLM13_CT


title: RNA-seq_p10_ehet_rep3


title: 2_THP1_CT


title: KDM5 Y874C 3

description:
Y874C_3
counts.csv

data_processing:
R
Reads were trimmed using fastp
Reads were aligned using Rsubread (RNA-Seq) or RNA-STAR (Ribo-Seq)
Counts were obtained using featureCounts (RNA-Seq) or ORFik (Ribo-Seq)
Differential expression analysis was performed with DESeq2
Assembly: dm6
Supplementary files format and content: RNA-Seq comma separated values (csv) of raw counts
Supplementary files format and content: Ribo-Seq differential expression analyses using the R package ORFik.


title: KDM5 Y874C 2

description:
Y874C_2
counts.csv


title: 3_MOLM13_AZA


title: 2_THP1_AZA


title: 2_SKM1_CT


title: RNA-seq_p10_ehet_rep1


title: KDM5 Y874C 1

description:
Y874C_1
counts.csv


title: RNA-seq_p10_ehet_rep2


title: RNA-seq_p10_khet_rep2


title: Ribo-Seq Ctl IP 3


title: KDM5 R873W 3

description:
R873W_3
counts.csv


title: 2_SKM1_AZA


title: RNA-seq_p10_wt_rep2


title: Ribo-Seq Ctl IP 1


title: RNA-seq_p10_wt_rep1


title: 2_OCIAML3_AZA


title: KDM5 R873W 1

description:
R873W_1
counts.csv


title: KDM5 R873W 2

description:
R873W_2
counts.csv


title: KDM5 L854F 3

description:
L854F_3
counts.csv


title: 2_MOLM13_CT


title: KDM5 L854F 2

description:
L854F_2
counts.csv


title: KDM5 L854F 1

description:
L854F_1
counts.csv


title: 2_MOLM13_AZA


title: CD45+Ter119- cells from bone marrow of 2208L tumor-bearing mice

city: Houston

first: Xiang

last: Zhang

state: Texas

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
The mm10 genome was used for reads mapping. Raw sequencing files were imported into 10x Genomics Cell Ranger toolkit (v3.1.0) with default settings for quantifications.
Assembly: mm10
Supplementary files format and content: Compressed .gz files contains the filtered_feature_bc_matrix output folder from Cellranger. Each .gz file contains a .mtx file which is the count matrix and two .tsv files that list the feature names and sample annotations.

source_name: 2208L tumor-bearing

extract_protocol:
PB was collected by retro-orbital sampling. To isolate the BM cells, the muscle tissue on the tibia and femur were completely removed, BM cells were flushed out with PBS(2%FBS) from long bone (tibia and femur) and filtered through a 70 µm strainer. red blood cells are depleted by resuspending BM cells in RBC lysis buffer (Tonbo). For each group, cells were sampled from five mice and pooled into one, then stained with DAPI, CD45-APC and TER-119-VF450. To get rid of erythroid cells, DAPI-CD45+TER119- singlet cells were purified by fluorescence-activated cell sorting (FACS)orted into single-cell suspension and immediately submitted to the Single Cell Genomics Core at Baylor College of Medicine.
The single-cell gene expression Library was prepared according to the Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics). In brief, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on the Chromium controller (10x Genomics) to generate single-cell GEMS (Gel Beads-In-Emulsions) where full-length cDNA was synthesized and barcoded for each single cell. Subsequently, the GEMS are broken and cDNA from each single cell is pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR. The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. The final library was generated by amplification. The libraries that passed the quality control, were sequenced by the NovaSeq 6000 (Illumina).

value: Bone marrow

value: BALB/c

tag: inoculated tumor cell line


title: RNAseq data for shctrl in GSC3565, replicate #2


title: CD45+Ter119- cells from bone marrow of T12 tumor-bearing mice

source_name: T12 tumor-bearing


title: CD45+Ter119- cells from bone marrow of T11 tumor-bearing mice

source_name: T11 tumor-bearing


title: CD45+Ter119- cells from bone marrow of Naïve BALB/c mice

source_name: Tumor-free


title: 1_THP1_AZA


title: 1_SKM1_CT