title: plasma_DWM_0mo_NURSE

tag: acrostic

value: NURSE

tag: group

value: DWM

tag: height (cm)

tag: mo

tag: albumin/creatinine ratio

tag: dbp (mmhg)

tag: body fat (%)

tag: fat mass (lb)

tag: fat free mass (lb)

tag: 6 min walk test distance (m)

tag: 6 min walk test heart rate (beats/min)

tag: alt (iu/l)

tag: ast (iu/l)

tag: hematocrit (%)

tag: white blood count (10^6 / ml)

value: meal tolerance test glucose time 0 min (mg/dl):144

value: meal tolerance test glucose time 15 min (mg/dl):160

value: meal tolerance test glucose time 30 min (mg/dl):165

value: meal tolerance test glucose time 60 min (mg/dl):186

value: meal tolerance test glucose time 120 min (mg/dl):172

value: meal tolerance test insulin time 0 min (mcU/ml):3.68700003623962

value: meal tolerance test insulin time 15 min (mcU/ml):22.238000869751

value: meal tolerance test insulin time 30 min (mcU/ml):30.5470008850098

value: meal tolerance test insulin time 60 min (mcU/ml):13.8809995651245

value: meal tolerance test insulin time 120 min (mcU/ml):17.4589996337891

tag: homair

tag: homab

tag: matsuda

value: FPG < 126 and HbA1c < 6.5 (0 = no; 1 = yes; 9 = missing):0

tag: instauc

value: insulin total area under curve (mcU/ml · 120 min):2196.945

tag: insiauc

value: insulin incremental area under curve (mcU/ml · 120 min):1754.505

value: change in insulin from 0 to 30 min (mcU/ml):26.86

value: change in glucose from 0 to 30 min (mg/dl):21

value: change in insulin from 0 to 30 min / change in glucose from 0 to 30 min (mcU/ml / mg/dl):1.279048

tag: odi

value: oral disposition index = dinsg030 / mttins0:0.3469074


title: A20_3787

status: Public on Aug 24 2021

type: SRA

city: Gainesville

first: Thomas

middle: C

last: Foster

state: Florida

address: 1149 S. Newell Dr.

department: Neuroscience

country: USA

institute: University of Florida

library_source: genomic

data_processing:
Input data sets were read in fastq format followed by short reads trimming using trimmomatic and quality control by FastQC and multiQC.
Reads were filtered using CSCALL to remove reads containing more than 10000 or more than 5.0% 'lone' cytosines.
Alignment of the input reads to the rn6 reference genome was done using BSMAP.
Methylation calling was performed with cscall v1.0  (Riva 2016) using the rn6-CG index.
Differential methylation was determined using the mcomp program.
Genome_build: rn6
Supplementary_files_format_and_content: comma separated values files which contains the methylation ratio for each sample.

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Brain hippocampal tissue

extract_protocol:
Animals were euthanized 6 hours after the last (E2/oil) injection and the brain CA1 region was dissected from dorsal hippocampi. The collected tissue was flash frozen in liquid nitrogen and stored in -80ᵒC. Genomic DNA was isolated using standard protocol involving SDS - Proteinase K treatment. Bisulfite conversion was performed with the EZ DNA Methylation-Direct kit (Zymo Research, catalog number: D5020).
Whole-genome bisulfite sequencing (WGBS) libraries for some samples were constructed with the Illumina TruSeq DNA Methylation kit (Illumina, catalog number: EGMK91324) and due to product discontinuation remaining libraries were made with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (Cat No. E7645S) according to manufacturer’s instructions.

treatment_protocol: Injections of 17β-estradiol-3-benzoate (10µg) or oil as control were given 6 weeks after OVX for two consecutive days 24 hours apart.

tag: strain

value: Fisher 344

tag: treatment

value: No treatment

tag: age

value: Young

tag: tissue

value: Brain hippocampal tissue


title: A5_3497


title: plasma_DWM_3mo_RODEO

type: protein

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

hyb_protocol: Hybridized by SomaLogic (http://somalogic.com/wp-content/uploads/2017/06/SSM-002-Technical-White-Paper_010916_LSM1.pdf)

scan_protocol: Scanned by SomaLogic (http://somalogic.com/wp-content/uploads/2017/06/SSM-002-Technical-White-Paper_010916_LSM1.pdf)

data_processing: Hybridization Control Normalization, Median Signal Normalization, and Calibration by SomaLogic.  The Relative fluorescence units provided in the sample data tables are the processed data provided by SomaLogic and these values were used to draw the conclusions for the study. Raw data were not provided by SomaLogic.

label: biotin

molecule: protein

organism: Homo sapiens

source_name: plasma

label_protocol: Biotin labeled by SomaLogic (http://somalogic.com/wp-content/uploads/2017/06/SSM-002-Technical-White-Paper_010916_LSM1.pdf)

extract_protocol: Extracted from plasma by SomaLogic (http://somalogic.com/wp-content/uploads/2017/06/SSM-002-Technical-White-Paper_010916_LSM1.pdf)

value: plasma

tag: acrostic

value: RODEO

tag: group

value: DWM

tag: height (cm)

tag: mo

tag: dbp (mmhg)

tag: sbp (mmhg)

tag: waist (cm)

tag: weight (kg)

tag: bmi

tag: basal metabolic rate

tag: body fat (%)

tag: fat mass (lb)

tag: fat free mass (lb)

tag: fasting plasma glucose (mg/dl)

tag: total cholesterol (mg/dl)

tag: ldl cholesterol (mg/dl)

tag: hdl cholesterol (mg/dl)

tag: triglycerides (mg/dl)

value: meal tolerance test glucose time 0 min (mg/dl):141

value: meal tolerance test glucose time 15 min (mg/dl):161

value: meal tolerance test glucose time 30 min (mg/dl):185

value: meal tolerance test glucose time 60 min (mg/dl):212

value: meal tolerance test glucose time 120 min (mg/dl):213

value: meal tolerance test insulin time 0 min (mcU/ml):3.15000009536743

value: meal tolerance test insulin time 15 min (mcU/ml):17.4029998779297

value: meal tolerance test insulin time 30 min (mcU/ml):11.7349996566772

value: meal tolerance test insulin time 60 min (mcU/ml):14.6409997940063

value: meal tolerance test insulin time 120 min (mcU/ml):29.0510005950928

tag: dmcure

value: insulin total area under curve (mcU/ml · 120 min):2079.083

value: insulin incremental area under curve (mcU/ml · 120 min):1701.083

value: change in insulin from 0 to 30 min (mcU/ml):8.584999

value: change in glucose from 0 to 30 min (mg/dl):44

value: change in insulin from 0 to 30 min / change in glucose from 0 to 30 min (mcU/ml / mg/dl):0.1951136

value: oral disposition index = dinsg030 / mttins0:0.0619408


title: 834418

type: RNA

city: San Francisco

first: Denise

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.

molecule: total RNA

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.

tag: tissue

value: breast cancer

tag: hr

tag: mp

tag: pcr

tag: arm

value: Control Arm


title: plasma_DWM_0mo_ORBIT

value: plasma

tag: acrostic

value: ORBIT

tag: group

value: DWM

tag: height (cm)

tag: mo

tag: albumin/creatinine ratio

tag: dbp (mmhg)

tag: sbp (mmhg)

tag: serum creatinine (mg/dl)

tag: waist (cm)

tag: weight (kg)

tag: 6 min walk test distance (m)

tag: 6 min walk test heart rate (beats/min)

tag: alt (iu/l)

tag: ast (iu/l)

tag: hematocrit (%)

tag: white blood count (10^6 / ml)

value: meal tolerance test glucose time 0 min (mg/dl):202

value: meal tolerance test glucose time 15 min (mg/dl):203

value: meal tolerance test glucose time 30 min (mg/dl):243

value: meal tolerance test glucose time 60 min (mg/dl):268

value: meal tolerance test glucose time 120 min (mg/dl):233

value: meal tolerance test insulin time 0 min (mcU/ml):27.6660003662109

value: meal tolerance test insulin time 15 min (mcU/ml):48.8800010681152

value: meal tolerance test insulin time 30 min (mcU/ml):71.390998840332

value: meal tolerance test insulin time 60 min (mcU/ml):56.6139984130859

value: meal tolerance test insulin time 120 min (mcU/ml):44.7309989929199

tag: homair

tag: homab

tag: matsuda

value: FPG < 126 and HbA1c < 6.5 (0 = no; 1 = yes; 9 = missing):0

tag: instauc

value: insulin total area under curve (mcU/ml · 120 min):6436.552

tag: insiauc

value: insulin incremental area under curve (mcU/ml · 120 min):3116.632

value: change in insulin from 0 to 30 min (mcU/ml):43.725

value: change in glucose from 0 to 30 min (mg/dl):41

value: change in insulin from 0 to 30 min / change in glucose from 0 to 30 min (mcU/ml / mg/dl):1.066463

tag: odi

value: oral disposition index = dinsg030 / mttins0:0.0385478


title: A6_3498

tag: strain

value: Fisher 344

tag: treatment

value: No treatment

tag: age

value: Young

tag: tissue

value: Brain hippocampal tissue


title: wild-type_mock_T10d_rep2

city: Piracicaba

first: Paulo

last: Teixeira

state: SP

address: Av. Pádua Dias, 11

department: Biology

country: Brazil

institute: University of São Paulo (ESALQ/USP)

library_source: transcriptomic

data_processing:
Illumina Casava version 1.8 was used for basecalling
Quality assessment of the sequencing reads was performed using FastQC
Trimmomatic was used to identify and discard reads containing Illumina adapter sequences
Quality-filtered reads were mapped to the Solanum Lycopersicum ITAG3.1 genome using HISAT2
The featureCounts function from the subread package was used to count reads that mapped to protein-coding genes
Genome_build: ITAG3.1
Supplementary_files_format_and_content: tab-delimited text file including read counts per gene for each sample

organism: Solanum lycopersicum

source_name: Shoots

growth_protocol: Wild-type MT and the transgenic line 35S::AtCKX2 were germinated in a 1:1 mixture of substrate:expanded vermiculite and grown under controlled conditions in a growth chamber at 25oC, 14 h photophase and 80% humidity.

extract_protocol:
TRIzol reagent
poly(A) RNA was isolated from 1000 ng total RNA and used to prepare Illumina RNA-seq libraries using the KAPA Stranded RNA-Seq kit.

treatment_protocol: The shoot apex and axillary buds of 17-d-old tomato seedlings of MT and the transgenic line 35S::AtCKX2 were inoculated with 70 µL of 10^6 basidiospores in 0.3% agar-water (w/v), and the plants were kept in a humid chamber for 48 h. Control plants were treated with 0.3% agar-water. Plants were kept under controlled conditions in a growth chamber at 25oC, 14 h photophase and 80% humidity.

tag: genotype

value: Wild-type

tag: cutivar

value: Micro-Tom

value: Mock

tag: time


title: wild-type_mock_T10d_rep1


title: plasma_RYGB_0mo_VISTA

value: plasma

tag: acrostic

value: VISTA

tag: group

value: RYGB

tag: height (cm)

tag: mo

tag: albumin/creatinine ratio

tag: dbp (mmhg)

tag: sbp (mmhg)

tag: serum creatinine (mg/dl)

tag: waist (cm)

tag: weight (kg)

tag: bmi

tag: basal metabolic rate

tag: body fat (%)

tag: fat mass (lb)

tag: fat free mass (lb)

tag: 6 min walk test distance (m)

tag: 6 min walk test heart rate (beats/min)

tag: alt (iu/l)

tag: fasting plasma glucose (mg/dl)

tag: total cholesterol (mg/dl)

tag: ldl cholesterol (mg/dl)

tag: hdl cholesterol (mg/dl)

tag: triglycerides (mg/dl)

value: meal tolerance test glucose time 0 min (mg/dl):171

value: meal tolerance test glucose time 15 min (mg/dl):192

value: meal tolerance test glucose time 30 min (mg/dl):222

value: meal tolerance test glucose time 60 min (mg/dl):257

value: meal tolerance test glucose time 120 min (mg/dl):228

value: meal tolerance test insulin time 0 min (mcU/ml):6.73000001907349

value: meal tolerance test insulin time 15 min (mcU/ml):14.6770000457764

value: meal tolerance test insulin time 30 min (mcU/ml):21.1620006561279

value: meal tolerance test insulin time 60 min (mcU/ml):28.1030006408691

value: meal tolerance test insulin time 120 min (mcU/ml):11.3039999008179

tag: dmcure

value: insulin total area under curve (mcU/ml · 120 min):2350.53

value: insulin incremental area under curve (mcU/ml · 120 min):1542.93

value: change in insulin from 0 to 30 min (mcU/ml):14.432

value: change in glucose from 0 to 30 min (mg/dl):51

value: change in insulin from 0 to 30 min / change in glucose from 0 to 30 min (mcU/ml / mg/dl):0.2829804

value: oral disposition index = dinsg030 / mttins0:0.0420476


title: wild-type_infected_T5d_rep4

tag: genotype

value: Wild-type

tag: cutivar

value: Micro-Tom

tag: treatment

value: Infected

tag: time


title: plasma_DWM_0mo_DAISY

tag: tissue

value: plasma

tag: acrostic

value: DAISY

tag: group

value: DWM

tag: height (cm)

tag: mo

tag: albumin/creatinine ratio

tag: dbp (mmhg)

tag: sbp (mmhg)

tag: serum creatinine (mg/dl)

tag: waist (cm)

tag: weight (kg)

tag: bmi

tag: basal metabolic rate

tag: ast (iu/l)

tag: hematocrit (%)

tag: white blood count (10^6 / ml)

value: meal tolerance test glucose time 0 min (mg/dl):157

value: meal tolerance test glucose time 15 min (mg/dl):198

value: meal tolerance test glucose time 30 min (mg/dl):229

value: meal tolerance test glucose time 60 min (mg/dl):254

value: meal tolerance test glucose time 120 min (mg/dl):236

value: meal tolerance test insulin time 0 min (mcU/ml):3.23699998855591

value: meal tolerance test insulin time 15 min (mcU/ml):15.1999998092651

value: meal tolerance test insulin time 30 min (mcU/ml):27.75

value: meal tolerance test insulin time 60 min (mcU/ml):24.0820007324219

value: meal tolerance test insulin time 120 min (mcU/ml):14.4630002975464

tag: homair

tag: homab

tag: matsuda

value: FPG < 126 and HbA1c < 6.5 (0 = no; 1 = yes; 9 = missing):0

tag: instauc

value: insulin total area under curve (mcU/ml · 120 min):2394.232

tag: insiauc

value: insulin incremental area under curve (mcU/ml · 120 min):2005.792

value: change in insulin from 0 to 30 min (mcU/ml):24.513

value: change in glucose from 0 to 30 min (mg/dl):72

value: change in insulin from 0 to 30 min / change in glucose from 0 to 30 min (mcU/ml / mg/dl):0.3404583

tag: odi

value: oral disposition index = dinsg030 / mttins0:0.1051771


title: 808714

tag: tissue

value: breast cancer

tag: hr

tag: mp

tag: pcr

tag: arm

value: Control Arm


title: wild-type_mock_T10d_rep3

tag: genotype

value: Wild-type

tag: cutivar

value: Micro-Tom

tag: treatment

value: Mock

tag: time


title: plasma_RYGB_24mo_MAGIC

value: plasma

tag: acrostic

value: MAGIC

tag: group

value: RYGB

tag: height (cm)

tag: mo

tag: albumin/creatinine ratio

tag: dbp (mmhg)

tag: sbp (mmhg)

tag: serum creatinine (mg/dl)

tag: waist (cm)

tag: weight (kg)

tag: bmi

tag: basal metabolic rate

tag: body fat (%)

tag: fat mass (lb)

tag: fat free mass (lb)

tag: 6 min walk test distance (m)

tag: 6 min walk test heart rate (beats/min)

tag: alt (iu/l)

tag: ast (iu/l)

tag: hematocrit (%)

tag: fasting plasma glucose (mg/dl)

tag: total cholesterol (mg/dl)

tag: ldl cholesterol (mg/dl)

tag: hdl cholesterol (mg/dl)

tag: triglycerides (mg/dl)

tag: dmcure


title: wild-type_infected_T5d_rep1

tag: genotype

tag: cutivar

tag: treatment

value: Infected

tag: time


title: wild-type_infected_T5d_rep3


title: plasma_DWM_36mo_ELBOW

tag: tissue

tag: acrostic

value: ELBOW

tag: group

value: DWM

tag: height (cm)

tag: mo

tag: albumin/creatinine ratio

tag: dbp (mmhg)

tag: sbp (mmhg)

tag: serum creatinine (mg/dl)

tag: waist (cm)

tag: weight (kg)

tag: bmi

tag: basal metabolic rate

tag: body fat (%)

tag: fat mass (lb)

tag: white blood count (10^6 / ml)


title: plasma_DWM_12mo_RADIO

value: RADIO

tag: fat free mass (lb)

tag: 6 min walk test distance (m)

tag: 6 min walk test heart rate (beats/min)

tag: alt (iu/l)

tag: ast (iu/l)

tag: hematocrit (%)

tag: fasting plasma glucose (mg/dl)

tag: total cholesterol (mg/dl)

tag: ldl cholesterol (mg/dl)

tag: hdl cholesterol (mg/dl)

tag: triglycerides (mg/dl)

value: meal tolerance test glucose time 0 min (mg/dl):130

value: meal tolerance test glucose time 15 min (mg/dl):159

value: meal tolerance test glucose time 30 min (mg/dl):194

value: meal tolerance test glucose time 60 min (mg/dl):192

value: meal tolerance test glucose time 120 min (mg/dl):180

value: meal tolerance test insulin time 0 min (mcU/ml):4.08199977874756

value: meal tolerance test insulin time 15 min (mcU/ml):7.56400012969971

value: meal tolerance test insulin time 30 min (mcU/ml):13.7399997711182

value: meal tolerance test insulin time 60 min (mcU/ml):7.68699979782104

value: meal tolerance test insulin time 120 min (mcU/ml):10.0319995880127

tag: homair

tag: homab

tag: matsuda

tag: dmcure

value: FPG < 126 and HbA1c < 6.5 (0 = no; 1 = yes; 9 = missing):0

tag: instauc

value: insulin total area under curve (mcU/ml · 120 min):1100.1

tag: insiauc

value: insulin incremental area under curve (mcU/ml · 120 min):610.26

value: change in insulin from 0 to 30 min (mcU/ml):9.658

value: change in glucose from 0 to 30 min (mg/dl):64

value: change in insulin from 0 to 30 min / change in glucose from 0 to 30 min (mcU/ml / mg/dl):0.1509062

tag: odi

value: oral disposition index = dinsg030 / mttins0:0.0369687


title: Sample A_C6_FSK

city: Shanghai

first: Minfeng

last: Shu

state: State...

address: No.131 Dongan Road II Xuhui district

country: China

institute: Fudan University

hyb_protocol: Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://www.mirbase.org/) and a spacer segment of polyethylene glycol toextend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 μL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device)

data_processing: Images were digitized using Array-Pro image analysis software (Media Cybernetics). Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression)

source_name: C6 cells

label_protocol: The assay started from 4 to 8μg total RNA sample were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.

growth_protocol: C6 Cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS, Yeasen),100 units/ml penicillin, and 100 μg/ml streptomycin in a humidified atmosphere of 5% CO2 at 37°C。

extract_protocol: Total RNA was extracted by Total RNA Purification Kit (LC Sciences, Cat. TRK-1001) following the manufacturer's instructions.

treatment_protocol: C6 Cells were treated with DMSO or FSK for 24 hours

tag: cell type

value: rat glioma cells

tag: treatment

value: FSK treatment


title: plasma_RYGB_36mo_HUMOR

tag: tissue

value: plasma

tag: acrostic

value: HUMOR

tag: group

value: RYGB

tag: height (cm)

tag: mo

tag: albumin/creatinine ratio

tag: dbp (mmhg)

tag: sbp (mmhg)

tag: serum creatinine (mg/dl)

tag: waist (cm)

tag: weight (kg)

tag: bmi

tag: basal metabolic rate

tag: body fat (%)

tag: fat mass (lb)

tag: fat free mass (lb)

tag: 6 min walk test distance (m)

tag: 6 min walk test heart rate (beats/min)

tag: alt (iu/l)

tag: white blood count (10^6 / ml)

value: FPG < 126 and HbA1c < 6.5 (0 = no; 1 = yes; 9 = missing):1


title: IR64_C_III_root

city: Tsukuba

first: Taiji

last: Kawakatsu

state: Ibaraki

address: 3-1-3 Kan-nondai

country: Japan

institute: National Agriculture and Food Research Organization

data_processing:
Reads were mapped to the IRGSP-1.0 genome assembly and MU7 gene models using the STAR aligner with options “--outFilterMultimapNmax 20 --outMultimapperOrder Random -- outSAMmultNmax 1 --alignIntronMax 3608 --twopassMode Basic”.  Uniquely mapped read counts were quantified using the featureCounts (ver. 1.6.4) with options “-s 2 -p -B -C”.
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: Tab-delimited text files include raw gene counts for every genes for each sample.

molecule: polyA RNA

organism: Oryza sativa

source_name: rice plants grown at three different positions in the growth chamber

growth_protocol: Two accessions were cultivated at three different positions in the growth chamber  in the pot filled with the calcined clay (Profile® Greens GradeTM, PROFILE Products LLC, http://www.profileevs.com). The calcined clay was irrigated with a modified Kimura B culture solution (273.2 µM K2SO4, 546.9 µM MgSO4･7H2O, 182.0 µM NaH2PO4･2H2O, 182.3 µM CaCl2･2H2O, 182.4 µM CaSO4･2H2O, 1.2 mM KNO3, 411.2 µM NH4Cl, and 4 mg/L FeC6H5O7･nH2O [pH 5.5]) before sowing.

extract_protocol:
Total RNA was extracted by the HighGI method (Yoshino et al., Breeding Science 2020).
Equal amounts of RNA extracted from three independent plants were pooled, then RNA-seq libraries were prepared using NEBNext Ultra II Directional mRNA-seq kit (New England Biolabs) following manufacturer's instruction.

tag: tissue

value: root tip

tag: cultivar


title: Sample A_C6_DMSO

tag: cell type

tag: treatment

value: DMSO treatment


title: IR64_C_II_root


title: wild-type_infected_T5d_rep5

tag: genotype

value: Wild-type

tag: cutivar

value: Micro-Tom

value: Infected

tag: time


title: plasma_RYGB_3mo_VIDEO

tag: acrostic

value: VIDEO

tag: group

tag: height (cm)

tag: mo

tag: dbp (mmhg)

tag: sbp (mmhg)

tag: waist (cm)

tag: weight (kg)

tag: ast (iu/l)

tag: hematocrit (%)

tag: fasting plasma glucose (mg/dl)

tag: total cholesterol (mg/dl)

tag: ldl cholesterol (mg/dl)

tag: hdl cholesterol (mg/dl)

tag: triglycerides (mg/dl)

value: meal tolerance test glucose time 0 min (mg/dl):99

value: meal tolerance test glucose time 15 min (mg/dl):151

value: meal tolerance test glucose time 30 min (mg/dl):149

value: meal tolerance test glucose time 60 min (mg/dl):135

value: meal tolerance test glucose time 120 min (mg/dl):117

value: meal tolerance test insulin time 0 min (mcU/ml):3.41599988937378

value: meal tolerance test insulin time 15 min (mcU/ml):41.367000579834

value: meal tolerance test insulin time 30 min (mcU/ml):12.1479997634888

value: meal tolerance test insulin time 60 min (mcU/ml):6.59499979019165

value: meal tolerance test insulin time 120 min (mcU/ml):8.54199981689453

tag: homair

tag: homab

tag: matsuda

tag: dmcure

value: FPG < 126 and HbA1c < 6.5 (0 = no; 1 = yes; 9 = missing):0

tag: instauc

value: insulin total area under curve (mcU/ml · 120 min):1472.49

tag: insiauc

value: insulin incremental area under curve (mcU/ml · 120 min):1062.57

value: change in insulin from 0 to 30 min (mcU/ml):8.732

value: change in glucose from 0 to 30 min (mg/dl):50

value: change in insulin from 0 to 30 min / change in glucose from 0 to 30 min (mcU/ml / mg/dl):0.17464

tag: odi

value: oral disposition index = dinsg030 / mttins0:0.0511241


title: wild-type_mock_T5d_rep2

tag: genotype

value: Wild-type

tag: cutivar

value: Micro-Tom

tag: treatment

value: Mock

tag: time


title: wild-type_mock_T5d_rep5


title: wild-type_mock_T5d_rep4


title: IR64_C_I_root

tag: tissue

value: root tip

tag: cultivar


title: plasma_DWM_0mo_HUMAN

value: plasma

tag: acrostic

value: HUMAN

tag: group

value: DWM

tag: height (cm)

tag: mo

tag: albumin/creatinine ratio

tag: dbp (mmhg)

tag: sbp (mmhg)

tag: serum creatinine (mg/dl)

tag: waist (cm)

tag: weight (kg)

tag: bmi

tag: basal metabolic rate

tag: body fat (%)

tag: fat mass (lb)

tag: fat free mass (lb)

tag: 6 min walk test distance (m)

tag: 6 min walk test heart rate (beats/min)

tag: alt (iu/l)

tag: ast (iu/l)

tag: hematocrit (%)

tag: white blood count (10^6 / ml)

tag: fasting plasma glucose (mg/dl)

tag: total cholesterol (mg/dl)

value: meal tolerance test glucose time 0 min (mg/dl):137

value: meal tolerance test glucose time 15 min (mg/dl):162

value: meal tolerance test glucose time 30 min (mg/dl):172

value: meal tolerance test glucose time 60 min (mg/dl):215

value: meal tolerance test glucose time 120 min (mg/dl):191

value: meal tolerance test insulin time 0 min (mcU/ml):11.4980001449585

value: meal tolerance test insulin time 15 min (mcU/ml):25.4790000915527

value: meal tolerance test insulin time 30 min (mcU/ml):41.7820014953613

value: meal tolerance test insulin time 60 min (mcU/ml):47.5769996643066

value: meal tolerance test insulin time 120 min (mcU/ml):32.0909996032715

value: insulin total area under curve (mcU/ml · 120 min):4512.21

value: insulin incremental area under curve (mcU/ml · 120 min):3132.45

value: change in insulin from 0 to 30 min (mcU/ml):30.284

value: change in glucose from 0 to 30 min (mg/dl):35

value: change in insulin from 0 to 30 min / change in glucose from 0 to 30 min (mcU/ml / mg/dl):0.8652571

value: oral disposition index = dinsg030 / mttins0:0.0752528


title: wild-type_mock_T5d_rep3

tag: genotype

value: Wild-type

tag: cutivar

value: Micro-Tom

tag: treatment

value: Mock

tag: time


title: wild-type_infected_T5d_rep2

value: Infected


title: wild-type_infected_T10d_rep3


title: plasma_RYGB_12mo_FENCE

tag: tissue

value: plasma

tag: acrostic

value: FENCE

tag: group

value: RYGB

tag: height (cm)

tag: mo

tag: albumin/creatinine ratio

tag: dbp (mmhg)

tag: sbp (mmhg)

tag: serum creatinine (mg/dl)

tag: waist (cm)

tag: weight (kg)

tag: bmi

tag: ldl cholesterol (mg/dl)

tag: hdl cholesterol (mg/dl)

tag: triglycerides (mg/dl)

value: meal tolerance test glucose time 0 min (mg/dl):96

value: meal tolerance test glucose time 15 min (mg/dl):181

value: meal tolerance test glucose time 30 min (mg/dl):186

value: meal tolerance test glucose time 60 min (mg/dl):162

value: meal tolerance test glucose time 120 min (mg/dl):120

value: meal tolerance test insulin time 0 min (mcU/ml):9.31900024414062

value: meal tolerance test insulin time 15 min (mcU/ml):48.318000793457

value: meal tolerance test insulin time 30 min (mcU/ml):41.2770004272461

value: meal tolerance test insulin time 60 min (mcU/ml):21.2250003814697

value: meal tolerance test insulin time 120 min (mcU/ml):13.496000289917

tag: homair

tag: homab

tag: dmcure

value: FPG < 126 and HbA1c < 6.5 (0 = no; 1 = yes; 9 = missing):1

tag: instauc

value: insulin total area under curve (mcU/ml · 120 min):3083.4

tag: insiauc

value: insulin incremental area under curve (mcU/ml · 120 min):1965.12

value: change in insulin from 0 to 30 min (mcU/ml):31.958

value: change in glucose from 0 to 30 min (mg/dl):90

value: change in insulin from 0 to 30 min / change in glucose from 0 to 30 min (mcU/ml / mg/dl):0.3550889

tag: odi

value: oral disposition index = dinsg030 / mttins0:0.0381038


title: IR64_B_II_root

tag: tissue

value: root tip

tag: cultivar


title: wild-type_mock_T5d_rep1

tag: genotype

value: Wild-type

tag: cutivar

value: Micro-Tom

tag: treatment

value: Mock

tag: time


title: 796558

value: breast cancer

tag: hr

tag: mp

tag: pcr

tag: arm

value: Control Arm


title: IR64_B_III_root


title: 783427


title: wild-type_infected_T48h_rep5

value: Infected


title: Saos-2_si-hsa_circ_0000073

city: Gui Yang

first: Xiaobin

last: Tian

address: Zhongshan East Road 83

institute: Guizhou Provincial People's Hospital

description: Gene expression data from OS cells transfected sh-circ_0000073

hyb_protocol: Put the sample into the GeneChip Hybridization Oven 645 hybridization oven for chip hybridization; use the GeneChip Fluidics Station 450 to wash and stain.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

source_name: Saos-2 cells with si-hsa_circ_0000073

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

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

treatment_protocol: Cells transfected with sh‐NC or sh-circ_0000073

tag: cell line

value: OS cell line (Saos-2)

tag: transfection


title: wild-type_infected_T48h_rep4


title: Saos-2_si-NC

description: Gene expression data from OS cells transfected with sh‐NC

source_name: Saos-2 cells with si-NC

value: sh-NC


title: wild-type_infected_T48h_rep1


title: IR64_A_III_root


title: IR64_B_I_root


title: FOXO3_3

city: Dalian

first: Lizhi

last: Bai

state: Liaoning

address: 6 Jiefang Road, Zhongshan

institute: Affiliated Zhongshan Hospital of Dalian University

description: Gene expression in A549 cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to LC Biotech Human lncRNA Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G5761A) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: circRNA-FOXO3 overexpression

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.25 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using the Plasma/Serum Circulating and Exosomal RNA Purification Mini Kit (Norgen Biotek,Ontario, Canada) following the manufacturer's recommendations.RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).


title: wild-type_infected_T48h_rep3


title: 752372


title: FOXO3_1

description: Gene expression in A549 cells


title: FOXO3_4

description: Gene expression in A549 cells


title: MG-63_si-NC

source_name: MG-63 cell with si-NC

value: OS cell line (MG-63)


title: wild-type_infected_T48h_rep2


title: A4_3496

tag: strain

value: Fisher 344

value: E2 Treatment

tag: age

value: Young

value: Brain hippocampal tissue


title: KP_C_II_root

value: Kinandang Patong


title: FOXO3_2

description: Gene expression in A549 cells


title: wild-type_mock_T48h_rep4


title: wild-type_mock_T48h_rep3


title: 752469


title: 748611


title: wild-type_mock_T48h_rep5


title: IR64_A_I_root


title: MG-63_si-hsa_circ_0000073

source_name: MG-63 cells with si-hsa_circ_0000073


title: Control_4

description: Gene expression in A549 cells

source_name: control


title: KP_C_III_root


title: KP_B_III_root


title: wild-type_mock_T48h_rep1


title: wild-type_infected_T24h_rep5


title: IR64_A_II_root


title: KP_C_I_root


title: wild-type_infected_T24h_rep4


title: KP_B_I_root


title: wild-type_mock_T48h_rep2


title: Control_2

description: Gene expression in A549 cells


title: Control_3

description: Gene expression in A549 cells


title: Control_1

description: Gene expression in A549 cells


title: KP_A_III_root


title: wild-type_infected_T24h_rep3


title: wild-type_infected_T24h_rep2


title: Z2551

city: Columbus

first: Janek

middle: S

last: Walker

state: Ohio

address: 410 W 12th Ave

department: Division of Hematology, Department of Internal Medicine

institute: The Ohio State University

data_processing:
Basecalls performed using Casava 1.8.2
Reads were trimmed using AdapterRemoval v2.2.0 to remove sequencing adapters
Reads were aligned against the mouse decontaminome using HISAT2 v2.0.6 using default parameters
Unaligned deconaminome reads were aligned against the mouse genome using HISAT2 v2.0.6 using default parameters
Reads were quantified using Subread FeatureCounts using GENCODE release M14
High quality transcripts were identified using CLEAR
VDJ/CDR3 quantification was performed using MiXCR (v3.0.5) with default parameters
Transcript-level abundances were estimated using Salmon, normalized with tximport, and differential expression computed with DESeq2.
With custom mouse reference, Transcript-level abundances were estimated using Salmon, normalized with tximport, and differential expression computed with DESeq2.
Genome_build: GRCm38p4
Supplementary_files_format_and_content: TSV Counts tables generated using Subread FeatureCounts, Unfiltered; MiXCR clonal output
Supplementary_files_format_and_content: Salmon abundance estimation results generated from untrimmed fastqs via Salmon quant v1.0.0 with flags --seqBias --gcBias --validateMappings
Supplementary_files_format_and_content: Salmon abundance estimation results generated from untrimmed fastqs via Salmon quant v1.0.0 with flags --seqBias --gcBias --validateMappings using a custom mouse genome with humn TCL1 and MTCP1 added.
Supplementary_files_format_and_content: CSV normalized abundance tables with transgene group comparisons from DESeq2 analysis for both mouse reference and custom mouse reference

organism: Mus musculus

source_name: Spleenic B cells

extract_protocol:
B cells were isolated using EasySepTM mouse pan B cell isolation kit (STEMCELL Technologies; Cat #19844). Cell pellets were captured and washed in PBS on ice prior to resuspension in TRIzol reagent and stored at -80°. Total RNA was isolated from TRIzol suspensions using a chloroform/ethanol extraction method and quantified via Qubit RNA HS Assay kit (Invitrogen).
The Clontech SMARTer v4 kit (Takara Bio USA, Inc.) was used for global preamplification. Illumina sequencing libraries were derived from the resultant cDNA using the Illumina Nextera XT DNA Library Prep Kit following manufacturer’s instructions. RNA-sequencing libraries were prepared with the Illumina Tru-Seq stranded kit and sequenced on a Hiseq 4000 targeting 40x10E6 fragments per sample.

tag: transgene


title: Z2606


title: KP_B_II_root


title: KP_A_I_root


title: Young BM derived macrophages 3 (RNA-Seq)

city: Heidelberg

first: Mark

last: Hartmann

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center (DKFZ)

data_processing:
nf-core RNAseq: v1.2
Cutadapt: v1.18
Trim Galore!: v0.50
STAR: v2.6.1a_08-27
HISAT2: v2.1.0
Picard: v.2.18.15
Samtools: v1.9
Stringtie: v1.3.4d
Genome_build: mm10
Supplementary_files_format_and_content: counts_BMDM.txt

source_name: Bone marrow

growth_protocol: BM derived macrophages (F4/80+CD169+) obtained from young (3 weeks old) versus old (>78 weeks old) mice

extract_protocol:
The RNA of 10,000 cells per replicate was extracted using the RNeasy Plus Micro Kit (Qiagen)
SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara, 634891) until cDNA amplification, fragmentation of cDNA using Covaris, library preparation using NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina (NEB, E6240)
HiSeq 4000 Paired-End 100bp

tag: cell type

value: BM derived macrophage F4/80+CD169+

value: BALB/c

value: WT

value: Bone marrow


title: Young BM derived macrophages 2 (RNA-Seq)


title: Old BM derived macrophages 2 (RNA-Seq)

value: Old


title: Old BM derived macrophages 1 (RNA-Seq)


title: Old BM derived macrophages 3 (RNA-Seq)


title: Young BM derived macrophages 1 (RNA-Seq)


title: wild-type_mock_T24h_rep4

value: Wild-type

value: Micro-Tom

value: Mock


title: wild-type_mock_T24h_rep5


title: KP_A_II_root

value: root tip


title: IR64_B_III_leaf

value: leaf


title: Z2641


title: 706639

value: breast cancer

value: Control Arm


title: wild-type_infected_T24h_rep1

value: Infected


title: 706169


title: B4376


title: IR64_C_III_leaf


title: IR64_A_III_leaf


title: Z2755

value: none (wildtype)


title: Myeloid cells from malignant pleural effusion_2

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

institute: Universitätsklinikum Hamburg-Eppendorf

data_processing:
Pair-ended UMI-indexed Illumina reads were demultiplexed with Cellranger (v. 3.0.1) mkfastq followed by CellRanger count to perform alignment to the Mm10 genome, read filtering and UMI counting for each sample.
Genome_build: mm10
Supplementary_files_format_and_content: Sparse matrix output files from Cellranger

source_name: pleural fluid

extract_protocol:
After euthanization of the mice, all fluid was aspirated from the pleural cavity. The cell suspension was filtered through 100 μm and 40 μm cell strainers and centrifuged at 400 x g, 5 min at 4 ℃. Cells were resuspended in cell blood lysis buffer (0.15 M NH4Cl, 10 mM KHCO3, 0.1 mM EDTA) for 5 min, washed in PBS, resuspended in FACS-buffer (PBS, 2 mM EDTA, 25 mM HEPES) at a concentration of 1 million cells/100 μl and incubated for 20 min on ice with anti-CD45 andanti-CD11b antibodies. Labelled cells were washed with PBS and resuspended in FACS-buffer. FACS sorted alive CD45+ CD11b+ single cells were encapsulated in droplets using 10X Genomics GemCode Technology (Single Cell 3' v2 kit) and processed following manufacturer’s specifications.
Single Cell 3' v2

treatment_protocol: Mice were anaesthetized using isoflurance inhalation and received intrapleural injections of 100ul PBS containing 150,000 murine tumor cells (LLC)

value: pleural fluid

value: Myeloid cells

tag: disease state

value: malignant pleural effusion


title: 689076

tag: tissue


title: 711476


title: IR64_C_II_leaf

tag: cultivar


title: wild-type_mock_T24h_rep3

tag: genotype


title: B4437


title: IR64_C_I_leaf


title: C1594


title: Z2754


title: wild-type_mock_T24h_rep2

tag: cutivar


title: wild-type_mock_T24h_rep1

tag: treatment


title: 688955


title: Myeloid cells from malignant pleural effusion_1


title: IR64_B_II_leaf


title: wild-type_infected_T12h_rep5

tag: time


title: KP_C_III_leaf

value: Kinandang Patong


title: Z2785


title: wild-type_infected_T12h_rep2


title: IR64_B_I_leaf


title: wild-type_infected_T12h_rep4


title: 679787

tag: hr


title: iWAT, Notum, S_2041

city: Los Angeles

first: Alice

last: Mouton

address: 610 Charles E. Young Dr. East

department: Ecology and Evolutionary Biology

institute: UCLA

description:
rawcount.txt
normalizedcount.txt

data_processing:
Reads were QC’d using FastQC in batch mode
Mapped to the mouse genome (mm10) using STAR aligner version 2.3.1
Differential expression analysis was performed using DEseq2 (R package).
Genome_build: mm10 ensembl 93
Supplementary_files_format_and_content: tab-delimited text files of rawcounts and normalizedcounts

source_name: inguinal white adipose tissue

extract_protocol:
miRNA isolation kit (Qiagen, Germantown, MD)
Illumina TruSeq kits (Illumina, San Diego, CA).

treatment_protocol: Eight week old male C57BL6/J mice were each injected through the tail vein 1x10^12 genome copies of adeno associated viruses that overexpress either GFP or Notum in a liver specific fashion. After 4 weeks of chow diet feeding, the mice were fasted for 4 hours, euthanized for the collection of inguinal white adipose tissue for RNA-seq experiment.

tag: Sex

value: Male

tag: aav treatment duration

value: 4 weeks

tag: diet

value: chow

tag: dob

tag: sac date

tag: rna isolation date

tag: rin

value: overexpress Notum in a liver specific fashion

value: inguinal white adipose tissue


title: iWAT, Notum, S_2042

description:
rawcount.txt
normalizedcount.txt

tag: strain


title: IR64_A_I_leaf


title: wild-type_infected_T12h_rep1

value: Wild-type

value: Micro-Tom


title: 631337

tag: mp

tag: pcr

tag: arm


title: iWAT, GFP, S_2021

description:
rawcount.txt
normalizedcount.txt

value: overexpress GFP  in a liver specific fashion

tag: tissue


title: wild-type_mock_T12h_rep4

tag: genotype

value: Mock


title: KP_C_I_leaf

value: leaf

tag: cultivar


title: IR64_A_II_leaf


title: wild-type_mock_T12h_rep5

tag: cutivar

tag: treatment


title: KP_C_II_leaf


title: wild-type_mock_T12h_rep3

tag: time


title: iWAT, Notum, S_2034

description:
rawcount.txt
normalizedcount.txt

tag: Sex


title: KP_B_II_leaf


title: iWAT, Notum, S_2033

description:
rawcount.txt
normalizedcount.txt

tag: aav treatment duration


title: KP_B_III_leaf


title: wild-type_mock_T12h_rep2


title: wild-type_infected_T12h_rep3


title: iWAT, Notum, S_2032

description:
rawcount.txt
normalizedcount.txt

tag: diet


title: wild-type_mock_T12h_rep1


title: KP_A_III_leaf


title: iWAT, GFP, S_2022

description:
rawcount.txt
normalizedcount.txt

tag: dob


title: iWAT, GFP, S_2014

description:
rawcount.txt
normalizedcount.txt

tag: sac date


title: KP_A_II_leaf


title: iWAT, GFP, S_2013

description:
rawcount.txt
normalizedcount.txt

tag: rna isolation date


title: KP_A_I_leaf


title: iWAT, GFP, S_2012

description:
rawcount.txt
normalizedcount.txt

tag: rin


title: iWAT, GFP, S_2011

description:
rawcount.txt
normalizedcount.txt

tag: strain


title: Retina Con

first: Qihuang

last: Jin

address: 85 Wujin Road

department: Department of Ophthalmology

institute: Shanghai General Hospital

data_processing:
Basecalls and data filtering performed using Cell Ranger Version 3.0.1
Reads were aligned to the mm10 genome assembly using Cell Ranger Version 3.0.1
Read count were calculated using Cell Ranger Version 3.0.1
Cluster classified using Seurat 3.0, and cluster definied using SingleR.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Retina

extract_protocol: Cells were loaded onto the 10X Chromium Single Cell Platform (10X Genomics) at a concentration of 1,000 cells per μl (Single Cell 3′ library and Gel Bead Kit v.3) as described in the manufacturer’s protocol.

treatment_protocol: C57BL/6J male mice at 3-5 weeks were intraperitoneally injected with STZ (Sigma Aldrich) at a dose of 55mg/kg. After 3 days of injection, the blood glucose concentration was measured by a glucose meter and strips (Glucomen, Menarini) weekly. Development of diabetes was defined by blood glucose levels higher than 300 mg/dL. The mice kept high blood glucose concentration for 25 weeks before sacrificed to prepare retinal cell suspension for scRNA-Seq.

value: retina

value: untreated


title: Day14.no3, mouse

city: New York

first: Jinyang

last: Li

state: New York

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Transcript quantification using Salmon
Calculate TPM values
Genome_build: mm38
Supplementary_files_format_and_content: txt file for TPM values

source_name: mouse pancreatic tumor cell - 6620c1

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

tag: cell line

value: mouse pancreatic tumor cell line 6620c1


title: Day14.no2, mouse


title: Day14.no1, mouse


title: KP_B_I_leaf


title: iWAT, Notum, S_2031

description:
rawcount.txt
normalizedcount.txt


title: Retina STZ

value: treated


title: Day2.no3, mouse


title: Day2.no2, mouse


title: iAstrocyte_Vehicle_3

first: Kun

last: Leng

state: Calfironia

address: 675 Nelson Rising Lane, 3rd Floor

department: Institute for Neurodegenerative Diseases

institute: University of California San Francisco

data_processing:
Alignment and quantification were performed using Salmon (version 1.4.082), with the --noLengthCorrection flag and an index generated from the human transcriptome (GRCh38, Gencode release 37)
Genome_build: GRCh38, Gencode release 37

source_name: hiPSC-derived astrocytes generated using the protocol described in the publication associated with this submission

growth_protocol: iAstrocytes were plated at 20,000 cells/cm2 on Matrigel-coated plates and maintained in Astrocyte Media (ScienCell cat. no. 1801) for 5 days prior to cytokine treatment.

extract_protocol:
Zymo Quick-RNA microprep kit
Lexogen QuantSeq 3' mRNA FWD

treatment_protocol: iAstrocytes were treated with vehicle or IL1a (3 ng/mL) +TNF (30 ng/mL) + C1q (400 ng/mL) for 24 hours.

tag: cytokine treatment

value: Vehicle

tag: library type

value: QuantSeq 3' mRNA FWD


title: iAstrocyte_IL1a+TNF+C1q_1


title: iAstrocyte_IL1a+TNF+C1q_3


title: iAstrocyte_Vehicle_2


title: Day2.no1, mouse


title: Proliferative Zone (PZ) of mandibular condylar cartilage (MCC),  laser-capture microdissection (LCM)

city: Riyadh

first: Aisha

middle: Mohammed

last: Basudan

state: Riyadh

address: Arrimayah

country: Saudi Arabia

institute: King Abdulaziz Medical City

description: Gene expression data from Proliferative Zone (PZ) of mandibular condylar cartilage (MCC)

hyb_protocol: 12.5ug of fragmented and labeled aRNA was used and was incubated for 17 hours at 44oC for hybridization. GeneChip Hybridization, Wash and Stain Kit (P/N 900720) and Fluidics Station 450 were used to wash and stain the probe arrays (GeneChip Rat Genome 230 2.0 Array, Affymetrix, Santa Clara, CA, USA) according to the Affymetrix GeneChip Expression Analysis Technical Manual.

scan_protocol: GeneChip Scanner 3000 7G was used to scan the probe arrays. For image processing, Affymetrix GeneChip Command Console (AGCC) software was used.

data_processing: The data were analyzed with Microarray Suite version 5 (MAS5.0 Affymetrix, Santa Clara, CA, USA) software enables both probe set summarization, as well as initial quality examination of data. MAA data were further analyzed using GeneSpring GX version 12 software (Agilent Technologies Inc., Santa Clara, CA, USA) where the Biological Significance Analysis workflow was selected. In this workflow type, default parameters for data processing are applied, and according to the RMA (Robust Multichip Averaging) normalization approach, absolute expression values were baselined to a median of all samples expression value, normalized using the quantile scheme, and then transformed into log2 based value of relative intensity for each probe set.

source_name: Proliferative Zone (PZ) of mandibular condylar cartilage (MCC) of Sprague-Dawley 5-week-old male rat

label_protocol: Two-cycle linear amplification process was performed in accordance to the protocol provided with the Arcturus® RiboAmp® HS Plus amplification Kit (Applied Biosystems, CA, USA). Labeling of aRNA transcripts was performed using the Arcturus® Turbo Labeling™ Biotin Reagent Kit (Applied Biosystems, Amsterdam, The Netherlands) and according to the manufacturer’s instructions. After quantification, 16.8 µg of the labeled aRNA samples were hydrolyzed in a fragmentation buffer (5X) solution of the GeneChip® 3' IVT Express Kit (Affymetrix, Santa Clara, CA, USA)

extract_protocol: LCM was performed and the collected dissected cells were immediately lysed in 50 μL of lysis buffer (Arcturus®  PicoPure RNA Isolation Kit, Applied Biosystems, CA, USA) as recommended by the manufacturer. The cell lysate of 30 microdissected tissue sections from each zone were pooled to create single samples. RNA was isolated from the pooled samples using Arcturus PicoPure RNA Isolation Kit (Applied Biosystems).

treatment_protocol: To obtain homogeneous cell populations, we followed our optimized laser-capture microdissection (LCM) protocol described earlier to dissect cells from each of the four MCC zones individually. Briefly, frozen sections were cut at  7μm thickness using a cryostat set to -24°C to -30°C, and were mounted on glass microscope slide. Slides were processed using Arcturus HistoGene™ LCM Frozen Section Staining Kit (CA, USA) was used according to the manufacturer’s instructions. The slides were individually placed onto the microscope platform of the Arcturus PixCell®  II Laser Capture Microdissection System (CA, USA).

tag: tissue

value: Sprague-Dawley

value: wild type

tag: age

value: male


title: siCtrl_replicate1

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

hyb_protocol: Affymetrix GeneChip® Human Gene 1.0 ST arrays were washed, stained and scanned according to the protocol described in GeneChip® WT Terminal Labeling and Hybridization User Manual (Fluidics Protocol FS450_0007)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.1

label: Biotin

source_name: Human mature adipocytes, de-novo differentiated in cell culture from isolated stromal vascual fraction of lipoaspirates; control sample, transfected with control siRNA, replicate 1

label_protocol: 100ng of total RNA were amplified and labeled using the Ambion Whole Transcript Expression Kit (Catalog Number 4425209, Ambion, Austin, TX) and Affymetix Genechip Whole Transcript Terminal Labeling Kit (Catalog Number 900671, Affymetrix, Santa Clara, CA)

extract_protocol: Rneasy mini kit (Qiagen)

treatment_protocol: Treated Human mature adipocytes, de-novo differentiated from stromal vascular fraction (SVF) derived from lipoaspirates from 2 different donors. One pool of adipocytes was transfected with a non-targeting siRNA (siCtrl) and the other pool was transfected with a siRNA targeting human LMO3 gene.

tag: sirna

value: control siRNA


title: Mature chondrocytes Zone (MZ) of mandibular condylar cartilage (MCC),  laser-capture microdissection (LCM)

description: Gene expression data from Mature chondrocytes Zone (MZ) of mandibular condylar cartilage (MCC)

source_name: Mature chondrocytes Zone (MZ) of mandibular condylar cartilage (MCC) of Sprague-Dawley 5-week-old male rat

tag: genotype


title: Fibrous Zone (FZ) of mandibular condylar cartilage (MCC),  laser-capture microdissection (LCM)

description: Gene expression data from Fibrous Zone (FZ) of mandibular condylar cartilage (MCC)

source_name: Fibrous Zone (FZ) of mandibular condylar cartilage (MCC) of Sprague-Dawley 5-week-old male rat


title: Hypertrophic chondrocytes Zone (HZ) of mandibular condylar cartilage (MCC),  laser-capture microdissection (LCM)

description: Gene expression data from Hypertrophic chondrocytes Zone (HZ) of mandibular condylar cartilage (MCC)

source_name: Hypertrophic chondrocytes Zone (HZ) of mandibular condylar cartilage (MCC) of Sprague-Dawley 5-week-old male rat


title: 580541

source_name: Breast cancer biopsy (pre-treatment)

value: breast cancer

tag: hr

tag: mp

tag: pcr

tag: arm

value: Control Arm


title: Day0.no3, mouse

tag: time


title: iAstrocyte_Vehicle_1


title: iAstrocyte_IL1a+TNF+C1q_2


title: NPC_IL1a+TNF+C1q_2

source_name: hiPSC-derived neural progenitor cells


title: siCtrl_replicate2

source_name: Human mature adipocytes, de-novo differentiated in cell culture from isolated stromal vascual fraction of lipoaspirates; control sample, transfected with control siRNA, replicate 2


title: Femoral condylar cartilage (FCC), laser-capture microdissection (LCM)

description: Gene expression data from Femoral condylar cartilage (FCC)

source_name: Femoral condylar cartilage (FCC) of Sprague-Dawley 5-week-old male rat

value: Femoral condylar cartilage (FCC)

tag: Sex


title: siLMO3_replicate1

source_name: Human mature adipocytes, de-novo differentiated in cell culture from isolated stromal vascual fraction of lipoaspirates; exprerimental sample, transfected with LMO3 targeting siRNA, replicate 1


title: Murine epididymal  adipose tissue from (rAAV-Lmo3) transduced mice (pool of n=2 mice) after 12 weeks of HFD,  3

hyb_protocol: Affymetrix GeneChip® Mouse Gene 1.0 ST arrays were washed, stained and scanned according to the protocol described in GeneChip® WT Terminal Labeling and Hybridization User Manual (Fluidics Protocol FS450_0007)

source_name: Murine epididymal  adipose tissue from (rAAV-Lmo3) transduced mice (pool of n=2 mice) after 12 weeks of HFD, replicate 3

label_protocol: 100ng of total RNA were amplified and labeled using the GeneChip® WT PLUS Reagent Kit (Catalog Number 902281, Affymetrix, Santa Clara, CA)

growth_protocol: Animals were exposed to a High Fat Diet (Reseach Diets cat.No. D12492) at an age of 6 weeks for a total of 12 weeks.

extract_protocol: RNA was isolated using Trizol method.

treatment_protocol: Visceral (epididymal) adipose tissue from obese rAAV-LacZ (control) or rAAV-Lmo3 (experimental) transduced C57BL6/J mice was collected after 12 weeks of high fat diet (HFD).

tag: group

value: (rAAV-Lmo3) transduced

value: Murine epididymal  adipose tissue


title: 532183


title: siLMO3_replicate2

source_name: Human mature adipocytes, de-novo differentiated in cell culture from isolated stromal vascual fraction of lipoaspirates; exprerimental sample, transfected with LMO3 targeting siRNA, replicate 2


title: Day0.no2, mouse


title: 517870


title: NPC_IL1a+TNF+C1q_1


title: Day0.no1, mouse


title: NPC_Vehicle_2


title: Murine epididymal  adipose tissue from (rAAV-Lmo3) transduced mice (pool of n=2 mice) after 12 weeks of HFD,  2

source_name: Murine epididymal  adipose tissue from (rAAV-Lmo3) transduced mice (pool of n=2 mice) after 12 weeks of HFD, replicate 2


title: Sorafenib sensitive group A(SA)

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.

tag: cell type

value: Hepatocellular carcinoma

tag: strain/cell line

value: PDX MODEL

tag: tissue source

value: Liver of NCG mice


title: Li astrocyte_IL1a+TNF+C1q_3

source_name: hiPSC-derived astrocytes generated using the protocol from Li et al. (PMID: 30269954)


title: Li astrocyte_Vehicle_3


title: Krencik astrocyte_IL1a+TNF+C1q_3

source_name: hiPSC-derived astrocytes generated using the protocol from Krencik et al. (PMID: 22011653)


title: Sorafenib sensitive group B(SB)


title: Murine epididymal  adipose tissue from (rAAV-Lmo3) transduced mice (pool of n=2 mice) after 12 weeks of HFD,  1

source_name: Murine epididymal  adipose tissue from (rAAV-Lmo3) transduced mice (pool of n=2 mice) after 12 weeks of HFD, replicate 1

tag: strain


title: Sorafenib primary response group(PR)


title: iNeuron_IL1a+TNF+C1q_1

source_name: hiPSC-derived neurons generated using the protocol from Fernandopulle et al. (PMID: 29924488)

tag: cytokine treatment


title: Murine epididymal  adipose tissue from (rAAV-YFP) transduced control mice (pool of n=2 mice) after 12 weeks of HFD,  3

source_name: Murine epididymal  adipose tissue from (rAAV-YFP) transduced control mice (pool of n=2 mice) after 12 weeks of HFD, replicate 3

value: control


title: MEF-2

city: BeiJing

first: Mao

last: Yihuan

address: No. 3 A, Datun Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

description: passage 4

data_processing:
RNA-seq reads were aligned to the mouse reference genome assembly (GRCm38/mm10) using STAR (version 2.7.1a)  with default parameters.
A customized script was used to filter the uniquely mapped reads.
Normalized gene expression level (Fragments Per Kilobase Million or FPKM) was obtained using Stringtie (version 2.0).
Differentially expressed gene (DEG) analysis was performed using Cuffdiff (version 2.2.1) with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: gene FPKM txt files

source_name: Embryonic fibroblast cells

extract_protocol:
RNA was harvested using Trizol reagent (Thermo Fisher Scientific, 15596018).
NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, E7530L)  was used for the construction of sequencing libraries. Poly-T-oligo-attached magnetic beads were used to isolate mRNA from total RNA, and first strand cDNA was obtained by reverse transcription PCR. The cDNA was then purified, end-paired, A-tailed, adapter-added and amplified by PCR.

tag: cell types

value: Embryonic fibroblast cells

tag: culture media

value: DMEM plus 10% FBS


title: MEF-1

description: passage 4


title: 2iL-iPS-3

description: passage 2

source_name: Induced pluripotent stem cells

value: Induced pluripotent stem cells

value: reprogramming, 2iL + DOX;daily cuture, N2B27 + DOX


title: 2iL-iPS-6

description: passage 3


title: iNeuron_IL1a+TNF+C1q_2

tag: library type

value: QuantSeq 3' mRNA FWD


title: Young BM derived macrophages 1 (ATAC-Seq)

description: Young BM derived macrophages replicate 1, multiplexed on 4 lanes

data_processing:
Sequencing reads were quality and adapter trimmed using Trim Galore v. 0.4.4 [1] in combination with Cutadapt v. 1.14 by deploying the non-default parameters “--paired”, “--nextera”, “--length_1 35”, “--length_2 35”.
Sequencing reads were aligned against the Genome Reference Consortium Mouse Build version 38.86 using Bowtie2 v. 2.2.6 with the “--very-sensitive” flag enabled and the maximal insertion length set to 2500 bp.
Aligned reads of the same library preparation that were sequenced on multiple lanes were combined using SAMtools merge v. 1.5.
Picard MarkDuplicates v. 2.17.4 was applied to remove PCR duplicates.
Reads that did not map in a proper pair or that exhibited a mapping quality below 20 on the Phred scale were filtered out by means of SAMtools view.
All read pairs showing an insert size smaller than 38 bp were removed.
To reconstruct the 29 bp transposase binding regions, the 5’ end of each read was extended by 19 bp into 5’ direction and 10 bp into 3’ direction.
Peak calling was performed using MACS2 callpeak v. 2.1.0.20140616 with a q-value cutoff of 0.005 and the non-default arguments “--broad”, “--nomodel”, “--keep-dup”, and “--gsize mm”.
The analysis workflow was described using the Common Workflow Language v. 1.0 and is publicly available at www.doi.org/10.5281/zenodo.3365923.
Genome_build: mm10
Supplementary_files_format_and_content: broadPeak

source_name: Bone marrow

extract_protocol:
50,000 cells per replicate were used to perform the Omni-ATAC protocol (Corces et al. 2017 Nature Methods)
Omni-ATAC protocol (Corces et al. 2017 Nature Methods), Illumina High Seq 2000 v4 Paired-End 125 bp
HiSeq 2000 v4 Paired-End 125bp

value: BM derived macrophage F4/80+CD169+

value: BALB/c

value: WT

tag: tissue

value: Bone marrow

tag: age

value: Young


title: Old BM derived macrophages 3 (ATAC-Seq)

description: Old BM derived macrophages replicate 3, multiplexed on 4 lanes

tag: genotype

value: Old


title: Young BM derived macrophages 3 (ATAC-Seq)

description: Young BM derived macrophages replicate 3, multiplexed on 4 lanes


title: Old BM derived macrophages 2 (ATAC-Seq)

description: Old BM derived macrophages replicate 2, multiplexed on 4 lanes


title: Old BM derived macrophages 1 (ATAC-Seq)

description: Old BM derived macrophages replicate 1, multiplexed on 4 lanes


title: Young BM derived macrophages 2 (ATAC-Seq)

description: Young BM derived macrophages replicate 2, multiplexed on 4 lanes


title: iNeuron_Vehicle_2

value: Vehicle


title: Murine epididymal  adipose tissue from (rAAV-YFP) transduced control mice (pool of n=2 mice) after 12 weeks of HFD,  2

source_name: Murine epididymal  adipose tissue from (rAAV-YFP) transduced control mice (pool of n=2 mice) after 12 weeks of HFD, replicate 2

value: male

value: Murine epididymal  adipose tissue


title: NPC_Vehicle_1

source_name: hiPSC-derived neural progenitor cells


title: OSKM-iPS-3

description: passage 6

value: reprogramming, N2B27 + DOX;daily cuture, N2B27 + DOX


title: iNeuron_Vehicle_1


title: OSKM-iPS-1

description: passage 7


title: Input_mESC

city: Barcelona

first: Mar

last: Gonzalez-Ramirez

address: C/ Dr Aiguader 88

country: Spain

institute: Center for Genomic Regulation (CRG)

description: ChIP-seq experiment

data_processing:
ChIP-seq analysis: Alignment: Sequence reads of the samples without were mapped to the mouse genome (mm10) using BOWTIE (PubMed ID 19261174) with the option -m 1. ChIPseq profiles were produced by SeqCode (http://ldicrocelab.crg.eu/) using buildChIPprofile function, in BedGraph format.
Genome_build: mm10
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide ChIP-seq)

growth_protocol: E14Tg2A ESCs were cultured feeder-free on 15-cm plates coated with 0.1% gelatin. Coating was achieved by covering the plates with gelatin 15 minutes at 37 °C. After removing any remaining gelatin, ESCs were cultured with Glasgow minimum essential medium (Sigma) supplemented with β-mercaptoethanol, sodium pyruvate, penicillin–streptomycin, non-essential amino acids, GlutaMAX, 20% fetal bovine serum (Hyclone), and leukemia inhibitory factor (LIF).

extract_protocol:
Cells were grown in 15-cm plates until 70% confluency and crosslinked in 1% formaldehyde in growth medium for 10 minutes at room temperature (RT) in a shaker. To stop the fixation glycine was added to a final concentration of 0.125 M and incubated for 5 minutes at RT. Cells were then washed twice with ice cold PBS and harvested by gently scrapping on ice in PBS plus protease inhibitors. Cells from two 15-cm plates were pooled together and centrifuged at 3,400 x g, 4ºC, 5 minutes.
Libraries were prepared according to Illumina instructions.

value: embryonic stem cells

tag: cell line

tag: chip antibody


title: 493519

first: Denise

last: Wolf

address: 2340 Sutter st

institute: University of California, San Francisco

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)

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: H4K20me3_mESC

description: ChIP-seq experiment

tag: cell type

value: H4K20me3 (Abcam, ab9053)


title: Krencik astrocyte_Vehicle_3


title: 2iL-ES_d38_2

description: unchanged, switched from 2iL to 2iL for 38 days

source_name: Embryonic stem cells

value: (C57BL/6 x 129S4/SvJae)F1  x (CBA/CaJ X C57BL/6J)F2

value: Embryonic stem cells

value: unchanged,  2iL


title: H3_mESC

description: ChIP-seq experiment

value: H3 (Abcam, Ab1791)


title: Murine epididymal  adipose tissue from (rAAV-YFP) transduced control mice (pool of n=2 mice) after 12 weeks of HFD,  1

source_name: Murine epididymal  adipose tissue from (rAAV-YFP) transduced control mice (pool of n=2 mice) after 12 weeks of HFD, replicate 1

tag: group

value: control

tag: Sex


title: Li astrocyte_Vehicle_2

value: QuantSeq 3' mRNA FWD


title: Li astrocyte_IL1a+TNF+C1q_1


title: Li astrocyte_Vehicle_1


title: 2iL-ES_d25_1

description: unchanged, switched from 2iL to 2iL for 25 days

tag: strain


title: 2iL-ES_d25_2


title: Li astrocyte_IL1a+TNF+C1q_2

tag: cytokine treatment


title: H3K4me3_mESC

description: ChIP-seq experiment

value: H3K4me3 (Diagenode, C15410003)


title: Krencik astrocyte_IL1a+TNF+C1q_2


title: H3K79me2_mESC

description: ChIP-seq experiment

value: H3K79me2 (Abcam, ab3594)


title: 2iL-ES_d18_1

description: unchanged, switched from 2iL to 2iL for 18 days

tag: cell types


title: H3K36me3_mESC

description: ChIP-seq experiment

value: H3K36me3 (Abcam, ab9050)


title: H3K27me3_mESC

description: ChIP-seq experiment


title: Krencik astrocyte_IL1a+TNF+C1q_1


title: H3K27me2_mESC

description: ChIP-seq experiment

value: H3K27me2 (Cell Signaling, #9728)


title: OSKM-ES_d38_2

description: switched from 2iL to N2B27 + DOX for 38 days

tag: culture media

value: switched from 2iL to N2B27 + DOX


title: H3K4me1_mESC

description: ChIP-seq experiment

value: H3K4me1 (Abcam, ab8895)


title: Krencik astrocyte_Vehicle_2

value: Vehicle

tag: library type


title: 2iL-ES_d18_2


title: OSKM-ES_d38_1


title: OSKM-ES_d25_2

description: switched from 2iL to N2B27 + DOX for 25 days


title: TCW astrocyte_IL1a+TNF+C1q_3

source_name: hiPSC-derived astrocytes generated using the protocol from TCW et al. (PMID: 28757165)


title: H3K27me1_mESC

description: ChIP-seq experiment

value: embryonic stem cells

value: H3K27me1 (Active Motif, #61015)


title: OSKM-ES_d25_1


title: TCW astrocyte_Vehicle_3


title: H2Bub1_mESC

description: ChIP-seq experiment

value: H2Bub (Cell Signaling, #5546)


title: OSKM-ES_d18_2

description: switched from 2iL to N2B27 + DOX for 18 days


title: 2iL-ES_d38_1


title: 10xRNA_ITC_GEMwell4

data_processing:
Alignment and quantification were performed on 10X single-cell RNA-seq libraries and sgRNA-enriched libraries using Cell Ranger (version 5.0.1) with default parameters and reference genome GRCh38-3.0.0.
Cellranger aggr was used to aggregate counts belonging to the same sample across different GEM wells.
sgRNA unique molecular identifier (UMI) counts for each cell barcode were obtained using the pipeline described in Hill et al. [PMID: 29457792]
sgRNAs were assigned to cells using demuxEM [PMID: 31266958]
Genome_build: GRCh38-3.0.0

source_name: hiPSC-derived astrocytes

extract_protocol: 10x Next GEM v3.1

value: 10x RNA


title: TCW astrocyte_Vehicle_2


title: OSKM-ES_d18_1

value: (C57BL/6 x 129S4/SvJae)F1  x (CBA/CaJ X C57BL/6J)F2


title: 10xRNA_ITC_GEMwell3


title: Krencik astrocyte_Vehicle_1


title: 421917

tag: tissue

value: breast cancer

value: Control Arm


title: Microglia EYFP  rep4

first: Zhilin

last: Wang

address: 138 Yixueyuan Road

institute: Fudan University

data_processing:
Quality of reads was evaluated using fastp v0.20.1 and all samples passed quality control.
Reads were aligned to mm10 (GRCm38 from Ensembl) using hisat2-2.0.5
Mapped reads were counted using featureCounts(Yang Liao et al., Bioinformatics. 2014)
Genome_build: mm10 (GRCm38 from Ensembl)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Microglia

extract_protocol:
The mice were perfused with ice-cold 1× PBS and hippocampi were isolated and incubated with enzyme mix to dissociate   into single cell suspension. Debris was removed using debris removal solution. Microglias were enriched using CD11b microBeads. RNA in microglia was extracted with Trizol.
Libraries were prepared following the instructions in VAHTS mRNA-seq V3 Library Kit for illumina.

treatment_protocol: Mice were co-injected AAV-RAM-Cre either with AAV-Dio-Atg7-Flag or AAV-Dio- EYFP in dorsal dentate gyrus to   overexpress ATG7 in the DG memory engrams

value: dorsal hippocampus

value: Microglia

tag: age

value: 6-8 Weeks


title: 10xRNA_Veh_GEMwell1


title: Microglia ATG7  rep3

tag: genotype

value: ATG7 overexpression


title: TCW astrocyte_Vehicle_1

value: QuantSeq 3' mRNA FWD


title: Microglia ATG7  rep2


title: TCW astrocyte_IL1a+TNF+C1q_1


title: 10xRNA_Veh_GEMwell2


title: Microglia ATG7  rep1


title: Chip_Alveolus_Day10_2

city: Boston

first: S. Jordan

last: Kerns

address: 27 Drydock Ave

institute: Emulate

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
TPMs, FPKMs were calculated using the hit counts and the corresponding gene lengths (using R).
Genome_build: GRCh38
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files

source_name: Epithelial cells from Alveolus-Chip

growth_protocol:
Colon Intestine-Chips were seeded with colonic epithelial cells obtained from dissociation of colonic organoids (introduced in the top channel of an Organ-on-Chip) and Human Intestinal Microvascular Endothelial Cells (HIMEC) (introduced into the bottom channel of an Organ-on-Chip). The chips were maintained under constant perfusion of fresh media at 30 µl/hr through the top channel with expansion medium and bottom channel with EGM2-MV medium. Peristalsis-like stretch deformations of the tissue attached to the membrane (2% strain 0.2 Hz at Day 2; 10% strain 0.2Hz at Day 3-8).
Alveolar Lung-Chips were seeded with human alveolar epithelial cells obtained (introduced in the top channel of an Organ-on-Chip) and Human Lung Microvascular Endothelial Cells (HMVEC-L) (introduced into the bottom channel of an Organ-on-Chip). The chips were maintained under constant perfusion of fresh media at 30 µl/hr through the top channel with SAGM medium and bottom channel with EGM2-MV medium. An air-liquid interface was introduced at Day 5 of culture where air was introduced into the top channel and perfusion of HMVEC-L medium at 30uL/hr. Breathing-like stretch deformations of the tissue attached to the membrane was introduced at Day 7 (5% strain 0.2 Hz).

extract_protocol:
RNA was extracted using TRIzol (Life Technologies) according to manufacturer’s guidelines.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Not applicable.

tag: applied mechanostimulation

value: Bottom channel flow (30 ul/hr) and stretch (10% at Day 7)

value: alveolus epithelial cells

tag: air liquid interface

value: Day 5 - Air Liquid Interface


title: Microglia EYFP  rep2

value: control


title: Microglia EYFP  rep3


title: H3K27ac_mESC

description: ChIP-seq experiment

tag: cell line

tag: chip antibody

value: H3K27Ac (Millipore, #07-360)


title: Chip_Alveolus_Day10_3


title: Microglia EYFP  rep1


title: Chip_Alveolus_Day10_1


title: Chip_Alveolus_Day5_3

value: flow (30 ul/hr)


title: Chip_Alveolus_Day5_2


title: ASPcKOP7cKO tumor 4

city: Memphis

first: Hongjian

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60),  mapped to mouse genome assembly (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (vM22) .
Genome_build: GRCm38(mm10)
Supplementary_files_format_and_content: gene-level RSEM raw count, TPM, FPKM txt files

source_name: tumor

extract_protocol:
Tumors were excised and enzymatically (collagenase B/dispase II) and mechanically digested for 1 hour at 37C and filtered into single cells for flow cytometry. TdTomato+/PECAM1- population was used for RNA extraction with Qiazol's miRNeasy Micro Elution Kit.
The KAPA Hyper Prep library kit was used according to manufacturer's specifications.

value: Flow-cytometry sorted tumor cell

value: aP2-Cre; SmoM2/tdTom; Pten f/f; Pax7 f/f

tag: background

value: mixed


title: Chip_Alveolus_Day5_1


title: TCW astrocyte_IL1a+TNF+C1q_2

city: San Francisco


title: proband sample with WNT3A media, replicate 1

first: Rolf

last: Stottmann

state: OHIO

address: 575 Children's Crossroads

department: Pediatrics

institute: Nationwide Children's Hospital

data_processing:
All steps were performed by Novogene following a commercially available analysis service. Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling)
STAR software is used to accomplish the mapping.
Genome_build: hg38
Supplementary_files_format_and_content: excel file

source_name: cultured fibroblast

growth_protocol: Fibroblasts  were cultured in Dulbecco Modified Eagle Medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C and 5% CO2

extract_protocol:
RNA was extracted using the Trizol protocol as described above
RNA sequencing was performed by Novogene USA using standard protocols. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra  TM RNA  Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. BBriefly, mRNA was  purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand  Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis  was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of  3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in  length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptorligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and  Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Fibroblasts were grown in 6-well plates to 80% confluency, serum starved for 24 hours and treated for 12 hrs with either SAG (400nM), WNT3A conditioned media (cells from ATCC; media prepared in-house according to vendor protocol), or control media.

tag: sample type

value: proband

tag: treatment

value: WNT3A treated


title: proband sample with WNT3A media, replicate 2


title: 363669

value: breast cancer

tag: hr

tag: mp

tag: pcr

tag: arm

value: Control Arm


title: proband sample with WNT3A media, replicate 3


title: ASPcKOP7cKO tumor 3


title: ASPcKOP7cKO tumor 2


title: proband sample with control media, replicate 3

value: untreated


title: proband sample with control media, replicate 2


title: proband sample with control media, replicate 1


title: Flask_Alveolus_2

source_name: Epithelial cells from Alveolus

tag: cell type


title: Flask_Alveolus_3


title: ASPcKO tumor 4

value: aP2-Cre; SmoM2/tdTom; Pten f/f


title: ASPcKOP7cKO tumor 1


title: proband sample with SAG media, replicate 3

value: SAG treated


title: control sample with WNT3A media, replicate 3


title: control sample with WNT3A media, replicate 2


title: Chip_Colon_3

source_name: Epithelial cells from Colon Intestine-Chip

value: flow (30 ul/hr) and stretch (2% at Day 3-4; 10% at Day 4-8)

value: colon epithelial cells


title: Chip_Colon_2


title: ASPcKO tumor 2


title: proband sample with SAG media, replicate 2


title: proband sample with SAG media, replicate 1


title: Organoids_Colon_3

source_name: Epithelial cells from Colon Organoids


title: ASPcKO tumor 1


title: Chip_Colon_1


title: control sample with WNT3A media, replicate 1


title: Organoids_Colon_2


title: Flask_Alveolus_1

value: alveolus epithelial cells


title: control sample with SAG media, replicate 2


title: Young miR-146b Conditional KO

city: Saint Louis

first: Andrea

last: Santeford

state: MO

address: 660 S. Euclid Ave.

department: Opthalmology

institute: Washington University School of Medicine

description:
Single-cell RNA-Seq
mRNA

data_processing:
For miRNA analysis from RNAseq of 3 to 30 months C57Bl/6 WT samples: Sequencing reads were analyzed using Cofactor Genomics EXP software and aligned to the mouse mm9 genome. Overlapping reads were clustered together to assemble expressed loci and provide respective counts and coverage levels for each loci. Coverage was calculated by $alignedBases/$coveredBases. 6x cutoff of cluster depth corresponding to Integer(sequencedBases/integer(genomeBases)). In order to allow cross sample comparative expression between small-RNAs, all counts and expression levels were normalized to the sample with the fewest reads. A pair-wise comparison was performed between samples and logs2 ratios were computed for each expressed small-RNA.
For RNAseq analysis of macrophages from miR-146b knockout and wildtype littermate controls: Second mate was used for sample demultiplexing. Individual single-end fastqs were aligned to mm10 genome using STAR with following options --outFilterMultimapNmax 15 --outFilterMismatchNmax 6 --outReadsUnmapped Fastx --outSAMstrandField All. Gene expression was obtained via ht-seq and DESeq2 for differential expression. Gene expression was obtained using in-house scripts based on MACS and HTSeq (https://github.com/ctlab/quant3p).
For scRNA-seq: Data was analyzed first using Cellranger 3.1.0 and mapped to the mouse mm10 genome with default parameters. Expression matrices were reanalyzed using Monocle3 (v0.2.1) (44). Initial clustering identified minor contamination (<1%) of cells not expressing macrophage markers (Emr1, Mertk, Csf1r, and Cd68) that were removed from further analyses. tSNE-dimension reduction was performed on the top principal components learned from the 317 genes with the highest variance across the cells that passed quality filters (>5000 mRNA counts) and the Louvain method was used to define clusters. The Monocle3 fit_models() function with the following parameters (model_formula_str = "~library + 1") was used to asses differential gene expression.
Genome_build: For miRNA analysis of C57Bl/6 3-30 month macrophages: mmu9 (MGSCv37)
Genome_build: For RNAseq and single-cell RNAseq analyses of Lys2 Cre+/-; miR146b conditional knockout macrophages and littermate controls: mmu10 (GRCm38)
Supplementary_files_format_and_content: mirSeq_3-30months.txt
Supplementary_files_format_and_content: counts.txt
Supplementary_files_format_and_content: *.tar: Tar archives of barcodes.tsv, features.tsv, and matrix.mtx files.

source_name: peritoneal macrophage

growth_protocol: Macrophages were harvested by peritoneal lavage 4 days post-IP injection with 4% Thioglycollate and plated in DMEM containing 10% FBS, 1% L-glutamine, and 1% Penicillin/Streptomycin. Cells were allowed to adhere to the plate overnight, followed by 3-4 washes in DPBS to remove non-adherent cells. Complete DMEM was replaced and cells were rested for 24hours prior to harvest for RNA isolation.

extract_protocol:
Macrophage total mRNA was extracted using RNeasy RNA Isolation kit (Qiagen).
Libraries for single-cell RNA-seq were prepared using 10x Genomics chromium single cell 3' (v3) chemistry.

tag: strain

value: Lyz2 Cre +/- X miR-146b flox/flox; C57Bl/6J

value: 3 months

value: Peritoneal macrophage


title: control sample with SAG media, replicate 3

value: control


title: Young Control

description:
Single-cell RNA-Seq
mRNA


title: Old miR-146b Conditional KO

description:
Single-cell RNA-Seq
mRNA

value: 17 months


title: control sample with control media, replicate 3


title: control sample with SAG media, replicate 1


title: Organoids_Colon_1


title: sCAb33L3

city: MADISON

first: Donna

last: Peters

state: WI- WISCONSIN

address: 1300 UNIVERSITY AVE

department: Pathology & Laboratory Medicine

institute: UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE

data_processing:
Sequencing reads were checked for quality using fastqc
skewer trimming software was used to preprocess raw fastq files.
quality control: combined per cycle base quality
quality control: per cycle base frequencies
quality control: per cycle average base quality
quality control:relative 3k-mer diversity
quality control: Phred quality distribution
quality control:mean quality distribution
quality control: read length distribution
quality control: read occurrence distribution
reads were aligned against the reference genome using STAR (Spliced Transcripts Alignment to a Reference)
Low-abundance genes with a read count < 1 Log CPM (counts per million) in two or more samples were excluded
Each RNA-Seq sample was normalized by the method of trimmed mean M-values
Identification of the differentially expressed genes were annotated using Ensembl Genes version GRCH38.p12
Supplementary_files_format_and_content: Excel worksheet including gene and transcript ENSEMBL IDs, TPM and FPKM data
Supplementary_files_format_and_content: The "edgeRglm_GENE…" and "edgeRglm_ISOFORM…" files in the first four processed data file columns are spread sheets containing the edgeR DGE analysis contrasting the 3 cell lines used in this study. 3 contrasts were examined: CAb3 vs EV, WTb3 vs EV and WTb3 vs CAb3. Contrasts were performed at both the gene and transcript level.
Supplementary_files_format_and_content: The 5th and 6th processed data file columns list files that containin FPKM and TPM data generated from the analysis at both the gene and transcript level.

source_name: TM-1 CAb3

growth_protocol: all cell lines grown in high glucose DME, 10% FBS, 2 mM L-glutamine, 0.2% Primocin, 0.05% gentamicin, 2 mg/mL puromycin

extract_protocol:
All cells were lifted up with trypsin, washed 1X in PBS, pelleted via centrifugation. RNA was isolated from each sample using the RNeasy Micro kit with QIAshredder (Qiagen) according to the manufacturer’s instructions.
RNA libraries were prepared using 1µg of RNA/sample with the TruSeq RNA sample preparation kit (Illumina)

treatment_protocol: all cell lines cultured at 100% confluence in high glucose DME, 1% FBS, 2 mM L-glutamine, 0.2% Primocin, 0.05% gentamicin, 2 mg/mL puromycin for 24 hrs

tag: tissue origin

value: trabecular meshwork

value: SV40 immortalized trabecular meshwork cells

tag: transfected with

value: overexpressing constitutively active b3 integrin


title: control sample with control media, replicate 2


title: 294739

tag: tissue


title: sCAb34L3


title: 293142


title: control sample with control media, replicate 1


title: escape.e2.no3

data_processing:
fastq files were processed using Salmon for alignment-independent quantification
DESeq2 was used for differential gene expression and rlog value generation
Genome_build: mm10
Supplementary_files_format_and_content: TPM count table and DESeq2 normalized rlog value table

source_name: mouse pancreatic tumor cells

growth_protocol: Tumor cells were cultured in vitro with DMEM + 10% FBS

extract_protocol:
RNA was extracted using Qiagen kit
RNA-seq libraries wered prepared by a commercial company, BGI at CHOP at UPenn, with standard protocol

treatment_protocol: no treatment

tag: genetic background


title: escape.e2.no2


title: sCAb32L3


title: ASPcKO tumor 3

value: Flow-cytometry sorted tumor cell

tag: genotype

value: mixed


title: sCAb31L3


title: escape.e2.no1


title: CC_Ic9

city: ChengDu

first: Yong

last: Lv

state: SiChuan

department: Department of pediatric surgery

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: fusiform 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: fusiform choledochal cyst

tag: type

value: Ic


title: escape.e1.no3


title: sWTb34L3

source_name: TM-1 WTb3

value: overexpressing wild type b3 integrin


title: CC_Ic10


title: Old Control

description:
Single-cell RNA-Seq
mRNA

tag: age


title: escape.e1.no2


title: CC_Ic7


title: escape.e1.no1


title: sWTb32L3


title: sWTb33L3


title: sWTb31L3


title: parental.no3


title: parental.no1


title: CC_Ic6


title: parental.no2


title: sEV4L3

source_name: TM-1 EV

value: expressing an empty vector


title: PCNA 211F-2

city: Taichung

first: Shao-Chun

address: No. 6 Xueshi Rd

country: Taiwan

institute: China Medical University Hospital

description:
tumor isolating from 10wks old mouse, single cell performed by GentlMACS and EpCAM antibody captured the epithelial cell.
genes.fpkm_table.txt

data_processing:
The reads were aligned with TopHat 2.0.13 to mouse genome (GRCm38) with default parameters and then were assembled by Cufflink 2.2.1, using Ensembl v90 annotations. and then were assembled by Cufflink 2.2.1, using Ensembl v79 annotations.
Transcript abundance was measured in fragments per kb of exon per million fragments mapped (FPKM).
The differentially expressed genes between WT and Y211F mouse were identified by DESeq2 package of R language.
For the differential expressed genes associated with genotypes, we used fgsea package of R language to perform Gene Set Enrichment Analysis (GSEA) to interpret their biological functions. The significant functions were identified by p < 0.05
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: mammary gland

growth_protocol: Cells were routinely plated at cell density of 100000 in DMEM/F-12 medium (Hyclone, Logon, UT) supplemented with 10%FBS and 1% PSA

extract_protocol:
RNA extraction is performed by Direct-zol RNA MiniPrep plus (Zymo Research, USA). Purified RNA was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology,USA), qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 LabChip kit (Agilent Technologies, USA) and sequenced on Illumina NovaSeq 6000 system
All RNA sample preparation procedures were carried out to the offical Illumina protocol. Agilent's SureSelect Strand-Specific RNA Library Preparation Kit were used for library construction folllowed by AMPure XP Beads size selection.
The sequence was directly determined using Illumina's sequencing-by-synthessis technology. Sequencing data were generated by Welgene's pipeline based on Illumina's basecalling program bc12fastq v2.2.0

value: epithelial adenocarcinoma

tag: molecular subtype

value: luminal

tag: genotype/variation


title: CC_Ic5


title: sEV3L3


title: CC_Ic3


title: CC_Ic2


title: sEV1L3


title: 259899

source_name: Breast cancer biopsy (pre-treatment)

value: breast cancer

value: Control Arm


title: 233191


title: CC_Ic4


title: sEV2L3


title: PCNA 211F-1


title: PCNA WT-2

value: WT


title: CC_Ic1


title: CC_Ic8


title: CC_Ia12

source_name: cystic choledochal cysts

value: cystic choledochal cyst

value: Ia


title: patient10

first: JAE WON

last: CHO

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: wild type


title: patient9

description: single-cell RNA sequencing


title: patient7

description: single-cell RNA sequencing

value: mutation


title: PCNA WT-1


title: CC_Ia10


title: CC_Ia9


title: patient5

description: single-cell RNA sequencing


title: patient6

description: single-cell RNA sequencing


title: CC_Ia7


title: CC_Ia6


title: patient4

description: single-cell RNA sequencing


title: CC_Ia8


title: OAT rep2

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

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

source_name: CD11b+ FACS sorted

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

tag: treatment


title: CHECK rep2

description: GL261 luc+ tdT+ implanted mice


title: OAT rep1

description: GL261 luc+ tdT+ implanted mice


title: COM rep3

description: GL261 luc+ tdT+ implanted mice

value: COMB


title: CC_Ia5


title: patient3

description: single-cell RNA sequencing


title: COM rep2

description: GL261 luc+ tdT+ implanted mice


title: 219545

tag: hr

tag: mp


title: CC_Ia4


title: patient1

description: single-cell RNA sequencing


title: patient8

description: single-cell RNA sequencing


title: 172168

tag: pcr

tag: arm


title: 252748


title: CTR rep2

description: GL261 luc+ tdT+ implanted mice

tag: strain

value: CTR


title: CHECK rep1

description: GL261 luc+ tdT+ implanted mice


title: CC_Ia11


title: CTR rep1

description: GL261 luc+ tdT+ implanted mice


title: CC_Ia2


title: LiverPBS_3_5

city: Fukuoka

first: Fumiko

last: Matsuzaki

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

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.

value: 10 week

value: IP of PBS

value: Liver (left lobe)