title: MGT703#2

status: Public on Apr 30 2024

type: SRA

city: Buk-gu

first: Chan-Ho

last: Lee

address: Yongbongro 77

department: Animal Science

country: South Korea

institute: Chonnam national university

description: MGT 703#2

library_source: transcriptomic

data_processing:
Potentially existing sequencing adapters and raw quality bases in the raw reads were trimmed by Skewer ver 0.2.2.
The cleaned high quality reads after trimming the low quality bases and sequencing adapters were mapped to the reference genome by STAR ver 2.5 software.
Since the sequencing libraries were prepared strand-specifically by using Illumina’s strand-specific library preparation kit, the strand-specific library option, --library-type=fr-firststrand was applied in the mapping process.
To quantify the mapped reads on the reference genome in to the gene expression values, Cuffquant in Cufflinks ver 2.2.1 with the strand-specific library option,--library-type=fr-firststrandand other default options was used.
The gene annotation of the reference genome canfam3 from UCSC genome (https://genome.ucsc.edu) in GTF format was used as gene models and the expression values were calculated in Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) unit.
Assembly: canfam3
Supplementary files format and content: text files include RPKM values for each Sample

molecule: total RNA

organism: Canis lupus familiaris

growth_protocol: MGT cells were maintained in DMEM/F-12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using hybrid-R (GeneAll). 1 ug of total RNA was used processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI)   according to manufacturer’s instruction
RNA libraries for RNA-seq were prepared using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.

tag: cell line


title: MGT421#1

description: MGT 421#1


title: MGT506#3

description: MGT 506#3


title: MGT612

description: MGT 612


title: MGT316

description: MGT 316


title: MGT408#2

description: MGT 408#2


title: MGT122

description: MGT 122


title: MDCK

description: MDCK

source_name: MDCK

value: MDCK


title: TP53 K/O fibroblast

description: TP53 K/O fibroblast

source_name: TP53 K/O fibroblast

value: TP53 K/O fibroblast


title: NK cells, cultured, d5, rep2, IP sample

city: Esch-sur-Alzette

first: Sebastian

last: Scheer

address: 29, rue Henri Koch

department: Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

library_source: genomic

data_processing:
Raw paired end fastq files were aligned to the UCSC mm10 genome with Bowtie2 (parameters: --no-mixed --no-discordant -X 1000)
Aligned bam files were then filtered to remove reads in black-listed regions, duplicate reads were marked using Picard MarkDuplicates
Bam files were filtered again to remove low quality reads (samtools view -q 10 -F 1800)
Bamcoverage was applied on Bam files
Assembly: UCSC mm10
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Mus musculus

source_name: spleen

growth_protocol: Splenic NK cells isolated with STEMCELL NK cell isolation kit; cultured in IMDM (10% FCS), P/S, Glutamax, β-ME for 5 days.

extract_protocol:
2 µg of anti-H3K79me2 (ab3594) was used to perform ChIP. DNA was purified using the NucleoSpin Gel and PCR Clean-up kit according to the manufacturer's specifications
MGITech MGIEasy DNA FS Library preparation kit V3 (according to the manufacturer's instructions: document revision A0)

tag: tissue

value: spleen

tag: chip antibody

tag: cell type

value: NK cell

tag: genotype

value: WT

tag: treatment

value: IMDM (10% FCS) + 50 ng/ml IL-15


title: NK cell, cultured, d5, knockout, rep3

description: column 7

data_processing:
Raw paired end fastq files were aligned to the UCSC mm10 genome with RNAStar, followed by featureCounts and DESeq2 (standard parameters)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: enriched splenic NK cells

growth_protocol: cultured for 5 days in complete IMDM containing 50 ng/ml recombinant human IL15

extract_protocol:
Macherey Nagel NucleoSpin RNA kit according to manufacturer's instructions
MGIEasy V3 chemistry

value: enriched splenic NK cells

value: NK cells

value: DOT1L KO

value: 5 days in culture (50 ng/ml IL-15)


title: NK cells, cultured, d5, rep2, input

value: no primary


title: NK cell, cultured, d5, knockout, rep1

description: column 5


title: NK cells, cultured, d5, rep1, input


title: NK cell, cultured, d5, knockout, rep2

description: column 6


title: NK cell, cultured, d5, wild type, rep3

description: column 4


title: splenic sorted NK cells, knockout, d2 MCMV, rep1

description: column 10

data_processing:
Raw paired end fastq files were aligned to the UCSC mm10 genome with RNAStar, followed by featureCounts and DESeq2 (standard parameters)
Assembly: UCSC mm10
Supplementary files format and content: tab-delimited text files include CPM values for each sample

source_name: sorted splenic NK cells

extract_protocol:
bulk RNA was isolated from sorted, splenic NK1.1+ CD3/TCRβ- Ly49H+ cells using the Nucleospin RNA isolation kit
MGIEasy V3 chemistry

value: sorted splenic NK cells

value: NK cells (Ly49H+)

tag: time

value: NK cell enrichment followed by FACS sort for Ly49H+ NK1.1+ CD3-


title: splenic sorted NK cells, knockout, d2 MCMV, rep3

description: column 12


title: NK cell, cultured, d5, wild type, rep1

description: column 2


title: MGT414#2

description: MGT 414#2


title: splenic sorted NK cells, wild type, d2 MCMV, rep1

description: column 8


title: splenic sorted NK cells, knockout, rep3

description: column 7


title: splenic sorted NK cells, wild type, rep1

description: column 2


title: NK cell, cultured, d5, wild type, rep2

description: column 3


title: NK cells, cultured, d5, rep1, IP sample


title: splenic sorted NK cells, knockout, d2 MCMV, rep2

description: column 11


title: splenic sorted NK cells, wild type, d2 MCMV, rep2

description: column 9


title: splenic sorted NK cells, knockout, rep2

description: column 6


title: PT286-PLM rep1

city: Hefei

first: Bingbing

last: Ren

state: Anhui

address: University  of  Science  and  Technology  of  China,  443  Huangshan  Road, Hefei, Anhui

country: China

data_processing:
Libraries were sequenced using PE150 (Pair End 150bp) on an Illumina HiSeq 6000 instrument (Novogene, China). Low quality reads (one end low quanlity base > 50%), N-containing reads (unidentified reads ratio > 0.002) and reads with adapters are removed from the raw data to generate clean reads for further analysis.
Clean reads were mapped onto the fission yeast genome released on Pombase using HISAT2
The expressions of mRNA and lncRNA were evaluated with Stringtie followed by the annotation references
Genome_build: reference sequence based on Pombase(https://www.pombase.org/)

organism: Schizosaccharomyces pombe

growth_protocol: Strain PT286 was grown at 30℃ to mid-log phase in YES medium.

extract_protocol:
Total RNA was extracted from harvested cells using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For the stress experiments, cells were cultured in YES medium and harvested at 16h. Then changed medium to induce stress and harvested at 8h after addition of different DNA damage-inducing agents to the culture. Different DNA damage conditions were induced as follows. Camptothecin (APExBIO) was added to a fifinal concentration of 20 μM. Hydroxyurea (Sigma) was added to a fifinal concentration of 10 mM. Methyl methanesulfonate (Sigma) was added to a fifinal concentration of 0.02%. Phleomycin (APExBIO) was added to a fifinal concentration of 5 μg/mL.

value: treated with phleomycin (5 ug/mL) for 8h

tag: strain


title: PT286-HU rep1

institute: University of Science and Technology of China

value: treated with hydroxyurea (10 mM) for 8h


title: PT286-CPT rep2

value: treated with camptothecin (20 uM) for 8h


title: PT286-MMS rep1

value: treated with methyl methanesulfonate (0.02%) for 8h


title: splenic sorted NK cells, wild type, rep2

description: column 3


title: PT286-WT rep2

value: untreated


title: PT286-MMS rep2


title: PT286-HU rep2


title: splenic sorted NK cells, knockout, rep1

description: column 5


title: splenic sorted NK cells, wild type, rep3

description: column 4


title: H7.0-24

city: Shanghai

first: Yihong

last: Chen

state: China

address: Department of Cardiology, Shanghai Changzheng Hospital, Second Military Medical University, No. 415, Fengyang Road, Huangpu District

department: Department of Cardiology

data_processing:
cDNA library construction and sequencing were performed with BGISEQ-500 platform.
Raw reads were filtered with software SOAPnuke v1.5.2. In brief, 1) Remove reads with adaptors; 2) Remove reads in which unknown bases(N) are more than 10%; 3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 15 is greater than 50% in a read).
Clean reads were aligned to the human reference genome (GRCh37) using Bowtie2 v2.2.5 with parameters (-q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1 ,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200). The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM) using RNA-seq by Expectation Maximization (RSEM).
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel files include the FPKM values for each sample.

organism: Homo sapiens

source_name: Palpebral adipose tissues

growth_protocol: The stem cells were isolated from human adipose tissues and cultured with DMEM/F12 plus 10% FBS and 1% Penicillin Streptomycin (complete medium,pH=7.4) .

extract_protocol:
The RNA samples were harvested with Trizol reagent after discarding the medium .Then ,the total RNA was isolated with chloroform and isopropanol. At last, the total RNA was dissolved in RNase-free water.
Briefly, the protocol was as below: 1)mRNA enrichment: Oligo dT Selection or rRNA depletion;2)RNA fragment and reverse transcription: Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer;3)End repair, add A tailing and adaptor ligation:The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments;4)PCR amplification:The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer;5)Denature and cyclization:Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase;6) Sequencing on BGISEQ-500 platform.

treatment_protocol: The second day of  seeding  cells in the culture wells as normal way, the complete medium was changed  with different pH  conditions (pH=7.4/7.2/7.0/6.5) as  treatments. All the treatments were  kept for 24/48 h.

value: Adipose-derived stem cells

tag: passages

tag: Sex

value: Female

tag: ph

tag: time point


title: H6.5-24

institute: Department of Cardiology, Shanghai Changzheng Hospital


title: PT286-PLM rep2


title: TG_H, snRNAseq

city: Beijing

first: Jiakun

last: Miao

address: No. 2 Yuanmingyuan West Road

department: Institute of Animal Science

institute: Chinese Academy of Agricultural Sciences

description: 10× Genomics

library_source: transcriptomic single cell

data_processing:
Reads were mapped to the Sscrofa11.1 reference genome (Ensembl release104, http://asia.ensembl.org ) using the 10× Genomics Cell Ranger software (version 3.1.0) with default parameters.
After mapping, UMI sequences were corrected for sequencing errors, with empty droplets removed according to the EmptyDrops method. The cell by gene matrices were produced via UMI counting and cell barcodes calling. The cell by gene matrices for each sample were individually imported to Seurat (version 3.1.1) for downstream analysis.
Cells with the following criteria were filtered out: (1) unusually high number of UMIs (≥ 8000) (2) percentage of mitochondrial genes ≥ 10% (3) genes fewer than 500 or more than 4000 (4) doublet GEMs. We utilized the DoubletFinder tool (version 2.0.3) to filter doublet GEMs.
After removing unwanted cells from the dataset, we employed a global-scale normalization method "LogNormalize" to normalize the gene expression measurements of each cell to the total expression
Assembly: Sscrofa11.1 reference genome (Ensembl release104, http://asia.ensembl.org )
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

organism: Sus scrofa

source_name: heart(myocardium)

extract_protocol:
Frozen heart tissue from the left ventricular free wall was minced with a blade and transferred to a Dounce homogenizer containing 500 µl of chilled lysis buffer. Samples were gently homogenized five to ten times without rotation, then incubated on ice for 5 minutes. A 700 µl lysis buffer was added to the lysate and filtered gently through a 70 µm filter into a 50 ml centrifuge tube. Then 1 ml 50% of iodixanol was added to the filtrate and mixed gently. A total of 2 ml of the nuclei suspension was transferred into a 15 ml centrifuge tube containing 3 ml of chilled iodixanol gradient solution (1 ml 33% iodixanol, 2 ml 30% iodixanol). Nuclei were recovered after centrifugation and resuspended gently in wash buffer, followed by counting on a hemocytometer.
Nuclei were processed with the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 from 10× Genomics. In brief, cellular suspensions were loaded on a 10× Genomics GemCode Single-cell instrument to generate single-cell Gel Bead-In-EMlusion (GEMs). After dissolution of the Gel Bead in a GEM, reverse transcription, barcoding, complementary DNA amplification and purification for sequencing libraries preparation was performed according to the Single Cell 3' protocol.

value: heart(myocardium)

tag: tissue region

value: left ventricular free wall

value: triple-transgenic Bama pig

value: 12 months high-fat-high-sucrose diet intervention


title: WT_H, snRNAseq

description: 10× Genomics

value: wild-type Bama pig


title: PT286-CPT rep1


title: PT286-WT rep1


title: H6.5-48


title: AP7357

city: L'Hospitalet de Llobregat

first: Isabel

last: Fabregat

state: Barcelona

address: Avinguda de la Granvia de l’Hospitalet, 199

department: Oncobell Program

country: Spain

institute: Bellvitge Biomedical Research Institute - IDIBELL

data_processing:
RNA-seq reads were mapped using STAR aligner version 2.7.8a. Annotated genes from GENCODE version M31 were quantified with RSEM version 1.3.0.
Assembly: GRCm39
Supplementary files format and content: RSEM output (tab-delimited file)

source_name: Primary mouse hepatocytes

extract_protocol:
Total RNA was isolated from cells by RNA STAT 60
KAPA Stranded mRNA-Seq Illumina® Platforms Kit

value: Primary mouse hepatocytes

tag: condition

value: ΔEGFR


title: AP7356


title: AP7353

value: Mineral Oil


title: AP7352


title: AP7354


title: AP7351


title: AP7350


title: AP7345

value: WT


title: AP7346


title: AP7355


title: AP7347


title: H7.2-24


title: AP7344


title: H7.4-48


title: H7.4-24


title: AP7342


title: AP7343


title: E7T-seq_wt_14dpp_onIce_3d

city: New York

first: Soonjoung

last: Kim

email: kims16@mskcc.org, soonjk@yuhs.ac

state: New York

address: 430 East 67th Street

department: Molecular Biology

country: USA

institute: Memorial Sloan Kettering Cancer C

data_processing:
After Qubit quantification and quality control by Agilent BioAnalyzer, libraries were pooled equimolar and run on an Illumina sequencer. A spike-in of PhiX was added to the run to increase diversity when necessary and for quality control purposes. Base calls were perfomed using bcl2fastq software v.2.20 or bcl-convert software v.3.9.3 to 3.10.5 for samples sequenced on Illumina NextSeq 500, NextSeq 2000, or NovaSeq 6000.  Reads were trimmed and filtered by Trim Galore version 0.6.6 with the arguments --paired --length 15 <http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>
Sequence reads were mapped onto the mouse reference genome (mm10) by bowtie2 version 2.3.5.1 (ref. 1) with the arguments -N 1 -X 1000. (ref. 1) Langmead et al., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009). Duplicated reads were removed by Picard <https://broadinstitute.github.io/picard/>. Uniquely and properly mapped reads (MAPQ ≥ 20) were extracted by samtools with the arguments -q 20 <http://www.htslib.org/>.
Reads for S1, Exo7/T, or ExoT-seq were counted at which a nucleotide next to biotinylated adaptor DNA was mapped (this corresponds to a position of ssDNA). Adaptors were swapped for some samples (indicated by sample names), and reads were counted at which a nucleotide next to the other (unbiotinylated) adaptor DNA was mapped. Maps were analyzed using R version 4.0.3 <http://www.r-project.org>.
Assembly: mm10
Supplementary files format and content: bigWig files contain read counts at positions of ssDNA. Reads were not normalized to RPM (reads per million mapped). Letter "F" or "R" in sample names indicates that reads were mapped on forward or reverse strand, respectively

source_name: testis

extract_protocol:
Testis cells from mice at indicated age were obtained as described previously (ref. 1). Cells were embedded in plugs of low-melting point agarose to protect DNA from shearing, and DNA was liberated by treatment with SDS and proteinase K as described previously (ref. 1). In-plug overhang removal with S1 endonuclease for S1-seq, exonuclease VII and exonuclease T for Exo7/T-seq, or exonuclease T for ExoT-seq, and adaptor ligation were performed as described previously (ref. 1, 2, 3) with minor modifications. In brief for S1-seq, plugs were washed in 0.5 ml of modified S1 buffer (50 mM sodium acetate, 280 mM NaCl, 4.5 mM ZnSO4, pH 4.7) for 30 min four times, treated with 9 units of S1 nulcease in 500 µl of modified S1 buffer at 37°C for 20 min and washed once with 1ml TE. For Exo7/T-seq, plugs were washed in 1 ml of exonuclease VII buffer for 15 min twice, treated with 50 units of exonuclease VII in 100 µl of exonuclease VII buffer at 37°C for 60 min and washed once with 1ml TE and followed by exonulcease T treamtment. For ExoT-seq, plugs were washed in 1 ml of NEBuffer 4 for 15 min 3 times, treated with 75 units of exonuclease T in 100 µl of NEBuffer 4 at 24°C for 90 min and washed 3 times with 8 ml of TE for 15 min. The nuclease treated ssDNA ends were further polished with T4 polymerase before the first adaptor ligation as previously described (ref. 1, 2, 3). After ligation to biotinylated adaptors, DNA was purified from the agarose, sheared by sonication, purified with streptavidin, ligated to second-end adaptors, amplified, and sequenced as described previously (ref. 1, 2, 3). (ref. 1) Yamada et al., Molecular structures and mechanisms of DNA break processing in mouse meiosis. Genes Dev 34, 806-818 (2020). (ref. 2) Mimitou et al., S. A global view of meiotic double-strand break end resection. Science 355, 40-45 (2017). (ref. 3) Mimitou et al., S1-seq Assay for Mapping Processed DNA Ends. Methods Enzymol 601, 309-330 (2018).
After Qubit quantification and quality control by Agilent BioAnalyzer, libraries were pooled equimolar and run on an Illumina sequencer. A spike-in of PhiX was added to the run to increase diversity when necessary and for quality control purposes. Base calls were perfomed using bcl2fastq software v.2.20 or bcl-convert software v.3.9.3 to 3.10.5 for samples sequenced on Illumina NextSeq 500, NextSeq 2000, or NovaSeq 6000.  Reads were trimmed and filtered by Trim Galore version 0.6.6 with the arguments --paired --length 15 <http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>. Sequence reads were mapped onto the mouse reference genome (mm10) by bowtie2 version 2.3.5.1 (ref. 1) with the arguments -N 1 -X 1000. (ref. 1) Langmead et al., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009). Duplicated reads were removed by Picard <https://broadinstitute.github.io/picard/>. Uniquely and properly mapped reads (MAPQ ≥ 20) were extracted by samtools with the arguments -q 20 <http://www.htslib.org/>. Reads for S1, Exo7/T, or ExoT-seq were counted at which a nucleotide next to biotinylated adaptor DNA was mapped (this corresponds to a position of ssDNA). Maps were analyzed using R version 4.0.3 <http://www.r-project.org>.
S1-seq, Exo7/T-seq, ExoT-seq

value: testis

value: Spermatocytes

value: wild type

tag: age

value: 14 days post partum

tag: group

value: Exo7/T cell storage condition test


title: S1-seq_wt_timecourse_16dpp_rep1

value: 16 days post partum

value: S1 timecourse


title: E7T-seq_wt_14dpp_onIce_5d


title: S1-seq_wt_timecourse_13dpp_rep1

value: 13 days post partum


title: AP7348


title: S1-seq_wt_timecourse_15dpp_rep1

value: 15 days post partum


title: H7.2-48

value: Adipose-derived stem cells

value: Female


title: S1-seq_wt_timecourse_12dpp_rep1

value: 12 days post partum


title: BM_embTRMp, rep2

city: Jena

first: Konstantin

last: Riege

address: Beutenbergstraße 11

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

data_processing:
Sequence information was converted to FASTQ format using bcl2fastq v2.20.0.422
Raw data was quality trimmed and clipped for Nextera Transposase adapter. Potential sequencing errors were detected and corrected using Rcorrector. Rrna fragments have been depleted using SortMeRNA.
Reads were mapped on GRCm39 (mm11) using segemehl and quantified on Ensembl v109 derived gene annotation utilizing featureCounts. Variance stabilized counts were inferred by DESeq2.
Assembly: mm11 (Ensembl v109)
Supplementary files format and content: Tab delimited text files include raw, variance stabilized and TPM normalized read counts for each sample.

molecule: polyA RNA

source_name: Bone marrow

extract_protocol:
Bone marrow myeloid cells were sorted into QIAzol Lysis Reagent (Qiagen, #79306). RNA isolation was performed with miRNeasy Micro Kit (Qiagen, #217084).
For library preparation 2 µl cDNA was tagmented according to the Illumina DNA Prep Kit.

value: Bone marrow

value: Macrophage

value: eYFPpos

value: female


title: BM_embTRMp, rep3


title: BM_adMono_Ly6Chi, rep1

value: Monocyte


title: BM_embTRMp, rep1


title: BM_adTRMp, rep2

value: eYFPneg


title: BM_adMono_Ly6Chi, rep2


title: BM_adTRMp, rep1


title: BM_adMono_Ly6Clo, rep2


title: BM_adMono_Ly6Clo, rep3


title: S1-seq_wt_timecourse_14dpp_rep1

value: testis

value: Spermatocytes


title: CD8+ TIL, control, rep4

city: Daejeon

first: Seung Hyuck

last: Jeon

address: 291 Daehak-ro, Yuseong-gu

institute: Korea Advanced Institute of Science and Technology

description: Control_4_1, CD8+ TIL

data_processing:
FASTQ files were mapped to the mouse genomic DNA reference (GRCm38/mm10) using Hisat2
StringTie was used to quantify gene expression based on the aligned reads.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM expression for each Sample

source_name: CD8+ tumor-infiltrating T cells

extract_protocol:
Total RNA was extracted from the sorted cells using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara).
Libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara).

value: CD8+ tumor-infiltrating T cells

value: primary

value: CD8+ T cell

value: C57BL/6 hPD-1/hPD-L1/h4-1BB mice

value: Control


title: CD8+ TIL, pembrolizumab treated, rep3

description: Pembro_3_1, CD8+ TIL

value: Pembrolizumab


title: CD8+ TIL, control, rep2

description: Control_2_1, CD8+ TIL


title: CD8+ TIL, pembrolizumab treated, rep1

description: Pembro_1_1, CD8+ TIL


title: CD8+ TIL, control, rep1

description: Control_1_1, CD8+ TIL


title: CD8+ TIL, ABL503+pembrolizumab treated, rep5

description: Combi_5_1, CD8+ TIL


title: CD8+ TIL, control, rep5

description: Control_5_1, CD8+ TIL


title: CD8+ TIL, pembrolizumab treated, rep5

description: Pembro_5_1, CD8+ TIL


title: CD8+ TIL, ABL503+pembrolizumab treated, rep4

description: Combi_4_1, CD8+ TIL


title: BM_adMono_Ly6Clo, rep1


title: CD8+ TIL, ABL503+pembrolizumab treated, rep3

description: Combi_3_1, CD8+ TIL


title: BM_adMono_Ly6Chi, rep3


title: CD8+ TIL, ABL503+pembrolizumab treated, rep1

description: Combi_1_1, CD8+ TIL


title: BM_adTRMp, rep3


title: CD8+ TIL, ABL503 treated, rep5

description: ABL_5_1, CD8+ TIL


title: CD8+ TIL, pembrolizumab treated, rep2

description: Pembro_2_1, CD8+ TIL


title: CD8+ TIL, ABL503 treated, rep3

description: ABL_3_1, CD8+ TIL


title: CD8+ TIL, control, rep3

description: Control_3_1, CD8+ TIL


title: CD8+ TIL, pembrolizumab treated, rep4

description: Pembro_4_1, CD8+ TIL


title: CD8+ TIL, ABL503 treated, rep4

description: ABL_4_1, CD8+ TIL


title: CD8+ TIL, ABL503 treated, rep2

description: ABL_2_1, CD8+ TIL


title: CD8+ TIL, ABL503 treated, rep1

description: ABL_1_1, CD8+ TIL


title: CD8+ TIL, ABL503+pembrolizumab treated, rep2

description: Combi_2_1, CD8+ TIL


title: IREPKO_pituitary scRNA-seq_01

city: Iowa City

first: Ling

last: Yang

state: Iowa

address: 169 Newton RD

department: Anatomy & Cell Biology

institute: university of Iowa

description: 10X Genomics

data_processing:
RNA seq reads were made using Kallisto BUStool
Assembly: mm10
Supplementary files format and content: H5

source_name: pituitary

extract_protocol:
10x Chromium single-cell RNAseq of cells from pituitary glands
Library was performed according to single cells 3' v3.1 protocol

value: pituitary

value: all cell types

value: IREPKO

value: RD


title: IREPKO_pituitary scRNA-seq_02

description: 10X Genomics


title: HFD_pituitary scRNA-seq_01

description: 10X Genomics

value: HFD


title: HFD_pituitary RNA-seq_02

data_processing:
sequencing reads were trimmed and mapped to mm10 (mouse)
Assembly: mm10
Supplementary files format and content: csvs file include raw counts for each sample

extract_protocol:
Pituitary RNA was extracted using Rneasy mini kit (Qiagen)
RNA libraries for RNA seq were using oligo-dT purification of polyadenylated RNA following manufacturer's protocol

value: male


title: IREfl_pituitary scRNA-seq_01

description: 10X Genomics

value: IREfl


title: HFD_pituitary scRNA-seq_02

description: 10X Genomics


title: RD_pituitary scRNA-seq_01

description: 10X Genomics


title: IREfl_pituitary scRNA-seq_02

description: 10X Genomics


title: RD_pituitary RNA-seq_03


title: RD_pituitary RNA-seq_01


title: HFD_pituitary RNA-seq_03


title: IREPKO_liver RNA-seq_01

source_name: liver

extract_protocol:
Liver RNA was extracted using Rneasy mini kit (Qiagen)
RNA libraries for RNA seq were using oligo-dT purification of polyadenylated RNA following manufacturer's protocol

value: liver


title: RD_pituitary RNA-seq_02


title: IREPKO_liver RNA-seq_02


title: HFD_pituitary RNA-seq_01


title: IREfl_liver RNA-seq_02


title: IREfl_liver RNA-seq_03


title: IREfl_liver RNA-seq_01


title: pFUS_UC_4

city: Palo Alto

first: Avnesh

last: Thakor

state: California

address: 3155 Porter Drive,

institute: Stanford University

data_processing:
Sequenced reads were trimmed for adaptor sequence,
Then mapped to mouse genome Mus Musculus using HISTAT
HTSeq was used to generate the raw read counts
DESeq2 was used for differential gene expression analysis
Assembly: (GRCm39/mm39)
Supplementary files format and content: tab-delimited text file include FPKM values for all samples
Supplementary files format and content: tab-delimited text file include raw counts for all samples

source_name: kidney

extract_protocol:
total RNA was extracted from each replicate using the RNAeasy minikit (qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

value: MSC

value: cisplatin +pFUS+UC


title: UC_4

value: cisplatin+ UC


title: pFUS_UC_2

value: primary


title: pFUS_UC_3


title: UC_3


title: pFUS_UC_1


title: UC_2


title: UC_1


title: AKI_4

value: cisplatin


title: AKI_2


title: RD_pituitary scRNA-seq_02

description: 10X Genomics


title: AKI_1


title: AKI_3


title: Lung, LPS, rep2

city: Wuhan

first: xiufang

last: weng

address: 13# Hangkong Rd, Wuhan, Hubei

institute: Huazhong University of Science and Technology

data_processing:
Illumina nova seq platform used for basecalling.
Raw image Data files obtained by Illumina nova are analyzed by CASAVA Base Calling and converted into Raw Data of sequencing sequences，and the results are stored in FASTQ (.fastq) file format. The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html).
The clean reads obtained by filtering were compared to the reference sequence.Based on the comparison results, new transcript prediction, differential splicing gene detection, SNP and Indel detection, fusion gene detection and other analyses were performed.
HISAT2 was used to compare clean reads to reference genes.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: Matrix table with read counts for every gene and every sample

source_name: Lung

extract_protocol:
Total RNA of lung tissue was havested by Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung

value: WT

value: LPS


title: Lung, LPS+TSLP, rep3

value: LPS+TSLP


title: Lung, LPS, rep3


title: Lung, LPS, rep1


title: Lung, LPS+TSLP, rep1


title: Lung, LPS+TSLP, rep4


title: RGCOlig3_3

first: Xiuqing

last: Fu

state: Shanghai

address: 393 Middle Huaxia Road, Pudong

department: School of Life Science and Technology (SLST)

institute: ShanghaiTech University

data_processing:
Mus musculus Genomics
Quality distribution plot and base content distribution were generated by FASTQC.
HISAT2 software is used to align clean data to reference genome.
Read counts for individual transcripts of each sample were produced with HTSeq-count.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: retina

extract_protocol:
For the isolation of single RGCs, magnetic beads coupled with CD90.2 antibody, which specifically recognizes RGC cells, were employed. The beads-isolated GFP-positive RGCs were manually selected for RNA-seq analysis. All RGCs settled in a 35 mm dish for 5 minutes, and subsequently, 10 ~ 15 RGCs were collected into the RNA lysate buffer (SMART-Seq® HT Kit) using UnipicK (DCU ID = 20 μm) under an inverted fluorescence microscope (Olympus).
Whole transcriptome amplification in PCR tubes were performed following SMART-Seq® HT Kit protocol. Briefly, 10~20 picked cells (~0.2μl) were lysed in 10μl lysis buffer (with RNase Inhibitor). Next, samples were mixed well with 1μl 3’-SMART-Seq CDS Primer II A, and then incubated at 72°C for 3 minutes and immediately placed on ice for 2 minutes. Then, we incubated samples with 12.5μl One-Step Master Mix at 42°C for 90 minutes and amplified for 20 PCR cycles. The cells’ cDNA was purified by immobilization on AMPure XP beads and cDNA is eluted with 17μl Elution Buffer. After purification, 1μl the profile of the cDNA was evaluated using the Agilent 2100 Bioanalyzer and Agilent’s High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626).

value: retina

value: Retina ganglion cells

value: AAV-Olig3 injection for 14 days and ONC for 14 days


title: Lung,Vehicle, rep2

value: Vehicle


title: Lung, LPS+TSLP, rep2


title: Lung,Vehicle, rep3


title: Lung,Vehicle, rep1


title: RGCGFP_3

value: AAV-GFP injection for 14 days and ONC for 14 days


title: RGCOlig2_1

value: AAV-Olig2 injection for 14 days and ONC for 14 days


title: RGCOlig3_1


title: RGCOlig2_3


title: Allogeneic treated Nintedanib rep 3

city: Düsseldorf

first: Jörg

last: Distler

address: Merowingerplatz 1A

department: Department of Rheumatology

institute: University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University

description:
Nin_3
L1_1 and L2_1 are from the same read-end (forward read), but run in different lane. L1_2 and L2_2 are from the same read-end (reverse read), but run in different lane.

data_processing:
Reads were checked and filtered by FastQC and Trimmomatic
Reads were mapped to mouse genome (GRCm39) by Spliced Transcripts Alignment to a Reference (STAR)
Uniquely mapped reads were assigned to annotated genes using the “featureCounts” from R package “Rsubread” (version 1.22.2)
Assembly: GRCm39
Supplementary files format and content: text document containing raw counts all groups of sample

source_name: skin

growth_protocol: Recipient mice (BALB/c (H-2d)) with an age of 8 weeks received total body irradiation with 700 cGy. Six hours after irradiation, all BALB/c (H-2d) recipients received bone marrow from either BALB/c (H-2d) in a syngeneic or B10.D2 (H-2d) in an allogeneic transplantation manner.

extract_protocol:
Total RNA was extracted from 3mm-diameter area of skin using the Nucleo Spin RNA isolation kit (Macherey-Nagel).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. 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 NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized 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, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptorligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. 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: To reflect the clinical situation with treatment only upon clinical signs of cGvHD, treatment was started 21 days after bone marrow transplantation and thus after the first clinically detectable manifestations of cGvHD in allogeneically transplanted mice. The outcome of treatment was analyzed seven weeks after transplantation. Antibodies were given i.p twice a week, with a first loading dose at 20 mg/kg and the following doses at 10 mg/kg. Nintedanib was given at 50 mg/kg p.o. daily.

value: skin

value: Balb/c

value: Nintedanib


title: Allogeneic treated Nintedanib rep 2

description:
Nin_2
L1_1 and L2_1 are from the same read-end (forward read), but run in different lane. L1_2 and L2_2 are from the same read-end (reverse read), but run in different lane.


title: RGCOlig3_2


title: RGCGFP_2


title: H7.0-48

value: Adipose-derived stem cells

value: Female


title: Allogeneic treated anti-IL1RAP ab rep 4

value: anti-IL1RAP ab mCAN10


title: RGCGFP_1


title: RGCOlig2_2


title: Allogeneic treated Nintedanib rep 5

description:
Nin_5
L1_1 and L2_1 are from the same read-end (forward read), but run in different lane. L1_2 and L2_2 are from the same read-end (reverse read), but run in different lane.


title: Allogeneic treated Nintedanib rep 4


title: Allogeneic treated anti-IL1RAP ab rep 1


title: Allogeneic treated ddH2O rep 3


title: Allogeneic treated Nintedanib rep 1


title: Allogeneic treated ddH2O rep 1

description:
Allo_H_1
L1_1 and L2_1 are from the same read-end (forward read), but run in different lane. L1_2 and L2_2 are from the same read-end (reverse read), but run in different lane.


title: Allogeneic treated ddH2O rep 4


title: Allogeneic treated anti-IL1RAP ab rep 3


title: Allogeneic treated isotype control ab rep 1

value: isotype control ab


title: Allogeneic treated isotype control ab rep 4


title: Allogeneic treated anti-IL1RAP ab rep 2


title: Syngenic rep 4


title: Syngenic rep 2


title: Syngenic rep 3


title: Allogeneic treated isotype control ab rep 2


title: Allogeneic treated isotype control ab rep 3


title: mouse_CD-1_DMSO_72_0_na_A03

city: Asheville

first: Melissa

middle: Marie

last: Heintz

state: NC

address: 31 College Place, Suite B118

institute: ToxStrategies

description: Illumina NovaSeq X plus

data_processing:
Sequencing reads are demultiplexed using the standard sequencing instrument software for each sample using the barcodes to give a FASTQ file for each
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
bcl2fastq v2.17.1.14 or v2.18.0.12 for demultiplexing
fastqs were aligned to a pseudo transcriptome using Bowtie allowing up to 2 mismatches
Assembly: probe-based targeted sequencing
Supplementary files format and content: comma-separated text files include raw count values for each gene_probe

source_name: primary hepatocytes

growth_protocol: Hepatocytes were isolated from the livers of 8 – 12 week-old male CD-1 mice (CD-1 IGS, strain code: 022) purchased from Charles River (Raleigh, NC) and 11 week-old male B6129SF2/J mice (stock #101045) and 11 week-old male PPARa-null mice (B6;129S4-Pparatm1Gonz/J, stock #008154) purchased from The Jackson Laboratory (Bar Harbor, ME). Rat hepatocytes were isolated from the livers of 8 – 12 week-old male Sprague Dawley (SD, strain code: 001) rats purchased from Charles River. Human hepatocytes were isolated from a pool of 10 donor livers (5 male and 5 female). Hepatocytes from all species/strains were isolated using a two-step enzymatic digestion of liver tissue as described in Mudra and Parkinson (2001).   Primary hepatocytes were plated in a collagen-sandwich configuration on 48-well plates. Hepatocytes were maintained in Modified Eagle's medium, Dr. Chee’s modification (MCM; Gibco, Grand Island, NY) supplemented with 11.5% NaHCO3 (Sigma Aldrich), 0.88% L-arginine (Sigma Aldrich), 3% L-glutamine (Sigma Aldrich), 0.05% thymidine (Sigma Aldrich), 1% (v/v) ITS+ (BD Biosciences, Bedford, MA), 1% (v/v)  penicillin/streptomycin (5,000 U/mL penicillin, 5,000 μg/mL streptomycin (Sigma Aldrich), and  0.001% 10 mM dexamethasone (Sigma Aldrich). Cell cultures were incubated in a humidified culture chamber (37 ± 2 °C at 95% relative humidity, 95/5% air/CO2).

extract_protocol:
Following treatment with HFPO-DA or positive controls (i.e., GW7647, rosiglitazone, acetaminophen or d-galactosamine) for 12, 24 or 72 h, hepatocytes were lysed using TempO-Seq® Enhanced Lysis Buffer and processed according to the TempO-Seq® protocol by BioSypder Technologies.
TempO-Seq® protocol by BioSypder Technologies

treatment_protocol: Using 48-well plates, CD-1, B6129SF2/J and PPARa-KO mouse hepatocytes were seeded at a density of 0.6 x 10^6 cells/mL, and rat and human hepatocytes were seeded at a density of 1.3 x 10^6 cells/mL. After a 24 h adaptation period, hepatocytes from each species/strain were treated for 12, 24 or 72 h with supplemented MCM media containing solvent control in the presence or absence of HFPO-DA (0.1, 5, 50 or 500 μM) or one of the following positive controls: GW7647 (0.01, 0.1, 1 or 10 μM), rosiglitazone (0.01, 0.1, 1 or 10 μM), acetaminophen (0.3, 1, 3 or 10 mM) or d-galactosamine (0.3, 1, 3 or 10 mM). Deionized water (1%) served as the solvent control for HFPO-DA and dimethylsulfoxide (DMSO, 0.1%; cell culture grade; Sigma Aldrich) served as the solvent control for the remaining test chemicals. Treatment solutions were replaced every 24 h. For each species/strain, treatment groups were performed in triplicate wells for 12 and 72 h treatment durations, and quadruplicate wells for the 24 h treatment duration.

value: primary hepatocytes

tag: chemical

value: DMSO

tag: concentration

value: solvent control

tag: concentration units

tag: exposure duration_(hours)


title: mouse_CD-1_DMSO_72_0_na_A01

description: Illumina NovaSeq X plus

tag: cell type


title: mouse_CD-1_Deionized_water_72_0_na_F04

description: Illumina NovaSeq X plus


title: mouse_CD-1_Deionized_water_72_0_na_F06

description: Illumina NovaSeq X plus


title: mouse_CD-1_Deionized_water_72_0_na_F05

description: Illumina NovaSeq X plus


title: mouse_CD-1_DMSO_72_0_na_A02

description: Illumina NovaSeq X plus


title: Allogeneic treated ddH2O rep 2

description:
Allo_H_2
L1_1 and L2_1 are from the same read-end (forward read), but run in different lane. L1_2 and L2_2 are from the same read-end (reverse read), but run in different lane.

tag: tissue

tag: genotype


title: Syngenic rep 1

tag: treatment


title: mouse_CD-1_HFPO_DA_72_500_uM_A06

description: Illumina NovaSeq X plus

tag: strain

value: uM


title: mouse_CD-1_HFPO_DA_72_500_uM_A05

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_72_500_uM_A04

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_72_50_uM_H01

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_72_50_uM_H03

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_72_10_uM_E06

description: Illumina NovaSeq X plus

value: Rosiglitzone


title: mouse_CD-1_HFPO_DA_72_50_uM_H02

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_72_10_uM_E02

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_72_10_mM_F07

description: Illumina NovaSeq X plus

value: mM


title: mouse_CD-1_Rosiglitzone_72_10_uM_E04

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_72_5_uM_G01

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_72_10_uM_E05

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_72_5_uM_G02

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_72_10_uM_E03

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_72_5_uM_G03

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_72_10_mM_F08

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_72_10_mM_B09

description: Illumina NovaSeq X plus

value: Acetominophen


title: mouse_CD-1_GW7647_72_10_uM_E01

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_72_10_mM_B08

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_72_10_mM_F09

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_72_3_mM_A07

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_72_1_uM_D06

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_72_10_mM_B07

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_72_1_uM_D05

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_72_1_uM_D04

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_72_3_mM_E09

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_72_3_mM_E08

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_72_3_mM_A08

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_72_1_mM_D09

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_72_1_uM_D01

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_72_3_mM_A09

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_72_1_uM_D02

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_72_1_uM_D03

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_72_1_mM_D08

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_72_1_mM_H06

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_72_1_mM_H04

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_72_1_mM_D07

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_72_0.3_mM_C08

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_72_1_mM_H05

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_72_0.3_mM_C07

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_72_3_mM_E07

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_72_0.01_uM_B04

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_72_0.1_uM_C04

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_72_0.3_mM_G05

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_72_0.3_mM_G04

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_72_0.01_uM_B06

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_72_0.3_mM_G06

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_72_0.1_uM_C05

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_72_0.01_uM_B05

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_72_0.1_uM_C06

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_72_0.1_uM_F03

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_72_0.3_mM_C09

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_72_0.01_uM_B03

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_72_0.1_uM_F01

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_72_0.1_uM_C03

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_72_0.1_uM_F02

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_72_0.1_uM_C02

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_72_0.1_uM_C01

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_72_0.01_uM_B02

description: Illumina NovaSeq X plus


title: IREPKO_liver RNA-seq_03

value: liver

value: HFD


title: mouse_CD-1_GW7647_72_0.01_uM_B01

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_24_10_mM_F3

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_24_10_mM_F2

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_24_10_mM_F1

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_24_10_mM_B4

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_24_10_mM_B3

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_24_10_mM_B1

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_24_3_mM_E4

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_24_10_mM_B2

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_24_3_mM_E3

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_24_3_mM_E1

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_24_3_mM_A3

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_24_1_mM_D1

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_24_1_mM_D2

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_24_3_mM_A4

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_24_1_mM_D4

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_24_3_mM_A1

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_24_0.3_mM_C3

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_24_1_mM_D3

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_24_0.3_mM_C1

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_24_3_mM_E2

description: Illumina NovaSeq X plus


title: mouse_CD-1_DMSO_24_0_na_A01

description: Illumina NovaSeq X plus


title: mouse_CD-1_Deionized_water_24_0_na_F07

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_24_3_mM_A2

description: Illumina NovaSeq X plus


title: mouse_CD-1_DMSO_24_0_na_A04

description: Illumina NovaSeq X plus


title: mouse_CD-1_DMSO_24_0_na_A03

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_24_0.3_mM_C4

description: Illumina NovaSeq X plus


title: mouse_CD-1_DMSO_24_0_na_A02

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_24_500_uM_A07

description: Illumina NovaSeq X plus


title: mouse_CD-1_Deionized_water_24_0_na_F08

description: Illumina NovaSeq X plus


title: mouse_CD-1_Deionized_water_24_0_na_F05

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_24_500_uM_A08

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_24_500_uM_A06

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_24_50_uM_H04

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_24_500_uM_A05

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_24_50_uM_H02

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_24_50_uM_H03

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_24_50_uM_H01

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_24_10_uM_E08

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_24_10_uM_E07

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_24_10_uM_E06

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_24_10_uM_E04

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_24_10_uM_E05

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_24_10_uM_E02

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_24_10_uM_E03

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_24_0.3_mM_C2

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_24_10_uM_E01

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_24_5_uM_G04

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_24_5_uM_G02

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_24_1_uM_D04

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_24_5_uM_G03

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_24_1_uM_D05

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_24_1_uM_D08

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_24_1_uM_D03

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_24_5_uM_G01

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_24_1_uM_D06

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_24_1_uM_D07

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_24_1_mM_H08

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_24_1_uM_D01

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_24_1_mM_H07

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_24_1_mM_H06

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_24_1_uM_D02

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_24_0.3_mM_G08

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_24_1_mM_H05

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_24_0.3_mM_G05

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_24_0.1_uM_C08

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_24_0.3_mM_G06

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_24_0.1_uM_C06

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_24_0.01_uM_B08

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_24_0.1_uM_C07

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_24_0.01_uM_B07

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_24_0.1_uM_C05

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_24_0.01_uM_B06

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_24_0.3_mM_G07

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_24_0.01_uM_B05

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_24_10_mM_F4

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_24_0.1_uM_F03

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_24_0.1_uM_A03

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_24_0.1_uM_C04

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_24_0.1_uM_F01

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_24_0.01_uM_A04

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_24_0.1_uM_F02

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_24_0.01_uM_A03

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_24_0.01_uM_A01

description: Illumina NovaSeq X plus


title: mouse_CD-1_DMSO_12_0_na_A02

description: Illumina NovaSeq X plus


title: mouse_CD-1_Deionized_water_12_0_na_F06

description: Illumina NovaSeq X plus


title: mouse_CD-1_Deionized_water_12_0_na_F05

description: Illumina NovaSeq X plus


title: mouse_CD-1_DMSO_12_0_na_A01

description: Illumina NovaSeq X plus


title: mouse_CD-1_Deionized_water_12_0_na_F04

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_12_500_uM_A06

description: Illumina NovaSeq X plus


title: mouse_CD-1_DMSO_12_0_na_A03

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_24_0.1_uM_F04

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_12_50_uM_H01

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_12_10_uM_E05

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_12_50_uM_H02

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_24_0.1_uM_A02

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_12_50_uM_H03

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_12_10_uM_E03

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_24_0.1_uM_A01

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_24_0.01_uM_A02

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_12_10_uM_E02

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_12_10_uM_E04

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_12_10_mM_F07

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_12_10_mM_F08

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_12_500_uM_A05

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_12_10_mM_B09

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_12_10_mM_B07

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_12_500_uM_A04

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_12_10_uM_E06

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_12_5_uM_G03

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_12_10_mM_F09

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_12_5_uM_G02

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_12_3_mM_E08

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_12_3_mM_A08

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_12_3_mM_A07

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_12_5_uM_G01

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_12_1_uM_D02

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_12_1_uM_D04

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_12_10_uM_E01

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_12_1_uM_D03

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_12_1_uM_D06

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_12_1_mM_D09

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_12_10_mM_B08

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_12_1_mM_H06

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_12_1_mM_D08

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_12_3_mM_E09

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_12_1_mM_H05

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_12_0.3_mM_C09

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_12_3_mM_A09

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_12_0.3_mM_C08

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_12_0.3_mM_G06

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_12_3_mM_E07

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_12_0.3_mM_C07

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_12_0.1_uM_C06

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_12_0.3_mM_G05

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_12_1_uM_D05

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_12_0.3_mM_G04

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_12_0.01_uM_B06

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_12_1_uM_D01

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_12_0.01_uM_B05

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_12_0.01_uM_B04

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_12_0.1_uM_F01

description: Illumina NovaSeq X plus


title: mouse_CD-1_D_Galactosamine_12_1_mM_D07

description: Illumina NovaSeq X plus


title: mouse_CD-1_Rosiglitzone_12_0.1_uM_C04

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_12_0.1_uM_C03

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_12_0.1_uM_C01

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_12_0.01_uM_B03

description: Illumina NovaSeq X plus


title: mouse_CD-1_Acetominophen_12_1_mM_H04

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_12_0.01_uM_B01

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_12_0.01_uM_B02

description: Illumina NovaSeq X plus


title: mouse_CD-1_GW7647_12_0.1_uM_C02

description: Illumina NovaSeq X plus


title: ΔMBH-2_BAP1-3xT7_H3K4me1

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2.
Peaks were called using SICERv2 with following configuration - For ChIP-Seq of histone modifications: Windows (200), Gaps (200), FDR (1e-3); for ChIP-Seq of MLL4 and T7 tag: Windows (50), Gaps (50), FDR (1e-10)
Assembly: mm10
Supplementary files format and content: wig files were generated using in-house script and the scores represent RPKM

source_name: Embryonic stem cells (ESCs)

growth_protocol: Mouse ES cells were maintained on 0.1% gelatin and cultured in 2i+LIF medium (47.75% Advanced DMEM/F-12, 47.75%  Neurobasal, 0.5% N-2 supplement, 1% B-27 supplement minus Vitamin A, 1% GlutaMax, 1% Penicillin-Streptomycin, 1% EmbryoMax 2-mercaptoethanol supplemented with 1 µM MEK inhibitor PD0325901, 3 µM GSK3 inhibitor CHIR99021 HCl and 1,000 units/mL mouse LIF protein).

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min and quenched by 125 mM glycine for 10 min. 30 million fixed cells were swelled in cold buffer containing 5mM PIPES (pH 8.0), 85mM KCl, 1% NP-40 and protease inhibitors for 20 min, and centrifuged at 2,000 g for 5 min at 4°C. Nuclei were resuspended with 3 mL TE buffer (pH 8.0), and subjected to sonication. Sheared chromatin was clarified by centrifugation at 4,000 g for 10 min at 4°C. The supernatant was transferred to a new tube and further supplemented with 150mM NaCl, 0.1% SDS, 1% Triton-X100 and protease inhibitors. 2% of the total material was set aside as input and 20 ng of spike-in chromatin (Active Motif, #53083) was added to each ChIP material. For each ChIP material, 2 - 8 µg of target antibodies and 1.5 μg of spike-in antibody (anti-H2Av, Active Motif, #61686) pre-bound with protein A Dynabeads (ThermoFisher) were added and incubated on a rotator at 4°C overnight. Beads were then collected on a magnetic rack and washed twice with 1 mL cold RIPA buffer, once with 1 mL cold RIPA buffer containing 500mM NaCl, twice with 1 mL cold LiCl buffer and once with 1 mL TE buffer. Finally, beads were eluted with 100 μL buffer containing 0.1M NaHCO3, 1% SDS, and 100 μg Proteinase K at 65°C overnight. Samples were then purified using QIAquick PCR purification kit (Qiagen) and eluted in 50 μL 10mM Tris-HCl.
Libraries were prepared according to NEB (Illumina kit) instructions. DNA were used to construct libraries using NEBNext® Ultra™ II DNA Library Prep kit with AMPure XP magnetic beads (Beckman Coulter).

treatment_protocol: ESCs were infected with Doxycycline-inducible lentiviral pCW57.1 vector expressing T7-tagged BAP1. Cells were treated with 1 μg/mL Doxycycline for 1 day to induced robust BAP1-T7 expression.

value: Embryonic stem cells (ESCs)

value: ASXL1/2 [Delta]MBH

value: Doxycycline


title: ΔMBH-2_BAP1-3xT7_H3K27ac


title: WT_BAP1-3xT7_H3K27ac

value: wild type


title: mouse_CD-1_Rosiglitzone_12_0.1_uM_C05

description: Illumina NovaSeq X plus


title: WT_BAP1-3xT7_H3K4me1


title: ΔMBH-2_BAP1-3xT7_MLL4


title: ΔMBH-2_BAP1-3xT7_T7


title: WT_BAP1-3xT7_MLL4


title: mouse_CD-1_HFPO_DA_12_0.1_uM_F02

description: Illumina NovaSeq X plus


title: mouse_CD-1_HFPO_DA_12_0.1_uM_F03

description: Illumina NovaSeq X plus


title: ΔMBH-1_BAP1-3xT7_H3K27ac


title: ΔMBH-1_BAP1-3xT7_T7


title: ΔMBH-1_BAP1-3xT7_input


title: WT_BAP1-3xT7_input


title: 105096-001-053

city: Groningen

first: Reinoud

last: Gosens

address: Antonius Deusinglaan 1

department: Molecular Pharmacology

country: Netherlands

institute: University of Groningen

description: Mouse 4

data_processing:
Library preparation was checked by calculating ribosomal (and globin) content.
Checks for possible sample and barcode contamination were performed and a set of standard quality metrics for the raw dataset was determined using quality control tools (FstQC v0.34 and FastQA).
Prior to alignment, the reads were trimmed for adapter sequences using Trimmomatic v0.30.
Assembly: To align the reads of each sample, the  mouse reference GRCm39 was used. Data was analyzed with DESEQ2 package 1.34.0 in R studio
Supplementary files format and content: Count files

growth_protocol: 300,000 freshly isolated mouse Epcam+ cells were mixed in a 1:1 ratio with proliferation-inactivated CCL206 fibroblasts and seeded into 6-well plates as described above. Cultures were exposed to treatments for 72 hours, after which the medium was removed, and Matrigel was digested using 1 mL dispase (Sigma-Aldrich, #SCM133) for 1 hour at 37 °C. Organoids were disrupted by 1 mL trypsin for 5 minutes at 37 °C, and the resulting cells were resorted into Epcam+ and CCL206 fractions using mouse Epcam (CD326) microbeads.

extract_protocol:
Total RNA was isolated using the RNA purification kit NucleoSpin RNA (Macherey-Nagel 740955, Germany) according to the manufacturer’s guide. Cells were lysed by adding a mixture of buffer RA1 and dithiothreitol (Sigma-Aldrich, 3483-12-3). The yield of the isolated RNA was then measured using the NanoDrop 1000 spectrophotometer.
RNA-seq was conducted using the Illumina NovaSeq 6000 sequencer by GenomeScan (https://www.genomescan.nl/). The procedure included data quality control, adapter trimming, alignment of short reads and feature counting. Library preparation was checked by calculating ribosomal (and globin) content. Checks for possible sample and barcode contamination were performed and a set of standard quality metrics for the raw dataset was determined using quality control tools (FstQC v0.34 and FastQA). Prior to alignment, the reads were trimmed for adapter sequences using Trimmomatic v0.30. To align the reads of each sample, the the  mouse reference GRCm39 was used. Data was analyzed with DESEQ2 in R studio

treatment_protocol: Organoids were exposed to either vehicle, TGF-beta 2 ng/ml, IPF cocktail (IPFc), composed of 9 factors which are increased in IPF lungs (CCL2, IL-1β, IL-4, IL-8, IL-13, IL-33, TGF-β, TNFα and TSLP) or exacerbation cocktail (EC) composed of 4 factors that are increased during an exacerbation of COPD (TNFα, IL-1β, IL-6, IL-8).

value: Lung

value: CD45-/CD31-/Epcam+ cells

value: WT

value: IPFc


title: 105096-001-054

description: Mouse 4

value: TGFb


title: 105096-001-052

description: Mouse 4

value: EC


title: 105096-001-051

description: Mouse 4

value: Vehicle


title: 105096-001-050

description: Mouse 3


title: 105096-001-049

description: Mouse 3


title: 105096-001-048R

description: Mouse 3


title: 105096-001-045R

description: Mouse 2


title: 105096-001-046R

description: Mouse 2


title: ΔMBH-1_BAP1-3xT7_H3K4me1


title: ΔMBH-1_BAP1-3xT7_MLL4


title: mouse_CD-1_Deionized_water_24_0_na_F06

description: Illumina NovaSeq X plus

value: primary hepatocytes

value: solvent control


title: 105096-001-043R

description: Mouse 2


title: WT_BAP1-3xT7_T7


title: 105096-001-042R

description: Mouse 1


title: 105096-001-041R

description: Mouse 1


title: 105096-001-040R

description: Mouse 1


title: 105096-001-039R

description: Mouse 4

tag: cell line


title: 105096-001-037R

description: Mouse 4


title: 105096-001-038R

description: Mouse 4


title: 105096-001-036R

description: Mouse 4


title: 105096-001-034R

description: Mouse 3


title: 105096-001-032

description: Mouse 3


title: 105096-001-033R

description: Mouse 3


title: 105096-001-031

description: Mouse 2


title: ΔMBH-2_BAP1-3xT7_input


title: 105096-001-030

description: Mouse 2


title: 105096-001-029

description: Mouse 2


title: 105096-001-028

description: Mouse 1


title: 105096-001-025

description: Mouse 1


title: 105096-001-026

description: Mouse 1


title: 105096-001-027

description: Mouse 1


title: ACREB virus transduction, VIP treatment, rep 3

city: Singapore

first: Jessica

middle: R

last: Gaunt

address: 11 Mandalay Road

department: LKC Medicine

country: Singapore

institute: Nanyang Technological University

data_processing:
Raw FASTQ files were processed using the Gekko high-performance cluster computing system at Nanyang Technological University, Singapore). First, Illumina adapters were trimmed (≤ 2 seed mismatches; paired-end alignment score ≥ 10; adapter length ≥ 3) and reads with an average quality score below 15 or length below 30 bases were removed using Trimmomatic (v0.39) (Bolger, Lohse, & Usadel, 2014).
Paired reads were then aligned to the mouse genome assembly GRCm38 (mm10) using STAR (v2.7.1a) (Dobin et al., 2013) and quantified using HTseq (v0.11.2)(Anders, Pyl, & Huber, 2015).
Analyses of gene expression count matrices were conducted in R 3.6.1 (R Core Team, 2019) using packages available through Bioconductor (R. C. Gentleman et al., 2004).
Data were filtered to retain genes with CPM > 1 in a minimum of three samples (N = 15,345) and then upper quartile normalised. Differential expression tests were conducted using the robust quasi-likelihood F-test pipeline in edgeR (Lun, Chen, & Smyth, 2016; Robinson, McCarthy, & Smyth, 2010; Zhou, Lindsay, & Robinson, 2014). RUVseq (Risso, Ngai, Speed, & Dudoit, 2014) was used to correct for batch effects and other sources of unwanted variability, by identifying the top two latent factors of variation in the expression of empirically-determined negative control genes (selected by excluding the top 5000 genes in a first-pass ANOVA-like test; N = 10,345) and incorporating these factors into the design matrix.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Raw count files generated by HTseq with Ensembl gene IDs

source_name: astrocyte-enriched cortical cultures

growth_protocol: For cortical astrocytes, mouse forebrains from C57BL6/J mouse pups (post-natal day 0-2) were dissected in cold HBSS (Invitrogen) and digested in 0.25% trypsin for 20 min in a 37 °C water bath. The tissue was triturated with a glass pipette and cell suspension was sieved and resuspended in A10 astrocytes media which contains minimum essential media (MEM) (PAN-Biotech), supplemented with 10% horse serum (Gibco) and 1X Glutamax (Gibco). Cells were further processed and plated on PDL (40 kDa; 0.1 mg/ml; Sigma) coated dishes (Greiner Bio-one). All cultures were maintained in a 37 ºC, 5% CO2 incubator with replacement of A10 media every 2 days. When cortical cultures reach confluency at DIV 7, cells were agitated to detach other glial subtypes, trypsinized and re-plated into the appropriate PDL-coated tissue culture dishes to obtain astrocyte-enriched cultures for further experiments.

extract_protocol:
Cortical astrocytes were washed with 1X PBS and lysed directly using 1 mL of TRIZOL. From TRIZOL mix, the total RNA was column purified using the Qiagen RNeasy Kit.
Strand-specific cDNA libraries (~250-300bp) were prepared for RNA-seq by NovogeneAIT Genomics (Singapore) and 20M 150bp paired-end reads per sample were generated by sequencing on the Illumina Novaseq 6000 platform.

treatment_protocol: Cortical astrocytes were transduced with Control or ACREB expression vectors for 5 days as follows. Lentiviral particles were diluted in serum-free MEM and incubated with cortical astrocytes in reduced volume for 24 hours before being replaced with A10 media with media changes every 2 days. Cells were bath-applied with PBS or VIP (0.5 µM) for 30 min followed by a 1.5 h recovery before harvesting RNA for RNA-seq.

value: astrocyte-enriched cortical cultures

tag: viral transduction

value: VIP (0.5 uM)

tag: time

value: 30 min bath-application + 90 min recovery


title: 105096-001-044R

description: Mouse 2


title: ACREB virus transduction, VIP treatment, rep 1


title: ACREB virus transduction, VIP treatment, rep 2


title: ACREB virus transduction, PBS treatment, rep 3

value: PBS


title: ACREB virus transduction, PBS treatment, rep 2


title: ACREB virus transduction, PBS treatment, rep 1


title: Control virus transduction, VIP treatment, rep 3

value: pCIG3 (pCMV-IRES-GFP)


title: Control virus transduction, VIP treatment, rep 2


title: Control virus transduction, VIP treatment, rep 1


title: Control virus transduction, PBS treatment, rep 2


title: Control virus transduction, PBS treatment, rep 3


title: Control virus transduction, PBS treatment, rep 1


title: WT, Batch 2, rep 3

data_processing:
Initial processing steps were performed on the Gekko high-performance computing system (Nanyang Technological University, Singapore). First, adapters and low-quality bases were trimmed using Trimmomatic (v0.39; Bolger et al., 2014). STAR (v2.7.1a, Dobin et al., 2013) was then used to align paired-end reads to GENCODE mouse genome assembly release M24 supplemented with the human APOE RNA sequence obtained from Jackson laboratories. Reads per gene were quantified using HTseq (v0.11.2, Anders et al., 2015).
Using R v4.0.2, counts for human and mouse APOE were combined. Data were filtered to retain genes with CPM > 1 in a minimum of three samples (N = 16,171) and then upper quartile normalised. Robust likelihood ratio tests for differential expression were conducted separately for each batch using edgeR (Robinson et al., 2010; McCarthy et al., 2012; Zhou et al., 2014) to compare each genotype to WT and APP-TKI to DM. A false discovery rate threshold of 10% was used to identify differentially expressed genes (DEGs) and non-protein-coding genes were removed.
Assembly: GENCODE M24
Supplementary files format and content: Raw count files with Ensembl gene IDs

source_name: Hippocampus

extract_protocol:
Whole hippocampi were dissected on ice from female mice aged 3 months and snap-frozen in TRIzol reagent (Invitrogen). Samples were homogenised in TRIzol, extracted using chloroform and 100% ethanol, and then column-purified.
Directional polyA-enriched mRNA libraries were prepared and 150bp paired-end reads were obtained by sequencing on the Illumina Novaseq 6000 platform by NovogeneAIT Genomics (Singapore).

value: Hippocampus

tag: Sex

value: Female

value: 3 months

value: Wild-type


title: WT, Batch 2, rep 1


title: WT, Batch 2, rep 2


title: APOE, Batch 2, rep 2


title: WT, Batch 1, rep 3


title: WT, Batch 1, rep 1


title: WT, Batch 1, rep 2


title: APOE, Batch 2, rep 1


title: DM, Batch 1, rep 1


title: DM, Batch 1, rep 2


title: APP, Batch 1, rep 3

value: AppNL-G-F/NL-G-F


title: Small intestine IMQ [SI11]

city: Inchon

first: YunJae

last: Jung

address: 155 Gaetbeol-ro, Yeonsu-gu

department: Microbiology

institute: College of Medicine, Gachon University

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to mm10 whole genome by using HISAT2 version 2.1.0 with parameter -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
FPKM were calculated by using StringTie version 2.1.3b, with parameter --rf -l -o -G -A -e
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Small intestine IMQ

growth_protocol: Six-to-eight-week-old female or male BALB/c mice were purchased from Orientbio (Gyeonggi-do, Korea). The mice were kept under standard temperature and humidity conditions in a specific pathogen-free environment. All procedures involving mice were reviewed and approved by the Center of Animal Care and Use of the Lee Gil Ya Cancer and Diabetes Institute, Gachon University (Number: LCDI-2020-0113).

extract_protocol:
RNA from the skin and small intestines of the mice was extracted using QIAzol and purified using an RNeasy mini kit. The purified RNA was processed with DNase I  to remove genomic DNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Prior to the experimentation, the mice were shaved. At 8-10 weeks of age, the mice received a daily topical dose of 62.5 mg IMQ cream (5%) (Aldara™) or vehicle cream (Vaseline) on their shaved back and right ear for a period of 5-8 consecutive days.

value: BALB/c

value: Small intestine

value: Imiqiumod

value: Psorisis


title: Small intestine Con [SI8]

source_name: Small intestine Con

value: Vaseline

value: Nomal


title: Small intestine Con [SI9]


title: Small intestine IMQ [SI10]


title: DM, Batch 1, rep 3


title: Small intestine Con [SI7]


title: Skin IMQ [Skin6]

source_name: Skin IMQ

value: Skin


title: APP, Batch 1, rep 1


title: Skin IMQ [Skin4]


title: Skin Con [Skin3]

source_name: Skin Con


title: Skin Con [Skin1]


title: Skin Con [Skin2]


title: APOE, Batch 2, rep 3


title: Skin IMQ [Skin5]


title: cre_plus_4055_l

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Samples were sequenced using Novaseq 6000(Illumina) using 100 cycles. 200M reads were targeted for each sample, targeting20,000 reads per nuclei/cell. Samples were analyzed using Cell Ranger and Loupe (10x Genomics).
Raw reads were aligned to the mouse genome (mm10), and the digital expression matrix was generated using cellranger count.
Assembly: mm10
Supplementary files format and content: Raw count expression matrix

source_name: Single nuclei form injured heart tissue, serpina3n CKO, 7 days post MI

extract_protocol:
For sc-RNA-seq, 7 days post MI Serpina3nCKO and control mice hearts were harvested and digested by 0.1μg/ml liberase TH. After digestion, cells were incubated with 10μM Calcein AM and flow sorted to identify live cells followed by library preparation. For snRNA-seq, Serpina3nCKO and control mice hearts were harvested at Day 7 after MI, then the injured regions of the heart were dissected and homogenized using nuclei lysis buffer. Nuclei pellet was resuspended in nuclei wash buffer and filtered through 100m and 20um pluristrainer.
Single cell gene expression libraries were created using Chromium Next GEM Single Cell 3' (v3.1 Chemistry) (10x Genomics), Chromium Next GEM Chip G Single Cell Kit (10x Genomics), and Single Index Kit T Set A (10x Genomics) according to the manufacturer’s instructions.
snRNA-seq / scRNA-seq

value: injured heart

value: heart cells

value: Serpina3n CKO

value: myocardial injury (MI)


title: cre_plus_4024_L


title: cre_plus_4021_na


title: cre_minus_4020_na

source_name: Single nuclei form injured heart tissue, WT,  7 days post MI

value: WT


title: Cre-plus-4032-r

source_name: Single cells form injured heart tissue, serpina3n CKO, 7 days post MI


title: APP, Batch 1, rep 2

value: Hippocampus


title: cre_minus_4020_r


title: 105096-001-047R

description: Mouse 3

value: Lung

value: CD45-/CD31-/Epcam+ cells

value: Vehicle


title: cre_minus_4020_L


title: Cre-plus-4032-1


title: Cre-minus-4034-L

source_name: Single cells form injured heart tissue, WT, 7 days post MI


title: Cre-minus-4034-R


title: Cre-minus-4034-1


title: lung, CLP+GW4869, rep3

city: wuhan

first: chaoqun

last: wang

address: bayi road

institute: wuhan University

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep  and Sickle with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method.RSEM was used to quantify gene abundances.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: lung

extract_protocol:
RNA-seq transcriptome library was prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA) using 1 μg of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Sham:sham surgery;    CLP:cecal ligation and puncture;   CLP+GW:GW4869 (2.5μg/g) was given by intraperitoneal injection (IP) 1 h before cecal ligation and puncture;   Lungs of all mice were collected 24 h after surgery.

value: lung


title: lung, CLP+GW4869, rep2


title: lung, CLP, rep1

value: CLP


title: lung, sham, rep2

value: sham


title: lung, CLP, rep3


title: lung, CLP+GW4869, rep1


title: lung, sham, rep3


title: lung, CLP, rep2


title: lung, sham, rep1


title: Cre-plus-4035-R


title: U4

city: kunming

first: Rui-ze

last: Niu

address: Chunrong West Road

institute: kunming medical university

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

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

value: USCs treatment


title: U2

description: 10x Genomics


title: P3

description: 10x Genomics

value: PBS treatment


title: U1

description: 10x Genomics


title: P4

description: 10x Genomics


title: U3

description: 10x Genomics


title: Th17, Dex+IL-1B, 2

city: Cleveland

first: William

last: Miller-Little

address: 10900 Euclid Ave

institute: Case Western Reserve University

data_processing:
Reads were mapped to GRCm38 using STAR 2.7.0a. HTSeq v0.6.1 was used to count the read numbers mapped to each gene, and FPKM (fragments per kilobase of exon per million mapped fragments of each gene) were calculated. Log(FPKM) values were used to calculateZscores for generating heatmaps using HemI 1.0. Differential gene analysis was performed using DESeq2 v 3.14.
Assembly: Mus_musculus_mm10
Supplementary files format and content: datatable, tab-delinieated, Readcount per sample

source_name: in vitro differentiated Th17

growth_protocol: naïve CD4+ T cells were polarized to Th17 cells in RPMI 37C and 5% Co2 using plate bound anti-CD3/anti-CD28 +TGF-B, IL-6, anti-IFN-g and anti-IL-4 for 72 hours

extract_protocol:
Trizol extraction
mRNA from Eukaryote organisms is purified from total RNA using poly-T oligo-attached magnetic beads (For prokaryotes, mRNA was purified through the removal of  rRNA by using kit). The mRNA is first fragmented randomly by addition of fragmentation. Then first strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to  prepare for hybridization(1). In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads.

treatment_protocol: Cells were treated with Dex, IL-1B, or Dex+IL-1B for 4 hours prior to harvesting

value: in vitro differentiated Th17

value: Wild-type

value: Dexamethasone + IL-1B (4h)


title: Th17, Dex+IL-1B, 3


title: P2

description: 10x Genomics


title: Th17, IL-1B, 3


title: Th17, Dex, 3

value: Dexamethasone (4h)


title: Th17, Dex+IL-1B, 1


title: Th17, IL-1B, 1


title: Th17, IL-1B, 2


title: P1

description: 10x Genomics


title: Th17, untreated, 3

value: Untreated


title: Th17, untreated, 2


title: Th17, Dex, 2


title: Th17, untreated, 1


title: M6 effector

city: Cologne

first: Martha

last: Kiljan

address: Elsenbornerstraße, 26

institute: University Hospital Cologne

data_processing:
sequences were aligned with STAR to the mm10 genome
reads were count with HTSeq
differential gene expression analysis was performed with DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw gene counts for each Sample

source_name: CD4 T cell

growth_protocol: naive T cells were isolated from spleens and differentiated to TH1 cells

extract_protocol:
Sorted cells were frozen in Trizol. Choroform was added and after centrifugation aqueous phase was mixed with 70% Ethanol and isolation was further processed according to MiniElute Kit (Mitenyi). At least 10 ng RNA were used for sequencing
RNA preparation was performed with the TruSeq Stranded RNA Kit (Illumina).

treatment_protocol: Naive T cells were stimulated for 6 hours; TH1 cells were differentiated for five days and then resimulated with antigen-pulsed macrophages for six hours

value: CD4 T cell

value: Effector


title: M6 reactivated effector

value: Reactivated Effector


title: M5 effector


title: M5 activated naive

value: Active naive


title: M6 activated naive


title: M5 reactivated effector


title: M4 reactivated effector


title: M6 naive

value: Naive


title: Th17, Dex, 1


title: M5 naive


title: M4 activated naive


title: M4 effector


title: M4 naive


title: M3 reactivated effector


title: M3 activated naive


title: M2 effector


title: M3 effector


title: M2 reactivated effector


title: M3 naive


title: M1 reactivated effector


title: M2 activated naive


title: M2 naive


title: M1 naive


title: M1 effector


title: M1 activated naive


title: Methyl-HiC PmutNgn2 rep2

city: Neuherberg

first: Boyan

last: Bonev

state: Deutschland

address: Ingolstädter Landstr. 1

institute: Helmholtz Zentrum München

data_processing:
Joint Hi-C / DNA methylation data were mapped to the mm10 genome using JuiceMe (Durand et al., 2016). Only uniquely mapping reads (mapq>30) were retained for further analysis. After removal of PCR duplicates, reads were translated into a pair of fragment-ends (fends) by associating each read with its downstream fend. CpG methylation was assessed using MethylDackel (https://github.com/dpryan79/MethylDackel), in a “mergeContext” mode with the first 6 nucleotides omitted from further analysis.
The bedGraph file contains genome-wide CpG methylation levels (1x coverage) with the number of methylated and non-methylated reads per cytosine. A detailed description of the file format can be found under https://github.com/dpryan79/MethylDackel. Compressed text file contains the mapped paired reads with mapq>=30 and belonging to different DpnII fragments in the Juicer short format which can be further analysed using Juicer Pre (https://github.com/aidenlab/juicer/wiki/Pre).
Assembly: mm10
Library strategy: Methyl-HiC

source_name: Methyl-HiC primary mouse astrocytes transduced with PmutNgn2 expressing doxycycline-inducible lentivirus rep2

extract_protocol:
The cortex of post-natal mice aged P5/6 was isolated, mechanically dissociated to obtain a single cell suspension and cultured in medium containing 10% FBS, glucose, pen/strep, B27 supplement, epidermal growth factor and fibroblast growth factor. After culturing for 7 days, the astrocyte enriched culture was reseded on to poly-D-lysine coated 6 well plates and infected with a doxycycline-inducible lentiviral construct. The lentiviral constructs were induced by addition of doxycycline (2ug/ml) for 2 consecutive days in medium containing glucose, pen/strep, glutamine and B27 supplement.  At 48 hours post-doxycycline induction, the transduced astrocytes were isolated with FACS  based on GFP expression and G0/G1 cell cycle state (DAPI staining)
The cortex of post-natal mice aged P5/6 was isolated, mechanically dissociated to obtain a single cell suspension and cultured in medium containing 10% FBS, glucose, pen/strep, B27 supplement, epidermal growth factor and fibroblast growth factor. After culturing for 7 days, the astrocyte enriched culture was reseded on to poly-D-lysine coated 6 well plates and infected with a doxycycline-inducible lentiviral construct. The lentiviral constructs were induced by addition of doxycycline (2ug/ml) for 2 consecutive days in medium containing glucose, pen/strep, glutamine and B27 supplement.  At 48 hours post-doxycycline induction, the transduced astrocytes were isolated with FACS  based on GFP expression and G0/G1 cell cycle state (DAPI staining)

value: Brain

value: primary mouse cortical astrocytes

value: R26-M2rtTA (homozygous)

value: Doxycycline (2 microg/ml) was freshly added to the differentiation medium every 24 hours


title: Yy1_scRNAseq_cell_multiplex_library

description:
Yy1_WT_barcodes.tsv.gz
Yy1_WT_features.tsv.gz
Yy1_WT_matrix.mtx.gz
Yy1_KO_barcodes.tsv.gz
Yy1_KO_features.tsv.gz
Yy1_KO_matrix.mtx.gz
Yy1_WT_Ngn2+_barcodes.tsv.gz
Yy1_WT_Ngn2+_features.tsv.gz
Yy1_WT_Ngn2+_matrix.mtx.gz
Yy1_KO_Ngn2+_barcodes.tsv.gz
Yy1_KO_Ngn2+_features.tsv.gz
Yy1_KO_Ngn2+_matrix.mtx.gz

library_source: genomic single cell

data_processing:
Fastq files were demultiplexed and reads were aligned to the GRCm38 reference (mm10) using cellranger-6.0.0
Processed data files represent filtered feature-barcode matrix (*mtx.gz) stored in the Market Exchange Format (MEX) for sparse matrices as well as gzipped TSV files with feature and barcode sequences corresponding to row and column indices respectively. Processed data files represent the demultiplexed output per sample. A detailed described of the content of the processed data files can be found at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/cellplex
Assembly: mm10

source_name: scRNAseq primary mouse astrocytes transduced transduced with doxycycline inducible lentivirus expressing Ngn2 in the context of Yy1 knock-out, scRNAseq_cell_multiplex_library

extract_protocol:
The cortex of post-natal mice aged P5/6 was isolated, mechanically dissociated to obtain a single cell suspension and cultured in medium containing 10% FBS, glucose, pen/strep, B27 supplement, epidermal growth factor and fibroblast growth factor. After culturing for 5 days, the astrocytes were infected with a lentivirus which constitutively expressed the Cre protein and tdTomato fluorescent protein. After culturing for 7 days, the astrocyte enriched culture was reseded on to poly-D-lysine coated 6 well plates and infected with a doxycycline-inducible lentiviral construct, which expressed Ngn2. The Ngn2 expressing lentiviral construct was induced by addition of doxycycline (2ug/ml) for 2 consecutive days in medium containing glucose, pen/strep, glutamine and B27 supplement
The experimental conditions were labelled according to manufacturer's instructions with the following CellPlex reagents from the 3' CellPlex Kit set A (10x genomics, PN: 1000261): Yy1_WT (CMO309), Yy1_KO (CMO310), Yy1_WT/Ngn2+ (CMO311), Yy1_KO/Ngn2+ (CMO312). Approximately, 25,000 events per condition were FACS sorted (Yy1_WT; untransduced, Yy1_KO; RFP+, Yy1_WT/Ngn2+; GFP+, Yy1_KO/Ngn2+; RFP+GFP+)  into an eppendorf tube. Approximately, 33,000 cells were loaded onto a Chromium Next GEM ChIP G (10x Genomics, PN:2000177) to obtain a targeted cell recovery of 20,000 cells. The gene expression library (PN:3000431) and the cell multiplexing library (PN:3000482) were prepared according to manufacturer's protocol (CG000388 Rev A). The gene expression library and the cell multiplexing library were quality controlled using the Agilent 2100 Bioanalyser (Agilent) and the libraries were sequenced according to manufacturer's specifications


title: Yy1_scRNAseq_gene_expression_library

source_name: scRNAseq primary mouse astrocytes transduced transduced with doxycycline inducible lentivirus expressing Ngn2 in the context of Yy1 knock-out, scRNAseq_gene_expression_library


title: Methyl-HiC PmutNgn2 rep1

source_name: Methyl-HiC primary mouse astrocytes transduced with PmutNgn2 expressing doxycycline-inducible lentivirus rep1


title: Methyl-HiC Ngn2 rep2

source_name: Methyl-HiC primary mouse astrocytes transduced with Ngn2 expressing doxycycline-inducible lentivirus rep2


title: Methyl-HiC Ngn2 rep1

source_name: Methyl-HiC primary mouse astrocytes transduced with Ngn2 expressing doxycycline-inducible lentivirus rep1


title: Multiome_scATAC-seq_PmutNgn2

data_processing:
Reads were aligned to the GRCm38 reference genome (mm10) and quantified using cellranger-arc-2.0.1.
Processed data files represent filtered peak-barcode matrix (*mtx.gz) stored in the Market Exchange Format (MEX) for sparse matrices as well as a BED file with peak. Furthermore the gzipped TSV files cotian barcode sequences as well as the genomic position of the obtained fragments, their barcodes and duplication count. A detailed described of the content of the processed data files can be found at https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/output/fragments and https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/output/peaks
Assembly: mm10

source_name: Multiome scATAC-seq primary mouse astrocytes transduced with PmutNgn2 expressing doxycycline-inducible lentivirus

extract_protocol:
The cortex of post-natal mice aged P5/6 was isolated, mechanically dissociated to obtain a single cell suspension and cultured in medium containing 10% FBS, glucose, pen/strep, B27 supplement, epidermal growth factor and fibroblast growth factor. After culturing for 7 days, the astrocyte enriched culture was reseded on to poly-D-lysine coated 6 well plates and infected with a doxycycline-inducible lentiviral construct. The lentiviral constructs were induced by addition of doxycycline (2ug/ml) for 2 consecutive days in medium containing glucose, pen/strep, glutamine and B27 supplement.  At 48 hours post-doxycycline induction, the transduced astrocytes were isolated with FACS based on GFP expression.
Directly after FACS isolation, the nuclei were isolated according to 10x Genomic protocol (CG000365) and scATAC-seq libraries (PN-1000230, PN-1000281, PN-3000427) were prepared by using 5000. nuclei for the astrocyte sample and 1250 nuclei for the GFP, Ngn2 and PmutNgn2 samples as input in the 10x Genomics Chromium Next GEM Single Cell mutiome ATAC + Genexpression kit (PN-1000285). The size distribution of the obtained libraries was assessed using an Agilent 2100 Bioanalyser.


title: Methyl-HiC GFP rep1

source_name: Methyl-HiC primary mouse astrocytes transduced with GFP expressing doxycycline-inducible lentivirus rep1


title: Methyl-HiC GFP rep3

source_name: Methyl-HiC primary mouse astrocytes transduced with GFP expressing doxycycline-inducible lentivirus rep3


title: Methyl-HiC GFP rep2

source_name: Methyl-HiC primary mouse astrocytes transduced with GFP expressing doxycycline-inducible lentivirus rep2


title: Multiome_scATAC-seq_Astro

source_name: Multiome scATAC-seq primary mouse astrocytes untransduced


title: Multiome_scATAC-seq_Ngn2

source_name: Multiome scATAC-seq primary mouse astrocytes transduced with Ngn2 expressing doxycycline-inducible lentivirus


title: Multiome_scATAC-seq_GFP

source_name: Multiome scATAC-seq primary mouse astrocytes transduced with GFP expressing doxycycline-inducible lentivirus


title: Multiome_scRNA-seq_PmutNgn2

data_processing:
Reads were aligned to the GRCm38 reference genome (mm10) and quantified using cellranger-arc-2.0.1.
Processed data files represent filtered feature-barcode matrix (*mtx.gz) stored in the Market Exchange Format (MEX) for sparse matrices as well as gzipped TSV files with feature and barcode sequences corresponding to row and column indices respectively. A detailed described of the content of the processed data files can be found at https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/output/matrices
Assembly: mm10

source_name: Multiome scRNA-seq primary mouse astrocytes transduced with PmutNgn2 expressing doxycycline-inducible lentivirus

extract_protocol:
The cortex of post-natal mice aged P5/6 was isolated, mechanically dissociated to obtain a single cell suspension and cultured in medium containing 10% FBS, glucose, pen/strep, B27 supplement, epidermal growth factor and fibroblast growth factor. After culturing for 7 days, the astrocyte enriched culture was reseded on to poly-D-lysine coated 6 well plates and infected with a doxycycline-inducible lentiviral construct. The lentiviral constructs were induced by addition of doxycycline (2ug/ml) for 2 consecutive days in medium containing glucose, pen/strep, glutamine and B27 supplement.  At 48 hours post-doxycycline induction, the transduced astrocytes were isolated with FACS based on GFP expression.
Directly after FACS isolation, the nuclei were isolated according to 10x Genomic protocol (CG000365) and scRNA-seq libraries (PN-1000230, PN-1000284, PN-3000431) were prepared by using 5000. nuclei for the astrocyte sample and 1250 nuclei for the GFP, Ngn2 and PmutNgn2 samples as input in the 10x Genomics Chromium Next GEM Single Cell mutiome ATAC + Genexpression kit (PN-1000285). The size distribution of the obtained libraries was assessed using an Agilent 2100 Bioanalyser.


title: Multiome_scRNA-seq_GFP

source_name: Multiome scRNA-seq primary mouse astrocytes transduced with GFP expressing doxycycline-inducible lentivirus


title: Multiome_scRNA-seq_Astro

source_name: Multiome scRNA-seq primary mouse astrocytes untransduced


title: Multiome_scRNA-seq_Ngn2

source_name: Multiome scRNA-seq primary mouse astrocytes transduced with Ngn2 expressing doxycycline-inducible lentivirus


title: CMV-siRE group, tumour [E3-Z]

city: Nanjing

first: Zheng

address: Xianlin district 163

institute: NJU

description: tumour.csv

data_processing:
Differential gene expression analysis was performed with the R package DESeq2.
Assembly: Ensembl v96 transcriptomes
Supplementary files format and content: csv profile of adjusted gene expression level

source_name: tumour tissue

extract_protocol:
Total RNA was extracted from mouse tissues using TRIzol Reagent (Invitrogen, 15596018, MA, USA) according to the manufacturer’s instructions.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: Tissues were harvested from EGFR DEL19 mice treated with the CMV-scrR, CMV-siRE or CMV-GE11-siRE circuit (10 mg/kg) 7 times over a 2-week period.

value: tumour tissue

value: EGFR DEL19

value: intravenously injected with genetic circuit  (10 mg/kg) every 2 days for a total of 7 injections.

value: Day 14


title: CMV-GE11-siRE group, tumour [G4-Z]

description: tumour.csv