title: P1205

type: genomic

city: Bethesda

first: Ariel

middle: Fernando

last: Martinez

address: 35 Convent Drive, Room 1B209

institute: National Institutes of Health

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926037_R05C02

hyb_protocol: According to the Infinium HD Assay Ultra protocol

data_processing:
BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).
The supplementary file on the series record contains the columns Genotype: AA,AB,BB,or NC (no call), Score, Theta, R, B Allele Freq, Log R Ratio, X Raw and Y Raw for each sample.  There is also a separate file with raw data only. Sample ID can be found in the 'description' field.

label: Cy3, Cy5

source_name: Blood

label_protocol: 200ng of genomic DNA were processed following the Infinium HD Assay Ultra protocol

extract_protocol: Extraction of genomic DNA from whole blood was performed using QIAGEN's QIAamp DNA Blood Maxi kit (cat No 51194)

value: Blood

tag: gender

value: F

tag: adhd affection status

value: Unaffected


title: MCF7 cells

status: Public on Apr 01 2020

type: RNA

city: Nanjing

first: kun

last: xu

address: 300 Guangzhou Road

country: China

institute: Department of Oncology, The First Affiliated Hospital of Nanjing Medical University

hyb_protocol: following Phalanx Internal Protocol

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1   using default parameters to obtain background subtracted and spatially  detrended Processed Signal intensities as the raw data. Raw data were normalized  in quantile algorithm with Genespring 13.0.

molecule: total RNA

organism: Homo sapiens

source_name: MCF7 cells

label_protocol: following ULS™ Small RNA Labeling Kit

growth_protocol: MCF7 cells were grown in RPMI 1640 (Gibco, USA) supplemented with 10% fetal bovine serum (FBS) (Hyclone USA)

extract_protocol: Total RNA was isolated from the four cell lines using the Trizol Reagent (Invitrogen, Carlsbad, CA, USA). Small RNA was extracted by using a mirVana kit (Ambion, Austin, USA).

treatment_protocol: without treatment

tag: cell line

tag: agent


title: 3-102-2-1b_S131

type: SRA

city: Lausanne

first: Gregory

last: Lefebvre

address: EPFL Scientific Parc

country: Switzerland

institute: Nestlé Institute of Health Science

library_source: transcriptomic

data_processing:
Sequence reads are trimmed from polyA and Lexogene reference sequences using bbduk software
Sequence reads are map to reference genome using RNAStar (v2.3.0e)
Matrix of counts is ctreated from HTSeq software
Genome_build: hs_GRCh38.p2
Supplementary_files_format_and_content: Text file containing counts for each genes (rows) for each sample (columns)

source_name: adipose tisue

extract_protocol: Lexogen QuantSeq - established 3' mRNA-Seq library prep protocol

tag: cid (cid1

value: baseline, cid2 :lcd, cid3 :di):CID1

tag: individual


title: 3-102-2-2_S2

value: baseline, cid2 :lcd, cid3 :di):CID2


title: SK-BR-3 cells, 4μM palbociclib, 48h

source_name: SK-BR-3 cells, 4μM palbociclib, 48h

growth_protocol: SK-BR-3 cells were grown in RPMI 1640 (Gibco, USA) supplemented with 10% fetal bovine serum (FBS) (Hyclone USA)

treatment_protocol: treated with 4μM palbociclib for 48 hours

value: SK-BR-3 treated with palbociclib

value: palbociclib


title: cKO_1_B10

city: New York

first: Hanseul

last: Yang

state: NY

address: 1230 York Avenue

country: USA

institute: Rockefeller University

description: processed data file: NFI_scRNA_TPM.txt

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm10) using the Bowtie2 program (version 2.2.9).
The expression values of each gene were quantified as transcript per million (TPM) using RSEM (v1.2.30).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: NFI_scRNA_TPM.txt: Tab-delimited text file includes TPM values for each Sample.

organism: Mus musculus

source_name: Mouse back skin

extract_protocol:
Single bulge hair follicle stem cells were FACS-purified, collected into 96 well plates containing lysis buffer and stored in -80oC.
Single cells were lyzed by incubating at 72oC for 3 min. Reverse transcription reaction and whole transcriptome amplification were performed according to Smart-seq2 protocol. The amplified cDNA libraries were purified by Ampure XP beads (Beckman Coulter), and tagmentation reaction was performed by Illumina Nextera XT DNA Library Prep Kit. The libraries were pooled and sequenced on Illumina Nextseq 500 with high-output 38/37cycles paired-end mode.

tag: strain

tag: Sex

value: Male

tag: age

tag: cell type

value: Hair follicle stem cells

tag: sorting markers

value: DAPI (neg), Sca-1 (neg), integrina6 (pos), YFP (pos)


title: 3-103-2-1b_S125


title: P1626

state: MD

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926037_R04C02

scan_protocol: According to the Infinium HD Assay Ultra protocol

molecule: genomic DNA

tag: tissue

value: M


title: cKO_1_A12

description: processed data file: NFI_scRNA_TPM.txt


title: MDA-MB-231 cells, 4μM palbociclib, 48h

source_name: MDA-MB-231 cells, 4μM palbociclib, 48h

growth_protocol: MDA-MB-231 cells were grown in RPMI 1640 (Gibco, USA) supplemented with 10% fetal bovine serum (FBS) (Hyclone USA)


title: P1012

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926037_R03C02

value: Affected


title: Hs578t cells

source_name: Hs578t cells

growth_protocol: Hs578t cells were grown in DMEM supplemented with 10% FBS


title: cKO_1_A1

description: processed data file: NFI_scRNA_TPM.txt


title: MCF7 cells, 4μM palbociclib, 48h

source_name: MCF7 cells, 4μM palbociclib, 48h


title: P1473

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926037_R02C02


title: 3-099-2-3_S184

value: baseline, cid2 :lcd, cid3 :di):CID3


title: MDA-MB-231 cells

source_name: MDA-MB-231 cells

growth_protocol: MDA-MB-231 cells were grown in RPMI MDA-MB-231 cells1640 (Gibco, USA) supplemented with 10% fetal bovine serum (FBS) (Hyclone USA)


title: 3-099-2-2_S116


title: P1828

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926037_R01C02


title: cKO_1_A11

description: processed data file: NFI_scRNA_TPM.txt


title: P1536

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926037_R06C01


title: Blast_Vehicle_Rep2

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

library_source: genomic

data_processing:
ATAC-seq libraries were sequenced as 75bp paired-end reads on Illumina Nextseq 500 machine. Raw sequencing reads were demultiplexed into Fastq file format using Illumina’s bcl2fastq v2.20. For data quality processing, 3’ Nextera adapter CTGTCTCTTATA was first removed using cutadapt for both pairs. In addition, reads with at least 8bp overlap and at most 20% mismatches were kept for alignment. Pairs whose trimmed reads (R1 or R2) have length less than 50 bp will be discarded as well. Then those trimmed high quality reads were aligned to mm10 genome using bowtie2 with parameters “-X 2000 –very-sensitve”. After alignment, reads that mapped to mitochondrial chromosome were removed using samtools. Also, duplicated reads were evaluated and removed using Picard. Peaks were called using MACS2 with parameters “-f BAMPE -q 0.05”. Fragments per million normalized tracks in bigwig format were generated using fragments that are primary alignments, proper-paired, and not duplicated for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Track files in bigwig format

source_name: Bone Marrow

extract_protocol:
Samples were prepared using Illumina Cat#FC-121-1030 following the protocol of PMID25559105
Library was constructed using Illumina Cat#FC-121-1030 following the protocol of PMID25559105

tag: genotype

value: Bone Marrow

value: Blast

tag: treatment

value: Vehicle (Control)


title: P1471

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926037_R05C01


title: P1613

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926037_R03C01


title: 3-099-2-1_S43


title: Blast_Vehicle_Rep1


title: P1353

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926037_R02C01


title: 3-097-2-1b_S48


title: SK-BR-3 cells

source_name: SK-BR-3 cells


title: P1571

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926037_R01C01


title: P1778

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926035_R05C02


title: Blast_LowDox_Rep2

value: [Low]DXR + Chemotherapy


title: P1416

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926035_R06C02

value: Blood


title: 3-093-2-3_S158


title: P1790

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926035_R04C02

value: F


title: 3-092-2-3_S54


title: P1280

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926035_R01C02

value: Unaffected


title: P1385

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926035_R04C01


title: P1505

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926035_R06C01


title: P1158

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926035_R05C01


title: P1360

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926035_R03C02


title: 3-094-2-3_S121


title: LSC_Vehicle_Rep2

value: LSC


title: 3-093-2-1b_S68

value: baseline, cid2 :lcd, cid3 :di):CID1


title: P1700

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926035_R03C01


title: P1378

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926035_R02C01


title: LSC_LowDox


title: LSC_Vehicle_Rep1


title: 3-092-2-2_S109

value: baseline, cid2 :lcd, cid3 :di):CID2


title: 3-092-2-1b_S80


title: P1338

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926035_R01C01


title: P1209

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926029_R05C02


title: 3-090-2-1_S174


title: P1304

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926029_R03C02


title: P1326

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926029_R04C02


title: Blast_LowDox_Rep1


title: TMAO-4

city: Niigata

first: Yohko

last: Yoshida

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

country: Japan

institute: Niigata University

description:
TMAO-treated
q4

data_processing:
Illumina BaseSpace was used for basecalling.
TopHat 2 (version 2.0.13) was used for mapping reads to the reference genome (Ensembl GRCm38/mm10) with annotation data downloaded from Ensembl Asia website (URL https://asia.ensembl.org/).
Expression of each transcript were quantified as fragments per kilobase of transcript per million fragments mapped (FPKM) and compared among each 3 groups by Cuffdiff (included in Cufflinks version 2.2.1).
Genome_build: Ensembl GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

source_name: Heart

extract_protocol:
Heart were removed, flash frozen in liquid nitrogen, and RNA was harvested using QIAzol Lysis Reagent. RNeasy Mini Kit (Qiagen, 74104) was used with 500ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) according to the manufacturer’s instruction.

treatment_protocol: Mice were administered with PBS or 100mg/kg BW/day of trimethylamine N-oxide (TMAO) using infusion pump for 2 weeks from 11 weeks of age.

value: Heart

value: 13 weeks of age

value: wild type


title: TMAO-3

description:
TMAO-treated
q3


title: TMAO-2

description:
TMAO-treated
q2


title: P1124

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926029_R02C02


title: 3-085-2-1_S54


title: Hs578t cells, 4μM palbociclib, 48h

source_name: Hs578t cells, 4μM palbociclib, 48h

value: palbociclib


title: P1394

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926029_R01C02

value: M


title: 3-084-2-3_S6


title: P1706

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926029_R06C01


title: P1388

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926005_R06C02

value: Affected


title: P1207

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926029_R02C01


title: P1308

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926029_R03C01


title: Control-3

description:
PBS-treated
q3


title: Control-4

description:
PBS-treated
q4


title: P1374

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926029_R05C01


title: P1306

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926029_R01C01


title: TMAO-1

description:
TMAO-treated
q1


title: 3-082-2-1b_S148


title: P1560

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926005_R05C02


title: 3-082-2-2_S51


title: P1648

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926005_R04C02


title: Control-1

description:
PBS-treated
q1


title: P1003

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926005_R03C02


title: P1474

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926005_R06C01


title: Null3

city: Boston

first: Mirazul

last: Islam

state: MA

address: D857A, Dana Farber Cancer Institute, 44 Binney St. Boston MA

department: Medical Oncology

institute: DFCI

data_processing:
Illumina NextSeq500 with single-end 75bp reads
Sequenced reads were aligned to the UCSC mm9 reference genome assembly and gene counts were quantified using STAR (v2.5.1b)
Supplementary_files_format_and_content: Raw Counts

source_name: null_esophageal cells

growth_protocol: Cells were grown in 10cm plastic dishes in KSFM

extract_protocol:
RNA was extracted using the Qiagen Rneasy mini kit
Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits

tag: strain background

value: mixed

tag: genotype/variation

value: p53 -/- null

value: esophageal epithelial cells


title: 3-081-1-1_S19


title: P1816

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926005_R05C01


title: P1504

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926005_R01C02


title: Mutant3

source_name: mutant_esophageal cells

value: p53R172H mutant


title: P1863

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926005_R04C01


title: 3-081-2-1b_S64


title: 3-084-2-1_S75


title: P1351

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926005_R02C01


title: P1145

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925155_R04C02


title: Control-2

description:
PBS-treated
q2


title: P1029

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925155_R05C02


title: 3-079-2-1_S49


title: Mutant1


title: P1341

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926005_R03C01


title: Mutant2


title: P1676

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925155_R02C02


title: 3-077-2-2_S196


title: 3-077-2-2_S14


title: P1652

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925155_R06C01


title: P1321

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925155_R01C02


title: P1569

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925155_R03C02


title: P1061

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925155_R05C01


title: Null1


title: 3-080-2-3_S156

value: baseline, cid2 :lcd, cid3 :di):CID3


title: WT1

source_name: WT_esophageal cells


title: P1662

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925155_R04C01

value: Blood


title: 3-077-2-1_S96


title: 3-076-2-1_S163


title: P1195

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925155_R03C01

value: F


title: P1288

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925155_R02C01


title: CD11b+ dendritic cells, Rep 2

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome by Rsubread 1.22.3.
Read counts were summarized by Entrez Gene ID using featureCounts and Rsubread's built-in NCBI annotation.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: Virgin adult mammary gland

extract_protocol:
RNA was isolated from freshly sorted cells with the RNeasyPlus Mini kit (Qiagen).
mRNA reverse transcription cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.

tag: background strain

value: mammary gland

value: CD11b+ dendritic cells


title: 3-080-2-1_S11

value: baseline, cid2 :lcd, cid3 :di):CID1


title: P1266

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926005_R01C01

source_name: Blood

tag: gender


title: P1245

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925155_R01C01

tag: adhd affection status


title: 3-069-2-2_S249

value: baseline, cid2 :lcd, cid3 :di):CID2


title: CD11b-CD103+ dendritic cells, Rep 2

value: CD11b-CD103+ dendritic cells


title: WT2


title: P1074

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744106_R06C02

value: Unaffected


title: P1854

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744106_R05C02


title: P1052

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744106_R04C02


title: 3-069-2-2_S183


title: Stromal macrophages, Rep 2

value: Stromal macrophages


title: 3-066-2-3_S8


title: P1552

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744106_R01C02


title: P1726

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744106_R03C02


title: 3-066-2-3_S238


title: P1630

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744106_R06C01


title: CD11b+ dendritic cells, Rep 1


title: Ductal macrophages, Rep 2

value: Ductal macrophages


title: 3-065-2-2_S210


title: P1250

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744106_R05C01


title: P1629

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744106_R04C01

value: M


title: P1263

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744106_R03C01

value: Affected


title: CD11b-CD103- dendritic cells, Rep 1

value: CD11b-CD103- dendritic cells


title: CD11b-CD103- dendritic cells, Rep 2


title: 3-065-2-2_S161


title: 3-065-2-1b_S14


title: Stromal macrophages, Rep 1


title: P1409

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744072_R06C02


title: P1376

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744106_R01C01


title: CD11b-CD103+ dendritic cells, Rep 1


title: 3-064-1-2_S150


title: P1468

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744106_R02C02


title: 3-063-1-1b_S172


title: P1419

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744072_R02C02


title: GIneuron7

city: Houston

first: Guangsheng

last: Pei

state: Texas

address: 7000 Fanin

institute: UTHealth

description:
GI-ERαvlVMH neuron
human joint progenitor-like cells

data_processing:
RNA-seq raw data files were trimmed using TrimGalore (version 0.4.1) and aligned against the mouse reference genome assembly (GRCm38.p6) using the STAR aligner (version 2.5.3a). One sample (“GIneuron3”) was removed from the following analysis due to low sequence read counts. Next, gene expression was assessed using featureCounts (version 1.6.0). To improve the identification of differentially regulated genes, unwanted variation between samples was removed using RUVseq. Then, DESeq2 was used to determine differential gene expression. Significance of differential expression was assessed by requiring both P<0.05 and |log2(fold change)| >2.
Genome_build: RNA-seq: GRCh38.83
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

source_name: mouse hypothalamic neuron

extract_protocol:
Four GI-ERαvlVMH neurons and four GE-ERαvlVMH neurons (from two different mice) were manually collected and suspended in PBS buffer.
Cell lysis, first-strand cDNA synthesis and cDNA amplification were performed according to the manufacturer’s instructions of SMART-Seq v4 Ultra Low Input RNA Kit (Clontech). Amplified cDNA was purified by Agencourt AMPure XP Kit (Beckman Coulter).
The Nextera Library Prep Kit (Illumina) was used to prepare libraries for sequencing (100 bp paired-end, RNA-seq) on a HiSeq 2500 platform (Illumina).

treatment_protocol: We used female ERα-ZsGreen mice to record glucose-sensing properties of ERα expressing neurons (labelled by ZsGreen green fluorescence) in the vlVMH under the current clamp mode in response to a 5--1--5 mM extracellular glucose fluctuation protocol. Those neurons that hyperpolarized and decreased their firing rate in response to low glucose (1 mM) and recovered in response to high glucose (5 mM) were identified as GE neurons; those neurons that depolarized and increased their firing rate in response to low glucose (1 mM) and recovered in response to high glucose (5 mM) were identified as GI neurons.

tag: diagnosis

value: show depolarization and increased firing frequency in response to hypoglycemia (5-1 mM glucose), while recovery of glucose level to 5 mM restore the activity


title: Ductal macrophages, Rep 1


title: P1300

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744072_R04C02


title: P1635

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744072_R01C02


title: P1334

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744072_R05C01


title: 3-061-2-2_S59

source_name: adipose tisue


title: P1268

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744072_R06C01


title: GIneuron3


title: GIneuron5


title: P1063

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744072_R04C01


title: P1107

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744106_R02C01


title: P1357

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744072_R02C01


title: P1273

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744072_R03C01


title: P1465

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744072_R01C01


title: 3-060-2-1_S89


title: GIneuron2


title: P1688

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726006_R06C02


title: GEneuron8

description:
GE-ERαvlVMH neuron
human embryonic chondroprogenitors

value: show hyperpolarization and decreased firing frequency in response to hypoglycemia (5-1 mM glucose), while recovery of glucose level to 5 mM restore the activity


title: P1621

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744072_R05C02


title: P1396

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744072_R03C02


title: 3-056-1-1_S161


title: 3-050-2-3_S242


title: P1451

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726006_R04C02


title: P1833

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726006_R05C02


title: 3-050-2-3_S162


title: P1312

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726006_R01C02


title: P1231

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726006_R03C02


title: GEneuron4


title: P1787

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726006_R02C02


title: 3-050-2-1_S51


title: 3-061-2-1_S47


title: P1775

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726006_R03C01


title: P1403

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726006_R02C01


title: P1725

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726006_R01C01


title: P1204

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926083_R06C02


title: Raldh1/3 DKO (1)

city: Philadelphia

first: Michael

last: Gonzalez

state: Pennsylvania

address: 3535 Market St

department: Translational Medicine and Human Genetics

institute: University of Pennsylvania

description: n=2 Raldh1/3 DKO tumors pooled into one sample; harvested Day 11 post-implantation; live CD45+ cells FACSorted

data_processing:
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent kit v3  per manufacturer’s instructions. Libraries were uniquely indexed using the Chromium i7 Sample Index Kit, pooled,  and sequenced on an Illumina NovaSeq SP sequencer in a paired-end, single indexing run. Sequencing for each library targeted 30,000 mean reads per cell. We had a mean of 30,695 reads per cell post-normalization. Data was then processed using the Cellranger pipeline (10x genomics, v.3.0.2) for demultiplexing and alignment of sequencing reads to the GRCh38 transcriptome and creation of feature-barcode matrices. Individual single cell RNAseq libraries were aggregated using the cellranger aggr pipeline. Libraries were normalized for sequencing depth across all libraries during aggregation. Downstream analysis of the single-cell RNA-sequenced samples was performed using Seurat (v. 3.1.0) in R (v. 3.6.0). Genes expressed in less than three cells were removed. Cells that expressed less than 500 genes or had over 14% mitochondrial content were filtered out. The four samples were merged and counts for all genes were log2 normalized and scaled (NormalizeData and ScaleData). Principal components (PCs) were determined using the 2000 most variable genes (FindVariableFeatures). Subsequently, the top 50 PCs were used for graph-based cluster identification and dimensionality reduction by t-distributed stochastic neighbor embedding (t-SNE). Myeloid clusters were subsetted out using Adgre1, Lyz2, S100a9, Itgax and negative for lymphoid markers and re-analyzed as described above. Genes separating TAM_1 and TAM_2 clusters were determined using the default Wilcoxon Rank Sum test in the FindMarkers function.
Genome_build: mm10
Supplementary_files_format_and_content: barcode, feature, matrix tsv files

source_name: Mouse fibrosarcoma tumor

extract_protocol:
Single cell suspensions were generated by digestion with collagenase B and DNAse I for 45 minutes at 37oC and filtration through 70uM cell strainer. Mouse blood was collected in EDTA tubes and RBCs were lysed using ACK lysing buffer. Samples were incubated for 5 minutes at room temperature with anti-mouse CD16/32 Fc Block, and subsequently stained on ice with primary-fluorophore conjugated antibodies for identification of cell populations by FACS. 7AAD (BioLegend) was used for dead cell discrimination. Cells were sorted on MoFlo Astrios or FACS Jazz at the Children’s Hospital of Philadelphia (CHOP) Flow Cytometry Core Laboratory.
Dataset consists of a total of four single-cell datasets generated using the 10x Genomics Chromium platform. Prior to GEM generation, the sample’s concentration (cells/ul) and viability (%) were determined by staining the cells with trypan blue and by manually counting using an inverted microscope. Next-generation sequencing libraries were prepared following the 10X Single Cell v3 protocol without modification. Sample quality was evaluated using Agilent’s Bioanalyzer High Sensitivity reagent kit following cDNA amplification and library construction. The completed libraries were quantified using the Kapa Library Quantification Kit and the Life Technologies Viia7 Real-time PCR instrument. Libraries were diluted to 2nM and sequenced in a paired-end, single-indexed format on the Illumina NovaSeq SP using the Rapid Run v3 chemistry.

treatment_protocol: untreated tumors

value: CD45+ leukocyte

value: Raldh1/3 DKO (1)

value: Untreated tumor


title: Raldh1/3 DKO (2)

value: Raldh1/3 DKO (2)


title: 3-048-1-3_S6

value: baseline, cid2 :lcd, cid3 :di):CID3


title: Cas9 Control (2)

description: n=2 Cas9 Control tumors pooled into one sample; harvested Day 11 post-implantation; live CD45+ cells FACSorted

value: Cas9 Control (2)


title: P1539

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926083_R05C02

value: Blood


title: P1111

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926083_R04C02


title: 3-048-1-1_S49

value: baseline, cid2 :lcd, cid3 :di):CID1


title: Cas9 Control (1)

value: Cas9 Control (1)


title: GEneuron6


title: 3-048-1-3_S197


title: P1086

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926083_R03C02

value: F

value: Unaffected


title: P1085

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926083_R02C02


title: P1342

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726006_R06C01


title: P1467

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926083_R01C02


title: Left atria, KO337

first: David

last: Milan

address: 185 Cambridge St

institute: MGH

data_processing:
Transcriptome mapping was performed with STAR (PMID:23104886) using the Ensembl annotation of mm9 reference genome. Read counts for individual genes were produced using HTSeq (PMID:25260700).
Differential expression analysis was performed using the EdgeR package (PMID:19910308) after normalizing read counts and including only those genes with CPM > 1 for at least one out of all samples.
Genome_build: mm9
Supplementary_files_format_and_content: HTSeq counts

source_name: Left atria, KO

extract_protocol: PolyA+ NEBNext Ultra Directional RNA Library Prep Kit for Illumina

value: heart (left atria)

tag: developmental stage

value: adult

value: cardiac CSK KO


title: P1509

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726006_R05C01

value: M


title: GEneuron1

description:
GE-ERαvlVMH neuron
human embryonic chondroprogenitors


title: 3-047-2-1_S9

tag: cid (cid1


title: P1424

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926083_R06C01


title: P1267

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926083_R05C01

value: Affected


title: P1602

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926083_R03C01


title: 3-047-1-2_S146

value: baseline, cid2 :lcd, cid3 :di):CID2

tag: individual


title: 3-049-1-1_S100


title: P1166

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926083_R04C01


title: Left atria, WT338

source_name: Left atria, WT

value: WT


title: Left atria, KO26


title: P1717

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926083_R01C01


title: 3-047-2-3_S71


title: P1171

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726006_R04C01


title: 3-050-2-1_S147


title: Left atria, WT35


title: 3-046-2-3_S172


title: P1077

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926080_R05C02


title: P1722

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926080_R04C02


title: P1437

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926080_R06C02


title: 3-046-2-1_S115


title: P1200

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926080_R03C02


title: Left atria, IBR2

source_name: Left atria, IBR

value: IBR


title: P1018

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926080_R01C02


title: Left atria, IBR3


title: 3-045-1-1_S176


title: P1350

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926080_R02C02


title: Left atria, IBR1


title: 3-040-2-1_S37


title: P1670

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926083_R02C01


title: P1845

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926080_R06C01


title: Left atria, CTL3

source_name: Left atria, CTL

value: CTL


title: P1294

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926080_R05C01


title: 3-037-2-3_S143


title: Left atria, CTL2


title: 3-037-2-2_S183


title: P1025

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926080_R02C01


title: P1038

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926080_R03C01


title: P1201

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926080_R04C01


title: P1322

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926073_R05C02


title: 3-038-2-1_S67


title: P1058

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926073_R04C02


title: NFIB/X-dKO_36

description: processed data file: WT_NFIBcKO_NFIXcKO_NFIBXdKO_TPM.txt

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm10) using the Bowtie2 program (version 2.2.9).
The expression values of each gene were quantified as transcript per million (TPM) using RSEM (v1.2.30).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.genes.results.txt: Tab-delimited text files include TPM values for each Sample.
Supplementary_files_format_and_content: WT_NFIBcKO_NFIXcKO_NFIBXdKO_TPM.txt: Tab-delimited text file includes TPM values for each Sample.

source_name: Mouse back skin

extract_protocol:
Mouse hair follicle stem cells were purified from Sox9-CreER;NFIBfl/fl;NFIXfl/fl and WT littermate mice at P70 2nd telogen.
FACS-isolated cells were directly lysed into TRIzol LS (Invitrogen). Total RNA was purified using the Direct-zol RNA MiniPrep kit (Zymo Research) per manufacturer’s instructions. Quality of the RNA for sequencing was determined using an Agilent 2100 Bioanalyzer; all samples used had RNA integrity numbers >8. Library preparation using the Illumina TruSeq mRNA sample preparation kit was performed at the Weill Cornell Medical College Genomic Core facility (New York), and RNAs were paired-end sequenced on Illumina HiSeq 4000 or HiSeq 2500 machines.

tag: strain

value: Male

value: Hair follicle stem cells

value: DAPI (neg), Sca-1 (neg), integrina6 (pos), CD34 (pos), YFP (pos)


title: 3-037-1-2_S160


title: 3-037-2-1_S56


title: NFIB/X-dKO_33

tag: Sex


title: P1228

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926073_R02C02

value: Blood


title: NFIX-cKO_32

tag: age


title: WT_34

tag: cell type

value: DAPI (neg), Sca-1 (neg), integrina6 (pos), CD34 (pos)


title: P1390

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926073_R01C02


title: P1371

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926073_R03C02


title: P1668

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926073_R06C02


title: 3-036-2-1_S140

value: baseline, cid2 :lcd, cid3 :di):CID1


title: P1650

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926073_R04C01


title: 3-036-1-1_S191


title: P1665

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926073_R03C01


title: P1189

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926080_R01C01


title: WCE_ctnnb1BF ESCs_covaris

description: DNA Input

data_processing:
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
ChIP-seq was aligned to genome mm10 using bowtie2
Bigwig files are normalized and extended to fragment length for IP samples
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq in bigwig files

source_name: Whole cell extract

extract_protocol:
ChIP-seq: A total of 2×10^7 ES cells were used per ChIP assay. Cells were washed with 1 x PBS and crosslinked with 1% paraformaldehyde for 10 min at RT and quenched with 1ml 2.5M glycine. Cells were washed with cold PBS three times and resuspended in 300μl lysis buffer. The cell suspension was sonicated in Bioruptor Pico sonication device with the setting of 30 sec on, 30 sec off for 16 cycles followed with centrifuga- tion at maximum speed for 10 min. The supernatant was saved and mixed with antibody coated protein G dynabeads(Invitrogen 10003D) at a ratio of 5μl per 1μg antibody for immunoprecip- itation overnight at 4°C . The next day the protein G dynabeads were washed with 800μl RIPA buffer three times. After the elution, 4μ l RNase A(10μ g/ml) was then added with the beads being incubated at 37°C for 2 hours, after which 2μl Protease K(Invitrogen 20mg/ml) was added and the beads were incubated at 55 °C for 2 hours. After the RNase A and Protease K treatment, the beads were incubated at 55 °C overnight for decrosslinking. The next day the DNA on beads was extracted by 300 μl phenol chloroform isoamyl alcohol(25:24:1) with centrifugation at 12,000 rpm for 5 min at RT. The supernatant was transferred to a new 1.5ml tube with 12μl of 5M NaCl and 2μl glycogen (20mg/ml). The DNA was precipitated by 750μl cold 100% ethanol with at least 30 min incubation at - 80 °C . The sample was centrifuged for 30 min in 4 °C at maximum speed and the ethanol was decanted. The pellet was washed with 800 μ l cold 70% ethanol, centrifuged and air dried. The DNA was resuspended in 55μl nuclease-free water.
ChIP-seq libraries were prepared using the TruSeq RNA kit for sequencing,

tag: chip antibody

value: none (input)

tag: cell line

value: Embryonic stem cells

tag: culture condition


title: Left atria, CTL1

tag: tissue

value: heart (left atria)

tag: treatment


title: 3-035-2-1b_S73


title: P1745

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926050_R06C02


title: P1694

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926073_R02C01


title: Cov_Flag_ctnnb1BF ESCs

description: DNA IP

source_name: Embryonic stem cells

value: Flag M2 monoclonal antibody


title: P1672

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926073_R01C01

value: F

value: Unaffected


title: P1047

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926050_R05C02

value: M


title: P1422

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926050_R04C02


title: Tcf4 Lin-/Tcf4 DP DropSeq (Pooled samples 4-6)

city: Salt Lake City

first: Mario

middle: R.

last: Capecchi

state: UT

address: 15 North 2030 East

institute: University of Utah

description: Pooled samples 4-6

data_processing:
Premade metadata for mixed mouse and human samples was obtained from the drop-seq tools homepage: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63269/suppl/GSE63269_hg19_mm10_transgenes_reference_metadata.tar.gz ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63269/suppl/GSE63269_hg19_mm10_transgenes_reference_metadata.tar.gz
Index files were created using STAR (v2.5.0)
Fastq data was converted into unaligned bam files using picard (v1.137) FastqToSam
Data was processed using drop-seq tools 'Drop-seq_alignment.sh' command (v1.12). https://github.com/broadinstitute/Drop-seq/releases
Mouse-specific alignment data was extracted using the drop-seq tools 'FilterBam' command
Top mouse barcodes were extracted using the drop-seq tools 'DigitalExpression' command
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing gene counts for the top barcodes.

source_name: Isolated colon cells

growth_protocol: Tcf4GfpCre/+ RosamTmG/+ animals were sacrificed at (4-10) months

extract_protocol:
Procedure to isolate solonic epithelium from underlying mesenchyme as described (Nik and Carlsson, 2013). To isolate crypts for single cell preparations, we adapted a procedure that separates colonic epithelium from the underlying mesenchyme (Nik and Carlsson, 2013). A gavage needle with silicone tip attached to a 3 ml syringe was inserted into the cleaned colon from the distal end and pulled all the way through to the proximal end. The plunger needed to be pulled out and the barrel filled with air. The proximal part of the colon was secured to the tip of the gavage needle with thread. Using a thumb, the colon was pulled over the tip of the needle, thus inverting it. Following inversion, the proximal end of the colon was ligated with thread while the other end was still fitted to the gavage needle. The inverted colon was then submerged in 3.8 mL of ice-cold Cell Recovery Solution (Corning) in a 5 mL round-bottom polystyrene tube (Corning) and placed on ice. The submerged colon was inflated and deflated every 5 minutes with occasional swirling in the solution for 1 hour. During this time, the Cell Recovery Solution dissolved the basement membrane and the air pressure pushed the crypts out of the crypt beds. A 10-minute digestion with TrypLETM Express (Thermo Fisher) at 37°C then generated a single cell suspension. Addition of FBS and wash buffer (DPBS containing 3% BSA) inhibited the TrypLETM digest. The single cell suspension was filter using a 100 µm cell strainer and washed. Wash buffer used to prepare cells for Drop-seq procedure contained 0.5 mM EDTA.
A total of 600pg of amplified cDNA was used for a Nextera XT library preparation (Illumina), and the New-P5-SMART PCR hybrid oligo, and a modified P7 Nextera oligo with 10 bp barcodes was used for sequencing. A 125 cycle paired-end sequence run was performed on an Illumina HiSeq 2500 instrument using HiSeq SBS kit v4 sequencing reagents and the Read1CustomSeqB primer as described (Macosko et al., 2015).
Sample 1-3 and 4-6 were pooled. Cells were collected into DPBS with 3% BSA and 0.5 mM EDTA. Using FACS, Calcein violet cell stain was used to screen live from dead cells and Tom+ cells were isolated from Samples 1-3 while Tom+ GFP+ cells were isolated from Samples 4-6. Isolated Tcf4 Lin- and Tcf4 MIX populations were separately combined with human cells to reach optimal cell number and concentration for Drop-seq, and single-cell suspensions were diluted to 270 cells/ml and processed as described previously (Macosko et al., 2015). Briefly, cells, barcoded microparticle beads (ChemGenes Corporation, Lot #113015B), and lysis buffer were co-flown into a microfluidic device and captured in nanoliter sized droplets. After droplet collection and breakage, the beads were washed, followed by cDNA synthesis on the bead using Maxima H-minus RT (Cat # Thermo Fisher Scientific). Excess oligos were removed via exonuclease I digestion. cDNA amplification was done from a pool of 2,000 beads using HotStart ReadyMix (Kapa Biosystems). Individual PCRs were purified and pooled for library generation..
DropSeq

treatment_protocol: no pretreatment

value: Isolated colon cells

tag: cre driver

value: Tcf4 GfpCre/+

tag: reporter

value: RosamTmG/+


title: 3-033-2-3_S180

value: baseline, cid2 :lcd, cid3 :di):CID3


title: Tcf4 Lin-/Tcf4 DP DropSeq (Pooled samples 1-3)

description: Pooled samples 1-3


title: 3-033-2-2_S148

value: baseline, cid2 :lcd, cid3 :di):CID2


title: P1185

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926073_R05C01

tag: gender


title: P1161

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926050_R03C02

tag: adhd affection status


title: P1234

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926050_R02C02

value: Affected


title: 3-032-2-1_S76


title: P1620

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926073_R06C01


title: P1565

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926050_R01C02


title: input microRNA control1

city: Stanford

first: Mark

middle: Emile

last: Pepin

state: CA

address: 870 Quarry Road

department: Cardiovascular Medicine

institute: Stanford University

description:
microRNA
Differential expression was calculated based on transgenic (both TGH and TGL) relative to non-transgenic C57BL/6J mice.
processed data file: results_miRNA_TG.v.NTG.xlsx

data_processing:
Illumina bcl2fastq version 1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using TrimGalore version 0.4.0 with parameters: --paired, --trim1
Alignment of reads to the mm10 genome was accomplished using NovoAlign® (Singapore, Malaysia), raw counts generated using Samtools, and differential gene expression performed using DESeq2 (1.18.1) within the R (3.4.2) statistical computing environment as described previously.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: results_miRNA_TG.v.NTG.xlsx: Excel file was generated to calculate differential expression of transgenic (CaNrf2-Low and CaNrf2-High) versus non-transgenic mice using DESeq2.

source_name: Left Ventricle

extract_protocol:
Cardiac samples were removed, flash frozen on dry ice, and total RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: strain/background

tag: genotype/variation

value: Non-Transgenic

tag: age (months)

value: Male

value: Left ventricle


title: 3-030-2-1b_S102

tag: cid (cid1

value: baseline, cid2 :lcd, cid3 :di):CID1

tag: individual


title: input microRNA control2

tag: Sex


title: P1256

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926050_R05C01

value: Blood


title: P1050

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926050_R06C01


title: input microRNA control0


title: P1227

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926050_R04C01


title: 3-030-2-1b_S211


title: P1289

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926050_R03C01


title: 3-028-2-2_S167


title: P1152

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926050_R02C01


title: input microRNA TGH2


title: P1117

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926050_R01C01


title: 3-028-2-1_S134


title: input microRNA TGH1


title: P1054

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926049_R06C02


title: P1206

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926049_R04C02


title: P1224

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926049_R05C02


title: 3-028-1-1_S45


title: P1398

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926049_R03C02


title: input microRNA TGH0


title: input microRNA TGL2


title: P1235

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926049_R01C02


title: P1043

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926049_R05C01


title: 3-026-2-3_S203


title: P1779

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926049_R06C01


title: 3-026-2-1_S66


title: input microRNA TGL1


title: P1711

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926049_R04C01


title: P1082

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926049_R03C01


title: 3-020-1-1_S80


title: P1067

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926049_R02C01


title: P1417

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926049_R01C01


title: input RNA TGH2

description:
Differential expression was calculated based on transgenic (both TGH and TGL) relative to non-transgenic C57BL/6J mice.
processed data file: results_CaNRF2_mRNA_TG.v.NTG.xlsx

data_processing:
Illumina bcl2fastq version 1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using TrimGalore version 0.4.0 with parameters: --paired, --trim1
Alignment of reads to the mm10 genome was accomplished using NovoAlign® (Singapore, Malaysia), raw counts generated using Samtools, and differential gene expression performed using DESeq2 (1.18.1) within the R (3.4.2) statistical computing environment as described previously.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: results_CaNRF2_mRNA_TG.v.NTG.xlsx: Excel file generated to calculate differential expression of transgenic (CaNrf2-Low and CaNrf2-High) versus non-transgenic mice using DESeq2.

extract_protocol:
Cardiac samples were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.


title: P1070

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926016_R06C02


title: 3-018-2-2_S104


title: P1410

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926016_R05C02


title: 3-018-2-1_S65


title: P1036

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926016_R04C02


title: input RNA TGH1


title: P1239

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926049_R02C02


title: 3-026-2-3_S44


title: input RNA TGH0


title: 3-017-1-2_S31


title: input RNA TGL2


title: P1157

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926016_R02C02


title: P1320

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926016_R06C01


title: P1463

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926016_R03C02


title: P1573

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926016_R05C01


title: input RNA TGL1


title: 3-017-1-1_S134


title: input microRNA TGL0

description:
microRNA
Differential expression was calculated based on transgenic (both TGH and TGL) relative to non-transgenic C57BL/6J mice.
processed data file: results_miRNA_TG.v.NTG.xlsx


title: 3-016-2-1_S32


title: P1405

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926016_R01C02


title: F-KO3

city: Xi'an

first: Bai

last: Ruan

state: Shannxi

address: No.169, Changle Road

institute: Fourth Military Medical University

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat2 v2.0.13 with parameters --read_mismatches 2 --read_gap_length 2 --read_edit_dist 2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and counts for each Sample

source_name: Sinusoidal endothelial cells

extract_protocol:
Control SECs and RBPj knock out SECs were isolated and total RNA was immediatly isolated from the cells using Trizol (Invitrogen) according to standard protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For conditional deletion of endothelial RBPj, male mice of four to six-week-old were injected intraperitoneally once a day with tamoxifen (2mg/20g body weight) for totally seven days, and were allowed to rest for another week after the last injection. To establish liver fibrosis, mice were subjected to intraperitoneal injection of CCl4 (0.6ul/g body weight, diluted in olive oil to yield a final concentration of 15%) twice a week for total six weeks. After the last CCl4 injection, SECs were isolated and RNA samples were obtained.

tag: strain

value: liver

tag: age

value: 12-14 weeks

value: Sinusoidal endothelial cells


title: input RNA control3


title: P1762

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926016_R02C01

data_processing:
BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).
The supplementary file on the series record contains the columns Genotype: AA,AB,BB,or NC (no call), Score, Theta, R, B Allele Freq, Log R Ratio, X Raw and Y Raw for each sample.  There is also a separate file with raw data only. Sample ID can be found in the 'description' field.

extract_protocol: Extraction of genomic DNA from whole blood was performed using QIAGEN's QIAamp DNA Blood Maxi kit (cat No 51194)

value: F


title: input RNA control2


title: F-KO2

tag: cell type


title: input RNA TGL0


title: 3-012-2-1_S58


title: P1066

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926016_R01C01

value: Unaffected


title: F-KO1


title: P1051

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926016_R03C01


title: P1220

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926006_R06C02

value: M


title: input RNA control1


title: P1027

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926016_R04C01


title: 3-010-2-1_S60


title: F-CT3


title: P1737

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926006_R05C02


title: 3-010-2-2_S160


title: 3-008-2-1_S130


title: input RNA control0

description:
Differential expression was calculated based on transgenic (both TGH and TGL) relative to non-transgenic C57BL/6J mice.
processed data file: results_CaNRF2_mRNA_TG.v.NTG.xlsx


title: F-CT2


title: P1736

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926006_R04C02


title: 3-006-2-2_S46


title: 3-016-2-1_S128


title: P1544

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926006_R03C02


title: 3-004-2-2_S147


title: LSCVehicle9weekB3

data_processing:
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
RNA-seq was aligned to genome mm10 from UCSC using tophat 2.0.13.
FPKM was generated using Cufflinks v2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs

extract_protocol:
1,000 cells per sample were sorted into 96-well plates with 7 ul lysis buffer containing RNase inhibitor (2 U/μl) from BM. First-strand cDNA synthesis and cDNA libraries were constructed using the SMARTer ultra low input RNA kit for sequencing - v3 (Clontech) following the manufacturer’s instructions. cDNA quality was determined by Agilent high sensitivity DNA kit on Agilent 2100 BioAnalyzer (Agilent Technologies).
RNA-seq libraries were prepared using the SMARTer ultra low input RNA kit for sequencing - v3 (Clontech Nextera)

tag: genotype

value: Bone Marrow

value: LSC

value: Vehicle (Control)

tag: time


title: P1503

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926006_R02C02

tag: tissue


title: F-CT1


title: 3-003-2-2_S101

data_processing:
Sequence reads are trimmed from polyA and Lexogene reference sequences using bbduk software
Sequence reads are map to reference genome using RNAStar (v2.3.0e)
Matrix of counts is ctreated from HTSeq software
Genome_build: hs_GRCh38.p2
Supplementary_files_format_and_content: Text file containing counts for each genes (rows) for each sample (columns)

extract_protocol: Lexogen QuantSeq - established 3' mRNA-Seq library prep protocol


title: Q-SEC3

extract_protocol:
Hepatic stellate cells and sinusoidal entothelial cells were isolated from control and CCl4-treated mice,total RNA was immediatly isolated from the cells using Trizol (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To establish liver fibrosis models, male mice of six to eight week-old were subjected to intraperitoneal injection of CCl4 (0.6ul/g body weight, diluted in olive oil to yield a final concentration of 15%) twice a week for total six weeks, with olive oil as normal control.


title: LSCVehicle7weekA3

tag: treatment


title: LSCVehicle9weekB1


title: P1734

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926006_R01C02


title: LSCVehicle7weekA2


title: LSCVehicle9weekB2


title: Q-SEC2


title: P1685

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926006_R06C01


title: 3-001-2-2_S52


title: 3-001-2-1_S145


title: Q-HSC3

source_name: Hepatic stellate cells

value: Hepatic stellate cells


title: LSCVehicle7weekA1


title: Q-SEC


title: P1010

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926006_R05C01


title: Q-HSC2


title: 2-113-2-3_S70

value: baseline, cid2 :lcd, cid3 :di):CID3


title: LSCLowDXRChemoB2

value: [Low]DXR + Chemotherapy


title: 2-111-2-3_S81


title: P1013

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926006_R03C01


title: Q-HSC


title: LSCLowDXRChemoB1


title: 2-111-2-2_S158

value: baseline, cid2 :lcd, cid3 :di):CID2


title: P1246

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926006_R02C01

value: Affected


title: F-SEC3


title: 2-111-2-1_S3


title: LSCLowDXRChemoA3


title: F-SEC2


title: LSCLowDXRChemoA2


title: F-SEC


title: P1484

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926006_R01C01


title: 2-111-1-2_S6


title: P1062

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744134_R06C02


title: LSCLowDXRChemoA1


title: 2-111-1-1_S16


title: F-HSC3


title: P1303

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744134_R05C02


title: LSCLowDXRB1

source_name: LSCLowDXR

value: [Low]DXR


title: 2-110-2-1_S96

value: baseline, cid2 :lcd, cid3 :di):CID1


title: P1713

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571926006_R04C01

value: Blood


title: LSCLowDXRA1


title: F-HSC2

value: liver


title: P1531

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744134_R04C02


title: P1633

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744134_R03C02


title: 2-108-2-2_S163


title: 2-108-2-1_S168


title: LSChighDXRB1

value: Clinical DXR


title: P1135

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744134_R02C02


title: 2-108-1-1_S91


title: NIC_Prmt6_2

city: Smithville

first: Jianqiang

last: Bao

address: 1808 Park Road 1C (P.O. Box 389), Smithville  TX 78957

department: Epigenetics and Molecular Carcinogenesis

institute: University of Texas MD Anderson Cancer Center

data_processing:
Basecalling was done by Illumina HiSeq Control Software (version 3.3.76).
The reads were mapped to mouse genome (mm10) by TopHat (version 2.0.10).
The number of fragments in each known gene from RefSeq database (downloaded from UCSC Genome Browser on July 17, 2015) was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genes with less than 10 fragments in all the samples were removed, and then the normalized fragment count for each gene was calculated by R/Bioconductor package DESeq (version 1.18.0).
Genome_build: mm10
Supplementary_files_format_and_content: The first column is gene symbol. The other columns are normalized expression values (estimated by DESeq) for all the samples.

source_name: mammary epithelial cells (MEC)

growth_protocol: each mammary epithelial cells (MEC) sample was isolated from the number #3 and #4 mammary glands through enzymatic digestion and pulse centrifugation. Cells were prepared using the DMEM/F12 medium. Purified cells were kept in Trizol reagent and stored at -80oC freeezer.

extract_protocol:
Trizol method followed by the Dnase I digestion to remove the potential genomic DNA. poly A selection
TruSeq RNA Library Prep Kit v2 (illumina)

value: FVB

value: Mammary gland

value: mammary epithelial cells (MEC)


title: NIC_Prmt6_1


title: LSCChemoB3

source_name: LSCChemo

value: Chemotherapy


title: P1115

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744134_R01C02

source_name: Blood

value: M


title: LSCChemoB2

value: Bone Marrow

value: LSC


title: P1284

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744134_R06C01

value: F


title: LSCChemoB1


title: P1459

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744134_R05C01

value: Unaffected


title: 2-105-2-1_S74

source_name: adipose tisue


title: NIC_Carm1_2


title: P1445

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744134_R04C01


title: NIC_Carm1_1


title: LSCChemoA3


title: 2-102-2-3_S17

value: baseline, cid2 :lcd, cid3 :di):CID3


title: LSCChemoA2


title: NIC_Prmt1_2


title: P1525

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744134_R02C01


title: P1462

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744134_R03C01


title: LSCChemoA1


title: LSChighDXRA2


title: 2-100-2-2_S157

value: baseline, cid2 :lcd, cid3 :di):CID2


title: NIC_Prmt1_1


title: P1002

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744134_R01C01


title: HSPCVehicle9weekB3

value: HSPC

value: Vehicle (Control)


title: 2-100-2-1_S72

value: baseline, cid2 :lcd, cid3 :di):CID1


title: 2-107-2-3_S7


title: 2-108-1-1_S187


title: NIC_Carm1_3


title: 2-099-1-3_S128


title: NIC_1

value: NIC


title: NIC_Prmt1_3


title: 2-099-1-1b_S36


title: HSPCVehicle9weekB2


title: HSPCVehicle7weekA3


title: P1214

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925145_R06C02

value: Blood

value: Affected


title: HSPCVehicle9weekB1


title: F-HSC

value: liver

value: 12-14 weeks

value: Hepatic stellate cells


title: 2-100-2-3_S136


title: 2-098-2-2_S22


title: P1639

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925145_R04C02


title: HSPCVehicle7weekA1


title: NIC_2

value: FVB

value: Mammary gland

value: mammary epithelial cells (MEC)


title: P1335

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925145_R02C02

value: M


title: P1587

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925145_R03C02


title: 2-098-2-1_S36


title: HSPCLowDXRChemoB2

value: Bone Marrow

value: [Low]DXR + Chemotherapy


title: 2-097-2-2_S6


title: P1116

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925145_R01C02

value: Unaffected


title: HSPCLowDXRChemoB1


title: P1064

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925145_R06C01


title: P1709

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925145_R05C02


title: 2-097-2-2_S102

value: baseline, cid2 :lcd, cid3 :di):CID2


title: HSPCLowDXRChemoA3

value: HSPC


title: 2-097-2-1_S15


title: P1191

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925145_R04C01

value: F


title: HSPCLowDXRChemoA2


title: P1080

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925145_R03C01


title: HSPCLowDXRChemoA1


title: 2-098-2-2_S118


title: 2-097-2-1_S111

value: baseline, cid2 :lcd, cid3 :di):CID1


title: 2-096-2-3_S75

value: baseline, cid2 :lcd, cid3 :di):CID3


title: 2-096-2-2_S178


title: HSPCLowDXRB1

source_name: HSPCLowDXR

value: [Low]DXR


title: P1318

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925145_R02C01

value: Blood

value: Affected


title: P1731

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925145_R01C01


title: HSPCVehicle7weekA2

value: Vehicle (Control)


title: 2-096-1-3_S125


title: HSPChighDXRB1

value: Clinical DXR


title: P1548

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925145_R05C01


title: Head and neck squamous cell carcinoma HN174 microRNA

city: Memphis

first: Jeremiah

middle: Ray

last: Holt

state: TN

address: 19 S. Manassas, Room 202

department: Medicine

institute: UTHSC

hyb_protocol: Biotin-labeled RNA was hybridized to the Affymetrix GeneChip miRNA-1_0 array overnight at 48℃.

scan_protocol: After hybridization and wash, the arrays were scanned with the GeneChip Scanner 3000

data_processing:
Probe-level intensity files were evaluated for quality using the ‘affy’ R package to process the raw CEL files. PM intensities were log2 transformed and then normalized using the 'affy' expresso() function, and batch effects were corrected for using the ComBat() function in the 'sva' package in R.
Log2 transformed and quantile normalized RMA expression values.

label: biotin

label_protocol: One microgram total RNA was labeled with FlashTaq RNA labeling kit from Genisphere (Genisphere Inc. Hatfield, PA), and then poly-(A) tailing was added to RNA, before ligating a biotinylated signal molecule to the target RNA sample

growth_protocol: not applicable

extract_protocol: RNA was extracted using TRIzol from Invitrogen and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). RNA quality was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: not applicable

value: Tumor

tag: race

value: White

value: Female

tag: smoking packyears

tag: alcohol use

value: light or moderate

tag: differentiation

value: Moderately Differentiated

tag: tumor site

value: Larynx

tag: Stage

value: I

tag: tumor status

value: not available

tag: node status

value: Radiation Alone

tag: hpv status

value: negative


title: Right brain, 5-min inhalation of DMHF vapor, biological rep3

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

hyb_protocol: Following fragmentation, 12.5 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were quantified with the distribution free weighted method (DFW), using the statistical language R (R-2.7.2) and Bioconductor 2.2.

organism: Rattus norvegicus

source_name: Right brain excised from DMHF vapor inhalated rat

label_protocol: biotinylated cRNA was obtained from 100 ng of purified total RNA using a GeneChip 3’ IVT PLUS Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using ISOGEN II reagent (Nippon Gene Co., Tokyo, Japan), then purified with an RNeasy mini kit (Qiagen K.K., Tokyo, Japan).

treatment_protocol: Excised brain sample was divided into half at the midline, and the right brain was snap frozen in liquid nitrogen and stored at -80ºC until use.

value: Wistar

tag: Sex

value: Male

value: 7 weeks

value: Brain


title: Right brain, 5-min inhalation of DMHF vapor, biological rep4

tag: strain


title: Right brain, 5-min inhalation of DMHF vapor, biological rep2

tag: age


title: 2-095-2-1_S137

tag: cid (cid1

value: baseline, cid2 :lcd, cid3 :di):CID1

tag: individual


title: Right brain, 5-min inhalation of DW vapor (control), biological rep5

source_name: Right brain excised from DW vapor inhalated rat

value: distilled water (control)


title: Head and neck squamous cell carcinoma HN173 microRNA

tag: gender

value: IVA

value: Chemotherapy Alone-Palliative


title: Right brain, 5-min inhalation of DW vapor (control), biological rep4

tag: tissue


title: Right brain, 5-min inhalation of DW vapor (control), biological rep2

tag: treatment


title: Right brain, 5-min inhalation of DW vapor (control), biological rep3


title: HSPChighDXRA2

tag: genotype

value: Bone Marrow

tag: cell type

value: HSPC

value: Clinical DXR


title: P1271

first: Ariel

last: Martinez

institute: National Institutes of Health

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925134_R05C02

value: Blood

value: M

tag: adhd affection status

value: Affected


title: Right brain, 5-min inhalation of DW vapor (control), biological rep1


title: Right brain, 5-min inhalation of DMHF vapor, biological rep5


title: Right brain, 5-min inhalation of DMHF vapor, biological rep1


title: Head and neck squamous cell carcinoma HN172 microRNA

value: Tumor

tag: race

value: American Indian or Alaskan Native

tag: smoking packyears

tag: alcohol use

tag: differentiation

value: Moderately Differentiated

value: Larynx

value: Surgery and Concurrent Chemoradiation


title: HSPCChemoB3

source_name: HSPCChemo

value: Chemotherapy


title: P1457

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925134_R04C02

value: F


title: HSPCLowDXRA1

value: [Low]DXR


title: HSPCChemoB2


title: P1702

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925134_R06C02


title: 2-094-1-1b_S222

value: baseline, cid2 :lcd, cid3 :di):CID1


title: P1486

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925134_R02C02

value: Unaffected


title: P1120

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925134_R03C02


title: HSPCChemoB1


title: 2-093-2-1_S45


title: Head and neck squamous cell carcinoma HN170 microRNA

value: White

value: Male

tag: tumor site

tag: Stage

value: not available

tag: tumor status

tag: node status

value: Radiation Alone


title: Head and neck squamous cell carcinoma HN169 microRNA

tag: age

value: heavy use currently:>3 drinks per day

value: III

tag: hpv status

value: negative


title: HSPCChemoA3

value: Bone Marrow

value: HSPC


title: 2-095-1-1_S135

tag: cid (cid1

tag: individual


title: Head and neck squamous cell carcinoma HN167 microRNA

tag: tissue

value: Tumor

tag: gender

value: Unknown

value: light or moderate

value: Well Differentiated

value: IVA

value: Surgery Alone


title: P1108

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925134_R06C01

value: Blood

value: F

value: Affected


title: Head and neck squamous cell carcinoma HN168 microRNA

value: Black or African American

value: Male

value: Moderately Differentiated

value: Oropharynx

tag: treatment

value: Concurrent Chemoradiation


title: HSPCChemoA2

tag: genotype

tag: cell type

value: Chemotherapy


title: HSPCChemoA1

value: Bone Marrow


title: 2-091-2-1b_S123

value: baseline, cid2 :lcd, cid3 :di):CID1


title: 2-091-2-2_S19

value: baseline, cid2 :lcd, cid3 :di):CID2


title: 2-090-2-3_S118

value: baseline, cid2 :lcd, cid3 :di):CID3


title: P1857

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925134_R05C01

tag: adhd affection status


title: Head and neck squamous cell carcinoma HN165 microRNA

value: Tumor

tag: race

value: White

value: Female

tag: smoking packyears

value: heavy use currently:>3 drinks per day

value: Larynx

value: I

value: negative


title: 2-094-1-2_S84


title: P1793

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925134_R04C01

value: Blood

value: M

value: Unaffected


title: Head and neck squamous cell carcinoma HN171 microRNA

value: Male

tag: alcohol use

value: light or moderate

tag: differentiation

value: Moderately Differentiated

value: Hypopharynx

value: IVA

value: Surgery and Concurrent Chemoradiation


title: ControlLym2

source_name: ControlLym

value: Wild-type (C57Bl6)

value: Bone Marrow

value: Lym


title: P1391

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925134_R03C01

value: F


title: Head and neck squamous cell carcinoma HN164 microRNA

value: Tumor

value: Black or African American

value: heavy use currently:>3 drinks per day

value: Well Differentiated

tag: tumor site

value: Oropharynx

tag: Stage

value: III

value: Concurrent Chemoradiation


title: P1487

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925134_R02C01

value: Blood

value: M

value: Unaffected


title: ControlLym1


title: Head and neck squamous cell carcinoma HN163 microRNA

value: White

value: Male

tag: tumor status

tag: node status

value: negative


title: ControlHSPC3

source_name: ControlHSPC

value: Wild-type (C57Bl6)

value: HSPC


title: 2-090-2-1_S97

value: baseline, cid2 :lcd, cid3 :di):CID1


title: P1605

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925134_R01C01

value: Affected


title: P1181

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925134_R01C02


title: Head and neck squamous cell carcinoma HN162 microRNA

value: Tumor

tag: age

value: Unknown

value: Not evaluated

value: Hypopharynx

value: not available

value: Surgery Alone

tag: hpv status


title: Head and neck squamous cell carcinoma HN166 microRNA

value: light or moderate

value: Moderately Differentiated

value: IVB

value: Concurrent Chemoradiation


title: ControlLym3

value: Bone Marrow

value: Lym


title: 2-090-2-2_S24

tag: cid (cid1

value: baseline, cid2 :lcd, cid3 :di):CID2

tag: individual


title: 2-089-2-3_S124

value: baseline, cid2 :lcd, cid3 :di):CID3


title: P1035

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925114_R06C02

tag: tissue

value: Blood

tag: gender

value: M

value: Unaffected


title: ControlHSPC2

tag: genotype

value: Wild-type (C57Bl6)

value: HSPC

tag: treatment


title: ControlHSPC1

tag: cell type


title: 2-090-1-2_S169


title: Head and neck squamous cell carcinoma HN160 microRNA

value: Tumor

tag: race

value: White

value: Male

value: Larynx

value: III

value: negative


title: 2-090-1-3_S52


title: P1218

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925114_R05C02

tag: adhd affection status


title: BlastCellVehicle9weekB3

value: BlastCell

value: Vehicle (Control)

tag: time


title: P1616

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925114_R04C02

value: Affected


title: BlastCellVehicle9weekB2

value: Bone Marrow


title: P1241

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925114_R03C02


title: Head and neck squamous cell carcinoma HN161 microRNA

value: Female

tag: smoking packyears

tag: alcohol use

tag: differentiation

value: Well Differentiated

value: IVA

value: Concurrent Chemoradiation


title: 2-089-2-1_S31

value: baseline, cid2 :lcd, cid3 :di):CID1


title: Head and neck squamous cell carcinoma HN158 microRNA

value: light or moderate

value: Poorly Differentiated

tag: tumor site

value: Oropharynx

tag: Stage

tag: tumor status

value: positive


title: 2-089-2-2_S63

value: baseline, cid2 :lcd, cid3 :di):CID2


title: Head and neck squamous cell carcinoma HN159 microRNA

value: Tumor

tag: age

value: White

value: Male

value: Not evaluated

tag: node status

tag: hpv status


title: 2-090-2-1_S1

tag: cid (cid1

tag: individual


title: P1255

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925114_R02C02

tag: tissue

value: Blood

tag: gender

value: M

value: Unaffected


title: BlastCellVehicle9weekB1

tag: genotype

value: Bone Marrow

tag: cell type

value: BlastCell

tag: treatment

value: Vehicle (Control)


title: 2-089-1-3_S13

value: baseline, cid2 :lcd, cid3 :di):CID3


title: P1359

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925114_R01C02

tag: adhd affection status

value: Affected


title: BlastCellVehicle7weekA3

tag: time


title: 2-088-1-3_S173


title: Head and neck squamous cell carcinoma HN157 microRNA

tag: race

tag: smoking packyears

tag: alcohol use

value: heavy use > 6 months ago

value: IVA

value: Concurrent Chemoradiation

value: negative


title: Head and neck squamous cell carcinoma HN153 microRNA

value: light or moderate

tag: differentiation

value: Moderately Differentiated

tag: tumor site

tag: Stage

value: II

value: Surgery Alone


title: BlastCellVehicle7weekA2


title: 2-088-1-1_S87

value: baseline, cid2 :lcd, cid3 :di):CID1


title: Head and neck squamous cell carcinoma HN151 microRNA

value: Tumor

tag: age

value: White

value: Male

value: Well Differentiated

value: Larynx

value: not available

tag: tumor status

tag: node status


title: P1021

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925114_R06C01

value: Blood

value: M

value: Unaffected


title: P1715

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925114_R05C01


title: Head and neck squamous cell carcinoma HN150 microRNA

value: American Indian or Alaskan Native

value: Female

value: IVA

tag: hpv status


title: BlastCellLowDXRChemoB3

tag: tissue

value: Bone Marrow

value: BlastCell

value: [Low]DXR + Chemotherapy


title: 2-087-1-2_S124

tag: cid (cid1

value: baseline, cid2 :lcd, cid3 :di):CID2

tag: individual


title: Head and neck squamous cell carcinoma HN147 microRNA

tag: gender

value: heavy use currently:>3 drinks per day

value: Moderately Differentiated

value: II

value: Surgery Alone

value: negative


title: 2-087-1-2_S28


title: P1732

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925114_R04C01

value: F


title: BlastCellLowDXRChemoB2

tag: genotype

tag: cell type

tag: treatment


title: 2-086-1-2_S103


title: 2-087-1-1_S134

value: baseline, cid2 :lcd, cid3 :di):CID1


title: Head and neck squamous cell carcinoma HN145 microRNA

value: Tumor

tag: race

value: White

value: Male

value: heavy use > 6 months ago

value: Surgery and Radiation


title: BlastCellLowDXRChemoB1


title: Head and neck squamous cell carcinoma HN146 microRNA

tag: smoking packyears

value: light or moderate

value: III

value: Surgery and Concurrent Chemoradiation


title: BlastCellLowDXRChemoA3

value: Bone Marrow

value: BlastCell

value: [Low]DXR + Chemotherapy


title: Head and neck squamous cell carcinoma HN143 microRNA

value: Black or African American

tag: alcohol use

value: Moderately Differentiated

value: Oropharynx

value: IVA

value: not available

value: Concurrent Chemoradiation


title: 2-085-2-2_S151

value: baseline, cid2 :lcd, cid3 :di):CID2


title: P1614

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744150_R06C02

value: Blood

value: M

tag: adhd affection status

value: Affected


title: Head and neck squamous cell carcinoma HN140 microRNA

value: Tumor

value: White

value: Male

tag: differentiation

value: Well Differentiated

tag: tumor site


title: BlastCellLowDXRChemoA2

value: Bone Marrow


title: 2-085-2-1_S90

value: baseline, cid2 :lcd, cid3 :di):CID1


title: P1494

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925114_R01C01


title: BlastCellLowDXRB3

source_name: BlastCellLowDXR

value: BlastCell

value: [Low]DXR


title: P1065

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925114_R03C01

value: F

value: Unaffected


title: BlastCellVehicle7weekA1

value: Vehicle (Control)

tag: time


title: P1850

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744150_R05C02


title: P1538

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744150_R04C02


title: Head and neck squamous cell carcinoma HN138 microRNA

tag: age

value: Female

value: light or moderate

value: Moderately Differentiated

tag: Stage

value: not available

tag: tumor status

value: Surgery Alone


title: BlastCellLowDXRB2

tag: tissue


title: BlastCellLowDXRB1


title: Head and neck squamous cell carcinoma HN129 microRNA

value: Black or African American

value: Oropharynx

tag: node status

value: Concurrent Chemoradiation

tag: hpv status

value: negative


title: 2-083-1-2_S178

tag: cid (cid1

value: baseline, cid2 :lcd, cid3 :di):CID2

tag: individual


title: BlastCellLowDXRChemoA1

tag: genotype

value: Bone Marrow

tag: cell type

value: [Low]DXR + Chemotherapy


title: 2-085-1-1_S89

value: baseline, cid2 :lcd, cid3 :di):CID1


title: P1042

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744150_R01C02

value: Blood

tag: gender

value: M


title: P1183

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744150_R02C02

value: F

value: Unaffected


title: 2-082-2-3_S59

value: baseline, cid2 :lcd, cid3 :di):CID3


title: Head and neck squamous cell carcinoma HN127 microRNA

value: Tumor

tag: race

value: White

value: Male

tag: smoking packyears

value: heavy use > 6 months ago

value: Not evaluated

value: Larynx

value: II

value: Tis

tag: treatment


title: BlastCellLowDXRA3

value: BlastCell

value: [Low]DXR


title: P1579

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925114_R02C01

tag: adhd affection status

value: Affected


title: P1599

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744150_R03C02


title: Head and neck squamous cell carcinoma HN128 microRNA

value: Female

tag: alcohol use

value: heavy use currently:>3 drinks per day

tag: differentiation

value: Moderately Differentiated

tag: tumor site

value: Oropharynx

value: IVA

value: Concurrent Chemoradiation

value: negative


title: Head and neck squamous cell carcinoma HN126 microRNA

value: Tumor

tag: age

value: White

tag: Stage

value: III

value: not available

value: Surgery and Radiation


title: BlastCellLowDXRA2

tag: tissue

value: Bone Marrow


title: 2-081-2-1_S104

value: baseline, cid2 :lcd, cid3 :di):CID1


title: 2-082-2-1b_S174


title: 2-085-1-2_S84

value: baseline, cid2 :lcd, cid3 :di):CID2


title: Head and neck squamous cell carcinoma HN136 microRNA

value: Well Differentiated

tag: tumor status

tag: node status

value: Surgery Alone


title: P1749

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744150_R05C01

value: Blood

value: M

value: Affected


title: Head and neck squamous cell carcinoma HN124 microRNA

value: Black or African American

value: Male

value: light or moderate

value: Moderately Differentiated

value: Hypopharynx

value: II

value: Radiation Alone

tag: hpv status


title: Head and neck squamous cell carcinoma HN122 microRNA

value: Tumor

value: Female

value: not available

value: Surgery and Concurrent Chemoradiation

value: negative


title: 2-081-1-1_S36

tag: cid (cid1

value: baseline, cid2 :lcd, cid3 :di):CID1

tag: individual


title: BlastCellhighDXRB2

tag: genotype

value: Bone Marrow

tag: cell type

value: BlastCell

value: Clinical DXR


title: BlastCellhighDXRB3


title: Head and neck squamous cell carcinoma HN117 microRNA

tag: race

value: White

tag: gender

value: Surgery and Radiation

value: unknown because of low HAPB signal from sample


title: P1314

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744150_R06C01

value: Blood

value: M

value: Unaffected