title: LiverPBS_3_4


title: COM rep1

status: Public on Aug 24 2021

type: SRA

city: Warsaw

first: Adria-Jaume

last: Roura

address: Ludwika Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology, Polish Academy of Sciences

description: GL261 luc+ tdT+ implanted mice

library_source: transcriptomic

data_processing:
Illumina-specific adapters, short reads and low quality 5' and 3' bases were filtered out in the FASTQ format files using Trimmomatic tool.
Resulting RNA sequencing reads were aligned to a reference mouse genome sequence (mm10) with the STAR aligner using the twopassMode Basic option.
Duplicate reads were identified and marked using Picard Tools and mapped read quantification and summarization by genes was perform employing HTSeq-count, enabling paired mode (-p), reverse stranded mode (-s reverse) and only considering reads with MapQ values of 10 or higher.
Low-expressed features were pre-filtered out and a differential expressed genes analysis was performed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample - HTSeq_raw_counts.tab

molecule: polyA RNA

organism: Mus musculus

source_name: CD11b+ FACS sorted

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: treatment

value: COMB


title: LiverPBS_3_3

city: Fukuoka

first: Fumiko

last: Matsuzaki

address: 3-1-1 Maidashi, Higashi-ku

country: Japan

institute: Kyushu University

data_processing:
Libraries were sequenced on an Illumina HiSeq 1500 using 50 base read lengths in single-end mode.
RNA-seq reads were aligned to the mouse genome GRCm38 (version 81, indexes grcm38_tran) using HISAT2 (version 2.1.0) with default parameters except for -k of 30.
The generated sam files were converted to a sorted bam format with SAMtools (version 1.9).
Transcript abundance was estimated using Stringtie (version 2.0.3) with Ensembl GTF (release 98) as a reference.
The obtained values of reads per kilobase of exon per million mapped reads (RPKM) were compiled using the ballgown package in R environment.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: LiverPBS_liver (left lobe)

extract_protocol:
Total RNA was extracted from the liver tissue samples with the use of RNeasy Mini Kit (Qiagen), and integrity was confirmed using a Bioanalyzer (Agilent Technologies).
mRNA-seq libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: After one-week acclimation, mice were fasted for 12–16 h followed by IP of human insulin (0.7 U/kg; Sigma-Aldrich) or PBS.

tag: age

value: 10 week

value: IP of PBS

tag: tissue

value: Liver (left lobe)


title: PC3CR

type: RNA

city: Tokyo

first: Hiroshi

last: Hongo

state: Tokyo

address: 35, Shinanomachi, Shinjuku-ku

department: Urology

institute: Keio University School of Medicine

description: strain: PC3CR  cell type: Prostate cancer  tissue: prostate  established from PC3 cells as an acquired cabazitaxel resistant subline

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized on the GeneChip Human Gene 2.0 ST Array using  the GeneChip Hybridization Oven 645. GeneChips were washed and stained in the  GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console v1.4(Affymetrix) and Transcriptome Analysis Console v3.1 (Affymetrix). RMA was used as summarization algorithm.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Prostate cancer

label_protocol: cDNA synthesis, amplification and labeling were performed with WT PLUS Reagent Kit (Affymetrix).

growth_protocol: PC3, and PC3CR were routinely maintained in RPMI-1640 (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (Dainippon Pharmaceutical, Tokyo, Japan) at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol: Total RNA was isolated purified using RNeasy Mini kit (Qiagen).

treatment_protocol: PC3CR cells were were grown and passaged upon reaching confluence in medium containing CBZ over a 18-month period. Examinations were performed after 3 months without CBZ exposure.

tag: cell line


title: CC_Ia3

city: ChengDu

first: Yong

last: Lv

state: SiChuan

department: Department of pediatric surgery

country: China

institute: West China hospital of Sichuan university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: gene_fpkm.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: cystic choledochal cysts

extract_protocol:
Choledochal cysts were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: cystic choledochal cyst

tag: type

value: Ia


title: PC3

description: strain: PC3  cell type: Prostate cancer  tissue: prostate


title: LiverPBS_3_2


title: Day14.no3, human

city: New York

first: Jinyang

last: Li

state: New York

address: 1230 York Ave

country: USA

institute: The Rockefeller University

data_processing:
Transcript quantification using Salmon
Calculate TPM values
Genome_build: hg19
Supplementary_files_format_and_content: txt file for TPM values

source_name: human pancreatic tumor cell - PANC-1

growth_protocol: DMEM supplemented with 2.5 mM glucose, 0.5% fetal calf serum, and 20% of standard amino acid concentration as the nutrient and oxygen deprivation condition

extract_protocol:
Qiagen RNA extraction kit
RNAseq library was built by a commercial company, Novogene

treatment_protocol: No additional treatment

value: human pancreatic tumor cell line PANC-1

tag: time


title: LiverPBS_3_1


title: Day14.no2, human


title: patient2

city: Boston

first: JAE WON

last: CHO

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

description: single-cell RNA sequencing

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and aggregation of multiple sequencing runs were performed using the Cell Ranger analysis pipeline (v2.1.1)
Background and non-cellular garcodes are removed
Genome_build: GRCh38
Supplementary_files_format_and_content: .tsv and .mtx: barcodes, genes, and count matrix

source_name: lung cancer

extract_protocol:
We performed meticulous mechanical and enzymatic dissociation using a gentle MACS dissociator (Miltenyi Biotec, Cat#130-093-235) and the Human Tumor Dissociation Kit (Miltenyi Biotec, Cat#130-095-929) following the manufacturer's instructions. After incubation for an hour at 37℃, the resuspend samples were filter out with 70 µmMACS SmartStrainer (Miltenyi Biotec, Cat# 130-098-462) in the RPMI-1640 medium (Corning Inc., Corning, NY) with 10% FBS (FBS; Biowest, Riverside, MO) and centrifuged at 300g for 10 minutes. The pelleted cells were suspended into PBS with 2% FBS. For FACSsorting analysis, single cell suspensions were stained for 20 minutes at 4℃ with indicated fluorescent-conjugated antibodies following: LIVE/DEAD™ Fixable Red Dead Cell Stain Kit (Invitrogen, Cat#L23102) and CD45 (Biolegend, clone 2D1). The samples were sorted using a FACS Aria III (BD) into live and single CD45-positive cells. Then the sorted cell population was analyzed to ensure successful cell sorting. Viability of cells was assessed by Luna FL Fluorescence Cell Counter (Logos Biosystems, Cat#L20001) and confirmed to be 75-98% in all samples.
Single cell sample preparation for constructing libraries and sequencing was processed in the use of the Chromium controller according to the 10x Single Cell 3’ v2 protocol (10x Genomics). To acquire 10,000 targeted cells, the cells were diluted in nuclease-free water and mixed with master mix. Thereafter, the single cell suspension was loaded with Single Cell 3′ Gel Beads and Partitioning Oil (GEM) into a Single Cell 3′ Chip. Following to generate the GEMs, single cells were uniquely barcoded and subsequently cDNAs were used to construct libraries according to the manufacturer’s instructions. The libraries were sequenced using HiSeq 2500 (Illumina)

tag: diagnosis

value: NSCLC

tag: egfr status

value: mutation


title: Day2.no2, human


title: Day2.no3, human


title: LiverPBS_2_5


title: T cells engineered with IL12-CAR_3

city: Cologne

first: Agapios

last: Sachinidis

state: NRW

address: Robert-Kochstr. 39

department: Institute of Neurophysiology

country: Germany

institute: University of Cologne

description: SAMPLE 6

hyb_protocol: 2.3 µg fragmented biotin-labeled ds cDNA were hybridized to Clariom™ S arrays using the Fluidics Station 450   Arrays were scanned using the Gene-Chip Scanner 3000 7G (Affymetrix, United Kingdom) according to the manufacturer's instructions

scan_protocol: After hybridization and stainning  arrays were scanned using the and scanned using the Gene-Chip Scanner 3000 7G (Affymetrix, United Kingdom) according to the manufacturer's instructions

data_processing: The quality control (QC) matrices were confirmed with expression console software (Affymertix, USA) and  QC passed CEL files were further analyzed using the Affymetrix Transcriptome Analysis Console (TAC) 4.0 Software. . All CEL files were RMA background corrected, quantile normalized and all probe sets were summarized using median polish algorithm.

label: botin

source_name: T cells engineered with IL12-CAR

label_protocol: 250 ng total RNA   were labelled using the GeneChip™ WT PLUS Reagent Kit

growth_protocol: CAR T-cells were split and cultivated for 48 hrs in XVIVO15 medium + 5% HI FCS and 400 U/ml IL2) in 6 well plates (5x 10(6)/well) that were coated with 4 µg/ml of the CAR specific anti-idiotypic mAb BW2064/36 or for control with PBS

extract_protocol: Total RNA from cells was isolated by PureLink RNA Mini Kit (Life technologies, # 12183018A)

treatment_protocol: treated: T cells engineered with IL12-CAR  versus untreated: T cells engineered with conventional CAR

tag: cell type

value: T cells from 3 different healthy donors


title: LiverPBS_2_4


title: T cells engineered with IL12-CAR_2

description: SAMPLE 5


title: Day2.no1, human


title: LiverPBS_2_3


title: Day14.no1, human


title: T cells engineered with conventional CAR_3

description: SAMPLE 3


title: T cells engineered with conventional CAR_2

description: SAMPLE 2


title: SJRHB015721_X1_shDBX1_B_Rep 3

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

description:
MEH202
SJRHB015721_X1_shDBX1_B_R3

hyb_protocol: Samples were hybridized with the WT Plus Assay Kit (#902280, ThermoScientific) according to manufacturer's protocol.

scan_protocol: Samples were scanned on a Gene Chip Scanner 3000 7G.

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data and metrics for Quality Controls. The distribution of raw data show no outlier experiment. Affymetrix probe-set data were normalized using the robust multi-array average (RMA) method.

source_name: SJRHB015721_X1 FN-RMS cells

label_protocol: Samples were labeled with the WT Plus Assay Kit (#902280, ThermoScientific) according to manufacturer's protocol.

growth_protocol: SJRHB015721_X1 cells are maintained in complete neurobasal medium as described in (Drummond et al., (2018) Cancer Cell).

extract_protocol: RNA harvested with Qiagen't miRNeasy RNA protocol.

treatment_protocol: Cells were transduced with pLKO.3G.Scr or pLKO.3G.shDBX1-A (or B) overnight. The virus was removed the next morning. RNA was harvested 72 hours post-transduction.


title: 104268

city: San Francisco

first: Denise

middle: M

last: Wolf

state: CA

address: 2340 Sutter st

institute: University of California, San Francisco

hyb_protocol: Performed by Agendia Inc (Irvine, CA)

scan_protocol: Performed by Agendia Inc (Irvine, CA)

data_processing:
gnormalized signal (log2) data, as provided in the raw files on each patient, was extracted and aligned to the 75th quantile across arrays by Agendia. All values indicated for non-conformity, as indicated by the 'gIsFeatNonUnifOL' column in the raw files, are NA'd out. Probeset level data per array were mean-collapsed to the gene level, and genes common to the two platforms identified.  Expression data from the first ~900 I-SPY 2 patients distributed over the two platforms were combined into a single gene-level dataset over the set of common genes after batch-adjusting using ComBat [PMID:16632515].  The data matrix for this study constitutes 233 samples from this larger COMBAT-combined expression set.  Linear adjustment factors were derived from the larger ComBat operation, per platform, and can be used against these 233 samples for batch correcting on raw files.  The linear adjustment factors and updated probe annotation files per platform are provided.
The data matrix provided contains platform corrected, normalized expression values from two different platforms.  Data is collapsed on the gene level as was used in the analysis.

source_name: Breast cancer biopsy (pre-treatment)

label_protocol: Performed by Agendia Inc (Irvine, CA)

extract_protocol: Extraction, labeling, hybridization, and scanning are performed by Agendia Inc (Irvine, CA).  This company is referenced by the platforms used: GPL20078 and GPL16233.

value: breast cancer

tag: hr

tag: mp

tag: pcr

tag: arm

value: Control Arm


title: 116603


title: LiverPBS_2_2


title: LiverPBS_2_1


title: Day0.no2, human


title: HUH-7 cell (WT) serum starvation 6h+ALB

city: Changchun

first: Xin

last: Guan

address: No.1163 Xinmin Street

institute: School of Pharmaceutical Sciences, Jilin University

data_processing:
bulk RNA-seq:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
scRNA-seq:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 80%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: bulk RNA-seq: TXT file contain counts for each sample
Supplementary_files_format_and_content: scRNA-seq: tab-delimited text files include counts for each cell

source_name: Liver

growth_protocol: Bulk RNA-seq: The human HCC line Huh-7 (WT) (Serial, TCHu182) was purchased from the National Collection of Authenticated Cell Cultures and cultured in DMEM (BI, Cat# 061055571A) with 10% (vol/vol) fetal bovine serum (FBS, Gibco, Cat# 12483020).The human HCC line sorafenib resistance Huh-7(SR) (XC509) was purchased from MEIXUAN Biological Science and Technology Ltd (Shanghai, China), and cultured in RPMI-1640 medium (BI, Cat# 011001A) with 10% (vol/vol) FBS mixed with sorafenib (2 μg/mL final concentration). The cells were cultured at 37 °C in a 5% CO2 incubator. (typically 5 × 106 cells into a T75 flask)

extract_protocol:
The tissues were removed surgically and placed in MACS Tissue Storage Solution (Miltenyi Biotec, Cat# 130100008) until further processing. Briefly, the samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1 mm3) on ice, and digested with 200 U/mL collagenase I (Worthington, Cat# LS004197) and 200 U/mL DNase I (Worthington, Cat# LS002147) for 45 min at 37 °C, with agitation. Subsequently, the samples were sieved through a 70-µm cell strainer and harvested by centrifugation at 300 ×g for 5 min at room temperature. After washing with PBS containing 0.04% bovine serum albumin (BSA), the cell pellets were re-suspended in PBS containing 0.04% BSA and re-filtered through a 35-μm cell strainer. The viability of the dissociated single cells was assessed using Calcein-AM (Thermo Fisher Scientific, Cat# c3099) and Draq7 (BD Biosciences, Cat# 564904).
Bulk RNA-seq: RNA libraries were prepared for sequencing using standard Illumina protocols
scRNA-seq: Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

treatment_protocol: Bulk RNA-seq: We divided HUH-7 SR and huh-7 WT cell lines into four experimental groups: serum starvation for 6 h and 10% ALB supplementation after 6 h of starvation.

value: Hepatocellular carcinoma

tag: strain/cell line

tag: tissue source

value: Liver of human


title: Day0.no1, human


title: LiverPBS_1_5


title: sg2.day2.no3

tag: transduction


title: T cells engineered with IL12-CAR_1

description: SAMPLE 4


title: HUH-7 cell (sorafenib resistance) serum starvation 6h+ALB

value: HUH-7(sorafenib resistance)


title: LiverPBS_1_4

tag: strain


title: sg1.day2.no3


title: SJRHB015721_X1_shDBX1_A_Rep 3

description:
MEH196
SJRHB015721_X1_shDBX1_A_R3

tag: treatment


title: 136536


title: LiverPBS_1_3

tag: age


title: SJRHB015721_X1_Scr_Rep 3

description:
MEH195
SJRHB015721_X1_Scr_R3

value: Scr


title: LiverPBS_1_2

tag: tissue


title: HUH-7 cell (WT) serum starvation 6h


title: T cells engineered with conventional CAR_1

description: SAMPLE 1


title: ev.day2.no3

tag: cell line

value: ev


title: HUH-7 cell (sorafenib resistance) serum starvation 6h


title: SJRHB015721_X1_shDBX1_B_Rep 2

description:
MEH194
SJRHB015721_X1_shDBX1_B_R2


title: SJRHB015721_X1_shDBX1_B_Rep 1

description:
MEH191
SJRHB015721_X1_shDBX1_B_R1


title: Day0.no3, human


title: sg2.day2.no2


title: SJRHB015721_X1_Scr_Rep 2

description:
MEH192
SJRHB015721_X1_Scr_R2


title: CTN-48h

city: Kunming

first: Jie

last: Song

state: Yunnan

address: Number 935 Jiaoling Load

institute: Institute of Medical Biology, Chinese Academy of Medicine Science and Peking Union Medical College

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
count counting
Genome_build: GRCh_38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Human neuroblastoma cell line SH-SY5Y

growth_protocol: The human neuroblastoma cell line SH-SY5Y, purchased from Jennino Biological Technology, was propagated in Dulbecco’s modified Eagle’s medium (DMEM) (Corning, USA) with the addition of 10% fetal bovine serum (FBS; Gibco, USA), 2 mmol/L glutamine, 100 units/mL penicillin and 100 μg/mL streptomycin (Gibco, USA) at 37℃ in a humidified 5% CO2/95% air atmosphere.

extract_protocol:
prefrontal cortex were rharvested , flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The CTN strain, isolated from the brain tissue of rabies patients who died in Shandong Province in 1957, was used in this study. SH-SY5Y cells were seeded into 6-well plates at a density of 5 × 105 cells/well and infected with CTN at a multiplicity of infection (MOI) of 1. Subsequently, the infected cells were harvested at 0, 12 and 24 h post infection (hpi). Moreover, cells treated with CTN for 0 hpi were defined as control group.

value: Human neuroblastoma cell line SH-SY5Y

value: 48 hpi


title: LiverPBS_1_1

value: 10 week

value: IP of PBS


title: sg1.day2.no2


title: CTN-24h

value: 24 hpi


title: LiverInsulin_3_4

source_name: LiverInsulin_liver (left lobe)

value: IP of human insulin (0.7 U/kg; Sigma-Aldrich)

value: Liver (left lobe)


title: ev.day2.no2

value: human pancreatic tumor cell line PANC-1


title: CTN-0h

value: 0 hpi


title: LiverInsulin_3_5


title: sg2.day2.no1


title: sg1.day2.no1


title: SJRHB015721_X1_shDBX1_A_Rep 2

description:
MEH193
SJRHB015721_X1_shDBX1_A_R2


title: LiverInsulin_3_2


title: SJRHB015721_X1_shDBX1_A_Rep 1

description:
MEH190
SJRHB015721_X1_shDBX1_A_R1


title: EAE NG2 Rep2

city: San Francisco, CA

first: Katerina

last: akassoglou

address: 1650 Owens st

institute: Gladstone Institutes

data_processing:
For each sample, read 1 and read 2 FASTQ files were separately catenated, and Illumnia adaptors were trimmed and FASTQ files were quality checked using FASTQC. Next, sequencing reads were aligned to mouse reference genome mm10 with STAR and then counts per gene were quantified by featureCounts as previously described (PMID: 32284594). Differentially expressed genes (DEGs) were identified by EdgeR (version 3.24.3) (pmid:19910308), using cutoffs of log2 fold change of > 1 or < -1 and false discovery rate (FDR) p-value < 0.05.
Genome_build: mm10

source_name: spinal cord

extract_protocol:
Spinal cord tissues were collected from perfused female mice as previously described (PMID: 32284594). Single-cell suspensions were prepared from entire spinal cords following the adult brain dissociation (ABD) kit manufacturer’s instructions with modification (Miltenyi Biotec). Briefly, minced tissues were individually incubated with ABD Mix 1 containing 15 μM actinomycin D (ActD; Sigma) (PMID: 29024657) for 15 min at 34°C, and then ABD Mix 2 was added to solution for 10 min at 34°C. Tissues were gently triturated and then incubated for 10 min at 34°C. Homogenized tissue solutions were passed through 70-μm smartstrainer (Miltenyi Biotec), washed with cold Dulbecco’s phosphate-buffered saline and centrifuged at 450xg for 7 min at 4°C. Tissue debris was removed following the ABD Kit debris removal step instructions and then passed through 30-μm smartstrainer (Miltenyi Biotec) and centrifuged at 450xg for 7 min at 4°C. All steps above were performed in the presence of 3 μM ActD. Single-cell suspensions were incubated with 1 μM Sytox blue live/dead stain (Thermo Fisher Scientific) for 5 min at 4°C and then cell sorting was performed on an FACSARIA II (BD Biosciences). Sytox blue– NG2-tdtomato+ cells were sorted directly into tubes containing RLT plus lysis buffer (Qiagen) supplemented with 1% 2-mercaptoenthanol (Sigma) and 0.25% reagent DX (Qiagen). Cell lysates were frozen on dry ice and immediately stored at -80°C until use
Frozen NG2 cell lysates in RLT buffer were thawed at 24°C and then lysed using the QIAshredder (Qiagen) following manufacturer’s instructions. Total RNA was isolated from cell lysates using the RNAeasy micro kit without modification (Qiagen). RNA quality and quantity were determined by Bioanalyzer pico chip analysis (Agilent) and all samples with RNA integrity number > 8 were used for RNA-seq library preparation. cDNA libraries were generated from total RNA using the Ovation RNA-seq System V2 (NuGEN). Libraries were quantified and quality checked by KAPA qPCR (Roche) and Bioanalyzer DNA chip analysis (Agilent), respectively. Libraries were pooled and paired-end 75 base pair read length sequenced across 8 lanes on a Nextseq500 (Illumnia), for a sequencing depth of >40 million reads per library. FASTQ files were generated in Biospace following manufacturer’s guidelines (Illumina).

value: spinal cord

tag: genotype

tag: condition

value: EAE


title: LiverInsulin_3_1


title: EAE NG2 Rep1


title: Control NG2 Rep3

value: Control


title: sg2.day0.no3

tag: time


title: EAE NG2 Rep3


title: Control NG2 Rep2


title: LiverInsulin_2_4


title: sg1.day0.no3


title: ev.day0.no3


title: SJRHB015721_X1_Scr_Rep 1

description:
MEH189
SJRHB015721_X1_Scr_R1


title: LiverInsulin_2_3


title: sg2.day0.no2


title: Control NG2 Rep1


title: OPH3

city: Brno

first: Martina

last: Zapletalová

address: Kamenice 5

department: Department of Biochemistry

country: Czech Republic

institute: Masaryk University

data_processing:
Quality control of reads was performed using FastQC, RSeQC, and MultiQC packages.
Samples were trimmed using cutadapt tool.
Samples were aligned to the reference genome using STAR aligner.
R package DeSeq2 was used for exploration and differential expression of the count data.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file

source_name: Chondroblasts

growth_protocol: Cells for micromass cultures were obtained from mouse fore limbs at embryonic day (E) 12. Fresh post mortem limbs were removed to PSA buffer (Puck’s Saline A liquid) and cut in pieces by needle. Pieces of tissue were incubated 1-2 hours in 37 °C with Dispase (Gibco, final activity 1U/ml) solved in PSA buffer with 10 % foetal bovine serum (FBS, Sigma-Aldrich). Dispase was inactivated by adding culture medium, cells were passed through a 40 μm cell strainer (Corning), centrifuged (100 g/5 min) washed with fresh medium and counted. Subsequently, cells at a concentration of 2x107/ml were spotted in 10 µl drops on the culture plate and left 5% CO2/37°C to adhere. After 60 minutes, spots were covered by fresh culture medium. Culture medium which supports chondrogenic differentiation was composed of DMEM (Sigma-Aldrich) and Nutrient Mixture F12 (Sigma-Aldrich) in proportion 2:3, 10 % FBS (Sigma Aldrich), Penicillin/streptomycin (Sigma-Aldrich, final concertation 100 U/ml and 100 µg/ml), L-Glutamine (Sigma-Aldrich), final concentration 2mM), β-Glycerol phosphate (Sigma-Aldrich, final concentration 10mM) and Ascorbic acid (Sigma-Aldrich, final concentration 50 µg/ml).   Cell were cultured without treatment until the following morning in order to attach to the surface.

extract_protocol:
After 6 days of caspase inhibition, the cultured cells were harvested into 350 µl RLT lysis buffer (Qiagen) with β-mercaptoethanol (Sigma-Aldrich). RNeasy Mini Kit (Qiagen) with included DNase treatment was used for RNA isolation.
The library for sequencing was constructed using QuantSeq 3´mRNA-Seq Library Prep kit FWD for Illumina (Lexogen) and Lexogen i5 6 nt Unique Dual Indexing Add-on kit (Lexogen).

treatment_protocol: For caspase inhibition, pharmacological inhibitors Z-VAD-FMK (FMK001, R&D Systems) and Q-VD-OPH (OPH001, R&D Systems) were applied to the micromass cultures at a concentration of 100 μM, according to the manufacturer’s recommendation and previous studies. In the controls, DMSO as an inhibitor vehicle was added and the control micromass cultures were run in parallel. The medium with caspase inhibitors or DMSO was changed every second day. The experiments were performed in three biological replicates.

value: Limb-derived chondroblasts

value: OPH

value: embryonic day 12


title: LiverInsulin_3_3


title: LiverInsulin_2_2


title: ev.day0.no2


title: LiverInsulin_2_1


title: ev.day2.no1


title: OPH2


title: LiverInsulin_1_5


title: OPH1


title: sg1.day0.no1


title: FMK3

value: FMK


title: LiverInsulin_1_4


title: LiverInsulin_2_5


title: sg2.day0.no1


title: EphA CAR-b transduced T cell after co-culture

city: Beijing

first: yi

last: hu

address: No.10 Yangfangdian Road

institute: Beijing Shijitan Hospital

description:
S26_count
after co-culture.anno.xls

data_processing:
Raw data were first processed through custom Perl a scripts. Clean data (clean reads) were read by removing reads containing poly-N with 5′-adapter contaminants, without 3′ adapter or the insert tag, or containing poly-A or -T or -G or -C from raw data, as well as low-quality reads.
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
DEGseq was used for differential gene expression analysis between two samples with non biological replicates. Under the assumption that the number of reads derived from a gene (or transcript isoform) follows abinomial distribution, DEGseq is proposed based on MA-plot and widely used for differential gene expression analysis. The P-value could be assigned to each gene and adjusted by the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes (DEGs). DESeq2 was designed for differential gene expression analysis between two samples with biological replicates under the theoretical basis obeys the hypothesis of negative binomial distribution for the value of count. Differing from DESeq, DESeq2 estimates the depth parameters of samples and gene-specific, as well as uses "linear regression" for dispersion to "shrink", which was mainly considering genes of the same expression level may share the similarity deviations or own their the expression characteristics. DESeq2 estimates the expression level of each gene in per sample by the linear regression, then calculates the p-value with Wald test. Finally the p-value was corrected by the BH method. Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes (DEGs).
Genome_build: ensemble release-80
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: T cell

growth_protocol: Human peripheral blood mononuclear cells(PBMCs) were seperated from healthy donors by gradient centrifugation

extract_protocol:
Total RNA was extracted from cell using Trizol Reagent (Invitrogen) following the manufacturer’s instructions. The quantity and purity of RNA were measured on a Nanodrop Technologies ND-1000 spectrophotometer (Thermo Fisher Scientific, Inc.). Only samples with the appropriate absorbance measurements (A260/A280 of ~2.0, and A260/A230 of 1.9-2.2) were considered for inclusion in the present study
A total amount of 2 µg total RNA per sample was used as input material for generating the sequencing libraries using NEBNext®Ultra™ RNA Library Prep Kit (#E7530L, NEB, USA) following the manufacturer’s. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair, A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed.

treatment_protocol: T cells in PBMCs were isolated and stimulated with anti-CD3 and anti-CD28 beads, and then transduced with retrovirus. On day 5, the transduced T cells were subjected to CAR expression detection and then expanded in X-VIVOTM15 serum-free medium which containing 10% GemCellTM Human Serum AB(Gemini Bio) and IL-2. One day 7, the cells were subjected to cytotoxicity assay and in vivo tumor treatment.

value: T cell

tag: car-t treatment

value: EphA2 CAR transduced

tag: culture method

value: co-culture with U251 cells

tag: car-t type


title: LiverInsulin_1_2

value: 10 week


title: LiverInsulin_1_3


title: FMK2


title: FMK1


title: EphA CAR-a transduced T cell after co-culture

description:
S24_count
after co-culture.anno.xls

tag: cell type


title: DMSO3

value: DMSO


title: LiverInsulin_1_1


title: DMSO2


title: EphA CAR-b transduced T cell

description:
control26_count
before co-culture.anno.xls

value: without tumor cell co-culture


title: DMSO1


title: sg1.day0.no2


title: mA-3T3L1-LMO3-replicate_3

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

data_processing:
fastq generation, bcl2fastq via Basespace
alignment and extraction of counts/gene, STAR aligner (STAR_2.5.0b) via Basespace,
differential gene expression analysis, DESeq2 (1.6.3) via Basespace
Genome_build: UCSC mm10
Supplementary_files_format_and_content: plain text, raw counts per gene, one file per sample

source_name: mature 3T3-L1 adipocytes

growth_protocol: At 2 days post-confluency 3T3-L1 cells were treated with a differentiation cocktail containing: DMEM, 10% CS, insulin (870 nM), TZD (5µM), Dex (1 µM), and IBMX (500 µM). On day 3 of differentiation, cells were switched to differentiation cocktail excluding IBMX and Dex for remaining duration of differentiation.

extract_protocol:
Total RNA was isolated from cultured cells using Qiagen Rneasy mini kit according to the manufacturers protocol
Library preparation and RNA-Seq was carried out by the Core facility Genomics, Medical University of Vienna, Vienna, Austria. Briefly, sequencing libraries were prepared using the NEBNext® Ultra™ II RNA Library Prep Kit according to manufacturer’s instructions and sequenced on a Illumina NextSeq500 platform in a 75bp single-read mode

treatment_protocol: 3T3-L1 adipocytes were infected with 100 pfu/cell on day 7 of differentiation. Experiments were performed 3 days after adenoviral transduction.

value: Lmo3 Adenovirus (experimental)

value: 3T3-L1 cells were induced to differentiate into matutre adipocytes fr a period of 7 days after which cell were infected with Adenovirus (Lmo3)


title: mA-3T3L1-LMO3-replicate_2


title: PC9 siNC

city: Hamamatsu

first: Kazuo

last: Tsuchiya

department: Tumor pathology

institute: Hamamatsu University School of Medicine

description: Gene expression data from PC9 cells

hyb_protocol: 5μL (100-300ng) of each RNA sample was mixed with 8μL of the Master Mix (reporter codeSet and hybridization buffer). 2μL of the capture probeSet was added; the solution was mixed and spun down. It was placed in a 65°C thermocycler (Bio-Rad Laboratories Inc, Hercules, California, USA) for 16 hours (maximum hybridization time should not exceed 48 hours).

scan_protocol: The samples were transferred to the preparation station (NanoString Technologies, Seattle, WA) with prepared nCounter Master Kit and a cartridge. The samples binding to the cartridge. The preparation station 12 lanes per run in approximately 2.5 to 3 hours. The cartridges were transferred to the Digital Analyzer (NanoString Technologies, Seattle, WA) for analysis. Cartridges were then scanned on the Digital Analyzer at 555 fields of view.

data_processing: To quantify gene expression values, first normalization step was analyzed by geNormalgorithm in nCounter Advanced Analysis ver2.0.115.

label: NanoString Oligonucleotide Probe

source_name: siNC

label_protocol: The RNA samples were run on the NanoString nCounter Analysis System (NanoStringTechnologies, Inc., WA, USA) according to the manufacturer's directions.

growth_protocol: Cells were maintained in a 5% CO2 and 95% air incubator at 37℃.

extract_protocol: Total RNA was extracted using RNeasy Plus Mini Kit (#74136, Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Cells were cultured for 24 hours prior to transfection and transfected with 15 nM of final concentrations of siRNAs. Total RNA were extracted  at 48 h after transfection.

value: lung adenocarcinoma

tag: genotype/variation

value: siNC


title: NH

city: Guangzhou

first: Yu

last: Zhou

state: Guangdong

address: No. 106, Zhognshan Er Road

department: General Surgery

institute: Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences

description: Normal liver tissue near the metastatic lesion

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:MT% < 40%;   Cell Gene Number < Median Gene Number * 2; Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: Normal liver tissue

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3' Reagent Kit v3 (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

value: Normal liver tissue

tag: location

value: Liver

tag: sampling time

value: Immediately after resection


title: PBMC

description: Mononuclear cells enriched from 15ml venous blood collected preoperatively

source_name: Peripheral blood mononuclear cells

value: Blood

value: Peripheral venous blood

value: The first day before operation


title: mA-3T3L1-LMO3-replicate_1


title: PC9 siYTHDF2 #2

description: Gene expression data from PC9 cells

source_name: siYTHDF2 #2


title: ev.day0.no1

value: human pancreatic tumor cell line PANC-1

value: ev


title: H5

description: Cells from liver metastatic tissue

source_name: Metastatic lesion

value: Liver metastatic tumor tissue of pancreatic neuroendocrine tumor


title: T2

description: Cells from primary tumor tissue located at the pancreatic body

source_name: Primary tumor

value: Primary pancreatic neuroendocrine tumor tissue

value: Pancreatic body


title: PC9 siYTHDF1 #2

description: Gene expression data from PC9 cells

source_name: siYTHDF1 #2


title: PC9 siYTHDF2 #1

description: Gene expression data from PC9 cells

source_name: siYTHDF2 #1


title: mA-3T3L1-LACZ-replicate_3

value: LacZ Adenovirus (control)

value: 3T3-L1 cells were induced to differentiate into matutre adipocytes fr a period of 7 days after which cell were infected with Adenovirus (LacZ)


title: mA-3T3L1-LACZ-replicate_2


title: Chuong-ChIP-233

city: Los Angeles

first: Ya-Chen

last: Liang

address: 2011 Zonal Ave., HMR 304A

department: Department of Pathology

institute: University of Southern California

description: input gDNA control for related ChIP

library_source: genomic

data_processing:
RNA-seq analysis. The RNA-seq analysis pipeline was adapted according to the publication (Trapnell et al., 2012). Manipulation. Tools: fastq_groomer (Galaxy Version 1.1.1) and fastq_trimmer_by_quality (window size 3; min score >= 20). Mapping. Tool: TopHat2 (Galaxy Version 2.1.1). Quantification and differentially expressed gene analysis. Tools: Cufflinks package (Trapnell et al., 2010)–including Cufflinks (Galaxy Version 2.2.1.2), Cuffmerge (Galaxy Version 2.2.1.1), Cuffquant (Galaxy Version 2.2.1.1), and Cuffdiff (Galaxy Version 2.2.1.3). Deeptools bamCoverage (Galaxy Version 3.1.2.0.0) was used to normalize the reads to 1X sequencing depth and wig_to_bigwig (Galaxy Version 1.1.1) was used to generate bigWig files of read coverages.
ChIP-seq analysis. Manipulation. Tools: fastq_groomer (Galaxy Version 1.1.1), fastq_quality_filter (Galaxy Version 1.0.2), fastq_trimmer_by_quality (Galaxy Version 1.1.1; window size 3; min score >= 20). Mapping. Tool: bowtie2 (Galaxy Version 2.3.4.2; genome: UCSC galGal4, --very-sensitive). Filtering. Tools: samtool_filter2 (Galaxy Version 1.8; -q 1), samtools_sort (Galaxy Version 2.0.1), samtools_rmdup (Galaxy Version 1.0.1; BAM is single-end). Peak-calling. Tools: MACS2 (Galaxy Version 2.1.1.20160309.4; for H3K27ac-ChIP, --gsize 1065365425 --nomodel --extsize 147 --bdg --broad --broad-cutoff 0.1; for CTCF/KLF-ChIP, --gsize 1065365425 --nomodel --extsize value obtained from macs2_predictd tool) and macs2_bdgcmp (Galaxy Version 2.1.1.20160309.0; -m FE and -m logLR -p 0.00001). To normalize MACS2 results from different libraries for comparison, we followed a “Build Signal Track” instruction from https://github.com/taoliu/MACS/wiki/Build-Signal-Track#Run_MACS2_bdgcmp_to_generate_foldenrichment_and_logLR_track.  Convert format. Tool: wig_to_bigWig (Galaxy Version 1.1.1).
NG Capture-C analysis. Double Capture-C results were analyzed according to the publication (Davies et al., 2016). The analysis pipeline was well documented and can be downloaded from “https://github.com/Hughes-Genome-Group/captureC/releases/download/VS2.0/UserManualforCaptureCanalysis.pdf". In brief, 1) download the CaptureC analyser package including CCanalyser3.pl, dpngenome3_1.pl, dpnII2E.pl from “https://github.com/Hughes-Genome-Group/captureC/releases", 2) generate in silico DpnII digested chicken genome ver. Ensemble galGal4 Release 72 with alpha and beta keratins, 3) perform adapter trimmer using the tool trim_galore (Dr. Felix Krueger at the Babraham Institute), 4) Merge overlapping reads by using the tool FLASH (Magoc and Salzberg, 2011), 5) in silico DpnII digest the FLASH-merged reads; 6) install Bowtie 1.2 (Langmead et al., 2009), 7) build up bowtie index using the original genome used in the Step 2, 8) align digested FLASH-merged reads (output of Step 5) using Bowtie1.2, and 9) run CCanalyser3.pl. wig_to_bigwig (Galaxy Version 1.1.1) was used to generate bigWig files from wig files of CCanalyser3 outputs.
Genome_build: UCSC Genome Browser assembly ID: galGal4
Supplementary_files_format_and_content: Bigwig files were generated using the wig/bedgraph_to_bigwig tool. Detail processes of RNA-seq, ChIP-seq, and NG Capture-C are described above.

molecule: genomic DNA

organism: Gallus gallus

source_name: E14 non-keratinized feather filament

growth_protocol: White Leghorn chicken eggs were used. Eggs were incubated in a humidified egg incubator with an automatic egg turner.

extract_protocol:
Please find detailed protocols for ChIP and Capture-C DNA preparation in Methods of this publication. RNA extraction for RNA-seq: Total RNAs of indicated tissues were extracted followed by the standard Trizol extraction protocol (Invitrogen, Cat.15596026). ChIPed-DNA preparation for ChIP-seq: The protocol was adapted from Dr. Ruchi Bajpai’s laboratory (Bajpai et al., 2010). 3C library preparation for NG Capture-C: The protocol was adapted from Dr. Wange Lu’s laboratory (Davies et al., 2016; Davies et al., 2017).
For RNA-seq library preparation: TruSeq RNA Prep Kit v2 (Illumina, RS-122-2001/-2002). For ChIP-seq library preparation: NEBNext Ultra End Repair/dA-Tailing Module (New England Biolabs, Cat. E7442S), NEBNext Ultra Ligation Module (New England Biolabs, Cat. E7445S), and KAPA HiFi HotStart ReadyMix (Kapa Biosystems, Cat. KK2601). For NG Capture-C library preparation: 5 µg of sheared 3C-DpnII DNA was used in adaptor ligation for pre-capture library using NEBNext DNA Library Prep Master Mix Set for Illumina (NEB, Cat. E6040). Adaptors were from NEBNext Multiplex Oligos for Illumina (NEB, Cat. E7500). The indexed 3C DNA was amplified using a primer pair of P5 (5’-aatgatacggcgaccaccga) and P7 (5’-caagcagaagacggcatacgagat) and purified using 1.8X AMPure XP beads. To perform the first capture, SeqCap EZ Hybridization and Wash Kit (Roche, Cat. 05634261001) was used. For one library, the indexed sequencing library, 5 µg of a Cot-1 DNA equivalent chicken Hybloc DNA (Applied Genetics Lab, Cat. CHB), 1 µl of 1xGen Universal Blocking Oligo—TS-p5 (1 nmole/µl), and 1 µl of 1xGen Universal Blocking Oligo—TS-p7(6nt) (1 nmole/µl) were mixed well and dried completely in a low retention PCR tube (Axygen, Cat. PCR-02-L-C). The dried pellet was then resuspended in Nimblegen Hybridization Buffer and Component A, mixed with 2 µl of a capture probe pool (3 pmole in total), and incubated for hybridization at 47℃ for 72 hours. After the first hybridization, biotinylated-probe-hybridized DNA (captured DNA) was mixed with 40 µl of prepared streptavidin magnetic beads (Invitrogen, Cat. 65001) and incubated at 47℃ for 45 min. The mixture was further washed using the SeqCap Wash Kit. The captured DNA was then purified using 1.8X AMPure XP beads and eluted in final 44 µl of nuclease-free water and amplified using the P5/P7 primer pair for 12 cycles. This 1st-captured DNA was finally cleaned up with 1.8X AMPure XP beads and eluted in 25 µl of water. To perform the second capture, the 1st-captured DNA was mixed with components described in the first capture part and incubated for hybridization at 47℃ for 24 hours. The double-captured DNA was then washed, pulled down by using the streptavidin beads, purified, amplified, and cleaned up as described before.

treatment_protocol: No treatment

tag: chip antibody

value: input genomic DNA

tag: skin region

value: dorsal back

tag: skin/appendage layer

value: whole skin


title: PC9 siYTHDF1 #1

description: Gene expression data from PC9 cells

source_name: siYTHDF1 #1

value: lung adenocarcinoma


title: T1

description: Cells from primary tumor tissue located at the pancreatic head

value: Pancreatic head


title: Chuong-ChIP-238


title: mA-3T3L1-LACZ-replicate_1

tag: strain


title: Chuong-ChIP-73

tag: age


title: EphA CAR-a transduced T cell

description:
control24_count
before co-culture.anno.xls

value: T cell

value: EphA2 CAR transduced

value: without tumor cell co-culture


title: MEF10_MN+FRG_Day6_rep2 [ATAC-seq]

status: Public on Aug 23 2021

first: Fei

last: Ji

address: 185 Cambridge St

institute: Massachusetts General Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome mm9 using BWA.
Peaks were called using HOMER with default parameter.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.bed: bed files include peak calls.

growth_protocol: MEFs harboring Rosa-rtTA, Col1a1-tetO-MyoD and Pax7-nGFP were isolated from E13.5 embryos and were maintained in DMEM (GIBCO) containing 1X glutaMAX (GIBCO), 1X MEM non essential Amino Acid Solution (GIBCO), 100 U/ml penicillin, 100 μg/mL streptomycin (GIBCO), 0.1% β-mercaptoethanol (GIBCO) and 10% Fetal Bovine Serum (HyClone). For dedifferentiation into iMPCs, MEFs were maintained in knockout DMEM (GIBCO) containing 1X glutaMAX (GIBCO), 1X MEM non essential Amino Acid Solution (GIBCO), 100 U/ml penicillin, 100 μg/mL streptomycin (GIBCO), 0.1% β-mercaptoethanol (GIBCO), 10% KnockOut Serum Replacement (GIBCO), 10% Fetal Bovine Serum (HyClone), 10ng/ml basic FGF (Peprotech), 5μM Forskolin (Sigma), 5μM RepSox (Sigma), 3μM GSK3β inhibitor CHIR99021 (Tocris) and 2μg/ml Doxycycline (Sigma). For transdifferentiation into myotubes, MEFs were maintained in knockout DMEM (GIBCO) containing 1X glutaMAX (GIBCO), 1X MEM non essential Amino Acid Solution (GIBCO), 100 U/ml penicillin, 100 μg/mL streptomycin (GIBCO), 0.1% β-mercaptoethanol (GIBCO), 10% KnockOut Serum Replacement (GIBCO), 10% Fetal Bovine Serum (HyClone), 10ng/ml basic FGF (Peprotech) and 2μg/ml Doxycycline (Sigma). Hypoxia experiments were performed in 5% O2 level. Primary satellite cells were isolated from adult Pax7-nGFP mice (10-12 weeks). Expanded satellite cells were maintained in F10 (GIBCO) with 20% Horse Serum (GIBCO), 1X glutaMAX (GIBCO) and 100 U/ml penicillin, 100 μg/mL streptomycin (GIBCO). 5ng/ml basic FGF (Sigma) was daily added.

extract_protocol:
DNA was extracted using MiniElute Kit according to the manufacturer’s instructions.
ATAC-seq was performed as previously described (Buenrostro et al., 2013). 60,000 cells were washed once with 100ml PBS and resuspended in 50ml lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.2% IGEPAL CA-630). The suspension of nuclei was then centrifuged for 10min at 500 g at 4°C, followed by the addition of 50ml transposition reaction mix (25ml TD buffer, 2.5ml Tn5 Transposase and 22.5ml Nuclease Free H2O) and incubation at 37°C for 30min. DNA was isolated using MiniElute Kit (QIAGEN). Libraries were amplified by PCR (13 cycles). After the PCR reaction, the library was selected for fragments between 100 and 1000bp with AmpureXP beads (Beckman Coulter). Libraries were purified with Qiaquick PCR (QIAGEN) and integrity checked on a Bioanalyzer before sequencing.

treatment_protocol: Cells were harvested following trypsin treatment and processed for transposition reaction.


title: MEF10_MN+FRG_Day6_rep1 [ATAC-seq]


title: MEF10_MyoD+FRG_Day6_rep2 [ATAC-seq]


title: MEF10_MyoD+FRG_Day6_rep1 [ATAC-seq]


title: MEF14_FRG_Day8_rep2 [ATAC-seq]


title: MEF14_FRG_Day8_rep1 [ATAC-seq]


title: MEF14_Dox+_Day8_rep2 [ATAC-seq]


title: RA synovium W0 patient 4

city: Brussels

first: Clement

last: Triaille

address: avenue Hippocrate, 10

department: IREC (Institut de Recherche Expérimentale et Clinique)

country: Belgium

institute: UCLouvain

description: Gene Expression data from rheumatoid arthritis synovial biopsy.

hyb_protocol: GeneChip Human Genome U133 Plus 2.0 arrays were hybridized overnight at 45°C with 10 μg fragmented biotinylated cRNA. The slides were then washed and stained using a EukGE‐WS2v5 fluidics protocol on a GeneChip Fluidics Station 450.

scan_protocol: Washed and stained chips were scanned on a GeneChip Scanner 3000 (Affymetrix).

data_processing: Analyses of the microarray data were performed using GeneSpring GX software (Agilent). Fluorescence intensity data were normalized using robust multiarray analysis.

source_name: RA synovium W0

label_protocol: Complementary RNA (cRNA) was synthesized from 100 ng total RNA, and biotin-labelled according to a standard Affymetrix procedure (GeneChip 3′ IVT Plus kit (Affymetrix)).

extract_protocol: Total RNA was extracted using Tripure Isolation Reagent (Roche) after mechanical disruption with an Ultra-turrax (Sigman Aldrich). RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips.

treatment_protocol: Samples were stored at -80°C after overnight incubation in RNA-Later solution (Invitrogen).

tag: patient

tag: diagnosis

value: Rheumatoid arthritis

tag: tissue

value: Rheumatoid arthritis synovium

tag: treatment

tag: time point

value: Week 0

tag: acpa/rf seropositivity

value: N

tag: das28crp w0

tag: das28crp w16

tag: gender

value: Female

tag: age w0 (years)


title: RA synovium W16 patient 3

source_name: RA synovium W16

value: Abatacept

value: Week 16

value: Y

value: H


title: MEF14_Dox+_Day4_rep2 [ATAC-seq]

tag: cell type


title: RA synovium W0 patient 2


title: MEF14_Dox+_Day8_rep1 [ATAC-seq]


title: CC_Ia1

first: Yong

last: Lv

institute: West China hospital of Sichuan university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: gene_fpkm.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: cystic choledochal cysts

extract_protocol:
Choledochal cysts were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: cystic choledochal cyst

tag: type

value: Ia


title: Pre-treatment breast cancer biopsy  112606

city: Novato

first: Christina

last: Yau

address: 8001 Redwood Blvd

institute: Buck Institute of Age Research

hyb_protocol: Extraction, labeling, hybridization, and scanning are performed by Agendia Inc (Irvine, CA).

data_processing: gnormalized signal (log2) data, as provided in the raw files on each patient, was extracted and aligned to the 75th quantile across arrays by Agendia. All values indicated for non-conformity, as indicated by the 'gIsFeatNonUnifOL' column in the raw files, are NA'd out. Probeset level data per array were mean-collapsed to the gene level, and genes common to the two platforms identified.  Expression data from the first ~900 I-SPY 2 patients distributed over the two platforms were combined into a single gene-level dataset over the set of common genes after batch-adjusting using ComBat [PMID:16632515].  The data matrix for this study constitutes 127 samples from this larger COMBAT-combined expression set.  Linear adjustment factors were derived from the larger ComBat operation, per platform, and can be used against these 127 samples for batch correcting on raw files.  The linear adjustment factors and updated probe annotation files per platform are provided.

source_name: Breast cancer biopsy (pre-treatment)

tag: hr

tag: mp

tag: pcr

tag: arm

value: TH Control


title: RA synovium W16 patient 10


title: RA synovium W16 patient 7


title: MEF14_Dox+_Day4_rep1 [ATAC-seq]


title: RA synovium W16 patient 6


title: RA synovium W16 patient 1


title: RA synovium W0 patient 9


title: RA synovium W0 patient 5


title: RA synovium W16 patient 2


title: RA synovium W16 patient 9


title: RA synovium W0 patient 8


title: RA synovium W16 patient 4


title: RA synovium W0 patient 10


title: RA synovium W16 patient 5


title: quiescent_SCs_rep2 [ATAC-seq]


title: activated_SCs_rep1 [ATAC-seq]


title: activated_SCs_rep2 [ATAC-seq]


title: quiescent_SCs_rep1 [ATAC-seq]


title: MEF14_Dox+FRG_Day10_GFP_rep2 [ATAC-seq]


title: RA synovium W16 patient 8


title: RA synovium W0 patient 3


title: MEF14_Dox+FRG_Day10_GFP_rep1 [ATAC-seq]


title: RA synovium W0 patient 6


title: RA synovium W0 patient 7


title: RA synovium W0 patient 1


title: MEF14_Dox+FRG_Day8_GFP_rep1 [ATAC-seq]


title: MEF14_Dox+FRG_Day8_GFP_rep2 [ATAC-seq]


title: MEF14_Dox+FRG_Day8_rep2 [ATAC-seq]


title: MEF14_Dox+FRG_Day8_rep1 [ATAC-seq]


title: MEF14_Dox+FRG_Day6_rep1 [ATAC-seq]


title: MEF14_Dox+FRG_Day2_rep2 [ATAC-seq]


title: MEF14_Dox+FRG_Day4_rep1 [ATAC-seq]


title: MEF14_Dox+FRG_Day4_rep2 [ATAC-seq]


title: MEF14_Day0_rep2 [ATAC-seq]


title: MEF14_Dox+FRG_Day2_rep1 [ATAC-seq]


title: Pax7_low_rep2 [RNA-seq]

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome mm9 using STAR.
Transcript abundance was calculated using Htseq.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.count.txt: Tab-delimited text files include raw count for each gene.

extract_protocol:
RNA was extracted using miRNeasy Mini Kit according to the manufacturer’s instructions.
RNA-seq libraries were constructed from polyadenosine (polyA)-selected RNA using NEBNext Ultra Directional RNA library prep kit for Illumina (New England BioLabs). Libraries were amplified for 14 cycles. Post library constructions, the samples were validated using 2200 Tapestation System and High Sensitivity D1000 ScreenTape kit. Libraries were quantified using the Kapa Biosystems Library Quantification kit (KK4828) and the BioRad CFX96 instrument. Each lane of sequencing was pooled into a 19-plex (19 samples per lane) with unique barcodes. Pooled libraries are also quantified using the Kapa Biosystems Library Quantification kit (KK4828) and the BioRad CFX96 instrument. These pools are then denatured to 16 pM with 1% PhiX and sequenced on the Illumina HiSeq2000 instrument, resulting in approximately 30 million reads per sample on average.

treatment_protocol: Cells were harvested following trypsin treatment and processed for RNA extraction.


title: Pax7_high_rep2 [RNA-seq]


title: Pax7_low_rep1 [RNA-seq]


title: MC36.V2.Old

city: Toulouse

first: Nathalie

last: Viguerie

address: Avenue Poulhes

country: France

institute: INSERM

hyb_protocol: 825 ng of Cy5 labelled probe was cohybridized the same amount of Cy3 labelled control probe. We used the Whole Human Genome Microarray Kit, 4x44K from Agilent with the gene expression hybridization kit according to the manufacturer’s protocol

scan_protocol: Micro-arrays were scanned on a InnoScan 710 scanner (Innopsys, Carbonne, France, EU) and data were extracted with Mapix software version 7.2.0 (Innopsys).

data_processing: Features with a signal to background ratio strictly below 2 in both color as well as control spots were discarded. The data without background subtraction were normalized with the Loess procedure and quantiles method by use of R/limma.

source_name: mix of liver, adipose tissue and skeletal muscle (Ambion First Choice Human Total RNA Survey Panel, Catalog #AM6000)

label_protocol: Total RNA quality was checked by capillary electrophoresis (Experion, BioRad) and quantified using Nanodrop ND-1000 Spectrophotometer (Labtech). Only good quality RNA extracts only were used for microarray hybridization. Fluorescent probes were obtained by amplifying and labelling 200ng of RNA with the low RNA input linear amplification kit (Agilent).

extract_protocol: Adipose tissue was crushed in QIAzol (Qiagen) and total RNA was extracted with the RNeasy mini kit (Qiagen) according to manufacturer instructions.

treatment_protocol: Individuals followed an 8-week lifestyle intervention including a moderate calorie restriction of 20% below their daily energy requirement aerobic combined to two sessions of resistance exercise per weeks.

tag: Sex

value: mix of male and female

source_name: Abdominal subcutaneous adipose tissue

value: Male

tag: group

value: Elderly

value: after lifestyle intervention


title: MEF14_Dox+FRG_Day6_rep2 [ATAC-seq]


title: Pax7_high_rep1 [RNA-seq]


title: MC36.V1.Old

value: baseline


title: CF05.V1.Yng

value: Young


title: CF05.V2.Yng


title: DJ10.V2.Old


title: SB18.V2.Yng


title: MEF14_Day0_rep1 [ATAC-seq]


title: MEF10_MN+FRG_Day6_rep2 [RNA-seq]


title: DG21.V2.Old


title: WT BMDM infected 3hr with B. thailandensis rep_2

first: Geoffrey

last: Neale

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Biotin-labeled cDNA (5 - 6 ug) was hybridized to an Affymetrix Clariom S Mouse Genechip Array (ThermoFisher Scientific, P/N 902930).

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Array signals were quantile normalized and transformed into log2 transcript expression values by using the robust multi-array average (RMA) algorithm (Affymetrix Expression Console v1.1).

label: Biotin

source_name: BMDMs isolated from wild-type mouse

label_protocol: Total RNA (200 ng) was converted into biotin-labeled cDNA by using an Affymetrix Whole Transcript Plus Expression kit (ThermoFisher Scientific, P/N 902281).

growth_protocol: Primary bone marrow–derived macrophages (BMDMs) were grown for 6 days in DMEM (11995073, Thermo Fisher Scientific, Waltham, MA) supplemented with 10% FBS (TMS-013-B, Millipore, Billerica, MA or S1620, BioWest, Riverside, MO), 30% L929-conditioned media and 1x penicillin-streptomycin (15070063, Thermo Fisher Scientific). BMDMs were seeded in antibiotic–free media at a concentration of 1 x 106 cells onto 12-well plates and incubated overnight. Cells were further washed and cultured in antibiotic-free DMEM with 10% FBS before infection.

extract_protocol: At 3hr post-infection, total RNA was extracted using TRIzol reagent (P/N 15596026, Thermo Fisher Scientific)

treatment_protocol: Cells were rinsed with PBS, then PBS was replaced with fresh antibiotic-free DMEM containing 10% FBS. Log-phase B. thailandensis (MOI 5) was pelleted onto cells at 300 x g for 5 min. Cells were were washed after 1 h, incubated with DMEM (1000 μg/mL kanamycin) for 1 h, washed again, and finally incubated in DMEM (250 μg/mL kanamycin) for the remainder of the treatment time.

value: bone marrow-derived macrophages

tag: strain

tag: genotype

value: wild type

value: infected 3hr with B. thailandensis


title: DJ10.V1.Old


title: SB18.V1.Yng


title: Ifnar1-/- BMDM infected 3hr with B. thailandensis rep_1

source_name: BMDMs isolated from Ifnar1-/- mouse

tag: treatment


title: ALE_EV2

city: Seoul

first: Sang Woo

last: Seo

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
Library strategy: whole genome resequencing
The quality of the sequence reads was checked by FastQC.
Sequencing reads were mapped onto the reference genome and analized using Breseq analysis software.
Genome_build: CP002185.1, CP002186.1, CP002187.1
Supplementary_files_format_and_content: html, region and type of mutation on the genome
Supplementary_files_format_and_content: gd, text files that represent region and type of mutation on the genome

organism: Escherichia coli

source_name: ATCC 9637

growth_protocol: Each strain was cultured in modified M9 medium supplemented with 100mM glycerol.

extract_protocol:
Genomic DNA was extracted from an overnight cultured sample (3 mL cell broth) using the GeneAll ExgeneTM Cell SV kit (GeneAll Biotechnology) according to the manufacturer’s protocol.
Sequencing libraries were constructed using the KAPA HyperPlus kit (Kapa Biosystems, Wilmington, MA, USA) according to the manufacturer’s instructions.

value: W


title: WT BMDM infected 3hr with B. thailandensis rep_1


title: Ifnar1-/- BMDM infected 3hr with B. thailandensis rep_2


title: MEF10_MyoD+FRG_Day6_rep2 [RNA-seq]

city: Boston


title: MEF10_MN+FRG_Day6_rep1 [RNA-seq]


title: ALE_EV1


title: MEF10_MyoD+FRG_Day6_rep1 [RNA-seq]


title: BP15.V1.Yng

tag: time point


title: MEF14_FRG_Day8_rep2 [RNA-seq]


title: MEF14_Dox+_Day8_rep2 [RNA-seq]


title: MEF14_FRG_Day8_rep1 [RNA-seq]


title: CJ44.V1.Old


title: DG21.V1.Old


title: BP15.V2.Yng


title: ALE_parental


title: BJ25.V2.Yng


title: BJ25.V1.Yng


title: CJ44.V2.Old


title: MEF14_Dox+_Day4_rep2 [RNA-seq]


title: activated_SCs_rep2 [RNA-seq]


title: MEF14_Dox+_Day4_rep1 [RNA-seq]


title: quiescent_SCs_rep2 [RNA-seq]


title: activated_SCs_rep1 [RNA-seq]


title: WCmHP_1

description: rRNA poorly depleted

data_processing:
The quality of the sequence reads obtained from RNA-seq was checked by FastQC.
The sequence reads were aligned to the reference genome using bowtie (version 1.2.2).
Reads generated from rRNA were firstly removed by alignment to rRNA, and rest of reads that were unaligned to rRNA were used for further studies.
The Cufflink package (http://cufflinks.cbcb.umd.edu/) was run to obtain transcriptomic data.
Genome_build: CP002185.1, CP002186.1, CP002187.1
Supplementary_files_format_and_content: gff, raw counts of sequencing reads (log scale)

growth_protocol: Parental, WAmHP, and WCmHP strains were cultured in 50mL modified minimal medium supplemented with glycerol and appropriate antibiotics, followed by 2μM coenzyme B12 and 0.1mM IPTG induction at 0.9-1.0 OD600.

extract_protocol:
Total RNA was extracted and purified using the Qiagen RNeasy Plus Mini Kit (Qiagen) in accordance with the manufacturer’s instructions. Ribosomal RNAs were depleted using the RiboMinus™ Transcriptome Isolation Kit (Thermo Fisher Scientific, Waltham, MA, USA).
The RNA-seq library was then constructed from the subtracted RNA using the KAPA Stranded RNA-seq Library Preparation Kit (Kapa Biosystems) in accordance with the manufacturer’s instructions.

treatment_protocol: Cell culture samples were harvested after 12-h induction and treated with RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany).

value: CRP(T168P) mutant


title: WAmHP_1

description: rRNA poorly depleted

value: AC(S254R) mutant


title: WAmHP_2

description: rRNA poorly depleted


title: MEF14_Dox+FRG_Day10_GFP_rep2 [RNA-seq]


title: WLBK2_2

description: rRNA poorly depleted

value: wild-type


title: MEF14_Dox+FRG_Day10_GFP_rep1 [RNA-seq]


title: quiescent_SCs_rep1 [RNA-seq]


title: MEF14_Dox+FRG_Day8_GFP_rep2 [RNA-seq]


title: RP29.V2.Yng


title: MEF14_Dox+_Day8_rep1 [RNA-seq]


title: WCmHP_2

description: rRNA poorly depleted


title: WLBK2_1

description: rRNA poorly depleted


title: RP29.V1.Yng


title: MEF14_Dox+FRG_Day8_rep1 [RNA-seq]


title: MEF14_Dox+FRG_Day8_rep2 [RNA-seq]


title: MEF14_Dox+FRG_Day8_GFP_rep1 [RNA-seq]


title: BE04.V1.Yng


title: MEF14_Dox+FRG_Day6_rep2 [RNA-seq]


title: BE04.V2.Yng


title: SY26.V2.Old


title: S4 (25°C_CPA)

city: Sendai

first: Yuta

last: Chiba

state: Miyagi

address: 4-1 Seiryo-cho, Aoba-ku

institute: Tohoku University

description: total RNA

data_processing:
First strand cDNAs were transcribed to the 5’ end of capped RNAs, attached to CAGE "bar code" tags and the sequenced CAGE tags were mapped to the mouse mm9 genomes using BWA software (v0.5.9) after discarding ribosomal or non-A/C/G/T base- containing RNAs.
For tag clustering, CAGE-tag 5' coordinates were input for Reclu clustering,with maxmum irreproducible discovery rate (IDR) 0.1 and minimum Tags per million (TPM) value 0.1 (Ohmiya et al, BMC Genomics 2014, 15:269).
Genome_build: GRCh38
Supplementary_files_format_and_content: Datasheet(All Samples).xlsx includes raw counts for all samples

source_name: Cultured tooth germ

growth_protocol: Mice tooth germs were dissected at E13.5 then seeded into cell culture inserts (BD Falcon, BD Biosciences, Franklin Lakes, NJ, USA) and cultured using an air–liquid interface culture technique in Dulbecco‘s modified Eagle’s medium (DMEM)/F-12, supplemented with 20% fetal bovine serum (FBS) (Gibco/Life Technologies, Waltham, MS, USA), 180 μg/mL ascorbic acid (Sigma, St. Louis, MS, USA), 2 mM l-glutamine (Gibco/Life Technologies, Waltham, MS, USA), and 1% penicillin/streptomycin (Gibco/Life Technologies, Waltham, MS, USA) at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
To construct each cDNA library, total RNA of mice tooth germ was extracted using TRIzol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tooth germs were cultured in a medium supplemented with 0.25 mM CPA at 25°C for 3 days. Then, we changed to a fresh medium, only by adding DMSO, and tooth germs were cultured for an additional 4 days.

value: ICR

tag: tissue

value: Tooth germ

tag: developmental stage

value: embryonic day 14.5


title: MEF14_Dox+FRG_Day6_rep1 [RNA-seq]


title: S3 (25°C_DMSO)

description: total RNA


title: S2 (37°C_CPA)

description: total RNA


title: S1 (37°C_DMSO)

description: total RNA


title: GW42.V2.Yng


title: MEF14_Dox+FRG_Day2_rep1 [RNA-seq]


title: MEF14_Dox+FRG_Day4_rep1 [RNA-seq]


title: MEF14_Day0_rep2 [RNA-seq]


title: MEF14_Dox+FRG_Day2_rep2 [RNA-seq]


title: SY26.V1.Old


title: SMCs_4

city: Durham

first: Rana

middle: K

last: Gupta

state: North Carolina

address: Carmichael Building, 300 North Duke St.

department: Duke Molecular Physiology Institute

institute: Duke University

data_processing:
Reads with phred quality scores <20 and <35 bp after trimming were removed from further analysis using trimgalore version 0.4.1.
Quality-filtered reads were then aligned to the mouse reference genome GRCm38 (mm10) using the HISAT (v2.0.1) using default settings.
Duplicates were marked using Sambamba version 0.6.6.
Aligned reads were quantified using ‘featurecount’ (v1.4.6).
Generation of normalized counts and analysis of differential gene expression was done using the R package DEseq2 (v1.6.3).
Genome_build: mm10
Supplementary_files_format_and_content: Normalized_count_table.tabular.txt: Tab-delimited text file of normalized counts for every sample and every gene.

source_name: epidydimal white adipose tissue

growth_protocol: Adipose tissue PDGFRb+ cells were isolated by flow cytometry.

extract_protocol:
Total RNA of freshly isolated cells was extracted using RNAqueous micro RNA isolation kit. 250ng total RNA of each sample was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Ultra II RNA Library Prep Kit following manufacturer's instructions.

value: White adipose tissue Pdgfrb+ cells

tag: cell subpopulation

value: SMCs

tag: age

value: Postnatal Day 7


title: SMCs_3


title: GW42.V1.Yng

value: mix of male and female

value: Male


title: MEF14_Dox+FRG_Day4_rep2 [RNA-seq]


title: SMCs_2


title: SMCs_1


title: MEF14_Day0_rep1 [RNA-seq]


title: SL07.V1.Old

value: Elderly

value: baseline


title: MLCs_4

value: MLCs


title: BJ08.V2.Yng

value: Young

value: after lifestyle intervention


title: MLCs_3


title: SL07.V2.Old


title: MLCs_2


title: BJ08.V1.Yng


title: RS20.V2.Yng


title: MLCs_1


title: FIPs_4

value: FIPs


title: MG22.V2.Old


title: MG22.V1.Old


title: RS20.V1.Yng


title: FIPs_3


title: GA16.V2.Old


title: TF38.V2.Yng


title: TF38.V1.Yng


title: FIPs_2


title: FIPs_1


title: GA16.V1.Old


title: BC23.V1.Yng


title: BC23.V2.Yng


title: APCs_4

value: APCs


title: CF44V2_Skeletal muscle from obese individual; after lifestyle intervention

source_name: Reference mix of liver, adipose tissue and skeletal muscle

extract_protocol: Skeletal muscle was crushed in QIAzol (Qiagen) and total RNA was extracted with the RNeasy mini kit (Qiagen) according to manufacturer instructions. Reference RNA = Ambion (First Choice Human Total RNA Survey Panel, Catalog #AM6000).

source_name: Skeletal muscle

value: Skeletal muscle

tag: age group

tag: disease state

value: obese


title: APCs_3

tag: cell type


title: CF44V1_Skeletal muscle from obese individual; baseline

value: mix of liver, adipose tissue and skeletal muscle


title: P88UT Genomic DNA Untransduced T-cells

type: genomic

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

description: Peripheral-blood mononuclear cells were isolated from a fresh leukapheresis product and activated in T-cell medium. High molecular weight DNA was extracted from paired T-cell samples consisting of CART19 untransduced and transduced T-cells before infusion into patients.

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting. Briefly, 600 ng of DNA of the studied samples was used to hybridize the BeadChip 850K microarray and scanned using HiScan SQ system (Illumina)

data_processing: Raw signal intensity data were initially QC’d and preprocessed from resulting idat files in R statistical environment (v4.0.3) using minfi Bioconductor package (v1.36.0). A number of quality control steps were applied to minimize errors and remove erratic probe signals, such as failed probes (probes with detection P value > 0.01 in at least 10% of samples were removed. If probe P value > 0.01 in less than 10% of samples, the Beta values of those probes in the failed samples were marked as NAs and later imputed using the median), cross-reacting probes, and probes that overlapped SNPs within ±1 bp of CpG sites, followed by background correction and dye-based normalization using ssNoob algorithm (single-sample normal-exponential out-of-band). All analyses were performed under R statistical environment (v4.0.3)

label: Cy5 and Cy3

source_name: High molecular weight DNA extracted from untransduced T-cells before infusion into patients

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: patient id

tag: matching transduced untransduced samples

value: Yes

tag: transduction status

value: Untransduced

tag: gender

value: F

tag: disease

value: NHL


title: APCs_2

value: White adipose tissue Pdgfrb+ cells

value: Postnatal Day 7


title: P83UT Genomic DNA Untransduced T-cells


title: P85UT Genomic DNA Untransduced T-cells

value: M


title: P81UT Genomic DNA Untransduced T-cells

value: ALL


title: P84UT Genomic DNA Untransduced T-cells


title: APCs_1


title: TF38V1_Skeletal muscle from obese individual; baseline

tag: Sex

value: mix of male and female

value: Male

value: baseline


title: TF38V2_Skeletal muscle from obese individual; after lifestyle intervention

value: Young

value: after lifestyle intervention


title: P86UT Genomic DNA Untransduced T-cells


title: P87UT Genomic DNA Untransduced T-cells


title: P73UT Genomic DNA Untransduced T-cells


title: P82UT Genomic DNA Untransduced T-cells


title: P76UT Genomic DNA Untransduced T-cells


title: P78UT Genomic DNA Untransduced T-cells


title: P75UT Genomic DNA Untransduced T-cells


title: P77UT Genomic DNA Untransduced T-cells


title: P71UT Genomic DNA Untransduced T-cells


title: P68UT Genomic DNA Untransduced T-cells


title: P80UT Genomic DNA Untransduced T-cells


title: P64UT Genomic DNA Untransduced T-cells


title: P67UT Genomic DNA Untransduced T-cells


title: P70UT Genomic DNA Untransduced T-cells


title: LM45V1_Skeletal muscle from obese individual; baseline

value: Elderly


title: P74UT Genomic DNA Untransduced T-cells


title: SB18V2_Skeletal muscle from obese individual; after lifestyle intervention

value: Skeletal muscle


title: LM45V2_Skeletal muscle from obese individual; after lifestyle intervention

value: obese


title: P69UT Genomic DNA Untransduced T-cells


title: C-DM-W3 miRNA-seq

city: Qingdao

first: Bin

last: Zhang

state: Shandong

address: Yanerdao Road 5

institute: Shangdong Eye Institue

data_processing:
Sequenced read quality was checked with FastQC.
After quality control, the reads were 3’-adaptor trimmed and fltered <= 15 bp reads with cutadapt software.
The trimmed reads were aligned to reference genome with bowtie software.
The expression level (Reads count) of miRNA were calculated using miRDeep2.
Diﬀerentially expressed miRNAs analyses were performed with R package edgeR. The number of identifed miRNA per group was calculated based on the mean of CPM in group >= 1.
Genome_build: GRCm38
Supplementary_files_format_and_content: Expression_miRNA.xlsx

source_name: regenerative corneal epithelium

extract_protocol:
The regenerative corneal epithelium was disrupted in TRIzol reagent (Invitrogen, USA) immediately and stored at -80°C until further experiments could be performed. The RNA obtained was run on agarose gels to measure degradation and contamination. RNA quantity and quality were also estimated using the NanoDrop ND-1000 system.
Complementary DNA (cDNA) libraries were prepared using NEB Multiplex Small RNA Library Prep Set (Illumina, USA) for miRNA. Then, the quality of the amplified libraries was verified with a 2100 Bioanalyzer (Agilent, USA). Sequencing of high-quality miRNA was carried out using the Illumina NextSeq 500 (Illumina, USA).

tag: strain

value: C57BL/6 + STZ

value: post treatment 16 weeks


title: P66UT Genomic DNA Untransduced T-cells

value: Yes

value: Untransduced


title: P79UT Genomic DNA Untransduced T-cells

value: NHL


title: P62UT Genomic DNA Untransduced T-cells


title: P63UT Genomic DNA Untransduced T-cells


title: SB18V1_Skeletal muscle from obese individual; baseline

value: mix of liver, adipose tissue and skeletal muscle


title: C-DM-W2 miRNA-seq


title: P72UT Genomic DNA Untransduced T-cells

value: F


title: C-DM-W1 miRNA-seq


title: P61UT Genomic DNA Untransduced T-cells

value: M


title: P114_Genomic DNA CART 19

description: Patients were treated with a second generation retroviral vector encompassing the variable regions derived from the anti-CD19 monoclonal antibody FMC63 with a CD34 16aa peptide trackable marker in the hinge region fused to the 4-1BB costimulatory domain and the CD3 zeta chain and linked to the iC9 suicide gene. For CAR CD19 T-cells generation, autologous peripheral blood-derived mononuclear cells were activated using anti-CD3/anti-CD28 antibodies, transduced and subsequently expanded during 14 days in IL-7 and IL-15 containing media and at that point cells were cryopreserved until infusion.

source_name: High molecular weight DNA extracted from CART 19 transduced T-cells before infusion into patients

value: No

value: Transduced

value: ALL


title: MC36V2_Skeletal muscle from obese individual; after lifestyle intervention

value: mix of male and female

value: Male


title: P59UT Genomic DNA Untransduced T-cells


title: P113_Genomic DNA CART 19


title: P57UT Genomic DNA Untransduced T-cells


title: C-Ctrl-W2 miRNA-seq

value: counterpart


title: RS20V2_Skeletal muscle from obese individual; after lifestyle intervention

value: Young

value: after lifestyle intervention


title: P112_Genomic DNA CART 19


title: MC36V1_Skeletal muscle from obese individual; baseline

value: Skeletal muscle

value: Elderly

value: obese

value: baseline


title: P111_Genomic DNA CART 19


title: P110_Genomic DNA CART 19


title: RS20V1_Skeletal muscle from obese individual; baseline


title: C-Ctrl-W1 miRNA-seq


title: P65UT Genomic DNA Untransduced T-cells

value: Yes

value: Untransduced


title: P60UT Genomic DNA Untransduced T-cells


title: Light-H3k4me3

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

data_processing:
ChIP-seq reads were aligned with BWA v0.7.16a to the reference sequence (mm10 from UCSC). Reads were filtered for MAPQ >10 and duplicated reads were removed using samtools. MACS2 v2.1.1 was used to identify peaks. Bedtools v2.25.0 was used to integrate dark/light ChIP-seq data. HOMER v4.9.1 was used for motif analysis.
Genome_build: Mouse mm10
Supplementary_files_format_and_content: bed-files including coordinates of the detected peaks from ChIP-Seq.

source_name: Superchiasmatic Nuclei

extract_protocol:
DNA was extracted using a True MicroChIP Kit (Diagenode) and fragmentation was performed using a Covaris-S2 sonicator.
ChIP libraries were constructed using a True MicroChIP Kit (Diagenode)

tag: experiment

value: ChIP-seq

tag: genotype

value: WT

tag: condition

value: Light

value: Superchiasmatic Nuclei

value: 11-12 weeks

value: male

tag: batch

tag: protocol

value: Protocol 2


title: P108_Genomic DNA CART 19

value: No

value: Transduced

value: M

value: ALL


title: P106_Genomic DNA CART 19


title: P107_Genomic DNA CART 19

value: F


title: SY26V1_Skeletal muscle from obese individual; baseline

tag: tissue

value: mix of liver, adipose tissue and skeletal muscle

value: mix of male and female

value: Skeletal muscle

value: Male

value: Elderly

tag: time point


title: P109_Genomic DNA CART 19

tag: age


title: SY26V2_Skeletal muscle from obese individual; after lifestyle intervention

tag: age group

tag: disease state

value: obese

value: after lifestyle intervention


title: P58UT Genomic DNA Untransduced T-cells

tag: patient id

value: Yes

value: Untransduced

value: NHL


title: P103_Genomic DNA CART 19

tag: matching transduced untransduced samples


title: P105_Genomic DNA CART 19

tag: transduction status


title: P104_Genomic DNA CART 19

tag: gender


title: P52UT Genomic DNA Untransduced T-cells

tag: disease


title: 2188_Unstim_wt

city: Bonn

first: Joachim

last: Schultze

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description:
2188_Unstim_wt
2188

data_processing:
base calling and de-multipexing using CASAVA version 1.8
Alignment and quatification with Kallisto l using the default parameters
reads mapped to each transcript against the RefSeq mm38 annotation download on March 2018
Normalization using DeSeq2
Genome_build: mm38
Supplementary_files_format_and_content: comma separated files include DeSeq2 normalized counts for each Sample.
Supplementary_files_format_and_content: comma separated files log ttransformed counts corrected for the experimental day for each Sample.

source_name: microglia

extract_protocol:
miRNeasy micro Kit (Qiagen)  according to the manufacturers' recommendations. Total RNA was eluted in RNAse free water.
Samples with more than 100 ng total RNA were converted into NGS libraries using the TruSeq RNA Library Prep Kit v2 (Illumina) at 100 ng input according to manufacturer’s recommendations. The size-distribution of the libraries was determined using the Agilent D1000 assay on a Tapestation 2200 system (Agilent). Libraries were quantified using a Qubit HS dsDNA assay. 75 bp single-end sequencing was performed on a HiSeq1500 system using Rapid v2 chemistry. Base calling from base call files and demultiplexing was performed with CASAVA v1.8 (Illumina). Low input Samples were converted into libraries of double stranded cDNA molecules as a template for high throughput sequencing following the SMART-Seq2 protocol. Shortly, mRNA was primed for SMART reverse transcription from 5 ng of total RNA using poly-T oligos. cDNA was pre-amplified by SMART ISPCR. Fragmentation was performed using the Illumina Nextera XT kit, followed by PCR amplification and indexing. Size-selection and purification of library fragments preferentially 300-400 bp in length was performed using SPRIBeads (Beckman-Coulter). The size-distribution of cDNA libraries was measured using the Agilent high sensitivity D5000 assay on a Tapestation 4200 system (Agilent). cDNA libraries were quantified using a Qubit high sensitivity dsDNA assay. 75 bp single-end sequencing was performed on a NextSeq500 system using High Output v2.5 chemistry. Base calling from base call files and file conversion to fastq files were achieved by Illumina standard pipeline scripts (bcl2fastq2 v.2.20).

treatment_protocol:
Briefly, after decapitation, extracted brains were collected in ice-cold PBS. Cortices of both hemispheres were collected after removal of meninges and triturated until a single-cell suspension was achieved. Isolated cells were cultivated as mixed glia culture until they reached confluency after approximately 14 days. Cells were cultivated in DMEM high glucose (Gibco, Darmstadt, Germany) containing 10 % fetal calf serum (FCS) (PAA, Freiburg, Germany), 1 % penicillin/streptomycin (Gibco). The medium was changed twice weekly. Microglia cells were harvested by shaking for 1 h at 200 rpm and re-seeded in 24-well plates for stimulation experiments at a density of 1.5 x 105 cells/ml. After re-seeding, cells were rested for 24 h.
For stimulation experiments, cells were treated for 30 min or 16 h with E. coli LPS serotype 0127:B8 (100 ng/ml) (Sigma-Aldrich, Taufkirchen, Germany) and IFNγ (20 ng/ml) (R&D Systems, Wiesbaden, Germany), CpG (1 nmol/mL), or PolyI:C (50g/mL).

value: brain

tag: developmental stage

value: neonatal

value: WT

tag: agent


title: Dark-H3k4me3

tag: experiment

value: ChIP-seq

value: Dark

value: Superchiasmatic Nuclei

value: 11-12 weeks

tag: Sex

value: male

value: Protocol 2


title: 2186_Unstim_wt

description:
2186_Unstim_wt
2186

tag: strain

tag: genotype


title: P50UT Genomic DNA Untransduced T-cells

value: F


title: P54UT Genomic DNA Untransduced T-cells

value: M


title: P51UT Genomic DNA Untransduced T-cells

value: ALL


title: 2059_Poly_IC_CB2_KO

description:
2059_Poly_IC_CB2_KO
2059


title: P98_Genomic DNA CART 19

value: No

value: Transduced


title: P99_Genomic DNA CART 19


title: C-Ctrl-W3 miRNA-seq

tag: treatment

value: counterpart


title: P97_Genomic DNA CART 19


title: P53UT Genomic DNA Untransduced T-cells

value: Yes

value: Untransduced


title: 2058_Poly_IC_CB2_KO

description:
2058_Poly_IC_CB2_KO
2058

tag: tissue

value: brain


title: P96_Genomic DNA CART 19


title: P48UT Genomic DNA Untransduced T-cells

value: NHL


title: P100_Genomic DNA CART 19


title: DJ10V2_Skeletal muscle from obese individual; after lifestyle intervention

value: mix of liver, adipose tissue and skeletal muscle

value: mix of male and female

value: Skeletal muscle

value: Male

value: Elderly

value: obese

tag: time point

value: after lifestyle intervention


title: RP29V1_Skeletal muscle from obese individual; baseline

value: Young

value: baseline


title: DJ10V1_Skeletal muscle from obese individual; baseline


title: P102_Genomic DNA CART 19

value: M

tag: age

value: ALL


title: P101_Genomic DNA CART 19

value: No

value: Transduced


title: PY13V2_Skeletal muscle from obese individual; after lifestyle intervention

tag: age group


title: P95_Genomic DNA CART 19


title: 2057_Poly_IC_CB2_KO

description:
2057_Poly_IC_CB2_KO
2057

value: neonatal


title: 2056_CpG_CB2_KO

description:
2056_CpG_CB2_KO
2056

value: CpG


title: P49UT Genomic DNA Untransduced T-cells

value: Yes

value: Untransduced


title: P93_Genomic DNA CART 19

value: F


title: P56UT Genomic DNA Untransduced T-cells

value: NHL


title: P94_Genomic DNA CART 19


title: 2055_CpG_CB2_KO

description:
2055_CpG_CB2_KO
2055

value: brain


title: 2054_CpG_CB2_KO

description:
2054_CpG_CB2_KO
2054


title: P46UT Genomic DNA Untransduced T-cells


title: P91_Genomic DNA CART 19


title: 2053_LPS_IFNg_CB2_KO

description:
2053_LPS_IFNg_CB2_KO
2053


title: P92_Genomic DNA CART 19


title: 2052_LPS_IFNg_CB2_KO

description:
2052_LPS_IFNg_CB2_KO
2052


title: P90_Genomic DNA CART 19


title: PY13V1_Skeletal muscle from obese individual; baseline

value: mix of liver, adipose tissue and skeletal muscle

value: mix of male and female

value: Skeletal muscle

value: Male

tag: disease state


title: P89_Genomic DNA CART 19

tag: patient id


title: LJ39V2_Skeletal muscle from obese individual; after lifestyle intervention

value: Elderly

value: obese

value: after lifestyle intervention


title: JS03V2_Skeletal muscle from obese individual; after lifestyle intervention

value: Young


title: 2050_Unstim_CB2_KO

description:
2050_Unstim_CB2_KO
2050


title: DG21V1_Skeletal muscle from obese individual; baseline

value: baseline


title: LJ39V1_Skeletal muscle from obese individual; baseline


title: P55UT Genomic DNA Untransduced T-cells

tag: matching transduced untransduced samples

value: M


title: P88_Genomic DNA CART 19

description: Peripheral-blood mononuclear cells were isolated from a fresh leukapheresis product and activated in T-cell medium. On day 2 of culture, activated cells were transduced with the CD19 CAR retrovirus. This construct comprises the variable regions of anti-CD19 monoclonal antibody FMC63 fused to the CD28 costimulatory domain and to the CD3 zeta chain, which were cloned into a mouse stem-cell virus gamma-retroviral backbone. CAR-T-cells were then further expanded in IL-2 containing T- cell medium until day 9–10. High molecular weight DNA was extracted from paired T-cell samples consisting of CART19 untransduced and transduced T-cells before infusion into patients.

tag: transduction status

value: Transduced


title: P87_Genomic DNA CART 19

tag: gender


title: 2048_Unstim_CB2_KO

description:
2048_Unstim_CB2_KO
2048

value: neonatal


title: DG21V2_Skeletal muscle from obese individual; after lifestyle intervention


title: MG22V2_Skeletal muscle from obese individual; after lifestyle intervention


title: 2049_Unstim_CB2_KO

description:
2049_Unstim_CB2_KO
2049


title: P86_Genomic DNA CART 19

value: Yes

tag: disease


title: 2051_LPS_IFNg_CB2_KO

description:
2051_LPS_IFNg_CB2_KO
2051

tag: developmental stage


title: GW42V1_Skeletal muscle from obese individual; baseline


title: GW42V2_Skeletal muscle from obese individual; after lifestyle intervention


title: L4_batch2

description:
Single-nuclei seq
SCN_COUNTS_META.RData

data_processing:
Bulk RNA-seq reads were aligned with STAR v2.7.1a to the reference sequence (mm10 from UCSC). Mouse reference was used for gene annotation and counting (gencode M21). Uniquely mapped reads were quantified using HTSeq v0.9.1 suite using protein coding genes by gene.
Genome_build: Mouse mm10
Supplementary_files_format_and_content: Input tables are included as tab separated files.
ChIP-seq
ChIP-seq reads were aligned with BWA v0.7.16a to the reference sequence (mm10 from UCSC). Reads were filtered for MAPQ >10 and duplicated reads were removed using samtools. MACS2 v2.1.1 was used to identify peaks. Bedtools v2.25.0 was used to integrate dark/light ChIP-seq data. HOMER v4.9.1 was used for motif analysis.
Genome_build: Mouse mm10
Supplementary_files_format_and_content: bed-files including coordinates of the detected peaks from ChIP-Seq.
Single-nuclei RNA-seq
Single-nuclei RNA-seq data was processed using mkfastq command from 10X Genomics CellRanger v3.0.1. UMI-tools were used to match barcode and reads. Single-nuclei RNA-seq reads were aligned with STAR v2.5.2b to the reference sequence (mm10 from UCSC). Human reference was used for gene annotation and counting (gencode M17). Gene level expression was calculated using featureCounts v1.6.2. Downstream analysis was performed using Seurat v3.0
Genome_build: Mouse mm10
Supplementary_files_format_and_content: Rdata containing count and meta data tab separated tables

extract_protocol:
Nuclei wer extracted following  a modified protocal based on CG00055_SamplePrepDemonstratedProtocol_-_MouseNeuralTissue_RevA (10x Genomics)
10X libraries were constructed using CG000075_Chromium_Single_Cell_3__V2_Ref_Cards_Rev_C (10x Genomics)

value: snSCN

value: WT

tag: condition

value: Light

value: Superchiasmatic Nuclei

value: 11-12 weeks

value: male

tag: batch

tag: protocol

value: Protocol 3


title: JS03V1_Skeletal muscle from obese individual; baseline

value: mix of liver, adipose tissue and skeletal muscle

tag: Sex

value: mix of male and female

value: Skeletal muscle

value: Male


title: MG22V1_Skeletal muscle from obese individual; baseline

value: Elderly

value: obese


title: RP29V2_Skeletal muscle from obese individual; after lifestyle intervention

value: Young

value: after lifestyle intervention


title: L3_batch2

description:
Single-nuclei seq
SCN_COUNTS_META.RData

tag: experiment

tag: genotype


title: P84_Genomic DNA CART 19

value: Transduced

value: F

value: NHL


title: L2_batch2

description:
Single-nuclei seq
SCN_COUNTS_META.RData

value: snSCN

value: WT

tag: tissue


title: P82_Genomic DNA CART 19

value: Yes


title: 2187_Unstim_wt

description:
2187_Unstim_wt
2187

tag: strain

value: brain

value: neonatal

tag: agent


title: L1_batch2

description:
Single-nuclei seq
SCN_COUNTS_META.RData

value: Light

value: Superchiasmatic Nuclei

tag: age

value: 11-12 weeks

value: male

value: Protocol 3


title: CF05V1_Skeletal muscle from obese individual; baseline

value: mix of liver, adipose tissue and skeletal muscle

value: mix of male and female

value: Skeletal muscle

value: Male

tag: age group

tag: disease state

tag: time point

value: baseline


title: P81_Genomic DNA CART 19

tag: patient id

tag: matching transduced untransduced samples

tag: transduction status

value: Transduced

value: F

value: ALL


title: DJ24V2_Skeletal muscle from obese individual; after lifestyle intervention

value: Elderly

value: obese

value: after lifestyle intervention


title: CF05V2_Skeletal muscle from obese individual; after lifestyle intervention

value: Young


title: P80_Genomic DNA CART 19

value: Yes

tag: gender

tag: disease

value: NHL


title: D4_batch2

description:
Single-nuclei seq
SCN_COUNTS_META.RData

value: snSCN

value: WT

tag: condition

value: Dark

value: Superchiasmatic Nuclei

value: 11-12 weeks

tag: batch


title: D3_batch2

description:
Single-nuclei seq
SCN_COUNTS_META.RData

tag: Sex

value: male

tag: protocol

value: Protocol 3


title: DJ24V1_Skeletal muscle from obese individual; baseline

value: mix of liver, adipose tissue and skeletal muscle

value: mix of male and female

value: Skeletal muscle

value: Male

value: baseline


title: P47UT Genomic DNA Untransduced T-cells

value: Untransduced

value: F


title: P79_Genomic DNA CART 19

value: Transduced

value: M


title: D2_batch2

description:
Single-nuclei seq
SCN_COUNTS_META.RData

tag: experiment

tag: genotype


title: BP15V2_Skeletal muscle from obese individual; after lifestyle intervention

tag: tissue

value: Young

value: obese

value: after lifestyle intervention


title: BP15V1_Skeletal muscle from obese individual; baseline


title: P78_Genomic DNA CART 19

value: Yes

value: ALL


title: D1_batch2

description:
Single-nuclei seq
SCN_COUNTS_META.RData

value: snSCN

value: WT

value: Dark

value: Superchiasmatic Nuclei

value: 11-12 weeks


title: P77_Genomic DNA CART 19

value: NHL


title: PV33V2_Skeletal muscle from obese individual; after lifestyle intervention

value: mix of liver, adipose tissue and skeletal muscle

value: mix of male and female

value: Skeletal muscle

value: Male

value: Elderly


title: PV33V1_Skeletal muscle from obese individual; baseline

value: baseline


title: BJ25V2_Skeletal muscle from obese individual; after lifestyle intervention

value: Young


title: P85_Genomic DNA CART 19

value: Transduced

value: M


title: P76_Genomic DNA CART 19

value: Yes

value: F


title: P83_Genomic DNA CART 19


title: D0_batch1

description:
Single-nuclei seq
SCN_COUNTS_META.RData

value: snSCN

value: male

value: Protocol 3


title: BJ25V1_Skeletal muscle from obese individual; baseline

value: obese


title: L0_batch1

description:
Single-nuclei seq
SCN_COUNTS_META.RData

value: WT

value: Light

value: Superchiasmatic Nuclei

value: 11-12 weeks


title: P75_Genomic DNA CART 19

value: NHL


title: Light-Input

value: ChIP-seq

value: Protocol 2


title: P74_Genomic DNA CART 19

value: ALL


title: GA16V2_Skeletal muscle from obese individual; after lifestyle intervention

value: mix of liver, adipose tissue and skeletal muscle

value: mix of male and female

value: Skeletal muscle

value: Male

value: Elderly

value: after lifestyle intervention


title: Light-H3k27ac

value: male


title: GA16V1_Skeletal muscle from obese individual; baseline

value: baseline


title: P73_Genomic DNA CART 19

value: Yes

value: Transduced

value: M


title: P72_Genomic DNA CART 19

value: F


title: Yami73

city: Tartu

first: Tuuli

last: Reisberg

address: Riia 23

country: Estonia

institute: University of Tartu

description: Genomic DNA extracted from blood was genotyped using HumanOmniExpress 24 v1.1 BeadChip (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Genomestudio v2.0 with GT module 2.0.4 (Illumina).

label: Cy3, Cy5

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: population

value: Yami

tag: region

value: East Asia


title: BJ08V2_Skeletal muscle from obese individual; after lifestyle intervention

tag: age group

value: Young

value: obese


title: Yami68


title: Yami64


title: P71_Genomic DNA CART 19

tag: age

value: ALL


title: WL3

description:
Raw_Counts_NPAS4.txt
Rpkm_NPAS4.txt

extract_protocol:
mRNA was extracted from SCN tissue using a Dynabead mRNA DIRECT Micro Kit (Ambion) according to the manufacturer’s instructions. All mRNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer (Agilent).
Samples were randomized for library preparation and sequencing. Libraries were constructed following Truseq protocols (Illumina) and sequencing was performed at the McDermott Sequencing Core at UTSW.

value: WT

value: Light

value: Superchiasmatic Nuclei

value: 11-12 weeks

value: Protocol 1


title: Yami70


title: Dark-Input

value: ChIP-seq

value: Dark

value: Protocol 2


title: BJ08V1_Skeletal muscle from obese individual; baseline

value: mix of liver, adipose tissue and skeletal muscle

value: mix of male and female

value: Skeletal muscle

value: Male

tag: disease state

tag: time point

value: baseline


title: Yami59

value: Yami

value: East Asia


title: Dark-H3k27ac

value: male


title: SL07V2_Skeletal muscle from obese individual; after lifestyle intervention

value: Elderly

value: obese

value: after lifestyle intervention


title: P70_Genomic DNA CART 19

tag: patient id

tag: matching transduced untransduced samples

value: Yes

value: Transduced

value: M

value: ALL


title: WL2

description:
Raw_Counts_NPAS4.txt
Rpkm_NPAS4.txt

value: WT

value: Light

value: Superchiasmatic Nuclei

value: 11-12 weeks

value: Protocol 1


title: Yami60


title: Yami53


title: BE04V2_Skeletal muscle from obese individual; after lifestyle intervention

value: mix of liver, adipose tissue and skeletal muscle

value: mix of male and female

value: Skeletal muscle

value: Male

value: Young


title: Yami56

value: Yami

value: East Asia


title: P69_Genomic DNA CART 19

tag: transduction status

tag: gender

value: F

value: NHL


title: Yami32


title: SL07V1_Skeletal muscle from obese individual; baseline

value: Elderly

value: obese

value: baseline


title: Yami58


title: Yami21


title: Yami25


title: P68_Genomic DNA CART 19

value: Yes

value: Transduced

tag: disease


title: WD3

description:
Raw_Counts_NPAS4.txt
Rpkm_NPAS4.txt

value: WT

tag: condition

value: Dark

value: Superchiasmatic Nuclei

value: male

tag: batch


title: WD2

description:
Raw_Counts_NPAS4.txt
Rpkm_NPAS4.txt

value: 11-12 weeks

tag: Sex

tag: protocol

value: Protocol 1


title: BE04V1_Skeletal muscle from obese individual; baseline

value: mix of liver, adipose tissue and skeletal muscle

value: mix of male and female

value: Skeletal muscle

value: Male