title: STAG1_CTRL_rep-1


title: RAD21_CTRL_rep-2

status: Public on Jul 21 2020

type: SRA

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

country: USA

institute: University of Cincinnati

description:
Rad21CTRL_Input_optimal_IDR_thresholded_peaks_mm10.narrowPeak
Rad21CTRL_nodup_pooled_signal_p_value_mm10.bw
Rad21CTRL_nodup_pooled_fold_change_over_imput_mm10.bw

library_source: genomic

data_processing:
Data were processed with ENCODE pipeline
Single reads were aligned to mm10 using bowtie
Insert size was assessed by spp
MACS2 was used to call differentiated peaks between treatments on pooled samples.
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak, bigWig

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse Hepatoma Cell Line

growth_protocol: Cells were grown in Alpha-MEM medium (Gibco) supplemented with 5% FBS and 1% Penicillin-Streptomycin solution and passaged at approximately 80% confluency.

extract_protocol:
Cells were fixed with 1% formaldehyde and the reaction subsequently quenched using 0.125 M glycine.  After fixation, cells were lysed to release nuclei, which were washed and re-suspended in nuclei lysis buffer before sonicating the chromatin using a Diagenode Bioruptor.  Fragmented chromatin was diluted and separated into equivalent aliquots prior to antibody application and complex retrieval.
A ChIP-seq script was selected for sequencing library preparation using PrepX DNA Library kit and Apollo 324 NGS automatic library prep system (WaferGen, Fremont, CA). Overhangs in samples of double-strand DNA fragments (~5 ng) were first blunt-ended, and adenylated at the 3' ends for TA ligation to the sequencing adaptors. The ligated library was enriched by 8 cycles of PCR using index-specific primers, followed by automated AMPure XP beads (Beckman Coulte, Brea CA) purification. To check the quality and yield of the library, one µl of purified PCR library was analyzed by Bioanalyzer with DNA High Sensitivity chip. To accurately quantify the library concentration for cluster generation, the library was 1:104 diluted with dilution buffer (10 mM Tris-HCl, pH 8.0 with 0.05% Tween 20), and qPCR analyzed with NEBNext Library Quant Kit (New England Biolabs, Ipswich, MA) using ABI 9700HT real-time PCR system (Lifetech, Grand Island, NY). Individually indexed libraries were proportionally pooled for clustering in the cBot system (Illumina, San Diego, CA). Libraries at the final concentration of 16 pM were clustered onto a flow cell using Illumina TruSeq SR Cluster kit v3, and sequenced for 50 cycles using TruSeq SBS kit on Illumina HiSeq system. According to Illumina, for studies targeting transcription factors, ~10M reads per sample were generated.

treatment_protocol: Cells were treated with filter-sterilized potassium chromate dissolved in MilliQ-grade water for 90 mins prior to fixation and processing.

tag: cell line

tag: treatment

value: 0 µM chromium (Control)

tag: chip antibody

value: Anti-Rad21 antibody - ChIP Grade (abcam, ab992)

tag: pulldown target


title: H3K4me3_Cr1_rep-2

description:
H3K4me3Cr1_Input_optimal_IDR_thresholded_peaks_mm10.narrowPeak
H3K4me3Cr1_nodup_pooled_signal_p_value_mm10.bw
H3K4me3Cr1_nodup_pooled_fold_change_over_imput_mm10.bw

value: 1 µM chromium

value: Anti-trimethyl-Histone H3 (Lys4) Antibody (Millipore Sigma, 07-473)


title: H3K4me3_Cr1_rep-1


title: Active CD4 T2h BruChase-Seq Rep1

city: Washington DC

first: Weiqun

last: Peng

state: Washington DC

address: 800 22nd St NW

department: Physics

institute: George Washington University

library_source: transcriptomic

data_processing:
Library strategy: BruChase-Seq
The sequencing quality of Bru-Seq and BruChase-Seq libraries was assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bru-Seq and BruChase-Seq libraries were mapped to human genome using Tophat (v2.1.0, Trapnell et al., Bioinformatics). UCSC genes for human hg19 assembly from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
Genome_build: hg19
Supplementary_files_format_and_content: [.wig file] ERCC normalized expression levels

molecule: total RNA

organism: Homo sapiens

source_name: CD4 T cells

extract_protocol:
Human resting CD4+ T cells were sort-purified and then activated by CD3/CD28. Bromouridine (Bru) was added to the media of resting and activated CD4+ T cells. The Bru-labeled RNA was isolated from the total or cytoplasmic RNA of resting and activated CD4+ T cells.
Libraries were prepared for sequencing using stardard Illumina protocol

tag: genotype

value: wild type

tag: cell type

value: Activated CD4 T cells

tag: cell subset

tag: molecule subtype

value: Bru-labeled total RNA


title: Active CD4 T0.5h BruChase-Seq Rep1


title: Input_CTRL_rep-1

value: Total Input

value: Input


title: H3K9me3_CTRL_rep-2

description:
H3K9me3CTRL_Input_optimal_IDR_thresholded_peaks_mm10.narrowPeak
H3K9me3CTRL_nodup_pooled_signal_p_value_mm10.bw
H3K9me3CTRL_nodup_pooled_fold_change_over_imput_mm10.bw

value: Anti-Histone H3 (tri methyl K9) antibody - ChIP Grade (abcam, ab8898)


title: Active CD4 T2h Cyto BruChase-Seq

data_processing:
Library strategy: Bru-Seq
The sequencing quality of Bru-Seq and BruChase-Seq libraries was assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bru-Seq and BruChase-Seq libraries were mapped to human genome using Tophat (v2.1.0, Trapnell et al., Bioinformatics). UCSC genes for human hg19 assembly from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
Genome_build: hg19
Supplementary_files_format_and_content: [.wig file] ERCC normalized expression levels

value: Bru-labeled cytoplasmic RNA


title: H3K36me3_CTRL_rep-2

description:
H3K36me3CTRL_Input_optimal_IDR_thresholded_peaks_mm10.narrowPeak
H3K36me3CTRL_nodup_pooled_signal_p_value_mm10.bw
H3K36me3CTRL_nodup_pooled_fold_change_over_imput_mm10.bw

value: Anti-Histone H3 (tri methyl K36) antibody - ChIP Grade (abcam, ab9050)


title: H3K36me3_CTRL_rep-1


title: Active CD4 T0h Bru-Seq Rep1


title: Rest CD4 T0h Bru-Seq Rep3

description: This sample is a replicate and was used to check for the experiment and model reproducibility.

value: Resting CD4 T cells


title: H3K36me3_Cr1_rep-2

description:
H3K36me3Cr1_Input_optimal_IDR_thresholded_peaks_mm10.narrowPeak
H3K36me3Cr1_nodup_pooled_signal_p_value_mm10.bw
H3K36me3Cr1_nodup_pooled_fold_change_over_imput_mm10.bw


title: H3K27me3_CTRL_rep-2

description:
H3K27me3CTRL_Input_optimal_IDR_thresholded_peaks_mm10.narrowPeak
H3K27me3CTRL_nodup_pooled_signal_p_value_mm10.bw
H3K27me3CTRL_nodup_pooled_fold_change_over_imput_mm10.bw

value: Histone H3K27me3 antibody (mAb) (Active Motif, 61017)


title: Rest CD4 T0.5h BruChase-Seq Rep2


title: Rest CD4 T0h Bru-Seq Rep2


title: H3K27me3_Cr1_rep-2

description:
H3K27me3Cr1_Input_optimal_IDR_thresholded_peaks_mm10.narrowPeak
H3K27me3Cr1_nodup_pooled_signal_p_value_mm10.bw
H3K27me3Cr1_nodup_pooled_fold_change_over_imput_mm10.bw


title: H3K27me3_CTRL_rep-1


title: Rest CD4 T2h BruChase-Seq Rep3


title: H3K36me3_Cr1_rep-1


title: H3K27me3_Cr1_rep-1


title: H3K4me3_CTRL_rep-2

description:
H3K4me3CTRL_Input_optimal_IDR_thresholded_peaks_mm10.narrowPeak
H3K4me3CTRL_nodup_pooled_signal_p_value_mm10.bw
H3K4me3CTRL_nodup_pooled_fold_change_over_imput_mm10.bw


title: Rest CD4 T2h BruChase-Seq Rep1


title: Rest CD4 T0.5h BruChase-Seq Rep1


title: Rest CD4 T0h Bru-Seq Rep1


title: zgc

city: Shanghai

first: tao

last: lv

address: No. 160 Pujian Road,Shanghai 200127, China

department: Department of Neurosurgery

country: China

institute: Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University

description: S359_04A_CHG015109-NBC1017-C-ZGC-GTGGCC_L002

data_processing:
Basecalls performed using CASAVA version 1.7
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Raw reads after quality control testing were then mapping to genome using Hisat2 software
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: normal cerebellum sample

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue type

value: normal cerebellum


title: xyq

description: S358_01B_CHG015108-NBC1017-B-XYQ-TAGCTT_L008


title: H3K27Ac_CTRL_rep-1

description:
H3K27AcCTRL_Input_optimal_IDR_thresholded_peaks_mm10.narrowPeak
H3K27AcCTRL_nodup_pooled_signal_p_value_mm10.bw
H3K27AcCTRL_nodup_pooled_fold_change_over_imput_mm10.bw

value: Anti-Histone H3 (acetyl K27) antibody - ChIP Grade (abcam, ab4729)


title: sjy

description: S358_01B_CHG015108-NBC1017-B-SJY-CTTGTA_L008


title: qfs

description: S358_01B_CHG015108-NBC1017-B-QFS-GGCTAC_L008


title: H3K27Ac_CTRL_rep-2


title: Rest CD4 T0.5h BruChase-Seq Rep3


title: zhh

description: S359_04A_CHG015109-NBC1017-C-DHH-GTTTCG_L002

source_name: medulloblastoma sample

value: medulloblastoma


title: ly

description: S359_04A_CHG015109-NBC1017-C-LY-CGTACG_L002


title: H3K27Ac_Cr1_rep-1

description:
H3K27AcCr1_Input_optimal_IDR_thresholded_peaks_mm10.narrowPeak
H3K27AcCr1_nodup_pooled_signal_p_value_mm10.bw
H3K27AcCr1_nodup_pooled_fold_change_over_imput_mm10.bw


title: CTCF_CTRL_rep-2

description:
CTCF_CTRL_Input_optimal_IDR_thresholded_peaks_mm10.narrowPeak
CTCFCTRL_nodup_pooled_signal_p_value_mm10.bw
CTCFCTRL_nodup_pooled_fold_change_over_imput_mm10.bw

value: 0 µM chromium (Control)

value: CTCF antibody (pAb) (Active Motif, 61311)

value: CTCF


title: djh

description: S359_04A_CHG015110-NBC1017-D-DJH-ACTGAT_L003


title: Rest CD4 T2h BruChase-Seq Rep2


title: CTCF_CTRL_rep-1


title: djf

description: S359_04A_CHG015110-NBC1017-D-DJW-GAGTGG_L003


title: CTCF_Cr1_rep-2

description:
CTCF_Cr1_Input_optimal_IDR_thresholded_peaks_mm10.narrowPeak
CTCFCr1_nodup_pooled_signal_p_value_mm10.bw
CTCFCr1_nodup_pooled_fold_change_over_imput_mm10.bw

value: 1 µM chromium


title: CTCF_Cr1_rep-1


title: H3K27Ac_Cr1_rep-2


title: Input_CTRL_rep-2


title: ovarian follicular - good group1

first: Di

last: Zhang

state: Shanghai

address: 301 Yanchangzhonglu

institute: Center for Reproductive medicine, Shanghai Tenth People’s Hospital of Tongji University

description: MicroRNA

data_processing:
Raw data reads were trimmed by cutadapter in order to receive clean data reads.
Clean reads were blasted to blasted in miRNA database, RFam database and Repbase database to remove repeats, non-miRNA families and other low quality sequences. Then aligned to human genome GRCH37.
Reads count data was received from alignment result, then differential expression analysis was conducted on the basis of it.
Genome_build: GRCH37
Supplementary_files_format_and_content: gene expression matrix file

source_name: exosome

extract_protocol:
Ovarian follicular fluid was collected by transvaginal ultrasound-guided puncture. Immediately after oocytes were retrieved, follicular fluid was collected and processed to remove the blood. Follicular fluid was then centrifuged at 2000g for 10 min to collect the supernatant, and the supernatant was centrifuged twice at 100,000g for 70 min to pellet exosomes.
MicroRNA libraries were prepared using the TruSeq Small RNA Sample Prep Kit (Illumina Inc., San Diego, CA, USA) following the manufacturer’s instructions. Briefly, small RNAs were ligated with 3’ and 5’ adapters, followed by reverse transcription to produce single stranded cDNAs. The cDNAs were amplified by PCR in 11 cycles.

tag: tissue

value: ovarian follicular fluid

tag: oocyte status

value: good

tag: sequenced molecule

value: exosomal miRNA


title: ovarian follicular - bad group1

description: MicroRNA

value: bad


title: shQKI3

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

country: South Korea

institute: Dankook University

data_processing:
Illumina Casava1.7 software used for basecalling.
Poor quality (Phred score < 20) or sequencing adapter-contaminated portions of sequenced reads were trimmed using Trim Galore (version 0.4.3) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Trimmed reads were aligned to the human reference genome (hg38 assembly) using STAR (version 2.7.5a; Dobin et al. Bioinformatics 2013) with the following parameters: --readFilesCommand zcat –outSAMtype BAM SortedByCoordinate.
The abuandance of transcripts was estimated using StringTie (version 1.3.6; Pertea et al. Nat Protoc 2016) with the GENCODE gene annotation (release 34; https://www.gencodegenes.org/).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for every sample
Supplementary_files_format_and_content: Matrix table with raw read counts for every transcript and every sample

source_name: Oral squamous cell carcinoma

growth_protocol: CAL27 cells (ATCC, Manassas, VA) were cultured in Dulbecco’s modification of Eagle’s medium (Welgene, Gyeongsan, Korea) with 10% fetal bovine serum (HyClone, Logan, UT) at 37°C in the presence of 5% CO2.

extract_protocol:
Total RNAs were isolated from QKI knockdown and control cells using AccuPrep® universal RNA extraction kit (BIONEER, Daejeon, Korea).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: QKI shRNAs and non-targeting control (MISSION® shRNA lentiviral vectors) were from Sigma-Aldrich (St. Louis, MO) and introduced into CAL27 cells by lentiviral infection.

value: shRNA-mediated knock-down of the QKI gene


title: shQKI2


title: Cardiomyocytes_RNA_rep1-TCDD treated_96hrs

description:
countsTable.xls
APM7

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to mm10 using Tophat
number of read counts was calculated for each Entrez gene
differential expression analysis was performed using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: Cardiomyocytes

growth_protocol: Undifferentiated C57BL/6N-C2 ES cells were maintained in ES medium containing high-glucose Dulbecco’s minimal essential medium (DMEM; Gibcol Carlsbad, CA) supplemented with 15% ES cell qualified serum (Knockout Serum Replacement; Gibco), 2 mM glutamine, 1% nonessential amino acids, 1% sodium pyruvate, 100U/mL penicillin, 100 µg/mL streptomycin and 0.1 mM β-mercaptoethanol, and 1,000 U/mL ESGRO leukemia inhibitory factor (LIF; Bioscience Research Reagents, Temucula, CA). Cells were seeded on 0.1% gelatin-coated plates, incubated at 37OC (95% humidity, 5% CO2) and passaged every second or third day. The establishment and maintenance of the G418-resistant Nkx2.5-ES cell line containing the pNkx2.5PuroIRES2eGFP plasmid were performed as follows. Briefly, cells were transfected by the pNkx2.5PuroIRES2eGFP plasmid bearing as well a G418-resistance marker regulated by the CMV promoter, seeded on 0.1% gelatin-coated plates and ES medium, and allowed to attach for 24 hours before adding 600 µg/ml G418. The transfected cells were selected for 3-5 passages to insure all cells not resistant to G418 were removed. The media was then replaced with ES medium without G418. After 24 hours, cells were trypsinized and seeded into wells of gelatin-coated 6-well plates with 5x104 cells in ES medium. After 24 hours, ES medium was replaced with differentiation medium containing LIF-free DMEM supplemented with 15% non-ES qualified fetal bovine serum and subjected to differentiation treatment sequentially as follows: 150 ng/ml Noggin for 1 day, 5 ng/ml BMP4 for the next 2 days, and then 3 µg/ml puromycin for 4 days. Thereafter, Nkx2.5¬ positive cells were selected by treatment with 3µg/ml puromycin every 2-3 days and examined by microscopy until day 14 for the presence of beating cardiomyocytes.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Life Technologies, Carlsbad, CA) according to the manufacturer’s instructions.
Directional RNA-seq was performed by the Genomics, Epigenomics and Sequencing Core (GESC) at the University of Cincinnati. The RNA quality was determined by Bioanalyzer (Agilent, Santa Clara, CA). To isolate the polyA RNA, NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) was used with a total of 1 μg of good quality total RNA as input. The NEBNext Ultra II Directional RNA Library Prep Kit (New England BioLabs) was used for library preparation by dUTP-based stranded library. The library was indexed and amplified under a PCR cycle number of 8. After library Bioanalyzer QC analysis and quantification, individually indexed and compatible libraries were proportionally pooled and sequenced using Illumina Hiseq sequencer (Illumina, San Diego, CA). Under the sequencing setting of single read 1x51 bp, about 25 million pass filter reads per sample were generated.

treatment_protocol: Cardiomyocytes were treated with TCDD at a concentration of 5 nM, (a concentration commonly used for tissue culture studies of the high-affinity AHR of C57BL/6 mice), for 24, 72, and 96 hours. TCDD was dissolved in DMSO, which never exceeded 0.05% of the volume of medium in either treatment or vehicle control. Undifferentiated, untreated parental ES cells and differentiated untreated cardiomyocytes served as controls.

value: ES-derived cardiomyocytes

tag: strain

tag: time (hrs)

value: TCDD


title: Cardiomyocytes_RNA_rep2-TCDD treated_96hrs

description:
countsTable.xls
APM8


title: Cardiomyocytes_RNA_rep2-control treated_24hrs

description:
countsTable.xls
APM10

value: DMSO


title: Cardiomyocytes_RNA_rep2-TCDD treated_24hrs

description:
countsTable.xls
APM4


title: Cardiomyocytes_RNA_rep1-control treated_24hrs

description:
countsTable.xls
APM9


title: Cardiomyocytes_RNA_rep1-TCDD treated_72hrs

description:
countsTable.xls
APM5


title: Cardiomyocytes_RNA_rep2-TCDD treated_72hrs

description:
countsTable.xls
APM6


title: Splenic MDSCs PBS-treated mouse, biological rep3

type: RNA

city: Ulm

first: Jasmin

last: Scheurer

address: Eythstraße 24

country: Germany

institute: Dept of Pediatrics and Adolsecent medicine

description: Gene expression data from splenic MDSCs isolated 10 days after allogeneic bone marrow transplantation (parent into F1 bone marrow transplantation mouse model)

hyb_protocol: according to Affymetrix Whole Transcript (WT) Sense Target Labeling Assay

scan_protocol: according to Affymetrix protocols using a GeneChip 3000 Scanner

data_processing: Affymetrix® Expression Console™ Software for RMA normalization, BRB Array Tools for statistical analysis

label: biotin

source_name: splenic MDSCs isolated 10 days post-transplantation

growth_protocol: 10 days after allogeneic bone marrow transplantation splenic single cell suspensions were prepared and MDSCs were isolated by magnetic activated cell sorting using CD11b MicroBeads (Miltenyi) according to manufacturer’s protocol.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Zymo Research)

treatment_protocol: Lethally irradiated B6D2F1 recipient mice were reconstituted with T cell depleted bone marrow  from B6 mice  in the presence or absence of B6-derived spleen cells. 1.5 mg/kg rapamycin or PBS i.p. injections were administered every second day until day 10 post-trasplantion.

tag: mouse strain

tag: agent

value: PBS


title: Agpat3 KO liver 3

city: Shinjyuku-ku Tokyo

first: Daisuke

last: Hishikawa

address: Toyama 1-21-1

country: Japan

institute: NCGM

hyb_protocol: 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting

data_processing: The scanned images were analyzed with Feature Extraction Software; "75Percentile shift" within GeneSpring software for normalization.

source_name: Agpat3 KO liver

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit, One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

growth_protocol: C57BL/6 mice (10 weeks old, male)

extract_protocol: total RNA were extracted from frozen liver tissues using Rneasy mini kit.

tag: strain background

tag: Sex

value: male

tag: genotype/variation

value: Agpat3 KO

value: liver


title: sw480-Tet2

city: Guangzhou

first: Hao

last: Sun

address: 190 Kaiyuan Avenue

institute: Chinese Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Clean fastQ files were mapped to the Human genome (build Hg38) using bismark (version 0.20.1).
Genome_build: hg38
Supplementary_files_format_and_content: CpG reads

source_name: Colorectal Adenocarcinoma cell sw480

growth_protocol: Cancer cell lines were obtained from ATCC. Cell lines were cultured in High Glucose DMEM supplemented with 10% Fetal Bovine Serum (FBS, Excell), 1% nonessential amino acids (NEAA, Thermo Fisher), and 1% GlutaMAX (Thermo Fisher). Cells were maintained at 37 °C under 5% CO2.

extract_protocol:
Cultured cells were washed on ice with ice-cold PBS, detached using cell scrapers and collected by centrifugation. Nucleic acids were subsequently extracted using the Promega Wizard Genomic DNA Purification kit according to instructions and stored at -80°C until further processing.
DNA libraries were prepared using methylated adapters and the NEBNext DNA library prep master mix set following manufacturer recommendations. Libraries were bisulfite-converted using the Imprint DNA modification kit , and PCR amplified for 12 cycles using barcoded primers according to manufacturers instructions.

treatment_protocol: Lentivirus was packaged by co-transfection of vectors encoding target genes and the packaging plasmids pMD2.G and psPAX2 into HEK293T cells. Viruses were collected and used to infect cell lines. 5 μg/ml puromycin was used to select cell lines with genomic incorporation and stable expression of the target genes.

value: Colorectal Adenocarcinoma

tag: tag


title: sw480-vector


title: Agpat3 KO liver 4


title: Agpat3 KO liver 2


title: Splenic MDSCs Rapamycin-treated mouse, biological rep3

label_protocol: Whole Transcript (WT) Sense Target Labeling Assay

value: Rapamycin


title: Splenic MDSCs Rapamycin-treated mouse, biological rep1


title: Splenic MDSCs Rapamycin-treated mouse, biological rep2


title: Cardiomyocytes_RNA_rep1-TCDD treated_24hrs

description:
countsTable.xls
APM3

tag: treatment


title: Agpat3 WT liver 2

source_name: Agpat3 WT liver

value: Agpat3 WT


title: Agpat3 WT liver 1


title: Agpat3 KO liver 1


title: Agpat3 WT liver 4


title: ES cells_RNA_rep2

description:
countsTable.xls
APM2

source_name: ES cells

value: ES cells

value: untreated


title: shQKI1

tag: cell line


title: Splenic MDSCs PBS-treated mouse, biological rep1


title: Agpat3 WT liver 3


title: Splenic MDSCs PBS-treated mouse, biological rep2


title: sw620-vector

source_name: Colorectal Adenocarcinoma cell sw620

tag: cell type


title: ES cells_RNA_rep1

description:
countsTable.xls
APM1


title: NTC3

value: wild type


title: B-231NC-3

city: wuxi

first: ming

last: chen

address: zhongshan road

institute: nanjing medical university

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
HTSeq count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: breast cancer cells

extract_protocol:
Total RNA from MDA-MB-231 shNC/shBry was prepared and kept at 80°C. The RNA quality was determined using a Bioanalyzer 2200 (Agilent, SantaClara, CA, USA). RNA with RIN (RNA integrity number)>8.0 was considered acceptable for cDNA library construction. Sequencing and bioinformatic analysis were performed byShanghai Novelbio. Genes were considered to be significantly differentially expressed between groups when the P-value was<0.05 and the fold change of expression was more than 1.5
RNA libraries were prepared for sequencing using standard Illumina protocols

value: breast cancer cells

tag: shRNA

value: shNC


title: sw620-Tet2


title: B-231NC-2


title: NTC2


title: NTC1


title: B-231NC-1


title: A-231SH-3

value: shBry


title: A-231SH-2


title: A-231SH-1


title: Patient 7_After_PBMC

city: Jinan

first: Ming

last: Hou

state: Shandong

address: 107 West Wenhua Road

department: Department of Hematology

institute: Qilu Hospital, Cheeloo College of Medicine, Shandong University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Clean data were mapped to human transcriptome hg19, and read counts for each gene were generated by featureCounts v1.5.0-p3.
Fragments Per Kilobase Million (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two groups was performed using the EdgeR R package (1.16.1).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: PBMCs

extract_protocol:
PBMCs were isolated from patient blood and RNA of PBMCs was harvested using Trizol reagent. A total amount of 3 μg RNA per sample was used as input material for the RNA sequencing library preparations.  Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell types

value: peripheral blood mononuclear cells

value: low-dose decitabine

tag: therapeutic effect

value: Non responder


title: Patient 4_After_PBMC

value: Responder


title: Patient 5_After_PBMC


title: Patient 6_After_PBMC


title: Patient 3_After_PBMC


title: Donor 3, CAMK2G transcripts, rep.2

city: Amherst

first: Roman

last: Sloutsky

state: MA

address: 710 North Pleasant Street LGRT 1106

department: Biochemistry and Molecular Biology

institute: UMass Amherst

data_processing:
Base calling, standard Illumina sequence quality filtering, and adapter trimming were performed on the MiSeq instrument. FASTQ files were exported from the instrument for subsequent analysis.
For Donor 1 rep. 2, Donor 2, and Donor 3 libraries from genes CAMK2B, CAMK2G, and CAMK2D, reads from Nano and full-size flow cells were combined. For each gene from each sample, reads were clustered by sequence similarity, producing clusters with >90% read sequence similarity and two or fewer insertions / deletions. See Sloutsky et al. (https://doi.org/10.1101/721589) for details.
The consensus sequence of each cluster was aligned to exons of the four CaMKII genes (CAMK2A, CAMK2B, CAMK2G, and CAMK2D) from genome build GRCh38.p12, retrieved from Ensembl release 95, to determine the exon order in the splice variant represented by the read cluster.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Spreadsheets (in tabs) with read counts and percentages of mapped reads from each sample (Donor 1 rep. 1, Donor 1 rep. 2, Donor 2, Donor 3) for each CaMKII gene.

source_name: Donor 3 hippocampal tissue

extract_protocol:
purchased total RNA samples
First strand cDNA was reverse-transcribed from total RNA using the NEB ProtoScript II First Strand cDNA Synthesis Kit (E6560). Transcripts of individual CaMKII-encoding genes were sub-amplified from cDNA in separate PCR reactions using gene-specific primers. Illumina sequencing libraries were constructed from gene-specific amplicon pools using a PCR approach based on Kanizay et al. Plant Genome 2015 (https://doi.org/10.3835/plantgenome2014.10.0070). See Sloutsky et al. (https://doi.org/10.1101/721589) for details.

tag: tissue

value: hippocampus

tag: donor age

tag: donor sex

tag: sample type

value: Full-size flow cell


title: Donor 3, CAMK2D transcripts, rep.2

value: male


title: Donor 3, CAMK2D transcripts, rep.1

value: library balancing Nano flow cell


title: Donor 3, CAMK2G transcripts, rep.1


title: Patient 2_After_PBMC


title: Donor 3, CAMK2B transcripts, rep.2


title: PBS_control_fish5

city: St. John's

first: Khalil

last: Eslamloo

state: Newfoundland and Labrador

address: 0 Marine Lab Rd.

department: Ocean Sciences

country: Canada

institute: Memorial University of Newfoundland

hyb_protocol: The labeled aRNA (i.e. 825 ng) of each experimental sample was mixed with an equal amount of labeled aRNA of the common reference, and the resulting pool was fragmented based on the manufacturer's instructions (Agilent, Mississauga, ON). Each labelled aRNA pool (i.e. an individual sample and common reference) was co-hybridized to a cGRASP-designed Agilent 44K salmonid oligonucleotide microarray (GEO accession # GPL11299). The arrays were hybridized at 65°C for 17 h with 10 rpm rotation in an Agilent hybridization oven. The array slides were washed immediately following hybridization as per the manufacturer's instructions.

scan_protocol: The microarray slides were scanned at 5 µm resolution using SureScan Microarray Scanner System (Agilent Technologies, Santa Clara, CA) and Microarray Scan Control Software following the Agilent HD 2-color gene expression microarrays scan protocol.

data_processing: Agilent Feature Extraction Software v12.0 (Agilent Technologies) was used to extract and Loess-normalize the signal intensity data. Thereafter, using GeneSpring Software v14.9 (Agilent Technologies), the data were quality-checked so that probes with low and marginal quality as well as absent values in more than 25% of all 12 arrays were removed from the dataset.

organism: Salmo salar

source_name: PBS-injected fish at 24 h post-stimulation.

label_protocol: Six individuals per group (6 PBS group and 6 High-Rs group; 12 samples in total) were used for microarray experiment. The microarray experiment was conducted using a common reference design. The mRNA of each sample was amplified and then labelled using 1 µg of DNase-treated and column-purified RNA and Amino Allyl MessageAmp™ II aRNA Amplification kit (Ambion®, Carlsbad, CA, USA), according to the kit’s procedure. A common reference was prepared using a pool of all 12 samples (15 µg aRNA from each sample) involved in microarray experiment. The experimental samples (PBS and High-Rs) were labelled with Cy5 (GE Healthcare, Buckinghamshire, UK), whereas the common reference samples were labelled with Cy3 (GE Healthcare), based on the manufacturer’s protocol.

extract_protocol:
Bacterin injection and sampling: Twelve Atlantic salmon were anesthetised using MS222 (50 mg L-1) and intraperitoneally injected with a high (5×10^7 cells/kg; High-Rs; n = 6) dose of formalin-killed R. salmoninarum or phosphate-buffered saline (PBS control; n = 6). Fish were held in the tank for 24 h after injection, and then were euthanized using an overdose of MS222 (400 mg L-1) before dissection. The head kidney of the each individual was sampled and used for transcriptome analyses.
Total RNA was extracted from TRIzol-lysed samples, following the manufacturer’s instructions. The RNA samples were treated with Dnase-I (Qiagen, Mississauga, Ontario, Canada) for removing any residual genomic DNA contamination, and then purified using RNeasy MinElute Cleanup Kit (Qiagen) according to the manufacturer’s instructions.  The high-purity RNA samples (e.g. A260/230 and A260/280 ratios > 1.8) with tight 18S and 28S ribosomal RNA bands were used for the microarray analysis.

value: head kidney

tag: life stage

value: adult

source_name: pool of RNAs from all samples involved in the microarray experiment


title: PBS_control_fish6


title: Patient 1_After_PBMC


title: High_R. salmoninarum_bacterin_fish6

source_name: R. salmoninarum bacterin-injected fish at 24 h post-stimulation.


title: Cardiac cells from postnatal 3 weeks old mouse

first: Zhen

last: Jiang

address: 393 Middle Huaxia Road, L Building B328

department: Life Science and Technology School

institute: ShanghaiTech University

data_processing:
Aligned reads and gene-barcode matrices were then generated using Cell Ranger (v.3.1.0) processing pipeline.
Analysed of processed scRNA-seq data in R (v.3.6.1) using the Seurat package (v.3.1.5).
Genome_build: mm9
Supplementary_files_format_and_content: Cell gene expression table

source_name: Cardiac cells

extract_protocol:
Single cardiac cells were isolated from infant mouse at postnatal 3 weeks by retrograde Langendorff perfusion
Single cell library was generated using 10x Genomic Chromium system with the v3 single cell reagent kit. Sequencing of library was performed on Illumina NovoSeq 6000 platform.

tag: strain

value: C57BL/6 ICR

value: heart

tag: age

value: postnatal 3 weeks

tag: genotype


title: High_R. salmoninarum_bacterin_fish2


title: PBS_control_fish3


title: High_R. salmoninarum_bacterin_fish4


title: High_R. salmoninarum_bacterin_fish1


title: High_R. salmoninarum_bacterin_fish3


title: PBS_control_fish2


title: High_R. salmoninarum_bacterin_fish5


title: Patient 7_Before_PBMC


title: Patient_EA627_Serum_v1_prediabetes_v2_prediabetes

city: Bialystok

first: Iwona

last: Sidorkiewicz

address: Sklodowska-Curie Street 24a

department: Clinical Research Centre

country: Poland

institute: Medical University of Bialystok

hyb_protocol: The samples were prepared for nCounter miRNA expression profiling according to the manufacturer’s recommendations (NanoString Technologies, USA). Briefly, 3 ng miRNA samples were prepared by ligating a specific miR-tag onto 3′ end of each mature miRNA followed by an overnight hybridization (65 °C) to nCounter Reporter and Capture probes. Subsequently, samples were placed into the nCounter Prep Station for automated sample purification and subsequent reporter capture.

scan_protocol: Each sample was scanned on the nCounter Digital Analyzer for data collection.

data_processing: nSolver 4.0 Analysis software (NanoString) was used for data analysis including normalization using the average geometric mean of the top 100 probes detected. The p-values were adjusted using the False Discovery Rate (FDR) correction for multiple comparisons, which was limited to 0.05

label: oligonucleotide probe

source_name: serum

label_protocol: Specific oligonucleotide probe pairs that are bound to barcoded tags (nanostring technologies inc.) were conducted according to the manufacturer's protocol.

extract_protocol: miRNeasy Serum/Plasma Kit (Qiagen, Germany) according to the manufacturer’s instructions

tag: status after 5 years

value: Prediabetes

tag: gender

value: F

tag: bmi


title: Patient_EA217_Serum_v1_prediabetes_v2_prediabetes


title: Patient 6_Before_PBMC

tag: treatment


title: PBS_control_fish4


title: Donor 3, CAMK2A transcripts, rep.1

value: Nano flow cell


title: Patient_EA755_Serum_v1_prediabetes_v2_prediabetes

value: M


title: Adult mechanoreceptor RAMA responder 7

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
Illumina BaseCaller: Sequence images to BCL files
Illumina bcl2fastq v2.17.1.14: Demultiplexing to fastq files
FastQC v0.11.5: Quality checks
Cutadapt 1.9.1: removal of Nextera adapter
STAR aligner v2.5.2a: alignment to reference genome Mus musculus mm10 version 96, allowing for 2 mismatches within 50 bases
R v3.6.1, edgeR v3.22.5: read count analysis and TPM calculation
Genome_build: mm10 version 96
Supplementary_files_format_and_content: Text files containing tab-delimited matrices of raw read counts or Transcripts Per Million (TPM)

growth_protocol: DRG were isolated from male C57BL/6J mice at the indicated ages. In brief, DRG neurons were promptly isolated and digested with collagenase (Life Technologies) and papain (Worthington). Neurons were plated on poly-D-lysine (1 mg/mL, Milipore) coated coverslips, which were additionally coated with laminin (20 µg/mL, Life Technologies). Growth medium (Ham’s F12/DMEM 1:1 ratio with L-glutamine; Gibco) was supplemented with 10 % horse serum (Life Technologies) and 100 ng/ml NGF, 50 ng/ml GDNF, 50 ng/ml BDNF, 50 ng/ml NT-3, and 50 ng/ml NT-4 (all growth factors procured from R&D Systems). Experiments were performed 24 h after culturing to ensure reliable adhesion to the coated surface before mechanical stimulation. See Coste et al., 2010; Narayanan et al., 2016; Narayanan et al., 2018; Michel et al. 2020.

extract_protocol:
After patch clamp recordings negative pressure was applied to the patch pipette in whole-cell-mode to aspirate cytosolic contents as suggested (Fuzik et al., 2016; Cadwell et al., 2017). The content of the patch pipette was transferred, by applying positive pressure, to a 1.5 ml centrifuge tube filled with 100 µl of cool lysis buffer containing TCEP from the NucleoSpin RNA XS kit (MACHEREY-NAGEL GmbH & Co. KG, Germany). Often, pipettes were broken inside the tube to ensure full transfer of cellular material to the buffer. After harvest samples were flash frozen in liquid nitrogen and stored at -80 °C. RNA purification was performed according to the manufacturer’s instructions of the NucleoSpin RNA XS kit (MACHEREY-NAGEL GmbH & Co. KG, Germany).
cDNAs were constructed using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories, Inc., USA /Takara) according to the manufacturer's protocol. The amplified and purified cDNAs were validated at the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit (Agilent). The libraries for sequencing were prepared using Nextera XT DNA Sample Preparation kit (Illumina, Inc., USA) following the manufacturer’s protocol (input cDNA: 1 ng). Before sequencing, library quality was controlled at the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit (Agilent). Libraries were sequenced on the NovaSeq 6000 sequencing system (Illumina; paired-end 150 bp fragments).

treatment_protocol: DRG neuron somata were mechanically stimulated using a blunt glass probe at -70 mV holding potential and room temperature up to 11 µm in standard NaCl-based bath solution and standard KCl-based pipette solution in whole-cell voltage clamp. Action potentials were evoked using current injection in whole-cell current clamp experiments under the same conditions. Action potentials were categorized as noci or mec according to their waveform (full width at half maximum and presence of a bump in the falling phase); categories given here match the resulting RNA-profile (expression of common marker genes). Please see for details: Michel et al. 2020 “Maturational changes in mouse cutaneous touch and Piezo2-mediated mechanotransduction”.

value: WT

tag: Sex

value: post natal day 113

value: dorsal root ganglion neuron

tag: action potential type

value: mechanoreceptor

tag: mechanically activated rapidly adapting current (na)


title: Patient 5_Before_PBMC

tag: cell types

value: peripheral blood mononuclear cells

value: low-dose decitabine

value: Non responder


title: Adult mechanoreceptor RAMA responder 9

value: male

tag: cell type


title: Adult mechanoreceptor RAMA responder 8


title: Donor 2, CAMK2D transcripts, rep.1

source_name: Donor 2 hippocampal tissue

tag: tissue

value: hippocampus

value: library balancing Nano flow cell


title: PBS_control_fish1

value: head kidney

value: adult


title: Patient_EA533_Serum_v1_prediabetes_v2_prediabetes


title: Patient_EA723_Serum_v1_prediabetes_v2_prediabetes


title: Donor 2, CAMK2D transcripts, rep.2

tag: donor age

value: Full-size flow cell


title: Donor 3, CAMK2B transcripts, rep.1

tag: donor sex


title: Adult mechanoreceptor RAMA responder 6

value: post natal day 102


title: Patient 4_Before_PBMC

tag: therapeutic effect

value: Responder


title: Donor 2, CAMK2G transcripts, rep.2

tag: sample type


title: Donor 2, CAMK2G transcripts, rep.1


title: Adult mechanoreceptor RAMA responder 4

tag: strain


title: Patient 3_Before_PBMC


title: Adult mechanoreceptor RAMA responder 5

tag: age


title: Patient_EA622_Serum_v1_prediabetes_v2_prediabetes

value: Prediabetes


title: Patient_EA571_Serum_v1_prediabetes_v2_prediabetes

value: MF


title: Patient_EA541_Serum_v1_prediabetes_v2_prediabetes

value: M


title: Patient 2_Before_PBMC


title: Donor 2, CAMK2B transcripts, rep.2


title: Donor 2, CAMK2B transcripts, rep.1


title: 12 TLK1 siTLK2-2

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

data_processing:
Reads were aligned to the human genome version hg19 using Bowtie (v.0.12.9) with options: -m 1 -n 1. SAM files were converted to BAM and sorted using sambamba (v.0.5.8)
Peak calling was performed with MACS (v.1.4.2) with no matched controls and deafult parameters
Genome_build: hg19
Supplementary_files_format_and_content: BED files of peak calling with MACS

source_name: HeLa

growth_protocol: Cells were grown in DMEM (Thermo Fisher Scientific) supplemented with 10% FBS (Sigma-Aldrich) and penicillin–streptomycin at 37°C in a 5% CO2 incubator.

extract_protocol:
75000 cells were resuspended in 50 μl of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Igepal CA-630) for nuclei preparation and treated with Nextera Tn5 Transposase (Nextera DNA Library Preparation Kit, Illumina) at 37°C for 30 min. DNA was purified using MinElute PCR Purification Kit (Qiagen).
ATAC libraries were prepared using NEBNext High-Fidelity 2x PCR Master Mix (NEB) following manufacturer's instructions for 11 cycles. Amplified libraries were purified using PureLink PCR Purification Kit (Thermo Fisher Scientific).

treatment_protocol: Human HeLa LT WT and TLK1-knockout cells were transfected in biological duplicate with siRNAs (siCont, siTLK2) and 48 hours post-transfection cells were collected by trypsinization. 75000 cells were subsequently used for nuclei preparation.

tag: cell line

value: HeLa

tag: genotype

value: TLK1 KO

tag: replicate

tag: sirna


title: Patient 1_Before_PBMC

tag: treatment


title: Patient_EA503_Serum_v1_prediabetes_v2_prediabetes

tag: status after 5 years

tag: gender

value: F

tag: bmi


title: Adult mechanoreceptor RAMA responder 2

value: WT

tag: Sex

value: post natal day 94

value: dorsal root ganglion neuron

tag: action potential type

value: mechanoreceptor

tag: mechanically activated rapidly adapting current (na)


title: Donor 2, CAMK2A transcripts, rep.1

tag: tissue

value: hippocampus

tag: donor age

value: male

value: Nano flow cell


title: 11 TLK1 siTLK2-1


title: 10 TLK1 siGFP-2

value: siCont


title: Patient_EA276_Serum_v1_prediabetes_v2_prediabetes


title: Juvenile mechanoreceptor RAMA responder 9

value: post natal day 28

tag: cell type


title: Donor 1, CAMK2G transcripts, rep. 3

source_name: Donor 1 hippocampal tissue

tag: donor sex

tag: sample type

value: Full-size flow cell


title: Adult mechanoreceptor RAMA responder 1

tag: strain

tag: age

value: post natal day 90


title: Patient_EA614_Serum_v1_prediabetes_v2_prediabetes

value: Prediabetes


title: Juvenile mechanoreceptor RAMA responder 8

tag: genotype


title: Donor 1, CAMK2D transcripts, rep. 3


title: 9 TLK1 siGFP-1

tag: cell line

tag: replicate


title: Adult mechanoreceptor RAMA responder 3

value: post natal day 85


title: Donor 1, CAMK2D transcripts, rep. 2

value: library balancing Nano flow cell


title: Juvenile mechanoreceptor RAMA responder 6

value: post natal day 30


title: Donor 1, CAMK2G transcripts, rep. 2


title: Donor 1, CAMK2B transcripts, rep. 3


title: Patient_EA740_Serum_v1_prediabetes_v2_T2DM

value: Diabetes


title: Patient_EA629_Serum_v1_prediabetes_v2_T2DM

value: F


title: Juvenile mechanoreceptor RAMA responder 4

value: WT


title: Patient_EA630_Serum_v1_prediabetes_v2_T2DM

value: M


title: 1 siGFP-1

value: HeLa

tag: sirna


title: ChIPH3.3siT-B19.10

data_processing:
Reads were aligned to the human genome version hg19 using Bowtie (v.0.12.9) with options: -m 1 -n 1. SAM files were converted to BAM and sorted using sambamba (v.0.5.8)
Peak calling was performed with MACS (v.1.4.2) using matched inputs with options: --broad -q 0.01
Genome_build: hg19
Supplementary_files_format_and_content: BED files of peak calling with MACS

extract_protocol:
Cells were crosslinked with 1% Formaldehyde in DMEM for 10 min at room temperature and quenched with Glycine at a final concentration of 125 mM. Cells were washed with PBS, pelleted by centrifugation and dry pellets were snap frozen. For nuclear extract preparation, pelleted cells were thawed on ice, resuspended in cold Swelling buffer (25 mM Hepes pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1x protease (Roche) and phosphatase inhibitors (Sigma-Aldrich)) for 10 min and passed through a douncer 50 times. Nuclei were pelleted by centrifugation at 3000 g for 5 min at 4ºC, and resuspended in 300 ul of 1% SDS in ChIP buffer (10 mM Tris-HCl pH 7.5,150 mM NaCl, 1% Triton X-100, 5 mM EDTA, 0.5 mM DTT, 1x protease (Roche) and phosphatase inhibitors (Sigma-Aldrich)). The extracts were incubated for 15 min on ice and sonicated in a Bioruptor Pico sonication device (Diagenode) for 30 cycles 30’’ on/30’’ off. Chromatin was cleared by centrifugation at top speed 15 min at 4ºC. For H3.3 (Millipore 09-838) ChIP, 5 ug of total chromatin was diluted 1:10 in ChIP buffer and incubated with 1 ug of antibody on rotation at 4ºC overnight. 50 ul of prewashed Dynabeads Protein G (Thermo Fisher Scientific) were added on rotation for 2h at 4ºC. Beads were washed with Low Salt buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1% Triton X-100, 1x protease (Roche) and phosphatase inhibitors (Sigma-Aldrich)), High Salt buffer (50 mM HEPES pH 7.5, 500 mM NaCl, 1% Triton X-100, 1x protease (Roche) and phosphatase inhibitors (Sigma-Aldrich)) and eluted by incubating in a thermomixer with Elution buffer (1% SDS, 100 mM NaHCO3) for 30 min at 65ºC and 1000rpm. Samples were reverse-crosslinked by incubating at 65ºC overnight and incubated with Proteinase K for 1h at 45ºC. Chipped DNA was purified using the MinElute PCR Purification Kit (Qiagen) and eluted in 40 ul.
Library construction was done with the kit NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, catalog # E7645), following manufacturer´s instructions and 9-10 cycles of amplification

treatment_protocol: U-2-OS cells were transfected in biological duplicate with siRNAs (siCont and siTLK1+2) and 48 hours post-transfection were harvested by trypsinization.

value: H3.3 ChIP

value: siTLK

value: B


title: Juvenile mechanoreceptor RAMA responder 5

value: male

value: dorsal root ganglion neuron

value: mechanoreceptor


title: ChIPH3.3siT-A19.10

value: A


title: Donor 1, CAMK2A transcripts, rep. 2

value: hippocampus

value: Nano flow cell


title: Juvenile mechanoreceptor RAMA responder 3


title: Juvenile mechanoreceptor RAMA responder 7

value: post natal day 31


title: Patient_EA73_Serum_v1_prediabetes_v2_prediabetes

tag: status after 5 years

value: Prediabetes


title: Patient_EA617_Serum_v1_prediabetes_v2_T2DM

tag: gender


title: Patient_EA591_Serum_v1_prediabetes_v2_T2DM

tag: bmi


title: 2 siGFP-2

value: siCont


title: ChIPH3.3siG-B19.10

value: ctrl


title: Donor 1, CAMK2D transcripts, rep. 1


title: Juvenile mechanoreceptor RAMA responder 2

tag: Sex

value: post natal day 29


title: ChIPH3.3siG-A19.10


title: Donor 1, CAMK2G transcripts, rep. 1


title: Patient_EA573_Serum_v1_prediabetes_v2_T2DM

value: Diabetes


title: ChIP1%inputsiT-B19.10

value: input


title: ChIP1%inputsiT-A19.10


title: Donor 1, CAMK2A transcripts, rep. 1


title: Patient_EA452_Serum_v1_prediabetes_v2_T2DM

value: M


title: uninfected

city: Seattle

first: Nicole

middle: A P

last: Lieberman

state: WA

address: 850 Republican St S130

department: Laboratory Medicine

institute: University of Washington

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired end reads were adapter and quality trimmed and aligned to the human transcriptome by Kallisto v0.44.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human Airway Epithelial Cells

extract_protocol:
RNA from uninfected and infected HAE was extracted using Direct-zol RNA MicroPrep (Zymo).
Libraries were generated using the TruSeq Stranded mRNA kit (Illumina) and 2x100bp paired-end reads sequenced on a Novaseq

tag: sars-cov-2 infection

value: uninfected

value: Human Airway Epithelial Cells


title: Patient_EA287_Serum_v1_prediabetes_v2_T2DM


title: Patient_EA263_Serum_v1_prediabetes_v2_T2DM

value: F


title: X3_DPI

value: male

value: infected


title: X7_DPI


title: ChIP1%inputsiG-A19.10


title: 12 week old NOD pancreas - sample 8

city: Stanford

first: Linda

last: Yip

state: CA

address: 269 Campus Drive West, CCSR Building Rm. 2240

department: Medicine

institute: Stanford University

description: Gene expression in pancreas of a 12 week old NOD mouse compared to a pool of 8 age-matched NOD.B10 pancreas

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit and the Agilent Microarray Hybridization Chamber as instructed by the manufacturer. Samples were hybridized for 17 h at 65ºC, and slides were washed with Gene Expression Wash Buffer (Agilent) according to maufacturer's instructions.

scan_protocol: Microarray chips were scanned using the DNA microarray scanner (Agilent Technologies) with the following parameters: 2 color scan; scan resolution 5 um, single pass, red and green dye channels. Data was extracted using Feature Extraction software (version 10.5.1.1)

data_processing: Data were processed using Genespring 12.6.1

source_name: pancreas

label_protocol: 1 ug of total RNA from each individual  NOD mouse, or 1 ug of total RNA from a pool of 8  NOD.B10 mice were labeled using the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies) according to manufacturer's instructions.

growth_protocol: NOD and NOD.B10 mice were bred at the Stanford School of Medicine Animal facility.  All mice were maintained under pathogen-free conditions according to institutional guidelines under approved protocols in the Stanford Medical Center’s Department of Comparative Medicine.

extract_protocol: Total RNA was extracted from NOD and NOD.B10 pancreas using Trizol (Invitrogen) combined with the RNeasy mini kit (Qiagen).

treatment_protocol: Pancreas tissues were isolated from mice and immediately homogenized in Trizol Reagent (Invitrogen).

value: NOD

value: 12 weeks old

value: female


title: Donor 1, CAMK2B transcripts, rep. 2

value: hippocampus

value: library balancing Nano flow cell


title: B7 siTLK2

extract_protocol:
50000 cells were resuspended in 50 μl of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Igepal CA-630) for nuclei preparation and treated with Nextera Tn5 Transposase (Nextera DNA Library Preparation Kit, Illumina) at 37°C for 30 min. DNA was purified using MinElute PCR Purification Kit (Qiagen).
ATAC libraries were prepared using NEBNext High-Fidelity 2x PCR Master Mix (NEB) following manufacturer's instructions for 11 cycles. Amplified libraries were purified using PureLink PCR Purification Kit (Thermo Fisher Scientific).

treatment_protocol: U-2-OS cells were transfected in biological duplicate with siRNAs (siCont, siTLK1, siTLK2, siTLK1+2) and 48 hours post-transfection cells were collected by trypsinization. 50000 cells were subsequently used for nuclei preparation.


title: B6 siTLK1


title: B8 siTLK1+TLK2


title: Patient_EA535_Serum_v1_prediabetes_v2_T2DM


title: Donor 1, CAMK2B transcripts, rep. 1

value: Nano flow cell


title: Juvenile mechanoreceptor RAMA responder 1

value: WT

value: post natal day 28

value: dorsal root ganglion neuron

tag: action potential type

value: mechanoreceptor

tag: mechanically activated rapidly adapting current (na)


title: B5 WT U2OS


title: OCM1 CTCF ChIP-seq  rep3

first: Peiwei

last: Chai

address: No.833 Zhizaoju Road

institute: Shanghai Jiao Tong University school of medcine

data_processing:
Mapping : bowtie -m 2 --maxIns 350, hg38 For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts) Generating bigwig tracks (ucsctools bedGraphToBigWig)
Genome_build: hg38
Supplementary_files_format_and_content: bigWig : DEEPtools bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above)from bam to bigwig, (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

source_name: melanoma cells

growth_protocol: All cell lines were cultured in Dulbecco’s modified Eagle medium (DMEM; Gibco, USA) supplemented with 10% certified heat-inactivated fetal bovine serum (FBS; Gibco, USA), penicillin (100 U/ml) and streptomycin (100 μg/ml) at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: sciencell epithelial media

value: ocular melanoma cells

tag: antibody

value: CTCF


title: Patient_EA138_Serum_v1_prediabetes_v2_T2DM

value: Diabetes


title: ChIP1%inputsiG-B19.10

value: input

value: ctrl

value: B


title: Patient_EA90_Serum_v1_prediabetes_v2_T2DM

value: M


title: Patient_EA171_Serum_v1_prediabetes_v2_T2DM


title: Patient_EA79_Serum_v1_prediabetes_v2_T2DM

value: F


title: 12 week old NOD pancreas - sample 6

value: NOD

value: 12 weeks old


title: OCM1 CTCF ChIP-seq  rep2

tag: cell type


title: 12 week old NOD pancreas - sample 5

value: female


title: 12 week old NOD pancreas - sample 4


title: 12 week old NOD pancreas - sample 7


title: A4 siTLK1+TLK2


title: 12 week old NOD pancreas - sample 3


title: Patient_EA65_Serum_v1_prediabetes_v2_T2DM


title: Patient_EA182_Serum_v1_prediabetes_v2_T2DM


title: OCM1 input rep2


title: OCM1 input  rep3


title: Vg1 RNP

city: Notre Dame

first: Chao

last: Yang

state: IN

address: 437 Stepan Chemistry Hall

department: Chemistry and Biochemistry

institute: University of Notre Dame

description: pulldown RNA

data_processing:
Sequencing was done on an Illumina MiSeq v2 300 cycle micro reagent kit using 100 x 100 bp reads
Base calling was done by Illumina MiSeq Control Software (MCS v2.6)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Xla.v91 genome and .gff3 file using Tophat/bowtie2
Fragments Per Kilobase Million (FPKM) were calculated and differentially compared using Cufflinks/Cuffdiff. FPKMs were also converted in Transcripts Per Million (TPM)
Genome_build: bowtie2  Xla.v91.fa

organism: Xenopus laevis

source_name: Oocytes

growth_protocol: Oocytes were cultured in oocytes culturing media (50% Leibovitz’s L-15 medium, 15 mM HEPES pH 7.6, 1 mg/ml L-glutamine, 5 mg/ml vitellogenin, 1µg/ml insulin, 100 U/ml penicillin G, 100 µg/ml streptomycin, 100 µg/ml gentamicin, 50 U/ml nystatin). The media is freshly prepared on a daily basis.

extract_protocol:
Briefly, oocytes were manually breaked down to get the extract and the Biotin-Vg1RNP was pulled down by incubating with streptavidin-conjugated beads. RNA was extracted by phenol and precipitated by ethanol.
Library was prepared using the NEBNext Ultra II Directional RNA library prep kit with RiboZero depletion module H/M/R.

treatment_protocol: 6 nl of 300 pg/nl biotin-Vg1 mRNA was injected into each oocyte followed by culturing for 35 hours in oocyte culturing media in 18 degree.

tag: oocyte stage

value: Stage III-early stage IV oocytes

value: Xenopus oocytes

tag: rna pulldown beads

value: Streptavidin conjugated sephorase beads


title: A3 siTLK2


title: OCM1 CTCF ChIP-seq  rep1


title: 12 week old NOD pancreas - sample 2

tag: strain


title: Patient_EA53_Serum_v1_prediabetes_v2_T2DM

tag: age


title: OCM1 input rep1


title: A2 siTLK1

tag: genotype


title: Sequence2 (mixed samples)

first: Jes

last: Alexander

address: 3720 15th Ave NE, Foege Building S-210

department: Genome Sciences

description:
Mixed sample (non-demultiplexed):
No IR Brain 1 (Normal brain from a PDGF-driven mouse model of glioma)
No IR Tumor 1 (Tumor from a PDGF-driven mouse model of glioma)
No IR Tumor 2 (Tumor from a PDGF-driven mouse model of glioma)
No IR Tumor 3 (Tumor from a PDGF-driven mouse model of glioma)
IR 8hr Brain 1 (Normal brain from a PDGF-driven mouse model of glioma harvested at 8 hours after 10 Gy of ionizing radiation)
IR 8hr Brain 2 (Normal brain from a PDGF-driven mouse model of glioma harvested at 8 hours after 10 Gy of ionizing radiation)
IR 8hr Tumor 1 (Tumor from a PDGF-driven mouse model of glioma harvested at 8 hours after 10 Gy of ionizing radiation)
IR 8hr Tumor 2 (Tumor from a PDGF-driven mouse model of glioma harvested at 8 hours after 10 Gy of ionizing radiation)
IR 72hr Brain 1 (Normal brain from a PDGF-driven mouse model of glioma harvested at 72 hours after 10 Gy of ionizing radiation)
IR 72hr Brain 2 (Normal brain from a PDGF-driven mouse model of glioma harvested at 72 hours after 10 Gy of ionizing radiation)
IR 72hr Tumor 1 (Tumor from a PDGF-driven mouse model of glioma harvested at 72 hours after 10 Gy of ionizing radiation)
293T/NIH3T3 (50:50 mix of 293T (human) and NIH3T3 (mouse) cell lines used as a control for determining collision rate)

Processed data files:
MouseGliomaCDS.rds
MouseGliomaCells.tsv
MouseGliomaGenes.tsv
MouseGliomaMatrix.mtx
BarnyardCDS.rds
BarnyardCells.tsv
BarnyardGenes.tsv
BarnyardMatrix.mtx
Sequence2Barcodes.tsv

data_processing:
Demultiplexing was performed using bcl2fastq v2.16.  Barcodes used are in Sequence1Barcodes.tsv for Sequence1_S0_R1_001.fastq.gz and Sequence1_S0_R2_001.fastq.gz, Sequence2Barcodes.tsv for Sequence2_S0_R1_001.fastq.gz and Sequence2_S0_R2_001.fastq.gz, Sequence3Barcodes.tsv for Sequence3_S0_R1_001.fastq.gz and Sequence3_S0_R2_001.fastq.gz, and Sequence4Barcodes.tsv for Sequence4_S0_R1_001.fastq.gz and Sequence4_S0_R2_001.fastq.gz.
Poly-A tails and adaptors were clipped using trim_galore v 0.4.1
Using STAR v2.5.2b, trimmed reads were aligned to a reference genome including human (hg19) and mouse (mm10) genomes with annotations from GENCODE V19 for human and VM11 for mouse
Reads not mapping uniquely and duplicates based on unique molecular index (UMIs), reverse transcription index, and rear 2 end coordinate were removed.
Reads were mapped to cells by further demultiplexing using the reverse transcription index (RTBarcodes.tsv).
A digital gene expression matrix was created by counting, in a strand-specific manner, the number of unique sequences based on UMIs that map to either exonic or intronic regions of each gene using bedtools (version 2.26.0)
RCAS virus reads were added back to the matrix by first aligning previously unaligned reads to the RCAS LTR reference sequence using bowtie v2.2.3
Aligned reads were deduplicated based on the UMIs, reverse transcription index, and rear 2 end coordinates.
Counts were then added for the RCAS LTR transcript (RCAS, ENSMUSG00000000LTR.1) to the appropriate cell in the digital gene expression matrix based on the barcodes.
Cells with < 90% of UMIs mapping to a single species and cells with < 100 UMIs total were filtered out.
Genome_build: hg19 and mm10, RCAS LTR: >RCAS_ASLV_LTR  AATGTAGTCTTATGCAATACTCTTGTAGTCTTGCAACATGGTAACGATGAGTTAGCAACATGCCTTACAAGGAGAGAAAAAGCACCGTGCATGCCGATTGGTGGAAGTAAGGTGGTACGATCGTGCCTTATTAGGAAGGCAACAGACGGGTCTGACATGGATTGGACGAACCACTGAATTCCGCATTGCAGAGATATTGTATTTAAGTGCCTAGCTCGATACAATAAACGCCATTTGACCATTCACCACA
Supplementary_files_format_and_content: MouseGliomaCDS.rds: R data file (.rds) containing a Monocle 3alpha CellDataSet Object with labeled mouse glioma data after removing cells with <= 100 transcripts and < 90% mouse transcripts.
MouseGliomaCells.tsv: Tab-separated value (.tsv) file containing the names of cells (i.e., barcodes representing cells) for the mouse glioma dataset.
MouseGliomaGenes.tsv: Tab-separated value (.tsv) file containing the Ensembl IDs for the mouse glioma dataset.
MouseGliomaMatrix.mtx: Matrix Market (.mtx) file containing transcript counts for the mouse glioma dataset (cells are columns and Genes are rows).
BarnyardCDS.rds: R data file (.rds) containing a Monocle 3alpha CellDataSet Object with labeled 293T/NIH3T3 mixed cell data after removing cells with <= 100 transcripts.
BarnyardCells.tsv: Tab-separated value (.tsv) file containing the names of cells (i.e., barcodes representing cells) for the barnyard (293T/NIH3T3 mix) dataset.
BarnyardGenes.tsv: Tab-separted value (.tsv)  file containing the Ensembl IDs for the barnyard (293T/NIH3T3 mix) dataset.
BarnyardMatrix.mtx: Matrix Market (.mtx) file containing transcript counts for the  barnyard (293T/NIH3T3 mix) dataset.  Cells are columns and Genes are rows.

organism:
Homo sapiens
Mus musculus

source_name: Brain, 293T and NIH 3T3 cell lines

growth_protocol: Ink4a/Arf-/- mice were injected intracranially as pups with RCAS-PDGFB virus to generate glioma-like tumors.

extract_protocol:
Nuclei were extracted and fixed using the single-cell combinatorial indexed RNA sequencing protocol (Cao et al. Science. 2017. 357:661-7.)
Library construction was as per the single-cell combinatorial indexed RNA sequencing protocol (Cao et al. Science. 2017. 357:661-7.)

treatment_protocol: At symptom onset, tumor and normal brain was immediately harvested or mice were either irradiated with 10Gy of ioninzing radiation (X-rays) and tumor and normal brain was harvested at 8 +/- hours or 72 hours after radiation.

tag: tissue

value: mixed sample (Normal Brain, Tumor, cell lines 293T and NIH 3T3 )

tag: treatment

value: mixed sample (IR, No IR)

tag: hours after ionizing radiation (ir)

value: mixed sample (8hr after IR, 72hr after IR, No IR)


title: Patient_EA39_Serum_v1_prediabetes_v2_T2DM

tag: status after 5 years


title: Sequence1 (mixed samples)

description:
Mixed sample (non-demultiplexed):
No IR Brain 1 (Normal brain from a PDGF-driven mouse model of glioma)
No IR Tumor 1 (Tumor from a PDGF-driven mouse model of glioma)
No IR Tumor 2 (Tumor from a PDGF-driven mouse model of glioma)
No IR Tumor 3 (Tumor from a PDGF-driven mouse model of glioma)
IR 8hr Brain 1 (Normal brain from a PDGF-driven mouse model of glioma harvested at 8 hours after 10 Gy of ionizing radiation)
IR 8hr Brain 2 (Normal brain from a PDGF-driven mouse model of glioma harvested at 8 hours after 10 Gy of ionizing radiation)
IR 8hr Tumor 1 (Tumor from a PDGF-driven mouse model of glioma harvested at 8 hours after 10 Gy of ionizing radiation)
IR 8hr Tumor 2 (Tumor from a PDGF-driven mouse model of glioma harvested at 8 hours after 10 Gy of ionizing radiation)
IR 72hr Brain 1 (Normal brain from a PDGF-driven mouse model of glioma harvested at 72 hours after 10 Gy of ionizing radiation)
IR 72hr Brain 2 (Normal brain from a PDGF-driven mouse model of glioma harvested at 72 hours after 10 Gy of ionizing radiation)
IR 72hr Tumor 1 (Tumor from a PDGF-driven mouse model of glioma harvested at 72 hours after 10 Gy of ionizing radiation)
293T/NIH3T3 (50:50 mix of 293T (human) and NIH3T3 (mouse) cell lines used as a control for determining collision rate)

Processed data files:
MouseGliomaCDS.rds
MouseGliomaCells.tsv
MouseGliomaGenes.tsv
MouseGliomaMatrix.mtx
BarnyardCDS.rds
BarnyardCells.tsv
BarnyardGenes.tsv
BarnyardMatrix.mtx
Sequence1Barcodes.tsv


title: U2OS siTLK1 siTLK2 B4

description:
sample name in processed data file:
9942016

data_processing:
Reads were aligned to the human genome version hg19 using Bowtie (v.0.12.9) with default options. SAM files were converted to BAM and sorted using sambamba (v.0.5.8)
Aligned reads for each sample and gene were computed using function "featureCounts" from the Rsubread R package and built-in annotation hg19
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts matrix. Row identifiers: gene entrez ID

extract_protocol:
RNA was isolated using the PureLink RNA Mini Kit (Thermo Fisher Scientific) following the manufacturer's instructions for TRIzol Plus Total Transcriptome Isolation.
RNA libraries were prepared for sequencing using the kits Ribo-Zero Gold rRNA Removal Kit (Illumina Cat#MRZG12) and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (New England Biolabs Cat#E7770), following manufacturer´s instructions and 7 cycles of amplification.

treatment_protocol: U-2-OS cells were transfected in biological duplicate with siRNAs (siCont, siTLK1, siTLK2, siTLK1+2) and 48 hours post-transfection were washed twice with cold PBS and collected by scraping in Tri-Reagent (Sigma-Aldrich).

tag: cell line

tag: replicate


title: HAE_SARSCoV2_3

city: Atlanta

first: Mehul

middle: Shamal

last: Suthar

state: GA

address: 954 Gatewood Road, Office 2022

institute: Emory University

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the human (GRCh38 Ensemble release 100) and SARS-CoV2 (MT246667.1)  genomic reference with STAR (v2.7.3a) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
A value of '1' was added to each of the normalized read counts.  This provides a value to genes which show no read counts and allows for appropriate calculations of fold change.  Low abundance transripts are moe influenced by highly expressed transcripts.
Genome_build: GRCh38 Ensembl release 100 (primary assembly) and MT246667.1 reference. ORF7b was annotated in MT246667.1 based on NC_045512.2 reference
Supplementary_files_format_and_content: STARv2.7.3a was used to generate the raw read counts.  Read counts were normalized using DESeq2 through R software.

source_name: SARS-CoV-2 HAE 48 hours 3

extract_protocol:
Total RNA was extracted using the Zymo Quick-RNA MiniPrep kit (VWR, R1055) according to the manufacturers protocol.
Libraries were generated using the Clontech SMART-Seq v4 kit, barcoding and sequencing primers were added using NexteraXT Library Prep kit.  Libraries were validated by microelectrophoresis, quantified, pooled and sequenced on an Illumina NovaSeq 6000 in 100-base single-read reactions.

treatment_protocol: pHAE cultures were infected at MOI= 0.5 for 48 hours. RNA was harvested from mock and infected pHAE cultures (n=3) by gently scraping the Transwell insert with a plunger to dislodge the cells, which were then lysed by treatment with RNA lysis buffer for > 5 minutes.

value: Primary Human Airway Epithelial (pHAE) Culture

tag: agent


title: HAE_SARSCov2_1

source_name: SARS-CoV-2 HAE 48 hours 1


title: U2OS siTLK1 B2

description:
sample name in processed data file:
9922016


title: DMSO+AB 3

first: Chen

last: Liu

state: Guangdong

address: No.58, Zhongshan Er Road

institute: The First Affiliated Hospital of Sun Yat-sen University

data_processing:
the sequencing data was filtered with SOAPnuke(v1.5.2).
removing reads whose low-quality base ratio(base quality less than or equal to 5) is more than 20%,removing reads whose inknown base ('N' base) ratio os more than 5%,afterwars clean reads were obtained and stored in FASTQ format.
the clean reads were mapped to the reference genome using HISAT2(v2.0.4)
Bowtie2(v2.2.5) was applied to align the clean reads to the reference coding gene set
Genome_build: the expression level of gene was calculated by RSEM(v.1.2.12). Differential expression analysis was performed using the DESeq2(V 1.4.5).
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Left ventricular muscle of heart

growth_protocol: 8 weeks old mouses were conducted with arotic banding or Sham surgery, 4 weeks later, samples were haversted.

extract_protocol:
Left ventricular muscles of mouse hearts were extracted, flash frozen on dry ice, and RNA was harvested using Trizol reagent and a phenol-chloroform extraction was performed to isolate RNA. Then, total RNA was qualified and quantified using a Nano Drop and Aligent 2100 bioanalyzer(Thermo Fisher Scientific, MA, USA).
Oligo(dt)-attached magnetic beads were used to purified mRNA. Then, double strained products were purified, heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball(DNB). DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated in BGIseq500 platform.

treatment_protocol: mouses were treated with DMSO or hispidulin(20 mg/kg/day, i.p., once daily) one day before surgery to 4 weeks after surgery.

value: Left ventricular muscle of heart

value: DMSO+AB


title: Hispidulin+AB 3

value: Hispidulin+AB


title: Hispidulin+AB 1


title: DMSO+AB 2


title: Hispidulin+AB 2


title: HAE_Mock_3

source_name: Mock HAE 48 hours 3

value: Mock infection


title: DMSO+AB 1


title: HAE_Mock_2

source_name: Mock HAE 48 hours 2


title: U2OS siGFP B1

description:
sample name in processed data file:
9912016

value: WT

value: B


title: Hispidulin+Sham 3

value: Hispidulin+Sham


title: 12 week old NOD pancreas - sample 1

value: NOD

tag: Sex


title: Irf2AhcKO_ISCs_rep4

city: Tokyo

first: Taku

last: Sato

address: 1-5-45 Yushima Bunkyo-ku

department: Department of Biodefense Research

institute: Medical Research Institute, Tokyo Medical and Dental University (TMDU)

description: Gene expression in ISCs of Irf2AhcKO Lgr5ki mouse  1 mo after beta-Naphthoflavone injection

hyb_protocol: 2.0ug of Cy3-labelled cDNA was filled up to 50 ul containing 1x Agilent blocking agent and 1x Agilent hybridization buffer, and hybridized to SurePrint G3 Mouse GE 8x60K Microarray (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Irf2AhcKOl_Lgr5ki mouse, Intestinal stem cells, replicate 4

label_protocol: DNA were amplified by Ovation® Pico WTA System V2（NuGEN Technologies) from 20ng※ total RNA according to the manufacturer's instructions. Amplified cDNA yield were checked with the NanoDrop ND-2000 Spectrophotometer. Cyanine-3 (Cy3) labeled cDNA was prepared from 2.0ug cDNA using SureTag Complete DNA Labeling Kit (Agilent) according to the manufacturer's instructions, followed by Amicon Ultra-0.5 mL Centrifugal Filters for DNA Purification and Concentration (Merck Millipore). Dye incorporation and cDNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: The total RNA was extracted from each cell sample using the RNeasy Mini Kit (Qiagen).

value: Lgr5^hi Intestinal stem cells

tag: strain/genotype


title: A1 WT U2OS


title: U2OS siTLK1 siTLK2 A4

description:
sample name in processed data file:
9902016

value: A


title: HAE_Mock_1

source_name: Mock HAE 48 hours 1


title: Irf2AhcKO_ISCs_rep3

source_name: Irf2AhcKOl_Lgr5ki mouse, Intestinal stem cells, replicate 3

value: 1 mo after beta-Naphthoflavone injection


title: U2OS siTLK2 A3

description:
sample name in processed data file:
9892016


title: P2-day7

city: Hefei

first: Bin

last: Li

address: NO. 96 Jinzhai Road

institute: University of Science and Technology of China

data_processing:
The raw sequencing data of patients and health donors were processed using Cell Ranger (version 3.1.0) against the GRCh38 human reference genome with default parameters
We retained cells with detected gene numbers between 500 and 6,000 and mitochondrial unique molecular identifiers (UMIs) less than 10%.
We used the default parameters for Scrublet (i.e. min_gene_variability_pctl=85, n_prin_comps=30, threshold=0.25) and detected 50 doublets from the patients.
Genome_build: hg38
Supplementary_files_format_and_content: Porcessed data files are tcv/csv or mtx format, which contain the single-cell expression matrix and the source of each single-cell.

source_name: PBMC

extract_protocol:
Peripheral blood samples were obtained from two severe COVID-19 patients. The patient severity was defined by the "Diagnosis and Treatment of COVID-19 (Trial Version 6)” which was released by The General Office of the National Health Commission and the Office of the National Administration of Traditional Chinese Medicine.
We collected 2ml peripheral blood each time from the COVID-19 patients. Peripheral blood mononuclear cells (PBMC) were freshly isolated from the whole blood by using a density gradient centrifugation using Ficoll-Paque and cryopreserved for subsequent generation of single-cell RNA library.
We generated single-cell transcriptome library following the instructions of single-cell 3’ solution v2 reagent kit (10x Genomics). Briefly, after thawing, washing and counting cells, we loaded the cell suspensions onto a chromium single-cell chip along with partitioning oil, reverse transcription (RT) reagents, and a collection of gel beads that contain 3,500,000 unique 10X Barcodes. After generation of single-cell gel bead-in-emulsions (GEMs), RT was performed using a C1000 TouchTM Thermal Cycler (Bio-Rad). The amplified cDNA was purified with SPRIselect beads (Beckman Coulter). Single-cell libraries were then constructed following fragmentation, end repair, polyA-tailing, adaptor ligation, and size selection based on the manufacturer’s standard parameters.

value: Blood

tag: disease stage

value: remission

tag: disease

value: 400 mg Tocilizumab at day 1

tag: collection timepoint

value: day 7


title: Hispidulin+Sham 2


title: U2OS siTLK1 A2

description:
sample name in processed data file:
9882016


title: HAE_SARSCoV2_2

source_name: SARS-CoV-2 HAE 48 hours 2

tag: cell type


title: Hispidulin+Sham 1


title: U2OS siTLK2 B3

description:
sample name in processed data file:
9932016


title: Irf2AhcKO_ISCs_rep1

source_name: Irf2AhcKOl_Lgr5ki mouse, Intestinal stem cells, replicate 1


title: P2-day5

value: day 5


title: Control_ISCs_rep4

description: Gene expression in ISCs of control Lgr5ki mouse  1 mo after beta-Naphthoflavone injection

source_name: Irf2^fl/fl_Lgr5ki mouse, Intestinal stem cells, replicate 4


title: U2OS siGFP A1

description:
sample name in processed data file:
9872016


title: P2-day1

value: severe

value: day 1


title: P1-day5-rep2


title: DMSO+Sham 2

value: Left ventricular muscle of heart

value: DMSO+Sham


title: MC-47_RNA-Seq [FGC1247_s_3_1_AGCGATAG-CCTATCCT]

city: Philadelphia

first: Minal

last: Caliskan

state: PA

address: 415 Curie Blvd., Room 540

department: Genetics

institute: University of Pennsylvania

data_processing:
RNA-Seq: (1) Low quality base calls and sequencing adapters were trimmed using Trim Galore! (2) Trimmed reads were aligned to the reference human genome (hg19) and transcriptome (GENCODE v19 annotations) using STAR v2.5 in 2-pass mode (3) Aligned reads were sorted and filtered to retain only primary aligned reads using SAMtools-1.3.1 (4) RSEM was used to estimate gene-level expression as Transcripts Per Million (TPM)
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq: Feature counts RNA-Seq:TPM values

source_name: Liver

extract_protocol:
Illumina TruSeq Stranded mRNA kit
QIAGEN’s AllPrep DNA/RNA/miRNA Universal Kit

tag: cohort

value: Penn Cohort 2

value: liver

tag: individual


title: MC-47_RNA-Seq [FGC1247_s_2_1_AGCGATAG-CCTATCCT]


title: DMSO+Sham 1

tag: strain

tag: age


title: Control_ISCs_rep3

source_name: Irf2^fl/fl_Lgr5ki mouse, Intestinal stem cells, replicate 3


title: MC-47_RNA-Seq [FGC1244_s_2_1_AGCGATAG-CCTATCCT]

tag: tissue


title: P1-day1-rep2

tag: treatment


title: P1-day5-rep1


title: P1-day1-rep1


title: Irf2AhcKO_ISCs_rep2

source_name: Irf2AhcKOl_Lgr5ki mouse, Intestinal stem cells, replicate 2


title: MC-47_RNA-Seq [FGC1244_s_1_1_AGCGATAG-CCTATCCT]


title: DMSO+Sham 3


title: Control_ISCs_rep1

source_name: Irf2^fl/fl_Lgr5ki mouse, Intestinal stem cells, replicate 1


title: Control_ISCs_rep2

source_name: Irf2^fl/fl_Lgr5ki mouse, Intestinal stem cells, replicate 2


title: AR1KO_ISCs_1wk_polyIC_rep2

description: Gene expression in ISCs of Ifnar1-/- Lgr5ki mouse  1 wk after poly(I:C) injection

source_name: Ifnar1-/- Lgr5ki mouse, Intestinal stem cells, 1 wk, poly(I:C) ip, replicate 2

value: 1 wk after poly(I:C) injection


title: AR1KO_ISCs_1wk_polyIC_rep1

source_name: Ifnar1-/- Lgr5ki mouse, Intestinal stem cells, 1 wk, poly(I:C) ip, replicate 1


title: Control_ISCs_1wk_polyIC_rep2

description: Gene expression in ISCs ofl Lgr5ki mouse  1 wk after poly(I:C) injection

source_name: Control Lgr5ki mouse, Intestinal stem cells, 1 wk, poly(I:C) ip, replicate 2


title: Control_ISCs_1wk_polyIC_rep1

description: Gene expression in ISCs of Lgr5ki mouse  1 wk after poly(I:C) injection

source_name: Control Lgr5ki mouse, Intestinal stem cells, 1 wk, poly(I:C) ip, replicate 1


title: Control

city: Fukui city

first: Takuma

last: Neo

state: Fukui

address: 3-9-1, Bunkyo

institute: Fukui university

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute. • Transfer 130μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm • Fluidics washing is FS450_0002

scan_protocol: Gene ChIP Scanner 3000 7G System

data_processing:
Data were processed using R. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: RabGene-1_0-st.pgf
meta-probeset file: RabGene-1_0-st.mps

label: Biotin

organism: Oryctolagus cuniculus

source_name: retina, untreated

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: retina

value: untreated


title: RVO

source_name: retina, retinal vein occlusion

value: retinal vein occlusion


title: ICSI_CTRL_47

status: Public on Jul 20 2020

type: genomic

city: Cusano Milanino

first: Luciano

last: Calzari

state: MI

address: Via Zucchi 18

country: Italy

institute: IRCCS Istituto Auxologico Italiano

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

scan_protocol: Fluorescence intensities were captured by using the fluorescent scanner Illumina HiScan SQ (Illumina).

data_processing: Quality control, pre-processing and generation of β-values matrix were performed by using the ChAMP (release 2.16.1) package (Morris TJ et al., 2014) implemented R environment (version 3.6.2). Sites with a detection p-value above 0.01 (n=9840) and a bead count <3 in at least 5% of samples (n=256) were removed. Moreover, also non-GpG probes (n=2726), potentially SNP affected probes (n=57449) (Zhou Wet al., 2017) probes aligning to multiple locations (n=11) (Nordlund J et al., 2013) and of X and Y chromosomes (n=9496) were filtered out. As a final outcome of the filtering procedures, a total of 405734CpG sites were retained.

label: Cy3 and Cy5

source_name: Control

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from peripheral blood lymphocytes of probands and their parents (Automated Extractor, Tecan Group Ltd. and Wizard Genomic DNA Purification Kit (Ref: A1125), Promega). Quality control and quantification of DNA was assessed by visualization of genomic DNA (gDNA) on 1% agarose gel electrophoresis and by using NanoPhotometer Pearl (Implen GmbH).

value: Cord Blood

value: male

tag: group

value: control


title: ICSI_CTRL_57


title: ICSI_CTRL_52

value: female


title: ICSI_CTRL_51


title: ICSI_CTRL_59


title: ICSI_CTRL_55


title: ICSI_CTRL_28_BIS


title: ICSI_CTRL_31


title: ICSI_CTRL_48


title: ICSI_CTRL_33


title: ICSI_CTRL_45


title: ICSI_CTRL_46


title: ICSI_CTRL_42


title: ICSI_CTRL_50


title: ICSI_CTRL_40_BIS


title: ICSI_CTRL_30


title: ICSI_CTRL_34


title: ICSI_CTRL_58


title: ICSI_CTRL_43


title: ICSI_CTRL_36


title: ICSI_CTRL_54


title: ICSI_CTRL_44_BIS


title: ICSI_CTRL_49_BIS


title: ICSI_CTRL_38


title: ICSI_CTRL_56


title: ICSI_CTRL_35


title: ICSI_CTRL_32


title: ICSI_CTRL_27


title: ICSI_CTRL_39_BIS


title: ICSI_CTRL_29


title: ICSI_CTRL_26_BIS


title: ICSI_CTRL_24


title: ICSI_CTRL_23


title: ICSI_CTRL_15


title: ICSI_CTRL_20


title: ICSI_CTRL_22


title: ICSI_CTRL_17


title: ICSI_CTRL_10


title: ICSI_CTRL_19


title: ICSI_CTRL_21


title: ICSI_CTRL_16


title: ICSI_CTRL_14


title: ICSI_CTRL_08


title: ICSI_CTRL_12


title: CTRL_13


title: CTRL_17


title: ICSI_CTRL_03


title: ICSI_CTRL_11


title: ICSI_CTRL_25


title: ICSI_CTRL_09


title: CTRL_16


title: ICSI_CTRL_07


title: ICSI_CTRL_05


title: ICSI_CTRL_01


title: ICSI_CTRL_06


title: CTRL_12


title: ICSI_CTRL_02


title: ICSI_CTRL_04


title: CTRL_15


title: ICSI_CTRL_18


title: CTRL_14


title: CTRL_11


title: CTRL_03


title: CTRL_04


title: CTRL_10


title: CTRL_08


title: CTRL_05


title: CTRL_07


title: CTRL_06


title: GSS1403_107_F_AE

city: Mason

first: Joe

last: Sherrill

state: Ohio

address: 8700 Mason-Montgomery Rd

institute: Procter and Gamble

description: batch_subjectID_gender_sampling site

hyb_protocol: Biotinylated cRNA was fragmented by limited alkaline hydrolysis and then hybridized overnight to Affymetrix GeneTitan U219 microarray plates using the Affymetrix GeneTitan instrument

scan_protocol: ArrayPlates were scanned using the Affymetrix GeneTitan Instrument utilizing AGCC GeneTitan Instrument Control software version 4.2.0.1566

data_processing: The RMA algorithm was used as the processing protocol to normalize the data for subsequent analysis.

source_name: LCM-separated epidermis from human arm

label_protocol: Biotinylated cRNA were prepared  using the Affymetrix HT 3’ IVT Express kit (Cat. #901253) on a Beckman Biomek FXp Laboratory Automation Workstation (Beckman Cat. #A31842).

extract_protocol: Total RNA from LCM samples was isolated utilizing the Pico Pure RNA Isolation Kit (Life Technologies, Grand Island, NY) according to manufacturer's recommendations

treatment_protocol: Punch biopsy samples were frozen in OCT media. Laser capture microdissection (LCM) was performed to isolate the epidermal compartments for gene expression profiling.

value: LCM-separated epidermis

tag: collection time

tag: gender


title: GSS1403_155_F_AE

description: batch_subjectID_gender_sampling site


title: PRETERM_17

source_name: Case

value: preterm newborn


title: GSS1403_290_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_152_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_124_F_AE

description: batch_subjectID_gender_sampling site


title: PRETERM_05


title: PRETERM_11


title: GSS1403_173_F_AE

description: batch_subjectID_gender_sampling site


title: PRETERM_09


title: PRETERM_18


title: PRETERM_12


title: GSS1403_214_F_AE

description: batch_subjectID_gender_sampling site


title: CTRL_01


title: CTRL_09


title: PRETERM_16


title: PRETERM_15


title: CTRL_02


title: PRETERM_14


title: PRETERM_10


title: GSS1403_243_F_AE

description: batch_subjectID_gender_sampling site


title: PRETERM_13


title: PRETERM_02


title: PRETERM_06


title: PRETERM_07


title: PRETERM_04


title: PRETERM_03


title: PRETERM_08


title: PRETERM_01


title: GSS1403_166_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_159_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_139_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_300_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_242_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_122_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_200_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_249_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_260_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_142_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_262_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_144_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_227_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_112_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_314_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_167_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_150_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_213_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_281_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_127_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_186_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_183_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_177_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_286_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_269_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_238_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_103_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_162_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_128_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_135_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_111_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_138_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_133_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_108_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_230_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_125_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_271_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_140_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_226_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_171_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_320_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_189_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_134_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_219_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_207_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_141_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_221_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_158_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_222_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_121_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_179_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_307_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_268_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_118_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_310_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_123_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_168_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_188_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_198_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_115_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_185_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_194_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_294_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_233_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_277_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_129_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_109_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_137_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_131_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_248_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_237_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_212_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_190_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_160_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_114_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_218_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_176_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_288_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_130_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_113_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_170_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_203_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_251_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_223_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_274_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_196_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_206_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_208_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_181_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_161_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_318_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_273_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_259_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_154_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_184_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_295_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_148_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_174_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_284_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_255_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_311_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_132_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_231_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_272_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_151_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_216_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_211_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_265_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_117_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_169_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_136_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_195_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_116_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_283_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_302_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_250_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_192_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_172_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_252_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_321_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_258_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_175_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_210_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_215_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_228_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_308_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_317_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_153_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_106_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_143_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_119_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_147_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_201_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_199_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_110_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_157_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_282_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_101_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_191_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1403_224_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1376_233_F_BE

description: batch_subjectID_gender_sampling site

source_name: LCM-separated epidermis from human buttock


title: GSS1376_141_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1376_109_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1376_273_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1403_220_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1376_138_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1376_128_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1376_186_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1376_132_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1376_169_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1403_289_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1376_170_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1376_194_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1376_195_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1376_250_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1376_248_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1376_187_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1376_212_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1376_220_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1376_288_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1376_308_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1403_187_F_AE

description: batch_subjectID_gender_sampling site


title: GSS1376_258_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1376_168_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1376_224_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1376_214_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1376_143_F_BE

description: batch_subjectID_gender_sampling site