title: 360

tag: disease state

value: Coronary Artery Disease

value: M

tag: hr

tag: ef %

tag: dyslipidemia

value: Yes

tag: hypertension

value: No

value: Former

value: Y

value: MID


title: AUR-AD9G-TTM3-A-1-1-D-A531-37

status: Public on Jan 03 2023

type: genomic

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

country: USA

institute: University of Pittsburgh

hyb_protocol: DNA was bisulfite-converted using the Zymo EZ DNA Methylation Kit (Zymo Research), cleaned using the Zymo-Spin binding columns, and processed through the EPIC array protocol. For FFPE samples, BS converted eluate from the spin columns was used as input for the Infinium HD FFPE DNA Restore kit and processed through the separate restoration workflow. BS converted DNA was denatured, amplified, and hybridized to the EPIC bead chip.

scan_protocol: Array BeadChips were scanned on the Illumina iScan system to produce IDAT files.

data_processing: IDATs were processed with the R Bioconductor (release 3.8) package sesame (version 1.0.0) using the default openSesame pipeline. Probe masking was performed using the standard mask list in sesame, including probes that overlap with SNPs and repeat elements. De-identified files were generated by removing data from the SNP probes using the deidentify function in sesame.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Fresh frozen metastatic breast tumor

label_protocol: An extension reaction was performed using fluorophore-labeled nucleotides per the manufacturer’s protocol.

extract_protocol: DNA was extracted from frozen tissues and FFPE solid tissues using a modification of the AllPrep DNA/RNA kit (Qiagen) and the AllPrep DNA/RNA FFPE kit (Qiagen), respectively. DNA was quantified by Qubit fluorimetry (Life Technologies). Only cases yielding a minimum of 250ng of tumor DNA were included in this study.

tag: Sex

value: Female

tag: sample type

value: Metastatic tumor

tag: tissue

value: Adrenal

tag: tissue type

value: Fresh frozen

tag: autopsy

value: Autopsy


title: A38-LivN-R-150306-1R0i_CP-2767

type: SRA

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: HiSeq2500 HO

library_source: transcriptomic

data_processing:
(If necessary) merge multiple FASTQs together
Maps the data with STAR 2.7.6a
Quantifies the expression with Salmon 1.4.0
QC: (1) Create a sorted bam with samtools sort 1.10, (2) Picard 2.22.4 CollectRnaSeqMetrics, (3) Calculate max read length, flagstat, and a few other metrics, (4) With the unsorted bam, run FastQC 0.11.9
Once all of that is done per sample, a set of summary processes create cohort-wide matrices for expression, normalized expression
Genome_build: CGRh38/hg38 genome
Supplementary_files_format_and_content: (1) Raw read counts (salmon_gene.matrix_RAP101_plus_Normals24.txt)
Supplementary_files_format_and_content: (2) Raw read counts normalized to a fixed upper quartile (salmon_gene_normalized.matrix_RAP101_plus_Normals24.txt)

molecule: polyA RNA

source_name: Normal Liver tissue

extract_protocol:
Tumor tissue was disrupted using roto-stator homogenization. RNA was isolated using the RNeasy Mini Kit (QUIAGEN) according to manufacturer protocol. RNA was quantified using a NanoDrop® Spectrophotometer,  and the quality of RNA was  then  analyzed  via  2100 Bioanalyzer Instrumentwhich  using the  RNA 6000 Nano  assay (Agilent)  for determination  of  an  RNA  Integrity  Number  (RIN).
Briefly, 1 μg of total RNA was converted to RNAseq libraries using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) and sequenced on an Illumina HiSeq 2000 or HiSeq2500 using a 2x50bp configuration

tag: cell type

value: Healty tissue


title: AUR-AD9G-NT1-A-1-1-D-A531-37

source_name: Fresh frozen normal brain

value: Normal tissue

value: Brain


title: AUR-AD9G-TTM1-A-2-1-D-A531-37

value: Liver


title: 358

city: Washington

first: Timothy

last: McCaffrey

state: DC

address: 2300 I Street NW

department: Department of Biochemisty & Molecular Biology

institute: The George Washington University

data_processing:
Concatentate 4 lanes of forward reads
Concatentate 4 lanes of reverse reads
Trim ends using trimmomatic
align to HG38 genome using STAR aligner v 2.5.2b
Use quantMode Gene Counts
Assembly: HG38
Supplementary files format and content: single Excel file .xlsx with one patient per column
Supplementary files format and content: expression level is Transcripts per Million (TPM)

molecule: total RNA

source_name: Whole blood

extract_protocol:
Tempus Spin RNA Isolation Kit
Turbo DNAse treatment and RiboZero Depletion
Illumina TruSeq Stranded Total RNA kit
High-Output 2x75 bp kit on NextSeq 500

treatment_protocol: Tempus preserved whole human blood

value: Whole blood

tag: age

tag: bmi

tag: sbp

tag: dbp

tag: diabetes mellitus

tag: family history_of_cad

tag: smoking

value: Never

tag: asa

value: N

tag: cad

value: LOW

tag: %stenosis

tag: rnaseq group


title: 357

tag: disease state

value: Coronary Artery Disease

tag: Sex

value: M

tag: hr

tag: ef %

tag: dyslipidemia

value: Yes

tag: hypertension

value: No

value: Current


title: A25-LivN-130387-1R0i_CP-2766

description: HiSeq2500 HO

tag: cell type

tag: tissue type


title: A21-LivN-120915-2R0i_CP-2773

description: HiSeq2500 HO


title: AUR-AD9F-TTM2-A-2-1-D-A531-37

value: Female

tag: sample type

value: Metastatic tumor

tag: tissue

value: Lymph node

tag: autopsy


title: AUR-AD9F-TTM1-A-1-1-D-A531-37

value: Fresh frozen

value: Autopsy


title: 356

value: F

tag: age

tag: bmi

tag: sbp

tag: dbp

tag: diabetes mellitus

tag: family history_of_cad

value: Former


title: AUR-AD9E-TTM2-A-1-1-D-A531-37

value: Lung


title: 353

value: Whole blood

tag: disease state

tag: smoking

tag: asa

value: Y

tag: cad

value: CAD

tag: %stenosis

tag: rnaseq group


title: AUR-AD9E-NT1-A-2-1-D-A585-37

source_name: Fresh frozen normal liver

tag: Sex

value: Normal tissue

value: Liver


title: 351

value: Coronary Artery Disease

tag: hr

tag: ef %

tag: dyslipidemia

tag: hypertension

value: Never

value: MID


title: AUR-AD9E-TTM1-A-2-1-D-A531-37

tag: sample type

tag: tissue

value: Soft tissue

tag: tissue type

tag: autopsy


title: 352

value: M

tag: age

tag: bmi

tag: sbp

tag: dbp

value: Yes

tag: diabetes mellitus


title: A20-LivN-120769-2R0i_CP-2772

description: HiSeq2500 HO

tag: cell type

value: Healty tissue


title: A16-2-LivN-110855-2R0i_CP-2768

description: HiSeq2500 HO

value: Fresh frozen


title: 349

tag: disease state

value: No

tag: family history_of_cad

tag: smoking

tag: asa

tag: cad

tag: %stenosis


title: A19-LivN-120715-2R0i_CP-2770

description: HiSeq2500 HO


title: 348

tag: Sex

tag: hr

tag: ef %

tag: dyslipidemia

tag: hypertension

tag: rnaseq group


title: 346

tag: tissue

tag: age

tag: bmi

value: N

value: LOW


title: A17-2-LivN-111079-2R0i_CP-2769

description: HiSeq2500 HO

tag: tissue type


title: 345

value: F

tag: sbp

tag: dbp

tag: diabetes mellitus


title: A27-LungN-131214-2R0i_CP-2763

description: HiSeq2500 HO

source_name: Normal Lung tissue

tag: cell type


title: A28-LungN-131331-2R0i_CP-2764

description: HiSeq2500 HO


title: A32-LungN-R-140512-2R0i_CP-2765

description: HiSeq2500 HO


title: A26-LungN-130920-2R0i_CP-2762

description: HiSeq2500 HO


title: AUR-AD9F-TTM3-A-1-1-D-A531-37

value: Female

tag: sample type

value: Metastatic tumor

value: Adrenal

tag: autopsy

value: Autopsy


title: 344

value: Whole blood

tag: disease state

tag: family history_of_cad

tag: smoking

tag: asa

value: Y

tag: cad

value: CAD

tag: %stenosis


title: AUR-AD9G-TTM2-A-1-1-D-A531-37

tag: Sex

value: Liver


title: A21-LungN-L-120922-2R0i_CP-2760

description: HiSeq2500 HO


title: A25-LungN-130388-1R0i_CP-2761

description: HiSeq2500 HO


title: A34-BrainN-140837-1R0i_CP-2759

description: HiSeq2500 HO

source_name: Normal Brain tissue


title: 343

tag: tissue

value: Coronary Artery Disease

tag: hr

tag: ef %

tag: dyslipidemia

tag: hypertension

value: Never

tag: rnaseq group


title: 341

value: M

tag: age

tag: bmi

tag: sbp

tag: dbp

value: Yes

tag: diabetes mellitus


title: A30-BrainN-R-140019-2R0i_CP-2756

description: HiSeq2500 HO

tag: cell type

value: Healty tissue

tag: tissue type

value: Fresh frozen


title: 340

tag: disease state

tag: family history_of_cad

value: No

tag: smoking

value: Former

tag: asa


title: A27-BrainN-131226-2R0i_CP-2755

description: HiSeq2500 HO


title: 339

tag: tissue

tag: Sex

tag: cad

value: MID

tag: %stenosis


title: 338

tag: hr

tag: ef %

tag: dyslipidemia

tag: hypertension

value: N

value: LOW


title: A21-BrainN-Occi-120926-2R0i_CP-2754

description: HiSeq2500 HO


title: A19-BrainN-120718-2R0i_CP-2758

description: HiSeq2500 HO


title: 334

tag: age

tag: bmi

tag: sbp

tag: rnaseq group


title: A20-BrainN-120774-2R0i_CP-2752

description: HiSeq2500 HO

tag: cell type

tag: tissue type


title: 335

tag: disease state

value: F

tag: dbp

tag: diabetes mellitus

tag: family history_of_cad


title: 332

tag: tissue

tag: Sex

tag: smoking

tag: asa


title: 330

tag: hr

tag: ef %

tag: cad

tag: %stenosis


title: 333

tag: age

tag: bmi

tag: dyslipidemia

tag: hypertension


title: A36-PrimT-FFPER0i_CP-1367

description: HiSeq2500 (HS)

source_name: Primary breast tumor

tag: cell type

value: Primary breast cancer

tag: tissue type

value: Formalin-Fixed Paraffin-Embedded


title: A23-BrainN-121320-2R0i_CP-2753

description: HiSeq2500 HO


title: A34-PancreasMet_ROi_CP-2602

description: HiSeq2500 HO

source_name: Pancreas metastasis

value: Metastatic breast cancer


title: 329

value: Whole blood

tag: disease state

tag: sbp

tag: dbp

value: Y

value: CAD

tag: rnaseq group


title: A34-LivMet-R_ROi_CP-2600

description: HiSeq2500 HO

source_name: Liver metastasis


title: 342

tag: tissue

value: Coronary Artery Disease

tag: Sex

tag: diabetes mellitus

tag: family history_of_cad


title: 328

tag: hr

tag: ef %

tag: smoking

value: Never

tag: asa


title: 327

tag: age

tag: bmi

tag: cad

tag: %stenosis


title: A34-LivMet-L_ROi_CP-2599

description: HiSeq2500 HO

tag: cell type

tag: tissue type


title: A34-LN-Met-R0i_CP-2601

description: HiSeq2500 HO

source_name: Lymph node metastasis


title: 326

tag: disease state

value: M

tag: sbp

tag: dyslipidemia

tag: hypertension

value: Yes


title: A30-BrainN-Occi-140024-2R0i_CP-2757

description: HiSeq2500 HO

value: Healty tissue

value: Fresh frozen


title: A34-DuraMet_ROi_CP-2598

description: HiSeq2500 HO

source_name: Dura metastasis


title: 324

tag: tissue

tag: Sex

tag: dbp

value: No

value: Former

tag: rnaseq group


title: A34-BrainMet_ROi_CP-2597

description: HiSeq2500 HO

source_name: Brain metastasis


title: 337

tag: hr

tag: ef %

tag: diabetes mellitus

tag: family history_of_cad

value: N


title: 323

tag: age

tag: bmi

tag: smoking

value: Current

tag: asa

value: MID


title: A34-PrimT-FFPER0i_CP-1248

description: HiSeq2500 (HS)

tag: cell type

value: Primary breast cancer

tag: tissue type


title: A38-PrimT-FFPER0i_CP-1372

description: HiSeq2500 (HS)

value: Formalin-Fixed Paraffin-Embedded


title: 320

tag: disease state

tag: sbp

tag: cad

value: LOW

tag: %stenosis


title: 322

tag: tissue

value: Whole blood

tag: Sex

tag: dyslipidemia

tag: hypertension


title: 321

tag: dbp

tag: hr

tag: ef %

tag: rnaseq group


title: A30-LivMet-L_ROi_CP-2595

description: HiSeq2500 HO

value: Metastatic breast cancer


title: 319

value: F

tag: age

tag: bmi

tag: diabetes mellitus

tag: family history_of_cad

value: Y

value: CAD


title: 318

value: Coronary Artery Disease

value: M

tag: smoking

value: Never

tag: asa


title: A30-LivMet-R_ROi_CP-2596

description: HiSeq2500 HO

tag: cell type

tag: tissue type

value: Fresh frozen


title: A30-BrainMetOci_ROi_CP-2593

description: HiSeq2500 HO


title: SKNAS N-MYC-ER MYC-ON CT32

city: Rochester

first: Brian

middle: James

last: Altman

state: NY

address: 601 Elmwood Avenue Box 633

department: Biomedical Genetics

institute: University of Rochester

description:
SKNAS_MYC-ON_32
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

data_processing:
Raw reads were processed by Novogene to demultiplex, remove reads containing adaptors, remove reads containing N > 10% (N represents the base cannot be determined), and remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
Processed reads were mapped to transcripts using Salmon 1.3.0 in mapping-based mode for paired-end samples, using a decoy-aware transcriptome built from Gencode v35 GRCh38 primary assembly genome and v35 transcriptome.  Salmon further filtered out ambiguous reads or reads that corresponded to decoy fragments.
Transcripts were collapsed to gene-level using Tximport 1.12.3 using Gencode v35 transcriptome.  Genes were annotated with symbols using the Ensembl GRCh38.101 transcriptome annotations.
Tximport normalized raw counts to Transcripts-Per-Million (TPM).
Assembly: hg38
Supplementary files format and content: Tab-delimited text with GENEID (Column A), SYMBOL (Column B) and TPM data of samples (Columns C-CG)

source_name: neuroblastoma cancer

growth_protocol: Cells were cultured in DMEM high glucose with 10% fetal bovine serum in a 5% CO2 incubator.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plus kit according to manufacturer's instructions.
mRNA library with poly-A enrichment, second-strand synthesis, sequencing adaptor ligation, and PCR amplification.  Libraries were sequences on an Illumina NovaSeq 6000 as 150PE (paired-end), yielding an average of 54.7 million reads per sample (when adding together both paired ends).

value: neuroblastoma cancer

tag: cell line

value: SKNAS

value: neuroblastoma cancer cells

tag: genotype

value: N-MYC-ER overexpressing

tag: treatment

value: 4OHT (MYC-ON), dexamethasone


title: SKNAS N-MYC-ER MYC-ON CT48

description:
SKNAS_MYC-ON_48
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

tag: tissue


title: SKNAS N-MYC-ER MYC-ON CT44

description:
SKNAS_MYC-ON_44
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: SKNAS N-MYC-ER MYC-ON CT52

description:
SKNAS_MYC-ON_52
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: 317

tag: disease state

tag: Sex

tag: sbp

tag: dyslipidemia

value: No

tag: hypertension

value: Yes

tag: cad

tag: %stenosis


title: SKNAS N-MYC-ER MYC-ON CT68

description:
SKNAS_MYC-ON_68
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: SKNAS N-MYC-ER MYC-ON CT36

description:
SKNAS_MYC-ON_36
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: SKNAS N-MYC-ER MYC-ON CT40

description:
SKNAS_MYC-ON_40
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: SKNAS N-MYC-ER MYC-ON CT64

description:
SKNAS_MYC-ON_64
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: SKNAS N-MYC-ER MYC-ON CT60

description:
SKNAS_MYC-ON_60
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: SKNAS N-MYC-ER MYC-ON CT24

description:
SKNAS_MYC-ON_24
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: A30-BrainMet-L4_ROi_CP-2592

description: HiSeq2500 HO


title: SKNAS N-MYC-ER MYC-OFF CT72

description:
SKNAS_MYC-OFF_72
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

value: Ethanol (MYC-OFF, vehicle control), dexamethasone


title: 316

value: Whole blood

tag: age

tag: bmi

tag: dbp

tag: hr

tag: ef %

tag: diabetes mellitus

value: N

value: LOW

tag: rnaseq group


title: SKNAS N-MYC-ER MYC-ON CT72

description:
SKNAS_MYC-ON_72
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

tag: cell line

tag: cell type

tag: genotype


title: SKNAS N-MYC-ER MYC-OFF CT68

description:
SKNAS_MYC-OFF_68
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

tag: tissue

tag: treatment


title: A31-PrimT-FFPER0i_CP-1363

description: HiSeq2500 (HS)

value: Primary breast cancer

tag: tissue type

value: Formalin-Fixed Paraffin-Embedded


title: SKNAS N-MYC-ER MYC-ON CT56

description:
SKNAS_MYC-ON_56
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: 315

tag: disease state

value: Coronary Artery Disease

tag: Sex

tag: sbp

tag: dyslipidemia

tag: family history_of_cad

tag: smoking

value: Former

tag: asa

value: Y

value: CAD


title: SKNAS N-MYC-ER MYC-OFF CT64

description:
SKNAS_MYC-OFF_64
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

value: neuroblastoma cancer


title: SKNAS N-MYC-ER MYC-OFF CT60

description:
SKNAS_MYC-OFF_60
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

value: SKNAS


title: A30-PrimT-FFPER0i_CP-1362

description: HiSeq2500 (HS)


title: 314

value: M

tag: age

tag: bmi

tag: dbp

tag: hr

tag: hypertension

value: Current

tag: cad

tag: %stenosis


title: SKNAS N-MYC-ER MYC-OFF CT56

description:
SKNAS_MYC-OFF_56
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

tag: tissue

tag: cell line

tag: cell type

value: neuroblastoma cancer cells

tag: genotype

value: N-MYC-ER overexpressing


title: SKNAS N-MYC-ER MYC-ON CT28

description:
SKNAS_MYC-ON_28
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

tag: treatment

value: 4OHT (MYC-ON), dexamethasone


title: A30-BrainMet-R_ROi_CP-2594

description: HiSeq2500 HO

value: Metastatic breast cancer

tag: tissue type

value: Fresh frozen


title: SKNAS N-MYC-ER MYC-OFF CT52

description:
SKNAS_MYC-OFF_52
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

value: Ethanol (MYC-OFF, vehicle control), dexamethasone


title: A28-PancreasMet_ROi_CP-2591

description: HiSeq2500 HO


title: SKNAS N-MYC-ER MYC-OFF CT40

description:
SKNAS_MYC-OFF_40
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: A28-LungMet-LLL_ROi_CP-2589

description: HiSeq2500 HO

source_name: Lung metastasis


title: SKNAS N-MYC-ER MYC-OFF CT44

description:
SKNAS_MYC-OFF_44
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: SKNAS N-MYC-ER MYC-OFF CT36

description:
SKNAS_MYC-OFF_36
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: SKNAS N-MYC-ER MYC-OFF CT76

description:
SKNAS_MYC-OFF_76
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: SKNAS N-MYC-ER MYC-OFF CT28

description:
SKNAS_MYC-OFF_28
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: 311

value: Whole blood

tag: disease state

tag: Sex

tag: sbp

tag: ef %

tag: dyslipidemia

value: Yes

value: No

tag: diabetes mellitus

value: Never

tag: rnaseq group


title: SKNAS N-MYC-ER MYC-OFF CT48

description:
SKNAS_MYC-OFF_48
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: A28-LungMet-RUL_ROi_CP-2590

description: HiSeq2500 HO


title: 313

value: Coronary Artery Disease

tag: age

tag: bmi

tag: dbp

tag: hr

tag: family history_of_cad

tag: smoking

tag: asa

value: MID


title: SKNAS N-MYC-ER MYC-OFF CT24

description:
SKNAS_MYC-OFF_24
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

tag: tissue

tag: cell line

tag: cell type

tag: genotype


title: 310

tag: disease state

tag: Sex

value: F

tag: hypertension

value: N

tag: cad

value: LOW

tag: %stenosis


title: Shep N-MYC-ER Replicate 2 MYC-ON CT76

description:
SHEP_Rep2_MYC-ON_76
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

value: neuroblastoma cancer

value: Shep

tag: treatment


title: A28-LivMet-1_ROi_CP-2588

description: HiSeq2500 HO

tag: tissue type


title: 309

value: M

tag: age

tag: bmi

tag: sbp

tag: ef %

tag: dyslipidemia

tag: diabetes mellitus

tag: rnaseq group


title: A28-DuraMat-Met_ROi_CP-2587

description: HiSeq2500 HO


title: Shep N-MYC-ER Replicate 2 MYC-ON CT72

description:
SHEP_Rep2_MYC-ON_72
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

tag: tissue

tag: cell line

value: neuroblastoma cancer cells

value: N-MYC-ER overexpressing


title: A29-PrimT-FFPER0i_CP-1371

description: HiSeq2500 (HS)

tag: cell type

value: Primary breast cancer

value: Formalin-Fixed Paraffin-Embedded


title: A28-AdrenalMet_ROi_CP-2586

description: HiSeq2500 HO

source_name: Adrenal metastasis

value: Metastatic breast cancer

value: Fresh frozen


title: 308

value: Whole blood

tag: disease state

tag: dbp

tag: hr

value: Yes

tag: family history_of_cad

tag: smoking

tag: asa


title: Shep N-MYC-ER Replicate 2 MYC-ON CT64

description:
SHEP_Rep2_MYC-ON_64
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

tag: genotype

tag: treatment

value: 4OHT (MYC-ON), dexamethasone


title: 307

value: Coronary Artery Disease

tag: Sex

tag: age

tag: bmi

value: No

tag: hypertension

value: Never

value: Y

tag: cad

tag: %stenosis


title: Shep N-MYC-ER Replicate 2 MYC-ON CT56

description:
SHEP_Rep2_MYC-ON_56
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

tag: tissue


title: Shep N-MYC-ER Replicate 2 MYC-ON CT60

description:
SHEP_Rep2_MYC-ON_60
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

tag: cell line


title: SKNAS N-MYC-ER MYC-OFF CT32

description:
SKNAS_MYC-OFF_32
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

value: SKNAS

tag: cell type

value: Ethanol (MYC-OFF, vehicle control), dexamethasone


title: A25-PrimT-FFPER0i_CP-1364

description: HiSeq2500 (HS)

tag: tissue type


title: 306

tag: disease state

tag: sbp

tag: dbp

tag: ef %

tag: dyslipidemia

tag: diabetes mellitus

value: N

value: LOW

tag: rnaseq group


title: 305

tag: Sex

value: F

tag: hr

tag: family history_of_cad

tag: smoking

value: Former

tag: asa

value: CAD


title: Shep N-MYC-ER Replicate 2 MYC-ON CT48

description:
SHEP_Rep2_MYC-ON_48
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

value: neuroblastoma cancer

value: Shep

value: neuroblastoma cancer cells

tag: genotype

value: N-MYC-ER overexpressing

tag: treatment


title: 312

tag: tissue

value: Whole blood

value: M

tag: age

tag: bmi

value: Yes

tag: hypertension

tag: cad

tag: %stenosis


title: Shep N-MYC-ER Replicate 2 MYC-ON CT52

description:
SHEP_Rep2_MYC-ON_52
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

tag: cell line

tag: cell type

value: 4OHT (MYC-ON), dexamethasone


title: Shep N-MYC-ER Replicate 2 MYC-ON CT40

description:
SHEP_Rep2_MYC-ON_40
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Shep N-MYC-ER Replicate 2 MYC-ON CT36

description:
SHEP_Rep2_MYC-ON_36
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: 303

tag: disease state

value: Coronary Artery Disease

tag: sbp

tag: dbp

tag: ef %

tag: dyslipidemia

tag: diabetes mellitus

value: No

value: Current


title: A23-PleuraMet_ROi_CP-2583

description: HiSeq2500 HO

source_name: Pleura metastasis

value: Metastatic breast cancer

tag: tissue type

value: Fresh frozen


title: Shep N-MYC-ER Replicate 2 MYC-ON CT32

description:
SHEP_Rep2_MYC-ON_32
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

tag: genotype


title: Shep N-MYC-ER Replicate 2 MYC-ON CT44

description:
SHEP_Rep2_MYC-ON_44
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

tag: treatment


title: 301

tag: tissue

tag: Sex

tag: hr

tag: family history_of_cad

tag: smoking

value: Never

tag: asa

value: Y

tag: rnaseq group


title: Shep N-MYC-ER Replicate 2 MYC-OFF CT76

description:
SHEP_Rep2_MYC-OFF_76
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

tag: cell line

tag: cell type

value: Ethanol (MYC-OFF, vehicle control), dexamethasone


title: Shep N-MYC-ER Replicate 2 MYC-ON CT68

description:
SHEP_Rep2_MYC-ON_68
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Shep N-MYC-ER Replicate 2 MYC-OFF CT72

description:
SHEP_Rep2_MYC-OFF_72
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Shep N-MYC-ER Replicate 2 MYC-OFF CT68

description:
SHEP_Rep2_MYC-OFF_68
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: A28-PrimT-FFPER0i_CP-1361

description: HiSeq2500 (HS)

value: Primary breast cancer

value: Formalin-Fixed Paraffin-Embedded


title: A23-BrainMet_ROi_CP-2581

description: HiSeq2500 HO


title: Shep N-MYC-ER Replicate 2 MYC-OFF CT64

description:
SHEP_Rep2_MYC-OFF_64
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

value: neuroblastoma cancer

value: Shep


title: Mouse KO Neurospheres rep 3

city: Sacramento

first: Paul

last: Knoepfler

state: CA

address: 2425 Stockton Blvd, Room 633

department: Cell Biology and Human Anatomy

institute: University of California Davis

data_processing:
Reads were trimmed using Bbduk
Reads were quantified using Salmon (salmon v1.1.0)
Differential expression was calculated using EdgeR (bioconductor version 3.38.4)
Assembly: EnsDb.Mmusculus.v79

organism: Mus musculus

source_name: mouse neurospheres

growth_protocol: E13.5 embryos were used to generate primary cell lines. The head was removed to establish neural stem cell and precursor cell lines (neurospheres), internal organs were removed, and the remaining body tissue was used to form lines of mouse embryonic fibroblasts (MEFs).

extract_protocol:
RNA was extracted from neurospheres and MEFs using the Nucleospin RNA kit (MacheryNagel 740955.50)
Libraries were prepared using the QuantSeq 3′ mRNA‐Seq Library Prep Kit FWD for Illumina (Lexogen)
3' RNA-seq

value: mouse neurospheres

value: KO


title: Shep N-MYC-ER Replicate 2 MYC-OFF CT56

description:
SHEP_Rep2_MYC-OFF_56
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

value: neuroblastoma cancer cells

value: N-MYC-ER overexpressing


title: A23-AdrenalMet_ROi_CP-2580

description: HiSeq2500 HO


title: Shep N-MYC-ER Replicate 2 MYC-OFF CT52

description:
SHEP_Rep2_MYC-OFF_52
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: A23-LN-Met_ROi_CP-2582

description: HiSeq2500 HO


title: A23-PTcore2009-FFPER0i_CP-1359

description: HiSeq2500 (HS)


title: Shep N-MYC-ER Replicate 2 MYC-OFF CT48

description:
SHEP_Rep2_MYC-OFF_48
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: A23-LN-Met-2010postT-FFPER0i_CP-1360

description: HiSeq2500 (HS)


title: Mouse KO Neurospheres rep 2


title: Shep N-MYC-ER Replicate 2 MYC-OFF CT60

description:
SHEP_Rep2_MYC-OFF_60
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Shep N-MYC-ER Replicate 2 MYC-OFF CT32

description:
SHEP_Rep2_MYC-OFF_32
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: A21-LN-met-FFPE-R0i_CP-2733

description: HiSeq2500 HO


title: Shep N-MYC-ER Replicate 2 MYC-OFF CT44

description:
SHEP_Rep2_MYC-OFF_44
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Shep N-MYC-ER Replicate 2 MYC-OFF CT24

description:
SHEP_Rep2_MYC-OFF_24
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Shep N-MYC-ER Replicate 2 MYC-OFF CT36

description:
SHEP_Rep2_MYC-OFF_36
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Mouse WT Neurospheres rep 3

value: WT


title: A21-PrimT-FFPE-R0i_CP-2732

description: HiSeq2500 HO


title: A20-SPLEEN-MET_ROi_CP-2579

description: HiSeq2500 HO

source_name: Spleen metastasis


title: Mouse WT Neurospheres rep 1


title: Shep N-MYC-ER Replicate 2 MYC-OFF CT28

description:
SHEP_Rep2_MYC-OFF_28
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Shep N-MYC-ER Replicate 2 MYC-ON CT24

description:
SHEP_Rep2_MYC-ON_24
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt

value: 4OHT (MYC-ON), dexamethasone


title: Mouse WT Neurospheres rep 2


title: Shep N-MYC-ER Replicate 1 MYC-ON CT76

description:
SHEP_Rep1_MYC-ON_76
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Shep N-MYC-ER Replicate 1 MYC-ON CT72

description:
SHEP_Rep1_MYC-ON_72
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Mouse KO MEFs rep 5

source_name: mouse embryonic fibroblasts

value: mouse embryonic fibroblasts


title: A20-LUNG-MET-R_ROi_CP-2578

description: HiSeq2500 HO


title: Shep N-MYC-ER Replicate 1 MYC-ON CT68

description:
SHEP_Rep1_MYC-ON_68
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Mouse KO MEFs rep 4


title: A20-LUNG-MET-L_ROi_CP-2577

description: HiSeq2500 HO


title: Shep N-MYC-ER Replicate 2 MYC-OFF CT40

description:
SHEP_Rep2_MYC-OFF_40
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Shep N-MYC-ER Replicate 1 MYC-ON CT60

description:
SHEP_Rep1_MYC-ON_60
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: A20-LN-Met_ROi_CP-2576

description: HiSeq2500 HO


title: Mouse KO MEFs rep 3


title: Shep N-MYC-ER Replicate 1 MYC-ON CT64

description:
SHEP_Rep1_MYC-ON_64
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Shep N-MYC-ER Replicate 1 MYC-ON CT56

description:
SHEP_Rep1_MYC-ON_56
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Shep N-MYC-ER Replicate 1 MYC-ON CT52

description:
SHEP_Rep1_MYC-ON_52
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: A20-LIVER-MET_ROi_CP-2575

description: HiSeq2500 HO


title: Mouse KO MEFs rep 2


title: A20-BRAIN-MET_ROi_CP-2574

description: HiSeq2500 HO


title: A20-ADRENAL-MET_ROi_CP-2573

description: HiSeq2500 HO


title: Shep N-MYC-ER Replicate 1 MYC-ON CT36

description:
SHEP_Rep1_MYC-ON_36
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Shep N-MYC-ER Replicate 1 MYC-ON CT48

description:
SHEP_Rep1_MYC-ON_48
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Shep N-MYC-ER Replicate 1 MYC-ON CT32

description:
SHEP_Rep1_MYC-ON_32
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Mouse WT MEFs rep 2


title: Shep N-MYC-ER Replicate 1 MYC-ON CT44

description:
SHEP_Rep1_MYC-ON_44
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Shep N-MYC-ER Replicate 1 MYC-ON CT40

description:
SHEP_Rep1_MYC-ON_40
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Mouse KO MEFs rep 1


title: Shep N-MYC-ER Replicate 1 MYC-ON CT28

description:
SHEP_Rep1_MYC-ON_28
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: A17-LivMet1_ROi_CP-2572

description: HiSeq2500 HO


title: Mouse WT MEFs rep 1


title: A17-9ChestMet_ROi_CP-2571

description: HiSeq2500 HO

source_name: Chest metastasis


title: Shep N-MYC-ER Replicate 1 MYC-OFF CT72

description:
SHEP_Rep1_MYC-OFF_72
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Shep N-MYC-ER Replicate 1 MYC-OFF CT76

description:
SHEP_Rep1_MYC-OFF_76
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: A17-PrimT-FFPER0i_CP-1369

description: HiSeq2500 (HS)


title: Shep N-MYC-ER Replicate 1 MYC-OFF CT68

description:
SHEP_Rep1_MYC-OFF_68
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Mouse WT MEFs rep 3


title: Shep N-MYC-ER Replicate 1 MYC-OFF CT60

description:
SHEP_Rep1_MYC-OFF_60
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Shep N-MYC-ER Replicate 1 MYC-OFF CT64

description:
SHEP_Rep1_MYC-OFF_64
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Mouse KO Neurospheres rep 1


title: A15-LUNG-MET_ROi_CP-2568

description: HiSeq2500 HO


title: Shep N-MYC-ER Replicate 1 MYC-OFF CT56

description:
SHEP_Rep1_MYC-OFF_56
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Shep N-MYC-ER Replicate 1 MYC-OFF CT52

description:
SHEP_Rep1_MYC-OFF_52
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Shep N-MYC-ER Replicate 1 MYC-OFF CT44

description:
SHEP_Rep1_MYC-OFF_44
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Shep N-MYC-ER Replicate 1 MYC-ON CT24

description:
SHEP_Rep1_MYC-ON_24
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Shep N-MYC-ER Replicate 1 MYC-OFF CT36

description:
SHEP_Rep1_MYC-OFF_36
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: A15-MEDIAST-MET_ROi_CP-2569

description: HiSeq2500 HO


title: Shep N-MYC-ER Replicate 1 MYC-OFF CT40

description:
SHEP_Rep1_MYC-OFF_40
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: RNA-seq_SRSF6_OE_Hyp_rep2.fq.gz

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

country: Germany

institute: Goethe University Frankfurt

description: RNA-seq

data_processing:
RNA-seq: Reads were mapped to the human genome hg38 using STAR (v2.6.1d) with default parameters.
Mapped reads were counted with htSeq-count.
Assembly: hg38
Supplementary files format and content: Count tables in .txt format.

source_name: HeLa

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and pennicilin/streptomycin antibiotics at 37˚C with 5% CO2.  (Hypoxia).

extract_protocol:
Total RNA was isolated using the Trizol method.
For RNA-seq, total RNA was subjected to Ribodepletion and Illumina library preparation following standard procedures. RNA-seq libraries were sequenced on an Illumina NovaSeq60000 instrument (paired-end 150-nt reads; 60 million reads per replicate).

treatment_protocol: Cells were grown either with 21% oxygen (Normoxia) or 0.2% oxygen.


title: Shep N-MYC-ER Replicate 1 MYC-OFF CT24

description:
SHEP_Rep1_MYC-OFF_24
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Shep N-MYC-ER Replicate 1 MYC-OFF CT32

description:
SHEP_Rep1_MYC-OFF_32
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: Shep N-MYC-ER Replicate 1 MYC-OFF CT28

description:
SHEP_Rep1_MYC-OFF_28
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: A15-PriT070427B_ROi_CP-2570

description: HiSeq2500 HO


title: RNA-seq_SRSF6_OE_Hyp_rep1.fq.gz

description: RNA-seq


title: A12-SKULL-MET_ROi_CP-2565

description: HiSeq2500 HO

source_name: Skull metastasis


title: A15-ChestMet_ROi_CP-2566

description: HiSeq2500 HO


title: A15-LiverMet_ROi_CP-2567

description: HiSeq2500 HO


title: A12-PLEURA-MET_ROi_CP-2563

description: HiSeq2500 HO


title: RNA-seq_SRSF6_OE_Norm_rep1.fq.gz

description: RNA-seq


title: A12-MESENTE-MET_ROi_CP-2562

description: HiSeq2500 HO

source_name: Mesentary metastasis


title: Shep N-MYC-ER Replicate 1 MYC-OFF CT48

description:
SHEP_Rep1_MYC-OFF_48
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: TU0140_ATB_V1_NonClass_Mo

city: La Jolla

first: Julie

last: Burel

address: 9420 Athena Circle

institute: La Jolla Institute of Immunology

description: Microscaled (SmartSeq2) cDNA amplification - RNA seq

data_processing:
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The reads were then aligned to UCSC hg19 reference genome using TopHat (v 1.4.1) (Trapnell et al., 2009). DUST scores were calculated with PRINSEQ Lite (v 0.20.3) (Schmieder et al., 2011) and low-complexity reads (DUST > 4) were removed from the BAM files.  The alignment results were parsed via the SAMtools (Li et al., 2009) to generate SAM files. Read counts to each genomic feature were obtained with the htseq-count program (v 0.6.0) (Anders et al., 2014) using the “union” option.
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were against the GRCh38 reference genome and Gencode v27 annotations using STAR v2.6.1 (default options)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: GRCh38.gencode.v27B
Supplementary_files_format_and_content: read count matrix with rows as genes and columns as cells

source_name: Cryopreserved PBMC

growth_protocol: Cells were directly isolated post thawing of cryopreserved PBMC samples and lysed, no culture were involved.

extract_protocol:
Cryopreserved PBMC were thawed, stained with antibodies, and 100,000 memory CD4 T cells sorted using BD Aria 3 cell sorter direclty in Trizol. Memory cells were defined as the combination of CCR7-CD45RA-, CCR7-CD45RA+ and CCR7+CD45RA- populations. Total RNA was purified using a miRNAeasy micro kit (Qiagen, USA) and quantified by qPCR as described previously (Seumois et al., 2012).
Purified total RNA (1 to 5 ng) was amplified following the smart-seq2 protocol (16 cycles of cDNA amplification) (Picelli et al., 2014). cDNA was purified using AMPure XP beads (Beckman Coulter). From this step, 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina).

treatment_protocol: No specific treatment involved

tag: disease group

tag: geographic location

value: USA:San Diego

tag: cell subset

value: Non-classical CD14-CD16+ monocytes


title: A12-LN-MET_ROi_CP-2560

description: HiSeq2500 HO

value: Metastatic breast cancer

value: Fresh frozen


title: XT0082_TBneg_NonClass_Mo

value: TBneg


title: XT0130_TBneg_NonClass_Mo


title: XT0134_LTBI_NonClass_Mo

value: LTBI


title: TU0124_ATB_V1_NonClass_Mo


title: TU0137_LTBI_NonClass_Mo


title: A12-LIVER-MET_ROi_CP-2559

description: HiSeq2500 HO


title: TU0113_ATB_V1_NonClass_Mo


title: TU0110_TBneg_NonClass_Mo


title: TU0085_TBneg_NonClass_Mo


title: TU0084_TBneg_NonClass_Mo


title: RNA-seq_SRSF6_OE_Norm_rep2.fq.gz

description: RNA-seq


title: A12-ADREN-MET_ROi_CP-2558

description: HiSeq2500 HO


title: TU0081_LTBI_NonClass_Mo


title: A12-PriT020076B_ROi_CP-2564

description: HiSeq2500 HO

source_name: Primary breast tumor

value: Primary breast cancer


title: Shep N-MYC-ER Replicate 2 MYC-ON CT28

description:
SHEP_Rep2_MYC-ON_28
Shep_Sknas_N-MYC-ER_RNA-Seq_TPM_Circadian.txt


title: PPO2 [ATAC-seq]

city: CINCINNATI

first: Richard

middle: Q.

last: Lu

state: OH

address: 3333 Burnet Avenue

department: CBDI

institute: Cincinnati Childrens Hosp Med Ctrl

library_source: genomic

data_processing:
Adaptor sequence were trimmed by cutadapt. Reads mapped to mm10 whole genome by Bowtie2 with default options. Use Picard to delete the duplicate reads. Convert bam to wig by bam2wig
Assembly: mm10
Supplementary files format and content: bigWig, bed

growth_protocol: DMEM/F12, serum free media, supplemented with FGF, EGF, ITS, Heparin, progesterone. Cells were cultured at 37C at 5% CO2.

extract_protocol: Genome DNA was extracted based on the protocol of QIAamp DNA Micro Kit, and the ATAC-seq was performed by the ATAC-seq protocol.

value: Mouse Brain Glioma

value: Ptenfl/fl; Trp53 fl/fl; Olig2Cre


title: A11-THYRO-MET_ROi_CP-2557

description: HiSeq2500 HO

source_name: Thyroid metastasis


title: A24-PrimT-FFPER0i_CP-1368

description: HiSeq2500 (HS)

value: Formalin-Fixed Paraffin-Embedded


title: A11-RIB-MET_ROi_CP-2556

description: HiSeq2500 HO

source_name: Rib metastasis


title: TU0075_LTBI_NonClass_Mo


title: TU0078_LTBI_NonClass_Mo


title: TU0070_LTBI_NonClass_Mo


title: TU0064_LTBI_NonClass_Mo


title: PPO1 [ATAC-seq]

value: Ptenfl/fl; Trp53 fl/fl; Olig1Cre


title: TU0071_TBneg_NonClass_Mo


title: A12-LUNG-MET_ROi_CP-2561

description: HiSeq2500 HO


title: A11-CELEBE-MET_ROi_CP-2553

description: HiSeq2500 HO


title: TU0056_TBneg_NonClass_Mo


title: TU0057_TBneg_NonClass_Mo


title: A11-LUNG-MET_ROi_CP-2555

description: HiSeq2500 HO


title: TU0054_TBneg_NonClass_Mo


title: TU0059_TBneg_NonClass_Mo


title: TU0046_LTBI_NonClass_Mo


title: TU0036_LTBI_NonClass_Mo


title: TU0035_LTBI_NonClass_Mo


title: TU0063_LTBI_NonClass_Mo


title: A8-PrimT-030222B-R0i_CP-2731

description: HiSeq2500 HO


title: TU0025_LTBI_NonClass_Mo


title: A11-LIVER-MET_ROi_CP-2554

description: HiSeq2500 HO

source_name: Liver metastasis


title: A7-RIB-MET_ROi_CP-2551

description: HiSeq2500 HO


title: TU0024_LTBI_NonClass_Mo


title: TU0022_LTBI_NonClass_Mo


title: TU0011_LTBI_NonClass_Mo


title: A7-KIDNEY-MET_ROi_CP-2549

description: HiSeq2500 HO

source_name: Kidney metastasis


title: TU0013_LTBI_NonClass_Mo


title: TU0010_LTBI_NonClass_Mo


title: A11-BRAIN-MET_ROi_CP-2552

description: HiSeq2500 HO

source_name: Brain metastasis


title: DOX-4

type: RNA

city: Bengbu City

first: hongwei

last: ye

state: Anhui Province

address: 2600 Donghai Avenue

country: China

institute: Bengbu Medical College

hyb_protocol: Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C)

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).
Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.

organism: Mus

source_name: DOX

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

growth_protocol: Male C57BL/6J mice were subjected to the standard humidity/temperature-controlled environment with a12h-12h light-dark cycle and were fed with sterile rodent food and water.

extract_protocol: RNA quantity and quality were measured by NanoDrop ND-1000

treatment_protocol: The mice were given with saline or DOX through single intraperitoneal injection.

tag: strain

value: male

value: heart


title: TT0120_ATB_V2_NonClass_Mo

description: The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns

value: South Africa


title: DOX-2

value: DOX through single intraperitoneal injection


title: TU0005_LTBI_NonClass_Mo


title: A7-BRAIN-MET_ROi_CP-2548

description: HiSeq2500 HO


title: DOX-5


title: A7-1LiverMet_ROi_CP-2547

description: HiSeq2500 HO


title: DOX-1


title: TT0119_ATB_V1_NonClass_Mo


title: TT0120_ATB_V1_NonClass_Mo


title: GFP+, scRNAseq

city: Nantong

first: Wei

last: Guanyun

address: 9 of Seyuan Lu

institute: Nantong University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCz11
Supplementary files format and content: FASTQ

organism: Danio rerio

source_name: GFP+cells from Tg(Brn3c:mGFP) zebrafish

extract_protocol:
The Tg(Brn3c:mGFP) transgenic zebrafsh larvae at 6 days post-fertilization (dpf) were anesthetized and then treated with 0.25% trypsin to dissociate into single cells, which were divided into GFP-positive and GFP-negative cells through the fuorescent activated cell sorter, and the RNA expressed in GFP-positive cells were then obtained and sequenced using the 10×Genomics platform.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: hair cell

tag: age

value: 6 days


title: TU0033_LTBI_NonClass_Mo

value: USA:San Diego


title: TT0116_ATB_V2_NonClass_Mo

value: Non-classical CD14-CD16+ monocytes


title: Disseminative (biol rep 2)

city: Baltimore

first: Joel

middle: S

last: Bader

state: MD

address: 3400 North Charles Street

department: Biomedical Engineering

institute: Johns Hopkins University

source_name: breast tumor

extract_protocol:
RNA was extracted using Trizol (Invitrogen) according to manufacturer’s protocol.
Total RNA extracts were sent to the Johns Hopkins Transcriptomic and Deep sequencing core for library preparation and RNA sequencing.

value: breast tumor

tag: group

value: Disseminative


title: A7-PrimT020552B_ROi_CP-2546

description: HiSeq2500 HO

tag: tissue type

value: Fresh frozen


title: TU0023_LTBI_NonClass_Mo

value: LTBI


title: TT0116_ATB_V1_NonClass_Mo


title: TT0114_ATB_V2_NonClass_Mo


title: C2

source_name: Control

tag: treatment

value: saline through single intraperitoneal injection


title: A5-SkinMet-R_ROi_CP-2544

description: HiSeq2500 HO

source_name: Skin metastasis

value: Metastatic breast cancer


title: TT0114_ATB_V1_NonClass_Mo


title: Disseminative (biol rep 1)

tag: tissue

tag: genotype


title: Disseminative (biol rep 3)


title: TT0111_ATB_V2_NonClass_Mo


title: A5-SkinMet-R-R0i_CP-3050

description: HiSeq2500 HO


title: C1

tag: Sex


title: TT0111_ATB_V1_NonClass_Mo


title: TT0109_ATB_V2_NonClass_Mo


title: A5-CHESTwal-MET_ROi_CP-2543

description: HiSeq2500 HO


title: TT0107_ATB_V1_NonClass_Mo


title: Non-invasive (biol rep 3)

value: Non-invasive


title: A5-PrimT030065B_ROi_CP-2545

description: HiSeq2500 HO

value: Primary breast cancer


title: Non-invasive (biol rep 1)


title: Invasive (biol rep 3)

value: Invasive


title: TT0108_ATB_V2_NonClass_Mo


title: A4-LULungMet_ROi_CP-2541

description: HiSeq2500 HO

source_name: Lung metastasis


title: TT0105_ATB_V1_NonClass_Mo


title: TT0106_ATB_V1_NonClass_Mo


title: Invasive (biol rep 2)


title: TT0107_ATB_V2_NonClass_Mo


title: A4-LUL-LungMet-R0i_CP-3049

description: HiSeq2500 HO


title: Invasive (biol rep 1)


title: A4-PrimT020306B__ROi_CP-2542

description: HiSeq2500 HO


title: TT0075_TBneg_NonClass_Mo

value: TBneg


title: TT0069_ATB_V2_NonClass_Mo


title: Non-invasive (biol rep 2)


title: TT0059_ATB_V2_NonClass_Mo


title: TT0057_TBneg_NonClass_Mo


title: TT0058_TBneg_NonClass_Mo


title: A1-AxLN-Met_ROi_CP-2540

description: HiSeq2500 HO

source_name: Lymph node metastasis


title: TT0059_ATB_V1_NonClass_Mo


title: A2-PrimT-FFPER0i_CP-1365

description: HiSeq2500 (HS)

value: Formalin-Fixed Paraffin-Embedded


title: Muscle 10 days post NTX [FAP_CCR2KO: 10d-3]

city: Vancouver

first: Fabio

last: Rossi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

country: Canada

institute: University of British Columbia

data_processing:
Illumina base call files were de-multiplexed by bcl2fastq2 on Basespace. Adaptor sequences were trimmed and low-quality reads (< 35 base pairs) were discarded. Additionally, Bowtie was used to remove read pairs that aligned against abundant sequences. Demultiplexed read sequences were then aligned to the mm10 genome reference using STAR aligner. The number of aligned reads to each annotated gene was tallied with RnaReadCounter to generate read-count matrices for all samples, which were used as inputs for downstream analyses. Bowtie, STAR, and RnaReadCounter are tools built under RNA-Seq Alignment (v 1.1).
Assembly: mm10
Supplementary files format and content: Matrix table with raw counts for every gene and sample

source_name: Skeletal muscle (Tibialis Anterior)

extract_protocol:
Muscle were digested, single cell suspension stained and the different cell populations were sorted as following: FAP as CD45-/CD31-/EGFP+, inflammatory cells as CD45+/CD31-, myogenic progenitors as CD45-/CD31-/a7+/VCAM+, and endothelial cells as CD45-/CD31+ using PDGFRa EGFP wild type B6 background and CCR2KO mouse. Pericytes were sorted as CD45-/CD31-/Sca1-/NG2+ using the NG2 DsRed wild type B6 background mouse. Total tissue was digested from wild type B6 background mouse. RNA extraction was performed with RNAzol based protocol.
Sample quality control was performed using the Agilent 2100 Bioanalyzer. Qualifying samples were then prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs). Sequencing was performed on the Illumina NextSeq 500 with Paired End 43bp × 43bp reads.

treatment_protocol: Skeletal muscle (Tibialis Anterior) was injected with myotoxin (notexin).

value: Muscle 10 days post NTX

value: FAP

tag: sorted as

value: CD45-/CD31-/PDGFRa EGFP+


title: Muscle 14 days post NTX [FAP_CCR2KO: 14d]

value: Muscle 14 days post NTX


title: TT0050_TBneg_NonClass_Mo

value: South Africa


title: TT0051_TBneg_NonClass_Mo

value: Non-classical CD14-CD16+ monocytes


title: TT0049_LTBI_NonClass_Mo


title: Muscle 10 days post NTX [FAP_CCR2KO: 10d-1]


title: TT0048_LTBI_NonClass_Mo


title: A1-4-SPIN-MET_ROi_CP-2537

description: HiSeq2500 HO

source_name: Spine metastasis


title: A1-13-LIVER-MET_ROi_CP-2539

description: HiSeq2500 HO


title: TT0047_TBneg_NonClass_Mo


title: Muscle 10 days post NTX [FAP_CCR2KO: 10d-2]


title: A7-LUNG-MET_ROi_CP-2550

description: HiSeq2500 HO


title: A1-10-ADREN_MET_ROi_CP-2538

description: HiSeq2500 HO

source_name: Adrenal metastasis


title: TT0044_TBneg_NonClass_Mo

source_name: Cryopreserved PBMC


title: C3

value: male

value: heart


title: Muscle 7 days post NTX [FAP_CCR2KO: 7d-2]

value: Muscle 7 days post NTX


title: TT0046_LTBI_NonClass_Mo

value: LTBI


title: Muscle 7 days post NTX [FAP_CCR2KO: 7d-1]


title: TT0040_TBneg_NonClass_Mo


title: Muscle 6 days post NTX [FAP_CCR2KO: 6d]

value: Muscle 6 days post NTX


title: TT0041_TBneg_NonClass_Mo


title: TT0039_LTBI_NonClass_Mo


title: A1-1-R-LUNG-MET_ROi_CP-2536

description: HiSeq2500 HO

value: Metastatic breast cancer

value: Fresh frozen


title: A1-PrimT_ROi_CP-2535

description: HiSeq2500 HO

source_name: Primary breast tumor

value: Primary breast cancer


title: TT0033_ATB_V1_NonClass_Mo


title: Muscle 5 days post NTX [FAP_CCR2KO: 5d]

value: Muscle 5 days post NTX


title: Muscle 3 days post NTX [FAP_CCR2KO: 3d-3]

value: Muscle 3 days post NTX


title: Muscle 4 days post NTX [FAP_CCR2KO: 4d]

value: Muscle 4 days post NTX


title: TT0027_ATB_V1_NonClass_Mo


title: TT0028_LTBI_NonClass_Mo


title: 3-3.Input

city: Tianjin

first: Yang

last: Li

state: Tianjin

address: Pingjiang Road 23th

institute: the Second Hospital of Tianjin Medical University

data_processing:
MeRIP-Seq was performed by Cloudseq Biotech Inc. (Shanghai, China) according to the published procedure (Meyer et al., 2012) with slight modifications. Briefly, fragmented RNA was incubated with anti-m6A polyclonal antibody (Synaptic Systems, 202003) in IPP buffer for 2 hours at 4°C. The mixture was then immunoprecipitated by incubation with protein-A beads (Thermo Fisher) at 4°C for an additional 2 hours. Then, bound RNA was eluted from the beads with N6-methyladenosine (BERRY & ASSOCIATES, PR3732) in IPP buffer and then extracted with Trizol reagent (Thermo Fisher) by following the manufacturer’s instruction. Purified RNA was used for RNA-seq library generation with NEBNext® Ultra™ RNA Library Prep Kit (NEB). Both the input sample without immunoprecipitation and the m6A IP samples were subjected to 150 bp paired-end sequencing on Illumina HiSeq sequencer.
Briefly, Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of input libraries were aligned to reference genome (UCSC HG19) by STAR software. Then circRNAs were identified by DCC software using the STAR alignment results. After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA, LncRNA and circRNA were figured out and choosed by home-made scripts. GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes, the associated genes of differentially methylated LncRNAs and the source genes of differentially methylated circRNAs separately.
Assembly: hg19
Supplementary files format and content: bed

source_name: PROSTATE CANCER(CRPC)

extract_protocol:
Total RNAs from  tissue samples were extracted with TRIzol (Invitrogen).
MeRIP-Seq was performed by Cloudseq Biotech Inc. (Shanghai, China) according to the published procedure (Meyer et al., 2012) with slight modifications. Briefly, fragmented RNA was incubated with anti-m6A polyclonal antibody (Synaptic Systems, 202003) in IPP buffer for 2 hours at 4°C. The mixture was then immunoprecipitated by incubation with protein-A beads (Thermo Fisher) at 4°C for an additional 2 hours. Then, bound RNA was eluted from the beads with N6-methyladenosine (BERRY & ASSOCIATES, PR3732) in IPP buffer and then extracted with Trizol reagent (Thermo Fisher) by following the manufacturer’s instruction. Purified RNA was used for RNA-seq library generation with NEBNext® Ultra™ RNA Library Prep Kit (NEB). Both the input sample without immunoprecipitation and the m6A IP samples were subjected to 150 bp paired-end sequencing on Illumina HiSeq sequencer.

tag: cancer

value: prostrate cancer

tag: cancer subtype

value: CRPC

tag: merip antibody

value: none (input)


title: 3-2.Input


title: TT0032_LTBI_NonClass_Mo


title: TT0027_ATB_V2_NonClass_Mo


title: TT0026_LTBI_NonClass_Mo


title: Muscle 3 days post NTX [FAP_CCR2KO: 3d-2]

value: FAP

value: CD45-/CD31-/PDGFRa EGFP+


title: 3-1.Input


title: TT0022_ATB_V1_NonClass_Mo

value: South Africa

value: Non-classical CD14-CD16+ monocytes


title: Muscle 3 days post NTX [FAP_CCR2KO: 3d-1]


title: 2-3.Input

source_name: PROSTATE CANCER(CSPC)

value: CSPC


title: TT0030_LTBI_NonClass_Mo


title: TT0017_LTBI_NonClass_Mo


title: TT0019_LTBI_NonClass_Mo


title: 2-1.Input


title: TT0013_LTBI_NonClass_Mo


title: Muscle 2 days post NTX [FAP_CCR2KO: 2d]

value: Muscle 2 days post NTX


title: 3-3.IP

value: anti-m6A polyclonal antibody (Synaptic Systems, 202003)


title: Muscle 1 day post NTX [FAP_CCR2KO: 1d-3]

value: Muscle 1 day post NTX


title: TT0011_LTBI_NonClass_Mo

value: LTBI


title: TT0020_LTBI_NonClass_Mo


title: TT0006_LTBI_NonClass_Mo


title: TT0007_LTBI_NonClass_Mo


title: Muscle undamaged [FAP_CCR2KO: 0d-2]

value: Muscle undamaged


title: TT0022_ATB_V2_NonClass_Mo


title: 3-1.IP


title: Muscle 1 day post NTX [FAP_CCR2KO: 1d-1]


title: Muscle 1 day post NTX [FAP_CCR2KO: 1d-2]


title: 3-2.IP


title: TT0008_TBneg_NonClass_Mo

value: TBneg


title: 2-2.Input


title: TT0016_LTBI_NonClass_Mo


title: TT0005_LTBI_NonClass_Mo


title: Muscle undamaged [FAP_CCR2KO: 0d-1]


title: 2-3.IP


title: 2-2.IP


title: TT0012_LTBI_NonClass_Mo


title: TT0001_ATB_V2_NonClass_Mo


title: Muscle 10 days post NTX [EC_CCR2KO: 10d-2]

value: Muscle 10 days post NTX

value: Endothelial cells


title: XT0130_TBneg_Int_Mo

value: USA:San Diego

value: Intermediate CD14+CD16+ monocytes


title: XT0082_TBneg_Int_Mo


title: XT0134_LTBI_Int_Mo


title: Muscle 14 days post NTX [EC_CCR2KO: 14d]

value: Muscle 14 days post NTX


title: 2-1.IP

value: prostrate cancer


title: TU0137_LTBI_Int_Mo


title: TT0010_LTBI_NonClass_Mo


title: TU0084_TBneg_Int_Mo


title: TU0081_LTBI_Int_Mo


title: TU0110_TBneg_Int_Mo


title: Muscle 7 days post NTX [EC_CCR2KO: 7d-3]

value: Muscle 7 days post NTX


title: Muscle 7 days post NTX [EC_CCR2KO: 7d-2]


title: U2OS MYC-ER Replicate 2 MYC-ON CT72

data_processing:
Raw reads were demultiplexed using bcl2fastq2-v2.17.1.14.
Processed reads were mapped to transcripts using Salmon 1.3.0 in mapping-based mode for paired-end samples, using a decoy-aware transcriptome built from Gencode v35 GRCh38 primary assembly genome and v35 transcriptome.  Salmon further filtered out ambiguous reads or reads that corresponded to decoy fragments.
Transcripts were collapsed to gene-level using Tximport 1.12.3 using Gencode v35 transcriptome.  Genes were annotated with symbols using the Ensembl GRCh38.101 transcriptome annotations.
Tximport normalized raw counts to Transcripts-Per-Million (TPM).
Assembly: hg38
Supplementary files format and content: Tab-delimited text with GENEID (Column A), SYMBOL (Column B) and TPM data of samples (Columns C-CG)

source_name: osteosarcoma cancer

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plus kit according to manufacturer's instructions.
For replicate 1, Illumina TruSeq Stranded Kit with ribosomal depletion. For replicate 2, Illumina TruSeq Stranded PolyA Kit.  Libraries were sequenced on an Illumina HiSeq 4000 as 100SR (single-end),  yielding an average of 74.3 million reads per sample for Replicate 1, and 40.9 million reads per sample for Replicate 2. .  Note that each sample was run on 5-7 lanes.

value: osteosarcoma cancer

tag: cell line

value: osteosarcoma cancer cells

value: MYC-ER

value: 4OHT (MYC-ON), dexamethasone

tag: time


title: U2OS MYC-ER Replicate 2 MYC-ON CT70

tag: cell type


title: U2OS MYC-ER Replicate 2 MYC-ON CT68


title: TT0001_ATB_V1_NonClass_Mo

tag: disease group

tag: geographic location

value: South Africa

value: Non-classical CD14-CD16+ monocytes


title: TU0075_LTBI_Int_Mo

tag: cell subset


title: U2OS MYC-ER Replicate 2 MYC-ON CT66


title: TU0071_TBneg_Int_Mo


title: Muscle 6 days post NTX [EC_CCR2KO: 6d]

value: Muscle 6 days post NTX


title: U2OS MYC-ER Replicate 2 MYC-ON CT64


title: TU0070_LTBI_Int_Mo

value: LTBI


title: TU0064_LTBI_Int_Mo


title: U2OS MYC-ER Replicate 2 MYC-ON CT62


title: Muscle 3 days post NTX [EC_CCR2KO: 3d]

value: Muscle 3 days post NTX


title: U2OS MYC-ER Replicate 2 MYC-ON CT60


title: TU0063_LTBI_Int_Mo


title: Muscle 2 days post NTX [EC_CCR2KO: 2d]

value: Muscle 2 days post NTX


title: TU0057_TBneg_Int_Mo

value: TBneg


title: TU0059_TBneg_Int_Mo


title: TU0056_TBneg_Int_Mo


title: Muscle 10 days post NTX [EC_CCR2KO: 10d-1]

value: Muscle 10 days post NTX

value: Endothelial cells


title: TU0085_TBneg_Int_Mo

value: USA:San Diego

value: Intermediate CD14+CD16+ monocytes


title: U2OS MYC-ER Replicate 2 MYC-ON CT58


title: TU0078_LTBI_Int_Mo


title: U2OS MYC-ER Replicate 2 MYC-ON CT56


title: Muscle 5 days post NTX [EC_CCR2KO: 5d]

value: Muscle 5 days post NTX


title: TU0054_TBneg_Int_Mo


title: TU0046_LTBI_Int_Mo


title: U2OS MYC-ER Replicate 2 MYC-ON CT54


title: Muscle 1 day post NTX [EC_CCR2KO: 1d-1]

value: Muscle 1 day post NTX


title: U2OS MYC-ER Replicate 2 MYC-ON CT52

value: osteosarcoma cancer


title: TU0035_LTBI_Int_Mo


title: TU0024_LTBI_Int_Mo


title: TU0033_LTBI_Int_Mo


title: TU0023_LTBI_Int_Mo


title: U2OS MYC-ER Replicate 2 MYC-ON CT50

value: osteosarcoma cancer cells


title: Muscle undamaged [EC_CCR2KO: 0d-1]

value: Muscle undamaged


title: Muscle undamaged [EC_CCR2KO: 0d-2]


title: TU0022_LTBI_Int_Mo


title: Muscle 10 days post NTX [MP_CCR2KO: 10d-2]

value: Myogenic Progenitors


title: U2OS MYC-ER Replicate 2 MYC-ON CT48

value: MYC-ER

value: 4OHT (MYC-ON), dexamethasone


title: U2OS MYC-ER Replicate 2 MYC-ON CT46


title: TU0011_LTBI_Int_Mo


title: Muscle 1 day post NTX [EC_CCR2KO: 1d-3]


title: TU0010_LTBI_Int_Mo


title: TT0121_ATB_V2_Int_Mo

value: South Africa


title: Muscle 10 days post NTX [MP_CCR2KO: 10d-1]


title: TT0121_ATB_V1_Int_Mo


title: TT0120_ATB_V2_Int_Mo


title: TU0036_LTBI_Int_Mo

value: LTBI


title: TU0025_LTBI_Int_Mo


title: Muscle 1 day post NTX [EC_CCR2KO: 1d-2]


title: U2OS MYC-ER Replicate 2 MYC-ON CT42


title: U2OS MYC-ER Replicate 2 MYC-ON CT44


title: Muscle 6 days post NTX [MP_CCR2KO: 6d]

value: Muscle 6 days post NTX


title: TU0005_LTBI_Int_Mo


title: Muscle 5 days post NTX [MP_CCR2KO: 5d]


title: U2OS MYC-ER Replicate 2 MYC-ON CT40


title: TU0013_LTBI_Int_Mo


title: Muscle 4 days post NTX [MP_CCR2KO: 4d]

value: Muscle 4 days post NTX


title: TT0117_ATB_V1_Int_Mo


title: TT0117_ATB_V2_Int_Mo


title: U2OS MYC-ER Replicate 2 MYC-ON CT38


title: TT0116_ATB_V2_Int_Mo


title: TT0119_ATB_V1_Int_Mo


title: TT0108_ATB_V1_NonClass_Mo

value: Non-classical CD14-CD16+ monocytes


title: TT0119_ATB_V2_Int_Mo


title: TT0114_ATB_V1_Int_Mo


title: Muscle 3 days post NTX [MP_CCR2KO: 3d-2]

value: Muscle 3 days post NTX


title: U2OS MYC-ER Replicate 2 MYC-ON CT36


title: TT0116_ATB_V1_Int_Mo


title: TT0114_ATB_V2_Int_Mo


title: Muscle 3 days post NTX [MP_CCR2KO: 3d-1]


title: U2OS MYC-ER Replicate 2 MYC-ON CT32


title: U2OS MYC-ER Replicate 2 MYC-ON CT30


title: Muscle undamaged [MP_CCR2KO: 0d]


title: TT0112_ATB_V2_Int_Mo


title: Muscle 14 days post NTX [total_tissue_WT: 14d-1]

value: Muscle 14 days post NTX

value: Skeletal Muscle

value: WT

value: Total muscle lysate


title: TT0109_ATB_V1_Int_Mo

value: Intermediate CD14+CD16+ monocytes


title: TT0111_ATB_V2_Int_Mo


title: U2OS MYC-ER Replicate 2 MYC-ON CT34

value: osteosarcoma cancer


title: TT0108_ATB_V1_Int_Mo


title: TT0109_ATB_V2_Int_Mo


title: Muscle 14 days post NTX [total_tissue_WT: 14d-2]


title: Muscle 1 day post NTX [MP_CCR2KO: 1d]

value: Muscle 1 day post NTX


title: TT0111_ATB_V1_Int_Mo


title: TT0108_ATB_V2_Int_Mo


title: U2OS MYC-ER Replicate 2 MYC-ON CT28

value: osteosarcoma cancer cells


title: TT0107_ATB_V2_Int_Mo


title: TT0112_ATB_V1_Int_Mo


title: TT0107_ATB_V1_Int_Mo


title: U2OS MYC-ER Replicate 2 MYC-ON CT26


title: U2OS MYC-ER Replicate 2 MYC-ON CT24


title: Muscle 10 days post NTX [total_tissue_WT: 10d-2]

value: Muscle 10 days post NTX


title: TT0106_ATB_V2_Int_Mo


title: Muscle 10 days post NTX [total_tissue_WT: 10d-1]


title: TT0106_ATB_V1_Int_Mo


title: U2OS MYC-ER Replicate 2 MYC-OFF CT72

value: MYC-ER

value: Ethanol (MYC-OFF, vehicle control), dexamethasone


title: TT0105_ATB_V2_Int_Mo

value: South Africa


title: Muscle 7 days post NTX [total_tissue_WT: 7d-2]

value: Muscle 7 days post NTX


title: TT0075_TBneg_Int_Mo

value: TBneg


title: TT0105_ATB_V1_Int_Mo


title: U2OS MYC-ER Replicate 2 MYC-OFF CT70


title: Muscle 7 days post NTX [total_tissue_WT: 7d-1]


title: U2OS MYC-ER Replicate 2 MYC-OFF CT68


title: TT0070_ATB_V1_Int_Mo


title: TT0070_ATB_V2_Int_Mo


title: U2OS MYC-ER Replicate 2 MYC-OFF CT66


title: TT0059_ATB_V2_Int_Mo


title: TT0059_ATB_V1_Int_Mo


title: TT0069_ATB_V2_Int_Mo


title: U2OS MYC-ER Replicate 2 MYC-OFF CT62


title: TT0058_TBneg_Int_Mo


title: Muscle 6 days post NTX [total_tissue_WT: 6d-1]

value: Muscle 6 days post NTX


title: TT0069_ATB_V1_Int_Mo


title: Muscle 6 days post NTX [total_tissue_WT: 6d-2]


title: U2OS MYC-ER Replicate 2 MYC-OFF CT64


title: U2OS MYC-ER Replicate 2 MYC-OFF CT60


title: TT0057_TBneg_Int_Mo


title: Muscle 5 days post NTX [total_tissue_WT: 5d-2]

value: Muscle 5 days post NTX


title: TT0050_TBneg_Int_Mo


title: Muscle 5 days postNTX [total_tissue_WT: 5d-1]

value: Muscle 5 days postNTX


title: TT0051_TBneg_Int_Mo


title: Muscle 4 days post NTX [total_tissue_WT: 4d-2]

value: Muscle 4 days post NTX


title: U2OS MYC-ER Replicate 2 MYC-OFF CT58


title: U2OS MYC-ER Replicate 2 MYC-OFF CT56


title: TT0049_LTBI_Int_Mo

value: LTBI


title: Muscle 6 days post NTX [total_tissue_WT: 6d-3]

value: Skeletal Muscle

value: WT


title: TT0046_LTBI_Int_Mo

value: Intermediate CD14+CD16+ monocytes


title: TT0048_LTBI_Int_Mo


title: TT0041_TBneg_Int_Mo


title: TT0044_TBneg_Int_Mo


title: U2OS MYC-ER Replicate 2 MYC-OFF CT54

value: osteosarcoma cancer


title: TT0040_TBneg_Int_Mo


title: Muscle 3 days post NTX [total_tissue_WT: 3d-2]

value: Muscle 3 days post NTX

value: Total muscle lysate


title: U2OS MYC-ER Replicate 2 MYC-OFF CT52

value: osteosarcoma cancer cells


title: Muscle 3 days post NTX [total_tissue_WT: 3d-1]


title: Muscle 2 days post NTX [total_tissue_WT: 2d-2]

value: Muscle 2 days post NTX


title: U2OS MYC-ER Replicate 2 MYC-OFF CT48

value: MYC-ER

value: Ethanol (MYC-OFF, vehicle control), dexamethasone


title: TT0033_ATB_V2_Int_Mo

value: South Africa


title: TT0036_ATB_V1_Int_Mo


title: TT0036_ATB_V2_Int_Mo


title: U2OS MYC-ER Replicate 2 MYC-OFF CT50


title: TT0033_ATB_V1_Int_Mo


title: TT0039_LTBI_Int_Mo


title: U2OS MYC-ER Replicate 2 MYC-OFF CT46


title: TT0030_LTBI_Int_Mo


title: Muscle 2 days post NTX [total_tissue_WT: 2d-1]


title: Muscle 1 day post NTX [total_tissue_WT: 1d-2]

value: Muscle 1 day post NTX


title: TT0047_TBneg_Int_Mo

value: TBneg


title: TT0029_LTBI_Int_Mo


title: U2OS MYC-ER Replicate 2 MYC-OFF CT44


title: Muscle 4 days post NTX [total_tissue_WT: 4d-1]


title: TT0028_LTBI_Int_Mo


title: Muscle 1 day post NTX [total_tissue_WT: 1d-1]


title: sciatic nerve, ctrl, p60

city: shanghai

first: Ximing

last: Nian

state: Shanghai

address: Chongqing Nanlu 227

institute: Shanghai Jiao Tong University

data_processing:
RNA from control and Seh1cKO sciatic nerve were subjected to 50-bp single-end sequencing with a BGISEQ-500 sequencer
At least 20 million clean reads of sequencing depth were obtained for each sample
Assembly: mm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: Sciatic nerve

extract_protocol:
Total RNA fraction was extracted using Eastep®Super Total RNA Extraction Kit (Promega)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sciatic nerve

value: wild type

value: post natal day 60


title: U2OS MYC-ER Replicate 2 MYC-OFF CT42


title: Muscle undamaged [total_tissue_WT: 0d-2]

value: Muscle undamaged


title: sciatic nerve, cko, p60


title: U2OS MYC-ER Replicate 2 MYC-OFF CT38


title: TT0032_LTBI_Int_Mo

value: LTBI


title: TT0026_LTBI_Int_Mo


title: sciatic nerve, ctrl, p30

value: post natal day 30


title: Muscle 14 days post NTX [FAP_WT: 14d-2]

value: Muscle 14 days post NTX

value: FAP

value: WT

value: CD45-/CD31-/PDGFRa EGFP+


title: sciatic nerve, cko, p30


title: TT0022_ATB_V2_Int_Mo

value: Intermediate CD14+CD16+ monocytes


title: U2OS MYC-ER Replicate 2 MYC-OFF CT36

value: osteosarcoma cancer

value: osteosarcoma cancer cells


title: Muscle undamaged [total_tissue_WT: 0d-1]

value: Skeletal Muscle

value: Total muscle lysate


title: TT0022_ATB_V1_Int_Mo

value: South Africa


title: U2OS MYC-ER Replicate 2 MYC-OFF CT34

value: MYC-ER

value: Ethanol (MYC-OFF, vehicle control), dexamethasone


title: Muscle 14 days post NTX [FAP_WT: 14d-1]


title: sciatic nerve, ctrl, p14

value: Sciatic nerve

value: wild type

value: post natal day 14


title: TT0020_LTBI_Int_Mo

value: LTBI


title: Muscle 10 days post NTX [FAP_WT: 10d-2]

value: Muscle 10 days post NTX


title: Muscle 10 days post NTX [FAP_WT: 10d-3]


title: TT0019_LTBI_Int_Mo


title: U2OS MYC-ER Replicate 2 MYC-OFF CT30


title: sciatic nerve, cko, p4

value: post natal day 4


title: TT0027_ATB_V1_Int_Mo


title: U2OS MYC-ER Replicate 2 MYC-OFF CT28


title: sciatic nerve, ctrl, p4


title: U2OS MYC-ER Replicate 2 MYC-OFF CT40


title: TT0027_ATB_V2_Int_Mo


title: Muscle 7 days post NTX [FAP_WT: 7d]

value: Muscle 7 days post NTX

value: FAP


title: TT0017_LTBI_Int_Mo


title: U2OS MYC-ER Replicate 2 MYC-OFF CT32


title: U2OS MYC-ER Replicate 2 MYC-OFF CT26


title: OPN3

data_processing:
RNA-seq reads in FASTQ format were first subjected to quality control to assess the need for trimming of adapter sequences or bad quality segments. The programs used in these steps were FastQC v0.11.7 (1), Trim Galore! v0.4.2 (2) and cutadapt v1.8.1 (3). The trimmed reads were aligned to the reference mouse genome version GRCm38/mm10 with the program STAR v2.6.1e (4). Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8 (5). Gene-level expression was assessed by counting features for each gene, as defined in the NCBI's RefSeq database (6). Read counting was done with the program featureCounts v1.6.2 from the Rsubread package (7). Raw counts were normalized as transcripts per million (TPM).
The differential expression analysis is done by R using DESeq2 package using raw read as input. The significant gene is defined with atleast log2 fold change of atleast2 and FDR <0.05 value
Assembly: mm10
Supplementary files format and content: tab-delimited text files compiled matrix through DESEq
Supplementary files format and content: tab-delimited text files compiled matrix TPM Values through DESEq

source_name: Glioma

extract_protocol: The RNA extraction from mouse tissues and cells are RNeasy Kits (Qiagen, Mini and Midi Cat. Nos. 74104 and 75144) following manufacturer’s protocol and preserved at -80C.

value: Glioma

tag: stain

value: Mixed

value: Nf1fl/fl; Trp53 fl/fl; Olig1Cre

value: Brain Tumor


title: sciatic nerve, cko, p14


title: TT0013_LTBI_Int_Mo

value: Intermediate CD14+CD16+ monocytes


title: U2OS MYC-ER Replicate 2 MYC-OFF CT24

value: osteosarcoma cancer

value: osteosarcoma cancer cells


title: Muscle 6 days post NTX [FAP_WT: 6d-1]

value: Muscle 6 days post NTX

value: WT

value: CD45-/CD31-/PDGFRa EGFP+


title: Muscle 10 days post NTX [FAP_WT: 10d-1]


title: TT0011_LTBI_Int_Mo

value: South Africa


title: TT0012_LTBI_Int_Mo


title: Muscle 6 days post NTX [FAP_WT: 6d-3]


title: PPO2-iv

value: Ptenfl/fl; Trp53 fl/fl; Olig2Cre


title: Muscle 6 days post NTX [FAP_WT: 6d-2]


title: PPO2-iii


title: U2OS MYC-ER Replicate 1 MYC-ON CT68

value: MYC-ER

value: 4OHT (MYC-ON), dexamethasone


title: PPO2-ii


title: U2OS MYC-ER Replicate 1 MYC-ON CT64


title: PPO2-i


title: Muscle 4 days post NTX [FAP_WT: 4d-3]

value: Muscle 4 days post NTX


title: Muscle 5 days post NTX [FAP_WT: 5d]

value: Muscle 5 days post NTX


title: U2OS MYC-ER Replicate 1 MYC-ON CT60


title: TT0008_TBneg_Int_Mo

value: TBneg


title: Muscle 4 days post NTX [FAP_WT: 4d-2]

value: FAP


title: PPO1-iv

value: Glioma

value: Mixed

value: Ptenfl/fl; Trp53 fl/fl; Olig1Cre


title: U2OS MYC-ER Replicate 1 MYC-ON CT56


title: Muscle 4 days post NTX [FAP_WT: 4d-1]


title: OPN2

value: Nf1fl/fl; Trp53 fl/fl; Olig1Cre

value: Brain Tumor


title: PPO1-iii


title: TT0006_LTBI_Int_Mo

value: LTBI

value: Intermediate CD14+CD16+ monocytes


title: PPO1-ii


title: Muscle 3 days post NTX [FAP_WT: 3d-6]

value: Muscle 3 days post NTX

value: WT


title: Muscle 3 days post NTX [FAP_WT: 3d-5]

value: CD45-/CD31-/PDGFRa EGFP+


title: TT0005_LTBI_Int_Mo

value: South Africa


title: TT0010_LTBI_Int_Mo


title: PPO1-i


title: U2OS MYC-ER Replicate 1 MYC-ON CT48

value: osteosarcoma cancer

value: osteosarcoma cancer cells

value: MYC-ER


title: U2OS MYC-ER Replicate 1 MYC-ON CT44

value: 4OHT (MYC-ON), dexamethasone


title: TT0003_ATB_V1_Int_Mo


title: U2OS MYC-ER Replicate 1 MYC-ON CT40


title: TT0003_ATB_V2_Int_Mo


title: Muscle 3 days post NTX [FAP_WT: 3d-3]


title: WT_Ctrl_1

data_processing:
RNA-seq reads in FASTQ format were first subjected to quality control to assess the need for trimming of adapter sequences or bad quality segments. The programs used in these steps were FastQC v0.11.7 (1), Trim Galore! v0.4.2 (2) and cutadapt v1.8.1 (3). The trimmed reads were aligned to the reference mouse genome version GRCm38/mm10 with the program STAR v2.6.1e (4). Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8 (5). Gene-level expression was assessed by counting features for each gene, as defined in the NCBI's RefSeq database (6). Read counting was done with the program featureCounts v1.6.2 from the Rsubread package (7). Raw counts were normalized as transcripts per million (TPM).
The differential expression analysis is done by R using DESeq2 package using raw read as input. The significant gene is defined with atleast log2 fold change of atleast2 and FDR <0.05 value
Assembly: mm10
Supplementary files format and content: tab-delimited text files compiled FPKM Values
Supplementary files format and content: tab-delimited text files compiled matrix through DESEq
Supplementary files format and content: tab-delimited text files compiled matrix TPM Values through DESEq

source_name: Brain

growth_protocol: NO

extract_protocol: RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.

value: Brain

tag: development stage


title: Muscle 3 days post NTX [FAP_WT: 3d-4]

value: FAP


title: TT0001_ATB_V1_Int_Mo


title: Muscle 3 days post NTX [FAP_WT: 3d-2]


title: PPO2_4

value: End-Stage


title: U2OS MYC-ER Replicate 1 MYC-ON CT36


title: U2OS MYC-ER Replicate 1 MYC-ON CT32


title: TT0001_ATB_V2_Int_Mo


title: Muscle 3 days post NTX [FAP_WT: 3d-1]


title: PPO2_3

value: Mixed


title: XT0134_LTBI_Class_Mo

value: USA:San Diego

value: Classical CD14+CD16- monocytes


title: TT0016_LTBI_Int_Mo


title: Muscle 2 days post NTX [FAP_WT: 2d-6]

value: Muscle 2 days post NTX


title: U2OS MYC-ER Replicate 1 MYC-ON CT28


title: Muscle 2 days post NTX [FAP_WT: 2d-5]


title: XT0130_TBneg_Class_Mo

value: TBneg


title: XT0082_TBneg_Class_Mo


title: U2OS MYC-ER Replicate 1 MYC-OFF CT72

value: Ethanol (MYC-OFF, vehicle control), dexamethasone


title: PPO2_2


title: TU0140_ATB_V1_Class_Mo


title: U2OS MYC-ER Replicate 1 MYC-ON CT24


title: U2OS MYC-ER Replicate 1 MYC-OFF CT64


title: TU0137_LTBI_Class_Mo

value: LTBI


title: Muscle 2 days post NTX [FAP_WT: 2d-4]

value: WT


title: U2OS MYC-ER Replicate 1 MYC-OFF CT68


title: Muscle 2 days post NTX [FAP_WT: 2d-3]

value: CD45-/CD31-/PDGFRa EGFP+


title: Control_3

city: Changsha

first: Liao

last: yuan

state: Hunan

address: 139 renmin zhong lu, furong district

department: dermatology department

institute: Second Xiang Ya Hospital of Central South University

data_processing:
Sub-pixel Registration  used for basecalling.
This project use the filtering software SOAPnuke for statistics and trimmomatic for filtering
Clean reads were compared to the reference gene sequences using Bowtie2, and then the expression levels of genes and transcripts were calculated using RSEM.
For the transcription factor, we compared all Unigene to the AnimalTFDB2.0 database to check the corresponding gene information, function, binding sites and other information of the TF family.
Correcting p-values to q-values through strategies Benjamini, y. — Hochberg, y. and Storey, j. —Tibshirani, r.In order to improve the accuracy of DEGs, we defined genes with difference multiples of more than twice and q-value ≤0.001 as significantly differentially expressed genes.
According to the results of differential gene detection, pheatmap function in R software was used for hierarchical clustering analysis.
According to the GO annotation results and t KEGG annotation results, we classified the differential genes into functional classification and biological pathway classification, and enriched them by using the phyper function in R software.Then the pvalue was corrected by FDR, and the function with Qvalue <= 0.05 was considered to be significantly enriched
Genome_build: GRCh38.p11(hg38)
Supplementary_files_format_and_content: The file format of proceed file was Fastq, including  fpkm.txt of differentially expressed genes.

source_name: Hacat cell

growth_protocol: cultured in DMEM (Gibco，Grand Island，USA) with 10% foetal bovine serum (FBS, HyClone) and 1% penicILlin (Solarbio ,China). The cells were mantained in a 37°C humidified air incubator with 5% CO2.

extract_protocol:
Total RNA was extracted from the cell using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. The cell was transferred into a  EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
DNase I was used to digest double-stranded and single-stranded DNA in total RNA, then, magnetic beads were purified to recover the reaction products, RNase H or Ribo-Zero method (human, mouse, plants) (Illumina, USA) was used to remove the rRNA. Purified mRNA from previous steps was fragmented into small pieces with fragment buffer at appropriate temperature. Then, First-strand cDNA was generated in First Strand Reaction System by PCR, and the second-strand cDNA was generated as well. The reaction product was purified by magnetic beads, afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to carry out end repair. The cDNA fragments with adapters were amplyfied by PCR, and the products were purified by Ampure XP Beads. Library was validating on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products above were heated denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29(Thermo Fisher Scientific, MA, USA) to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGISEQ500 platform (BGIShenzhen, China).

treatment_protocol: Hacat was transfected with WT1 overexpressed plasmids and blank  plasmids

value: Normal human skin immortalized keratinocytes

value: Hacat

tag: transfection

value: blank plasmid


title: Muscle 2 days post NTX [FAP_WT: 2d-2]


title: TU0124_ATB_V1_Class_Mo


title: U2OS MYC-ER Replicate 1 MYC-OFF CT56

value: osteosarcoma cancer

value: osteosarcoma cancer cells

value: MYC-ER

tag: treatment


title: Control_2


title: Control_1


title: WT1_3

value: overexpressing WT1 plasmid


title: PPO2_1

tag: tissue

value: Brain

value: End-Stage


title: Muscle 1 day post NTX [FAP_WT: 1d-4]

value: Muscle 1 day post NTX

value: FAP

tag: genotype


title: Muscle 2 days post NTX [FAP_WT: 2d-1]

value: Muscle 2 days post NTX


title: WT1_2


title: U2OS MYC-ER Replicate 1 MYC-OFF CT52


title: WT_Ctrl_2

value: Mixed


title: Muscle 1 day post NTX [FAP_WT: 1d-2]


title: TU0085_TBneg_Class_Mo

value: TBneg

value: USA:San Diego

value: Classical CD14+CD16- monocytes


title: WT1_1


title: U2OS MYC-ER Replicate 1 MYC-OFF CT44

value: Ethanol (MYC-OFF, vehicle control), dexamethasone


title: U2OS MYC-ER Replicate 1 MYC-OFF CT60


title: Muscle 1 day post NTX [FAP_WT: 1d-1]

value: WT

value: CD45-/CD31-/PDGFRa EGFP+


title: U2OS MYC-ER Replicate 1 MYC-OFF CT40


title: U2OS MYC-ER Replicate 1 MYC-ON CT52

value: 4OHT (MYC-ON), dexamethasone


title: TU0081_LTBI_Class_Mo

value: LTBI


title: Muscle undamaged [FAP_WT: 0d-3]

value: Muscle undamaged


title: TU0078_LTBI_Class_Mo


title: TU0113_ATB_V1_Class_Mo


title: Ctrl rep2

city: Jinan

first: Min

last: Wu

state: Shandong

address: Wenhua West Road

institute: Shandong University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Assembly: mm10
Supplementary files format and content: fpkm.csv

growth_protocol: Raw264.7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics.

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

treatment_protocol: AG group was induced by treatment of 1,5-Anhydroglucitol (0.5mM,J&K Scientific,China) for 24h.

value: macrophage cell line


title: AG rep1


title: Ctrl rep1


title: TU0071_TBneg_Class_Mo


title: Muscle undamaged [FAP_WT: 0d-1]


title: TT0007_LTBI_Int_Mo

value: South Africa

value: Intermediate CD14+CD16+ monocytes


title: U2OS MYC-ER Replicate 1 MYC-OFF CT32

value: osteosarcoma cancer

value: osteosarcoma cancer cells

value: MYC-ER


title: U2OS MYC-ER Replicate 1 MYC-OFF CT36


title: Muscle 1 day post NTX [FAP_WT: 1d-3]

value: Muscle 1 day post NTX

value: FAP


title: TU0110_TBneg_Class_Mo

value: TBneg


title: TU0070_LTBI_Class_Mo

value: USA:San Diego


title: Osteoclasts, Slc37a2 WT, biol rep 3

city: Crawley

first: Nathan

middle: J

last: Pavlos

state: WA

address: 35 Stirling Highway

department: School of Biomedical Sciences

country: Australia

institute: The University of Western Australia

description:
CAGRF20083572-WT_F_v_KO_F-top1000_genes.csv
CAGRF20083572-WT_F_v_KO_F-all_genes.csv

data_processing:
Image analysis was performed in real time by the NovaSeq Control Software (NCS) v1.7.0 and Real Time Analysis (RTA) v3.4.4, running on the instrument computer. RTA performs real-time base calling on the NovaSeq instrument computer. Then the Illumina bcl2fastq 2.20.0.422 pipeline was used to generate the sequence data. The data generated here meet the AGRF quality standards.
edgeR (version 3.30.3) to perform differential expression analysis.
(https://bioconductor.org/packages/release/bioc/html/edgeR.html) using R
4.0.0.
Assembly: mm10
Supplementary files format and content: The processed data files contain:
Supplementary files format and content: GeneID from the reference genome annotation
Supplementary files format and content: logFC: log2-fold change of expression between WT and KO groups
Supplementary files format and content: logCPM: average log count per million for the gene across all samples
Supplementary files format and content: LR: likelihood ratio test for the gene across all samples
Supplementary files format and content: PValue: p-values for test of expression
Supplementary files format and content: FDR: False discovery rate
Supplementary files format and content: SamplesCounts: Raw gene counts for each sample

source_name: bone

growth_protocol: Bone marrow macrophages were maitained in aMEM-supplemented with 10% fetal bovine serum (FBS), antibiotics and M-CSF (2ng/ml)in humidified atmosphere with 5% CO2 at 37C

extract_protocol: RNA was extracted using TRIzol reagent (Cat#. 15596026, Invitrogen), followed by purification using the PureLink RNA mini kit (Cat#. 12183020, Invitrogen) with in-column DNase I treatment (Cat# 12185010, Invitrogen) according to manufacturer's instruction.

treatment_protocol: Osteoclast differentation was induced by stimulating bone marrow macrophages for 5 days in the presence of RANKL (10ng/ml, R&D Systems) and M-CSF (2ng/ml).

value: bone

value: Bone marrow macrophage-derived osteoclasts

value: M-CSF/RANKL-stimulation (5-days)


title: U2OS MYC-ER Replicate 1 MYC-OFF CT48

value: Ethanol (MYC-OFF, vehicle control), dexamethasone


title: U2OS MYC-ER Replicate 1 MYC-OFF CT28


title: TU0075_LTBI_Class_Mo

value: Classical CD14+CD16- monocytes


title: AG rep2


title: Muscle 10 days post NTX [Pericyte_WT: 10d-2]

value: Muscle 10 days post NTX

value: Pericytes

value: WT


title: Osteoclasts, Slc37a2 WT, biol rep 2


title: U2OS MYC-ER Replicate 1 MYC-OFF CT24


title: N2A, basal, rep3

city: Kuopio

first: Nea

last: Korvenlaita

address: Neulaniementie 2

country: Finland

institute: University of Eastern Finland

description:
all_samples_peaks.bed columns: chr,start,stop,peak_id,score,dir,sample
SL3

data_processing:
Quality control was performed with FastQC
Cutadapt was applied to remove adapters and over-represented sequences, and to keep only reads with at least 24 bp and the quality score greater than 20 for each base.
STAR was applied for the alignment. Reads with inconsistent or non-canonical introns were filtered out. Alignment was performed with no soft-clipping setting. Next, RmDup was applied to remove PCR duplicates and to obtain the final BAM sequences. Fingerprint plot reported good quality of the sequences.
Piranha was applied to perform peak detection. The method was applied without control. Each replicate was treated separately. After Piranha, SlopBed was applied to the peak regions obtained for each sample. SlopBed expanded the peak regions of 30 bp.
RNA Centric Annotation System was applied for the annotation and functional analysis of the peaks. It kept only the significant peaks detected in all the samples, annotated the peaks to transcripts and genes, how many peaks fall in the gene’s regions and kept the genes having at least one peak in the 3utr. We then enriched the peaks associated to the genes with the miRNAs targeting them using Mirwalk database.
Assembly: mm10
Supplementary files format and content: bed format and Piranha significant peaks for sample

source_name: N2A cells

growth_protocol: N2A cells were maintained in Kool-aid High Glucose media supplemented with 10% inactivated Fetal Bovine Serum and 1% penicillin-streptomycin.

extract_protocol:
When the cultures reached 80% confluency, media were replaced with PBS. The cells were crosslinked once at 400 mJ/cm2 and after that twice at 200 mJ/cm2 by using Stratagene UV Stratalinker 1800 (Stratagene, LaJolla, CA, USA). After crosslinking the cells were scraped off the plates and collected into tubes, pelleted, and stored at -80°C as a dry pellet until further processing. Each sample corresponded to approximately 60 million cells.
The frozen samples after crosslinking were lysed and they went through Ago immunoprecipitation and radiolabeling of RNA. Ago-RNA complexes were further purified by SDS-PAGE and nitrocellulose transfer and visualized by autoradiography. Products were then extracted from the membrane, amplified with PCR, analyzed with Bioanalyzer and sequenced (Illumina).

value: N2A cells

value: Neuroblastoma

tag: ip antibody

value: anti-Ago2 (Wako clone 2D4)

tag: protocol

value: HITS-CLIP seq


title: TU0064_LTBI_Class_Mo

value: LTBI


title: Muscle 10 days post NTX [Pericyte_WT: 10d-1]

tag: sorted as


title: Osteoclasts, Slc37a2 KO, biol rep 3

value: Slc37a2 KO


title: Muscle 5 days post NTX [Pericyte_WT: 5d]

value: Muscle 5 days post NTX


title: TU0063_LTBI_Class_Mo


title: Muscle undamaged [FAP_WT: 0d-2]

value: Muscle undamaged

value: FAP

value: CD45-/CD31-/PDGFRa EGFP+


title: N2A, basal, rep2

description:
all_samples_peaks.bed columns: chr,start,stop,peak_id,score,dir,sample
SL2


title: Muscle 3 days post NTX [Pericyte_WT: 3d-2]

value: Muscle 3 days post NTX


title: Osteoclasts, Slc37a2 KO, biol rep 2

value: bone

value: Bone marrow macrophage-derived osteoclasts

value: M-CSF/RANKL-stimulation (5-days)


title: N2A, basal, rep1

description:
all_samples_peaks.bed columns: chr,start,stop,peak_id,score,dir,sample
SL1


title: TU0059_TBneg_Class_Mo

value: TBneg

value: USA:San Diego

value: Classical CD14+CD16- monocytes


title: Muscle 3 days post NTX [Pericyte_WT: 3d-1]

value: Pericytes

value: WT


title: TU0057_TBneg_Class_Mo


title: Osteoclasts, Slc37a2 KO, biol rep 1


title: TU0054_TBneg_Class_Mo


title: mononuclear cells, mdx5cv diaphragm 14 weeks [D5CV]

city: New York

first: Gregory

middle: Robert

last: Smith

address: 1 Gustave L. Levy Pl

department: Neurology

institute: Mount Sinai Hospital

description: Chromium legacy

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: skeletal muslce

extract_protocol:
Cryo-preserved cells were used directely for library construction for scRNA-seq. Cells were thawed, washed, and resuspended at 1,000 cells/ul for processing 10x scRNAseq v3.1 protocol.
10X Genomics Single Cell 3' Reagent Kits V3.1, following the User Guidelines. Briefly, GEM RNAseq was performed as described (10x Genomics, Pleasanton, CA), following the Single Cell 3’ Reagents Kits V3 User Guides. Cells were filtered, counted on a Nexcelome instrument, and the final concentration was set at 1,000 cells/μl for cells. The amount of cells or nuclei loaded on the chip was determined based on the 10X Genomics protocol. The 10X chip (Chromium Single Cell 3’ v3 chip kit B PN-2000060) was loaded to target 5,000 cells final. Reverse-transcription was performed in the emulsion and cDNA was amplified before library construction following the Chromium protocols v3. Each library was tagged with a different index for multiplexing (Chromium i7 Multiplex kit PN-12062). Quality control and quantification of the amplified cDNA were assessed on a Bioanalyzer (High-Sensitivity DNA Bioanalyzer kit). Sequencing was carried out at the New York Genome Center on Illumina Novaseq using  98+26 paired-end reads.

value: skeletal muslce

tag: age

value: 14 weeks

value: multiple cell types


title: Pooled Jak2V167F Vav-Cre+ bone marrow cells obtained six months after transplant from two mice [HTOonly]

city: Memphis

first: Jeremy

middle: Chase

last: Crawford

state: TN

address: MS 221, 262 Danny Thomas Place

department: Department of Host-Microbe Interactions

institute: St. Jude Children's Research Hospital

description:
10x Genomics single-cell hashing oligo matrix (unfiltered). Read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
JCC358_B_6_months_HTOonly

library_source: other

data_processing:
library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)
Gene expression and HTO data were processed using CellRanger (v5.0.1, 10X Genomics) with the corresponding refdata-gex-mm10-2020-A reference. HTObarcodes.csv was used to identify matching HTOs. Filtered gene expression matrices and unfiltered HTO matrices are provided. For convenience to other researchers, gene expression processed data files also include HTO data from simultaneous processing. Corresponding molecule_info.h5 files are also included, which were used by authors to aggregate/normalize samples with CellRanger prior to downstream analysis in Seurat.
The 2mo_6mo_AggregationMatrices.tar supplementary file includes filtered matrices for the normalized aggregation (via CellRanger) of JCC358_A_2_months_GEXandHTO and JCC358_B_6_months_GEXandHTO libraries, including gene expression and HTO data. This output was used by authors for downstream analyses. Cells labeled with -1 are derived from the JCC358_A_2_months_GEXandHTO library, whereas cells labeled with -2 are derived from the JCC358_B_6_months_GEXandHTO library.
Assembly: refdata-gex-mm10-2020-A reference

molecule: protein

source_name: bone marrow

extract_protocol: Library was prepared using Chromium Single Cell 3ʹ v2 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ v2 protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp) and libraries were then constructed per manufacturer's instructions.

value: bone marrow

value: Jak2V167F Vav-Cre+

tag: library type

value: HTO only


title: Pooled Jak2V167F Vav-Cre+ bone marrow cells obtained two months after transplant from two mice [HTOonly]

description:
10x Genomics single-cell hashing oligo matrix (unfiltered). Read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
JCC358_A_2_months_HTOonly


title: Muscle 2 days post NTX [Pericyte_WT: 2d-2]

value: Muscle 2 days post NTX


title: Muscle 2 days post NTX [Pericyte_WT: 2d-1]


title: Pooled Jak2V167F Vav-Cre+ bone marrow cells obtained six months after transplant from two mice [GEXandHTO]

description:
10x Genomics single-cell expression matrix (filtered) with hashtag oligos (HTOs) indicating individual mouse. Raw reads only contain gene expression data. See corresponding JCC358_B_6_months_HTOonly sample for HTO processed and raw data.
JCC358_B_6_months_GEXandHTO

tag: molecule subtype

value: polyA RNA and protein

value: mRNA and HTO


title: mononuclear cells, mdx5cv quadriceps 14 weeks [Q5CV]

description: Chromium legacy


title: Osteoclasts, Slc37a2 WT, biol rep 1

value: bone

tag: cell line


title: TU0046_LTBI_Class_Mo

extract_protocol:
Cryopreserved PBMC were thawed, stained with antibodies, and 100,000 memory CD4 T cells sorted using BD Aria 3 cell sorter direclty in Trizol. Memory cells were defined as the combination of CCR7-CD45RA-, CCR7-CD45RA+ and CCR7+CD45RA- populations. Total RNA was purified using a miRNAeasy micro kit (Qiagen, USA) and quantified by qPCR as described previously (Seumois et al., 2012).
Purified total RNA (1 to 5 ng) was amplified following the smart-seq2 protocol (16 cycles of cDNA amplification) (Picelli et al., 2014). cDNA was purified using AMPure XP beads (Beckman Coulter). From this step, 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina).

value: LTBI


title: TU0036_LTBI_Class_Mo


title: Muscle undamaged [Pericyte_WT: 0d-2]

value: Muscle undamaged

tag: cell type


title: mononuclear cells, WT quadriceps 14 weeks [QW]

description: Chromium legacy


title: mononuclear cells, WT diaphragm 14 weeks [DW]

description: Chromium legacy


title: TU0035_LTBI_Class_Mo

tag: disease group


title: Pooled Jak2V167F Vav-Cre+ bone marrow cells obtained two months after transplant from two mice [GEXandHTO]

description:
10x Genomics single-cell expression matrix (filtered) with hashtag oligos (HTOs) indicating individual mouse. Raw reads only contain gene expression data. See corresponding JCC358_A_2_months_HTOonly sample for HTO processed and raw data.
JCC358_A_2_months_GEXandHTO


title: Bald-3 substrate hyphae rep3

city: Beijing

first: Zhenpeng

last: Zhang

address: 38 Life Science Park Road

institute: Beijing Proteome Research Center

description:
972M3_3
Achaeostreptomyces halophilum YIM 93972

data_processing:
cDNA libraries were sequenced by paired-end 100 bp sequencing on an Illumina HiSeq2000 system.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Achaeostreptomyces halophilum YIM 93972 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Transcript count, TPM and FPKM were calculated using a protocol.
Genome_build: Genome of Achaeostreptomyces halophilum YIM 93972 (Genome_Achaeostreptomyces_halophilum_93972.fasta, Annotation_Achaeostreptomyces_halophilum_93972.xlsx).
Supplementary_files_format_and_content: transcript counts: transcript counts.
Supplementary_files_format_and_content: transcript tpm: transcript tpm.
Supplementary_files_format_and_content: transcript fpkm: transcript fpkm.

organism: Halocatena halophila

source_name: Hyphae

growth_protocol: The wild and mutated strains of Achaeostreptomyces halophilum YIM 93972 were spread on a layer of 0.20 μm BioTrace NT Nitrocellulose Transfer Membrane (Pall China, Beijing, China) covered on an ISP 4 medium containing 25% NaCl and 2% agar in 85 mm diameter Petri dish.

extract_protocol:
The total RNA was extracted and analyzed as described previously. Briefly, total RNA was extracted with Trizol method. The TruSeqTM Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) was used to prepare the cDNA libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To obtain the poorly differentiated and undifferentiated strains, a NTG-based mutagenesis experiment was applied.

value: Bald type

value: Hyphae


title: Muscle undamaged [Pericyte_WT: 0d-1]

source_name: Skeletal muscle (Tibialis Anterior)


title: TU0033_LTBI_Class_Mo

data_processing:
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The reads were then aligned to UCSC hg19 reference genome using TopHat (v 1.4.1) (Trapnell et al., 2009). DUST scores were calculated with PRINSEQ Lite (v 0.20.3) (Schmieder et al., 2011) and low-complexity reads (DUST > 4) were removed from the BAM files.  The alignment results were parsed via the SAMtools (Li et al., 2009) to generate SAM files. Read counts to each genomic feature were obtained with the htseq-count program (v 0.6.0) (Anders et al., 2014) using the “union” option.
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were against the GRCh38 reference genome and Gencode v27 annotations using STAR v2.6.1 (default options)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: GRCh38.gencode.v27B
Supplementary_files_format_and_content: read count matrix with rows as genes and columns as cells

tag: geographic location

value: USA:San Diego

value: Classical CD14+CD16- monocytes