title: Dnmt1_Manipulation_21311

description:
Dnmt1 Manipulation
204875570065_R05C02

source_name: Muscle, Mouse DNA, Tissue

value: Muscle


title: ES_Cells_21701

status: Public on Apr 11 2022

type: genomic

city: Philadelphia

first: Wanding

last: Zhou

state: PA

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

country: USA

institute: Children's Hospital of Philadelphia

description:
Dnmt1 Manipulation
204637490012_R01C01

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
SeSAMe software v1.10
20210916_GEO_processed_matrix.csv (Normalized average Beta)
20210916_GEO_signal_intensity_matrix.csv (Unmethylated and methylated signal intensities)

label: Cy5 and Cy3

molecule: genomic DNA

organism: Mus musculus

source_name: NA, ES Cells, Cell Line

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated from tissue samples using the AllPrep DNA/RNA Mini Kit (QIAGEN)

tag: Sex

value: Male

tag: site

value: Lab 1

tag: strain

tag: cell line

value: J1 Passage 8

tag: tissue

tag: sorted cell type

tag: treatment

tag: pathology


title: Dnmt1_Manipulation_21643

description:
Dnmt1 Manipulation
204875570063_R05C02

value: Female

value: Mixed


title: ES_Cells_21707

description:
Dnmt1 Manipulation
204637490012_R01C02

value: J1 C/C


title: Dnmt1_Manipulation_21317

description:
Dnmt1 Manipulation
204875570020_R05C01

source_name: Small Intestine, Mouse DNA, Tissue

value: Small Intestine

value: Normal


title: Dnmt1_Manipulation_21699

description:
Dnmt1 Manipulation
204875570032_R01C02


title: Dnmt1_Manipulation_21306

description:
Dnmt1 Manipulation
204875570065_R06C01

source_name: Lung, Mouse DNA, Tissue

value: Lung


title: Dnmt1_Manipulation_21227

description:
Dnmt1 Manipulation
204875570036_R01C02


title: Dnmt1_Manipulation_21423

description:
Dnmt1 Manipulation
204879580028_R05C02


title: Dnmt1_Manipulation_21672

description:
Dnmt1 Manipulation
204875570053_R04C01

source_name: Ovary, Mouse DNA, Tissue

value: Ovary


title: Dnmt1_Manipulation_21419

description:
Dnmt1 Manipulation
204879580028_R06C01

source_name: Liver, Mouse DNA, Tissue

value: Liver


title: Dnmt1_Manipulation_21334

description:
Dnmt1 Manipulation
204875570019_R03C01


title: Dnmt1_Manipulation_21363

description:
Dnmt1 Manipulation
204879580028_R04C01


title: Dnmt1_Manipulation_21666

description:
Dnmt1 Manipulation
204875570025_R05C02


title: Dnmt1_Manipulation_21694

description:
Dnmt1 Manipulation
204875570032_R02C01


title: Dnmt1_Manipulation_21391

description:
Dnmt1 Manipulation
204879580028_R05C01


title: Dnmt1_Manipulation_21946

description:
Dnmt1 Manipulation
204879580028_R03C02


title: Dnmt1_Manipulation_21195

description:
Dnmt1 Manipulation
204879580028_R03C01


title: Dnmt1_Manipulation_21309

description:
Dnmt1 Manipulation
204875570065_R03C02

source_name: Kidney, Mouse DNA, Tissue

value: Kidney


title: Dnmt1_Manipulation_21641

description:
Dnmt1 Manipulation
204875570063_R03C02


title: Dnmt1_Manipulation_21669

description:
Dnmt1 Manipulation
204875570053_R01C01


title: Dnmt1_Manipulation_21225

description:
Dnmt1 Manipulation
204875570036_R05C01


title: Dnmt1_Manipulation_21697

description:
Dnmt1 Manipulation
204875570032_R05C01


title: Dnmt1_Manipulation_21283

description:
Dnmt1 Manipulation
204875570062_R03C01


title: Dnmt1_Manipulation_21339

description:
Dnmt1 Manipulation
204875570019_R02C02


title: Dnmt1_Manipulation_21337

description:
Dnmt1 Manipulation
204875570019_R06C01


title: Dnmt1_Manipulation_21222

description:
Dnmt1 Manipulation
204875570036_R02C01


title: Dnmt1_Manipulation_21636

description:
Dnmt1 Manipulation
204875570063_R04C01

source_name: Hind Brain, Mouse DNA, Tissue

value: Hind Brain


title: Dnmt1_Manipulation_21638

description:
Dnmt1 Manipulation
204875570063_R06C01


title: Dnmt1_Manipulation_21278

description:
Dnmt1 Manipulation
204875570058_R04C02


title: Dnmt1_Manipulation_21276

description:
Dnmt1 Manipulation
204875570058_R02C02


title: Dnmt1_Manipulation_21220

description:
Dnmt1 Manipulation
204875570033_R06C02


title: Dnmt1_Manipulation_21664

description:
Dnmt1 Manipulation
204875570025_R03C02


title: Dnmt1_Manipulation_21332

description:
Dnmt1 Manipulation
204875570019_R01C01


title: Dnmt1_Manipulation_21637

description:
Dnmt1 Manipulation
204875570063_R05C01

source_name: Heart, Mouse DNA, Tissue

value: Heart


title: Dnmt1_Manipulation_21333

description:
Dnmt1 Manipulation
204875570019_R02C01


title: Dnmt1_Manipulation_21305

description:
Dnmt1 Manipulation
204875570065_R05C01


title: Dnmt1_Manipulation_21277

description:
Dnmt1 Manipulation
204875570058_R03C02


title: Dnmt1_Manipulation_21223

description:
Dnmt1 Manipulation
204875570036_R03C01


title: Dnmt1_Manipulation_22485

description:
Dnmt1 Manipulation
204879580028_R02C02


title: Dnmt1_Manipulation_21221

description:
Dnmt1 Manipulation
204875570036_R01C01


title: Dnmt1_Manipulation_21665

description:
Dnmt1 Manipulation
204875570025_R04C02


title: Dnmt1_Manipulation_21693

description:
Dnmt1 Manipulation
204875570032_R01C01


title: Dnmt1_Manipulation_21303

description:
Dnmt1 Manipulation
204875570065_R03C01

source_name: Frontal Lobe Brain, Mouse DNA, Tissue

value: Frontal Lobe Brain


title: Dnmt1_Manipulation_21219

description:
Dnmt1 Manipulation
204875570033_R05C02


title: Dnmt1_Manipulation_21691

description:
Dnmt1 Manipulation
204875570044_R05C02


title: Dnmt1_Manipulation_21281

description:
Dnmt1 Manipulation
204875570062_R01C01


title: Dnmt1_Manipulation_21275

description:
Dnmt1 Manipulation
204875570058_R01C02


title: Dnmt1_Manipulation_21663

description:
Dnmt1 Manipulation
204875570025_R02C02


title: Dnmt1_Manipulation_21340

description:
Dnmt1 Manipulation
204875570019_R03C02


title: Dnmt1_Manipulation_21310

description:
Dnmt1 Manipulation
204875570065_R04C02

source_name: Fat, Mouse DNA, Tissue

value: Fat


title: Dnmt1_Manipulation_21282

description:
Dnmt1 Manipulation
204875570062_R02C01


title: Dnmt1_Manipulation_21304

description:
Dnmt1 Manipulation
204875570065_R04C01


title: Dnmt1_Manipulation_21226

description:
Dnmt1 Manipulation
204875570036_R06C01


title: Dnmt1_Manipulation_21670

description:
Dnmt1 Manipulation
204875570053_R02C01


title: Dnmt1_Manipulation_21331

description:
Dnmt1 Manipulation
204875570020_R06C02


title: Dnmt1_Manipulation_21642

description:
Dnmt1 Manipulation
204875570063_R04C02


title: Dnmt1_Manipulation_21285

description:
Dnmt1 Manipulation
204875570062_R05C01

source_name: Esophagus, Mouse DNA, Tissue

value: Esophagus


title: Dnmt1_Manipulation_21692

description:
Dnmt1 Manipulation
204875570044_R06C02


title: Dnmt1_Manipulation_21338

description:
Dnmt1 Manipulation
204875570019_R01C02


title: Dnmt1_Manipulation_21617

description:
Dnmt1 Manipulation
204875570053_R05C01


title: Dnmt1_Manipulation_21698

description:
Dnmt1 Manipulation
204875570032_R06C01


title: Dnmt1_Manipulation_21673

description:
Dnmt1 Manipulation
204875570044_R01C01


title: Dnmt1_Manipulation_21635

description:
Dnmt1 Manipulation
204875570063_R03C01


title: Dnmt1_Manipulation_21274

description:
Dnmt1 Manipulation
204875570058_R06C01

source_name: Colon, Mouse DNA, Tissue

value: Male

value: Colon


title: Dnmt1_Manipulation_21272

description:
Dnmt1 Manipulation
204875570058_R04C01

value: Lab 1


title: Dnmt1_Manipulation_21302

description:
Dnmt1 Manipulation
204875570065_R02C01


title: Dnmt1_Manipulation_21690

description:
Dnmt1 Manipulation
204875570044_R04C02

value: Female


title: Dnmt1_Manipulation_21201

description:
Dnmt1 Manipulation
204875570033_R01C01

value: Mixed


title: Dnmt1_Manipulation_21645

description:
Dnmt1 Manipulation
204875570019_R04C02


title: Dnmt1_Manipulation_21217

description:
Dnmt1 Manipulation
204875570033_R03C02


title: Dnmt1_Manipulation_21313

description:
Dnmt1 Manipulation
204875570020_R02C01


title: Dnmt1_Manipulation_21301

description:
Dnmt1 Manipulation
204875570065_R01C01


title: Dnmt1_Manipulation_21634

description:
Dnmt1 Manipulation
204875570063_R02C01


title: Dnmt1_Manipulation_21633

description:
Dnmt1 Manipulation
204875570063_R01C01


title: Dnmt1_Manipulation_21300

description:
Dnmt1 Manipulation
204875570062_R06C02


title: Dnmt1_Manipulation_21660

description:
Dnmt1 Manipulation
204875570025_R05C01


title: Dnmt1_Manipulation_21273

description:
Dnmt1 Manipulation
204875570058_R05C01


title: Dnmt1_Manipulation_21328

description:
Dnmt1 Manipulation
204875570020_R03C02


title: Dnmt1_Manipulation_21329

description:
Dnmt1 Manipulation
204875570020_R04C02


title: Dnmt1_Manipulation_21688

description:
Dnmt1 Manipulation
204875570044_R02C02


title: Dnmt1_Manipulation_21271

description:
Dnmt1 Manipulation
204875570058_R03C01

source_name: Cecum, Mouse DNA, Tissue

value: Cecum


title: Dnmt1_Manipulation_21661

description:
Dnmt1 Manipulation
204875570025_R06C01


title: Dnmt1_Manipulation_21632

description:
Dnmt1 Manipulation
204875570053_R06C02


title: Dnmt1_Manipulation_21689

description:
Dnmt1 Manipulation
204875570044_R03C02


title: Dnmt1_Manipulation_21216

description:
Dnmt1 Manipulation
204875570033_R02C02


title: Dnmt1_Manipulation_21218

description:
Dnmt1 Manipulation
204875570033_R04C02


title: Dnmt1_Manipulation_21631

description:
Dnmt1 Manipulation
204875570053_R05C02


title: Dnmt1_Manipulation_21662

description:
Dnmt1 Manipulation
204875570025_R01C02


title: Dnmt1_Manipulation_21327

description:
Dnmt1 Manipulation
204875570020_R02C02


title: Dnmt1_Manipulation_21257

description:
Dnmt1 Manipulation
204875570036_R03C02


title: Dnmt1_Manipulation_21659

description:
Dnmt1 Manipulation
204875570025_R04C01


title: Dnmt1_Manipulation_21330

description:
Dnmt1 Manipulation
204875570020_R05C02


title: Backcross_22551

description:
Backcross
204879580035_R01C02

source_name: Tail, Mouse DNA, Tissue

value: Tail


title: Dnmt1_Manipulation_21299

description:
Dnmt1 Manipulation
204875570062_R05C02


title: Backcross_22544

description:
Backcross
204879580034_R06C02

value: Normal


title: Backcross_22529

description:
Backcross
204879580031_R03C02


title: Backcross_22520

description:
Backcross
204879580029_R06C02


title: Backcross_22511

description:
Backcross
204879580029_R03C01


title: Backcross_22486

description:
Backcross
204879580026_R01C01


title: Backcross_20405

description:
Backcross
204875570046_R06C01


title: Backcross_20412

description:
Backcross
204875570020_R01C01


title: Dnmt1_Manipulation_21687

description:
Dnmt1 Manipulation
204875570044_R01C02


title: Dnmt1_Manipulation_21215

description:
Dnmt1 Manipulation
204875570033_R01C02


title: Backcross_22556

description:
Backcross
204879580035_R06C02


title: Backcross_20403

description:
Backcross
204875570046_R04C01


title: Backcross_20399

description:
Backcross
204875570043_R06C02


title: Input_Quantity_Titration_20009_P1_H3

description:
Input Quantity Titration
204617710011_R06C02

source_name: NA, Cell Line DNA, Cell Line


title: Input_Quantity_Titration_21021_P1_A3

description:
Input Quantity Titration
204617710011_R05C01

value: NIH/Swiss


title: Backcross_20397

description:
Backcross
204875570043_R04C02


title: Input_Quantity_Titration_21021_P1_B3

description:
Input Quantity Titration
204617710011_R06C01


title: Input_Quantity_Titration_20009_P1_D3

description:
Input Quantity Titration
204617710011_R02C02


title: Input_Quantity_Titration_21021_P1_F2

description:
Input Quantity Titration
204617710011_R02C01


title: Input_Quantity_Titration_21021_P1_E2

description:
Input Quantity Titration
204617710011_R01C01


title: Input_Quantity_Titration_20009_P1_F3

description:
Input Quantity Titration
204617710011_R04C02


title: Dnmt1_Manipulation_20393_P1_C8

description:
Dnmt1 Manipulation
204617710014_R05C02

value: J1 Passage 18


title: Input_Quantity_Titration_20009_P1_G3

description:
Input Quantity Titration
204617710011_R05C02


title: Dnmt1_Manipulation_20003_P1_C7

description:
Dnmt1 Manipulation
204617710014_R03C01

value: Untreated-Day 24


title: Tumor_DNA_Replicates_20364_P1_E3

description:
Reproducibility
204617710011_R03C02

source_name: NA, Mouse DNA, Tissue

value: Intestinal Tumor

value: Tumor


title: Input_Quantity_Titration_21021_P1_H2

description:
Input Quantity Titration
204617710011_R04C01


title: Tumor_DNA_Replicates_20364_P1_G2

description:
Reproducibility
204617710011_R03C01


title: Input_Quantity_Titration_20009_P1_C3

description:
Input Quantity Titration
204617710011_R01C02


title: Dnmt1_Manipulation_20005_P1_D7

description:
Dnmt1 Manipulation
204617710014_R04C01

value: DAC-Day 12


title: SNPs_20020_P1_H11

description:
Strain SNP
204617710004_R04C01

value: Liver


title: Human_DNA_Titration_20980_P1_D8

description:
Human-mouse Titration
204617710014_R06C02

organism: Homo sapiens

source_name: NA, Human DNA, Tissue

value: 100% Human Blood


title: Dnmt1_Manipulation_20391_P1_A8

description:
Dnmt1 Manipulation
204617710014_R03C02

source_name: NA, ES Cells, Cell Line

value: J1 Passage 7


title: Tissue_Age_Associated_Me_20184_P1_F12

description:
Tissue Biology
204617710004_R04C02

source_name: Small Intestine, Mouse DNA, Tissue

value: Small Intestine


title: Tumor_DNA_Replicates_20385_P1_H12

description:
Reproducibility
204617710004_R06C02

value: Male


title: Dnmt1_Manipulation_20002_P1_B7

description:
Dnmt1 Manipulation
204617710014_R02C01

value: Lab 1

value: Untreated-Day 12


title: SNPs_20022_P1_B12

description:
Strain SNP
204617710004_R06C01

value: Female

value: B6 x DBA/2J


title: SNPs_20021_P1_A12

description:
Strain SNP
204617710004_R05C01

value: NSG


title: Tissue_Age_Associated_Me_20199_P1_G12

description:
Tissue Biology
204617710004_R05C02

value: Normal


title: Tumor_DNA_Replicates_20385_P1_C12

description:
Reproducibility
204617710004_R01C02

value: Mixed


title: Dnmt1_Manipulation_20006_P1_E7

description:
Dnmt1 Manipulation
204617710014_R05C01

value: DAC-Day 24


title: SNPs_20019_P1_G11

description:
Strain SNP
204617710004_R03C01

value: FVB/NJ


title: Tissue_Age_Associated_Me_20050_P1_E12

description:
Tissue Biology
204617710004_R03C02


title: Intestinal_Tumor_Normal_20278_P2_D1

description:
Intestinal Tumor Biology
204617710016_R04C01


title: Dnmt1_Manipulation_20007_P1_F7

description:
Dnmt1 Manipulation
204617710014_R06C01

value: Untreated-Day 0


title: Tumor_DNA_Replicates_20384_P2_D2

description:
Reproducibility
204617710016_R06C02

value: Intestinal Tumor

value: Tumor


title: Intestinal_Tumor_Normal_20277_P2_C1

description:
Intestinal Tumor Biology
204617710016_R03C01


title: Tissue_Age_Associated_Me_20028_P2_F1

description:
Tissue Biology
204617710016_R06C01

value: Liver


title: SNPs_20186_P1_E11

description:
Strain SNP
204617710004_R01C01

source_name: Spleen, Mouse DNA, Tissue

value: Spleen


title: Intestinal_Tumor_Normal_20279_P2_E1

description:
Intestinal Tumor Biology
204617710016_R05C01


title: Tissue_Age_Associated_Me_21009_P2_G1

description:
Tissue Biology
204617710016_R01C02


title: Tumor_DNA_Replicates_21026_P2_A2

description:
Reproducibility
204617710016_R03C02

value: Colon


title: Tumor_DNA_Replicates_20385_P2_A1

description:
Reproducibility
204617710016_R01C01


title: Tissue_Age_Associated_Me_20238_P1_D11

description:
Tissue Biology
204617710021_R06C02

value: Small Intestine


title: Intestinal_Tumor_Normal_20276_P2_B1

description:
Intestinal Tumor Biology
204617710016_R02C01

value: Male


title: SNPs_20257_P1_F11

description:
Strain SNP
204617710004_R02C01

value: Lab 1


title: Tissue_Age_Associated_Me_20993_P1_C11

description:
Tissue Biology
204617710021_R05C02


title: Tissue_Age_Associated_Me_20059_P1_D12

description:
Tissue Biology
204617710004_R02C02


title: Tissue_Age_Associated_Me_20131_P1_E10

description:
Tissue Biology
204617710021_R05C01

value: Frontal Lobe Brain


title: Intestinal_Tumor_Normal_20275_P1_C10

description:
Intestinal Tumor Biology
204617710021_R03C01


title: Tissue_Age_Associated_Me_20237_P1_A11

description:
Tissue Biology
204617710021_R03C02

value: Heart


title: Intestinal_Tumor_Normal_20332_P1_B10

description:
Intestinal Tumor Biology
204617710021_R02C01

value: Female


title: Tissue_Age_Associated_Me_20240_P2_H1

description:
Tissue Biology
204617710016_R02C02


title: Tissue_Age_Associated_Me_20130_P1_H10

description:
Tissue Biology
204617710021_R02C02


title: Tissue_Age_Associated_Me_20025_P1_B11

description:
Tissue Biology
204617710021_R04C02


title: Tissue_Age_Associated_Me_20024_P1_G10

description:
Tissue Biology
204617710021_R01C02


title: Intestinal_Tumor_Normal_20331_P1_A10

description:
Intestinal Tumor Biology
204617710021_R01C01


title: Intestinal_Tumor_Normal_20334_P2_H3

description:
Intestinal Tumor Biology
204617710019_R06C02


title: Lung, Mock3

type: SRA

city: New

first: Sean

last: Houghton

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

library_source: transcriptomic

data_processing:
FastQC (v0.11.5) to check FASTQ quality.
STAR alignment (v 2.6.1)
Salmon quantification (0.11.2)
Genome_build: Mesocricetus_auratus (ensembl MesAur1)
Supplementary_files_format_and_content: Gene count matrix

molecule: total RNA

organism: Mesocricetus auratus

source_name: Mock infection

growth_protocol: Standard Golden Syrian Hamsters

extract_protocol:
Lung tissue was harvested and lysed in TRIZOL and subjected to RNA extraction using Trizol extraction protocol
RNA-seq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Mock infected or SARS-CoV-2 treated hamsters treated either with sesame oil vehicle or disulfiam

value: Lung

tag: infection

value: Mock


title: Input_Quantity_Titration_20009_P2_G3

description:
Input Quantity Titration
204617710019_R05C02


title: Tissue_Age_Associated_Me_20242_P2_B3

description:
Tissue Biology
204617710019_R06C01

value: Kidney

value: Normal


title: Lung, Mock2


title: Input_Quantity_Titration_20009_P2_F3

description:
Input Quantity Titration
204617710019_R04C02


title: Tissue_Age_Associated_Me_20236_P1_F10

description:
Tissue Biology
204617710021_R06C01


title: Tissue_Age_Associated_Me_21012_P2_A3

description:
Tissue Biology
204617710019_R05C01


title: Lung, Mock1


title: Lung, Disulfiram.PostTx6

source_name: Disulfiram post-treatment

value: Post Disulfiram treatment


title: Lung, Disulfiram.PostTx5


title: Input_Quantity_Titration_20009_P2_E3

description:
Input Quantity Titration
204617710019_R03C02


title: Lung, Disulfiram.PostTx3


title: Lung, Disulfiram.PostTx4


title: Lung, Disulfiram.PostTx2


title: Tissue_Age_Associated_Me_20030_P2_H2

description:
Tissue Biology
204617710019_R04C01

source_name: Lung, Mouse DNA, Tissue


title: Intestinal_Tumor_Normal_20274_P2_F2

description:
Intestinal Tumor Biology
204617710019_R02C01


title: Tumor_DNA_Replicates_20364_P2_G2

description:
Reproducibility
204617710019_R03C01


title: Input_Quantity_Titration_20009_P2_D3

description:
Input Quantity Titration
204617710019_R02C02


title: Tissue_Age_Associated_Me_20023_P1_D10

description:
Tissue Biology
204617710021_R04C01


title: Lung, Disulfiram.PreTx5

source_name: Disulfiram pre-treatment

value: Pre Disulfiram treatment


title: Lung, Disulfiram.PostTx1


title: Lung, Disulfiram.PreTx4


title: Input_Quantity_Titration_20009_P2_C3

description:
Input Quantity Titration
204617710019_R01C02


title: Tumor_DNA_Replicates_20385_P2_E2

description:
Reproducibility
204617710019_R01C01

value: Mixed

value: Intestinal Tumor


title: Lung, Disulfiram.PreTx3


title: Lung, Disulfiram.PreTx2


title: Human_DNA_Titration_20992_P1_H9

description:
Human-mouse Titration
204617710018_R06C02

value: Fat


title: Human_DNA_Titration_20991_P1_G9

description:
Human-mouse Titration
204617710018_R05C02

value: Spleen


title: Human_DNA_Titration_20990_P1_F9

description:
Human-mouse Titration
204617710018_R04C02

organism:
Homo sapiens
Mus musculus

source_name: NA, Mouse Human DNA, Tissue

value: 10% Human Blood, 90% Mouse Fat


title: Lung, Sesame_oil_Vehicle_daily3

source_name: Sesame oil vehicle daily

value: Sesame oil vehicle


title: Human_DNA_Titration_20984_P1_H8

description:
Human-mouse Titration
204617710018_R04C01

value: Male

value: 25% Human Blood, 75% Mouse Spleen


title: Human_DNA_Titration_20989_P1_E9

description:
Human-mouse Titration
204617710018_R03C02

value: Lab 1

value: 25% Human Blood, 75% Mouse Fat


title: Lung, Sesame_oil_Vehicle_daily6


title: Lung, Sesame_oil_Vehicle_daily4


title: Lung, Sesame_oil_Vehicle_daily2


title: Lung, Sesame_oil_Vehicle_daily5


title: Human_DNA_Titration_20983_P1_G8

description:
Human-mouse Titration
204617710018_R03C01

value: 50% Human Blood, 50% Mouse Spleen


title: Lung, Sesame_oil_Vehicle_daily1

value: Lung


title: Human_DNA_Titration_20981_P1_E8

description:
Human-mouse Titration
204617710018_R01C01

value: 90% Human Blood, 10% Mouse Spleen


title: Human_DNA_Titration_20987_P1_C9

description:
Human-mouse Titration
204617710018_R01C02

value: Female

value: 75% Human Blood, 25% Mouse Fat


title: Human_DNA_Titration_20988_P1_D9

description:
Human-mouse Titration
204617710018_R02C02

value: 50% Human Blood, 50% Mouse Fat


title: Tissue_Age_Associated_Me_20239_P1_H6

description:
Tissue Biology
204617710010_R06C02

value: Normal


title: Human_DNA_Titration_20986_P1_B9

description:
Human-mouse Titration
204617710018_R06C01

value: 90% Human Blood, 10% Mouse Fat


title: Tissue_Age_Associated_Me_20026_P1_B6

description:
Tissue Biology
204617710010_R06C01

source_name: Stomach, Mouse DNA, Tissue

value: Stomach


title: Intestinal_Tumor_Normal_20322_P1_A6

description:
Intestinal Tumor Biology
204617710010_R05C01

value: Small Intestine


title: Human_DNA_Titration_20985_P1_A9

description:
Human-mouse Titration
204617710018_R05C01

value: 10% Human Blood, 90% Mouse Spleen


title: Tissue_Age_Associated_Me_21013_P1_G6

description:
Tissue Biology
204617710010_R05C02

value: Spleen


title: Lung, Disulfiram.PreTx1

value: Pre Disulfiram treatment


title: matched normal skin of patient 40 [40B]

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

data_processing:
Paired ends reads were cleaned using Trimmomatic (Bolger & Giorgi, 2014) with the following parameters LEADING:10 TRAILING:10 SLIDINGWINDOW:4:15 MINLEN:40 to remove adaptors and low quality reads.
Treatment samples with a minimum of 2,000 reads were kept for further analysis. After this, the chimeric reads were searched against the 16S rRNA Gold database with the default UCHIME (4.2) parameters.
Next, the cleaned reads were merged with PEAR (0.9.10). Finally, OTUs were generated by open reference of QIIME1.9.1  pipeline.
The databases used for taxonomic assignment were Silva 128 97_otus_16S.fasta. Only OTUs with the minimum total observation count of greater than 312 across all samples were retained.
Alpha- and Beta- diversity were also analyzed using QIIME191. Paired t-test was done for differential analysis of significant OTUs between tumor and healthy tissues. P–value <0.05 and fold change above or below 1.5  was considered statistically significant. Heatmap of significant OTUs was generated using pheatmap.
Genome_build: hg19
Supplementary_files_format_and_content: otu_table.txt

organism: organismal metagenomes

source_name: skin swab from patients with MF_normal skin

growth_protocol: Microorganisms are naturally grown on the skinspatients.

extract_protocol:
MicrobiomeInsight did the extraction. DNA is extracted from samples using the Qiagen MagAttract PowerSoil DNA KF Kit (Formerly MO BIO PowerSoil DNA Kit) optimized for the Thermofisher KingFisher robot. This kit uses magnetic beads to specifically capture DNA while excluding organic inhibitors. In-house testing has shown this kit to have a good balance of DNA yield and quality as demonstrated on a variety of environmental sample types. DNA quantification and quality checks are done via Qubit. The high-fidelity Phusion polymerase for amplification of marker genes will be used. If extractions contain some carry-over inhibition or a high concentration of DNA, typically1:1 and 1:10 dilutions will be tested and run the PCR products on gels for verification. PCR is done with dual-barcoded primers targeting either the prokaryotic 16S DNA with modified V4 skin cutaneous microbiome protocol. Samples with failed PCRs (or spurious bands) are re-amplified by optimizing PCR conditions. The PCR reactions are cleaned-up and normalized using the high-throughput SequalPrep 96-well Plate Kit.
Samples are then pooled to make one library that is quantified accurately with the KAPA qPCR Library Quant kit. Library pools are sequenced on the Illumina MiSeq using the corresponding primer sets for prokaryotic 16S V4_skin.

treatment_protocol: samples were stored at -80C.

tag: cell type

value: skin swab

tag: type

value: stage IA

tag: molecule subtype

value: 16s rRNA


title: matched normal skin of patient 39 [39B]

value: stage IIIA


title: Tumor_DNA_Replicates_21026_P1_E6

description:
Reproducibility
204617710010_R03C02

source_name: Colon, Mouse DNA, Tissue

value: Male

value: Lab 1

value: Colon

value: Tumor


title: Intestinal_Tumor_Normal_20321_P1_H5

description:
Intestinal Tumor Biology
204617710010_R04C01

value: Female


title: Tissue_Age_Associated_Me_20253_P1_D6

description:
Tissue Biology
204617710010_R02C02


title: Human_DNA_Titration_20982_P1_F8

description:
Human-mouse Titration
204617710018_R02C01

value: 75% Human Blood, 25% Mouse Spleen


title: Intestinal_Tumor_Normal_20320_P1_G5

description:
Intestinal Tumor Biology
204617710010_R03C01

value: Normal


title: matched normal skin of patient 36 [36B]

value: stage IB

value: topical steroid


title: matched normal skin of patient 38 [38B]

value: stage IIIB

value: phototherapy


title: matched normal skin of patient 37 [37B]


title: Intestinal_Tumor_Normal_20319_P1_F5

description:
Intestinal Tumor Biology
204617710010_R02C01

value: Small Intestine


title: matched normal skin of patient 32 [32B]


title: Tissue_Age_Associated_Me_21006_P1_C6

description:
Tissue Biology
204617710010_R01C02

value: Stomach


title: Tumor_DNA_Replicates_20384_P1_E5

description:
Reproducibility
204617710010_R01C01

value: Intestinal Tumor


title: matched normal skin of patient 31 [31B]

value: skin swab

value: stage IA


title: matched normal skin of patient 30 [30B]

value: 16s rRNA


title: Tissue_Age_Associated_Me_20027_P1_F6

description:
Tissue Biology
204617710010_R04C02

value: Spleen


title: matched normal skin of patient 29 [29B]

value: topical bexarotene


title: DNA_Methylation_Titration_20012_P1_F1

description:
DNA Methylation Titration
204617710015_R06C01

source_name: NA, EpigenDX Mouse DNA, EpigenDX DNA

value: Lab 1

value: EpigenDX Mouse DNA


title: matched normal skin of patient 28 [28B]

value: stage IIB


title: Tumor_DNA_Replicates_20364_P1_C2

description:
Reproducibility
204617710015_R05C02

value: Male

value: Tumor


title: PC9/GR replicate 2

type: RNA

city: Shijiazhuang

first: Yunlong

last: Jia

state: Hebei

address: Tianshan Road

department: Department of Tumor Immunotherapy

country: China

institute: Fourth Hospital of Hebei Medical University

description: gene expression in gefitinib-resistant PC9/GR cells

hyb_protocol: 0.6 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 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Sino Human ceRNA 3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565CA) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized by Quantile algorithm,R package “limma”. Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: lung adenocarcinoma cell PC9/GR (derived from PC9)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The cells were maintained in RPMI-1640 supplemented with 10% FBS (Gibco) at 37°C, with 5% CO2 and humidified atmosphere

extract_protocol: RNA was extracted by Trizol (Thermo Fisher Scientific, 15596026) following the manufacturer's instructions

treatment_protocol: To generate a gefitinib-resistant cell line, we exposed PC9 cells to increasing concentrations of gefitinib. Gefitinib concentrations were increased stepwise from 8 to 100 nM when the cells resumed growth kinetics similar to the untreated parental cells. Cells with the ability to grow in 100 nM of gefitinib were obtained 6 months after the initial drug exposure. PC9/GR cell line was isolated as a clone.

tag: phenotype

value: gefitinib-resistant


title: matched normal skin of patient 34 [34B]

value: stage IB


title: PC9 replicate 3

description: gene expression in gefitinib-sensitive PC9 cells

source_name: lung adenocarcinoma cell PC9 (parental)

value: gefitinib-sensitive


title: DNA_Methylation_Titration_20015_P1_E1

description:
DNA Methylation Titration
204617710015_R05C01

value: Female


title: PC9/GR replicate 3


title: PC9 replicate 2


title: PC9/GR replicate 1


title: matched normal skin of patient 33 [33B]


title: matched normal skin of patient 27 [27B]

value: topical steroid


title: DNA_Methylation_Titration_20010_P1_D1

description:
DNA Methylation Titration
204617710015_R04C01


title: PC9 replicate 1


title: DNA_Methylation_Titration_20012_P1_C1

description:
DNA Methylation Titration
204617710015_R03C01


title: DNA_Methylation_Titration_20011_P1_H1

description:
DNA Methylation Titration
204617710015_R02C02


title: matched normal skin of patient 26 [26B]

value: stage IVA


title: DNA_Methylation_Titration_20010_P1_A1

description:
DNA Methylation Titration
204617710015_R01C01


title: matched normal skin of patient 22 [22B]

value: stage IIA


title: DNA_Methylation_Titration_20013_P1_A2

description:
DNA Methylation Titration
204617710015_R03C02


title: matched normal skin of patient 21 [21B]

value: skin swab


title: matched normal skin of patient 23 [23B]

value: stage IA


title: matched normal skin of patient 19 [19B]

value: 16s rRNA


title: matched normal skin of patient 24 [24B]

value: nitrogen mustard


title: DNA_Methylation_Titration_20015_P1_B1

description:
DNA Methylation Titration
204617710015_R02C01


title: matched normal skin of patient 20 [20B]


title: matched normal skin of patient 25 [25B]


title: DNA_Methylation_Titration_20014_P1_G1

description:
DNA Methylation Titration
204617710015_R01C02


title: Input_Quantity_Titration_21021_P1_D2

description:
Input Quantity Titration
204617710015_R06C02

source_name: NA, Cell Line DNA, Cell Line

value: NIH/Swiss


title: Tumor_DNA_Replicates_20384_P1_D5

description:
Reproducibility
204617710012_R06C02

source_name: NA, Mouse DNA, Tissue

value: Lab 1

value: Intestinal Tumor


title: matched normal skin of patient 18 [18B]


title: DNA_Methylation_Titration_20016_P1_B2

description:
DNA Methylation Titration
204617710015_R04C02

value: EpigenDX Mouse DNA


title: Input_Quantity_Titration_20009_P1_F4

description:
Input Quantity Titration
204617710012_R06C01

value: Male


title: matched normal skin of patient 17 [17B]


title: matched normal skin of patient 16 [16B]


title: Input_Quantity_Titration_20009_P1_C5

description:
Input Quantity Titration
204617710012_R05C02


title: Input_Quantity_Titration_20009_P1_E4

description:
Input Quantity Titration
204617710012_R05C01


title: matched normal skin of patient 14 [14B]


title: Input_Quantity_Titration_20009_P1_B5

description:
Input Quantity Titration
204617710012_R04C02


title: Input_Quantity_Titration_20009_P1_D4

description:
Input Quantity Titration
204617710012_R04C01


title: matched normal skin of patient 15 [15B]


title: matched normal skin of patient 13 [13B]


title: Tumor_DNA_Replicates_20384_P1_A5

description:
Reproducibility
204617710012_R03C02

value: Tumor


title: matched normal skin of patient 10 [10B]


title: matched normal skin of patient 9 [9B]

value: stage IIB


title: matched normal skin of patient 11 [11B]

value: Imiquimod


title: Tumor_DNA_Replicates_21026_P1_B4

description:
Reproducibility
204617710012_R02C01

value: Colon


title: Intestinal_Tumor_Normal_20333_P1_C4

description:
Intestinal Tumor Biology
204617710012_R03C01

value: Female

value: Small Intestine


title: matched normal skin of patient 12 [12B]

value: topical steroid


title: Intestinal_Tumor_Normal_20317_P1_G4

description:
Intestinal Tumor Biology
204617710012_R01C02


title: matched normal skin of patient 3 [3B]


title: matched normal skin of patient 6 [6B]

value: stage IB


title: matched normal skin of patient 8 [8B]

value: skin swab

value: stage IVA


title: Intestinal_Tumor_Normal_20318_P1_H4

description:
Intestinal Tumor Biology
204617710012_R02C02

value: Normal


title: matched normal skin of patient 7 [7B]

value: stage IA

value: nitrogen mustard

value: 16s rRNA


title: Input_Quantity_Titration_20009_P1_H3_REP

description:
Input Quantity Titration
204637490027_R06C02

value: Lab 2


title: Input_Quantity_Titration_21021_P1_A3_REP

description:
Input Quantity Titration
204637490027_R05C01

value: NIH/Swiss


title: matched normal skin of patient 4 [4B]

value: topical steroid/Imiquimod


title: Tumor_DNA_Replicates_21026_P1_A4

description:
Reproducibility
204617710012_R01C01

value: Male

value: Lab 1

value: Tumor


title: Input_Quantity_Titration_21021_P1_B3_REP

description:
Input Quantity Titration
204637490027_R06C01


title: Input_Quantity_Titration_20009_P1_F3_REP

description:
Input Quantity Titration
204637490027_R04C02


title: Input_Quantity_Titration_20009_P1_G3_REP

description:
Input Quantity Titration
204637490027_R05C02


title: matched normal skin of patient 5 [5B]

value: stage IIB


title: matched normal skin of patient 2 [2B]

value: phototherapy


title: matched normal skin of patient 1 [1B]

value: topical steroid/bexarotene/phototherapy


title: Input_Quantity_Titration_21021_P1_H2_REP

description:
Input Quantity Titration
204637490027_R04C01


title: CTCL lesion of patient 40 [40A]

source_name: skin swab from patients with MF_Affected skin


title: CTCL lesion of patient 39 [39A]

value: stage IIIA


title: CTCL lesion of patient 38 [38A]

value: stage IIIB


title: Tumor_DNA_Replicates_20364_P1_E3_REP

description:
Reproducibility
204637490027_R03C02

value: Intestinal Tumor


title: Tumor_DNA_Replicates_20364_P1_G2_REP

description:
Reproducibility
204637490027_R03C01


title: Input_Quantity_Titration_20009_P1_D3_REP

description:
Input Quantity Titration
204637490027_R02C02


title: Input_Quantity_Titration_20009_P1_C3_REP

description:
Input Quantity Titration
204637490027_R01C02


title: Input_Quantity_Titration_21021_P1_F2_REP

description:
Input Quantity Titration
204637490027_R02C01


title: Human_DNA_Titration_20980_P1_D8_REP

description:
Human-mouse Titration
204637490025_R06C02

source_name: NA, Human DNA, Tissue

value: Female

value: 100% Human Blood


title: CTCL lesion of patient 33 [33A]

value: skin swab

value: stage IA


title: Dnmt1_Manipulation_20006_P1_E7_REP

description:
Dnmt1 Manipulation
204637490025_R05C01


title: CTCL lesion of patient 37 [37A]

value: stage IB

value: 16s rRNA


title: Dnmt1_Manipulation_20007_P1_F7_REP

description:
Dnmt1 Manipulation
204637490025_R06C01

value: Lab 2


title: Input_Quantity_Titration_21021_P1_E2_REP

description:
Input Quantity Titration
204637490027_R01C01

value: NIH/Swiss


title: CTCL lesion of patient 36 [36A]

value: topical steroid


title: CTCL lesion of patient 34 [34A]


title: Dnmt1_Manipulation_20005_P1_D7_REP

description:
Dnmt1 Manipulation
204637490025_R04C01


title: Dnmt1_Manipulation_21025_P1_B8_REP

description:
Dnmt1 Manipulation
204637490025_R04C02

source_name: NA, ES Cells, Cell Line

value: Male

value: J1 PH/+


title: CTCL lesion of patient 31 [31A]


title: CTCL lesion of patient 28 [28A]

value: stage IIB


title: CTCL lesion of patient 32 [32A]


title: Dnmt1_Manipulation_20393_P1_C8_REP

description:
Dnmt1 Manipulation
204637490025_R05C02

value: J1 P/H


title: CTCL lesion of patient 30 [30A]


title: CTCL lesion of patient 29 [29A]

value: topical bexarotene


title: CTCL lesion of patient 26 [26A]

value: stage IVA


title: Dnmt1_Manipulation_20003_P1_C7_REP

description:
Dnmt1 Manipulation
204637490025_R03C01


title: Dnmt1_Manipulation_20391_P1_A8_REP

description:
Dnmt1 Manipulation
204637490025_R03C02


title: CTCL lesion of patient 27 [27A]


title: CTCL lesion of patient 25 [25A]


title: CTCL lesion of patient 24 [24A]

value: nitrogen mustard


title: Dnmt1_Manipulation_21027_P1_H7_REP

description:
Dnmt1 Manipulation
204637490025_R02C02


title: Dnmt1_Manipulation_20002_P1_B7_REP

description:
Dnmt1 Manipulation
204637490025_R02C01


title: CTCL lesion of patient 22 [22A]

value: stage IIA


title: Dnmt1_Manipulation_20008_P1_G7_REP

description:
Dnmt1 Manipulation
204637490025_R01C02

value: Female


title: Dnmt1_Manipulation_20001_P1_A7_REP

description:
Dnmt1 Manipulation
204637490025_R01C01


title: CTCL lesion of patient 21 [21A]


title: Tumor_DNA_Replicates_20385_P1_H12_REP

description:
Reproducibility
204637490021_R06C02

value: Mixed

value: Intestinal Tumor

value: Tumor


title: Tissue_Age_Associated_Me_20199_P1_G12_REP

description:
Tissue Biology
204637490021_R05C02

source_name: Small Intestine, Mouse DNA, Tissue

value: Small Intestine

value: Normal


title: CTCL lesion of patient 20 [20A]

value: skin swab

value: 16s rRNA


title: CTCL lesion of patient 18 [18A]

value: stage IB


title: Tissue_Age_Associated_Me_20184_P1_F12_REP

description:
Tissue Biology
204637490021_R04C02

value: Lab 2


title: CTCL lesion of patient 19 [19A]


title: SNPs_20021_P1_A12_REP

description:
Strain SNP
204637490021_R05C01

source_name: Liver, Mouse DNA, Tissue

value: Male

value: NSG

value: Liver


title: SNPs_20019_P1_G11_REP

description:
Strain SNP
204637490021_R03C01

value: FVB/NJ


title: CTCL lesion of patient 16 [16A]


title: CTCL lesion of patient 14 [14A]

value: topical steroid


title: SNPs_20020_P1_H11_REP

description:
Strain SNP
204637490021_R04C01


title: SNPs_20022_P1_B12_REP

description:
Strain SNP
204637490021_R06C01

value: B6 x DBA/2J


title: CTCL lesion of patient 15 [15A]

value: stage IA


title: CTCL lesion of patient 13 [13A]


title: CTCL lesion of patient 12 [12A]

value: stage IIB


title: CTCL lesion of patient 23 [23A]


title: Tumor_DNA_Replicates_20385_P1_C12_REP

description:
Reproducibility
204637490021_R01C02

value: Mixed


title: SNPs_20257_P1_F11_REP

description:
Strain SNP
204637490021_R02C01

value: Colon


title: Tumor_DNA_Replicates_20384_P2_D2_REP

description:
Reproducibility
204637490019_R06C02

value: Intestinal Tumor

value: Tumor


title: SNPs_20186_P1_E11_REP

description:
Strain SNP
204637490021_R01C01

source_name: Spleen, Mouse DNA, Tissue

value: Female

value: Spleen

value: Normal


title: Intestinal_Tumor_Normal_20330_P2_C2_REP

description:
Intestinal Tumor Biology
204637490019_R05C02

value: Small Intestine


title: CTCL lesion of patient 17 [17A]

value: skin swab

value: 16s rRNA


title: Tissue_Age_Associated_Me_20059_P1_D12_REP

description:
Tissue Biology
204637490021_R02C02

value: Lab 2


title: CTCL lesion of patient 9 [9A]


title: CTCL lesion of patient 7 [7A]

value: nitrogen mustard


title: CTCL lesion of patient 10 [10A]

value: stage IB


title: Tissue_Age_Associated_Me_20050_P1_E12_REP

description:
Tissue Biology
204637490021_R03C02


title: CTCL lesion of patient 6 [6A]


title: Tumor_DNA_Replicates_21026_P2_A2_REP

description:
Reproducibility
204637490019_R03C02

value: Male


title: CTCL lesion of patient 4 [4A]

value: topical steroid/Imiquimod


title: Tissue_Age_Associated_Me_20240_P2_H1_REP

description:
Tissue Biology
204637490019_R02C02

value: Liver


title: CTCL lesion of patient 2 [2A]

value: stage IA

value: phototherapy


title: Intestinal_Tumor_Normal_20277_P2_C1_REP

description:
Intestinal Tumor Biology
204637490019_R03C01


title: Intestinal_Tumor_Normal_20276_P2_B1_REP

description:
Intestinal Tumor Biology
204637490019_R02C01


title: Tissue_Age_Associated_Me_21009_P2_G1_REP

description:
Tissue Biology
204637490019_R01C02

value: Mixed


title: CTCL lesion of patient 11 [11A]

value: Imiquimod


title: CTCL lesion of patient 1  [1A]

value: topical steroid/bexarotene/phototherapy


title: Tissue_Age_Associated_Me_20028_P2_F1_REP

description:
Tissue Biology
204637490019_R06C01

value: Female


title: CTCL lesion of patient 8 [8A]

value: stage IVA

value: topical steroid


title: Tissue_Age_Associated_Me_20238_P1_D11_REP

description:
Tissue Biology
204637490017_R06C02

value: Small Intestine

value: Normal


title: Tissue_Age_Associated_Me_20993_P1_C11_REP

description:
Tissue Biology
204637490017_R05C02


title: CTCL lesion of patient 5 [5A]

value: skin swab

value: stage IIB

value: 16s rRNA


title: Intestinal_Tumor_Normal_20329_P2_B2_REP

description:
Intestinal Tumor Biology
204637490019_R04C02

value: Lab 2

value: Tumor


title: Tissue_Age_Associated_Me_20236_P1_F10_REP

description:
Tissue Biology
204637490017_R06C01

source_name: Frontal Lobe Brain, Mouse DNA, Tissue

value: Male

value: Frontal Lobe Brain


title: Tissue_Age_Associated_Me_20025_P1_B11_REP

description:
Tissue Biology
204637490017_R04C02


title: Tissue_Age_Associated_Me_20131_P1_E10_REP

description:
Tissue Biology
204637490017_R05C01


title: Intestinal_Tumor_Normal_20279_P2_E1_REP

description:
Intestinal Tumor Biology
204637490019_R05C01


title: Intestinal_Tumor_Normal_20278_P2_D1_REP

description:
Intestinal Tumor Biology
204637490019_R04C01


title: Tissue_Age_Associated_Me_20023_P1_D10_REP

description:
Tissue Biology
204637490017_R04C01


title: CTCL lesion of patient 3 [3A]

value: stage IA


title: Tissue_Age_Associated_Me_20237_P1_A11_REP

description:
Tissue Biology
204637490017_R03C02

source_name: Heart, Mouse DNA, Tissue

value: Heart


title: Intestinal_Tumor_Normal_20332_P1_B10_REP

description:
Intestinal Tumor Biology
204637490017_R02C01


title: Tissue_Age_Associated_Me_20130_P1_H10_REP

description:
Tissue Biology
204637490017_R02C02


title: Intestinal_Tumor_Normal_20275_P1_C10_REP

description:
Intestinal Tumor Biology
204637490017_R03C01


title: Tumor_DNA_Replicates_20385_P2_A1_REP

description:
Reproducibility
204637490019_R01C01

value: Mixed

value: Intestinal Tumor


title: Tissue_Age_Associated_Me_20024_P1_G10_REP

description:
Tissue Biology
204637490017_R01C02


title: Intestinal_Tumor_Normal_20331_P1_A10_REP

description:
Intestinal Tumor Biology
204637490017_R01C01


title: Intestinal_Tumor_Normal_20334_P2_H3_REP

description:
Intestinal Tumor Biology
204637490016_R06C02


title: Tissue_Age_Associated_Me_21012_P2_A3_REP

description:
Tissue Biology
204637490016_R05C01

source_name: Kidney, Mouse DNA, Tissue

value: Kidney


title: Tissue_Age_Associated_Me_20242_P2_B3_REP

description:
Tissue Biology
204637490016_R06C01


title: Input_Quantity_Titration_20009_P2_G3_REP

description:
Input Quantity Titration
204637490016_R05C02


title: Tissue_Age_Associated_Me_20030_P2_H2_REP

description:
Tissue Biology
204637490016_R04C01

source_name: Lung, Mouse DNA, Tissue

value: Female

value: Lung


title: Input_Quantity_Titration_20009_P2_F3_REP

description:
Input Quantity Titration
204637490016_R04C02


title: Tumor_DNA_Replicates_20364_P2_G2_REP

description:
Reproducibility
204637490016_R03C01


title: Input_Quantity_Titration_20009_P2_D3_REP

description:
Input Quantity Titration
204637490016_R02C02


title: Input_Quantity_Titration_20009_P2_E3_REP

description:
Input Quantity Titration
204637490016_R03C02


title: Male-natural-1467-3

first: Yemin

last: Lan

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Mouse Methylation Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Sesame R package

source_name: Term placenta

growth_protocol: All animals were housed in polysulfone cages containing drinking water and chow (Laboratory Autoclavable Rodent Diet 5010, LabDiet) ad libitum.

extract_protocol: Genomic DNA was extracted and purified from Placentas samples using Phenol:Chloroform according to lab protocols. Then samples were Bisulfite-treated using Qiagen EpiTect Bisulfite Conversion Kit.

treatment_protocol: Placentas were collected at E18.5, snap frozen in liquid nitrogen and stored at -80C for DNA extraction.

tag: gender

value: Term placenta

tag: sample type

value: natural


title: Male-natural-1123-7


title: Male-natural-1135-9


title: Male-blastocyst-1458-2

value: blastocyst


title: Male-natural-1466-1


title: Input_Quantity_Titration_20009_P2_C3_REP

description:
Input Quantity Titration
204637490016_R01C02


title: Tumor_DNA_Replicates_20385_P2_E2_REP

description:
Reproducibility
204637490016_R01C01


title: Male-morula-1064-1

value: morula


title: Male-natural-1122-5


title: Male-morula-1624-5


title: Male-morula-1109-3


title: Female-natural-1466-4


title: Male-blastocyst-1362-2


title: Male-morula-1290-5


title: Male-morula-1049-2


title: Human_DNA_Titration_20986_P1_B9_REP

description:
Human-mouse Titration
204637490009_R06C01

source_name: NA, Mouse Human DNA, Tissue

value: 90% Human Blood, 10% Mouse Fat


title: Male-blastocyst-1637-3


title: Male-blastocyst-1363-1


title: Human_DNA_Titration_20992_P1_H9_REP

description:
Human-mouse Titration
204637490009_R06C02

source_name: Fat, Mouse DNA, Tissue

value: Fat


title: Male-morula-1109-1


title: Human_DNA_Titration_20991_P1_G9_REP

description:
Human-mouse Titration
204637490009_R05C02

value: Lab 2

value: Spleen


title: Female-morula-1624-6


title: Human_DNA_Titration_20985_P1_A9_REP

description:
Human-mouse Titration
204637490009_R05C01

value: Male

value: 10% Human Blood, 90% Mouse Spleen


title: Intestinal_Tumor_Normal_20274_P2_F2_REP

description:
Intestinal Tumor Biology
204637490016_R02C01

value: Small Intestine

value: Tumor


title: Female-natural-1122-3


title: Female-natural-1135-7


title: Female-natural-1123-10


title: Male-blastocyst-1358-2


title: Female-morula-1290-4


title: Female-morula-1610-1


title: Male-blastocyst-1620-2


title: Human_DNA_Titration_20989_P1_E9_REP

description:
Human-mouse Titration
204637490009_R03C02

value: 25% Human Blood, 75% Mouse Fat


title: Female-natural-1467-9


title: Human_DNA_Titration_20988_P1_D9_REP

description:
Human-mouse Titration
204637490009_R02C02

value: 50% Human Blood, 50% Mouse Fat


title: Human_DNA_Titration_20984_P1_H8_REP

description:
Human-mouse Titration
204637490009_R04C01

value: 25% Human Blood, 75% Mouse Spleen


title: Human_DNA_Titration_20982_P1_F8_REP

description:
Human-mouse Titration
204637490009_R02C01

value: 75% Human Blood, 25% Mouse Spleen


title: Female-morula-1109-5

value: Female


title: Human_DNA_Titration_20987_P1_C9_REP

description:
Human-mouse Titration
204637490009_R01C02

value: 75% Human Blood, 25% Mouse Fat


title: WT.4h_TGFB1.R4

city: Melbourne

first: Melissa

last: Davis

state: Victoria

address: 1G Royal Parade

department: Bioinformatics Division

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
fastqc was used to assess the quality of reads and to check for any adapter contamination. trimmomatic was used to trim any bases with sequencing quality less than 20 from the end of the reads and to remove Illumina adapters. Only reads largers than 20bp in length after trimming were kept.
Reads were aligned to mm10 using subread. Duplicate reads in the resulting BAM  les were marked using picard tool.
The aligned reads were sorted and indexed in samtools. Reads were summarised at the gene level using featureCounts.
Assembly: mm10
Supplementary files format and content: Tab-delimited txt file of raw gene counts in rows and samples in columns. Gene ids are ENTREZ ids

source_name: Natural Killer cells

extract_protocol:
Single-cell suspensions from indicated organs were prepared; 106 NK cells per replicate or culture condition were prepared for RNA sequencing. RNA was extracted from sorted ex vivo NK cells using the RNeasy Plus Mini Kit (#74134, QIAGEN, Hilden, Germany), according to the manufacturer’s instructions.
Purified RNA was measured using an Agilent 2200 TapeStation System (Agilent) with High Sensitivity (HS) RNA ScreenTapes (#5067-5579, Agilent). Next-generation sequencing libraries were generated from 100 ng of high-quality RNA samples with clear 18S and 28S peaks and RNA Integrity Number values ³ 9, using the NEBNext Ultra II Directional RNA Library Prep Kit (#E7760L, New England Biolabs) for Illumina, according to the manufacturer’s instructions.

tag: condition

value: WT

tag: biological replicate


title: TGFBRII_KO.24h_TGFB1.R1


title: TGFBRII_KO.4h_TGFB1.R3


title: WT.4h_TGFB1.R1


title: CIS_KO.4h_TGFB1.R1


title: Human_DNA_Titration_20981_P1_E8_REP

description:
Human-mouse Titration
204637490009_R01C01

tag: Sex

value: 90% Human Blood, 10% Mouse Spleen


title: CIS_KO.24h_TGFB1.R3


title: Female-morula-1064-3

value: Term placenta

value: morula


title: CIS_KO.24h_TGFB1.R4


title: WT.unstimulated.R2

value: unstimulated


title: Tissue_Age_Associated_Me_21013_P1_G6_REP

description:
Tissue Biology
204637490007_R05C02

tag: site

value: Lab 2

value: Normal


title: Tissue_Age_Associated_Me_20239_P1_H6_REP

description:
Tissue Biology
204637490007_R06C02

value: Male

tag: strain

value: Spleen


title: Intestinal_Tumor_Normal_20322_P1_A6_REP

description:
Intestinal Tumor Biology
204637490007_R05C01

tag: cell line

value: Small Intestine


title: WT.unstimulated.R3


title: Tissue_Age_Associated_Me_20027_P1_F6_REP

description:
Tissue Biology
204637490007_R04C02

tag: tissue


title: CIS_KO.4h_TGFB1.R2


title: WT.unstimulated.R4


title: Intestinal_Tumor_Normal_20321_P1_H5_REP

description:
Intestinal Tumor Biology
204637490007_R04C01

tag: sorted cell type

value: Tumor


title: Female-morula-1049-1


title: CIS_KO.unstimulated.R1

tag: treatment


title: Tissue_Age_Associated_Me_20026_P1_B6_REP

description:
Tissue Biology
204637490007_R06C01

source_name: Stomach, Mouse DNA, Tissue

value: Stomach

tag: pathology


title: Female-blastocyst-1637-1

value: blastocyst


title: Intestinal_Tumor_Normal_20320_P1_G5_REP

description:
Intestinal Tumor Biology
204637490007_R03C01


title: Tumor_DNA_Replicates_21026_P1_E6_REP

description:
Reproducibility
204637490007_R03C02

source_name: Colon, Mouse DNA, Tissue

value: Colon


title: Female-blastocyst-1458-1


title: Tissue_Age_Associated_Me_20253_P1_D6_REP

description:
Tissue Biology
204637490007_R02C02


title: CIS_KO.unstimulated.R4


title: Female-blastocyst-1620-1


title: CIS_KO.unstimulated.R3


title: CIS_KO.unstimulated.R2


title: Female-blastocyst-1363-4


title: Tissue_Age_Associated_Me_21006_P1_C6_REP

description:
Tissue Biology
204637490007_R01C02


title: TGFBRII_KO.24h_TGFB1.R2


title: TGFBRII_KO.24h_TGFB1.R3


title: Tumor_DNA_Replicates_20384_P1_E5_REP

description:
Reproducibility
204637490007_R01C01

source_name: NA, Mouse DNA, Tissue

value: Intestinal Tumor


title: Input_Quantity_Titration_21021_P1_D2_REP

description:
Input Quantity Titration
204637490005_R06C02

source_name: NA, Cell Line DNA, Cell Line

value: NIH/Swiss


title: WT.24h_TGFB1.R1


title: DNA_Methylation_Titration_20012_P1_F1_REP

description:
DNA Methylation Titration
204637490005_R06C01

source_name: NA, EpigenDX Mouse DNA, EpigenDX DNA

value: Female

value: EpigenDX Mouse DNA


title: WT.24h_TGFB1.R2

value: WT


title: DNA_Methylation_Titration_20015_P1_E1_REP

description:
DNA Methylation Titration
204637490005_R05C01


title: Tumor_DNA_Replicates_20364_P1_C2_REP

description:
Reproducibility
204637490005_R05C02


title: CIS_KO.4h_TGFB1.R3


title: Female-blastocyst-1358-6

value: Term placenta


title: DNA_Methylation_Titration_20016_P1_B2_REP

description:
DNA Methylation Titration
204637490005_R04C02


title: Human_DNA_Titration_20990_P1_F9_REP

description:
Human-mouse Titration
204637490009_R04C02

value: 10% Human Blood, 90% Mouse Fat


title: TGFBRII_KO.unstimulated.R1

value: unstimulated


title: Female-blastocyst-1358-7


title: Human_DNA_Titration_20983_P1_G8_REP

description:
Human-mouse Titration
204637490009_R03C01

value: Lab 2

value: 50% Human Blood, 50% Mouse Spleen


title: TGFBRII_KO.unstimulated.R2


title: DNA_Methylation_Titration_20013_P1_A2_REP

description:
DNA Methylation Titration
204637490005_R03C02


title: WT.24h_TGFB1.R4


title: TGFBRII_KO.unstimulated.R3


title: WT.24h_TGFB1.R3


title: DNA_Methylation_Titration_20014_P1_G1_REP

description:
DNA Methylation Titration
204637490005_R01C02


title: WT.unstimulated.R1


title: DNA_Methylation_Titration_20011_P1_H1_REP

description:
DNA Methylation Titration
204637490005_R02C02


title: TGFBRII_KO.4h_TGFB1.R2


title: DNA_Methylation_Titration_20010_P1_A1_REP

description:
DNA Methylation Titration
204637490005_R01C01

value: Male


title: DNA_Methylation_Titration_20012_P1_C1_REP

description:
DNA Methylation Titration
204637490005_R03C01


title: DNA_Methylation_Titration_20010_P1_D1_REP

description:
DNA Methylation Titration
204637490005_R04C01


title: DNA_Methylation_Titration_20015_P1_B1_REP

description:
DNA Methylation Titration
204637490005_R02C01


title: GS_cells_rep2

city: Kyoto

first: Satoshi

last: Watanabe

state: Kyoto

address: 53, Kawahara-cho, Shogoin, Sakyo

department: Graduate School of Medicine

country: Japan

institute: Kyoto University

data_processing:
Basecalls were performed using bcl2fastq v2.17.1.14.
The low-quality bases at the 3' read ends and the adaptor sequences were trimmed by cutadapt-1.16.
The ribosomal RNA (rRNA) sequence reads were filtered out using Bowtie 2.3.4.1.
The sequenced reads were mapped to the mm10 mouse reference genome using HISAT2 (version 2.1.0) with the mouse GENCODE (version M19) annotation gtf file.
The mapped reads with high mapping quality (MAPQ >= 20) were used for further analyses.
FPKM values were determined by Cuffdiff within Cufflinks version 2.2.1 package with the mouse GENCODE (version M19, protein_coding)
Genome_build: mm10
Supplementary_files_format_and_content: The tab-delimited text file include FPKM values for each sample.

source_name: Already established cutured SSCs (GS cells)

growth_protocol: DBA/2 GS cells and adult DBA/2 testicular cells purified by magnetically sorted using anti-CD9 antibody were cultured in culture medium based on Iscove’s modified MEM (Invitrogen, Carlsbad, CA), which was supplemented with 10 ng/ml human FGF2, 15 ng/ml recombinant rat GDNF (both from Peprotech, London, UK) and 1% fetal bovine serum (FBS) (Kanatsu-Shinohara et al, 2014).

extract_protocol:
Total RNA were extracted by TRIzol (Qiagen) and purified by RNeasy mini kit  (Qiagen)
RNA-seq libraries were generated from 200 ng total RNA with the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's protocol.

tag: culture time

value: GS cells


title: CIS_KO.24h_TGFB1.R2


title: Input_Quantity_Titration_20009_P1_F4_REP

description:
Input Quantity Titration
204637490002_R06C01


title: TGFBRII_KO.4h_TGFB1.R1


title: CIS_KO.24h_TGFB1.R1


title: CIS_KO.4h_TGFB1.R4


title: Input_Quantity_Titration_20009_P1_C5_REP

description:
Input Quantity Titration
204637490002_R05C02


title: Input_Quantity_Titration_20009_P1_E4_REP

description:
Input Quantity Titration
204637490002_R05C01


title: GS_cells_rep1

treatment_protocol: adult DBA/2 testicular cells purified by magnetically sorted using anti-CD9 antibody

tag: cell type

value: Already established cutured SSCs (GS cells)


title: Input_Quantity_Titration_20009_P1_B5_REP

description:
Input Quantity Titration
204637490002_R04C02


title: 3week_rep1

source_name: SSCs cultured for 3 weeks

value: 3 weeks

value: spermatogonial stem cells (SSCs)


title: 3week_rep2


title: 2week_rep2

source_name: SSCs cultured for 2 weeks

value: 2 weeks


title: Tumor_DNA_Replicates_20384_P1_A5_REP

description:
Reproducibility
204637490002_R03C02

value: Tumor


title: Intestinal_Tumor_Normal_20333_P1_C4_REP

description:
Intestinal Tumor Biology
204637490002_R03C01

source_name: Small Intestine, Mouse DNA, Tissue

value: Small Intestine


title: Tumor_DNA_Replicates_20384_P1_D5_REP

description:
Reproducibility
204637490002_R06C02

value: Intestinal Tumor


title: 1week_rep2

source_name: SSCs cultured for 1 week

value: 1 week


title: 1week_rep1


title: 0week_rep1

source_name: SSCs cultured for 0 week

value: 0 week


title: Tumor_DNA_Replicates_21026_P1_A4_REP

description:
Reproducibility
204637490002_R01C01

value: Colon


title: Intestinal_Tumor_Normal_20317_P1_G4_REP

description:
Intestinal Tumor Biology
204637490002_R01C02

value: Female


title: 0week_rep2


title: Tissue_Age_Associated_Me_20117

description:
Tissue Biology
204875570048_R02C02

source_name: Testis, Mouse DNA, Tissue

value: Lab 1

value: Testis

value: Normal


title: Tissue_Age_Associated_Me_20261

description:
Tissue Biology
204875570051_R01C02


title: Tissue_Age_Associated_Me_20092

description:
Tissue Biology
204875570014_R02C01


title: Developmental_Biology_22301

description:
Tissue Biology
204879580043_R06C01

source_name: Tail, Embryonic DNA, Tissue

value: Tail


title: Mutant3-5mpf-scATAC-seq

city: Birmingham

first: Rui

last: Monteiro

state: Select One

address: Medical School, Vincent Drive, IBR West

department: Institute of Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birminhgam

description: aggr_ATAC_upload.rds, associated with fragments.tsv.gz

library_source: genomic

data_processing:
scRNA-Seq samples were processed using CellRanger (10x Genomics: v3.1.0)
For scATAC-Seq, peaks were called using MACS2 using the following commands: macs3 callpeak -t  ~/ MUT1/outs/possorted_bam.bam ~/MUT2/outs/possorted_bam.bam  ~/ /MUT3/outs/possorted_bam.bam -n MUT -g 1.3E9 and callpeak -t  ~/ WT1/outs/possorted_bam.bam ~/WT2/outs/possorted_bam.bam  ~/ /WT3/outs/possorted_bam.bam -n WT -g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC (10x  Genomics: v1.2.0) and peaks were specified using the output from MACS2 during the cellrnager-atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples
Assembly:  GRCz11

organism: Danio rerio

source_name: wkm

growth_protocol: all samples were obtained from zebrafish marrow at the indicated timepoints (e.g. 12mpf)

extract_protocol:
10x genomics microfluidics system was used to isolate cells
3’-scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 (10x Genomics) and sequenced using a NextSeq 500 (Illumina). scATAC (assay for transposable accessible chromatin assay) -Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1, Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N, Set A (10x Genomics). Libraries were sequenced using   NextSeq 500 (Illumina).

treatment_protocol: cells were not treated

value: marrow

tag: age

tag: genotype


title: WT3-5mpf-scATAC-seq

value: WT


title: Mutant2-5mpf-scATAC-seq


title: WT2-5mpf-scATAC-seq


title: Input_Quantity_Titration_20009_P1_D4_REP

description:
Input Quantity Titration
204637490002_R04C01

value: Male

value: Lab 2


title: WT1-5mpf-scATAC-seq


title: Developmental_Biology_22284

description:
Tissue Biology
204879580022_R01C01


title: Mutant-5mpf-scRNAseq


title: 2week_rep1

value: spermatogonial stem cells (SSCs)


title: Developmental_Biology_22293

description:
Tissue Biology
204879580022_R04C02


title: Intestinal_Tumor_Normal_20318_P1_H4_REP

description:
Intestinal Tumor Biology
204637490002_R02C02


title: Mutant-12mpf-scRNAseq

description: MUT_rna_june2011.rds, associated with barcodes_of_cell_with_more_than_1000reads.xlsx (barcode of cells used for analysis from WT_Mutant 12mpf scRNAseq). Excel file of barcodes of cells with more than 1000 reads that were used in this analysis


title: WT-5mpf-scRNA-seq


title: Developmental_Biology_22277

description:
Tissue Biology
204879580021_R06C01


title: Developmental_Biology_22266

description:
Tissue Biology
204879580020_R01C02

value: Mixed


title: Developmental_Biology_22271

description:
Tissue Biology
204879580020_R06C02


title: Tumor_DNA_Replicates_21026_P1_B4_REP

description:
Reproducibility
204637490002_R02C01

value: Tumor


title: WT-12mpf-scRNAseq

description: WT_rna_june2011.rds, associated with barcodes_of_cell_with_more_than_1000reads.xlsx (barcode of cells used for analysis from WT_Mutant 12mpf scRNAseq). Excel file of barcodes of cells with more than 1000 reads that were used in this analysis


title: Mutant1-5mpf-scATAC-seq


title: Developmental_Biology_22260

description:
Tissue Biology
204879580020_R01C01


title: Tissue_Age_Associated_Me_20178

description:
Tissue Biology
204875570011_R02C01


title: Developmental_Biology_22254

description:
Tissue Biology
204879580009_R01C02


title: Developmental_Biology_22239

description:
Tissue Biology
204879580008_R04C01


title: Developmental_Biology_22242

description:
Tissue Biology
204879580008_R01C02


title: Developmental_Biology_22235

description:
Tissue Biology
204879580005_R06C02


title: Tissue_Age_Associated_Me_20125

description:
Tissue Biology
204875570071_R04C01

value: Stomach


title: Tissue_Age_Associated_Me_20205

description:
Tissue Biology
204875570038_R01C02


title: Tissue_Age_Associated_Me_20124

description:
Tissue Biology
204875570071_R03C01


title: Tissue_Age_Associated_Me_20254

description:
Tissue Biology
204875570051_R03C01


title: Tissue_Age_Associated_Me_20065

description:
Tissue Biology
204875570027_R02C02


title: Tissue_Age_Associated_Me_20064

description:
Tissue Biology
204875570027_R01C02


title: Tissue_Age_Associated_Me_20226

description:
Tissue Biology
204875570028_R06C02


title: Tissue_Age_Associated_Me_20168

description:
Tissue Biology
204875570023_R04C01


title: Tissue_Age_Associated_Me_20167

description:
Tissue Biology
204875570023_R03C01


title: Developmental_Biology_22248

description:
Tissue Biology
204879580009_R01C01


title: gWAT-KO-1

city: Niigata

first: Yohko

last: Yoshida

address: 1-757, Asahimachi-dori, Chuo-ku

institute: Niigata University

hyb_protocol: 600 ng of Cy3-labelled 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 SurePrint G3 Mouse GE microarray (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 028005_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Gonadal white adipose tissue (gWAT) from adipose tissue-specific Pgam1 knockout mouse

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (Low Input Quiuck Amp Labeling) (Agilent) according to the manufacturer's instructions.

growth_protocol: Mice were housed at 23℃ with free access to water and normal chaw under 12hr light / 12hr dark cycle.

extract_protocol: Total RNA was isolated from BAT or gWAT with RNeasy Lipid Tissue Mini Kit (QUIAGEN).RNA was quantified using a NanoDrop ND-1000 and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Gonadal white adipose tissue (gWAT)

value: 16 weeks of age


title: gWAT-WT-4

source_name: Gonadal white adipose tissue (gWAT) from littermate wild-type mouse


title: BAT-KO-4

source_name: Brown adipose tissue (BAT) from adipose tissue-specific Pgam1 knockout mouse

value: Brown adipose tissue (BAT)

value: 14 weeks of age


title: gWAT-KO-2


title: H1FOO_KD_Morula_rep3

city: Hangzhou

first: Kun

last: Zhang

address: 866 Yuhangtang Rd

institute: Zhejiang University

data_processing:
Reads were trimmed by Trimmomatic to remove the bases with low quality and adapter sequences
The trimmed reads were align to ARS-UCD1.2  by Hisat2
The raw reads counts of all expressed genes were quatified by FeatureCounts
The abundance of all expressed genes were normalized to FPKM by Cufflinks
Genome_build: ARS-UCD1.2-bosTau9
Supplementary_files_format_and_content: text file includes FPKM calculated by Cufflinks for each sample

molecule: polyA RNA

organism: Bos taurus

source_name: embryo

extract_protocol:
Total RNA was isolated from embryos using Picopure RNA isolation kit (Life Technologies, Grand Island, NY, USA) according to the manufacturer's instruction.
mRNAs were separated with oligo(dT)25 beads, and was used to prepare sequencing libraries with NEB Next Ultra RNA Library Prep Kit for Illumina (New England Biolabs). Briefly, mRNA was fragmented and reverse transcribed. The cDNA library was subject to end repair, poly(A)-tailing, adaptor ligation, and PCR amplification of 12–15 cycles for sequencing library construction.

tag: developmental stage

value: Morula

value: 5.5 day post insemination

value: embryos were injected with H1FOO siRNAs at zygote stage


title: H1FOO_KD_Morula_rep2


title: BAT-KO-3

tag: gender


title: gWAT-WT-3


title: gWAT-KO-4


title: gWAT-WT-2


title: BAT-WT-4

source_name: Brown adipose tissue (BAT) from littermate wild-type mouse


title: BAT-KO-1


title: BAT-WT-3


title: gWAT-WT-1


title: BAT-KO-2


title: H1FOO_KD_Morula_rep1


title: Tissue_Age_Associated_Me_20227

description:
Tissue Biology
204875570015_R01C01

source_name: Stomach, Mouse DNA, Tissue

value: Female

value: Lab 1

value: Normal


title: BAT-WT-2


title: gWAT-KO-3


title: NC_Morula_rep3

value: embryos were injected with negative control siRNAs at zygote stage


title: BAT-WT-1

value: Male


title: Tissue_Age_Associated_Me_20088

description:
Tissue Biology
204875570011_R04C02


title: NC_Morula_rep2


title: NC_Morula_rep1


title: Tissue_Age_Associated_Me_21007

description:
Tissue Biology
204875570022_R03C01


title: Intestinal_Tumor_Normal_20319_P1_F5_REP

description:
Intestinal Tumor Biology
204637490007_R02C01

value: Lab 2

value: Small Intestine


title: H1FOO_KD_16-cell_rep1

value: 4 day post insemination


title: Tissue_Age_Associated_Me_20087

description:
Tissue Biology
204875570011_R03C02


title: Tissue_Age_Associated_Me_20043

description:
Tissue Biology
204875570008_R01C02


title: NC_16-cell_rep2


title: NC_16-cell_rep1


title: Tissue_Age_Associated_Me_20120

description:
Tissue Biology
204875570048_R05C02

source_name: Spleen, Mouse DNA, Tissue

value: Spleen


title: axe1-5_rep1

city: Egham

first: Alessandra

last: Devoto

address: Egham Hill

institute: Royal Holloway University of London

description: without JA

hyb_protocol: 600 ng of cRNAs was hybridized to the microarray (Agilent design ID:21169) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer  (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: The microarray was scanned by Agilent DNA Microarray Scanner G2539A ver. C and  raw data was extracted using Feature Extraction program ver 9.1.

data_processing: RMA normalization was performed for signals of microarray probes using limma package on R program.

organism: Arabidopsis thaliana

label_protocol: 200 ng of each RNA sample was used to prepare for Cy3-labeled cRNA, using Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Whole A. thaliana seedlings of the Histone deacetylase 6 (HDA6) /Reduced potassium dependency 3 (RPD3), axe1-5 mutant and DR5 wild-type lines (Murfett et al 2001) were grown in vitro for 12 days on 1% Murashige and Skoog (MS) medium (Duchefa) supplemented with 1% sucrose, 0.8% phytoagar (Duchefa) and buffered to pH 5.8. Stratification of seeds was performed for 3 days at 4°C in the dark. Seeds were then grown with plates approximately 20° to vertical under 16h light/8h dark cycles for 12 days at 22°C and a light intensity of 100-120 µmol m-2s-1.

extract_protocol: Total RNA was extracted from whole plants using RNeasy Plant Mini Kit  (QIAGEN).

treatment_protocol: Twelve-day-old in vitro grown whole seedlings were transferred to 50 µM MeJA or mock plates and kept for 3 hours.

value: whole seedling

value: mock (only ethanol)-treated condition


title: axe1-5_rep2

description: without JA


title: Tissue_Age_Associated_Me_20212

description:
Tissue Biology
204875570028_R05C01


title: BR410 late post tx

city: Pittsburgh

first: Jishnu

last: Das

address: 203 Lothrop Street

department: Immunology

institute: University of Pittsburgh

data_processing:
RNA libraries generated using TruSeq Stranded Total RNA with Ribo-Zero Globin (Illumina, San Diego, CA) according to the manufacturer’s protocol. The libraries were validated using Fragment Analyzer (Agilent, Santa Clara, CA) and sequenced using Nextseq 500 platform (Illumina, San Diego, CA) to generate 75 bp paired end reads, up to 40 million reads per sample
The generated reads were pre-processed using FastQC (v0.10.1) and aligned to the human reference gtf annotation file ( GRCh37.68 genome using STAR)
Transcript abundances were quantified and normalized using RSEM.
Assembly: grch37.68
Supplementary files format and content: genes.results provides gene count matrix
Supplementary files format and content: isoforms.results provides isoform count matrix

source_name: whole blood (PBMC)

extract_protocol:
Trizol.
Illumina sequencing protocols.

tag: clinical metadata (time-point)

value: late post tx


title: BR388 late post tx


title: DR5_rep1

description: without JA


title: BR409 late post tx


title: BR399 late post tx


title: BR400 late post tx


title: Tissue_Age_Associated_Me_20074

description:
Tissue Biology
204875570045_R05C01


title: BR398 late post tx


title: 89_BR397  late post tx


title: Tissue_Age_Associated_Me_20174

description:
Tissue Biology
204875570023_R04C02


title: H1FOO_KD_16-cell_rep2


title: axe1-5_JA_rep2

description: with JA

value: JA-treated condition


title: li_Ola276

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

country: Germany

institute: German Diabetes Center

hyb_protocol: Amplified cDNA was hybridized on Affymetrix Mouse Gene ST 1.0 arrays (Affymetrix)

scan_protocol: Detection of probe intensities was performed using a GeneChip scanner 3000 7G (GDAS 1.4 package, Affymetrix).

data_processing: The data were analyzed with Affymetrix Expression Console using default analysis settings for RMA analyses for gene default and exon default .CHP files.

label: Affymetrix IVT

source_name: liver

label_protocol: 150 ng total RNAwas amplified using the Ambion WT Expression Kit and the WT Terminal Labeling Kit (Affymetrix, Freiburg, Germany).

growth_protocol: After weaning at the age of 21 days, all experimental animals received a high-fat diet (HFD) containing 45 kcal% fat, 20 kcal% protein and 35 kcal% carbohydrates with 4.73 kcal/gm energy (D12451 Research Diets Inc., New Jersey, USA).

extract_protocol: Total RNA extraction was made with RNeasy mini kit (Qiagen, Hilden, Germany) including DNAse digestion according to the manufacturer's instructions. RNA quality was evaluated using an Agilent 2100 Bioanalyzer and only high quality RNA (RIN > 8) was used for microarray analysis.

value: 6 weeks

value: liver

value: male


title: DR5_JA_rep1

description: with JA


title: BR390 late post tx


title: axe1-5_JA_rep1

description: with JA


title: DR5_JA_rep2

description: with JA


title: BR391 late post tx


title: Tissue_Age_Associated_Me_20995

description:
Tissue Biology
204875570051_R04C02


title: BR190 late post tx


title: BR204 late post tx


title: Tissue_Age_Associated_Me_20252

description:
Tissue Biology
204875570051_R02C01


title: Tissue_Age_Associated_Me_21002

description:
Tissue Biology
204875570051_R05C02


title: BR203 late post tx


title: BR389 late post tx


title: BR414 late post tx


title: BR413 late post tx


title: li_Ola298


title: li_Ola286


title: BR412 late post tx


title: Tissue_Age_Associated_Me_20094

description:
Tissue Biology
204875570014_R04C01


title: Tissue_Age_Associated_Me_20245

description:
Tissue Biology
204875570051_R01C01


title: BR403 late post tx


title: BR406 late post tx


title: BR402 late post tx


title: Tissue_Age_Associated_Me_20112

description:
Tissue Biology
204875570048_R03C01


title: Tissue_Age_Associated_Me_20105

description:
Tissue Biology
204875570048_R02C01


title: li_Ola306


title: BR393 late post tx


title: BR395 late post tx


title: Tissue_Age_Associated_Me_20103

description:
Tissue Biology
204875570048_R01C01


title: 109_BR392 late post tx


title: Tissue_Age_Associated_Me_20192

description:
Tissue Biology
204875570038_R02C01


title: BR383 late post tx


title: li_Ola304


title: li_NZO542

value: NZO/Hl (NZO; German Diabetes Centre Dusseldorf (HERBERG and COLEMAN 1977))


title: Tissue_Age_Associated_Me_20225

description:
Tissue Biology
204875570028_R05C02

value: Female


title: BR382 late post tx


title: BR407 late post tx


title: li_NZO545


title: li_NZO544


title: BR401 late post tx


title: BR396 late post tx


title: BR386 late post tx


title: Tissue_Age_Associated_Me_20218

description:
Tissue Biology
204875570028_R04C02

value: Lab 1


title: Tissue_Age_Associated_Me_20211

description:
Tissue Biology
204875570028_R04C01

value: Normal


title: BR394 late post tx


title: BR385 late post tx


title: BR198 late post tx


title: Tissue_Age_Associated_Me_20052

description:
Tissue Biology
204875570027_R02C01


title: li_NZO543


title: li_C3H111

value: C3H (000658, Jackson Lab)


title: BR196 late post tx


title: li_NZO658


title: BR416 late post tx


title: li_C3H112


title: Tissue_Age_Associated_Me_20163

description:
Tissue Biology
204875570015_R05C02

value: Male


title: BR194 late post tx


title: BR195 late post tx


title: BR193 late post tx


title: DR5_rep2

description: without JA


title: BR192 late post tx


title: li_C3H113


title: BR216 late post tx


title: Tissue_Age_Associated_Me_20154

description:
Tissue Biology
204875570015_R03C02


title: BR191 late post tx


title: li_C3H119


title: li_C3H109


title: BR217 late post tx


title: Tissue_Age_Associated_Me_20078

description:
Tissue Biology
204875570011_R06C01


title: BR215 late post tx


title: BR212 late post tx


title: Tissue_Age_Associated_Me_20156

description:
Tissue Biology
204875570015_R04C02


title: BR211 late post tx


title: li_Bl61555


title: BR214 late post tx


title: li_Bl61554


title: BR197 late post tx


title: Tissue_Age_Associated_Me_20076

description:
Tissue Biology
204875570011_R05C01


title: li_Bl61559


title: li_Bl61558


title: BR209 late post tx


title: Tissue_Age_Associated_Me_20033

description:
Tissue Biology
204875570008_R03C01


title: Tissue_Age_Associated_Me_20085

description:
Tissue Biology
204875570011_R01C02


title: Developmental_Biology_22291

description:
Tissue Biology
204879580022_R02C02

source_name: Placenta, Placental DNA, Tissue

value: Placenta


title: BR201 late post tx


title: BR208 late post tx


title: BR207 late post tx


title: BR213 late post tx


title: BR205 late post tx


title: BR200 late post tx


title: Developmental_Biology_22299

description:
Tissue Biology
204879580043_R04C01


title: Developmental_Biology_22265

description:
Tissue Biology
204879580020_R06C01

value: Mixed


title: BR210 late post tx


title: li_Bl61590


title: Tissue_Age_Associated_Me_20040

description:
Tissue Biology
204875570008_R04C01

value: Small Intestine


title: BR365 Early Post Tx

value: Early Post Tx


title: BR355 Early Post Tx


title: Developmental_Biology_22282

description:
Tissue Biology
204879580021_R05C02


title: BR199 late post tx


title: Developmental_Biology_22269

description:
Tissue Biology
204879580020_R04C02


title: Developmental_Biology_22275

description:
Tissue Biology
204879580021_R04C01


title: BR371 Early Post Tx


title: BR363 Early Post Tx


title: BR206 late post tx


title: BR364 Early Post Tx


title: GS cells-2

hyb_protocol: Fragmented and labelled cDNA was hybridized to GeneChip Mouse Gene 1.0 ST (Affymetrix).

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 TG.

data_processing: Mouse Gene 1.0 ST arrays were normalized using RMA16 implemented in the GeneSpring 12.6.

label: biotin

source_name: Already established cutured SSCs (GS cells)

label_protocol: GeneChip WT Terminal Labeling Kit (Affymetrix) were used according to Affymetrix protocol.

extract_protocol: Total RNA were extracted by TRIzol (Qiagen) and purified by RNeasy mini kit  (Qiagen)

value: spermatogonial stem cells (SSCs)


title: 2week-rep2

source_name: SSCs cultured for 2 weeks


title: GS cells-1


title: 3week-rep2

source_name: SSCs cultured for 3 weeks


title: BR345 Early Post Tx


title: BR354 Early Post Tx


title: BR372 Early Post Tx


title: Developmental_Biology_22268

description:
Tissue Biology
204879580020_R03C02


title: BR344 Early Post Tx


title: Developmental_Biology_22259

description:
Tissue Biology
204879580009_R06C02


title: 3week-rep1


title: 1week-rep2

source_name: SSCs cultured for 1 week


title: BR343 Early Post Tx


title: BR362 Early Post Tx


title: BR341 Early Post Tx


title: BR380 Early Post Tx


title: 1week-rep1


title: BR361 Early Post Tx


title: Developmental_Biology_22253

description:
Tissue Biology
204879580009_R06C01


title: 0week-rep2

source_name: SSCs cultured for 0 week


title: 2week-rep1


title: 0week-rep1


title: RNA_15min_-Glu_5min_+Glu_+PreTreat

city: La Jolla

first: Brian

middle: Matthew

last: Zid

state: California

address: 9500 Gilman Drive

department: Chemistry and Biochemistry

institute: University of California San Diego

description: RNA-seq

data_processing:
Cutadapt was used to remove the universal TruSeq adapter from raw fastqs, reads without adapters and less then 17nt following adapter removal were discarded
For files that required manual demultiplexing, Cutadapt was used again to demultiplex with a custom fasta containing the barcode sequence corresponding to a given biological sample
Unique molecular identifiers (UMIs) were removed from the read line of the fastq and appended to the header line with a custom python script for later deduplication of PCR artifacts
Bowtie was used to generate index files and align reads to the S. cerevisiae ncRNA with the following flags: -k 1 --best -t -S -q
Reads that did not align to ncRNA were filtered to remove low quality reads based on Phred score with fastqx_toolkit default settings
Bowtie was used again to align reads that passed QC filtering to the  S. cerevisiae genome
PCR duplicates were removed based on the header-appended UMIs using custom python scripts
Read features were counted using htseq-count and default settings
Polarity scores were calculated with custom python scripts
Assembly: R64-1-1
Supplementary files format and content: Unnormalized read counts and polarity scores for ribosome profiling libraries are in a .xlsx file with a unique sheet for each sample

organism: Saccharomyces cerevisiae

source_name: transcriptomic

growth_protocol: Cells were grown to OD ~0.4-0.6 except for the 1day and 5day samples which were grown to postdiauxic shift and stationary phase, respectively

extract_protocol:
Cells were harvested by vaccum filtration onto nitrocellulose membranes, flash frozen in liquid nitrogen, and cryogenically lysed with a planetary ball mill
Footprints: lysates were clarified by centrifugation, digested with RNase I, and footprints (~20-34nt) were recovered by size-selection and TBE-UREA gel-purification. The recovered footprints were dephosphorylated, ligated to oligonucleotide linkers, and again size selected and gel purified via TBE-UREA PAGE. Next, RiboZero treatment was performed on the indicated samples. All samples were then reverse transcribed and circularized. Circles were quantified by qPCR and taken through PCR amplification to ready them for sequencing. Total RNA: total RNA was extracted from whole frozen cells by SDS/hot acid phenol/chloroform extraction, fragmented in alkaline conditions, and gel purified. Fragmented RNA was ligated to linkers, reverse transcribed, and PCR amplified for sequencing.

treatment_protocol: Acute glucose starvation samples (1-30min time points) were transferred to media lacking gluose for the indicated amount of time prior to harvest. For glucose readdition, 2% gluose was added back to media following 15 minutes of acute glucose starvation.

value: wild-type

tag: cycloheximide pretreatment (ribosome profiling)

value: Not applicable

tag: molecule subtype

value: total RNA

tag: rrna removal


title: RNA_1day_-PreTreat

description: RNA-seq


title: RNA_5day_-PreTreat

description: RNA-seq

value: RiboZero


title: RNA_15min_-Glu_1min_+Glu_+PreTreat

description: RNA-seq


title: Developmental_Biology_22247

description:
Tissue Biology
204879580008_R06C02

tag: Sex

tag: site


title: BR369 Early Post Tx


title: Developmental_Biology_22308

description:
Tissue Biology
204879580010_R01C01

tag: strain

tag: cell line


title: BR353 Early Post Tx


title: BR357 Early Post Tx


title: Developmental_Biology_22240

description:
Tissue Biology
204879580008_R05C01

tag: tissue

tag: sorted cell type


title: BR350 Early Post Tx


title: Developmental_Biology_22236

description:
Tissue Biology
204879580008_R01C01

tag: treatment

tag: pathology


title: BR358 Early Post Tx


title: RNA_15min_-Glu_+PreTreat_Rep1

description: RNA-seq


title: BR349 Early Post Tx


title: BR378 Early Post Tx


title: RNA_logphase_+PreTreat_Rep2

description: RNA-seq


title: Developmental_Biology_22232

description:
Tissue Biology
204879580005_R03C02


title: BR379 Early Post Tx


title: BR370 Early Post Tx


title: Developmental_Biology_22231

description:
Tissue Biology
204879580005_R02C02


title: BR377 Early Post Tx


title: BR368 Early Post Tx


title: RNA_timecourse_pool_-PreTreat_Rep2

description: RNA-seq


title: Developmental_Biology_22241

description:
Tissue Biology
204879580008_R06C01


title: RNA_timecourse_pool_-PreTreat_Rep1

description: RNA-seq


title: Tissue_Age_Associated_Me_20049

description:
Tissue Biology
204875570027_R01C01

source_name: Ovary, Mouse DNA, Tissue

value: Ovary


title: RNA_logphase_+PreTreat_Rep1

description: RNA-seq


title: BR352 Early Post Tx


title: BR359 Early Post Tx


title: BR376 Early Post Tx


title: Tissue_Age_Associated_Me_21017

description:
Tissue Biology
204875570022_R05C02


title: BR366 Early Post Tx


title: Ribo_1day_-PreTreat

description: ribosome profiling

data_processing:
Cutadapt was used to remove the universal TruSeq adapter from raw fastqs, reads without adapters and less then 17nt following adapter removal were discarded
For files that required manual demultiplexing, Cutadapt was used again to demultiplex with a custom fasta containing the barcode sequence corresponding to a given biological sample
Unique molecular identifiers (UMIs) were removed from the read line of the fastq and appended to the header line with a custom python script for later deduplication of PCR artifacts
Bowtie was used to generate index files and align reads to the S. cerevisiae ncRNA with the following flags: -k 1 --best -t -S -q
Reads that did not align to ncRNA were filtered to remove low quality reads based on Phred score with fastqx_toolkit default settings
Bowtie was used again to align reads that passed QC filtering to the  S. cerevisiae genome
PCR duplicates were removed based on the header-appended UMIs using custom python scripts
Read features were counted using htseq-count and default settings
Polarity scores were calculated with custom python scripts
Assembly: R64-1-1
Supplementary files format and content: Unnormalized read counts and polarity scores for ribosome profiling libraries are in a .xlsx file with a unique sheet for each sample
Library strategy: Ribosome profiling

value: No

value: ribosome protected mRNA footprint


title: Tissue_Age_Associated_Me_20233

description:
Tissue Biology
204875570015_R06C01

value: Female


title: Tissue_Age_Associated_Me_20182

description:
Tissue Biology
204875570027_R05C02

value: Lab 1


title: Ribo_5day_-PreTreat

description: ribosome profiling


title: RNA_15min_-Glu_+PreTreat_Rep2

description: RNA-seq


title: Ribo_logphase_-PreTreat

description: ribosome profiling


title: BR360 Early Post Tx


title: BR348 Early Post Tx


title: BR346 Early Post Tx


title: Ribo_15min_-Glu_+PreTreat_Rep2

description: ribosome profiling

value: Yes


title: Tissue_Age_Associated_Me_20216

description:
Tissue Biology
204875570028_R03C02

source_name: Muscle, Mouse DNA, Tissue

value: Muscle

value: Normal


title: BR375 Early Post Tx


title: BR351 Early Post Tx


title: Tissue_Age_Associated_Me_20114

description:
Tissue Biology
204875570048_R05C01

value: Male


title: Ribo_15min_-Glu_5min_+Glu_+PreTreat

description: ribosome profiling


title: BR373 Early Post Tx


title: BR281 Early Post Tx


title: BR284 Early Post Tx


title: Ribo_15min_-Glu_1min_+Glu_+PreTreat

description: ribosome profiling


title: BR282 Early Post Tx


title: BR278 Early Post Tx


title: Tissue_Age_Associated_Me_20190

description:
Tissue Biology
204875570038_R01C01


title: Tissue_Age_Associated_Me_20176

description:
Tissue Biology
204875570023_R06C02


title: BR280 Early Post Tx


title: BR374 Early Post Tx


title: BR283 Early Post Tx


title: Ribo_15min_-Glu_+PreTreat_Rep1

description: ribosome profiling


title: BR276 Early Post Tx


title: Ribo_logphase_+PreTreat_Rep2

description: ribosome profiling


title: BR279 Early Post Tx


title: Ribo_logphase_+PreTreat_Rep1

description: ribosome profiling


title: BR274 Early Post Tx


title: Tissue_Age_Associated_Me_20069

description:
Tissue Biology
204875570027_R06C02


title: BR270 Early Post Tx


title: BR273 Early Post Tx


title: BR269 Early Post Tx


title: BR271 Early Post Tx


title: Tissue_Age_Associated_Me_20243

description:
Tissue Biology
204875570038_R06C02


title: Tissue_Age_Associated_Me_20098

description:
Tissue Biology
204875570014_R02C02


title: Ribo_timecourse_pool_-PreTreat_Rep2

description: ribosome profiling


title: Tissue_Age_Associated_Me_20031

description:
Tissue Biology
204875570008_R02C01


title: BR267 Early Post Tx


title: Ribo_timecourse_pool_-PreTreat_Rep1

description: ribosome profiling


title: BR264 Early Post Tx


title: BR266 Early Post Tx


title: Tissue_Age_Associated_Me_20241

description:
Tissue Biology
204875570038_R05C02

source_name: Lung, Mouse DNA, Tissue

value: Lung


title: BR295 Pre-Tx

value: Pre-Tx


title: BR285 Pre-Tx


title: Tissue_Age_Associated_Me_20119

description:
Tissue Biology
204875570048_R04C02


title: Bone marrow B cells, undigested, DNA methylation

city: Barcelona

first: Lars

last: Velten

address: C. Dr. Aiguader 88, P05

department: Bioinformatics and Genomics

country: Spain

institute: CRG

description: Bone marrow sample was sorted for the following 3 subpopulations: (S1) CD24+/CD38-, (S2) CD38+/CD34+/CD10+/CD123- and (S3) CD19+/CD34-, obtaining 9.25% of S1, 6.5% of S2 and 84.25% of S3. These subpopulations were mixed with the following ratio: 10% of S1, 22.9% of S2, and 67.1% of S3 for a total of 1M cells.

data_processing:
Library strategy: scTAM-seq
Raw sequencing data was processed using a customized version of the Mission Bio Tapestri Pipeline v2 (https://support.missionbio.com/hc/en-us/sections/360006255314-Tapestri-Pipeline). Reads were aligned to the reference genome version 'hg19' using bwa-mem2. We identified cells from the barcodes as follows: We exclusively used the control amplicons to determine barcodes that can reliably called as 'cells' according to their overall read counts. To determine a read count cutoff on a per amplicon and per cell basis, we focused on the number of amplicons in the panel and computed the threshold as the minimum of 10 and 0.2x(mean read counts of cells having more than 8 times the number of amplicons in the panel). Then, we call as cells those barcodes having more than the determined threshold of reads in at least 70% of the amplicons. The processing pipeline has been implemented in bash and is available from the GitHub repository (https://github.com/veltenlab/scTAM-seq-scripts).
Genome_build: hg19
Supplementary_files_format_and_content: The .tsv files contain the read count matrices for DNA methylation and surface protein expression (*_protein.tsv files) for the identified cells.

source_name: Bone marrow B cells

extract_protocol:
Cells were quantified using a Countess cell counter (Invitrogen) and the concentration of the cell suspension was adjusted to 3,500-4.000 cell/μl with Tapestri Cell Buffer. To obtain the single-cell emulsion, a total of 120,000-140,000 cells were loaded into a Tapestri microfluidics cartridge. Upon encapsulation, cells were lysed and barcoded.
To obtain the digested samples, the barcoding master mix was prepared as follows: 288 μl of Tapestri Barcoding Mix V2, 5 μl of custom high-concentrated HhaI enzyme (150,000 U/mL, NEB, Cat. Num. R0139B-HC1) while keeping the remaining regents as stated in the Tapestri protocol mentioned above. To allow the DNA digestion, barcoded cells were next incubated for 30 minutes at 37 ºC in a thermocycler. Upon DNA digestion, cells were subjected to PCR amplification as described in the Tapestri protocol of 592 targeted genomic regions, covering either CpGs showing dynamic methylation during B-cell differentiation or control regions. DNA digestion and targeted PCR steps were performed in a T100 Thermal Cycler (Bio-Rad). All Tapestri related reagents were part of a custom single-cell DNA sequencing kit purchased from Mission Bio, Inc
PCR products were retrieved from individual droplets, and purified with 0.7X Ampure XP beads (Beckman Coulter, Cat. num. A63881) to split scTAM-seq library, bound to the beads, from the oligo-tagged antibodies library, which reminds in the supernatant. scTAM-seq PCR products were used as a template to add the Illumina i5/i7 sequencing indices, followed by two steps of purification, using 0.6X and 0.65X Ampure XP beads.  Oligo-tagged antibodies PCR products were incubated with Tapestri Biotin Oligo at 96 °C for 5 minutes, followed by incubation on ice for 5 minutes, and next purified using Tapestri Streptavidin Beads. Afterward, beads were used as a PCR template for the incorporation of i5/i7 Illumina indices; followed by purification using 0.9X Ampure XP beads. The quality of all libraries, both scTAM-seq and Oligo-tagged antibodies were assessed by Bioanalyzer.

treatment_protocol: Cells were stained with oligo-tagged antibodies following the instruction in Tapestri® Single-Cell DNA + Protein Sequencing User Guide V2 (https://support.missionbio.com/hc/en-us/articles/360062406493-Tapestri-Single-cell-DNA-Protein-Sequencing-V2-User-Guide). Briefly, 1M cells were stained with TotalSeq-D Heme Oncology Cocktail (BioLegend, Cat. num. 399906) reconstituted in 59 μl of Cell Staining buffer (BioLegend, Cat. num. 420201) plus 1 μl of TotalSeq-D0154 anti-CD27 antibody (clone OX, BioLegend, Cat. num. 302861) for 30 minutes on ice. Next, cells were washed with Cell Staining Buffer, centrifuging 400 x g, 10 minutes, at 4 ºC.

value: bone marrow

tag: cell type

value: B cells

tag: disease state

value: healthy


title: BR265 Early Post Tx

value: Early Post Tx


title: Tissue_Age_Associated_Me_20188

description:
Tissue Biology
204875570045_R05C02

data_processing:
SeSAMe software v1.10
20210916_GEO_processed_matrix.csv (Normalized average Beta)
20210916_GEO_signal_intensity_matrix.csv (Unmethylated and methylated signal intensities)


title: SVF from KO mouse, scRNAseq

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Using CellRanger v3.0.1, the sequencing data was processed, and the count matrices were generated.
Data analysis of count matrices was performed by Seurat (version 3.1.5) on R ( version 4.0.1) and R studio (version 1.1.463).
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: gonadal adipose tissue

extract_protocol:
gWAT was excised, minced, and placed into 10 ml of PBS(–) containing 2 mg/ ml of type 2 collagenase (Worthington, Lakewood, NJ), 1.2 U/ ml of Dispase (Gibco, Carlsbad, CA), and 10 mM CaCl2 (Roche). Incubation was done for 20 minutes at 37°C with gentle agitation. After adding 10 ml of DMEM with 10% FBS, the lysate was centrifuged at 400×g for 5 minutes and the pellet was resuspended in 5 ml of erythrocyte lysis buffer and incubated for 5 minutes at room temperature. Then the lysate was filtered through a cell strainer (70 μm) into a 50 ml tube. Next, the lysate was centrifuged at 400×g for 5 minutes and the pellet was resuspended in 5 ml of PBS and filtered through a cell strainer (40 μm) into a 50 ml tube. The SVF cells were centrifuged at 400×g and resuspended in 500 μl of PBS for further analysis.
The scRNA-seq libraries was prepared using Chromium Single Cell 3ʹ Reagent Kits v3 and Chromium controller (10x Genomics).

value: gonadal adipose tissue

value: male

tag: age

value: 13 weeks of age

tag: genotype

value: Pgam1 knockout


title: BR297 Pre-Tx


title: SVF from WT mouse, scRNAseq

description: 10x Genomics

value: littermate wildtype


title: Tissue_Age_Associated_Me_20072

description:
Tissue Biology
204875570045_R03C01

extract_protocol: Genomic DNA was isolated from tissue samples using the AllPrep DNA/RNA Mini Kit (QIAGEN)

value: Female


title: BR328 Pre-Tx


title: BR296 Pre-Tx


title: BR330 Pre-Tx


title: BR286 Pre-Tx


title: Bone marrow B cells, undigested, surface protein expression

molecule: protein


title: BR263 Early Post Tx


title: Bone marrow B cells, HhaI digested, surface protein expression


title: Tissue_Age_Associated_Me_20214

description:
Tissue Biology
204875570028_R01C02

value: Lab 1


title: BR329 Pre-Tx


title: Tissue_Age_Associated_Me_20175

description:
Tissue Biology
204875570023_R05C02


title: BR318 Pre-Tx


title: BR320 Pre-Tx


title: Tissue_Age_Associated_Me_21014

description:
Tissue Biology
204875570022_R02C02


title: Tissue_Age_Associated_Me_20029

description:
Tissue Biology
204875570008_R01C01


title: Peripheral blood B cells, undigested, DNA methylation

source_name: Peripheral blood CD19+ mononuclear cells

value: blood


title: Bone marrow B cells, HhaI digested, DNA methylation


title: BR326 Pre-Tx


title: BR301 Pre-Tx


title: BR316 Pre-Tx


title: Peripheral blood B cells, HhaI digested, DNA methylation


title: Peripheral blood B cells, HhaI digested, surface protein expression


title: Developmental_Biology_22288

description:
Tissue Biology
204879580022_R05C01

source_name: Lung, Embryonic DNA, Tissue


title: BR315 Pre-Tx


title: Developmental_Biology_22305

description:
Tissue Biology
204879580043_R04C02


title: JN-DSRCT-1 shSIK1 +dox

city: New Orleasn

middle: Bong

last: Lee

state: LA

address: 1700 Tulane Ave

department: Pathology and Laboratory Medicine

institute: Tulane University

data_processing:
RNA-sequencing reads were pseudoaligned to the human transcriptome using kallisto
Genome_build: GRch38
Supplementary_files_format_and_content: TPM value for each transcripts ID

source_name: JN-DSRCT-1 cell line

growth_protocol: Dox-inducible JN and BER shSIK1 cells were grown in DMEM/F12 media supplemented with 10% FBS and Pen/Strep, and puromycin (0.5 µg/mL) and G418 (250 µg/mL).

extract_protocol:
Total RNAs were prepared using RNeasy kit (Qiagen)
The sequencing libraries were constructed from 100-500ng of total RNA using the Illumina TrueSeq Stranded Total RNA kit with Ribo-Zero following the manufacturer instruction.

treatment_protocol: Dox treated samples were grown for five days with regular growth media and doxycycline (1 µg/mL).

value: 1ug/mL Doxycycline


title: BR308 Pre-Tx

source_name: whole blood (PBMC)


title: BR327 Pre-Tx


title: BR356 Early Post Tx


title: BR310 Pre-Tx


title: Developmental_Biology_22298

description:
Tissue Biology
204879580043_R03C01

value: Normal


title: BR307 Pre-Tx


title: BER-DSRCT shSIK1 NT

source_name: BER-DSRCT cell line

value: BER-DSRCT

value: Not Treated


title: BR332 Pre-Tx

value: Pre-Tx


title: JN-DSRCT-1 shSIK1 NT


title: BR325 Pre-Tx


title: BR290 Pre-Tx


title: BR321 Pre-Tx


title: Tissue_Age_Associated_Me_20099

description:
Tissue Biology
204875570014_R03C02

value: Male

value: Lung


title: BR299 Pre-Tx


title: BR289 Pre-Tx


title: Developmental_Biology_22281

description:
Tissue Biology
204879580021_R04C02


title: Tissue_Age_Associated_Me_20213

description:
Tissue Biology
204875570028_R06C01

source_name: Liver, Mouse DNA, Tissue

value: Liver


title: BER-DSRCT shSIK1 +dox


title: BR340 Pre-Tx