title: 4mo Apoe(fl/fl) 5xFAD Csf1r-cre Hippocampus 4

tag: strain

value: C57BL/6, Apoe(fl/fl), 5xFAD, Csf1r-cre

tag: brain region

value: Hippocampus


title: WCA075

status: Public on Oct 15 2021

type: RNA

city: Boston

first: Sonu

last: Subudhi

state: MA

address: 100 Blossom St, Cox 7

department: Radiation Oncology

country: USA

institute: Massachusetts General Hospital

data_processing: Nanostring raw data was normalized to housekeeping genes (CLTC, GUSB, PGK1, SDHA and TUBB).

molecule: total RNA

organism: Homo sapiens

source_name: Human liver

extract_protocol: RNA extraction was performed on 5-20 μg of liver tissue using the miRNeasy Mini Kit (Qiagen) for flash-frozen samples or the RNA-later liver or High Pure FFPET RNA Isolation Kit (Roche Life Science) for Formalin-Fixed Paraffin-Embedded tissue (FFPET) samples, according to manufacturer’s instructions. RNA quantity and quality were assessed using an Agilent 2100 bioanalyzer (Santa Clara, CA). RIN numbers, ranging from 1.5 to 9 are appropriate for use with the nCounter Technology

tag: tissue

value: Human liver

tag: race

value: White

tag: bmi

tag: age

tag: Sex

value: Female

tag: diabetes

value: Yes

tag: alt

tag: ast

tag: nafld stage


title: WCA201


title: WCA395

value: Male

value: No


title: WCA129

value: Normal


title: CON-01a-PT

type: genomic

city: São Paulo

first: Caroline

middle: Perez

last: Camilo

state: São Paulo

address: Rua Doutor Ovídio Pires de Campos, 785

department: Institute of Psychiatry

country: Brazil

institute: University of São Paulo

hyb_protocol: DNA was bisulfite-converted using the EZ DNA methylation kit (Zymo Research, Irvine, California, USA), according to the manufacturer's instructions and hybridized in the Illumina Infinium HumanMethylation450 BeadChip (Illumina Inc., San Diego, California, USA), using standard Illumina protocol.

scan_protocol: Arrays were scanned with the iScan SQ scanner (Illumina).

data_processing:
Data processing were performed using GenomeStudio software (v.2011.1), with the methylation module v.1.9.0 (Illumina).
Average beta values.

label: Cy3, Cy5

molecule: genomic DNA

source_name: Control, ID 01a, DNA_putamen

label_protocol: Standard Illumina protocol.

extract_protocol: DNA was extracted using QIAsymphony DNA Kit (Qiagen, Hilden, Mettmann, Germany) on QIAsymphony platform, according to the manufacturer’s instructions.

tag: sample group

value: Control

tag: gender

tag: education (years)

tag: alcohol

value: Never

tag: tobacco

tag: brain volume (ml)

tag: brain weight (g)

tag: ph

tag: hemisphere

value: Right


title: WCA370

tag: tissue

tag: race


title: CON-01a-NAC

source_name: Control, ID 01a, DNA_nucleus accumbens

value: Brain_nucleus accumbens

tag: age


title: WCA396

tag: bmi

tag: Sex


title: 12mo Apoe(fl/fl) Hippocampus 1

type: SRA

city: Irvine

first: Kim

last: Green

state: CA

address: 3208 Biological Sciences 3

department: Neurobiology and Behavior

institute: University of California, Irvine

library_source: transcriptomic

data_processing:
Illumina HiSeq4000 was used to produce 50bp single-end reads.
Sequenced reads mapped to mm10 whole genome using STAR aligner.
featureCounts were calculated using function of the Rsubread package in R.
After filtering out low-count genes, count distributions were scaled using the calcNormFactors function of the edgeR package.
plotMDS function of the limma package in R was used to perform principal component analysis. Reads Per Kilobase of exon per Megabase of library size (RPKM)  were prepared and fitted to linear models using the voom and lmfit functions.
Genome_build: mm10
Supplementary_files_format_and_content: Excel Workbook file includes RPKM values for all Samples.

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
Brains were removed, microdissected into cortex, hippocampus, and thalamus/striatum, and flash frozen on dry ice.  RNA was extracted using Rneasy Mini Kit (Qiagen). cDNA synthesis, amplification, library construction and sequencing were performed by Novogene Inc. using Illumina NovaSeq and HiSeq platforms with paired-end 150 bp (PE 150) sequencing strategy.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: C57BL/6, Apoe(fl/fl)

tag: brain region


title: CON-01a-ACC

source_name: Control, ID 01a, DNA_anterior cingulate gyrus

value: Brain_anterior cingulate gyrus


title: 4mo Apoe(fl/fl) 5xFAD Csf1r-cre Hippocampus 3


title: 12mo Apoe(fl/fl) Csf1r-cre Hippocampus 1

value: C57BL/6, Apoe(fl/fl), Csf1r-cre


title: 4mo Apoe(fl/fl) 5xFAD Hippocampus 1

value: C57BL/6, Apoe(fl/fl), 5xFAD


title: 4452_SFC_MCI_2

city: Grand Rapids

first: Betul

last: Kara

state: Michigan

address: 400 Monroe Ave NW

institute: Michigan State University

description: Male, age: 72.7, Mild Cognitive Impairment, with various cognitive diagnoses and scores

hyb_protocol: Labeled cDNA (4 µg) was hybridized to NimbleGen 12 x 135K human arrays for 18 hrs at 42°C

scan_protocol: GenePix 4200A scanner.

data_processing:
log2 transformed data were batch corrected using comBat Bioconductor, sva v3.4
Probe intensity levels were quantified with RMA preprocessing (NimbleScan v2.5, Roche)
RMA data are Pre comBat and Quantile Normalization

source_name: Superior Frontal Cortex

label_protocol: Double-stranded cDNA was prepared and labeled with Cy3 (One-color DNA Labeling Kit, Nimblegen)

extract_protocol: 40-50 mg of frozen tissue was cut on a platform in dry ice and RNA was extracted from the samples using a total RNA isolation kit (Ambion)

treatment_protocol: Frozen frontal cortex (BA10) tissue from NCI, MCI, and mild/moderate AD cases (n = 12/group) representing both genders was acquired postmortem from participants in the Rush Religious Orders Study, a longitudinal clinical pathologic study of aging and AD in elderly Catholic clergy

tag: diagnosis

value: MCI

tag: cogdx

tag: globcog

tag: cerad

tag: braak

tag: niareagan


title: WCA386

value: Black or African American

tag: diabetes

tag: alt

tag: ast

tag: nafld stage


title: 4452_SFC_MCI_1


title: 4mo Apoe(fl/fl) 5xFAD Hippocampus 5

value: Hippocampus


title: WCA305

tag: tissue

value: Human liver

value: Other

value: Steatosis


title: 579_SFC_AD_2

description: Male, age: 83.8, Alzheimers Disease, with various cognitive diagnoses and scores

value: AD

value: Male


title: 4mo Apoe(fl/fl) 5xFAD Hippocampus 3


title: WCA393

tag: race

value: Female

value: No

value: Normal


title: 4mo Apoe(fl/fl) 5xFAD Csf1r-cre Hippocampus 2

value: C57BL/6, Apoe(fl/fl), 5xFAD, Csf1r-cre


title: 4mo Apoe(fl/fl) 5xFAD Hippocampus 4


title: 4mo Apoe(fl/fl) 5xFAD Csf1r-cre Hippocampus 1


title: WCA367

value: White

tag: age


title: 4mo Apoe(fl/fl) Csf1r-cre Hippocampus 6


title: WCA136

tag: bmi


title: 4287_SFC_MCI_2_2

description: Female, age: 90, Mild Cognitive Impairment, with various cognitive diagnoses and scores

tag: Sex


title: 4mo Apoe(fl/fl) 5xFAD Hippocampus 2

tag: strain


title: 579_SFC_AD_1


title: WCA234


title: WCA319


title: 718_SFC_MCI_2

description: Male, age: 80.5, Mild Cognitive Impairment, with various cognitive diagnoses and scores


title: WCA155

value: Yes


title: WCA390


title: 718_SFC_MCI_1


title: 4mo Apoe(fl/fl) Csf1r-cre Hippocampus 4

tag: brain region


title: 3863_SFC_AD_2

description: Male, age: 88, Alzheimers Disease, with various cognitive diagnoses and scores

tag: diagnosis


title: control_diet_training_rep8

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from liver of mice treated with control diet for 6 weeks, training, biological replicate 8

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

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

data_processing: SST-RMA gene-level probeset summary with standard settings of the Thermo Fisher Scientific Expression Console software (v.1.4.1.46)

label: biotin

source_name: liver, control diet for 6 weeks, training, biological replicate 8

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

growth_protocol: Male C57BL/6N mice were purchased at an age of 9 weeks from Charles River (Sulzfeld, Germany). Mice were maintained on a 12-h light-dark cycle with free access to water and food.

extract_protocol: Total RNA was isolated employing the RNeasy Mini kit (Qiagen, Hilden, Germany)

treatment_protocol: After 2 weeks of treadmill acclimatization of all animals, mice were randomized to 4 groups of n=8 for 6 weeks of dietary intervention and treadmill training: control diet, sedentary (CON_SED); control diet, training (CON_TRAIN); high-energy diet, sedentary (HED_SED); and high-energy diet, training (HED_TRAIN). The high-energy diet (Ssniff (Soest, Germany) E15744-344; 45 kJ% fat, 35 kJ% carbohydrates, 20 kJ% protein; corresponding to Research Diets D12451) contained additional sugar (10 weight% sucrose) and fat (20 weight% lard) and was otherwise similar to the matched control diet (E157453-04 / D12450J; 10 kJ% fat, 70 kJ% carbohydrates, 20 kJ% protein). Chow and tap water were provided ad libitum. Treadmill training was performed 3 times per week, separated by at least one day of rest, for 1 h and during the animals’ active phase, as previously described (Hoene et al., 2009). Treadmill conditions were: After 5 min warmup, 10 m/min at 12° uphill slope in week 1; 11 m/min, 12° in week 2; 12 m/min, 12° in week 3; 12 m/min, 10° in week 4, 12 m/min, 9° in week 5 and 12 m/min, 8° slope in week 6. After 5 weeks, an i.p. glucose tolerance test was performed as previously described, after 16h of fasting and with 1.5 g glucose (20% solution; B. Braun, Melsungen, Germany) per kg body weight. After 6 weeks, mice were analgosedated (150 mg ketamine and 10 mg xylazine /kg body weight) and exsanguinated by decapitation before removal of organs, which were immediately processed or flash-frozen in liquid nitrogen. Both glucose tolerance test and organ collection took place 48h after the preceding training session.

value: liver

value: 17 weeks

tag: gender

value: male

tag: genotype

value: wild type


title: control_diet_training_rep7

description: Gene expression data from liver of mice treated with control diet for 6 weeks, training, biological replicate 7

source_name: liver, control diet for 6 weeks, training, biological replicate 7


title: 4287_SFC_MCI_2_1 [350]

value: MCI

tag: cogdx

tag: globcog

tag: cerad


title: 3499_SFC_MCI_1

description: Male, age: 89.2, Mild Cognitive Impairment, with various cognitive diagnoses and scores

tag: braak

tag: niareagan


title: control_diet_training_rep6

description: Gene expression data from liver of mice treated with control diet for 6 weeks, training, biological replicate 6

source_name: liver, control diet for 6 weeks, training, biological replicate 6


title: 4mo Apoe(fl/fl) Hippocampus 6

value: C57BL/6, Apoe(fl/fl)

value: Hippocampus


title: 4mo Apoe(fl/fl) Hippocampus 7


title: control_diet_training_rep2

description: Gene expression data from liver of mice treated with control diet for 6 weeks, training, biological replicate 2

source_name: liver, control diet for 6 weeks, training, biological replicate 2


title: control_diet_training_rep3

description: Gene expression data from liver of mice treated with control diet for 6 weeks, training, biological replicate 3

source_name: liver, control diet for 6 weeks, training, biological replicate 3


title: 3400_SFC_NCI_2

description: Female, age: 82.9, NoCognitive Impairment, with various cognitive diagnoses and scores

value: NCI


title: control_diet_training_rep1

description: Gene expression data from liver of mice treated with control diet for 6 weeks, training, biological replicate 1

source_name: liver, control diet for 6 weeks, training, biological replicate 1


title: 3400_SFC_NCI_1


title: 4mo Apoe(fl/fl) Hippocampus 4


title: control_diet_sedentary_rep8

description: Gene expression data from liver of mice treated with control diet for 6 weeks, sedentary, biological replicate 8

source_name: liver, control diet for 6 weeks, sedentary, biological replicate 8


title: 3863_SFC_AD_1


title: control_diet_training_rep4

description: Gene expression data from liver of mice treated with control diet for 6 weeks, training, biological replicate 4

source_name: liver, control diet for 6 weeks, training, biological replicate 4


title: 4mo Apoe(fl/fl) Csf1r-cre Hippocampus 5

value: C57BL/6, Apoe(fl/fl), Csf1r-cre


title: 4mo Apoe(fl/fl) Csf1r-cre Hippocampus 2


title: 4mo Apoe(fl/fl) Csf1r-cre Hippocampus 1


title: 4mo Apoe(fl/fl) Hippocampus 8


title: control_diet_sedentary_rep6

description: Gene expression data from liver of mice treated with control diet for 6 weeks, sedentary, biological replicate 6

source_name: liver, control diet for 6 weeks, sedentary, biological replicate 6


title: 4mo Apoe(fl/fl) Hippocampus 5


title: 4mo Apoe(fl/fl) Csf1r-cre Hippocampus 3


title: 3499_SFC_MCI_2


title: 4mo Apoe(fl/fl) Hippocampus 3


title: 4mo Apoe(fl/fl) Hippocampus 2


title: 2701_SFC_AD_2_1 [320]

description: Male, age: 86.2, Alzheimers Disease, with various cognitive diagnoses and scores

value: AD


title: control_diet_sedentary_rep4

description: Gene expression data from liver of mice treated with control diet for 6 weeks, sedentary, biological replicate 4

source_name: liver, control diet for 6 weeks, sedentary, biological replicate 4


title: 2539_SFC_AD_1

description: Female, age: 85.6, Alzheimers Disease, with various cognitive diagnoses and scores


title: control_diet_training_rep5

description: Gene expression data from liver of mice treated with control diet for 6 weeks, training, biological replicate 5

source_name: liver, control diet for 6 weeks, training, biological replicate 5


title: 2539_SFC_AD_2


title: 4287_SFC_MCI_2_1

description: Female, age: 90, Mild Cognitive Impairment, with various cognitive diagnoses and scores


title: IM5.r3

city: Ramat Gan

first: Nitzan

last: Gonen

address: Bar-Ilan University

department: Life Sciences

country: Israel

institute: Bar-Ilan University

description: Bulk RNA-Seq

data_processing:
Cutadapt v1.9.1 (Martin, 2011) was used to trim adapter sequences from reads with the following options: -a AGATCGGAAGAGC –A AGATCGGAAGAGC -e 0.1 –q 10.
Gene-level abundance estimates were calculated with RSEM v1.3.0 (Li and Dewey, 2011), using STAR v2.5.2a (Dobin et al., 2013) to align reads against the GRCm38 genome assembly with Ensembl release 86 transcript annotations.
The pipeline used to create the abundance estimates is feely available here: https://github.com/crickbabs/BABS-RNASeq/tree/c3c13518a009fba9aa8afa228fab8cb779815ca5
Genome_build: GRCm38
Supplementary_files_format_and_content: *.genes.results.txt: RSEM gene-level abundance estimates including expected_count, TPM and FPKM. Gene ids are represented by Ensembl v86 identifiers.

source_name: Intermediate mesoderm-like cells condition 5 (FGF + BMP + RA + A + CHIR)

growth_protocol:
ESCs were routinely cultured on 0.1% Gelatin coated dishes with 2i/LIF media. For differentiation, ESCs cultured on 2i/LIF were seeded for 1 passage on dishes coated with Gel-MEF: 0.1% gelatin coating for 15 minutes followed by coating with MEF media for at least 2 hours [DMEM, 10% FCS, P/S, L-Glu]. ESCs were seeded in KSR media [Ad-DMEM/F12, 20% knock out serum replacement, P/S, L-Glu, Beta-mercaptoethanol and 1000 U/ml of LIF].
For epiblast-like cell (EpiLC) differentiation, 2.5x10^5 cells were seeded on Gel-MEF coated 6-well dish wells. EpiLC differentiation was performed as previously described (Hayashi et al., 2011). Briefly, EpiLCs were induced by culturing ESC in N2B27 minus Vitamin A medium containing 20 ng/ml activin A, 12 ng/ml bFGF and 1% knockout serum replacement for 2.5 days (~60 hours).
Early mesoderm differentiation was induced by growing the cells as previously described (Bernardo et al., 2011) in a chemically defined medium (CDM) containing PVA and supplemented with 20 ng/ml bFGF, 10 μM LY294002 and 10 ng/ml BMP4, named FLyB for 36 hours.

extract_protocol:
Total RNA was extracted using Trizol according to the manufacturer’s instructions. RNA quantity and quality were quantified using Nano-drop, Qbit and Tape station.
Libraries were prepared using the TruSeq Library Prep kit V2 (Illumina) according to the manufacturer’s instructions. Libraries were sequenced on the Illumina HiSeq 4000 following the manufacturer's protocols (Paired end, 75 bp).

treatment_protocol:
IM1: bFGF (5ng/ml) + BMP (20ng/ml).
IM2: bFGF (5ng/ml) + BMP (20ng/ml) + RA (100nM) + Activin A (10ng/ml).
IM3: bFGF (5ng/ml) + BMP (20ng/ml) + RA (100nM).
IM4: bFGF (5ng/ml) + BMP (20ng/ml) + RA (100nM) + CHIR 0.3 μM.
IM5: bFGF (5ng/ml) + BMP (20ng/ml) + RA (100nM) + Activin A (10ng/ml) + CHIR (0.3 μM).

tag: cell type

value: ES-derived intermediate mesoderm

tag: treatment

value: Condition 5

value: F1:C57BL/6 x CBA

value: Tesco-CFP; R26-rtTA XY cells, clone 7


title: control_diet_sedentary_rep3

description: Gene expression data from liver of mice treated with control diet for 6 weeks, sedentary, biological replicate 3

source_name: liver, control diet for 6 weeks, sedentary, biological replicate 3

tag: tissue


title: 2701_SFC_AD_1_1

value: Male


title: 2798_SFC_AD_1

description: Male, age: 87.4, Alzheimers Disease, with various cognitive diagnoses and scores


title: IM5.r2

description: Bulk RNA-Seq


title: iSC_2TF.r2

description: Bulk RNA-Seq

source_name: Induced embryonic Sertoli-like cells (induced by overexpression of Nr5A1 and Dmrt1)

value: ES-derived induced embryonic Sertoli-like cells


title: IM5.r1

description: Bulk RNA-Seq


title: 1770_SFC_AD_1_2

description: Male, age: 80.3, Alzheimers Disease, with various cognitive diagnoses and scores


title: 2798_SFC_AD_2


title: 4287_SFC_MCI_1_1

value: Female


title: 1988_SFC_NCI_2_2

description: Female, age: 92.2, NoCognitive Impairment, with various cognitive diagnoses and scores


title: IM4.r2

description: Bulk RNA-Seq

source_name: Intermediate mesoderm-like cells condition 4 (FGF + BMP + RA + CHIR)

value: Condition 4


title: iSC_2TF.r1

description: Bulk RNA-Seq


title: 4mo Apoe(fl/fl) Hippocampus 1

source_name: Hippocampus


title: 2701_SFC_AD_2_1

source_name: Superior Frontal Cortex


title: 1770_SFC_AD_1_1


title: control_diet_sedentary_rep5

description: Gene expression data from liver of mice treated with control diet for 6 weeks, sedentary, biological replicate 5

source_name: liver, control diet for 6 weeks, sedentary, biological replicate 5

value: liver

value: 17 weeks


title: high_energy_diet_training_rep5

description: Gene expression data from liver of mice treated with high energy diet for 6 weeks, training, biological replicate 5

source_name: liver, high energy diet for 6 weeks, training, biological replicate 5

value: male

value: wild type


title: high_energy_diet_training_rep3

description: Gene expression data from liver of mice treated with high energy diet for 6 weeks, training, biological replicate 3

source_name: liver, high energy diet for 6 weeks, training, biological replicate 3


title: 1474_SFC_NCI_1

description: Male, age: 76.3, NoCognitive Impairment, with various cognitive diagnoses and scores


title: control_diet_sedentary_rep2

description: Gene expression data from liver of mice treated with control diet for 6 weeks, sedentary, biological replicate 2

source_name: liver, control diet for 6 weeks, sedentary, biological replicate 2


title: 1988_SFC_NCI_2_1


title: control_diet_sedentary_rep7

description: Gene expression data from liver of mice treated with control diet for 6 weeks, sedentary, biological replicate 7

source_name: liver, control diet for 6 weeks, sedentary, biological replicate 7


title: IM4.r1

description: Bulk RNA-Seq


title: IM3.r1

description: Bulk RNA-Seq

source_name: Intermediate mesoderm-like cells condition 3 (FGF + BMP + RA)

value: Condition 3


title: 1770_SFC_AD_2_1


title: high_energy_diet_sedentary_rep6

description: Gene expression data from liver of mice treated with high energy diet for 6 weeks, sedentary, biological replicate 6

source_name: liver, high energy diet for 6 weeks, sedentary, biological replicate 6


title: high_energy_diet_training_rep6

description: Gene expression data from liver of mice treated with high energy diet for 6 weeks, training, biological replicate 6

source_name: liver, high energy diet for 6 weeks, training, biological replicate 6


title: high_energy_diet_training_rep7

description: Gene expression data from liver of mice treated with high energy diet for 6 weeks, training, biological replicate 7

source_name: liver, high energy diet for 6 weeks, training, biological replicate 7


title: 1291_SFC_AD_1

description: Male, age: 83.4, Alzheimers Disease, with various cognitive diagnoses and scores


title: high_energy_diet_training_rep2

description: Gene expression data from liver of mice treated with high energy diet for 6 weeks, training, biological replicate 2

source_name: liver, high energy diet for 6 weeks, training, biological replicate 2


title: IM4.r3

description: Bulk RNA-Seq


title: IM3.r2

description: Bulk RNA-Seq


title: IM2.r2

description: Bulk RNA-Seq

source_name: Intermediate mesoderm-like cells condition 2 (FGF + BMP + RA + A)

value: Condition 2


title: 959_SFC_NCI_1

description: Female, age: 85.2, NoCognitive Impairment, with various cognitive diagnoses and scores

value: NCI


title: 1770_SFC_AD_2_2


title: high_energy_diet_training_rep4

description: Gene expression data from liver of mice treated with high energy diet for 6 weeks, training, biological replicate 4

source_name: liver, high energy diet for 6 weeks, training, biological replicate 4


title: IM3.r3

description: Bulk RNA-Seq


title: 1988_SFC_NCI_1_1


title: 1291_SFC_AD_2


title: IM2.r3

description: Bulk RNA-Seq


title: IM1.r2

description: Bulk RNA-Seq

source_name: Intermediate mesoderm-like cells condition 1 (FGF + BMP)

value: Condition 1


title: IM1.r3

description: Bulk RNA-Seq


title: IM2.r1

description: Bulk RNA-Seq


title: mouse_FFPE_brain_hippocampus_7

city: Solna

first: Ludvig

middle: Ale

last: Larsson

state: Stockholm

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: SciLifeLab

data_processing:
library strategy: Spatial Transcriptomics (10x Visium)
bcl2fastq command line tool was used for base calling
Sequence reads were trimmed for adapter sequence (Template Switch Oligo) and polyA homopolymers using cutadapt (-g XAAGCAGTGGTATCAACGCAGAGTACATGGG;max_error_rate=0.1 -a AAAAAAAAAA ;max_error_rate=0--overlap 5 -n 2)
Reads were mapped, annotated and demultiplexed using the spaceranger v1.0.0 command line tool
Annotated reads were quantified and mapped to the Hematoxylin and Eosin image using the spaceranger v1.0.0 command line tool
Genome_build: mm10 for Mus musculus and GRCh38 for Homo sapiens
Supplementary_files_format_and_content: Matrix with raw counts for every gene and every spot, filtered to include spots under tissue
Supplementary_files_format_and_content: Hematoxylin and Eosin (HE) image in JPG format
Supplementary_files_format_and_content: Low resolution Hematoxylin and Eosin (HE) image in PNG format
Supplementary_files_format_and_content: Scalefactors in json format
Supplementary_files_format_and_content: Table with array and pixel coordinates

molecule: polyA RNA

source_name: FFPE mouse brain

extract_protocol:
Tissues were decrosslinked and enzymatically permeabilized
RNA libraries were prepared for sequencing following the 10x Genomics Visium protocol

treatment_protocol: Tissues were sectioned and placed on a glass slide followed by HE staining

value: hippocampus

tag: sample type

value: FFPE


title: mouse_FFPE_brain_hippocampus_6


title: mouse_FFPE_brain_hippocampus_5


title: mouse_FFPE_brain_hippocampus_4


title: control_diet_sedentary_rep1

description: Gene expression data from liver of mice treated with control diet for 6 weeks, sedentary, biological replicate 1

source_name: liver, control diet for 6 weeks, sedentary, biological replicate 1

tag: age


title: IM1.r1

description: Bulk RNA-Seq

value: ES-derived intermediate mesoderm


title: high_energy_diet_training_rep1

description: Gene expression data from liver of mice treated with high energy diet for 6 weeks, training, biological replicate 1

source_name: liver, high energy diet for 6 weeks, training, biological replicate 1


title: high_energy_diet_sedentary_rep2

description: Gene expression data from liver of mice treated with high energy diet for 6 weeks, sedentary, biological replicate 2

source_name: liver, high energy diet for 6 weeks, sedentary, biological replicate 2


title: M_FLyB.r2

description: Bulk RNA-Seq

source_name: Early mesodermal-like cells

value: ES-derived early mesodermal cells

value: F1:C57BL/6 x CBA


title: M_FLyB.r1

description: Bulk RNA-Seq

value: Tesco-CFP; R26-rtTA XY cells, clone 7


title: high_energy_diet_sedentary_rep1

description: Gene expression data from liver of mice treated with high energy diet for 6 weeks, sedentary, biological replicate 1

source_name: liver, high energy diet for 6 weeks, sedentary, biological replicate 1


title: high_energy_diet_sedentary_rep3

description: Gene expression data from liver of mice treated with high energy diet for 6 weeks, sedentary, biological replicate 3

source_name: liver, high energy diet for 6 weeks, sedentary, biological replicate 3


title: high_energy_diet_sedentary_rep4

description: Gene expression data from liver of mice treated with high energy diet for 6 weeks, sedentary, biological replicate 4

source_name: liver, high energy diet for 6 weeks, sedentary, biological replicate 4


title: high_energy_diet_sedentary_rep5

description: Gene expression data from liver of mice treated with high energy diet for 6 weeks, sedentary, biological replicate 5

source_name: liver, high energy diet for 6 weeks, sedentary, biological replicate 5


title: 959_SFC_NCI_2

source_name: Superior Frontal Cortex


title: L428-48H

city: Madrid

first: Sara

last: Fernández Robledo

state: Madrid

address: C/ Arturo Soria, 270

country: Spain

institute: Fundación MD Anderson

description: 48 hours of Ruxolitinib treatment

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 Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°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 (G2505B) 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: Scanning, quantification, and data normalization were done using a G4900DA SureScan Microarray Scanner System and Feature Extraction v12.0 (Agilent Technologies).   The extracted data were normalized and analyzed with the Subió platform (Subió Inc.). The normalization of one-color arrays was the Percentile Shift system.

source_name: L428 cells

label_protocol: Whole-transcriptome expression assays were performed using SurePrint G3 Human Gene Expression arrays 8×60K v2 (Agilent Technologies, Santa Clara, CA), profiling approximately 32,000 transcripts. Briefly, 200 ng of total RNA was isolated from all the untreated cell lines and after 6, 12, 24 and 48 h of drug incubation with ruxolitinib at the IC50 doses. Reverse transcription and cDNA labeling with Cy3-CTP were carried out according to the manufacturer’s instructions.

growth_protocol: Hodgkin lymphoma cell lines were growth in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: 200 ng of total RNA was isolated using the Recover All kit (ThermoFisher) following the manufacturer's recommendations.

treatment_protocol: Cell lines were incubated with or without ruxolitinib (HY-50856, MedChem, Monmouth Junction, NJ).

tag: agent

value: Ruxolitinib

tag: time point

value: 48 hours


title: KMH2-48H

description: 48 hours of Ruxolitinib treatment

source_name: KMH2 cells


title: L591-48H

description: 48 hours of Ruxolitinib treatment

source_name: L591 cells


title: mouse_FFPE_brain_hippocampus_3


title: EpiSC.r3

description: Bulk RNA-Seq

source_name: Epiblast Stem cell-like cells

value: ES-derived Epiblast stem cells

tag: strain


title: mouse_FFPE_brain_hippocampus_1


title: L540-48H

description: 48 hours of Ruxolitinib treatment

source_name: L540 cells


title: mouse_FFPE_brain_hippocampus_2


title: EpiSC.r2

description: Bulk RNA-Seq


title: PFA fixed lung_organoid_4

source_name: PFA fixed lung organoid

value: lung organoid

value: PFA fixed


title: L1236-48H

description: 48 hours of Ruxolitinib treatment

source_name: L1236 cells


title: L591-24H

description: 24 hours of Ruxolitinib treatment

value: 24 hours


title: M_FLyB.r3

description: Bulk RNA-Seq


title: KMH2-24H

description: 24 hours of Ruxolitinib treatment


title: L428-24H

description: 24 hours of Ruxolitinib treatment


title: EpiSC.r1

description: Bulk RNA-Seq


title: ESC.r3

description: Bulk RNA-Seq

source_name: Mouse Embryonic stem cells

value: ESC


title: ESC.r2

description: Bulk RNA-Seq


title: PFA fixed lung_organoid_2


title: PFA fixed lung_organoid_1


title: ESC.r1

description: Bulk RNA-Seq


title: PFA fixed kidney_organoid_3

source_name: PFA fixed kidney organoid

value: kidney organoid


title: PFA fixed kidney_organoid_1


title: PFA fixed kidney_organoid_2


title: pancreas TCF1lo_4 [PA-ND-2]

city: New York

first: Andrea

last: Schietinger

state: NY

address: 1275 York Avenue

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The quality of the sequenced reads was assessed with FastQC and QoRTs (for RNA-seq samples) (Andrews 2010, Hartley and Mullikin (2015)).
DNA sequencing reads were aligned with default parameters to the mouse reference genome (GRCm38) using STAR (Dobin et al. 2013). Gene expression estimates were obtained with featureCounts using composite gene models (union of the exons of all transcript isoforms per gene) from Gencode (version M17) (Liao, Smyth, and Shi 2014, Harrow et al. (2012)).
Differentially expressed genes (DEG) were determined with DESeq2.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include raw abundance values for each sample as obtained from featureCounts

source_name: pancreas TCF1lo

extract_protocol:
CD8+ T cells were isolated from the pancreatic lymph node or pancreas via FACS and sorted into FCS, washed with PBS, and resuspended in Trizol and frozen.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: NOD/ShiLtJ

value: 16 weeks

tag: mouse status

value: nondiabetic

value: pancreas

value: CD8+ T lymphocyte


title: pancreas TCF1lo_3 [PA-ND-1]


title: 10x: PBMC_PLA

city: Chicago

first: Hoang Van

last: Phan

state: Illinois

address: 5640 S Ellis Ave

department: Priztker School of Molecular Engineering

institute: The University of Chicago

description: Prox-seq analysis of PBMCs using 10x pipeline

data_processing:
Library strategy: PLA-seq
Sequencing data was aligned using a custom Java program (https://github.com/tay-lab/Prox-seq) to identify the Prox-seq probe barcodes. The list of probe barcodes is in Proxseq_probe_barcodes.xlsx
Count data was analyzed in Python and RStudio. Cells with fewer total UMI count lower than 10 were discarded.
Protein data caclulated from PLA count data was used to cluster the cells in Seurat v4.0.4
Genome_build: Human GRCh38
Supplementary_files_format_and_content: tab-separated text file

source_name: Peripheral blood mononuclear cells

growth_protocol: PBMCs are kept in RPMI media with 10% FBS

extract_protocol:
PLA products were extracted from single cells following 10x pipeline
Sequencing library was prepared from PLA products using PCR

value: Primary human white blood cells

tag: donor type

value: Healthy donor

tag: passages

tag: molecule subtype

value: RNA and protein


title: pancreas TCF1lo_6 [PA-ND-4]


title: PFA fixed lung_organoid_3


title: pancreas TCF1lo_2 [PA-D-4]

value: 20 weeks

value: diabetic


title: L591-12H

description: 12 hours of Ruxolitinib treatment

value: Ruxolitinib

value: 12 hours


title: pancreas TCF1lo_1 [PA-D-1]


title: naïve_3 [LNnaive-3]

source_name: naïve

value: 6 weeks

value: pancreatic lymph node


title: naïve_2 [LNnaive-2]


title: pancreas TCF1lo_5 [PA-ND-3]


title: L1236-24H

description: 24 hours of Ruxolitinib treatment

value: 24 hours


title: L428-12H

description: 12 hours of Ruxolitinib treatment


title: pLN TCF1lo_3 [LN14-LO-C]

source_name: pLN TCF1lo

value: 14 weeks


title: naïve_1 [LNnaive-1]


title: L1236-12H

description: 12 hours of Ruxolitinib treatment


title: KMH2-12H

description: 12 hours of Ruxolitinib treatment


title: KMH2-6H

description: 6 hours of Ruxolitinib treatment

value: 6 hours


title: L540-12H

description: 12 hours of Ruxolitinib treatment


title: L1236-6H

description: 6 hours of Ruxolitinib treatment


title: L591-6H

description: 6 hours of Ruxolitinib treatment


title: PDGF-BB_RNA-3

city: Pittsburgh

first: Delphine

last: Gomez

state: PA

address: 200 Lothrop Street

department: Medicine, division of Cardiology

institute: University of Pittsburgh

description: RNAseq_Expression Browser_TPM.xlsx

data_processing:
The 75 bp paired-end reads were mapped to Rattus Norvegicus reference genome Rn6 and gene ID were mapped to Rattus Norvegicus ensembl_v91 using default setting by CLC Genomic Workbench (Qiagen).
All mapped reads were normalized by Trimmed Mean of M values (TMM normalization) for differential gene expression analysis in CLC Genomic Workbench (Qiagen)
Genome_build: Rn6
Supplementary_files_format_and_content: Matrix table of normalized gene counts (TPM) for each sample

organism: Rattus norvegicus

source_name: Aortic SMC

growth_protocol: Cell lines were cultured in growth medium (DMEM/F12, Gibco) supplemented with FBS (10%, Corning), L-glutamine (1.6 mM, Gibco) and penicillin-streptomcyin (100 U/ml, Gibco). Before harvesting for RNAseq, cells were starved in a serum-free, insulin-free medium (ISFM)  for 72 hours.

extract_protocol:
RNA was extracted from cells using Rneasy Mini Kit (Qiagen) following manufacture's protocol. Genomic DNA was removed using Dnase I (Qiagen).
RNA library was prepared by TruSeq Stranded mRNA (Poly A+) according ot manufacturer's protocol.

treatment_protocol: SMC were starved in ISFM for 48 hours and then treated with human recombinant PDGF-BB constituted in 10 mM Acetic Acid at 30 ng/ml for treatment in ISFM for 24 hours.

tag: cell line

value: WT

value: Aortic SMC

value: PDGF-BB (30 ng/ml)


title: pLN TCF1lo_1 [LN14-LO-A]

value: NOD/ShiLtJ

value: nondiabetic


title: pLN TCF1lo_2 [LN14-LO-B]

value: CD8+ T lymphocyte


title: PDGF-BB_RNA-2

description: RNAseq_Expression Browser_TPM.xlsx


title: L540-6H

description: 6 hours of Ruxolitinib treatment


title: L428-6H

description: 6 hours of Ruxolitinib treatment


title: L591-0H

description: untreated

value: untreated


title: PDGF-BB_RNA-1

description: RNAseq_Expression Browser_TPM.xlsx


title: L540-0H

description: untreated


title: pLN TCF1hi_3 [LN14-HI-B]

source_name: pLN TCF1hi


title: KMH2-0H

description: untreated


title: STAT3f/f801-6w

city: Yokohama

first: Kosuke

last: Miyauchi

state: Kanagawa

address: 1-7-22 Suehiro-sho

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

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 whole mouse genome using STAR 2.7.0c (command --runThreadN 60 --outSAMtype BAM SortedByCoordinate) Genome: mm10 GRCm38.p6 ENSEMBL GTF: GRCm38.97 ENSEMBL
featurecounts v1.6.0 (command: -M -O -t exon -g gene_id -a) GTF: GRCm38.97 ENSEMBL
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for genes

extract_protocol:
Ear skins were removed, and total RNA was isolated using Trizol reagent. Lexogen 3'mRNA-seq library prep kit (Cat#015) was used with 10 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Lexogen 3'QuantSeq protocols
3'QuantSeq

value: Skin

tag: genotype


title: pLN TCF1hi_4 [LN14-HI-C]


title: Ctrl SMC_RNA-4

description: RNAseq_Expression Browser_TPM.xlsx


title: L428-0H

description: untreated


title: STAT3f/f796-6w


title: L540-24H

description: 24 hours of Ruxolitinib treatment


title: Ctrl SMC_RNA-1

description: RNAseq_Expression Browser_TPM.xlsx


title: Ctrl SMC_RNA-3

description: RNAseq_Expression Browser_TPM.xlsx


title: hSMC_5hmc_INPUT

library_source: genomic

data_processing:
Library strategy: hMeDIP-seq
Raw reads were aligned to hg38 using Bowtie2 after quality control. Peaks were called using MACS2 callpeak with cut off FDR (q-value) < 0.05 and INPUT files were used as the control group. Peaks were annotated by ChIPseeker with hg38.ncbiRefSeq as the annotation source.
Genome_build: Hg38
Supplementary_files_format_and_content: Annotated peak file

growth_protocol: Human coronary artery smooth muscle cells (hCASMCs, Lonza) were propagated in M199 medium (Gibco, 11150-067) supplemented with 10% FBS, 100 U/ml each penicillin-streptomycin, 2.7 ng/ml rhEGF (Biolegend, 713008), and 2ng/ml rhFGF (Biolegend, 71034). Before treatment, SMC were starved at 2.5% serum for 24 hours.

extract_protocol:
hydroxymethylated DNA was immunoprecipitated by Hydroxymethylated DNA IP Kit (Diagenode) following manufacturer's protocol. Precipitated genomic DNA was sonicated to 200 – 500 bp using the Covaris sonicator. 1 µg of fragmented genomic DNA was immunoprecipitated with a 5-hmC monoclonal antibody using the hMeDIP kit (Diagenode). The DNA-antibody mixture was then incubated with magnetic beads overnight at 4°C, washed and DNA purified using purification kit (Qiagen, 69504)
DNA library was prepared by NEBNext DNA library prep Master Mix set for illumina 6040 and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) E7335.

treatment_protocol: hCASMC were treated with 50nM rapamycin for 48 hours

tag: hmedip  antibody

tag: fraction

value: INPUT sample


title: pLN TCF1hi_1 [LN14-AD-HI]


title: pLN TCF1hi_2 [LN14-HI-A]


title: Ctrl SMC_RNA-2

description: RNAseq_Expression Browser_TPM.xlsx


title: STAT3f/f795-6w


title: hSMC_5hmC_IP

value: 5hmC monoclonal antibody (Diagenode)

value: IP sample


title: Myocd-LSD1NF_RNA-4

description: RNAseq_Expression Browser_TPM.xlsx


title: OX-484_MK-IgG

city: London

first: Tiago

last: Cunha Luis

address: South Kensington, Sir. Alexander Fleming Building

department: Department of Life Sciences

country: United Kingdom

institute: Imperial College London

description:
Megakaryocytes
counts.txt
122

data_processing:
Reads were trimmed with trimgalore settings  --stringency 3 --nextera
Reads were aligned to the mm10 genome reference with tophat version 2.0.10 and the refSeq annotation
Reads were sorted and indexed with samtools
Reads were filtered with samtools options -b F 0xF00
Reads were counted and assigned to mm10  transcripts in R with packages Rsamtools and GenomicAlignments
Genome_build: mm10
Supplementary_files_format_and_content: csv, raw counts

source_name: MK-IgG

extract_protocol:
Cells were FACS sorted directly into lysis buffer
Clonetech/SmartSeq kits; Libraries were sequenced on a HiSeq2500 or a HighSeq4000 sequecing machine.

treatment_protocol: Platelet depletion by injecting anti-CD42b antibody. Controls received an IgG Isotype control antibody

tag: background strain

tag: cell markers

value: FSChi CD41+ CD150+ VwfGFPhi

value: Megakaryocytes

value: IgG Isotype control Antibody


title: Control

city: Hiroshima

first: Mitsunori

last: Miyazaki

state: Hiroshima

address: 1-2-3 Kasumi, Minami-Ku

department: Graduate School of Biomedical and Health Sciences

institute: Hiroshima University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: skeletal muscle, control

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was prepared by using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s directions. The isolated RNA was quantified by using spectrophotometry (λ = 260 nm).

treatment_protocol: 1 × 10^6 C26 cells per individual were suspended with 100 μL of PBS and subcutaneously implanted into the flank region of the abdominal wall unilaterally using a 26G syringe as previously described. The control group was injected with an equal amount of PBS.

value: skeletal muscle

tag: gender

value: male

tag: treatment

value: PBS


title: Myocd-LSD1NF_RNA-3

description: RNAseq_Expression Browser_TPM.xlsx

tag: cell type


title: OX-483_MK-CD42b

description:
Megakaryocytes
counts.txt
121

value: GPIba/CD42b Antibody


title: RNAseq - HT115 cells, CSOX9_dox_pos_rep1

first: Nilay

middle: S

last: Sethi

address: 450 Brookline Ave

department: Department of Medical Oncology

institute: Dana Farber Cancer Institute

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 STAR 2.7.0a
A gene count matrix was obtained using featureCounts on bam files
Genome_build: hg38
Supplementary_files_format_and_content: featureCounts_HT115.txt
Supplementary_files_format_and_content: normalized_counts.xls

growth_protocol: HT-115 cell line was obtained from Millipore Sigma and cultured in DMEM + 2mM Glutamine + 15% Fetal Bovine Serum (FBS) + 1% (P/S).

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen) according to the manufacture`s instruction.
Matured mRNA fraction was captured and enriched via oligo(dT) beads, then mRNAs were fragmented randomly in fragmentation buffer and the first-strand cDNA is synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). The second strand was subsequently generated by dNTPs, DNA polymerase I and RNase H. Double-stranded cDNA molecules were purified by AMPure XP beads and overhanging ends are repaired to blunt ends by exonuclease/polymerase. After 5’ phosphorylation and 3’ adenylation, the cDNAs were ligated with P5/P7 sequencing adapters, then size selection (insert fragment of preferentially 150~200 bp in length) and library purification was performed using AMPure XP system (Beckman Coulter, Beverly, USA). The final library was created by amplification and subsequent AMPure XP beads purification.
RNA-Seq was performed using 150-bp paired-end sequencing chemistry (Illumina) at Novogene core facility.

treatment_protocol: GFP, SOX9 and mutant SOX9 was induced by doxycycline (0.5 µg/ml) for 24h. Each experiment was performed in duplicates.  Total RNA was extracted using RNeasy Mini kit (Qiagen) according to the manufacture`s instruction.

value: Colorectal Cancer cells

tag: doxycycline induction

tag: expression

value: Doxycycline induced overexpression of V5-tagged wildtype SOX9


title: RNAseq - HT115 cells, CSOX9_dox_pos_rep2


title: STAT3f/f793-6w

tag: tissue

tag: age

value: 6 weeks


title: STAT3f/fK5cre780-6w

tag: strain


title: C26

source_name: skeletal muscle, cancer cachexia

value: C26 cells


title: OX-482_MK-IgG

description:
Megakaryocytes
counts.txt
120


title: RNAseq - HT115 cells, CSOX9_dox_pos_rep3


title: L1236-0H

description: untreated

tag: agent


title: STAT3f/fK5cre792-6w


title: OX-481_MK-CD42b

description:
Megakaryocytes
counts.txt
119


title: OX-480_MK-CD42b

description:
Megakaryocytes
counts.txt
118


title: STAT3f/fK5cre773-6w


title: OX-479_MK-IgG

description:
Megakaryocytes
counts.txt
117


title: Myocd-LSD1NF_RNA-2

description: RNAseq_Expression Browser_TPM.xlsx

value: Aortic SMC


title: STAT3f/f796-5w

value: 5 weeks


title: RNAseq - HT115 cells, M379_dox_pos_rep1

value: Doxycycline induced overexpression of V5-tagged mutant SOX9


title: STAT3f/f801-5w

value: Skin


title: STAT3f/fK5cre800-6w


title: OX-496_CBM-PV-CD42b_IL1R-/-

description:
Central bone marrow perivascular cells
counts.txt
116

value: CD45- Ter119- CD31- LepR+

value: Central bone marrow perivascular cells


title: STAT3f/fK5cre779-6w


title: Myocd-LSD1NF_RNA-1

description: RNAseq_Expression Browser_TPM.xlsx

value: untreated


title: RNAseq - HT115 cells, M379_dox_pos_rep3


title: Myocd-LSD1_RNA-4

description: RNAseq_Expression Browser_TPM.xlsx


title: Myocd-LSD1_RNA-1

description: RNAseq_Expression Browser_TPM.xlsx


title: OX-494_CBM-PV-IgG_IL1R-/-

description:
Central bone marrow perivascular cells
counts.txt
114


title: RNAseq - HT115 cells, M303_dox_pos_rep3


title: RNAseq - HT115 cells, M228_dox_pos_rep3


title: OX-493_CBM-PV-IgG_IL1R-/-

description:
Central bone marrow perivascular cells
counts.txt
113


title: RNAseq - HT115 cells, M379_dox_pos_rep2


title: RNAseq - HT115 cells, M228_dox_pos_rep2


title: OX-492_CBM-PV-CD42b_IL1R-/-

description:
Central bone marrow perivascular cells
counts.txt
112


title: STAT3f/fK5cre792-5w


title: RNAseq - HT115 cells, M303_dox_pos_rep1


title: OX-491_CBM-PV-IgG_IL1R-/-

description:
Central bone marrow perivascular cells
counts.txt
111


title: STAT3f/f795-5w


title: siRNA (KMT5A) Input

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

data_processing:
The sequenced reads were aligned to the human genome (hg38) using Bowtie software (version 0.12.8; parameter -v3 -m1).
Genome_build: hg38
Supplementary_files_format_and_content: Input-normalized ChIP-seq signal tracks (bigWig) were generated using deepTools software (Ramirez et al., 2016) (version 3.3.1; parameter, bamCompare; --effectiveGenomeSize 2805636331 --normalizeUsing RPKM --scaleFactorsMethod None -bs 500 --smoothLength 50000).

source_name: hTERT-RPE1 cells

growth_protocol: hTERT-RPE1 cells  (ATCC, CRL-4000) were grown in a culture medium composed of Dulbecco’s modified Eagle’s medium high glucose supplemented with penicillin/streptomycin (100 units/mL penicillin, 100μg/mL streptomycin) and 10% fetal calf serum.

extract_protocol:
hTERT-RPE1 cells (7.5 × 10^6 cells) were first immersed in ice cold 0.2% Triton X-100 in 20 mM HEPES (pH7.4) containing 100 mM NaCl and 300 mM sucrose for 5 min and then cross-linked with 1% formaldehyde solution (Electron Microscopy Sciences, Hatfield, PA, USA) for 10 min at room temperature (approximately 22 °C), followed by the quenching step. Dynabeads M-280 sheep anti-mouse IgG (30 μL original suspension; Thermo Fisher Scientific) and anti-MCM3 (2 μg/tube, M038-3, MBL) were used for immunoprecipitation.
The ChIP-seq library of MCM3 was prepared using ThruPLEX DNA-seq Kit (Takara Bio) and sequencing was performed using HiSeq1500 (Illumina).

treatment_protocol: siRNA transfection was performed using Lipofectamine RNAiMAX (Thermo Fisher Scientific) according to the manufacturer's protocol with siRNAs (KMT5A, SASI_Hs01_00180215; Universal Negative Control #1, MISSION, Sigma-Aldrich). Confluent cells were prepared by leaving the cells for four days after covering almost the entire area of the adhesive surface, while the medium was changed every day.

value: hTERT-immortalized retinal pigment epithelial cells

tag: chip antibody

tag: transfection

value: siRNA


title: STAT3f/f793-5w


title: RNAseq - HT115 cells, M228_dox_pos_rep1

tag: cell line


title: Myocd-LSD1_RNA-3

description: RNAseq_Expression Browser_TPM.xlsx


title: STAT3f/fK5cre800-5w

tag: genotype


title: STAT3f/fK5cre779-5w


title: Confluent MCM3IP


title: Confluent  Input


title: STAT3f/fK5cre773-5w


title: RNAseq - HT115 cells, M303_dox_pos_rep2


title: P8_ACR_VDJ

first: Mark

middle: E

last: Snyder

address: 200 Lothrop Street, BST12

department: Medicine

description: single cell RNA_VDJ

data_processing:
Allignment, Filtering: CellRanger, CellRanger VDJ
Genome_build: GRCh38

source_name: BAL

growth_protocol: Primary cells from BAL of lung transplant recipients

extract_protocol:
FACS sorted - recipient-derived T cells based on recipient / donor HLA discrepancies
10x Genomics, 5' v1

treatment_protocol: Mixed lymphocyte reaction with irradiated donor cells for 5 hours in complete RPMI with human serum

value: T cell

tag: origin

value: Recipient

value: Rejection


title: STAT3f/f796-4w

value: 4 weeks


title: RNAseq - HT115 cells, GFP_dox_pos_rep1

value: Colorectal Cancer cells

value: Doxycycline induced overexpression of GFP control


title: STAT3f/f795-4w


title: RNAseq - HT115 cells, GFP_dox_pos_rep3


title: U251_siXRN2_1

city: Oklahoma City

first: Julio

middle: Cesar

last: Morales

state: OK

department: Department of Neurosurgery

institute: University of Oklahoma Health Science Center

description: XRN2 siRNA transected, replicate 1

data_processing:
Each library was indexed during library construction in order to multiplex for sequencing on the Illumina MiSeq platform.
Samples were normalized and sequenced in batches of 3 libraries per 2x150bp paired end sequencing run on the Illumina MiSeq. On average, a total of 44 million reads (7Gb) of sequencing data was collected per run.
Raw data for each sample was analyzed using CLC Genomics Workbench version 10.0.1 software from Qiagen (formerly CLCBio).
Raw sequence reads were mapped to the Homo sapiens genome for identification of genes expressed under each condition. Pairwise comparison of the expression results were performed using the total mapping results specified experimental groups.
Genome_build: Homo sapiens, GRCh37-hg19
Supplementary_files_format_and_content: tab delinated text files includes expression value and RPKM

source_name: cell line

growth_protocol: Cells were grown at 37 degrees, humidified in 5% CO2.  LN229 were grown in 5% FBS/DMEM and U251 were grown in 10% FBS/EMEM.  Both were supplemented with Pen/strep.

extract_protocol:
Total RNA was extracted using Qiagene's miRNeasy (cat no. 217084) using manufacturer's protocol.
RNAseq libraries were constructed using the Illumina TruSeq RNA LT v2 kit and established protocols.
The library construction was done using total RNA isolated from human GBM cell lines (1ug).  RNA quality for each prep was analyzed prior to construction using the Agilent Bioanalyzer 2100 and RNA nano total RNA chips.

treatment_protocol: Cells were reverse transfected either with mock, siControl or siXRN2.  Cells were allowed to grow for 72 hours before total RNA harvesting.

tag: disease

value: glioblastoma multiforme

tag: source

value: established cell line


title: P8_Treated_VDJ

description: single cell RNA_VDJ

value: Treated


title: U251_siXRN2_2

description: XRN2 siRNA transected, replicate 2


title: OX-490_CBM-PV-CD42b_IL1R-/-

description:
Central bone marrow perivascular cells
counts.txt
110

tag: background strain

tag: cell markers

value: GPIba/CD42b Antibody


title: STAT3f/fK5cre780-5w

value: 5 weeks


title: Myocd-LSD1_RNA-2

description: RNAseq_Expression Browser_TPM.xlsx

value: Aortic SMC

tag: treatment


title: Input ChIP

data_processing:
Overall sequencing quality was checked with the FastQC script.
Reads were aligned to the human genome with BOWTIE using default parameters.
Peak calling was performed with MACS2 using default parameters
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files were generated using deepTools

extract_protocol:
Chromatin Immunoprecipitation followed by DNA-sequencing (ChIP-seq). HT115 cells were washed with PBS and crosslinked with 1% formaldehyde for 10 minutes for H3K27ac immunoprecipitation or crosslinked with two agents starting with 2 mM DSG (Pierce) for 45 minutes at room temperature followed by 1 mL of 1% formaldehyde for 10 minutes for the V5. Cross-linked cell lines were quenched with 0.125 M glycine for 5 minutes at room temperature. Cross-linked material was resuspended in 1% SDS (50 mM Tris-HCl pH8, 10 mM EDTA) and sonicated for 5 minutes with a Covaris E220 instrument (5% duty cycle, 140 Peak Incident Power, 200 Cycles per burst, 1 mL AFA Fiber milliTUBEs). Soluble chromatin (40 µg) was immunoprecipitated with 10 μg V5 Tag Antibody (Invitrogen Cat# R96025 Lot# 1949337).
ChIP-seq libraries were constructed using Accel-NGS 2S DNA library kit from Swift Biosciences. Fragments of the desired size were enriched using AMPure XP beads (Beckman Coulter).
ChIP-Seq was performed using 36-bp paired-end reads were sequenced on a Nextseq instrument (Illumina).

treatment_protocol: GFP, SOX9 and mutant SOX9 was induced by doxycycline (0.5 µg/ml) for 24h. Each experiment was performed in duplicates.

tag: cell type

value: Input ChIP


title: STAT3f/f801-4w

value: Skin


title: STAT3f/f793-4w


title: RNAseq - HT115 cells, GFP_dox_pos_rep2

tag: doxycycline induction


title: V5-tag ChIP - SOX9_dox_pos_rep2

tag: expression

value: Doxycycline induced overexpression of V5-tagged wildtype SOX9

value: V5 Tag Antibody (Invitrogen Cat# R96025 Lot# 1949337)


title: Growth Phase Input

value: hTERT-immortalized retinal pigment epithelial cells


title: Growth Phase MCM3IP


title: P8_Early_VDJ

description: single cell RNA_VDJ

value: T cell


title: U251_siNT_OTP_2

description: Control siRNA transfected, replicate 2


title: P3_Treated_VDJ

description: single cell RNA_VDJ

value: Recipient


title: U251_Mock_2

description: Mock transfected, replicate 2


title: siRNA (KMT5A) MCM3IP

value: siRNA


title: V5-tag ChIP - SOX9_dox_pos_rep1


title: STAT3f/f794-4w

tag: tissue

value: 4 weeks


title: STAT3f/fK5cre792-4w

tag: age


title: V5-tag ChIP - SOX9_dox_neg_rep2

value: Colorectal Cancer cells

value: No doxycycline induced overexpression of V5-tagged wildtype SOX9


title: U251_siNT_OTP_1

description: Control siRNA transfected, replicate 1

value: glioblastoma multiforme


title: P8_Early_GEX

description: single cell RNA_GEX


title: STAT3f/fK5cre800-4w

tag: strain


title: V5-tag ChIP - M303_dox_pos_rep1

value: Doxycycline induced overexpression of V5-tagged mutant SOX9


title: V5-tag ChIP - M303_dox_neg_rep2

value: No doxycycline induced overexpression of V5-tagged mutant SOX9


title: P3_Treated_GEX

description: single cell RNA_GEX

value: Treated


title: STAT3f/fK5cre779-4w


title: P1_ACR_VDJ

description: single cell RNA_VDJ

value: Rejection


title: V5-tag ChIP - SOX9_dox_neg_rep1


title: LN229_siNT_OTP_1

description: Control siRNA transfected, replicate 1

value: established cell line


title: STAT3f/f801-3w

value: 3 weeks


title: P8_Treated_GEX

description: single cell RNA_GEX


title: V5-tag ChIP - GFP_dox_pos_rep2

value: Doxycycline induced overexpression of GFP control


title: P1_Treated_GEX

description: single cell RNA_GEX


title: LN229_siXRN2_2

description: XRN2 siRNA transected, replicate 2


title: STAT3f/f796-3w

value: Skin


title: V5-tag ChIP - M303_dox_pos_rep2

value: V5 Tag Antibody (Invitrogen Cat# R96025 Lot# 1949337)


title: U251_Mock_1

description: Mock transfected, replicate 1


title: LN229_siXRN2_1

description: XRN2 siRNA transected, replicate 1


title: LN229_Mock_1

description: Mock transfected, replicate 1


title: STAT3f/fK5cre773-4w


title: H3K27Ac ChIP - SOX9_dox_pos_rep2

extract_protocol:
Chromatin Immunoprecipitation followed by DNA-sequencing (ChIP-seq). HT115 cells were washed with PBS and crosslinked with 1% formaldehyde for 10 minutes for H3K27ac immunoprecipitation or crosslinked with two agents starting with 2 mM DSG (Pierce) for 45 minutes at room temperature followed by 1 mL of 1% formaldehyde for 10 minutes for the V5. Cross-linked cell lines were quenched with 0.125 M glycine for 5 minutes at room temperature. Cross-linked material was resuspended in 1% SDS (50 mM Tris-HCl pH8, 10 mM EDTA) and sonicated for 5 minutes with a Covaris E220 instrument (5% duty cycle, 140 Peak Incident Power, 200 Cycles per burst, 1 mL AFA Fiber milliTUBEs). Soluble chromatin (5 µg) was immunoprecipitated with 10 μg of H3K27ac (Diagenode C15410196 antibody).
ChIP-seq libraries were constructed using Accel-NGS 2S DNA library kit from Swift Biosciences. Fragments of the desired size were enriched using AMPure XP beads (Beckman Coulter).
ChIP-Seq was performed using 36-bp paired-end reads were sequenced on a Nextseq instrument (Illumina).

value: H3K27ac (Diagenode C15410196 antibody)

value: Doxycycline induced overexpression of V5-tagged wildtype SOX9


title: P3_ACR_GEX

description: single cell RNA_GEX

value: T cell

value: Recipient


title: H3K27Ac ChIP - SOX9_dox_pos_rep1


title: V5-tag ChIP - GFP_dox_pos_rep1


title: V5-tag ChIP - M303_dox_neg_rep1


title: P1_ACR_GEX

description: single cell RNA_GEX


title: LN229_siNT_OTP_2

description: Control siRNA transfected, replicate 2


title: STAT3f/fK5cre780-4w

value: 4 weeks


title: H3K27Ac ChIP - SOX9_dox_neg_rep2

value: Colorectal Cancer cells


title: STAT3f/f793-3w


title: STAT3f/f794-3w


title: STAT3f/fK5cre800-3w


title: P8_ACR_GEX

description: single cell RNA_GEX


title: PB IL-2 n°4

city: Besançon

first: Chrystel

last: Marton

address: 8 rue du Dr Jean-François-Xavier Girod

country: France

institute: UMR1098 INSERM

hyb_protocol: A hundred nanograms of total RNA were hybridized with the NanoString Technologies nCounter CAR T Characterization panel kit according to the CodeSet Hybridization Setup instructions and the nCounter SPRINT Profiler User Manual.

scan_protocol: The nCounter SPRINT Profiler was used to access to Nanostring molecular barcoding technology.

data_processing:
Gene expression data were analyzed using nSolver Analysis Software (version 4.0) and nCounter Advanced Analysis Software (version 158 2.0.134).
Normalization of the data was done using the algorithm automatically performed by the nCounter Advanced Analysis Software. Only endogenous gene normalzed counts were generated by the software and used for analysis.

source_name: PB IL-2 n°4

label_protocol: No label is used in Nanostring

growth_protocol: Peripheral and cord blood mononuclear cells were obtained from healthy human donors and cord blood units that were not compliant with banking standards. T cells were activated with anti-CD3/28 microbeads and expanded with IL-2 or with IL-7 and IL-15.

extract_protocol: Ten days after activation, transgenic T cells were lysed and RNA was extracted using Qiagen Rneasy Mini Kit according to manufacturer instructions.

treatment_protocol: T cells were transduced with a retroviral vector encoding an HLA-DRB1*04-restricted TCR targeting the human papillomavirus oncoprotein E7, and cultured with IL-2 or with IL-7 and IL-15.

value: peripheral blood

value: transgenic T cells

tag: culture condition


title: STAT3f/f795-3w


title: PB IL-2 n°1

source_name: PB IL-2 n°1


title: PB IL-2 n°2

source_name: PB IL-2 n°2


title: LN229_Mock_2

description: Mock transfected, replicate 2

value: glioblastoma multiforme


title: PB IL-2 n°3

source_name: PB IL-2 n°3


title: STAT3f/fK5cre792-3w


title: KI_rep1

city: Ann Arbor

first: Haocheng

last: Lu

address: 2800 plymouth road

department: Internal Medicine

institute: University of Michigan

hyb_protocol: Following labeling procedure, 5.2 ug of cDNA were hybridized at 48C on Mouse Gene 2.1 ST.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data was analyzed using the oligo and limma Bioconductor package implemented in the R-statistical language version 3.4.0. RMA was used to fit log2 transformed expression values.

source_name: liver

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA.

growth_protocol: All mice were maintained in an environment (22 degree) with a 12-hour light/dark cycle and had access to water and food ad libitum.

extract_protocol: Total RNA from the mouse liver was extracted using TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions.

treatment_protocol: Tm6sf2 KI mice and littermate wild type (Wt) mice were fed a high-sucrose fat free diet (HSD) (58.45% sucrose, 16.45% alphacel, non-nutritive bulk, 21.10% vitamin Free Casein, 4.00% salt mixture by mass; 74% kCal from sucrose. MP Biomedicals, 901683) or normal chow diet (22.5% protein, 11.8% fat, and 52% carbohydrate by mass) for 14 weeks.

value: liver

tag: gender

value: male

value: TM6SF2 E167K knock in


title: H3K27Ac ChIP - M303_dox_pos_rep2

city: Boston

tag: chip antibody

value: Doxycycline induced overexpression of V5-tagged mutant SOX9


title: CB IL-7 + IL-15 n°4

source_name: CB IL-7 + IL-15 n°4

value: cord blood


title: H3K27Ac ChIP - M303_dox_neg_rep2

tag: cell line

value: No doxycycline induced overexpression of V5-tagged mutant SOX9


title: CB IL-7 + IL-15 n°2

source_name: CB IL-7 + IL-15 n°2


title: H3K27Ac ChIP - M303_dox_pos_rep1


title: CB IL-7 + IL-15 n°3

source_name: CB IL-7 + IL-15 n°3


title: CB IL-7 + IL-15 n°1

source_name: CB IL-7 + IL-15 n°1


title: KI_rep2

tag: genotype


title: WT_rep2

value: wild type


title: STAT3f/fK5cre773-3w

value: Skin

value: 3 weeks


title: STAT3f/f801-2w

value: 2 weeks


title: STAT3f/fK5cre779-3w


title: KI_rep3


title: H3K27Ac ChIP - M303_dox_neg_rep1

value: H3K27ac (Diagenode C15410196 antibody)


title: H3K27Ac ChIP - GFP_dox_pos_rep2

value: Doxycycline induced overexpression of GFP control


title: H3K27Ac ChIP - SOX9_dox_neg_rep1

value: No doxycycline induced overexpression of V5-tagged wildtype SOX9


title: CAL1_ZRSR2_D7_3

first: Andrew

last: Lane

institute: Dana-Farber Cancer Institute

data_processing:
The raw FASTQ data were analyzed by the VIPER pipeline which combines STAR alignment and gene expression analysis such as unsupervised clustering, PCA based on Cufflinks and differential expression with DESEq2
Genome_build: hg19
Supplementary_files_format_and_content: RNA abundance expressed as fragments per kilobase of transcript per million mapped reads (FPKM)

growth_protocol: CAL1 cells transduced with control (CTRL) or ZRSR2 dox-inducible shRNAs were treated with doxycycline for 0, 2, or 7 days and then RNA was extracted

extract_protocol:
Arcturus PicoPure RNA Isolation Kit (Life Technologies)
TruSeq RNA Library Prep Kit (Illumina) using 1 ug of input total RNA and 15 cycles of amplificaftion

value: ZRSR2 shRNA

tag: time point

value: 7 days


title: STAT3f/f796-2w


title: CAL1_ZRSR2_D7_1


title: WT_rep4


title: OX_431_HSC_VWF_POS-IgG

description:
Hematopoietic stem cells VwfGFP+
counts.txt
OX_431

value: Lin- cKit+ Sca1+ Flt3- CD48- CD150hi VwfGFP+

value: Hematopoietic stem cells VwfGFP+

value: IgG Isotype control Antibody


title: KI_rep4

value: liver

value: male


title: CB IL-2 n°4

source_name: CB IL-2 n°4

value: transgenic T cells


title: CB IL-2 n°2

source_name: CB IL-2 n°2

value: cord blood


title: CAL1_ZRSR2_D2_2

value: 2 days


title: OX_429_BL-PaS-CD42b

description:
Bone lining mesenchymal progenitors
counts.txt
OX_429

value: CD45- Ter119- CD31- Alcam- Sca1+ Pdgfra+

value: Bone lining mesenchymal progenitors

value: GPIba/CD42b Antibody


title: OX_430_HSC_VWF_NEG-IgG

description:
Hematopoietic stem cells VwfGFP-
counts.txt
OX_430

value: Lin- cKit+ Sca1+ Flt3- CD48- CD150hi VwfGFP-

value: Hematopoietic stem cells VwfGFP-


title: WT_rep1

value: wild type


title: CAL1_ZRSR2_D2_3


title: WT_rep3


title: STAT3f/fK5cre792-2w

value: Skin

value: 2 weeks


title: OX_428_BL-PaS-IgG

description:
Bone lining mesenchymal progenitors
counts.txt
OX_428

source_name: BL-PaS-IgG


title: STAT3f/fK5cre780-3w

value: 3 weeks


title: CAL1_ZRSR2_D0_3

value: ZRSR2 shRNA

value: 0 days


title: OX_427_BL-OBP-CD42b

description:
Bone lining Osteoblast progenitors
counts.txt
OX_427

value: CD45- Ter119- CD31- Alcam- Sca1- OsxGFP+

value: Bone lining Osteoblast progenitors


title: CAL1_ZRSR2_D7_2

value: 7 days


title: OX_424_BL-OB-IgG

description:
Bone lining Osteoblasts
counts.txt
OX_424

source_name: BL-OB-IgG

value: CD45- Ter119- CD31- Alcam+ Sca1-

value: Bone lining Osteoblasts

value: IgG Isotype control Antibody


title: STAT3f/f795-2w


title: CAL1_CTRL_D7_1

value: control shRNA


title: STAT3f/fK5cre779-2w


title: CAL1_CTRL_D2_3

value: 2 days


title: heart, LPS-stressed 24 h mice_3

city: Beijing

first: Xiaoping

last: Wang

state: Beijing

address: No. 5, Dongdan Santiao, Dongcheng District, Beijing

country: China

institute: Peking Union Medical College

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 mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample, FPKMs

source_name: heart

extract_protocol:
Hearts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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: Heart

value: 8 weeks old

tag: stress

value: LPS


title: STAT3f/f793-2w


title: H3K27Ac ChIP - GFP_dox_pos_rep1

value: Colorectal Cancer cells

value: H3K27ac (Diagenode C15410196 antibody)

value: Doxycycline induced overexpression of GFP control


title: STAT3f/f794-2w

value: Skin

value: 2 weeks


title: OX_432_HSC_VWF_NEG-IgG

description:
Hematopoietic stem cells VwfGFP-
counts.txt
OX_432

value: Lin- cKit+ Sca1+ Flt3- CD48- CD150hi VwfGFP-

value: Hematopoietic stem cells VwfGFP-


title: CB IL-2 n°1

source_name: CB IL-2 n°1

tag: source

value: cord blood

value: transgenic T cells


title: OX_421_BL-EC-IgG

description:
Bone lining endothelial cells
counts.txt
OX_421

source_name: BL-EC-IgG

tag: background strain

value: Bone lining endothelial cells


title: OX_433_HSC_VWF_POS-IgG

description:
Hematopoietic stem cells VwfGFP+
counts.txt
OX_433

tag: cell markers

value: Lin- cKit+ Sca1+ Flt3- CD48- CD150hi VwfGFP+

value: Hematopoietic stem cells VwfGFP+


title: STAT3f/fK5cre800-2w


title: CAL1_CTRL_D0_3

source_name: cell line

tag: treatment

value: control shRNA

value: 0 days


title: heart, saline-injected control mice_5

value: Heart

value: saline


title: heart, LPS-stressed 24 h mice_4

value: 8 weeks old

value: LPS


title: OX_426_BL-OBP-IgG

description:
Bone lining Osteoblast progenitors
counts.txt
OX_426

source_name: BL-OBP-IgG

value: CD45- Ter119- CD31- Alcam- Sca1- OsxGFP+

tag: cell type

value: Bone lining Osteoblast progenitors

value: IgG Isotype control Antibody


title: OX_418_CBM-EC-IgG

description:
Central bone marrow endothelial cells
counts.txt
OX_418

source_name: CBM-EC-IgG

value: CD45- Ter119- CD31+ LepR-

value: Central bone marrow endothelial cells


title: heart, saline-injected control mice_4


title: CAL1_ZRSR2_D2_1

value: ZRSR2 shRNA

value: 2 days


title: OX_425_BL-OB-CD42b

description:
Bone lining Osteoblasts
counts.txt
OX_425

value: CD45- Ter119- CD31- Alcam+ Sca1-

value: Bone lining Osteoblasts

value: GPIba/CD42b Antibody


title: CAL1_ZRSR2_D0_1


title: STAT3f/fK5cre780-2w

value: Skin

value: 2 weeks


title: heart, saline-injected control mice_2


title: CAL1_CTRL_D7_2

value: control shRNA

value: 7 days


title: OX_422_BL-EC-IgG

description:
Bone lining endothelial cells
counts.txt
OX_422

value: Bone lining endothelial cells


title: heart, LPS-stressed 24 h mice_5

value: Heart

value: 8 weeks old


title: CAL1_CTRL_D2_2


title: OX_417_BL-EC-CD42b

description:
Bone lining endothelial cells
counts.txt
OX_417


title: CAL1_ZRSR2_D0_2

value: 0 days


title: CAL1_CTRL_D7_3


title: STAT3f/fK5cre773-2w


title: scBL4_mmuTHY4

city: Rochester

first: Stephan

last: Emmrich

address: 213 Hutchison Hall, River Campus

institute: University of Rochester

data_processing:
library strategy: single-cell CITE-Seq
Cellranger 3.1.0 was used to generate count matrices from either an ENSEMBL94 mouse reference ("mmuBM") or FRAMA naked mole-rat BM transcriptome assembly ("hglBM")
RNA features were uniquefied using data.table by sum-up each duplicate
ADT features from each sample were concatenated
Annotation of features, molecules/cells and samples was indexed against the feature matrices
Supplementary_files_format_and_content: R workspace containing RNA count matrix, ADT count matrix and cell annotation

source_name: hematopoietic system

growth_protocol: Naked mole-rat or Mouse primary lymphatic tissue cells from healthy specimen

extract_protocol:
Cells were DAPI-sorted as viable unfractionated lymphatic tissue
Chromium Single-Cell 3′ Library & Gel Bead Kit v3 (10X Genomics)

treatment_protocol: Cells were processed for TotalSeq™ CITE reagents according to the manufacturers instructions (BioLegend), using both human and mouse Fc blocking reagents (BioLegend)

value: thoracic thymus

value: 12 months

value: wildtype

tag: molecule type

value: 3' mRNA UMI


title: RPE_ChIP_H3k9me3_sg11C4

city: Amsterdam

first: Anna

last: Gonzalez Manjon

email: a.gonzalez@nki.nl, li.koob@nki.nl

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description: ChIP-seq in RPE-1 for H3k9me3 Taxol Resistant clone with EF1A integration on ABCB1 Clone sg11C4

data_processing:
Sequences were generated by the Illumina Hiseq 2500 (using 65bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA9. Reads with a BWA alignment quality score less than 20 were removed.
TDF files were generated from BAM files using the igvtools utility count (v2.3.67).
TLA data was processed as described before by (de Vree et al Nat Gen 2014).
Sequences were generated by the Illumina Hiseq 2500 (using 65bp reads) and were processed by the Illumina pipeline.  Reads were aligned to the Human Reference Genome (hg19) using BWA9. Reads with a BWA alignment quality score less than 20 were removed.  TDF files were generated from BAM files using the igvtools utility count (v2.3.67).
Genome_build: Hg19
Supplementary_files_format_and_content: tdf

source_name: RPE-1 cells

growth_protocol: RPE-1 cells were grown in DMEMF12 with 6% FCS and 1%Pen/Strep

extract_protocol:
Chromatin immunoprecipitations (ChIP) were performed as described (Stelloo et al. Oncogene 2018). For each ChIP 5 μg of specified antibody prebound to protein A beads were used.
Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303 KAPA biosystems kit).

treatment_protocol: Taxol resistant cells were cultured with 8nM Taxol

value: RPE-1 cells

tag: sgrna used

value: sgRNA #11 ABCB1

tag: clone name

tag: phenotype

value: Taxol resistant


title: heart, LPS-stressed 24 h mice_2

tag: strain

tag: tissue

tag: age

value: LPS


title: CAL1_CTRL_D2_1

value: 2 days


title: OX_423_BL-EC-IgG

description:
Bone lining endothelial cells
counts.txt
OX_423

value: IgG Isotype control Antibody


title: scBL3_mmuTHY3


title: OX_420_CBM-EC-IgG

description:
Central bone marrow endothelial cells
counts.txt
OX_420

value: CD45- Ter119- CD31+ LepR-

value: Central bone marrow endothelial cells


title: CB IL-2 n°3

source_name: CB IL-2 n°3

value: cord blood

value: transgenic T cells

tag: culture condition


title: RPE_ChIP_H3k9me3_sg11C3

description: ChIP-seq in RPE-1 for H3k9me3 Taxol Resistant clone with EF1A integration on ABCB1 Clone sg11C3

tag: cell line

tag: chip antibody


title: scBL2_mmuTHY2

value: 3 months

tag: genotype


title: scBL1_mmuTHY1


title: OX_412_CBM-EC-CD42b

description:
Central bone marrow endothelial cells
counts.txt
OX_412

value: GPIba/CD42b Antibody


title: OX_419_CBM-EC-IgG

description:
Central bone marrow endothelial cells
counts.txt
OX_419


title: OX_408_HSC_VWF_POS-IgG

description:
Hematopoietic stem cells VwfGFP+
counts.txt
OX_408

value: Lin- cKit+ Sca1+ Flt3- CD48- CD150hi VwfGFP+

value: Hematopoietic stem cells VwfGFP+


title: OX_414_BL-EC-CD42b

description:
Bone lining endothelial cells
counts.txt
OX_414

value: Bone lining endothelial cells


title: heart, LPS-stressed 24 h mice_1

value: Heart

value: 8 weeks old

tag: stress


title: CAL1_CTRL_D0_1

value: control shRNA

tag: time point

value: 0 days


title: heart, saline-injected control mice_3

value: saline


title: heart, saline-injected control mice_1


title: scBL3_mmuBM3

growth_protocol: Naked mole-rat or Mouse primary bone marrow cells from healthy specimen

extract_protocol:
Cells were DAPI-sorted as viable unfractionated marrow tissue
Chromium Single-Cell 3′ Library & Gel Bead Kit v3 (10X Genomics)

value: bone marrow

value: 12 months

value: wildtype

tag: molecule subtype

value: 3' mRNA UMI


title: CAL1_CTRL_D0_2


title: scBL1_mmuBM1


title: RPE_ChIP_H3k9me3_sg6C1

description: ChIP-seq in RPE-1 for H3k9me3 Taxol Resistant clone with EF1A integration on ABCB1 Clone sg6C1

value: RPE-1 cells

value: sgRNA #6 ABCB1

value: Taxol resistant


title: OX_405_HSC_VWF_NEG-CD42b

description:
Hematopoietic stem cells VwfGFP-
counts.txt
OX_405

tag: background strain

tag: cell markers

value: Lin- cKit+ Sca1+ Flt3- CD48- CD150hi VwfGFP-

value: Hematopoietic stem cells VwfGFP-


title: RPE_ChIP_H3k9me3_sg11C6

description: ChIP-seq in RPE-1 for H3k9me3 Taxol Resistant clone with EF1A integration on ABCB1 Clone sg11C6

value: sgRNA #11 ABCB1


title: RNAseq - LS180 cells, SOX9_dox_pos_rep2

growth_protocol: LS180 cell line was obtained from Millipore Sigma and cultured in DMEM + 2mM Glutamine + 15% Fetal Bovine Serum (FBS) + 1% (P/S).

tag: cell type

value: Colorectal Cancer cells

tag: doxycycline induction

tag: expression

value: Doxycycline induced overexpression of V5-tagged wildtype SOX9


title: OX_404_HSC_VWF_POS-CD42b

description:
Hematopoietic stem cells VwfGFP+
counts.txt
OX_404

value: Lin- cKit+ Sca1+ Flt3- CD48- CD150hi VwfGFP+

value: Hematopoietic stem cells VwfGFP+

tag: treatment

value: GPIba/CD42b Antibody


title: OX_413_CBM-EC-CD42b

description:
Central bone marrow endothelial cells
counts.txt
OX_413

value: CD45- Ter119- CD31+ LepR-

value: Central bone marrow endothelial cells


title: OX_403_HSC_VWF_NEG-CD42b

description:
Hematopoietic stem cells VwfGFP-
counts.txt
OX_403


title: RPE_ChIP_H3k9me3_sg12C5

description: ChIP-seq in RPE-1 for H3k9me3 Taxol Resistant clone with EF1A integration on ABCB1 Clone sg12C5

tag: sgrna used

value: sgRNA #12 ABCB1

tag: clone name

tag: phenotype


title: RPE_ChIP_H3k9me3_sg12C4

description: ChIP-seq in RPE-1 for H3k9me3 Taxol Resistant clone with EF1A integration on ABCB1 Clone sg12C4


title: OX_415_BL-EC-CD42b

description:
Bone lining endothelial cells
counts.txt
OX_415

value: Bone lining endothelial cells


title: OX_416_CBM-EC-CD42b

description:
Central bone marrow endothelial cells
counts.txt
OX_416


title: OX_407_HSC_VWF_NEG-IgG

description:
Hematopoietic stem cells VwfGFP-
counts.txt
OX_407

value: IgG Isotype control Antibody


title: 981posfxnVTA_S53

first: Michael

middle: J

last: Beckstead

address: 825 NW 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Foundation

data_processing:
Bases were called using Illumina Casava 1.8
RNAseq reads were trimmed (Q<30 and 2 bases from 3' and 5' ends) and aligned to build Mm10 of the mouse genome using Strand NGS v3.1.  Duplicate reads were removed. Quantitation was performed using DESeq algorithms, and transcripts with an averaged read count greater than 20 in at least 100% of samples in at least one group were quantified.
A students T-Test with Benjamini-Hochberg Multiple Testing Correction was used for statistical analysis and transcripts with a fold change greater than |1.25| were utilized for analysis.
Genome_build: Mm10 (2104.11.26)
Supplementary_files_format_and_content: Raw and normalized gene count matrix table

source_name: SNpc/VTA

extract_protocol:
Brain was rapidly removed and region of interest was disected and immediately placed in TRAP buffer for processing. NEB UltraII kit was used with 25 ng of total RNA for library construction.
RNA-seq libraries were preprared following NEB Ultra II protocols.

value: Astrocytes

tag: strain

tag: tissue

value: ventral midbrain


title: scBL4_mmuBM4

value: bone marrow

tag: age

value: 12 months

value: wildtype

value: 3' mRNA UMI


title: RPE_ChIP_H3k9me3_sg6C9

description: ChIP-seq in RPE-1 for H3k9me3 Taxol Resistant clone with EF1A integration on ABCB1 Clone sg6C9

tag: cell line

value: RPE-1 cells

value: sgRNA #6 ABCB1

value: Taxol resistant

tag: chip antibody


title: RPE_TLA_WT_R1

description: TLA in RPE-1 cells replicate 1

data_processing:
Library strategy: TLA
TLA data was processed as described before by (de Vree et al Nat Gen 2014).
TLA data was processed as described before by (de Vree et al Nat Gen 2014).
Sequences were generated by the Illumina Hiseq 2500 (using 65bp reads) and were processed by the Illumina pipeline.  Reads were aligned to the Human Reference Genome (hg19) using BWA9. Reads with a BWA alignment quality score less than 20 were removed.  TDF files were generated from BAM files using the igvtools utility count (v2.3.67).
Genome_build: Hg19
Supplementary_files_format_and_content: tdf

extract_protocol:
Sample collection was performed as described before by (de Vree et al Nat Gen 2014).
Library construction was performed as described before by (de Vree et al Nat Gen 2014).

value: Parental


title: 982posfxnVTA_S54


title: PB

data_processing:
library strategy: single-cell CITE-Seq
Cellranger 3.0.2 was used to generate count matrices from the FRAMA naked mole-rat BM transcriptome assembly
RNA features were uniquefied using data.table by sum-up each duplicate
ADT features from each sample were concatenated
Annotation of features, molecules/cells and samples was indexed against the feature matrices
Supplementary_files_format_and_content: R workspace containing RNA count matrix, ADT count matrix and cell annotation

organism: Heterocephalus glaber

growth_protocol: Naked mole-rat primary bone marrow cells from healthy specimen

extract_protocol:
Cells were sorted according to the manuscript methods description, then pooled as input to the 10X Chromium droplet device
Chromium Single-Cell 3′ Library & Gel Bead Kit v2 (10X Genomics)

treatment_protocol: Cells were processed for TotalSeq™ CITE reagents according to the manufacturers instructions (BioLegend), without Fc blocking reagents

value: Naked mole-rat

value: peripheral blood

value: 2-4 years

tag: genotype


title: RPE_ChIP_input

description: ChIP-seq in RPE-1 (input sample)


title: OX_406_HSC_VWF_POS-CD42b

description:
Hematopoietic stem cells VwfGFP+
counts.txt
OX_406

extract_protocol:
Cells were FACS sorted directly into lysis buffer
Clonetech/SmartSeq kits; Libraries were sequenced on a HiSeq2500 or a HighSeq4000 sequecing machine.

value: Lin- cKit+ Sca1+ Flt3- CD48- CD150hi VwfGFP+

value: Hematopoietic stem cells VwfGFP+

value: GPIba/CD42b Antibody


title: RNAseq - LS180 cells, SOX9_dox_pos_rep1

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen) according to the manufacture`s instruction.
Matured mRNA fraction was captured and enriched via oligo(dT) beads, then mRNAs were fragmented randomly in fragmentation buffer and the first-strand cDNA is synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). The second strand was subsequently generated by dNTPs, DNA polymerase I and RNase H. Double-stranded cDNA molecules were purified by AMPure XP beads and overhanging ends are repaired to blunt ends by exonuclease/polymerase. After 5’ phosphorylation and 3’ adenylation, the cDNAs were ligated with P5/P7 sequencing adapters, then size selection (insert fragment of preferentially 150~200 bp in length) and library purification was performed using AMPure XP system (Beckman Coulter, Beverly, USA). The final library was created by amplification and subsequent AMPure XP beads purification.
RNA-Seq was performed using 150-bp paired-end sequencing chemistry (Illumina) at Novogene core facility.

value: Colorectal Cancer cells

value: Doxycycline induced overexpression of V5-tagged wildtype SOX9


title: OX_401_HSC_VWF_NEG-CD42b

description:
Hematopoietic stem cells VwfGFP-
counts.txt
OX_401

value: Lin- cKit+ Sca1+ Flt3- CD48- CD150hi VwfGFP-

value: Hematopoietic stem cells VwfGFP-


title: Thy

value: thoracic thymus


title: RPE_ChIP_H3k9me3_WT

description: ChIP-seq in RPE-1 for H3k9me3 parental sample


title: RNAseq - LS180 cells, SOX9_dox_neg_rep1

value: No doxycycline induced overexpression of V5-tagged wildtype SOX9


title: scBL2_mmuBM2

value: bone marrow

value: 3 months

value: wildtype

value: 3' mRNA UMI


title: 88posfxnVTA_S55

value: Astrocytes

value: ventral midbrain


title: BM_2

value: Naked mole-rat


title: OX_402_HSC_VWF_POS-CD42b

description:
Hematopoietic stem cells VwfGFP+
counts.txt
OX_402


title: RNAseq - LS180 cells, SOX9_dox_neg_rep2


title: BM_3

value: 2-4 years


title: RPE_TLA_Taxol_Resistant_sg6-C9_R1

description: TLA in RPE-1 taxol resistant cells replicate 1

value: RPE-1 cells

value: sgRNA #6 ABCB1

value: Taxol resistant


title: 92posfxnVTA_S56


title: 982inputVTA_S49

value: CNS cell types


title: RNAseq - LS180 cells, M303_dox_pos_rep2

value: Colorectal Cancer cells

value: Doxycycline induced overexpression of V5-tagged mutant SOX9


title: OX_398_BL-PaS-IgG

description:
Bone lining mesenchymal progenitors
counts.txt
OX_398

value: CD45- Ter119- CD31- Alcam- Sca1+ Pdgfra+

value: Bone lining mesenchymal progenitors

value: IgG Isotype control Antibody


title: 981inputVTA_S48


title: 76w2_259_S2_L004

data_processing:
library strategy: single-cell CITE-Seq
Cellranger 3.1.0 was used to generate count matrices from both an ENSEMBL94 mouse reference and FRAMA for the same library
RNA features from each reference were labelled with a species tag
RNA features were uniquefied using data.table by sum-up each duplicate
ADT features from each sample were concatenated
Annotation of features, molecules/cells and samples was indexed against the feature matrices
Supplementary_files_format_and_content: R workspace containing RNA count matrix, ADT count matrix and cell annotation

growth_protocol: Naked mole-rat sorted HSPC populations (CP1 vs LTC) from donors aged 2-4 years were i.v. transplanted into preconditioned NSGS recipients and extracted from marrow 4 weeks post TX

extract_protocol:
Cells were sorted as viable xenograft according to FACS staining
Chromium Single-Cell 3′ Library & Gel Bead Kit v3 (10X Genomics)

value: bone marrow

tag: recipient strain

tag: recipient facs population

value: NOT Thy1.1-/CD34-

tag: donor facs population

tag: immunophenotype


title: OX_396_BL-PaS-CD42b

description:
Bone lining mesenchymal progenitors
counts.txt
OX_396

data_processing:
Reads were trimmed with trimgalore settings  --stringency 3 --nextera
Reads were aligned to the mm10 genome reference with tophat version 2.0.10 and the refSeq annotation
Reads were sorted and indexed with samtools
Reads were filtered with samtools options -b F 0xF00
Reads were counted and assigned to mm10  transcripts in R with packages Rsamtools and GenomicAlignments
Genome_build: mm10
Supplementary_files_format_and_content: csv, raw counts

tag: background strain

tag: cell markers

tag: cell type

value: GPIba/CD42b Antibody


title: 976posfxnVTA_S52


title: RNAseq - LS180 cells, M303_dox_pos_rep1

tag: doxycycline induction

tag: expression


title: OX_395_BL-PaS-IgG

description:
Bone lining mesenchymal progenitors
counts.txt
OX_395

tag: treatment


title: BM_1

value: wildtype

tag: molecule subtype

value: 3' mRNA UMI


title: 976inputVTA_S47

tag: strain

value: ventral midbrain


title: RNAseq - LS180 cells, M303_dox_neg_rep2

value: No doxycycline induced overexpression of V5-tagged mutant SOX9


title: 76w2_259_S2_L003

value: Naked mole-rat

tag: tissue

value: 2-4 years


title: 92inputVTA_S51


title: RNAseq - LS180 cells, M303_dox_neg_rep1


title: OX_394_BL-OB-IgG

description:
Bone lining Osteoblasts
counts.txt
OX_394

value: CD45- Ter119- CD31- Alcam+ Sca1-

value: Bone lining Osteoblasts


title: 76w2_259_S2_L002

tag: age


title: 88inputVTA_S50

value: CNS cell types


title: OX_393_BL-OB-CD42b

description:
Bone lining Osteoblasts
counts.txt
OX_393


title: OX_397_BL-PaS-CD42b

description:
Bone lining mesenchymal progenitors
counts.txt
OX_397


title: Cre PH 2

city: Raleigh

first: Raquel

last: Maeso-Diaz

state: United States

address: 3901 Sue Lane

institute: Duke University

description: Cre PH 2

data_processing:
Trim_galore trim off adapter and low quality reads
STAR aligning the reads (STAR/2.5.0c-fasrc01)
Samtools index sorted bam files
Picard remove duplicates
HTSeq quantify Gene Expression Data
Genome_build: mm10_STAR_genome_idx
Supplementary_files_format_and_content: BAM counts
Supplementary_files_format_and_content: File Counts Young and Old: Young Hepatocytes (Young 1, Young 2, Young 3), Young Regenerating Hepatocytes (YoungPH1, YoungPH2, YoungPH3), Old Hepatocytes (Old1 , Old2, Old3), Old Regenerating Hepatocytes (OldPH1, OldPH2, OldPH3)
Supplementary_files_format_and_content: File Counts Smo+ and Smo- : Smo + Hepaotcytes (Luci), Smo + Regenerating Hepatocytes (LuciPH), Smo - Hepatocytes (Cre 1, Cre2), Smo - Regenerating Hepatocytes (CrePH1, CrePH2)

source_name: Hepatocytes

growth_protocol: To obtain primary hepatocytes, livers were perfused with collagenase as described.  Hepatocyte preparations were evaluated by light microscopy to assure that viability and purity were at least 95%. Freshly isolated hepatocytes were immediately processed to obtain RNA.

extract_protocol:
Global transcriptome profiling of was performed by RNA-seq using freshly isolated hepatocytes from young and old wild type mice or Smo-floxed mice before and at 48 h after PH (n=3wild type mice/group/time point), n=1 Smo-flox-Luci mice/time point and n=2 Smo-flox-Cre mice/time point). Total RNA was extracted using RNeasy mini kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions.
mRNA library preparation (poly A enrichment)

treatment_protocol: C57BL/6J 3-month-old wild-type (Young) mice were obtained from Jackson Laboratories (Bar Harbor, ME). C57BL/6J 24-month-old wild-type (Old) mice were obtained from the NIA Aged Rodent Colonies (https://www.nia.nih.gov/research/dab/agedrodent-colonies-handbook). Adult male, C57BL/6J wild-type (WT) mice (Jackson Laboratory, Bar Harbor, ME) and adult male Smoothened (Smo) tm2Amc/J (Smo-flox) mice on a C57Bl6/J background were purchased from the Jackson Laboratory (Bar Harbor, ME) and studied at 2-3 months of age. All mice were housed in a barrier facility on 12 h:12 h light cycle with free access to water and standard chow diet (Rodent diet 20, 5033; Picolab, St. Louis, MO). Male Smo flox/flox mice were injected by tail vein with 5 × 1011 genome-equivalents of AAV8-TBG-Luc (control; Smo (+); n = 50 mice) or AAV8-TBG-Cre (Smo (-); n = 50 mice) to selectively delete the Smoothened (Smo) gene in hepatocytes. Viruses were obtained from the University of Pennsylvania Viral Vector Core.   70% partial hepatectomy (PH) (10, 16) was performed on young and old wild type mice and young Smo-floxed mice without or with Smo deletion (n=50 mice/group). Smo-floxed mice underwent PH 7 days after viral injection based on pilot studies showing reproducibly efficient deletion of floxed Smo alleles by this time point.

value: 3 months-old

tag: aav8-luci or cre

tag: quiescent or regenerating

value: Regenerating


title: 76w2_259_S2_L001

tag: genotype


title: RNAseq - LS180 cells, GFP_dox_pos_rep2

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 STAR 2.7.0a
A gene count matrix was obtained using featureCounts on bam files
Genome_build: hg38
Supplementary_files_format_and_content: featureCounts_HT115.txt
Supplementary_files_format_and_content: normalized_counts.xls

value: Colorectal Cancer cells

tag: cell line

value: Doxycycline induced overexpression of GFP control


title: 76w2_257_S1_L003

tag: recipient strain

tag: recipient facs population


title: OX_392_BL-OB-CD42b

description:
Bone lining Osteoblasts
counts.txt
OX_392


title: Cre PH 1

description: Cre PH 1


title: RNAseq - LS180 cells, GFP_dox_neg_rep1

value: No doxycycline induced overexpression of GFP control


title: 76w2_257_S1_L004

value: bone marrow

tag: donor facs population

tag: immunophenotype


title: OX_391_BL-OB-IgG

description:
Bone lining Osteoblasts
counts.txt
OX_391

tag: background strain

tag: cell markers

value: IgG Isotype control Antibody


title: RNAseq - LS180 cells, GFP_dox_neg_rep2

tag: cell type

tag: doxycycline induction


title: OX_390_BL-OBP-IgG

description:
Bone lining Osteoblast progenitors
counts.txt
OX_390

value: CD45- Ter119- CD31- Alcam- Sca1- OsxGFP+

value: Bone lining Osteoblast progenitors

tag: treatment


title: H292 SL_CAFs CM [N_3]

city: Wuhan

first: Jing

middle: Shu

last: Meng

address: 1095 Jiefang Avenue, Qiaokou District

department: Union Hospital, Tongji Medical College

institute: Huazhong University of Science and Technology

data_processing:
Raw sequencing data were filtered by Trimmomatic (version 0.36) to obtain clean data, which were then mapped using STRA software (version 2.5.3a).
Reads mapped to the exon region of each gene were counted by using featureCounts (Subread-1.5.1; Bioconductor).
And then RPKMs were calculated. Differential gene expression between two groups were identified by using edgeR package (version 3.12.1). A fold-change cutoff of 2 and p-value cutoff of 0.05 were used to judge the statistical significance of gene expression differences.
KEGG enrichment analysis was implemented by KOBAS software (version: 2.1.1) to judge statistically significant enrichment.
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: raw_counts; raw_rpkm

source_name: H292 SL_CAFs CM

growth_protocol: H292 cells were cultured in RPMI 1640 medium (Gibco) with 10% FBS and 1% penicillin/streptomycin at 37°C in a humidified atmosphere of 5% CO2

extract_protocol:
Total RNAs were extracted from H292 using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

treatment_protocol: H292 cells cultured with CAFs CM or SL-CAFs CM for 48 h

value: TP53 WT

value: SL-CAFs CM

value: huaman NSCLC cell line


title: OX_389_BL-OBP-CD42b

description:
Bone lining Osteoblast progenitors
counts.txt
OX_389

value: GPIba/CD42b Antibody


title: OX_388_BL-OBP-CD42b

description:
Bone lining Osteoblast progenitors
counts.txt
OX_388


title: H292 SL_CAFs CM [N_2]


title: RNAseq - LS180 cells, GFP_dox_pos_rep1

tag: expression


title: 117_hglTLN5

tag: strain

value: Naked mole-rat

value: cervical thymus

value: 3 years

value: wildtype

tag: molecule type

value: 3' mRNA UMI


title: Cre 1

description: Cre 1

tag: age

value: 3 months-old

value: Quiescent


title: Luci

description: Luci 1

tag: aav8-luci or cre


title: Old PH 3

description: Old PH 3

value: 24 months-old

value: No

tag: quiescent or regenerating

value: Regenerating


title: Cre 2

description: Cre 2


title: 116_hglTLN4

tag: tissue

tag: genotype


title: OX_387_BL-OBP-IgG

description:
Bone lining Osteoblast progenitors
counts.txt
OX_387

value: IgG Isotype control Antibody


title: H292 CAFs CM [A_4]

source_name: H292 CAFs CM

tag: cell line

value: CAFs CM


title: 76w2_257_S1_L002

value: bone marrow

value: 2-4 years

tag: recipient strain

tag: recipient facs population

value: NOT Thy1.1-/CD34-

tag: molecule subtype


title: H292 CAFs CM [A_2]

value: TP53 WT

value: huaman NSCLC cell line


title: 117_hglTHY5

value: Naked mole-rat

value: thoracic thymus


title: 115_hglTLN3

value: cervical thymus

value: 11 years


title: OX_386_BL-PV-IgG

description:
Bone lining perivascular cells
counts.txt
OX_386

source_name: BL-PV-IgG

tag: background strain

value: CD45- Ter119- CD31- LepR+

value: Bone lining perivascular cells


title: LuciPH

description: Luci PH

value: 3 months-old


title: OX_384_BL-PV-IgG

description:
Bone lining perivascular cells
counts.txt
OX_384

tag: cell markers


title: 76w2_257_S1_L001

value: wildtype

tag: donor facs population

tag: immunophenotype

value: 3' mRNA UMI


title: H292 CAFs CM [A_3]

tag: treatment

tag: cell type


title: H292 SL_CAFs CM [N_1]

value: SL-CAFs CM


title: Old PH 2

description: Old PH 2

tag: strain

value: 24 months-old

value: No

value: Regenerating


title: Young PH 3

description: Young PH 3


title: OX_382_CBM-PV-IgG

description:
Central bone marrow perivascular cells
counts.txt
OX_382

source_name: CBM-PV-IgG

value: Central bone marrow perivascular cells

value: IgG Isotype control Antibody


title: 116_hglBLN2

value: lymph node

value: 3 years

tag: molecule type


title: 114_hglTLN2

value: Naked mole-rat

tag: age


title: X_108_blood

first: Mingming

last: Shao

state: State...

address: 8 Gongren Tiyuchang Nanlu

institute: Beijing Chao-Yang Hospital

data_processing:
The data alignment to the reference genome with Cell Ranger using "mkfastq" and "count" commands and default parameters.
Used Seurat to create data objects from the matrix outputs.
Genes with an expression ratio of > 0.1% and cells with 200 to 6,000 detected genes were selected.
Genome_build: GRCh38.93
Supplementary_files_format_and_content: Matrix table with gene counts

extract_protocol:
Pleural fluid samples from each subject were collected in heparin-treated tubes within 24 hours after hospitalization, using standard thoracentesis techniques. Approximately 5 mL of venous blood were drawn simultaneously. The pleural effusion specimens were immediately immersed in ice and were then centrifuged at 1,200 rpm for 5 min. The cell-free supernatants of PE and sera were frozen at -80°C immediately after centrifugation. Mononuclear cells from pleural ﬂuid and blood were isolated by Ficoll-Hypaque gradient centrifugation within 1 hour and were resuspended in PBS.
Single-cell libraries were constructed using the Single Cell 5′ Library & Gel Bead Kit, Single Cell V(D)J Enrichment Kit, Human T Cell, or Single Cell V(D)J Enrichment Kit, Human B Cell. According to the cDNA synthesis and Chromium Single Cell A Chip Kits, cell suspensions were loaded on a Chromium Controller to generate single-cell gel beads in the emulsion. The cDNA libraries were constructed using Single Cell 5′ Library Construction Kit and i7 Multiplex Kit.

tag: diagnosis

value: lung adenocarcinoma

tag: Sex

value: male

value: blood


title: X_106_pleural effusion

source_name: Human_pleural effusion

tag: tissue

value: pleural effusion


title: X_108_pleural effusion


title: Old PH 1

description: Old PH 1

tag: aav8-luci or cre

tag: quiescent or regenerating


title: 115_hglTHY3

value: thoracic thymus

value: 11 years

tag: genotype


title: OX_380_BL-PV-CD42b

description:
Bone lining perivascular cells
counts.txt
OX_380

value: CD45- Ter119- CD31- LepR+

value: Bone lining perivascular cells

value: GPIba/CD42b Antibody


title: Young PH 2

description: Young PH 2

value: 3 months-old


title: OX_381_CBM-PV-IgG

description:
Central bone marrow perivascular cells
counts.txt
OX_381


title: Old 2

description: Old 2

value: 24 months-old

value: No

value: Quiescent


title: 113_hglBLN1

value: wildtype

value: 3' mRNA UMI


title: X_103_blood


title: Old 3

description: Old 3


title: 114_hglTHY2


title: OX_383_BL-PV-IgG

description:
Bone lining perivascular cells
counts.txt
OX_383

value: IgG Isotype control Antibody


title: OX_385_CBM-PV-IgG

description:
Central bone marrow perivascular cells
counts.txt
OX_385

value: Central bone marrow perivascular cells


title: Young PH 1

description: Young PH 1

value: Regenerating


title: Young 3

description: Young 3


title: OX_377_BL-PV-CD42b

description:
Bone lining perivascular cells
counts.txt
OX_377


title: 113_hglTHY1

value: Naked mole-rat

value: 3 years


title: X_31_blood

value: lung adenocarcinoma

value: female

value: blood


title: OX_378_BL-PV-CD42b

description:
Bone lining perivascular cells
counts.txt
OX_378

value: CD45- Ter119- CD31- LepR+


title: OX_376_CBM-PV-CD42b

description:
Central bone marrow perivascular cells
counts.txt
OX_376