title: CLL_484_ATACseq

city: Singapore

first: Melissa

last: Fullwood

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

data_processing:
For RNA-seq, kallisto (version 0.46.0) was used to quantify the abundance of transcripts. The reference transcriptome used was Ensembl release 75. kallisto reports transcripts per million (TPM) for the transcripts. The TPM values were not nromalized across samples.
For ATAC-seq, reads were aligned as paired-ends reads to hg19 genome assembly using BWA (version 0.7.17-r1188). The command used was bwa mem -M. Duplicates were marked and removed using MarkDuplicates function of Picard (version 2.22.2) from GATK. Paired-end reads with either end unmapped were filtered using samtools (version 1.6). macs2 (version 2.2.6) was used for peak calling with -BAMPE option.
For Hi-C, bwa (version 0.7.17-r1188) was used for aligning the paired-end reads to hg19 genome assembly. The command used was bwa mem -SP5M. The ENCODE HiC pipeline was used for filtering HiC alignments. Unmapped pairs and pairs with low quality mapping were removed. The pairs were deduplicated based on the mapping location of both ends. HiCCUPS from Juicer Tools (version 1.9.12) was used for calling loops. Contact domains were detected using Arrowhead from Juicer Tools.
Genome_build: hg19
Supplementary_files_format_and_content: ENCODE narrowPeak format generated by MACS2.
*_abundances.tsv is a plaintext file of the abundance estimates generated by Kallisto. Fields contained: 1. target_id. Transcript ID; 2. length. Transcript length; 3. eff_length. Effective length of the transcript; 4. est_counts. Estimated read counts given by the bootstrapping process of Kallisto; 5. tpm. Esmated transcript per million (TPM).
*_30.hic is a file contains Hi-C contact matrix of reads with a MAPQ score > 30 (produced by Juicer).

source_name: CLL 484 cells

extract_protocol:
Briefly 50,000 cells were lysed for nuclei isolation using ATAC-Resuspention Buffer containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin.
Transposition reaction was performed for 30 min at 37C using Nextera DNA library preparation kit (NEB). Transposed fragments were amplified by eight PCR cycles for library preparation. Primer dimers and long DNA fragments were removed by AMPure XP beads purification step. DNA concentration was measured by Qubit fluorometric assay and library quality was determined by Bioanalyzer. The library was sequenced in Nextseq 500 76bp paired-end configuration using Illumina platform.

value: Chronic Lymphocytic Leukemia

value: bone marrow aspirates

value: CLL 484 cells


title: Pten KO Cardiomyocyte RNA-seq-2

status: Public on Jul 09 2021

type: SRA

city: Hong Kong

first: Wuming

last: Wang

address: Sha Tin

country: China

institute: The Chinese University of Hong Kong

library_source: transcriptomic

data_processing:
The raw reads were cleaned using internal software SOAPnuke (Version v1.5.2, Website: https://github.com/BGI-flexlab/SOAPnuke) by removing adapter sequences, reads in which unknown bases are more than 10%, and low quality reads.
The clean reads were stored in FASTAQ format.
We used HISAT (Version v2.0.4, Website: http://www.ccb.jhu.edu/software/hisat) to do the mapping step, and calculated gene expression with a software package called RSEM (Version v1.2.12, Website: http://deweylab.biostat.wisc.edu/ RSEM).
FPKM method was used in calculated expression level, and the calculated gene expression can be directly used for comparing the difference of gene expression among sample.
Supplementary_files_format_and_content: FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: cardiomyocytes

growth_protocol: Mouse ESCs were cultured in DMEM/F12 containing GlutaMAX and sodium pyruvate (Life Technologies, 10565) with 15% fetal bovine serum (Hyclone, SH30071), nonessential amino acid solution (Life Technologies, 11140), b-mercaptoethanol (Life Technologies, 31350) with 1000 units/ml LIF (Millipore, ESG1106), 1  mM PD0325901 (Sigma, PZ0162), and 2.5 mM CHIR99021 (Sigma, SML1046). The mouse ESCs were grown on gelatin-coated plates and the medium was replaced every other day. The ESC cultures were passaged every 2 days.

extract_protocol:
Cardiomyocytes were collected, and RNA was harvested using Trizol reagent. The quality of the isolated RNA was determined with Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit). The RNA was converted into a template molecules library for sequencing on the BGISEQ-500.
For RNA-seq, total RNA samples were ribo-depleted and then fragmented. The fragmented samples were reversed transcribed to cDNA, end-repaired and 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. The ligation products were purified, and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer. Denature the PCR products by heat, and the single strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol: The Pten-/- ESCs were generated by the CRISPR-Cas9 system. ESCs were cultured in 6-well plates and transfected with donor plasmid and constructs containing Cas9 and target sequences using lipofectamine 3000, and these were then subjected to cell sorting of GFP-positive cells after transfection for 48 h. The enriched gene-modified cell populations were cultured in 60-mm dishes for 4-5 days, and each cell clone was passaged into 24-well plates. Finally, the Pten-/- cell lines were identified by sequencing, and the cells were stored in liquid nitrogen.

tag: cell type

value: ES-derived cardiomyocytes

tag: strain

value: cell line

tag: genotype

value: Pten-/-


title: CLL_401_ATACseq

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: CLL 401 cells

tag: disease state

tag: tissue

value: peripheral blood

value: CLL 401 cells


title: RNA-Seq of  HMCL-7304 treated with DECANOYL-L-CARNITINE at 100uM concentration K_26_03

city: Los Angeles

first: Brunilda

last: Balliu

state: CA

address: 621 Charles Young Drive South

department: Computational Medicine

country: USA

institute: UCLA

data_processing:
Reference genome (hg19) and gene model annotation files were downloaded from the UCSC genome browser website directly.
Indexes of the reference genome were built using STAR3 and paired-end clean reads were aligned to the reference genome using STAR (v2.6.0; with default option mismatch = 10).
Bam files were filtered for uniquely mapped reads, sorted, and indexed using SAMtools4 (v1.4.1).
HTSeq5 (v0.11.0) was used to count the read numbers mapped to each gene (with option -m union).
Genome_build: hg19

source_name: muscle skeletal

growth_protocol: HepG2, terminally differentiated SGBS, and HCML-7304 cells were starved for 6 hours in EMEA with no FBS (HepG2), DMEM/F12 supplemented with pan/bio and penicillin/streptomycin but no FBS (SGBS adipocytes) or HCML growth medium (PromoCell) without supplements. For the glucose condition DMEM no glucose medium (Thermo) was used.

extract_protocol: none provided by the submitter

treatment_protocol: After starvation and washing with PBS, the cells were exposed for 2 hours to the different compounds or the respective control media.

value: muscle skeletal

value: myocyte

tag: cell line

tag: treatment

value: DECANOYL-L-CARNITINE


title: RNA-Seq of  HEPG2 treated with TGF-B1 at 10ng/ml concentration H_14_03

source_name: liver

value: liver

value: hepatocyte


title: RNA-Seq of  HEPG2 treated with LAUROYL-L-CARNITINE at 100uM concentration H_13_02

value: LAUROYL-L-CARNITINE


title: Pten KO Cardiomyocyte RNA-seq-1


title: CLL_344_ATACseq

source_name: CLL 344 cells

value: CLL 344 cells


title: RNA-Seq of  HMCL-7304 treated with DECANOYL-L-CARNITINE at 100uM concentration K_26_02


title: RNA-Seq of  HEPG2 treated with LAUROYL-L-CARNITINE at 100uM concentration H_13_01


title: high_fat_diet_rep2

type: RNA

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from liver of mice treated with high fat diet for 22 weeks, biological replicate 2

hyb_protocol: According to the Thermo Fisher Scientific expression protocol (HWS kit)

scan_protocol: According to the Thermo Fisher Scientific expression protocol, Scanner 3000 7G

data_processing: SST-RMA gene-level probeset summary with standard settings of the Thermo Fisher Scientific Expression Console software (v.1.4.1.46). The provided SST-RMA data was obtained by including samples from an additional dataset (GSE137924)

label: biotin

source_name: liver_high fat diet treatment for 22 weeks

label_protocol: Total RNA (150 ng) was amplified using the WT PLUS Reagent Kit (Thermo Fisher Scientific Inc., Waltham, USA).

growth_protocol: All experiments were performed in adult male C57BL/6J mice purchased from Janvier Labs (Saint-Berthevin, Cedex, France). Mice were maintained on a 12-h light-dark cycle with free access to water and standard chow diet (Altromin, #1314) or 58% high fat diet (HFD) (Research Diets, D12331).

extract_protocol: Total RNA was isolated from liver tissue employing a commercially available kit (NucleoSpin RNA, #740955, Macherey-Nagel, Düren, Germany)

treatment_protocol: To promote diet-induced obesity (DIO), mice were ad-libitum fed with 58% high-fat diet (HFD) (Research Diets, D12331) for 22 weeks. Control mice were kept with normal chow. Mice were fasted for 4 hours and then sacrificed by cervical dislocation for organ withdrawal. Livers were removed immediately, flash frozen in liquid nitrogen and stored at -80°C until further analysis.

tag: genotype/variation

value: wild type

tag: Sex

value: male

tag: age

value: 30 weeks

tag: diet

value: high fat diet treatment for 22 weeks


title: WT Cardiomyocyte RNA-seq-3


title: CLL_324_ATACseq

source_name: CLL 324 cells

value: Chronic Lymphocytic Leukemia

value: bone marrow aspirates

value: CLL 324 cells


title: RNA-Seq of  HMCL-7304 treated with DECANOYL-L-CARNITINE at 100uM concentration K_26_01


title: RNA-Seq of  HEPG2 treated with IBMX at 250uM concentration H_12_03

value: IBMX


title: WT Cardiomyocyte RNA-seq-2

value: ES-derived cardiomyocytes

value: cell line


title: RNA-Seq of  HEPG2 treated with IBMX at 250uM concentration H_12_02


title: CLL_312_ATACseq

source_name: CLL 312 cells

value: CLL 312 cells


title: WT Cardiomyocyte RNA-seq-1


title: RNA-Seq of  HMCL-7304 CONTROL K_25_03

description: RNA-Seq of  HMCL-7304 CONTROL

value: muscle skeletal

value: myocyte

value: CONTROL (EMPTY EMEM MEDIUM) 4


title: RNA-Seq of  HMCL-7304 CONTROL K_25_02

description: RNA-Seq of  HMCL-7304 CONTROL


title: RNA-Seq of  HEPG2 treated with IBMX at 250uM concentration H_12_01

value: liver

value: hepatocyte


title: S44

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

data_processing:
mapping of reads was done using: bowtie2  --local using Escherichia coli K12 as template genome
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
The quality of the resulting fastq reads we checked using FastQC v0.11.9 (Babraham Bioinformatics, Cambridge and mapped on the reference genome using Bowtie2 v2.4.2 using default settings. Resulting SAM files were converted to BAM using SAMtools 1.11 and featuresCounts 2.0.1 was used to get the gene counts. The T-REx webserver was used to perform statistical analysis and determine differential gene expressions (DGE)
Genome_build: Priestia endophytica strain FH5 ; genome-build ASM383330v1 genome-build-accession NCBI_Assembly:GCA_003833305.1
Supplementary_files_format_and_content: Tab delimited text file

organism: Priestia endophytica

source_name: Bacterial

growth_protocol: 5 ul of Cells suspension of FH5 were inoculated in PDA agar plates at a distance of 2 cm from the PDA plug with or without fungi (R. solani) at 28 °C for 3 dyas

extract_protocol:
RNA was isolated as total RNA  using Roche RNA isolation kit with some modifications
The Zymo-Seq RiboFree™ Total RNA Library Kit (Zymo Research, USA) was used to prepare the library preps for Illumina sequencing using 800ng of the extracted total RNA. Samples were sequenced on the Illumina NexSeq 500 to generate 75 bases singel end reads (75SE) with an average read-depth of 12M reads per sample.

treatment_protocol: A 0.5-cm mycelium plug of 3-day-old R. solani was placed at the center of PDA plate and grow for 3 days at 28°C

value: R. solani exposure


title: S43

value: Untreated


title: YapKO cells, high density, replicate 2

city: Sioux Falls

first: Michael

last: Kareta

state: SD

address: 2301 East 60th Street North

department: Genetics & Genomics

institute: Sanford Research

data_processing:
Reads were aligned using HISAT2 (version 2.1.0) using the --dta --dta-cufflinks arguments. Cuffquant and cuffdiff (Cufflinks version 2.2.1) were used for transcriptome assembly and differential gene analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited files containing read count, fpkm, and pairwise DE gene analysis information.

molecule: polyA RNA

source_name: YapKO cells

growth_protocol: Human Schwann cells (hSC2λ) cells were obtained from the laboratory of Dr. Margaret Wallace. The cells were authenticated by short tandem repeat (STR) DNA profiling (DDC Medical). Cells were maintained in low glucose Dulbecco’s Modified Eagle’s Medium (DMEM) (Gibco) supplemented with 10% fetal bovine serum (Atlas Biologicals) and antibiotics (100 units/ml penicillin and 100 μg/ml Streptomycin) (Gibco), at 37°C in a humidified atmosphere of 5% CO2 (v/v). Cells were tested every 3 months for mycoplasma and confirmed free of contamination.

extract_protocol:
RNA was extracted from hSC2λ WT and YAP -/- cells using the RNeasy Mini Kit (Qiagen).
Libraries were prepared using the NEBNext Ultra II directional kit for Illumina (NEB) and sequenced using the NextSeq 500 High Output v2 Kit (Illumina) on the NextSeq 500 platform.

treatment_protocol: For YAP -/-, guide RNA (TCCGGACCCGGGCAACCG) targeting the first exon of YAP was cloned into the PX459 plasmid (Addgene #62988). hSC2λ cells were transfected using Lipofectamine 2000 (Life Technologies) and treated with 0.25 µg/mL puromycin (Gibco) for 48h. Single clones were selected, expanded, and subjected to Western blot analysis.

value: Human Schwann cells (hSC2lamda)

value: Yap knockout


title: YapKO cells, high density, replicate 3


title: RNA-Seq of  HMCL-7304 treated with RETINOIC ACID at 1uM concentration K_24_03

value: RETINOIC ACID


title: RNA-Seq of  HEPG2 treated with IGF1 at 100nM concentration H_11_03


title: YapKO cells, high density, replicate 1


title: RNA-Seq of  HEPG2 treated with IGF1 at 100nM concentration H_11_02


title: RNA-Seq of  HEPG2 treated with IGF1 at 100nM concentration H_11_01


title: YapKO cells, low density, replicate 3


title: RNA-Seq of  HMCL-7304 treated with RETINOIC ACID at 1uM concentration K_24_01


title: RNA-Seq of  HMCL-7304 treated with RETINOIC ACID at 1uM concentration K_24_02


title: YapKO cells, low density, replicate 2


title: RNA-Seq of  HMCL-7304 treated with WORTMANIN at 100nM concentration K_23_03

value: WORTMANIN


title: DAMAJ_S2_SLURRY

city: Barcelona

first: Claudia

middle: Sanz

last: Lanzas

state: Barcelona

address: Carrer Jordi Girona, 20

department: Environmental Toxicology

country: Spain

institute: IDAEA-CSIC

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMAJ

data_processing:
Library strategy: 16S rDNA metagenome-seq
Paired-end reads was assigned to samples based on their unique barcodes and truncated by cutting off the barcode and primer sequences. Paired-end reads were merged using FLASH (V1.2.7)[21] (see details http://ccb.jhu.edu/software/FLASH/), a very fast and accurate analysis tool, which was designed to merge paired-end reads when at least some of the reads overlap the read generated from the opposite end of the same DNA fragment, and the splicing sequences were called raw tags. Quality filtering on the raw tags were performed under specific filtering conditions to obtain the high-quality clean tags[22] according to the Qiime (V1.7.0)[23] (see details http://qiime.org/scripts/split_libraries_fastq.html) quality controlled process.
The tags were compared with the reference database (Gold database, see details http://drive5.com/uchime/uchime_download.html) using UCHIME algorithm (UCHIME Algorithm, see details http://www.drive5.com/usearch/manual/uchime_algo.html)[24] to detect chimera sequences (see details https://drive5.com/usearch/manual/chimeras.html). And then the chimera sequences were removed[25]. Then the Effective Tags finally obtained.
OTU cluster and Taxonomic annotation: Sequences analysis were performed by Uparse software (Uparse v7.0.1001, see details http://drive5.com/uparse/)[26] using all the effective tags. Sequences with ≥97% similarity were assigned to the same OTUs. Representative sequence for each OTU was screened for further annotation.
OTU cluster and Taxonomic annotation: For each representative sequence, Mothur software was performed against the SSUrRNA database of SILVA Database (see details http://www.arb-silva.de/)[27]for species annotation at each taxonomic rank (Threshold:0.8~1)[28] (kingdom, phylum, class, order, family, genus, species).
OTU cluster and Taxonomic annotation: To obtain the phylogenetic relationship of all OTUs representative sequences, the MUSCLE[29] (Version 3.8.31, see details http://www.drive5.com/muscle/) can compare multiple sequences rapidly.
OTU cluster and Taxonomic annotation: OTUs abundance information were normalized using a standard of sequence number corresponding to the sample with the least sequences. Subsequent analysis of alpha diversity and beta diversity were all performed basing on this output normalized data.
Genome_build: SILVA database
Supplementary_files_format_and_content: tab-delimited text files include normalized reads values (normalized counts) for each sample.

organism: soil metagenome

source_name: SOIL

growth_protocol: Soils were freezed at -20ºC prior to DNA extraction

extract_protocol:
DNeasy PowerSoil Kit (Qiagen Laboratories, Inc.)
Sequencing libraries were generated using NEBNext Ultra DNA Library Pre ®Kit for Illumina, following manufacturer's recommendations. Sequencing was carried out on an Illumina platform and 250 bp paired-end reads were generated

treatment_protocol: Soil directly added to the kit at a total amount of 0,25g following manufacturer´s indications

value: SLURRY

tag: geographic location

tag: sampling date

tag: soil type

value: Soil  fertilised with slurry


title: RNA-Seq of  HMCL-7304 CONTROL K_25_01

description: RNA-Seq of  HMCL-7304 CONTROL


title: DAMAI_S2_SLURRY

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMAI


title: DAMAH_S2_SLUDGE

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMAH

value: SLUDGE

value: Soil  fertilised with sludge


title: RNA-Seq of  HMCL-7304 treated with WORTMANIN at 100nM concentration K_23_02


title: CLL_102_ATACseq

source_name: CLL 102 cells

value: Chronic Lymphocytic Leukemia

value: bone marrow aspirates

value: CLL 102 cells


title: RNA-Seq of  HEPG2 treated with ISOPRENALINE at 100nM concentration H_10_02

value: ISOPRENALINE


title: YapKO cells, low density, replicate 1


title: RNA-Seq of  HMCL-7304 treated with WORTMANIN at 100nM concentration K_23_01

value: muscle skeletal

value: myocyte


title: DAMAG_S2_SLUDGE

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMAG


title: WT cells, high density, replicate 3

source_name: WT cells

value: wild-type


title: DAMAF_S1_SLUDGE

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMAF


title: DAMAK_S3_MINERAL

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMAK

value: MINERAL

value: Soil  fertilised with mineral


title: RNA-Seq of  HEPG2 CONTROL  H_09_03

description: RNA-Seq of  HEPG2 CONTROL

value: liver

value: hepatocyte

value: CONTROL (EMPTY EMEM MEDIUM) 2


title: RNA-Seq of  HEPG2 treated with ISOPRENALINE at 100nM concentration H_10_01


title: RNA-Seq of  HEPG2 CONTROL  H_09_02

description: RNA-Seq of  HEPG2 CONTROL


title: RNA-Seq of  HMCL-7304 treated with U0126 at 5uM concentration K_22_02


title: WT cells, high density, replicate 1

value: Human Schwann cells (hSC2lamda)


title: RNA-Seq of  HMCL-7304 treated with U0126 at 5uM concentration K_22_03


title: WT cells, high density, replicate 2


title: DAMAE_S1_USW

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMAE

value: USW

value: Soil  fertilised with usw


title: DAMAD_S1_SLURRY

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMAD

value: SLURRY

value: Soil  fertilised with slurry


title: RNA-Seq of  HEPG2 treated with ISOPRENALINE at 100nM concentration H_10_03


title: RNA-Seq of  HEPG2 CONTROL  H_09_01

description: RNA-Seq of  HEPG2 CONTROL


title: WT cells, low density, replicate 3


title: RNA-Seq of  HMCL-7304 treated with U0126 at 5uM concentration K_22_01


title: RNA-Seq of  HEPG2 treated with DEXAMETHASONE at 1uM concentration H_08_03

value: DEXAMETHASONE


title: WT cells, low density, replicate 2


title: RNA-Seq of  HEPG2 treated with DEXAMETHASONE at 1uM concentration H_08_02


title: RNA-Seq of  HMCL-7304 treated with SP600125 at 5uM concentration K_21_03


title: DAMAC_S1_MINERAL

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMAC


title: WT cells, low density, replicate 1


title: RNA-Seq of  HMCL-7304 treated with SP600125 at 5uM concentration K_21_02


title: RNA-Seq of  HEPG2 treated with DEXAMETHASONE at 1uM concentration H_08_01


title: RNA-Seq of  HMCL-7304 treated with SP600125 at 5uM concentration K_21_01


title: RNA-Seq of  HEPG2 treated with ROSIGLITAZONE at 2uM concentration H_07_02

value: ROSIGLITAZONE


title: RNA-Seq of  HMCL-7304 treated with SB203580 at 5uM concentration K_20_03


title: RNA-Seq of  HMCL-7304 treated with SB203580 at 5uM concentration K_20_02


title: RNA-Seq of  HEPG2 treated with ROSIGLITAZONE at 2uM concentration H_07_03


title: DAMA9_S1_SLUDGE

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA9

value: SLUDGE

value: Soil  fertilised with sludge


title: DAMAA_S0_NONE

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMAA

value: Initial soil, with no fertilization nor chemical nor organic


title: DAMA8_S1_USW

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA8


title: RNA-Seq of  HEPG2 treated with ROSIGLITAZONE at 2uM concentration H_07_01


title: RNA-Seq of  HEPG2 treated with IL-6 at 20ng/ml concentration H_06_03


title: DAMA67_S3_SLURRY

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA67


title: RNA-Seq of  HMCL-7304 treated with LEPTIN at 100ng/ml concentration K_19_02

value: muscle skeletal

value: myocyte

value: LEPTIN


title: RNA-Seq of  HMCL-7304 treated with SB203580 at 5uM concentration K_20_01


title: RNA-Seq of  HEPG2 treated with IL-6 at 20ng/ml concentration H_06_01


title: RNA-Seq of  HMCL-7304 treated with LEPTIN at 100ng/ml concentration K_19_01


title: DAMAB_S0_NONE

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMAB


title: RNA-Seq of  HMCL-7304 treated with ADIPONECTIN at 1nM concentration K_18_02

value: ADIPONECTIN


title: RNA-Seq of  HEPG2 treated with TNF-a at 10ng/ml concentration H_05_02

value: liver

value: TNF-a


title: DAMA65_S3_SLUDGE

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA65


title: DAMA66_S3_SLURRY

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA66


title: DAMA64_S3_SLUDGE

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA64


title: RNA-Seq of  HEPG2 treated with TNF-a at 10ng/ml concentration H_05_01

value: hepatocyte


title: RNA-Seq of  HMCL-7304 treated with ADIPONECTIN at 1nM concentration K_18_03


title: DAMA63_S3_SLUDGE

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA63


title: UNKC_2: UNKC tumor RNAseq

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

data_processing:
The RNAseq analysis was performed on Galaxy main server (usegalaxy.org). The raw reads were mapped to mouse genome mm10 using STAR aligner with default settings.
Reads mapped to annotated features were counted using featureCounts (Galaxy v1.6.3).
The DEseq2 v1.18.1 implemented in Galaxy (v2.11.40.2) was used to normalize the raw accounts and identify differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: DEseq2 output files including differential analysis results and normalized count table as well as raw count files generated by featureCounts

source_name: UN-KC-6141 orthotopic tumors from tumor-bearing mice

growth_protocol: PANC02-H7 and UN-KC-6141 cells were surgically injected to pancrease of C57BL/6 mice. Tumors were dissected from mice 20 days after tumor cell injection.

extract_protocol:
RNA was isolated using the ThermoFisher GeneJet RNA isolation kit
Novogene Corp Custome library construction

treatment_protocol: The mice were not treated

value: UN-KC-6141 orthotopic tumor

tag: site

value: Pancreas

tag: replicate

value: Replicate 2


title: DAMA7_S1_USW

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA7

value: USW

value: Soil  fertilised with usw


title: RNA-Seq of  HMCL-7304 treated with ADIPONECTIN at 1nM concentration K_18_01


title: UNKC_1: UNKC tumor RNA-seq

value: Replicate 1


title: RNA-Seq of  HMCL-7304 CONTROL K_17_03

description: RNA-Seq of  HMCL-7304 CONTROL

value: CONTROL (EMPTY EMEM MEDIUM) 3


title: DAMA62_S3_USW

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA62


title: RNA-Seq of  HEPG2 treated with IL-6 at 20ng/ml concentration H_06_02


title: RNA-Seq of  HMCL-7304 treated with LEPTIN at 100ng/ml concentration K_19_03


title: DAMA61_S3_USW

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA61


title: RNA-Seq of  HMCL-7304 CONTROL K_17_02

description: RNA-Seq of  HMCL-7304 CONTROL


title: N_2: Normal pancreas tissue RNA-seq

source_name: Normal whole pancreas from C57BL/6 mice

value: Normal pancreas


title: RNA-Seq of  HEPG2 treated with INSULIN at 100mM concentration H_04_01

value: INSULIN


title: DAMA68_S3_SLURRY

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA68

value: SLURRY

value: Soil  fertilised with slurry


title: RNA-Seq of  HMCL-7304 CONTROL K_17_01

description: RNA-Seq of  HMCL-7304 CONTROL

value: muscle skeletal

value: myocyte


title: N_1: Normal pancreas tissue RNA-seq


title: DAMA60_S3_USW

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA60


title: RNA-Seq of  HEPG2 treated with GLUCOSE at 10mM concentration H_03_03

value: GLUCOSE


title: RNA-Seq of  HEPG2 treated with TNF-a at 10ng/ml concentration H_05_03

value: liver


title: H7_2: H7 tumor RNA-seq

source_name: PANC02-H7 orthotopic tumors from tumor-bearing mice

value: PANC02-H7 orthotopic tumor


title: DAMA59_S3_MINERAL

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA59

value: MINERAL

value: Soil  fertilised with mineral


title: DAMA58_S3_MINERAL

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA58


title: RNA-Seq of  HEPG2 treated with GLUCOSE at 10mM concentration H_03_02

value: hepatocyte


title: H7_1: H7 tumor RNA-seq

value: Pancreas


title: DAMA57_S3_MINERAL

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA57


title: RNA-Seq of  HMCL-7304 treated with ATORVASTATIN at 1uM concentration K_16_03

value: ATORVASTATIN


title: RNA-Seq of  HEPG2 treated with INSULIN at 100mM concentration H_04_03


title: UNKC_2: UNKC tumor ChIP-seq

description: ChIP DNA

data_processing:
The ChIP-seq analysis was performed on Galaxy server. Adaptor and quality trimming were performed using Trim Glore! Modules (Galaxy v0.4.3.1). Trimmed reads were mapped to mouse genome mm10 using Bowtie2 (Galaxy v2.3.4.3) using default settings. Reads mapped to the mitochondria genome were removed using Filter SAM or BAM function under the samtools module (Galaxy v1.8), and PCR duplicates were removed using MarkDuplicates from Picard tool v2.20.2. The mapped reads overlapping with ENCODE blacklist regions (version 2) were filtered before calling peaks.
ChIP-seq peak calling was performed on Galaxy server using MACS2 v2.1.2 using default settings”.
DiffBind (Galaxy v. 2.6.6.4)  was used to identify differential peaks.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig

extract_protocol: Normal mouse pancreas and tumors from tumor-bearing mice were used for chromatin fragment preparation. Anti-H3K4me3 antibody was used for ChIP, followed by library construction and ChIP-sequencing.

value: UN-KC-6141 orthotopic tumor

tag: replicates

value: Replicate 2


title: DAMA56_S3_SLURRY

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA56


title: RNA-Seq of  HEPG2 CONTROL FOR GLUCOSE H_02_03

description: RNA-Seq of  HEPG2 CONTROL FOR GLUCOSE

tag: cell type

value: NO GLUCOSE (DMEM NO GLUCOSE)


title: RNA-Seq of  HEPG2 treated with INSULIN at 100mM concentration H_04_02


title: RNA-Seq of  HMCL-7304 treated with METFORMIN at 1mM concentration K_15_03

value: METFORMIN


title: UNKC_1: UNKC tumor ChIP-seq

description: ChIP DNA

value: Replicate 1


title: RNA-Seq of  HEPG2 CONTROL FOR GLUCOSE H_02_02

description: RNA-Seq of  HEPG2 CONTROL FOR GLUCOSE


title: RNA-Seq of  HMCL-7304 treated with METFORMIN at 1mM concentration K_15_02


title: DAMA55_S3_SLURRY

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA55

value: SLURRY


title: N_2: Normal pancreas tissue ChIP-seq

description: ChIP DNA

value: Normal pancreas


title: DAMA54_S3_SLURRY

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA54

value: Soil  fertilised with slurry


title: RNA-Seq of  HEPG2 CONTROL FOR GLUCOSE H_02_01

description: RNA-Seq of  HEPG2 CONTROL FOR GLUCOSE


title: RNA-Seq of  HMCL-7304 treated with TGF-B1 at 10ng/ml concentration K_14_03

value: muscle skeletal

value: myocyte


title: DAMA53_S3_SLUDGE

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA53

value: SLUDGE

value: Soil  fertilised with sludge


title: RNA-Seq of  HMCL-7304 treated with ATORVASTATIN at 1uM concentration K_16_02


title: RNA-Seq of  HMCL-7304 treated with METFORMIN at 1mM concentration K_15_01


title: H7_2: H7 tumor ChIP-seq

description: ChIP DNA

value: PANC02-H7 orthotopic tumor


title: H7_1: H7 tumor ChIP-seq

description: ChIP DNA

source_name: PANC02-H7 orthotopic  tumors from tumor-bearing mice


title: RNA-Seq of  HEPG2 CONTROL  H_01_02

description: RNA-Seq of  HEPG2 CONTROL

value: liver

value: CONTROL (EMPTY EMEM MEDIUM) 1


title: RNA-Seq of  HEPG2 treated with GLUCOSE at 10mM concentration H_03_01

value: hepatocyte

value: GLUCOSE


title: DAMA52_S3_SLUDGE

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA52


title: RNA-Seq of  HMCL-7304 treated with TGF-B1 at 10ng/ml concentration K_14_02


title: RNA-Seq of  HMCL-7304 treated with TGF-B1 at 10ng/ml concentration K_14_01


title: RNA-Seq of  HMCL-7304 treated with ATORVASTATIN at 1uM concentration K_16_01

value: ATORVASTATIN


title: DAMA50_S3_USW

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA50

value: USW

value: Soil  fertilised with usw


title: RNA-Seq of  HMCL-7304 treated with LAUROYL-L-CARNITINE at 100uM concentration K_13_03

value: LAUROYL-L-CARNITINE


title: HMM_3

city: Columbus

first: David

last: Brigstock

state: Ohio

address: 700 Children's Drive

institute: Nationwide Children's Hospital

data_processing:
Each sample was aligned to the GRCh38.p6 assembly of the human reference from NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000001405.32_GRCh38.p6) using version 2.5.1b of the RNA-Seq aligner STAR (http://bioinformatics.oxfordjournals.org/content/29/1/15)
Features were identified from the GFF file that came with the assembly from NCBI
Feature coverage counts were calculated using HTSeq (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html).
Differentially expressed features were calculated using DESeq2 (http://genomebiology.com/2014/15/12/550).
Genome_build: GRCh38.p6
Supplementary_files_format_and_content: RNA-seq_unfiltered list.xlsx (Excel spreadsheet containing normalized read counts and differential expression data for each comparison)

growth_protocol: HepG2/NTCP cells were maintained in the complete medium supplemented with 10% FBS,1% Pen/Step, and 8 μg/ml Blasticidin.

extract_protocol:
The cells were lysed in RLT buffer and total RNA was extracted with a QIAGEN RNAeasy kit and treated with DNase I
The library was prepared from first strand cDNA using ScriptSeq v2 RNA-Seq library preparation kit (Epicentre Biotechnologies,WI). Sequencing was performed using the Illumina HiSeq 4000 platform.

treatment_protocol: Cells were washed with PBS, changed with HMM or DMEM/10%FBS/2%DMSO medium, and cultured for 24hr before cell collection.

value: Hepatoma cell line

value: HMM

tag: passage number

tag: selection marker

value: Blasticidin


title: N_1: Normal pancreas tissue ChIP-seq

description: ChIP DNA

value: Normal pancreas

value: Pancreas

value: Replicate 1


title: DAMA5_S1_MINERAL

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA5

value: MINERAL

value: Soil  fertilised with mineral


title: dKO BM Tx rep3

city: Bonn

first: Lino

middle: Lars

last: Teichmann

address: Venusberg-Campus 1

department: Department of Medicine III

institute: University Hospital Bonn

description:
4816
DESeq2_results_spleen_CgasKO-BM-Tx_vs_dKO-BM-Tx.csv

data_processing:
Basecalling was performed with bcl2fastq 1.8.4
Adapter-trimmed raw reads were uploaded to Partek Genomics Suite (PGS, build 8.0.19.0819), trimmed for a Phred quality score > 20 and aligned to the mouse reference genome mm10 by STAR (version 2.6.1) with slightly modified standard settings (max mismatches = 14)
For mRNA quantification mm10 Ensembl transcripts (release 98) were used as annotation files
Raw gene counts were normalized and differentially expressed genes (defined by p value < 0.05) identified by DESeq2 (package version 1.25.16)
Genome_build: mm10
Supplementary_files_format_and_content: Comma separated value files contain DESeq2 results

source_name: spleen

extract_protocol:
Total RNA was isolated from single cell suspensions using the SPLIT RNA Extraction kit (Lexogen)
RNA libraries were prepared for sequencing using the Lexogen QuantSeq 3’-mRNA-Seq Library Prep Kit (FWD)

tag: strain

value: spleen


title: RNA-Seq of  HMCL-7304 treated with LAUROYL-L-CARNITINE at 100uM concentration K_13_02

tag: tissue

value: muscle skeletal

value: myocyte


title: dKO BM Tx rep5

description:
4822
DESeq2_results_spleen_CgasKO-BM-Tx_vs_dKO-BM-Tx.csv


title: DAMA49_S3_USW

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA49


title: RNA-Seq of  HEPG2 CONTROL  H_01_03

description: RNA-Seq of  HEPG2 CONTROL

value: liver

value: hepatocyte

tag: cell line

value: CONTROL (EMPTY EMEM MEDIUM) 1


title: Ctrl_3

tag: treatment

value: Ctrl


title: dKO BM Tx rep4

description:
4819
DESeq2_results_spleen_CgasKO-BM-Tx_vs_dKO-BM-Tx.csv


title: RNA-Seq of  HMCL-7304 treated with IBMX at 250uM concentration K_12_03

value: IBMX


title: DAMA48_S3_USW

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA48

value: USW

value: Soil  fertilised with usw


title: DAMA51_S3_SLUDGE

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA51

value: SLUDGE

value: Soil  fertilised with sludge


title: HMM_2

value: Hepatoma cell line

value: HMM

value: Blasticidin


title: Ctrl_2


title: RNA-Seq of  HEPG2 CONTROL  H_01_01

description: RNA-Seq of  HEPG2 CONTROL


title: HMM_1


title: dKO BM Tx rep1

description:
4796
DESeq2_results_spleen_CgasKO-BM-Tx_vs_dKO-BM-Tx.csv


title: DAMA47_S3_MINERAL

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA47

value: MINERAL


title: dKO BM Tx rep2

description:
4799
DESeq2_results_spleen_CgasKO-BM-Tx_vs_dKO-BM-Tx.csv


title: Cgas-/- BM Tx rep5

description:
4821
DESeq2_results_spleen_CgasKO-BM-Tx_vs_dKO-BM-Tx.csv


title: RNA-Seq of  HMCL-7304 treated with IBMX at 250uM concentration K_12_02


title: DAMA46_S3_MINERAL

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA46

value: Soil  fertilised with mineral


title: Ctrl_1


title: RNA-Seq of  HMCL-7304 treated with IBMX at 250uM concentration K_12_01


title: Cgas-/- BM Tx rep3

description:
4815
DESeq2_results_spleen_CgasKO-BM-Tx_vs_dKO-BM-Tx.csv

value: spleen


title: Distal sample JG-44

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

data_processing:
Base calling and demultiplexing with Illumina Casava 1.8.2
Adapter trimming using FLEXBAR (v2.4)
Alignment to hg19/GRCh37 reference genome using STAR version 2.3.0 with default settings
Reads per gene counted using Rsubread R package
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text giving raw number of counts mapped to each gene (identified by Entrez ID) in each sample

source_name: Sorted ILC3s

extract_protocol:
Sorted cells were used to prepare RNAseq libraries using the Clontech SMARTer Ultra Low Input RNA Kit V4 (Clontech Laboratories).
Standard Illumina protocols

tag: patient

value: Distal

value: Sorted ILC3s


title: RNA-Seq of  HMCL-7304 treated with IGF1 at 100nM concentration K_11_03

source_name: muscle skeletal

value: muscle skeletal

value: myocyte


title: Tumor sample JG-43

value: Tumor


title: DAMA42_S2_SLURRY

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA42

value: SLURRY

value: Soil  fertilised with slurry


title: Cgas-/- BM Tx rep2

description:
4798
DESeq2_results_spleen_CgasKO-BM-Tx_vs_dKO-BM-Tx.csv


title: RNA-Seq of  HMCL-7304 treated with IGF1 at 100nM concentration K_11_02


title: DAMA41_S2_SLUDGE

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA41


title: Cgas-/- BM Tx rep1

description:
4795
DESeq2_results_spleen_CgasKO-BM-Tx_vs_dKO-BM-Tx.csv


title: Distal sample JG-40


title: RNA-Seq of  HMCL-7304 treated with LAUROYL-L-CARNITINE at 100uM concentration K_13_01

value: LAUROYL-L-CARNITINE


title: RNA-Seq of  HMCL-7304 treated with IGF1 at 100nM concentration K_11_01


title: Distal smple JG-012-New

value: CRC- GI1280


title: RNA-Seq of  HMCL-7304 treated with ISOPRENALINE at 100nM concentration K_10_03

value: ISOPRENALINE


title: Tumor sample JG-011-New


title: DAMA40_S2_SLUDGE

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA40

value: SLUDGE

value: Soil  fertilised with sludge


title: Distal sample JG-010-New


title: Cgas-/- BM Tx rep4

description:
4818
DESeq2_results_spleen_CgasKO-BM-Tx_vs_dKO-BM-Tx.csv


title: DAMA43_S2_SLURRY

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA43


title: Tumor sample JG-09-New


title: Cgas-/- rep4

description:
4674
DESeq2_results_BM_CgasKO_vs_dKO.csv

source_name: bone marrow

value: bone marrow


title: DAMA4_S1_MINERAL

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA4


title: dkO rep4

description:
4259
DESeq2_results_BM_CgasKO_vs_dKO.csv


title: RNA-Seq of  HMCL-7304 CONTROL K_09_03

description: RNA-Seq of  HMCL-7304 CONTROL

value: CONTROL (EMPTY EMEM MEDIUM) 2


title: RNA-Seq of  HMCL-7304 treated with ISOPRENALINE at 100nM concentration K_10_02


title: Tumor sample JG-07-New


title: RNA-Seq of  HMCL-7304 treated with ISOPRENALINE at 100nM concentration K_10_01


title: Cgas-/- rep3

description:
4248
DESeq2_results_BM_CgasKO_vs_dKO.csv


title: DAMA39_S2_SLUDGE

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA39


title: dkO rep3

description:
4266
DESeq2_results_BM_CgasKO_vs_dKO.csv


title: DAMA38_S2_USW

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA38

value: USW

value: Soil  fertilised with usw


title: dkO rep2

description:
4267
DESeq2_results_BM_CgasKO_vs_dKO.csv


title: DAMA36_S2_USW

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA36


title: DAMA37_S2_USW

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA37


title: CLL_484_HiC

source_name: CLL 484 cells

extract_protocol:
Hi-C libraries were prepared using the Arima Genomics kit (Arima Genomics, San Diego, CA) in conjunction with the Swift Biosciences Accel-NGS 2S Plus DNA Library Kit (Cat # 21024) and Swift Biosciences Indexing Kit (Cat # 26148) following the manufacturer's recommendations. In brief, 1X 106 cells were fixed with formaldehyde in the nucleus. Fixed cells were permeabilized using a lysis buffer and then digested with a restriction enzyme cocktail supplied in the Arima HiC kit. The resulting overhangs were filled in with biotinylated nucleotides followed by ligation. After ligation, crosslinks were reversed, and the DNA was purified from protein. Purified DNA was treated to remove biotin that was not internal to ligated fragments. Hi-C material was then sonicated using a Covaris Focused-Ultrasonicator M220 instrument to achieve 300-500 bp fragment sizes. The sonicated DNA was double-size selected using Ampure XP beads.
Hi-C sequencing libraries were generated using low input Swift Biosciences Accel-NGS 2S Plus DNA Library Kit (Cat # 21024) and Swift Biosciences Indexing Kit (Cat # 26148). The Hi-C libraries were loaded on an Illumina flow cell for paired-end 150-nucleotide read length sequencing on the Illumina HiSeq 4000 following the manufacturer's protocols.

tag: disease state

value: Chronic Lymphocytic Leukemia

value: bone marrow aspirates

value: CLL 484 cells


title: dkO rep1

description:
4389
DESeq2_results_BM_CgasKO_vs_dKO.csv


title: RNA-Seq of  HMCL-7304 CONTROL K_09_02

description: RNA-Seq of  HMCL-7304 CONTROL

value: muscle skeletal


title: RNA-Seq of  HMCL-7304 CONTROL K_09_01

description: RNA-Seq of  HMCL-7304 CONTROL

value: myocyte


title: Cgas-/- rep2

description:
4249
DESeq2_results_BM_CgasKO_vs_dKO.csv


title: DAMA35_S2_MINERAL

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA35

value: MINERAL

value: Soil  fertilised with mineral


title: CLL_401_HiC

source_name: CLL 401 cells

value: peripheral blood

value: CLL 401 cells


title: RNA-Seq of  HMCL-7304 treated with DEXAMETHASONE at 1uM concentration K_08_03

value: DEXAMETHASONE


title: CLL_344_HiC

source_name: CLL 344 cells

value: CLL 344 cells


title: Cgas-/- rep1

description:
4250
DESeq2_results_BM_CgasKO_vs_dKO.csv


title: DAMA34_S2_MINERAL

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA34


title: DAMA33_S2_MINERAL

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA33


title: RNA-Seq of  HMCL-7304 treated with DEXAMETHASONE at 1uM concentration K_08_01


title: RNA-Seq of  HMCL-7304 treated with DEXAMETHASONE at 1uM concentration K_08_02


title: CLL_324_HiC

source_name: CLL 324 cells

value: CLL 324 cells


title: E17TDEP_WT_ATACseq_rep2

first: Neil

last: Segil

address: 1425 san pablo st, BCC 503K

department: BCC

institute: University of Southern California

data_processing:
For RNAseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using STAR. Reads were quantified against genes using RSEM, and differential gene expression analysis was conducted using DESeq2.
For ATACseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using bowtie2. PCR-duplicates were removed by Sambamba, and then peaks were called by MACS2 from individual replicate using filter p value < 0.01.
For Cut&Run, reads were trimmed based on quality score and then aligned to referene mouse genome (mm10) using STAR. PCR duplicates were removed based on UMI by umi_tools,  and then peaks were called by MACS2 for individual replicate using filter p value < 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: read count for genes in text format for RNAseq; peak regions in narrowPeak format for ATACseq and CUT&RUN

source_name: epidermis

extract_protocol:
Touch dome progenitor (TDEP) were purified from the skin of E17 wildtype animals by FACS sorting. Nuclei were extracted and chromatin were digested by tn5 transposase at 37°C for 20 minutes.DNA fragments were extracted using MiniElute columns (Qiagen), and then amplified by PCR.
Library were amplified by PCR with indexed primers

tag: developmental stage

value: embryonic day 17.5

value: Touch dome progenitor cells

tag: genotype

value: Wildtype


title: DAMA32_S2_SLURRY

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA32

value: SLURRY

tag: geographic location

value: Soil  fertilised with slurry


title: CLL_312_HiC

source_name: CLL 312 cells

value: Chronic Lymphocytic Leukemia

value: CLL 312 cells


title: RNA-Seq of  HMCL-7304 treated with ROSIGLITAZONE at 2uM concentration K_07_02

value: ROSIGLITAZONE


title: CLL_102_HiC

value: bone marrow aspirates

value: CLL 102 cells


title: DAMA27_S2_SLUDGE

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA27

source_name: SOIL

value: SLUDGE

tag: sampling date

value: Soil  fertilised with sludge


title: RNA-Seq of  HMCL-7304 treated with ROSIGLITAZONE at 2uM concentration K_07_03

value: muscle skeletal

value: myocyte


title: RNA-Seq of  HMCL-7304 treated with ROSIGLITAZONE at 2uM concentration K_07_01


title: E17TDEP_WT_ATACseq_rep1


title: E17Merkel_WT_POU4F3_CutnRun_rep2

data_processing:
Library strategy: CUT&RUN
For RNAseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using STAR. Reads were quantified against genes using RSEM, and differential gene expression analysis was conducted using DESeq2.
For ATACseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using bowtie2. PCR-duplicates were removed by Sambamba, and then peaks were called by MACS2 from individual replicate using filter p value < 0.01.
For Cut&Run, reads were trimmed based on quality score and then aligned to referene mouse genome (mm10) using STAR. PCR duplicates were removed based on UMI by umi_tools,  and then peaks were called by MACS2 for individual replicate using filter p value < 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: read count for genes in text format for RNAseq; peak regions in narrowPeak format for ATACseq and CUT&RUN

extract_protocol:
Merkel cells (Atoh1-GFP+) were purified from the skin of E17 wildtype animals by FACS sorting. Chromatin was digested using CUT&RUN method, and DNA fragments were extracted by phenol-chloroform method.
Libraries were prepared using Accel 2S Plus DNA library kit with MID and single indexed adapters

value: Merkel cells


title: DAMA31_S2_SLURRY

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA31

tag: soil type


title: E17Merkel_WT_POU4F3_CutnRun_rep1


title: RNA-Seq of  HMCL-7304 treated with IL-6 at 20ng/ml concentration K_06_03


title: CLL_344_RNAseq

extract_protocol:
Total RNA was extracted from the CLL samples using the All Prep DNA/RNA kit (Qiagen). The RNA was quantified using the Qubit BR RNA Assay kit.
RNA-seq libraries (strand specific and ribo zero) were constructed using Illumina Total RNA Prep kit (Illumina, San Diego, CA, USA) and sequenced 150 bases paired-end on the Illumina HiSeq 4000 following the manufacturer's instruction.

value: CLL 344 cells


title: DAMA26_S2_USW

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA26

value: USW

value: Soil  fertilised with usw


title: RNA-Seq of  HMCL-7304 treated with IL-6 at 20ng/ml concentration K_06_02


title: CLL_401_RNAseq

value: peripheral blood

value: CLL 401 cells


title: DAMA25_S2_USW

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA25


title: RNA-Seq of  HMCL-7304 treated with IL-6 at 20ng/ml concentration K_06_01


title: E17Merkel_WT_ATACseq_rep2

extract_protocol:
Merkel cells (Atoh1-GFP+) were purified from the skin of E17 wildtype animals by FACS sorting. Nuclei were extracted and chromatin were digested by tn5 transposase at 37°C for 20 minutes.DNA fragments were extracted using MiniElute columns (Qiagen), and then amplified by PCR.
Library were amplified by PCR with indexed primers

value: embryonic day 17.5

value: Wildtype


title: CLL_324_RNAseq

value: Chronic Lymphocytic Leukemia

value: CLL 324 cells


title: E17Merkel_WT_ATOH1_CutnRun_rep1


title: DAMA23_S2_MINERAL

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA23

value: MINERAL

value: Soil  fertilised with mineral


title: E17Merkel_WT_ATACseq_rep1


title: DAMA22_S2_MINERAL

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA22


title: CLL_312_RNAseq

value: bone marrow aspirates

value: CLL 312 cells


title: E17Merkel_Pou4f3KO_ATACseq_rep2

extract_protocol:
Merkel cells (Atoh1-GFP+) were purified from the skin of E17 Pou4f3 mutant animals by FACS sorting. Nuclei were extracted and chromatin were digested by tn5 transposase at 37°C for 20 minutes.DNA fragments were extracted using MiniElute columns (Qiagen), and then amplified by PCR.
Library were amplified by PCR with indexed primers

value: Pou4f3 KO


title: CLL_484_RNAseq

value: CLL 484 cells


title: RNA-Seq of  HMCL-7304 treated with TNF-a at 10ng/ml concentration K_05_03

value: muscle skeletal

value: myocyte

value: TNF-a


title: CLL_102_RNAseq

source_name: CLL 102 cells

value: CLL 102 cells


title: RNA-Seq of  HMCL-7304 treated with TNF-a at 10ng/ml concentration K_05_01


title: E17Merkel_WT_ATOH1_CutnRun_rep2

value: Merkel cells


title: RNA-Seq of  HMCL-7304 treated with INSULIN at 100mM concentration K_04_03

value: INSULIN


title: DAMA21_S2_MINERAL

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA21


title: E17HC_WT_POU4F3_CutnRun_rep2

source_name: Cochlea

extract_protocol:
Hair cells (Atoh1-GFP+) were purified from E17 wildtype cochlea  by FACS sorting. Chromatin were digested by CUT&RUN technique, and DNA fragements were purified by phenol-chloroform method.
Libraries were prepared using Accel 2S Plus DNA library kit with MID and single indexed adapters

value: hair cells

value: WT


title: E17Merkel_Pou4f3KO_ATACseq_rep1

value: embryonic day 17.5


title: RNA-Seq of  HMCL-7304 treated with INSULIN at 100mM concentration K_04_02

extract_protocol: none provided by the submitter


title: RNA-Seq of  HMCL-7304 treated with INSULIN at 100mM concentration K_04_01


title: RNA-Seq of  HMCL-7304 treated with TNF-a at 10ng/ml concentration K_05_02


title: DAMA18_S1_MINERAL

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA18


title: case_renal biopsy [BIOS-13-0007]

city: Dijon

first: Baptiste

last: Lamarthée

address: Bd du Mal De Lattre de Tassigny

department: RIGHT

country: France

institute: Inserm U1098

data_processing:
The normalization and all the data analysis were performed using Expression Suite software version 1.0.3. Assays with a cycle threshold (CT) values >35 were considered to be not expressed
For the normalization it uses the average of two housekeeping genes: RNU44 and RNU48
Target miRNA signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
All deltaCt based fold-change calculations from the uploaded raw threshold cycle data were calculated using R Studio.
The normalized_data.txt reports normalized signal (against housekeeping genes).

label: TaqMan

source_name: case_renal biopsy

label_protocol: Specific reverse transcription of 150 ng of total RNA was performed using Megaplex™ RT Primers Human Pool A v2.1 (Thermo Fisher Scientific, Les Ulis, France), on a Veriti Thermal Cycler (Applied Biosystems™, Thermo Fisher Scientific). No complementary (c)DNA preamplification was required.  MiRNA expression was assessed by qPCR, using TaqMan® Array Cards (Applied Biosystems™, Thermo Fisher Scientific), where the primers and probe of each miRNA were spotted and dried in duplicate wells of a microfluidic card. We used TaqMan® Array Human MicroRNA A+B Card Sets v3.0 (Thermo Fisher Scientific)

extract_protocol: Total RNA was extracted using the Allprep DNA/RNA/miRNA Universal Kit (Qiagen Benelux BV) on a QIAcube instrument (Qiagen Benelux BV). The quantity (absorbance at 260 nm) and purity (ratio of the absorbance at 230, 260, and 280 nm) of the isolated RNA were measured using the NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific/Life Technologies Europe BV, Ghent, Belgium). RNA integrity was evaluated with the Eukaryote nano/pico RNA Kit (Agilent Technologies Belgium NV, Diegem, Belgium) on the Bioanalyzer 2100 instrument (Agilent Technologies BelgiumNV)

value: renal, endothelial and immune cells

tag: outcome

value: MVI

tag: type of biopsy

value: Post kidney transplantation


title: E17HC_WT_POU4F3_CutnRun_rep1


title: DAMA2_S0_NONE

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA2

value: Initial soil, with no fertilization nor chemical nor organic


title: E17HC_WT_H3K27ac_CutnRun_rep2


title: E17HC_WT_H3K27me3_CutnRun_rep2


title: E17HC_WT_H3K27me3_CutnRun_rep1


title: RNA-Seq of  HMCL-7304 treated with GLUCOSE at 10mM concentration K_03_03

value: GLUCOSE


title: DAMA15_S1_USW

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA15

value: USW

value: Soil  fertilised with usw


title: DAMA24_S2_USW

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA24


title: RNA-Seq of  HMCL-7304 treated with GLUCOSE at 10mM concentration K_03_02


title: DAMA20_S1_SLURRY

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA20

value: SLURRY

value: Soil  fertilised with slurry


title: DAMA13_S1_SLURRY

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA13


title: case_renal biopsy [BIOS-13-0005]


title: DAMA14_S1_SLURRY

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA14


title: E17HC_WT_H3K27ac_CutnRun_rep1


title: RNA-Seq of  HMCL-7304 CONTROL FOR GLUCOSE K_02_02

value: muscle skeletal

value: myocyte

value: NO GLUCOSE (DMEM NO GLUCOSE)


title: DAMA11_S1_SLUDGE

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA11

value: SLUDGE

value: Soil  fertilised with sludge


title: E17HC_WT_H3K4me1_CutnRun_rep2

value: hair cells


title: case_renal biopsy [BIOS-09-0041]


title: case_renal biopsy [BIOS-13-0003]


title: case_renal biopsy [BIOS-13-0001]


title: RNA-Seq of  HMCL-7304 CONTROL FOR GLUCOSE K_02_01


title: RNA-Seq of  HMCL-7304 treated with GLUCOSE at 10mM concentration K_03_01


title: DAMA19_S1_SLURRY

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA19


title: RNA-Seq of  HMCL-7304 CONTROL FOR GLUCOSE K_02_03


title: E17HC_WT_H3K4me3_CutnRun_rep1

value: WT


title: control_renal biopsy [BIOS-09-0035]

source_name: control_renal biopsy

value: No MVI


title: control_renal biopsy [BIOS-09-0036]

value: renal, endothelial and immune cells


title: E17HC_WT_H3K4me1_CutnRun_rep1

value: embryonic day 17.5


title: DAMA10_S1_SLUDGE

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
DAMA10


title: RNA-Seq of  HMCL-7304 CONTROL K_01_03

description: RNA-Seq of  HMCL-7304 CONTROL

value: CONTROL (EMPTY EMEM MEDIUM) 1


title: E17HC_WT_ATOH1_CutnRun_rep2


title: case_renal biopsy [BIOS-09-0032]

value: MVI

value: Post kidney transplantation


title: RNA-Seq of  HMCL-7304 CONTROL K_01_02

description: RNA-Seq of  HMCL-7304 CONTROL


title: E17HC_WT_H3K4me3_CutnRun_rep2


title: case_renal biopsy [BIOS-09-0033]


title: 4450822

city: montreal

first: Yojiro

last: Yamanaka

state: Quebec

address: 1160 Pine Avenue West, room 416

department: Human Genetics

country: Canada

institute: McGill University (Goodman Cancer Research Centre)

data_processing:
Library strategy: WGS
For WGS - Raw reads were trimmed using Skewer and the resulting reads were aligned to the GRCm38 mouse reference genome using BWA-MEM. Duplicates were marked using Picard (http://broadinstitute.github.io/picard/).
Copy number variants (CNVs) were identified using CNVKit at default parameters in each tumour sample and normal tissue as reference. Heatmaps were generated using CNVKit’s heatmap command on all .cns segment files.
For scRNAseq - Raw BCL files from the Illumina HiSeq were demultiplexed into paired-end, gzip-compressed FASTQ files for each channel using Cell Ranger’s mkfastq.
Using Cell Ranger’s count, reads were aligned to the mouse reference transcriptome (mm10) containing the Tdtomato-WPRE-polyA transcript, and transcript counts quantified for each annotated gene within every cell.
The resulting UMI count matrix (genes × cells) were then provided as input to Seurat suite (version 2.3.4)
Cells were first filtered to remove those that contain less than 200 genes detected and those in which > 10% of the transcript counts were derived from mitochondrial-encoded genes.
Clustering was performed using the “FindClusters” function and Uniform Manifold Approximation and Projection (UMAP) visualization for all cells.
Cluster-specific gene markers were identified using Seurat’s FindMarkers with cutoffs avg_logFC > 0.5 and FDR < 0.05. CNV analysis was performed using the inferCNV package (10.18129/B9.bioc.infercnv)
Genome_build: GRCm38 for WGS and mouse reference transcriptome (mm10) containing the Tdtomato-WPRE-polyA transcript
Supplementary_files_format_and_content: Excel files containing CNAs and cluster gene markers.

source_name: Ovarian tumor

growth_protocol: Mice were housed under standard conditions on B6 background.

extract_protocol:
DNA was extracted from FFPE samples using Qiagen GeneRead DNA FFPE kit. RNA was isolated from the cell portion of ascities fluid after red blood cell removal
DNA libraries were prepared for sequencing using standard Illumina protocols. scRNA library was made using the Chromium Single Cell 3' kit V2.

treatment_protocol: Tumor formation was induced by in vivo electroportation of mouse fallopian tube epithelial cells with plasmids expressing Cas9, guide RNA and Cre.

value: Ovarian tumor

tag: lkb1 status

value: Intact

tag: pax8 expression

value: PAX8 +


title: 600913

value: Deletion


title: 760913

value: PAX8 -


title: E17HC_WT_ATOH1_CutnRun_rep1

tag: cell type


title: E17HC_WT_ATACseq_rep2

extract_protocol:
Hair cells (Atoh1-GFP+) were purified from E17 wildtype cochlea  by FACS sorting. Nuclei were extracted and chromatin were digested by tn5 transposase at 37°C for 20 minutes.DNA fragments were extracted using MiniElute columns (Qiagen), and then amplified by PCR.
Libraries were amplified by PCR with indexed primers


title: control_renal biopsy [BIOS-09-0031]


title: E17HC_WT_ATACseq_rep1


title: RNA-Seq of  HMCL-7304 CONTROL K_01_01

description: RNA-Seq of  HMCL-7304 CONTROL

value: muscle skeletal

value: myocyte


title: RNA-Seq of  SGBS treated with DECANOYL-L-CARNITINE at 100uM concentration B_26_02

source_name: adipose

value: adipose

value: adipocyte

value: SGBS

value: DECANOYL-L-CARNITINE


title: RNA-Seq of  SGBS treated with DECANOYL-L-CARNITINE at 100uM concentration B_26_03


title: 550912


title: case_renal biopsy [BIOS-09-0026]


title: control

source_name: WT fallopian tube / uterus

value: Fallopian tube and uterus


title: 540822


title: control_renal biopsy [BIOS-09-0022]

value: renal, endothelial and immune cells

value: No MVI


title: RNA-Seq of  SGBS treated with DECANOYL-L-CARNITINE at 100uM concentration B_26_01


title: E17HC_Pou4f3KO_H3K27ac_CutnRun_rep2

extract_protocol:
Hair cells (Atoh1-GFP+) were purified from E17 Pou4f3 mutant cochlea  by FACS sorting. Chromatin were digested by CUT&RUN technique, and DNA fragements were purified by phenol-chloroform method.
Libraries were prepared using Accel 2S Plus DNA library kit with single indexed adapters

value: embryonic day 17.5

value: hair cells


title: E17HC_Pou4f3KO_H3K27ac_CutnRun_rep1

extract_protocol:
Hair cells (Atoh1-GFP+) were purified from E17 Pou4f3 mutant cochlea  by FACS sorting. Chromatin were digested by CUT&RUN technique, and DNA fragements were purified by phenol-chloroform method.
Libraries were prepared using Accel 2S Plus DNA library kit with MID and single indexed adapters


title: 500921


title: control_renal biopsy [BIOS-09-0021]

value: Post kidney transplantation


title: control_renal biopsy [BIOS-13-0015]


title: RNA-Seq of  SGBS CONTROL B_25_03

description: RNA-Seq of  SGBS CONTROL

value: CONTROL (EMPTY EMEM MEDIUM) 4


title: 50822

value: Ovarian tumor


title: E17HC_Pou4f3KO_H3K4me1_CutnRun_rep2


title: case_renal biopsy [BIOS-09-0019]

value: MVI


title: 40921

value: Intact


title: E17HC_Pou4f3KO_H3K4me1_CutnRun_rep1

value: embryonic day 13.5


title: control_renal biopsy [BIOS-09-0018]


title: RNA-Seq of  SGBS CONTROL B_25_01

description: RNA-Seq of  SGBS CONTROL


title: control_renal biopsy [BIOS-09-0016]


title: E17HC_Pou4f3KO_ATOH1_CutnRun_rep2


title: RNA-Seq of  SGBS treated with RETINOIC ACID at 1uM concentration B_24_03

value: RETINOIC ACID


title: E17HC_Pou4f3KO_ATOH1_CutnRun_rep1


title: control_renal biopsy [BIOS-09-0015]


title: control_renal biopsy [BIOS-09-0013]


title: RNA-Seq of  SGBS treated with RETINOIC ACID at 1uM concentration B_24_02


title: RNA-Seq of  SGBS treated with RETINOIC ACID at 1uM concentration B_24_01


title: E17HC_Pou4f3KO_ATACseq_rep1

extract_protocol:
Hair cells (Atoh1-GFP+) were purified from E17 Pou4f3 mutant cochlea  by FACS sorting. Nuclei were extracted and chromatin were digested by tn5 transposase at 37°C for 20 minutes.DNA fragments were extracted using MiniElute columns (Qiagen), and then amplified by PCR.
Libraries were amplified by PCR with indexed primers


title: E17HC_Pou4f3KO_ATACseq_rep2


title: control_renal biopsy [BIOS-09-0012]


title: RNA-Seq of  SGBS treated with WORTMANIN at 100nM concentration B_23_02

value: WORTMANIN


title: Intestinal crypts, KO_3

city: Beijing

first: Yang

last: Xu

address: Beijing HaiDian District, Mingyuanxilu No.2

institute: China Agricultural University

description:
KO_MvsCtrl_WT_deg_all.txt
all_compare.txt
diff_stat.txt

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were masked for sequences containing adapter or undetermined base , and  masked for low-complexity or low-quality sequence
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Supplementary_files_format_and_content: Table with differentially expressed genes for every gene and every sample

source_name: Intestinal crypts

extract_protocol:
ntestinal crypt cells were isolated from the intestines of four KO mice and four littermate controls by incubation with 10 mM EDTA, 10 mM HEPES and 2% FBS in HBSS for 15 min at 37°C. The crypt fractions were collected by vigorous shaking and filtered through a 70 μm cell strainer. The gathered crypt cells were centrifuged at 1200 rpm for 5 min. Total RNA was isolated from the collected crypt cells using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Intestine

tag: age


title: Intestinal crypts, KO_4

tag: strain


title: control_renal biopsy [BIOS-09-0008]


title: RNA-Seq of  SGBS treated with WORTMANIN at 100nM concentration B_23_03

tag: tissue

value: adipose

value: adipocyte


title: Intestinal crypts, KO_1


title: E13PG_RNAseq_rep2

extract_protocol:
Progenitors (p27-GFP+) were purified from E13 cochlea by FACS sorting.RNA was extracted using Quick RNA micro-kit (Zymo).
PolyA RNA were enriched and used for library with Illumina Trueseq RNA library kit

value: progenitor cells

value: WT


title: RNA-Seq of  SGBS CONTROL B_25_02

description: RNA-Seq of  SGBS CONTROL

tag: cell line

value: SGBS


title: RNA-Seq of  SGBS treated with WORTMANIN at 100nM concentration B_23_01

tag: treatment


title: Intestinal crypts, KO_2


title: E13PG_ATACseq_rep2

extract_protocol:
Progenitors (p27-GFP+) were purified from E13 cochlea by FACS sorting. Nuclei were extracted and chromatin were digested by tn5 transposase at 37°C for 20 minutes.DNA fragments were extracted using MiniElute columns (Qiagen), and then amplified by PCR.
Libraries were amplified by PCR with indexed primers


title: control_renal biopsy [BIOS-09-0007]

value: renal, endothelial and immune cells

value: No MVI


title: case_renal biopsy [BIOS-09-0006]


title: RNA-Seq of  SGBS treated with U0126 at 5uM concentration B_22_03


title: E13PG_ATACseq_rep1


title: Intestinal crypts, Ctrl_4

value: Ctrl


title: case_renal biopsy [BIOS-09-0005]

value: Post kidney transplantation


title: Intestinal crypts, Ctrl_3


title: Intestinal crypts, Ctrl_2


title: RNA-Seq of  SGBS treated with U0126 at 5uM concentration B_22_02


title: MEF_Pou4f3_POU4F3_CutnRun_rep2

data_processing:
Library strategy: CUT&RUN
For ATACseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using bowtie2. PCR-duplicates were removed by Sambamba, and then peaks were called by MACS2 from individual replicate using filter p value < 0.01.
For Cut&Run, reads were trimmed based on quality score and then aligned to referene mouse genome (mm10) using STAR. PCR duplicates were removed based on UMI by umi_tools,  and then peaks were called by MACS2 for individual replicate using filter p value < 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: peak regions in narrowPeak format for ATACseq and CUT&RUN

source_name: embryo

extract_protocol:
Chromatin were digested by CUT&RUN technique, and DNA fragements were purified by phenol-chloroform method.
Libraries were prepared using Accel 2S Plus DNA library kit with MID and single indexed adapters

tag: infected genes


title: control_renal biopsy [BIOS-09-0004]


title: RNA-Seq of  SGBS treated with U0126 at 5uM concentration B_22_01


title: Intestinal crypts, Ctrl_1


title: control_renal biopsy [BIOS-09-0002]


title: MEF_Pou4f3_ATACseq_rep2

data_processing:
For ATACseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using bowtie2. PCR-duplicates were removed by Sambamba, and then peaks were called by MACS2 from individual replicate using filter p value < 0.01.
For Cut&Run, reads were trimmed based on quality score and then aligned to referene mouse genome (mm10) using STAR. PCR duplicates were removed based on UMI by umi_tools,  and then peaks were called by MACS2 for individual replicate using filter p value < 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: peak regions in narrowPeak format for ATACseq and CUT&RUN

extract_protocol:
Nuclei were extracted and chromatin were digested by tn5 transposase at 37°C for 20 minutes.DNA fragments were extracted using MiniElute columns (Qiagen), and then amplified by PCR.
Libraries were amplified by PCR with indexed primers


title: MEF_Pou4f3_POU4F3_CutnRun_rep1


title: Baseline (D0)

city: San Francisco

first: Sergio

middle: E

last: Baranzini

address: 675 Nelson Rising LN, STE 240

department: Neurology

institute: UCSF

data_processing:
raw sequence reads and generated gene count matrices using Cell Ranger v2.1.0
quality control, clustering, and differential gene expression analysis using Seurat v2.2
most variable genes were identified using PCA (principal component analysis) and performed tSNE (t-distributed stochastic neighbor embedding)
confirmation of each immune cell type by correlations with public datasets using SingleR software
Genome_build: mm10
Supplementary_files_format_and_content: The CellRanger software was used for alignment, deduplication. The matrix (mtx) includes sparse matrix of read counts, barcodes (tsv) for unique cell barcode and genes (tsv) for gene features.

source_name: CD11b+ cells

extract_protocol:
Retinas were removed, cell-sorting by FACS, prepared according to the 10x Genomics Cell Preparation Guideline,  single-cell RNA sequencing by ChromiumTM Single Cell 3’ Library and Gel Bead Kit and ChromiumTM Single Cell A Chip Kit
raw sequence reads and gene count matrices using Cell Ranger v2.1.0 & quality control, clustering, and differential gene expression analysis using Seurat v2.2.

treatment_protocol: Mice were immunized subcutaneously with 100 ug of MOG35-55 peptide (Genemed Synthesis, San Antonio, TX, USA) in complete Freund's adjuvant containing 400 ug Mycobacterium tuberculosis H37Ra (Difco Laboratories, Detroit, MI, USA). Mice received 200 ng pertussis toxin (List Biological,Campbell, CA, USA) by i.p. injection at the time of and post-immunization. Mice were 10 weeks old at baseline. Baseline samples were not immunized.

value: retina

tag: Sex

value: female

value: wildtype

tag: treatment / timepoint

value: Controls (0 dpi)


title: control_renal biopsy [BIOS-09-0001]


title: E13PG_RNAseq_rep1

tag: developmental stage

value: embryonic day 13.5

tag: genotype


title: control_renal biopsy [BIOS-06-0311]


title: MEF_Pou4f3_ATACseq_rep1


title: RNA-Seq of  SGBS treated with SP600125 at 5uM concentration B_21_01

data_processing:
Reference genome (hg19) and gene model annotation files were downloaded from the UCSC genome browser website directly.
Indexes of the reference genome were built using STAR3 and paired-end clean reads were aligned to the reference genome using STAR (v2.6.0; with default option mismatch = 10).
Bam files were filtered for uniquely mapped reads, sorted, and indexed using SAMtools4 (v1.4.1).
HTSeq5 (v0.11.0) was used to count the read numbers mapped to each gene (with option -m union).
Genome_build: hg19


title: Onset EAE (D6)

value: EAE - 25dpi


title: Chronic EAE (D25)

value: EAE - 6dpi


title: MEF_Gfp_ATACseq_rep2

value: Gfp


title: MEF_Gfp_ATACseq_rep1


title: control_renal biopsy [BIOS-06-0290]


title: RNA-Seq of  SGBS treated with SB203580 at 5uM concentration B_20_02

value: adipose


title: control_renal biopsy [BIOS-06-0277]


title: control_renal biopsy [BIOS-06-0265]


title: RNA-Seq of  SGBS treated with SB203580 at 5uM concentration B_20_01

value: adipocyte


title: MEF_Atoh1_Pou4f3_POU4F3_CutnRun_rep1


title: MEF_Atoh1_Pou4f3_POU4F3_CutnRun_rep2


title: case_renal biopsy [BIOS-06-0263]

value: MVI


title: RNA-Seq of  SGBS treated with LEPTIN at 100ng/ml concentration B_19_03

value: LEPTIN


title: tx-j+Choline_Input_2

city: Davis

first: Valentina

last: Medici

address: 451 E. Health Sciences Dr.

department: Department of Internal Medicine, Division of Hepatology/Gastroenterology

institute: University of California, Davis

data_processing:
The raw read data was filtered using HTStream (version 1.2.0) which included screening for contaminants (such as PhiX), removal of PCR duplicated reads, overlapping paired reads, quality-based trimming, and adapter trimming.
BWA MEM (version 0.7.16a) was used to align the processed data to the mouse genome (GRCm38).
Calling peaks was done using phantompeakqualtools (version 1.2.2). Bioconductor (version 3.11) package DiffBind (version 2.12.0) was used to combine raw count data for all peaks across replicates using R (version 3.6.3).
Bioconductor packages edgeR (version 3.26.8) and limma (version 3.40.6) were then used to perform differential expression analysis across the called peaks.
Finally, GREAT (version 4.0.4) was used to find the regulatory domains for the peaks and the genes within those domains.
Genome_build: GRCm38
Supplementary_files_format_and_content: bigWig files

source_name: Liver

extract_protocol:
After 24 weeks, Liver were removed, flash frozen in liquid nitrogne. Liver tissue lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Sequencing libraries were generated  by using KAPA Hyper Prep Kit (Kapa Biosystems, Wilmington MA, catalog. # KK8502) which included end repair, A-tailing, and adapter ligation with the KAPA Unique Dual-Indexed Adapter Kit (Kapa Biosystems, Wilmington, MA, catalog # KK8727) according to the manufacturer’s instructions.

treatment_protocol: From 12 to 24 weeks of age, Penicillamine (PCA )(Sigma, catalog #P4575;) was administered orally in the drinking water (100 mg/kg body weight/day) to a subgroup of tx-j control and choline-supplemented mice. Mice were euthanized at 24 weeks of age.

value: Liver

tag: treatment group

value: Untreated tx-j+Choline

value: Mutant (Atp7btx-J)

value: 24 weeks

tag: chip antibody


title: tx-j+Choline_Input_1


title: RNA-Seq of  SGBS treated with SP600125 at 5uM concentration B_21_03

value: SGBS


title: tx-j+PCA+Choline_Input_2

value: Untreated tx-j+PCA+Choline


title: MEF_Atoh1_Pou4f3_ATOH1_CutnRun_rep2


title: RNA-Seq of  SGBS treated with SP600125 at 5uM concentration B_21_02


title: control_renal biopsy [BIOS-06-0250]

value: renal, endothelial and immune cells

tag: outcome

value: No MVI

value: Post kidney transplantation


title: RNA-Seq of  SGBS treated with LEPTIN at 100ng/ml concentration B_19_02


title: MEF_Atoh1_Pou4f3_ATOH1_CutnRun_rep1


title: tx-j+PCA_Input_2

value: Untreated tx-j+PCA


title: RNA-Seq of  SGBS treated with LEPTIN at 100ng/ml concentration B_19_01


title: RNA-Seq of  SGBS treated with SB203580 at 5uM concentration B_20_03


title: control_renal biopsy [BIOS-06-0240]

tag: type of biopsy


title: tx-j+PCA+Choline_Input_1


title: control_renal biopsy [BIOS-06-0242]


title: MEF_Atoh1_Pou4f3_ATACseq_rep2


title: tx-j+PCA_Input_1


title: control_renal biopsy [BIOS-06-0238]


title: RNA-Seq of  SGBS treated with ADIPONECTIN at 1nM concentration B_18_03

value: ADIPONECTIN


title: tx-j_Input_2

value: Untreated tx-j


title: MEF_Atoh1_Pou4f3_ATACseq_rep1


title: tx-j_Input_1


title: RNA-Seq of  SGBS treated with ADIPONECTIN at 1nM concentration B_18_02


title: control_renal biopsy [BIOS-06-0226]


title: RNA-Seq of  SGBS treated with ADIPONECTIN at 1nM concentration B_18_01


title: C3H_Input_1

value: Wild type


title: C3H_Input_2


title: RNA-Seq of  SGBS CONTROL B_17_02

description: RNA-Seq of  SGBS CONTROL

value: adipose

value: CONTROL (EMPTY EMEM MEDIUM) 3


title: MEF_Atoh1_ATACseq_rep2


title: tx-j+PCA+Choline_H3K9ac_6

value: H3K9ac (Active Motif, Catalog-39918)


title: MEF_Atoh1_ATACseq_rep1


title: RNA-Seq of  SGBS CONTROL B_17_01

description: RNA-Seq of  SGBS CONTROL

value: adipocyte


title: P1CGP_ATAC_20000_cell_rep2

data_processing:
For ATACseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using bowtie2. PCR-duplicates were removed by Sambamba, and then peaks were called by MACS2 from individual replicate using filter p value < 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: peak regions in narrowPeak format for ATACseq

source_name: cerebellum

extract_protocol:
Atoh1-GFP positive cerebellar granule progenitor cells were FACS purified from postnatal day 1 animals. ATACseq was performed using 20,000 cells, and µATACseq was performed with 100, 500, 1000 cells. DNA fragments were extracted using MiniElute columns (Qiagen), and then amplified by PCR.
Libraries were prepared by PCR with indexed primers

value: postnatal day 1

tag: marker


title: tx-j+PCA+Choline_H3K9ac_5

value: Liver


title: control_renal biopsy [BIOS-06-0219]


title: case_renal biopsy [BIOS-06-0211]

value: MVI


title: P1CGP_ATAC_20000_cell_rep1


title: RNA-Seq of  SGBS treated with ATORVASTATIN at 1uM concentration B_16_02

value: ATORVASTATIN


title: RNA-Seq of  SGBS treated with ATORVASTATIN at 1uM concentration B_16_03

value: SGBS


title: MEF_Atoh1_ATOH1_CutnRun_rep2


title: tx-j+PCA+Choline_H3K9ac_4

value: Untreated tx-j+PCA+Choline

value: Mutant (Atp7btx-J)

value: 24 weeks


title: tx-j+PCA+Choline_H3K9ac_3


title: RNA-Seq of  SGBS treated with ATORVASTATIN at 1uM concentration B_16_01


title: P1CGP_ATAC_1000_cell_rep2


title: control_renal biopsy [BIOS-06-0224]

value: renal, endothelial and immune cells

value: No MVI

value: Post kidney transplantation


title: control_renal biopsy [BIOS-06-0198]


title: tx-j+PCA+Choline_H3K9ac_2


title: MEF_Atoh1_ATOH1_CutnRun_rep1


title: RNA-Seq of  SGBS CONTROL B_17_03

description: RNA-Seq of  SGBS CONTROL


title: RNA-Seq of  SGBS treated with METFORMIN at 1mM concentration B_15_03

value: METFORMIN


title: control_renal biopsy [BIOS-06-0222]


title: control_renal biopsy [BIOS-06-0197]


title: P1CGP_ATAC_500_cell_rep2


title: RNA-Seq of  SGBS treated with METFORMIN at 1mM concentration B_15_02


title: tx-j+Choline_H3K9ac_6

value: Untreated tx-j+Choline


title: P1CGP_ATAC_500_cell_rep1


title: control_renal biopsy [BIOS-06-0196]


title: RNA-Seq of  SGBS treated with METFORMIN at 1mM concentration B_15_01

value: adipose


title: P1CGP_ATAC_100_cell_rep2


title: control_renal biopsy [BIOS-06-0201]


title: control_renal biopsy [BIOS-06-0193]


title: tx-j+Choline_H3K9ac_5


title: RNA-Seq of  SGBS treated with TGF-B1 at 10ng/ml concentration B_14_03


title: tx-j+Choline_H3K9ac_4


title: control_renal biopsy [BIOS-06-0199]


title: control_renal biopsy [BIOS-06-0191]


title: P1CGP_ATAC_100_cell_rep1


title: RNA-Seq of  SGBS treated with TGF-B1 at 10ng/ml concentration B_14_02


title: P1CGP_ATAC_1000_cell_rep1


title: control_renal biopsy [BIOS-06-0187]


title: RNA-Seq of  SGBS treated with LAUROYL-L-CARNITINE at 100uM concentration B_13_03

value: LAUROYL-L-CARNITINE


title: tx-j+Choline_H3K9ac_2

value: H3K9ac (Active Motif, Catalog-39918)


title: control_renal biopsy [BIOS-06-0183]


title: P1SC_permissive_48h_H3K27ac_CutnRun_1

data_processing:
Library strategy: CutnRun
For RNAseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using STAR. Reads were quantified against genes using RSEM, and differential gene expression analysis was conducted using DESeq2.
For ATACseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using bowtie2. PCR-duplicates were removed by Sambamba, and then peaks were called by MACS2 from individual replicate using filter p value < 0.01.
For Cut&Run, reads were trimmed based on quality score and then aligned to referene mouse genome (mm10) using STAR. PCR duplicates were removed based on UMI by umi_tools,  and then peaks were called by MACS2 for individual replicate using filter p value < 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: Gene counts for RNAseq in text files, peak regions for ATACseq and H3K27ac CutnRun in narrowPeak files.

growth_protocol: P1 cochleae were cultured on SPI black filter membrane (SPI Supplies) in L15 Leibovitz media (Hyclone) supplemented with N2 (Invitrogen, 1:100), B27 (Gibco, 1:50), Penicillin G (Sigma, 100U/ml), EGF(Shenandoah Biotechnology, 5ng/ml), FGF (Shenandoah Biotechnology,2.5ng/ml) and HEPES (Invitrogen, 10mM).

extract_protocol:
Cultured organs were diggested were digested with Trypsin (Invitrogen, 0.125%) at 37°C for 8 minutes, and then dissociated by trituation with P200 pipettes. Lfng-CreER/TdT and Atoh1-GFP double positive supporting cells were FACS purified into 500μL PBS supplimented with 10% FBS. Purified cells were used for Cut&Run with H3K27ac antibody (Active Motif). DNA fragments were purified using  phenol-chloroform.
Libraries were prepared using Accel-NGS 2S Plus DNA Library Kit with single-indexed and UMI adaptors.

treatment_protocol: Cultured cochlear organs were treated with 10μ DAPT or equivalent amount of DMSO (VWR) for 24 hours or 48 hours

value: DAPT

tag: timepoint

value: Lfng-CreET/TdT, Atoh1-GFP

value: supporting cells


title: RNA-Seq of  SGBS treated with LAUROYL-L-CARNITINE at 100uM concentration B_13_02

tag: cell type

value: adipocyte


title: tx-j+PCA+Choline_H3K9ac_1

value: Liver

tag: age


title: tx-j+Choline_H3K9ac_1

tag: strain


title: P1SC_nonpermissive_48h_H3K27ac_CutnRun_2

extract_protocol:
Cultured organs were diggested were digested with Trypsin (Invitrogen, 0.125%) at 37°C for 8 minutes, and then dissociated by trituation with P200 pipettes. Lfng-CreER/TdT+ supporting cells were FACS purified into 500μL PBS supplimented with 10% FBS. Purified cells were used for Cut&Run with H3K27ac antibody (Active Motif). DNA fragments were purified using  phenol-chloroform.
Libraries were prepared using Accel-NGS 2S Plus DNA Library Kit with single-indexed and UMI adaptors.

value: postnatal day 1

value: Lfng-CreET/TdT


title: control_renal biopsy [BIOS-06-0176]


title: RNA-Seq of  SGBS treated with LAUROYL-L-CARNITINE at 100uM concentration B_13_01

extract_protocol: none provided by the submitter

tag: tissue

value: SGBS


title: P1SC_nonpermissive_48h_H3K27ac_CutnRun_1


title: RNA-Seq of  SGBS treated with IBMX at 250uM concentration B_12_03

tag: cell line

value: IBMX


title: P1SC_control_48h_H3K27ac_CutnRun_2

tag: treatment

value: DMSO


title: tx-j+PCA_H3K9ac_5

value: Untreated tx-j+PCA

value: Mutant (Atp7btx-J)

value: 24 weeks


title: RNA-Seq of  SGBS treated with IBMX at 250uM concentration B_12_02


title: control_renal biopsy [BIOS-06-0136]

extract_protocol: Total RNA was extracted using the Allprep DNA/RNA/miRNA Universal Kit (Qiagen Benelux BV) on a QIAcube instrument (Qiagen Benelux BV). The quantity (absorbance at 260 nm) and purity (ratio of the absorbance at 230, 260, and 280 nm) of the isolated RNA were measured using the NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific/Life Technologies Europe BV, Ghent, Belgium). RNA integrity was evaluated with the Eukaryote nano/pico RNA Kit (Agilent Technologies Belgium NV, Diegem, Belgium) on the Bioanalyzer 2100 instrument (Agilent Technologies BelgiumNV)

value: renal, endothelial and immune cells

value: No MVI

value: Post kidney transplantation


title: P1SC_control_48h_H3K27ac_CutnRun_1


title: RNA-Seq of  SGBS treated with IBMX at 250uM concentration B_12_01

value: adipose


title: tx-j+PCA_H3K9ac_4

value: H3K9ac (Active Motif, Catalog-39918)


title: tx-j+Choline_H3K9ac_3

value: Untreated tx-j+Choline


title: P1SC_permissive_48h_H3K27ac_CutnRun_2

value: DAPT

value: Lfng-CreET/TdT, Atoh1-GFP

value: supporting cells


title: RNA-Seq of  SGBS treated with IGF1 at 100nM concentration B_11_03

value: adipocyte


title: tx-j+PCA_H3K9ac_3

value: Liver


title: P1SC_permissive_48h_ATACseq_2

data_processing:
For RNAseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using STAR. Reads were quantified against genes using RSEM, and differential gene expression analysis was conducted using DESeq2.
For ATACseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using bowtie2. PCR-duplicates were removed by Sambamba, and then peaks were called by MACS2 from individual replicate using filter p value < 0.01.
For Cut&Run, reads were trimmed based on quality score and then aligned to referene mouse genome (mm10) using STAR. PCR duplicates were removed based on UMI by umi_tools,  and then peaks were called by MACS2 for individual replicate using filter p value < 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: Gene counts for RNAseq in text files, peak regions for ATACseq and H3K27ac CutnRun in narrowPeak files.

extract_protocol:
Cultured organs were diggested were digested with Trypsin (Invitrogen, 0.125%) at 37°C for 8 minutes, and then dissociated by trituation with P200 pipettes. Lfng-CreER/TdT and Atoh1-GFP double positive supporting cells were FACS purified into 500μL PBS supplimented with 10% FBS. Nuclei was extracted from sorted cells, and Tn5 transposation was carried out at 37°C for 20 minutes. DNA fragments were extracted using MiniElute columns (Qiagen), and then amplified by PCR.
Libraries were prepared by PCR with indexed primers

value: postnatal day 1


title: control_renal biopsy [BIOS-06-0098]


title: tx-j+PCA_H3K9ac_2


title: RNA-Seq of  SGBS treated with IGF1 at 100nM concentration B_11_02

value: SGBS


title: P1SC_permissive_48h_ATACseq_1


title: case_renal biopsy [BIOS-06-0095]

value: MVI


title: P1SC_nonpermissive_48h_ATACseq_2

extract_protocol:
Cultured organs were diggested were digested with Trypsin (Invitrogen, 0.125%) at 37°C for 8 minutes, and then dissociated by trituation with P200 pipettes. Lfng-CreER/TdT+ supporting cells were FACS purified into 500μL PBS supplimented with 10% FBS. Nuclei was extracted from sorted cells, and Tn5 transposation was carried out at 37°C for 20 minutes. DNA fragments were extracted using MiniElute columns (Qiagen), and then amplified by PCR.
Libraries were prepared by PCR with indexed primers

value: Lfng-CreET/TdT


title: tx-j_H3K9ac_6

value: Untreated tx-j

value: Mutant (Atp7btx-J)


title: RNA-Seq of  SGBS treated with IGF1 at 100nM concentration B_11_01


title: tx-j+PCA_H3K9ac_1

value: Untreated tx-j+PCA

value: 24 weeks


title: case_renal biopsy [BIOS-06-0088]

value: renal, endothelial and immune cells

value: Post kidney transplantation


title: control_renal biopsy [BIOS-06-0166]

value: No MVI


title: RNA-Seq of  SGBS treated with ISOPRENALINE at 100nM concentration B_10_03

value: adipose

value: ISOPRENALINE


title: tx-j+PCA_H3K9ac_6

value: H3K9ac (Active Motif, Catalog-39918)


title: tx-j_H3K9ac_5


title: case_renal biopsy [BIOS-06-0070]


title: RNA-Seq of  SGBS treated with ISOPRENALINE at 100nM concentration B_10_02


title: control_renal biopsy [BIOS-06-0130]


title: control_renal biopsy [BIOS-06-0100]


title: control_renal biopsy [BIOS-06-0065]


title: P1SC_control_48h_ATACseq_1

value: DMSO

value: supporting cells


title: tx-j_H3K9ac_4

value: Liver


title: tx-j_H3K9ac_3


title: control_renal biopsy [BIOS-06-0060]


title: P1SC_DAPT_24h_RNAseq_3

extract_protocol:
Cultured organs were diggested were digested with Trypsin (Invitrogen, 0.125%) at 37°C for 8 minutes, and then dissociated by trituation with P200 pipettes. GFP positive supporting cells were FACS purified into 300μL RNA lysis buffer (Zymo), and RNA was extracted with Quick-RNA Micro-prep kit (Zymo).
Poly-A tail RNA were enriched, and libraries were prepared using Illumina True-Seq mRNA-seq kit.

value: postnatal day 1

value: DAPT

value: Lfng-GFP


title: RNA-Seq of  SGBS CONTROL B_9_03

description: RNA-Seq of  SGBS CONTROL

value: adipocyte

value: SGBS

value: CONTROL (EMPTY EMEM MEDIUM) 2


title: control_renal biopsy [BIOS-06-0055]


title: P1SC_DAPT_24h_RNAseq_2


title: RNA-Seq of  SGBS CONTROL B_9_02

description: RNA-Seq of  SGBS CONTROL


title: tx-j_H3K9ac_1

value: Untreated tx-j

value: Mutant (Atp7btx-J)


title: P1SC_DAPT_24h_RNAseq_1


title: tx-j_H3K9ac_2

value: 24 weeks


title: RNA-Seq of  SGBS CONTROL B_9_01

description: RNA-Seq of  SGBS CONTROL


title: control_renal biopsy [BIOS-06-0050]

value: renal, endothelial and immune cells

value: Post kidney transplantation


title: P1SC_nonpermissive_48h_ATACseq_1

value: Lfng-CreET/TdT


title: C3H_H3K9ac_6

value: Wild type


title: control_renal biopsy [BIOS-06-0037]

value: No MVI


title: P1SC_DMSO_24h_RNAseq_3

value: DMSO


title: RNA-Seq of  SGBS treated with DEXAMETHASONE at 1uM concentration B_8_03

value: adipose

value: DEXAMETHASONE


title: C3H_H3K9ac_5

value: Liver

value: H3K9ac (Active Motif, Catalog-39918)


title: RNA-Seq of  SGBS treated with DEXAMETHASONE at 1uM concentration B_8_02


title: P1SC_control_48h_ATACseq_2

value: postnatal day 1

value: supporting cells


title: P1SC_DMSO_24h_RNAseq_2

value: Lfng-GFP


title: control_renal biopsy [BIOS-06-0034]


title: P1SC_DMSO_24h_RNAseq_1


title: C3H_H3K9ac_4


title: RNA-Seq of  SGBS treated with ISOPRENALINE at 100nM concentration B_10_01

value: adipocyte

value: SGBS

value: ISOPRENALINE


title: case_renal biopsy [BIOS-06-0032]

value: MVI


title: RNA-Seq of  SGBS treated with DEXAMETHASONE at 1uM concentration B_8_01


title: control_renal biopsy [BIOS-06-0029]

value: renal, endothelial and immune cells


title: C3H_H3K9ac_3

value: 24 weeks


title: E17HC_ATOH1_CutnRun_2

data_processing:
For RNAseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using STAR. Reads were quantified against genes using RSEM, and differential gene expression analysis was conducted using DESeq2.
For ATACseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using bowtie2. PCR-duplicates were removed by Sambamba, and then peaks were called by MACS2 from individual replicate using filter p value < 0.01.
For ChIPseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10 using STAR. PCR duplcates were removed by Sambamba, and then peaks were called by MACS2 from individual replicate using filter p value < 0.01.
For Cut&Run, reads were trimmed based on quality score and then aligned to referene mouse genome (mm10) using STAR. PCR duplicates were removed based on UMI by umi_tools,  and then peaks were called by MACS2 for individual replicate using filter p value < 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: Gene count text files for RNAseq, peak region narrowPeak files for ATACseq, ChIPseq and CUT&RUN.

extract_protocol: Atoh1-GFP positive sensory hair cells were FACS-sorted from E17.5 cochleae into 500μL PBS supplemented with 10% FBS. Purified cells were used for Cut&Run with GFP antibody against ATOH1-GFP fusion protein. DNA fragments were purified using  phenol-chloroform.

value: embryonic day 17.5

value: hair cells


title: RNA-Seq of  SGBS treated with ROSIGLITAZONE at 2uM concentration B_7_03

value: ROSIGLITAZONE


title: case_renal biopsy [BIOS-03-0058]

value: Post kidney transplantation


title: RNA-Seq of  SGBS treated with ROSIGLITAZONE at 2uM concentration B_7_02

value: adipose


title: E17HC_ATOH1_CutnRun_1