title: Primary_hepatocytes_PGC-1α

city: Oulu

first: Jukka

last: Hakkola

address: Aapistie 5

department: Research Unit of Biomedicine

country: Finland

institute: University of Oulu

description: Gene expression data from PGC-1α-Ad treated mouse primary hepatocytes.

hyb_protocol: Standard Affymetrix hybridization protocol.

scan_protocol: Standard Affymetrix scanning protocol.

data_processing: Probe sets were redefined according to Dai et al. (Nucleic Acids Res. 33, e175, 2005) using remapped Chip Definition File v9, based on the Entrez Gene database (build 36, v2). Expression estimates were done as described previously (Buler, M. et al. J. Biol. Chem. 287, 1847-1860, 2012).

label: Biotin

source_name: Primary hepatocyte

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA, pooled from 3 different samples.

growth_protocol: Primary hepatocytes were isolated from a male 9-week-old C57BL/6 mouse and cultured as described in Arpiainen, S. et al. Toxicol. Appl. Pharmacol. 232, 135–141 (2008).

extract_protocol: Total RNA was isolated using TRI-Reagent (Sigma-Aldrich) according to the manufacturer’s protocol and treated with DNase.

treatment_protocol: After the cells were attached, the cultures were infected with PGC-1α (MOI 1) or with GFP-Ad (MOI 1) for 36 h, after which cells were collected and RNA isolated.

tag: strain/background

tag: gender

value: 9 weeks

value: Primary hepatocytes

value: PGC-1alpha-Ad (MOI 1)


title: Allogeneic transplant - MC-deficient mouse 2

status: Public on Apr 10 2019

type: RNA

city: Lexington

first: Ethan

middle: Jesse

last: Strattan

state: KY

address: 900 South Limestone Street, Wethington Building, CTW453

department: Hematology/BMT

country: USA

institute: University of Kentucky

description: Total RNA was extracted from skin taken from the nape of the neck. RNA was assessed for quality by Bioanalyzer and 100ng was loaded into the Nanostring Myeloid Innate Immunity Panel.

hyb_protocol: In the NanoString kit, individual mRNA molecules are directly hybridized with barcoded fluorescent molecules per the manufacturer's instructions.

scan_protocol: Samples were scanned by a Nanostring Sprint system and number of barcoded spots was counted directly.

data_processing: Data was assessed using the NanoString nSolver software, which normalizes the readouts to a panel of ~20 housekeeping genes.

molecule: total RNA

organism: Mus musculus

source_name: skin after bone marrow transplant

label_protocol: RNA was assessed for quality by Agilent Bioanalyzer, then measured by QuBit and 100ng was loaded into the NanoString Myleoid Innate Immunity kit.

extract_protocol: Skin in RNAlater solution was transferred to 1ml of Trizol, then minced and homogenized. Trizol extraction of RNA was performed as per the manufacturer's instructions. RNA was assessed for quality by Agilent Bioanalyzer, then measured by QuBit and 100ng was loaded into the Myleoid Innate Immunity kit.

treatment_protocol: Recipient mice were irradiated with 850cGy ionizing radiation, then injected IV with 5e6 LP/J bone marrow cells and 2e6 LP/J splenocytes. GVHD symptoms were allowed to progress for 7 weeks, then mice were euthanized by CO2 and skin was isolated from the nape of the neck and stored in RNAlater solution at -20C

tag: transplant type

value: Allogeneic

tag: strain


title: C3647R_A

type: SRA

city: Chicago

first: Michelle

middle: C

last: Ward

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

library_source: transcriptomic

data_processing:
RNA-seq reads from each species were trimmed and mapped to each genome (hg19 or panTro3) using Tophat2 (version 2.0.11) (Kim et al. 2013).
The number of reads falling into orthologous meta-exons across 30,030 Ensembl genes from hg19, panTro3 and rheMac3 (Blekhman et al. 2010) was determined using featureCounts within subread (version 1.5.0) (Liao et al. 2014).
Only autosomal genes are retained.
Genome_build: hg19 & panTro3
Supplementary_files_format_and_content: RNA-seq counts for orthologous autosomal genes for all individuals

organism: Pan troglodytes

source_name: induced pluripotent stem cell-derived cardiomyocytes

growth_protocol: Human and chimpanzee iPSC-derived cardiomyocytes were maintained in Cardiomyocyte Maintenance Media  [500 mL DMEM without glucose (A14430-01, ThermoFisher Scientific), 50 mL FBS (S1200-500, Genemate), 990 mg Galactose (G5388, Sigma-Aldrich), 5 mL 100 mM sodium pyruvate (11360-070, ThermoFisher Scientific), 2.5 mL 1M HEPES (SH3023701, ThermoFisher Scientific), 5 mL Glutamax (35050-061, ThermoFisher Scientific), 5 mL Penicillin/Streptomycin)].

extract_protocol:
RNA was extracted from ~1.5 million cells using the ZR-Duet DNA/RNA extraction kit (D7001, Zymo, Irvine, CA, USA) in species-balanced batches. Samples had a median RIN score of 9.1
Samples were combined into 4 pools for RNA-seq library generation using the Illumina TruSeq RNA Library Prep kit.  Libraries were sequenced on the HiSeq3000/4000 following the manufacturer's protocols.

treatment_protocol: Four conditions per sample were collected per individual: A- normoxia at 10% oxygen, B- hypoxia at 1% oxygen for 6 hours, C- re-oxygenation at 10% oxygen for 6 hours and D- re-oxygenation at 10% oxygen for 24 hours.

tag: cell line

tag: Sex

value: Female

tag: population

value: Chimpanzee

tag: treatment

value: normoxia


title: Oxibendazole treated Female

first: Martin

middle: K

last: Nielsen

address: 1400 Nicholasville Road

data_processing:
Adaptor trimming and quality control were performed using TrimGalore Version 0.4.4 (Babraham Bioinformatics).
Reads were subsequently aligned to the Parascaris univalens reference genome (Wang et al., 2017) using STAR Version 2.5b (Dobin et al., 2013).
Reads were annotated to the Parascaris reference transcriptome (Wang et al., 2017) using Cufflinks (Release 2.2.1) (Trapnell et al., 2012).
Read counts were normalized as fragments per kilobase of exon per million mapped reads (FPKM) and differential gene expression analysis was performed on normalized read counts.
Genome_build: Parascaris univalens reference genome (doi:10.1101/gr.225730.117)
Supplementary_files_format_and_content: *genes.fpkm_tracking

organism: Parascaris sp.

source_name: Whole worm

growth_protocol: Worms were maintained as described my Scare et al. (2018). Briefly, worms were kept in tissue culture flasks in 200 mL of RPMI-1640 at 37C in an air incubator. Media was changed every 12 hours.

extract_protocol:
Whole worms were ground to a fine powder. 1 mL TRIzol reagent used for RNA isolation following the manufacturer's instructions.
RNA samples were sent to the University of Louisville CGeMM DNA Core Facility for library preparation and sequencing. Libraries were prepared with Illumina’s TruSeq stranded total RNA library kit (Illumina, San Diego, CA, USA) with Ribo-Zero Gold depletion. Libraries were sequenced using the NextSeq 500 High Output v2 75 cycles kit. Samples were run in 1x75 base pair configuration, generating up to 400 million reads total, approximately 40 million reads per sample.

treatment_protocol: Oxibendazole methyl carbamate, Sigma-Aldrich, St. Louis, MO, USA) prepared in 100% DMSO, then diluted to 10 ug/mL. Treatments provided after 24 hour acclimation period. Worms snap frozen after 24 hours of exposure.

tag: isolate

value: University of Kentucky, Main Chance Farm, barn 10

tag: tissue

value: Whole body

tag: developmental stage

value: Adult

value: Oxibendazole treated


title: C3647_D


title: Allogeneic transplant - MC-deficient mouse 1


title: Ivermectin control Male

treatment_protocol: No treatment given, but worm was snap frozen at the same time as the Ivermectin treated worm.

value: Male

value: Ivermectin control


title: C3647_C


title: Allogeneic transplant - WT mouse 3


title: Ivermectin treated male

treatment_protocol: Ivermectin (22,23-dihydroavermectin B1, Sigma-Aldrich, St. Louis, MO, USA) prepared in 100% DMSO, then diluted to 1 ug/mL. Treatments provided after 24 hour acclimation period. Worms snap frozen after 3 hours of exposure.

value: Ivermectin treated


title: C3647_B

value: hypoxia


title: Allogeneic transplant - WT mouse 1


title: C3647_A


title: Ivermectin treated Female


title: Allogeneic transplant - WT mouse 2


title: C3647R_C


title: Degradome-seq-T

city: Hefei

first: chaoling

last: Wei

state: Anhui

address: 130 West Changjiang Road

country: China

institute: Anhui Agricultural University

description: Results from Degradome sequencing.txt

data_processing:
The raw reads of sRNA-seq was generated from the Illumina GAIIX system and the degradome sequencing was sequenced on Illumina Hiseq2500
In sRNA-seq, the raw reads were filtered using the Illumina pipeline filter (Solexa 0.3), and then further processed with the in-house program (ACGT101-v4.2-miR, LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity reads, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences ranging from 18 to 26 nt in length were compared with known plant miRNAs in miRBase (Release 22; http://www.mirbase.org), using BLAST searches to identify known miRNAs with no more than two mismatches. After the analyses, known miRNAs were categorized into four groups (1a, 1b, 2a, and 3a).
In degradome sequencing ,raw sequencing reads were obtained using Illumina’s Pipeline v1.5 software and processed to remove adaptor sequences and low-quality sequencing reads. The unique sequencing reads with lengths of 20 nt and 21 nt were then used to identify potentially cleaved targets with a public software package (CleaveLand3.0 pipeline)
Genome_build: Camellia sinensis var. sinensis (Sequence Read Archive database accession No. SRA536878, http://pcsb.ahau.edu.cn:8080/CSS/)
Supplementary_files_format_and_content: precursors and mature miRNA sequences,tab-delimited text files include RPKM values for each Sample

organism: Camellia sinensis

source_name: Leaf

growth_protocol: Three-year-old cuttings were planted in pots (30-cm diameter, 35-cm height) and grown in a green house maintained at 23 ± 3 °C with 65 ± 5% room humidity and a 16/8 h (day/light) photoperiod. All experimental plants were irrigated once a day and fertilized once a month. Healthy Shuchazao cuttings with uniform growth (25−30 cm in height) were selected for experiments.

extract_protocol:
Total RNA was isolated from each frozen sample using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. The quantity and quality of the total RNA were determined using a Bioanalyzer 2100 (Agilent, CA, USA) and the RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Equal quantities of total RNA from C. gloeosporioides- and mock-inoculated leaves collected at four days post infection (4dpi) were used to prepare the sRNA libraries using the TruSeq Small RNA Sample Prep Kit (Illumina, San Diego, CA, USA). We performed single-end sequencing (36 bp) on an Illumina Hiseq 2500 at the LC-BIO (Hangzhou, China) using the vendor’s recommended protocol.

treatment_protocol: The pathogenic C. gloeosporioides was originally isolated from diseased leaves of Shuchazao at the field of Anhui Agricultural University, Hefei, China. C. gloeosporioides was cultured on potato dextrose agar and incubated at 25 °C ± 2 °C in darkness for 10 days to promote sporulation. Conidia were harvested and suspended in sterile water. The conidia concentration was determined using a hemocytometer and adjusted to 1×10^5 mL-1 for inoculation.

value: Shuchazao

value: gloeosporioides-inoculated

value: mature leaf


title: In vivo control Male

treatment_protocol: No treatment given. Worm remained within jejunum subsection prior to snap freezing. Worm was never maintained in vitro.

value: In vivo control


title: Syngeneic transplant - mouse 3

value: Syngeneic


title: Oxibendazole treated Male


title: Syngeneic transplant - mouse 2


title: Primary_hepatocytes_GFP

description: Gene expression data from GFP-Ad treated mouse primary hepatocytes.

tag: age

value: 9 weeks

tag: cell type

value: Primary hepatocytes

value: GFP-Ad (MOI 1)


title: Degradome-seq-CK

description: Results from Degradome sequencing.txt

value: control


title: In vivo control Female

value: University of Kentucky, Main Chance Farm, barn 10

value: Female


title: Syngeneic transplant - mouse 1


title: Ivermectin control Female

value: Whole body

value: Adult


title: C2

status: Public on Apr 09 2019

city: Richland

first: Hugh

middle: D

last: Mitchell

state: Washington

address: 902 Battelle Blvd, P.O. Box 999, MSIN J4-18

department: Computational Biology

institute: Pacific Northwest National Laboratory

description:
No treatment
C2 (Core 1)

data_processing:
Data quality was assessed with htseq-qa
Reads were aligned to the Arabidopsis thaliana TAIR10 genome (https://www.araport.org/downloads/TAIR10_genome_release/assembly) using TMAP 3.0.1 (https://github.com/iontorrent/TS/tree/master/Analysis/TMAP) , the ION Torrent aligner designed for ION data, with the –g parameter set to 0 (soft clip right and left ends of each read) and the –a parameter set to 1 (return only best alignment, random choice in case of ties).
BAM file outputs were then mapped to genes using htseq-count (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4287950/ ) using default settings, with TAIR10_GFF3_genes.gff (ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release/TAIR10_gff3) as the input annotation file.
Genome_build: TAIR10
Supplementary_files_format_and_content: .txt files are 2 columns: gene ID and raw counts

organism: Arabidopsis thaliana

source_name: Tissue of plant rosette core

growth_protocol: Plant seeds were sown on soil and cold treated at 4°C for 1 to 2 days. Plants were maintained in 16-hour photoperiods at 22°C with light intensity at 100 μE/(m2s).

extract_protocol:
RNA was extracted using Qiagen Mini RNeasy™ kit (cat#74104), followed by genomic DNA removal using Qiagen RNase-Free DNase Set kit (cat#79254). Integrity of the RNA samples was assessed using the Agilent 2100 Bioanalyzer.
The Ribo-Zero rRNA Removal Kit (Plant Leaf) (illumine cat#MRZPL116) was used to enrich the transcripts, followed by generation of cDNA template library using The Ion Total RNA-Seq Kit v2 (catalog number 4479789) according to the instruction manual. Briefly, the mRNA was fragmented using chemical hydrolysis followed by ligation with strand specific adapters and reverse transcript to generate cDNA.  This cDNA fragment size between 150 to 250 bp was isolated and the emulsion clonal bead amplification to generate bead templates for Ion Torrent platform was performed on the Ion Chef System (Thermo Fisher Scientific) with the Ion PI™ Hi-Q™ Chef Kit (Thermo Fisher Scientific, A27198) and Ion PI™ Chip Kit v3 (Thermo Fisher Scientific, cat#A26771). Sequencing was done using the Ion PI™ Hi-Q™ Sequencing 200 Kit (Thermo Fisher Scientific, cat# A26772) on Ion Proton sequencer with sequencing data processing using the Torrent Suite TM Software (Ver. 4.0.2) on the Torrent server.

treatment_protocol: The central 1.5-2 cm of the plant rosettes were used for the analyses.

tag: ecotype

value: rosette core

value: 31 day


title: C10

description:
No treatment
C10 (Core 3)


title: C4

description:
No treatment
C4 (Core 2)


title: C12

description:
No treatment
C12 (Core 4)


title: PBMC response to dietary mineral intake_6

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

description: Gene expression data from PBMCs isolated from whole blood

hyb_protocol: Snowball arrays (Freeman et al. in BMC Biol 2012, 10:90), see the ArrayExpress database, accession no. A-AFFY-189 Labelled DNA was hybridized for 16 hr at 42°C on Snowball Arrays. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and BioConductor. For normalization Robust Multichip Average (RMA) was used.

label: biotin

organism: Sus scrofa

source_name: PBMC

label_protocol: Each RNA sample was transcribed to DNA using the Ambion WT Expression Kit (Ambion, Austin, TX, USA). DNA preparations were fragmented and labelled with the WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using Qiazol reagent (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was column-purified using the RNeasy Kit (Qiagen, Hilden, Germany).

treatment_protocol: Diets varying in mineral content

tag: dietary group intake

value: low

value: m

tag: age (days post natum)

value: whole blood

value: PBMC


title: PBMC response to dietary mineral intake_17

value: high

value: f


title: PBMC response to dietary mineral intake_10


title: PBMC response to dietary mineral intake_19

value: medium


title: SAS NC

city: Gifu City

first: Katsuaki

last: Bunai

state: Gifu

address: 1-1 Yanagido

country: Japan

institute: Gifu University Graduate School of Medicine

hyb_protocol: Following fragmentation, 3.5 ug of cRNA were hybridized with rotation at 60 rpm for 16 hr at 45°C on GeneChip Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G

data_processing: Affymetrix Expression Console (EC) software

organism: Homo sapiens

source_name: Total RNA from SAS

label_protocol: Biotinylated cRNA were prepared using GeneChip WT PLUS Reagent Kit, according to the standard Affymetrix protocol from 250ng total RNA (GeneChip WT PLUS Reagent Kit User Manual, 2017, Affymetrix).

extract_protocol: Total RNAs were extracted using Rneasy mini kit (Qiagen) accoring to the the manufacturer's recommendations.

value: Human oral cancer cells

value: SAS

value: mock


title: PBMC response to dietary mineral intake_3


title: SAS 109

source_name: Total RNA from SAS 109 ARID1A siRNA

value: ARID1A siRNA


title: PBMC response to dietary mineral intake_1


title: PBMC response to dietary mineral intake_18


title: PBMC response to dietary mineral intake_20


title: PBMC response to dietary mineral intake_15


title: PBMC response to dietary mineral intake_11


title: SAS 108

source_name: Total RNA from SAS 108 ARID1A siRNA


title: PBMC response to dietary mineral intake_13


title: PBMC response to dietary mineral intake_5


title: PBMC response to dietary mineral intake_12


title: PBMC response to dietary mineral intake_8


title: PBMC response to dietary mineral intake_14


title: PBMC response to dietary mineral intake_9


title: H3b

city: Toronto

first: Rickvinder

last: Besla

state: ON

address: 101 college st, MaRS TMDT 3-901

country: Canada

institute: UHN

description: mRNA expression

hyb_protocol: 16 hr at 45°C

scan_protocol: Scanning was performed using the Affymetrix GeneChip Scanner 3000

data_processing:
Probe set expression levels were background corrected and normalized using Robust Multi-array Average (RMA). Probe sets corresponding to noncoding transcripts were filtered out.
Differentially expressed genes were defined based on >2 fold expression change and P < 0.05 determined using unpaired student’s t-test.

label: Biotin Allonamide Triphosphate

source_name: Spleen

label_protocol: Biotin Allonamide Triphosphate was used for labeling

growth_protocol: Mice were fed a high cholesterol diet for 12 weeks prior to sacrifice. Spleens were removed and processed, RBC lysed and stained for appropriate B cell subsets. Cells were sorted by BD influx cell sorter into FACS buffer

extract_protocol: mRNA was extracted from sorted cells using the PicoPure RNA isolation kit as per manufacturer's instructions. Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

tag: genotype

value: c-myb h/h LDL-R KO Mouse


title: PBMC response to dietary mineral intake_4


title: H2b

description: mRNA expression


title: H1c

description: mRNA expression


title: PBMC response to dietary mineral intake_16


title: TBX5 KO M2

first: Xinan

middle: Holly

last: Yang

address: 900 East 57th Street, KCBD Room 5121

department: Pediatrics

institute: universty of Chicago

data_processing:
After evaluating the quality of these 51bp single-ended RNAseq reads by fastqc, for each sample we left trimmed 3 bp reads with the lowest quality scores using fastx_toolkit (version 0.0.13).
The 47 bp length RNA-seq reads were alimented to the Mouse genome mm10 using tophat (version 2.0.11).
Featurecount was performed using Rsubread (version 1.14.2).
Differential expression was analyzed using DEseq2 Bioconductor package with the by default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file that was the output of DEseq2 that comparing TBX5 KO samples with CTRL samples

source_name: R26Cre driven TBX5 removal in adult animal

growth_protocol: Mice were raised according to university protocols (protocol # 71737).

extract_protocol:
Left and right atria were dissected from TBX5 removed and control 6‐8 week old mice. Tissues were mechanically homogenized in TRIzol Reagent (Invitrogen), chloroform was added, aqueous phase was isolated, ethanol was added, and then RNA was isolated using RNeasy Mini Columns. Overall, 12μg of total RNA for each sample was treated with the mouse GlobinClear kit (Ambion) to remove the majority of globin RNA. Libraries were prepared from this RNA starting with 1μg per sample and using the mRNA‐seq Sample Prep Kit (Illumina) as per recommended instructions. Cluster generation and sequencing were performed as per standard Illumina HiSeq2500 Rapid Run Mode protocols to generate single-end reads of 51bp. A single pool of libraries was sequenced in two individual lanes of the HiSeq2500 2‐lane flow cell.
Barcoded Libraries were prepared according to Illumina's instructions (2013) accompanying the TruSeq RNA Sample prep kit v2 (Part# RS‐122‐2001). Libraries were quantitated using the Agilent  Bio‐analyzer (model 2100) and pooled in equimolar amounts. The pooled libraries were sequenced on the HiSeq2500 in Rapid Run Mode following the manufacturer's protocols (2013).
Total RNA-seq (Ribozero purification removed only ribosomal RNA, remaining total RNA was sequenced) of 50bp

treatment_protocol: A tamoxifen inducible cre recombinase driven by the ubiquitous R26 promoter was used to excise exon 3 of TBX5 as previously described (Arnolds et al JCI 2012). Excision of TBX5 was induced by IP tamoxifen for 3 days, 0.167mg tamoxifen/day. Mice were sacrificed at 1 week post tamoxifen and right and left atrial appendage were dissected.

value: 8-10 weeks

value: Male

value: Tbx5 Null (Tbx5-/-)

value: left atria

tag: mouse strain

value: Mixed strain of C57B6, and 129 backgrounds


title: TBX5 KO M3

tag: gender


title: TBX5 KO F3

value: Female


title: H3c

description: mRNA expression


title: TBX5 KO F2


title: WT2b

description: mRNA expression

value: LDL-R KO Mouse


title: FOLFIRINOX_XRT_6

city: Atlanta

first: Gregory

middle: Brian

last: Lesinski

state: GA

address: 1365 Clifton Rd., NE

department: Hematology and Medical Oncology

institute: Emory University

hyb_protocol: scaled RNA was hybridized with biotin-labeled capture probes and fluorescently labeled reporter probes for 18 hours at 65° C

scan_protocol: samples were injected into a nanoString SPRINT cartridge and loaded onto the SPRINT instrument where excess capture probe and reporter probe were removed, and hybridized mRNAs were immobilized for imaging.

data_processing: Following image acquisition mRNA counts were extracted from raw RCC files using nSolver analysis software v3.0 (Nanostring) and exported as .csv files for further analysis.

label: Biotin-labeled capture probes

molecule: polyA RNA

source_name: PDAC tumor, prior FOLFIRINOX treatment, prior XRT

extract_protocol: For each patient, four 5-micron FFPE sections were scraped into 1.5 ml Eppendorf tubes. RNA was extracted with EZ FFPE RNA kit (Omega BioTek). RNA was eluted in 30 µl nuclease free water. RNA quality and quantity were determined using a Nanodrop 1000 (ThermoFisher) and 6000 RNA Nano assay (Aginelt). RNA input was scaled based on DV 300 value to 50ng (50ng/DV300 x 100) and processed according to the nCounter XT Assay User Manual (MAN-10023-11).

value: PDAC tumor

tag: race

value: African American

tag: initial staging

value: Locally Advanced

tag: cancer location (within pancreas)

value: Head

tag: differentiation status

value: Well

tag: surgical margin

value: Positive

tag: perineural invasion

value: Yes

tag: lymphovascular invasion

value: No


title: TBX5 KO F1

tag: tissue


title: TBX5 KO M1


title: H2a

description: mRNA expression


title: FOLFIRINOX_XRT_5

value: Borderline Resectable

value: Tail

value: Moderate

value: Negative


title: WT1b

description: mRNA expression


title: WT2a

description: mRNA expression


title: PBMC response to dietary mineral intake_7

value: high

tag: Sex

value: m

value: whole blood

value: PBMC


title: WT1a

description: mRNA expression

value: LDL-R KO Mouse


title: FOLFIRINOX_XRT_4

value: PDAC tumor

value: Male

value: Caucasian


title: H2c

description: mRNA expression

value: c-myb h/h LDL-R KO Mouse


title: WT3b

description: mRNA expression


title: PBMC response to dietary mineral intake_2

value: medium


title: WT3a

description: mRNA expression


title: FOLFIRINOX_XRT_2

value: Female

value: Head

value: Positive


title: FOLFIRINOX_XRT_3

value: Borderline Resectable

value: Poor

value: Yes


title: H1b

description: mRNA expression


title: H1a

description: mRNA expression


title: WT1c

description: mRNA expression


title: CTRL F1

source_name: Control adult mouse

tag: age

value: 8-10 weeks

value: Wildtype (Tbx5 +/+)

value: left atria

value: Mixed strain of C57B6, and 129 backgrounds


title: CTRL F2


title: H3a

description: mRNA expression

tag: cell type


title: CTRL M2


title: FOLFIRINOX_XRT_1

value: Locally Advanced

value: Tail

value: Moderate

value: Negative


title: FOLFIRINOX_SBRT_6

source_name: PDAC tumor, prior FOLFIRINOX treatment, prior SBRT

value: PDAC tumor

value: Caucasian


title: CTRL M1

value: Male


title: FOLFIRINOX_SBRT_4

value: Female

value: Asian

value: Not in database


title: FOLFIRINOX_SBRT_5

value: Borderline Resectable

value: Head

value: No


title: FOLFIRINOX_SBRT_2

value: Positive

value: Yes


title: FOLFIRINOX_6

source_name: PDAC tumor, prior FOLFIRINOX treatment

value: Well


title: FOLFIRINOX_SBRT_1


title: HPC2_pCHiC

city: Mainz

first: Daniel

last: Sasca

address: Langenbeckstr 1

department: Department of Hematology and Oncology

institute: University Medical Center Mainz

description: processed data in file: HPC1_and_HPC2_washU_text.txt

library_source: genomic

data_processing:
pCHiC pipeline: Samples were preprocessed with HiCUP. Raw HiCUP outputs were processed with the CHiCAGO pipeline (Babraham Institute).
washU browser txt files for pCHiC
Genome_build: mm10

molecule: genomic DNA

source_name: non-transduced HPC7 cells

growth_protocol: Cells were grown in standard media with addition of 100 ng/ul murine recombinant SCF

extract_protocol:
x-linking was performed with 1% Formaldehyde. Nuclei were homogenized with Dounce, DNA was enzymatically lysed with HindIII. Fragments were religated after 5' biotinylation.
pCHiC libraries were contructed via promoter capture with SureSelect hybridisation beads.

tag: cell line

value: Hematopoietic stem and progenitors

value: non-transduced HPC7 cells


title: FOLFIRINOX_SBRT_3


title: HPC1_pCHiC


title: HPC_H3K4me3_ChIP-seq

description: ChIP antibody: H3K4me3 (Diagenode, C15410003)

data_processing:
Chip Seq pipeline: Adapter sequences were trimmed for all reads and mapped against mm10 reference genome using Bowtie2. Uniquely mapped, deduplicated reads were retained and peaks were called using MACS2.
bedGraph files for ChIP Seq
Genome_build: mm10

extract_protocol:
x-linking was performed with 1% Formaldehyde. Lysates were clarified from sonicated nuclei and chromatin proteins were isolated with antibodies.
ChIP-Seq libraries were prepared for sequencing using a TruSeq ChIP Sample Prep Kit (Illumina) and standard Illumina protocols


title: miR-155 TCKO (day 9)

city: Holl

first: Ryan

last: O'Connell

state: UT

department: Pathology

institute: University of Utah

data_processing:
For each sample, demultiplex raw base call files (BCL) from Illumina with 10x Genomics' Single-Cell Gene Expression software, Cell Ranger, using the 'mkfastq' pipeline.
For each sample, perform alignment, filtering, barcode counting, and UMI (unique molecular identifier) counting with 10x Genomics' Single-Cell Gene Expression software, Cell Ranger (version 2.0.2), using the 'count' pipeline. Default parameters were used with exception of --expect-cells=6000,  in estimation of the expected number of recovered cells for samples 14795X1 and 14795X2. We used the mm10 genomic reference, 'refdata-cellranger-mm10-1.2.0',  prepared by 10x Genomics (see https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build#mm10_1-2-0 for details).
Genome_build: mm10
Supplementary_files_format_and_content: MEX-formatted UMI count matrices are available without normalization and are prefixed by sample identifiers (e.g. '14746X_'). Each sample's UMI count matrix contains the filtered gene-barcode output from 10x Genomics' Cell Ranger pipeline, which discards GEMs with insufficient total UMI count; details on this auto-filtering is available on 10x Genomics' website. More information on the formatting can be found at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices.

source_name: CD45+ tumor infiltrating immune cells

extract_protocol: Subcutaneous tumors were excised and minced by using scissors and tweezers. Mechanically disrupted tumors were incubated in Accumax (Innovative Cell Technologies) at room temperature on an orbital shaker for 30 minutes. Digested tumor samples were stained with anti-CD45-APC (Biolegend) antibody at 1:500 dilution in MACS buffer (PBS supplemented with 0.5% BSA and 2 mM EDTA). Live immune cells as defined by DAPI(-)CD45(+) staining pattern were FACS-sorted by using BS FACS Aria flow cytometer. Equal numbers of sorted cells were processed for single-cell 3' RNA-sequencing via 10X Genomics.

tag: strain

value: B16F10-OVA tumors

value: miR-155 TCKO

tag: timepoint

value: day 9


title: HPC_H3K4me1_ChIP-seq

description: ChIP antibody: H3K4me1 (Abcam, ab8895)

tag: genotype


title: miR-155 TCKO (day 12)

value: day 12


title: HPC_Pol2_ChIP-seq

description: ChIP antibody: Pol2 (Covance, MMS-126R)


title: HPC_Etv6_ChIP-seq

description: ChIP antibody: Etv6 (Santa Cruz, sc-8546x)


title: Wild-type (day 9)

value: WT


title: FOLFIRINOX_4

value: PDAC tumor

value: Male

value: Caucasian

value: Poor


title: Wild-type (day 12)


title: FOLFIRINOX_2

value: Female

value: African American

value: Borderline Resectable

value: Negative


title: FOLFIRINOX_3

value: Neck

value: Moderate

value: Yes

value: No


title: Input_Atg5_KO

city: Vancouver

last: Hirst

state: British Columbia

address: 2125 East Mall

department: Microbiology and Immunology

institute: University of British Columbia

data_processing:
Sequence reads were aligned to GRCm38/mm10 using Burrows-Wheeler Aligner 0.7.6a and converted to bam format by Sambamba 0.5.5.
Tracks for Input libraries were generated by converting bam files to Wiggle tracks and UCSC Wig2Bigwig was used to convert Wiggle tracks to BigWig for display on the UCSC browser.
Input control normalized tracks ChIPseq libraries were generated using MACS2.
MACS2 narrow Peak file was called using macs2 callpeak -t <ChIP bam> -c <Input bam> -f BAMPE -g hs -n <output name> -B -q 0.01
Genome_build: GRCm38
Supplementary_files_format_and_content: bigWig, Input and ChIP libraries tracks

extract_protocol:
Cells were lysed in non-ionic detergents and protease inhibitor cocktail. Cells were digested  by Micrococcal nuclease (MNase) at room temperature for 5 minutes and 0.25mM EDTA was used to stop the reaction. Antibodies, H3K27me3 and H3K4me3 were incubated with anti-IgA magnetic beads for 2 hours. Digested chromatin was incubated with magnetic beads alone for 1.5 hours. Digested chromatin was separated from beads and incubated with antibody-bead complex overnight in IP buffer. IPs were washed twice and eluted for 1.5 hours. Histones were digested by Protease for 30min and DNA fragments were purified using Sera Mag magnetic beads in 30% PEG.
Illumina sequencing libraries were generated by end repair, 3’ A-addition, and Illumina sequencing adaptor ligation.

tag: strain background

tag: tumour type

tag: genotype/variation

value: Cre-mediated deletion of Atg5

value: CD8+ tumour-infiltrating lymphocytes

tag: chip antibody


title: FOLFIRINOX_5

tag: gender

tag: race

tag: initial staging

value: Resectable

tag: cancer location (within pancreas)

value: Head


title: H3K27me3_Atg5_KO

tag: chip antibody ref.


title: H3K4me3_Atg5_KO

tag: chip antibody vendor

value: Cell Signaling Technology

tag: chip antibody cat.#

tag: chip antibody lot #


title: FOLFIRINOX_1

tag: tissue

value: PDAC tumor

tag: differentiation status

tag: surgical margin

tag: perineural invasion

tag: lymphovascular invasion


title: Surgery_Only_6

source_name: PDAC tumor, no prior treatment

value: Male

value: Tail


title: Surgery_Only_5

value: Caucasian

value: Positive


title: Input_Atg5_WT

source_name: wild-type

tag: strain background

value: wild type

tag: cell type


title: H3K27me3_Atg5_WT

tag: tumour type

tag: genotype/variation


title: H3K4me3_Atg5_WT

tag: chip antibody


title: sg5_E2

city: Singapore

first: Pushkar

last: Dakle

address: 14 Medical Drive, #12-01,

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
Paired end fastq files were pseudoaligned to Ensemble v82 transcritps using kallisto (VN: 0.43.1)
Transcript level expression and estimated counts were summarized to gene level using tximport Bioconductor package.
Differential expression analysis was performed with DESeq2 bioconductor package.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited output files - abundance.tsv generated by kallisto

source_name: Cell line NB-4

extract_protocol:
RNA was extracted using RNeasy Mini Kit(Qiagen)
TruSeq RNA Sample Preparation Kit (Illumina) was used for library preparation.

treatment_protocol: To induce ARID1A knockout, cells were cultured in media containing 1 μg/ml doxycycline for 7 days

tag: celltype

value: acute promyelocytic leukemia cell line

tag: genotype


title: sg1_E1


title: LacZ_E2

value: WT


title: sg1_E2


title: LacZ_E1


title: Surgery_Only_2

tag: gender

tag: race

value: Other

tag: initial staging

tag: cancer location (within pancreas)

value: Negative


title: mock control, no 4sU; rep2

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

description: purified newly transcribed RNA

data_processing:
Reads were mapped against the human genome (GRCh38) and rRNA sequences using ContextMap 2.7.7 with BWA as internal alignment program.
To calculate FPKM (Fragments Per Kilobase Of Exon Per Million Fragments Mapped) values, fragment counts per gene (from Gencode version 25) were calculated using the featureCounts program from the subread package (v1.4.6-p3).
Genome_build: GRCh38
Supplementary_files_format_and_content: featureCounts output containing read counts for genes

source_name: HeLa Flp-In cells

growth_protocol: Cells were grown in RPMI containing 10% FBS and P/S and split twice weekly

extract_protocol:
RNA was isolated using Triizol. 4sU residues in nascent transcripts were thiol-specifically biotinylated using Biotin-HPDP and purified using streptavidin-coated magnetic beads (Miltenyi). 4sU-RNA was recovered using Rneasy Minelute columns.
Replicate 1: TruSeq RNA Sample Prep Kit v2; Replicate 2: TruSeq Stranded mRNA LT Sample Prep Kit, performed by BGI Genomics

treatment_protocol: We mock treated or treated HeLa Flp-In cells for 1 or 2 hr with DMSO, 4-NQO, or 4-NQO + flavopiridol (FP). During the last 30 minutes of the treatments, we labeled the RNA or not with the nucleoside analogue 4-thiouridine (500µM 4sU) for 30 minutes.

tag: cell line

value: HeLa Flp-In cells

tag: library strand-specificity

value: strand-specific


title: 2 hr 4-NQO, 30 min 4sU; rep2

description: purified newly transcribed RNA


title: 1 hr 4-NQO, 30 min 4sU; rep2

description: purified newly transcribed RNA


title: 2 hr 4-NQO + FP, 30 min 4sU; rep1

description: purified newly transcribed RNA

value: not strand-specific


title: 2 hr DMSO, 30 min 4sU; rep2

description: purified newly transcribed RNA


title: 2 hr mock control, 30 min 4sU; rep2

description: purified newly transcribed RNA


title: 2 hr DMSO, 30 min 4sU; rep1

description: purified newly transcribed RNA


title: 2 hr 4-NQO, 30 min 4sU; rep1

description: purified newly transcribed RNA


title: Surgery_Only_1

tag: tissue

value: African American

tag: differentiation status

value: Poor

value: Yes


title: Surgery_Only_4

value: Resectable

value: Head

tag: surgical margin

tag: perineural invasion


title: 2 hr 4-NQO + FP, 30 min 4sU; rep2

description: purified newly transcribed RNA


title: mock control, no 4sU; rep1

description: purified newly transcribed RNA


title: 1 hr 4-NQO, 30 min 4sU; rep1

description: purified newly transcribed RNA


title: RNASeq_LY49H_LOW_02

city: New York

first: Endi

last: Santosa

state: New York

address: 417 E 68th St

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
BCL files were converted to fastq using bcl2fastq (v2.20.0.422).
RNA-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36).
Transcript quantification was performed by Salmon (v0.10.2) using arguments '-l IU --gcBias' and tximport (v1.9.12) using the UCSC mm10 known gene transcript assembly (v9).
DESeq2 (v1.12.17) was used to calculate differential expression.
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts (1 count = 1 read pair) are provided in the rawCounts_byEntrezID.txt file as quantified by Salmon (v.10.2). Row names are Entrez IDs of the gene.

source_name: NK cells

extract_protocol:
Spleens were removed 1.5 days post MCMV infection, and NK cells were sorted based on Ly49H expression (high and low: top and bottom 20%, respectively) into Trizol.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 2ng total RNA with RNA integrity numbers ranging from 8.1 to 10 underwent amplification using SMART-seq V4 Ultra Low Input RNA kit (Clonetech Cat# 63488), with 12 cycles of PCR. Subsequently, 10 ng of amplified cDNA was used to prepare Illumina HiSeq libraries using KAPA Hyper Prep DNA library preparation kit (KAPA Biosystems KK8504) using 8 cycles of PCR.

treatment_protocol: In vivo MCMV infection

tag: mouse strain

value: Spleen

value: NK cells

tag: cell subtype

tag: days post infection

value: Day 1.5

tag: infected with

value: MCMV


title: RNASeq_LY49H_LOW_04

tag: cell type


title: RNASeq_LY49H_LOW_03


title: RNASeq_LY49H_LOW_01


title: RNASeq_LY49H_HIGH_04


title: sg5_E1

tag: celltype


title: Surgery_Only_3

value: PDAC tumor

value: Male

value: Caucasian

value: Moderate

tag: lymphovascular invasion


title: RNASeq_LY49H_HIGH_02


title: RNASeq_LY49H_HIGH_01


title: 2 hr mock control, 30 min 4sU; rep1

description: purified newly transcribed RNA


title: Luc1_Ery_pCHiC

description: processed data in file: Luc1_and_Luc2_Ery_washU_text.txt

source_name: Luc inducible shRNA in EPO_induced cells

growth_protocol: Cells were grown in standard media with addition of 20 ng/ul murine recombinant SCF and 4 U/l EPO

treatment_protocol: 72 hours knock-down induction with Doxycycline

value: Hematopoietic stem and progenitors

tag: genotype


title: Luc2_Myelo_Smc1_ChIP-seq

description: ChIP antibody: Smc1 (Abcam, ab9262)

source_name: Luc inducible shRNA in IL3_induced cells

growth_protocol: Cells were grown in standard media with addition of 20 ng/ul murine recombinant SCF and 50 ng/ul IL-6

treatment_protocol: 75 hours knock-down induction with Doxycycline


title: RNASeq_LY49H_HIGH_03


title: shStag2_1_Ery_H3K27ac_ChIP-seq

description: ChIP antibody: H3K27Ac (Abcam, ab4729)

source_name: shStag2 inducible shRNA in EPO_induced cells

treatment_protocol: 74 hours knock-down induction with Doxycycline


title: Luc2_Myelo_Rad21_ChIP-seq

description: ChIP antibody: Rad21 (Abcam, ab992)

growth_protocol: Cells were grown in standard media with addition of 20 ng/ul murine recombinant SCF and 50 ng/ul IL-4

treatment_protocol: 73 hours knock-down induction with Doxycycline


title: Luc1_Myelo_Rad21_ChIP-seq

description: ChIP antibody: Rad21 (Abcam, ab992)

growth_protocol: Cells were grown in standard media with addition of 20 ng/ul murine recombinant SCF and 50 ng/ul IL-3


title: Luc1_Ery_H3K27ac_ChIP-seq

description: ChIP antibody: H3K27Ac (Abcam, ab4729)


title: Luc1_HPC_H3K27ac_ChIP-seq

description: ChIP antibody: H3K27Ac (Abcam, ab4729)

source_name: Luc inducible shRNA in HPC


title: 3094_DGC

city: San Diego

first: Jeremy

last: Rich

state: CA

address: 9500 Gilman Drive #0695

institute: University of California, San Diego

data_processing:
FASTQ files were trimmed with Trim Galore and aligned to the hg19 genome using BWA (for ChIPseq) as described in the methods.
SAM files were sorted and duplicates were removed using PicardTools as described in the methods
Bigwigs were generated from BAM files using DeepTools
Peaks were called using MACS2 as described in the methods
See methods section in manuscript for complete data processing details  sequencing analysis
Genome_build: hg19

source_name: Differentiated Glioma Cell

growth_protocol:
Cells from a primary patient derived GBM tumor model were injected intracranially into a immunocompromised NSG mouse and allowed to grow into a tumor. Cells were dissociated and passaged in vitro.
Cells were grown in neurobasal media supplemented with sodium pyruvate, B27, glutamax, EGF/FGF, and penicillin/streptomycin as described in more detail in the methods. Cells were treated with the indicated shRNA.

extract_protocol:
Chromatin immunoprecipitation was performed using EZ-ChIP chromatin immunoprecipitation kit (EMD Millipore).
ChIP libraries were then amplified with barcode using ThruPLEX DNA-seq library preparation kit (Rubicon Genomics).
1.0% agarose gel was used to select DNA fragments less than 1 kb, followed by 100 bp single-end sequencing performed with Hi-Seq 2000 (Illumina).

treatment_protocol: Differentiated Glioma Cells were generated by growing glioblastoma stem cell samples in 10% FBS for 1 week

tag: tumor type

value: Glioblastoma

tag: antibody


title: 3094_GSC

source_name: Glioma Stem Cell


title: GSC23_DGC


title: Luc1_HPC_RNA-seq (inhibitor)

data_processing:
RNA Seq pipeline: Rads were trimmed for adaptor sequence. Paired end reads were aligned to mm10 genome STAR version 2.4.0. To generate the bigwig file, we first extended each read to 200 bp along 5' end and generated count files using HTSeq.
HTSeq count files for RNA Seq
Genome_build: mm10

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) as per manufacturer’s protocol
RNA-seq libraries were prepared for sequencing using standard Illumina protocols


title: Input DNA

city: Saint Petersburg

first: Adel

last: Gazizova

address: Tikhoretsky av., 4

country: Russia

institute: Institute of Cytology RAS

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2.
Duplicates were marked with Picard.
Peaks were called using MACS2 with the following settings: -g mm; -B; -f BAMPE; -q 0.01; --SPMR.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using bedGraphToBigWig and converted to bigWig using WigToBigWig.

source_name: Embryonic stem cells

growth_protocol: Murine E14 Tg2a ESCs (BayGenomics) were passaged using 0.05% Trypsin–0.01% EDTA solution under standard feeder-free conditions on gelatinized tissue culture dishes in mES media: Knockout DMEM supplemented with 15% ES cell–qualified fetal bovine serum, 100 U/mL penicillin, 100 µg/mL streptomycin, 2 mM L-glutamine, 1× non-essential amino acids, 50 μM β-mercaptoethanol, and 500 U/mL of LIF.

extract_protocol:
Crosslinking was performed with 1% formaldehyde for 10 min at RT and stopped by adding glycine. After washings, chromatin was lysed in SDS-containing buffer (50 mM HEPESKOH, pH 7.9; 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS) with protease inhibitors cocktail (Roche) and sheared to 500-bp fragments by sonication. Sonicated chromatin was centrifuged twice at 16 000 g for 20 min, and used in immunoprecipitation experiments. For one experiment, about 10 mkg of antibodies and 8 mkL of MabSelect sepharose (GE healthcare) were taken; BSA were added to a final concentration of 1%. The precipitated chromatin was sequentially washed twice with SDS-containing buffer and with TE buffer (20mM Tris-HCl, pH 8.0; 1mM EDTA). Precipitated chromatin complexes were eluted by sequential incubation in two portions of elution buffer (50mM Tris-HCl, pH 8.0; 1mM EDTA, 1% SDS), 30 min each, at room temperature. The eluted chromatin solution was supplemented with 5 M NaCl (16 mkL per 500 mkL sample) and incubated at 65°C for 16 h on a thermoshaker for de-crosslinking. De-crosslinked chromatin was subjected to proteinase treatment (3 mkL of proteinase K and 5 mkL of 0.5M EDTA per 500 mkL sample) and incubated at 55°C for 4 h on thermoshaker. DNA was extracted with a phenol/chloroform mixture and precipitated with isopropanol. The precipitate was dissolved in TE buffer and subjected to library preparation.
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: E14 Tg2a

value: Embryonic stem cells

tag: chip antibody


title: hnRNP-K_ChIP-Seq

value: hnrnp-k (Abcam, ab70492)


title: GSC23_GSC


title: S269_LT_HSC

data_processing:
Paired end fastq files were pseudoaligned to Ensemble v82 transcritps using kallisto (VN: 0.43.1)
Transcript level expression and estimated counts were summarized to gene level using tximport Bioconductor package.
Differential expression analysis was performed with DESeq2 bioconductor package.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited output files - abundance.tsv generated by kallisto

source_name: FACS sorted cells from murine bone marrow

growth_protocol: Primary cells freshly harvested from mouse bone marrow

extract_protocol:
RNA was extracted from FACS-sorted LT-HSC cells using Qiagen RNeasy Micro Kit. RNA from purified CMP, GMP and MEP populations was extracted using Qiagen RNeasy Micro Kit.
For LT-HSCs, SMART-Seq v4 Ultra Low Input RNA Kit was used.  For CMP, GMP and MEP populations TruSeq RNA Sample Preparation Kit (Illumina) was used for library preparation.

value: murine hematopoietic stem cells

value: wild type


title: S270_LT_HSC


title: S245_LT_HSC


title: S244_LT_HSC


title: Luc2_Ery_pCHiC

tag: cell line


title: 309-MEP

value: murine myeloid precursors


title: T47D parental treated with E2 for 16 hours

city: San Antonio

first: Yufan

last: Zhou

state: TX

address: 7703 Floyd Curl Dr

institute: UT health Science Center at San Antonio

description: treated with E2 for 16 hours

data_processing:
Library strategy: TCC
For TCC, raw fastq is mapped to human genome, filtered and then generated first eigenvectors with HiCLib python package (Imakaev et al. 2012).
Genome_build: HG19
Supplementary_files_format_and_content: T47D_Compartment_TIME0_100K.bed, T47D_Compartment_TIME1_100K.bed, T47D_Compartment_TIME4_100K.bed, T47D_Compartment_TIME16_100K.bed, T47D_Compartment_TIME24_100K.bed, T47D_Compartment_TAMR_100K.bed are files of first eigenvectors generated by HiCLib

growth_protocol: Routine cell media for T47D parental and T47D Tamoxifen Resistant cell lines, respectively.

extract_protocol:
Extraction of cell nucleus and DNA were performed as described (Kalhor et al. 2012).
TCC was performed as described (Kalhor et al. 2012).

treatment_protocol: T47D parental cells were hormone-starved for 72hrs followed by the addition of 100nM β-Estradiol at 1hr, 4hr, 16hr and 24hr.

tag: cell types

value: immortalized breast epithelial cell line

tag: agent

tag: time point

value: 16 hours

tag: analysis

value: TCC


title: Luc1_Myelo_Smc1_ChIP-seq

description: ChIP antibody: Smc1 (Abcam, ab9262)

growth_protocol: Cells were grown in standard media with addition of 20 ng/ul murine recombinant SCF and 50 ng/ul IL-5


title: T47D parental treated with E2 for 4 hours

description: treated with E2 for 4 hours

value: 4 hours


title: T47D parental treated with E2 for 1 hour

description: treated with E2 for 1 hour

value: 1 hour


title: Luc1_Ery_RNA-seq

source_name: Luc inducible shRNA in erythroid cells

treatment_protocol: 72 hours knock-down induction with Doxycycline, followed by EPO-mediated differentiation (4 U/l EPO, 20 ng/ul SCF) for 48 hours


title: 309-GMP


title: 309-CMP


title: RNAseq_MCF7L_TamR_R3

data_processing:
For TCC, raw fastq is mapped to human genome, filtered and then generated compartment A/B with HiCLib python package (Imakaev et al. 2012).
For ChIP-seq, after raw fastq is mapped to human genome by Bowtie2, the peaks are called with MACS (Zhang et al. 2008) or the emission/transition probabilities are generated by ChromHMM (Ernst et al. 2012).
For RNA-seq, raw fastq is mapped to human genome by TopHat using default parameters, Cufflinks produces assembled transfrags for each replicate, Cuffmerge merges the assembly files, CuffDiff is used to detect differentially expressed genes between each two of cell population (Trapnell et al. 2012).
Genome_build: HG19
Supplementary_files_format_and_content: Compartment_TIME0_100K.bed, Compartment_TIME1_100K.bed, Compartment_TIME4_100K.bed, Compartment_TIME16_100K.bed, Compartment_TIME24_100K.bed, Compartment_TAMR_100K.bed are files of compartment A/B generated by HiCLib; MACS_peaks_TIME0_ER1.bed, MACS_peaks_TIME1_ER1.bed, MACS_peaks_TIME4_ER1.bed, MACS_peaks_TIME16_ER1.bed, MACS_peaks_TIME24_ER1.bed, MACS_peaks_TAMR_ER1.bed are ER alpha peaks called by MACS; MACS_peaks_TIME0_CTCF.bed, MACS_peaks_TIME1_CTCF.bed, MACS_peaks_TIME4_CTCF.bed, MACS_peaks_TIME16_CTCF.bed, MACS_peaks_TIME24_CTCF.bed, MACS_peaks_TAMR_CTCF.bed are CTCF peaks called by MACS; chromhmm_emission_10.txt, chromhmm_transitions_10.txt are generated by ChromHMM; DIFF_EXP_TAMR_GENE.txt is the differentally expressed gene produced by CuffDiff. C1 is MCF7L_Parental and C2 is RNAseq_MCF7L_TamR

source_name: MCF7L Tamoxifen Resistant

growth_protocol: Routine cell media for MCF7L parental and MCF7L Tamoxifen Resistant cell lines, respectively.

extract_protocol:
RNA extracted using Quick-RNA MiniPrep Kit from ZYMO Research
TCC was performed as described (Kalhor et al. 2012). ChIP-seq and RNA-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MCF7L-P cells were hormone-starved for 72hrs followed by the addition of 100nM β-Estradiol at 1hr, 4hr, 16hr and 24hr.

tag: replicate

value: Replicate 3


title: RNAseq_MCF7L_TamR_R2

value: Replicate 2


title: 308-MEP


title: T47D parental untreated

description: untreated

value: untreated


title: RNAseq_MCF7L_TamR

value: Replicate 1


title: 308-CMP


title: T47D TamR

source_name: T47D TamR

value: T47D TamR


title: ChIPseq_TAMR_CTCF

value: CTCF


title: 305-MEP


title: 305-GMP


title: 308-GMP


title: ChIPseq_TAMR_ER1

value: ERα


title: ChIPseq_TAMR_H3K27me3

description:
chromhmm_emission_10.txt
chromhmm_transitions_10.txt


title: T47D parental treated with E2 for 24 hours

description: treated with E2 for 24 hours

value: 24 hours


title: 304-MEP


title: 304-GMP


title: ChIPseq_TAMR_H3K9me3


title: 305-CMP


title: ChIPseq_TAMR_H3K4me1


title: ChIPseq_TAMR_H3K27ac


title: 304-CMP


title: Luc2_Ery_H3K27ac_ChIP-seq

description: ChIP antibody: H3K27Ac (Abcam, ab4729)

value: Hematopoietic stem and progenitors


title: 301-MEP


title: ChIPseq_TAMR_H3K4me3


title: 301-GMP


title: ChIPseq_TAMR_INPUT


title: 301-CMP


title: 300-MEP


title: RNAseq_MCF7L_Parental_R3

source_name: MCF7L parental


title: TCC_TAMR

data_processing:
Library strategy: TCC
For TCC, raw fastq is mapped to human genome, filtered and then generated compartment A/B with HiCLib python package (Imakaev et al. 2012).
For ChIP-seq, after raw fastq is mapped to human genome by Bowtie2, the peaks are called with MACS (Zhang et al. 2008) or the emission/transition probabilities are generated by ChromHMM (Ernst et al. 2012).
For RNA-seq, raw fastq is mapped to human genome by TopHat using default parameters, Cufflinks produces assembled transfrags for each replicate, Cuffmerge merges the assembly files, CuffDiff is used to detect differentially expressed genes between each two of cell population (Trapnell et al. 2012).
Genome_build: HG19
Supplementary_files_format_and_content: Compartment_TIME0_100K.bed, Compartment_TIME1_100K.bed, Compartment_TIME4_100K.bed, Compartment_TIME16_100K.bed, Compartment_TIME24_100K.bed, Compartment_TAMR_100K.bed are files of compartment A/B generated by HiCLib; MACS_peaks_TIME0_ER1.bed, MACS_peaks_TIME1_ER1.bed, MACS_peaks_TIME4_ER1.bed, MACS_peaks_TIME16_ER1.bed, MACS_peaks_TIME24_ER1.bed, MACS_peaks_TAMR_ER1.bed are ER alpha peaks called by MACS; MACS_peaks_TIME0_CTCF.bed, MACS_peaks_TIME1_CTCF.bed, MACS_peaks_TIME4_CTCF.bed, MACS_peaks_TIME16_CTCF.bed, MACS_peaks_TIME24_CTCF.bed, MACS_peaks_TAMR_CTCF.bed are CTCF peaks called by MACS; chromhmm_emission_10.txt, chromhmm_transitions_10.txt are generated by ChromHMM; DIFF_EXP_TAMR_GENE.txt is the differentally expressed gene produced by CuffDiff. C1 is MCF7L_Parental and C2 is RNAseq_MCF7L_TamR


title: 300-GMP


title: RNAseq_MCF7L_Parental


title: RNAseq_MCF7L_Parental_R2


title: 300-CMP


title: ChIPseq_TIME24_H3K9me3

value: treated with E2


title: WT_H3K4me3_E2

data_processing:
50 bp single-end reads were aligned to the mm10 reference genome using the bowtie aligner
PCR duplicates were marked were using picard tools
Peaks were identified using MACS2 with FDR cut-off of 0.01, while simultaneously generating bedgraph files in Reads Per Million scale.
Input signal was subtracted from ChIP-seq signal and bedgraph files were converted to binary bigwig files.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files representing input subtracted signal normalized to per million reads

source_name: bone marrow cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Immunoprecipitated DNA was extracted using QIAquick PCR Purification Kit (Qiagen) and DNA quality was assessed on 2100 Bioanalyzer. Following PCR amplification and size selection (100-300 bp), libraries were sequenced on HiSeq4000.

value: Lin- BM cells

value: H3K4me3 (Merck Millipore; 04-745)


title: WT_Input_E1


title: ChIPseq_TIME24_ER1

value: immortalized breast epithelial cell line


title: ChIPseq_TIME24_CTCF


title: ChIPseq_TIME24_H3K27me3


title: ChIPseq_TIME24_H3K4me1


title: KO_Input_E2


title: WT_H3K27Ac_E1

value: H3K27ac (Abcam; ab4729)


title: ChIPseq_TIME24_H3K4me3


title: WT_H3K27Ac_E2


title: KO_Input_E1


title: ChIPseq_TIME24_INPUT


title: KO_H3K27Ac_E2


title: ChIPseq_TIME16_CTCF

value: 16 hours


title: ChIPseq_TIME16_H3K9me3


title: ChIPseq_TIME24_H3K27ac


title: KO_H3K4me3_E2


title: ChIPseq_TIME16_ER1


title: ChIPseq_TIME16_H3K4me1


title: 396-KO

data_processing:
Paired end 50 bp reads were aligned to the mm10 reference genome using Bowtie2
PCR duplicate reads were removed using Picard MarkDuplicates
The reads were then filtered using samtools for a minimum mapping quality of 10 and only properly paired reads were used. Additionally, any reads aligning to the mitochondrial chromosome were removed.
Peaks were called subsequently using macs2 while simultaneously generating bedgraph files in Reads Per Million scale
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files representing signal normalized to per million reads

extract_protocol:
50,000 sorted cells were washed with cold PBS and suspended in lysis buffer for 10-15 min on ice.
DNA was purified using MinElute PCR Purification Kit (Qiagen). Transposed DNA was amplified using NEB Next High-Fidelity 2X PCR Master Mix and libraries were sequenced on HiSeq 4000. .

value: Lin-Kit+ BM cells


title: WT_Input_E2


title: WT_H3K4me3_E1


title: KO_H3K4me3_E1


title: 391-WT

value: wild type


title: ChIPseq_TIME16_H3K4me3


title: 390-KO


title: ChIPseq_TIME16_INPUT


title: 394-WT


title: 383-KO


title: 382-WT


title: ChIPseq_TIME4_CTCF

value: 4 hours


title: ChIPseq_TIME4_ER1


title: KO_H3K27Ac_E1


title: Donor 3, 28z CAR T cells, after co-culture

city: Cambridge

first: Jian

last: Ding

state: MA

address: 100 Binney Street, Suite 710

institute: TCR2 Therapeutics

description:
3G
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.

hyb_protocol: One microliter of the cell lysate was added to the Gene Expression Assay - Human Immunology V2 CodeSet in hybridization buffer an incubated at 65ºC for 16 hours. The hybrid was immobilized on to the cartridge by Prep Station.

scan_protocol: The prepared cartridges were scanned by MAX System Digital Analyzer, in approximately 2.5 hours per cartridge.

data_processing: The raw data (RCC files) were imported and analyzed in the NanoString data analysis tool nSolver 3.0. The data were normalized by positive controls normalization (based on the mean of POS control probes for each assay) and RNA content normalization (based on the geometric mean of housekeeping genes in the CodeSet).

label: NanoString

source_name: Peripheral blood mononuclear cells

label_protocol: Standard NanoString protocol.

growth_protocol: T cells were activated with Dynabeads (ThermoFisher) and human IL-2 (Peprotech, 300IU/mL) for 24 hours. The cells were then transduced with lentivirus encoding CD19-specific TRuC or CARs. The cells were expanded for 10 days.

extract_protocol: The T cell pellets were resuspended in 20 uL of RLT buffer provided by NanoString. The lysate was snap frozen on dry ice and sent to NanoString.

treatment_protocol: T cells were pelleted before co-culture with Raji cells, or at 4 hours after co-culture with Raji cells at 1:1 ratio. Raji cells were depleted from the co-culture.

value: T cells

tag: t cell transduction status

value: CD19-specific CD28z CAR

tag: t cell stimulation status

tag: donor

tag: disease status

value: Healthy


title: Donor 3, BBz CAR T cells, after co-culture

description:
3H
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.

tag: cell type

value: CD19-specific 41BBz CAR

value: 4 hours after co-culture with Raji cells


title: ChIPseq_TIME16_H3K27me3


title: P50_Depil5D

city: New York City

first: Etienne

last: Wang

state: NY

address: 1150 St Nicholas Avenue, Room 303

department: Dermatology

institute: Columbia University

data_processing:
cDNA was amplified and sequenced on an Illumina HiSeq 4000.
Cells with <500 or >2000 genes were excluded from analysis, as were cells with >105 UMIs (reflecting doublets) or mitochondrial genes >0.8% (reflecting dying cells).
Highly variable genes were identified based on their average expression and variance, and used for clustering analysis.
Principle component analysis (PCA) on variable genes was performed by JackStraw analysis to identify significant PCs (p<0.05), and t-Distributed Stochastic Neighbor Embedding (t-SNE) plots were made based on the first 28 PCs for all immune cells at all timepoints, and 10 PCs for just the macrophages at P45.
Further analysis and presentation of data was performed with the Seurat R package
Genome_build: mm10

source_name: CD45+ dermal immune cells

extract_protocol:
Dermal tissue was dissected, isolated and digested to yield a single-cell suspension. Cells were sorted for CD45+ live cells and sent for single-cell RNA sequencing on the 10X Genomics platform.
Individual cells are captured in droplets for lysis and reverse transcription in parallel. The droplets contain primers for cell- and and molecule-specific barcoding of cDNA. The resulting pooled, 3'-end libraries are typically sequenced in one lane of an Illumina HiSeq 4000.

value: CD45+ dermal immune cells


title: ChIPseq_TIME16_H3K27ac


title: ChIPseq_TIME4_H3K9me3


title: P80


title: Donor 3, TRuC T cells, after co-culture

description:
3F
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.

value: CD19-specific e-TRuC


title: Donor 3, non-transduced T cells, after co-culture

description:
3E
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.

value: Non-transduced


title: P63


title: Donor 3, BBz CAR T cells, before co-culture

description:
3D
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.

value: Before co-culture with Raji cells


title: ChIPseq_TIME4_H3K27me3

value: treated with E2


title: Donor 3, non-transduced T cells, before co-culture

description:
3A
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.


title: Donor 3, TRuC T cells, before co-culture

description:
3B
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.


title: P50


title: Donor 3, 28z CAR T cells, before co-culture

description:
3C
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.


title: ChIPseq_TIME4_H3K4me1


title: ChIPseq_TIME4_H3K4me3


title: ChIPseq_TIME4_H3K27ac


title: Donor 2, TRuC T cells, after co-culture

description:
2F
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.


title: Donor 2, BBz CAR T cells, after co-culture

description:
2H
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.


title: P45


title: Donor 2, BBz CAR T cells, before co-culture

description:
2D
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.


title: Donor 2, 28z CAR T cells, after co-culture

description:
2G
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.


title: Donor 2, non-transduced T cells, after co-culture

description:
2E
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.


title: Donor 2, 28z CAR T cells, before co-culture

description:
2C
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.


title: ChIPseq_TIME4_INPUT


title: WT2c

description: mRNA expression

data_processing:
Probe set expression levels were background corrected and normalized using Robust Multi-array Average (RMA). Probe sets corresponding to noncoding transcripts were filtered out.
Differentially expressed genes were defined based on >2 fold expression change and P < 0.05 determined using unpaired student’s t-test.

source_name: Spleen

extract_protocol: mRNA was extracted from sorted cells using the PicoPure RNA isolation kit as per manufacturer's instructions. Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: LDL-R KO Mouse


title: Donor 2, TRuC T cells, before co-culture

description:
2B
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.


title: ChIPseq_TIME1_CTCF

value: immortalized breast epithelial cell line

value: CTCF

value: 1 hour


title: Donor 2, non-transduced T cells, before co-culture

description:
2A
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.


title: ChIPseq_TIME1_H3K9me3

description:
chromhmm_emission_10.txt
chromhmm_transitions_10.txt


title: Donor 1, 28z CAR T cells, after co-culture

description:
1G
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.


title: Donor 1, TRuC T cells, after co-culture

description:
1F
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.


title: Donor 1, non-transduced T cells, after co-culture

description:
1E
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.


title: Donor 1, BBz CAR T cells, after co-culture

description:
1H
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.


title: ChIPseq_TIME1_H3K27me3


title: Donor 1, BBz CAR T cells, before co-culture

description:
1D
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.


title: dek15_rep3

city: Beijing

first: Yonghui

last: He

address: No.2 Yuanmingyuan West Rd, Haidian District, Beijing 100193, China

institute: China Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Clean reads were obtained by excluding poly-N, adapter polluted, and low-quality reads from raw reads using fqtools_plus (Annoroad). Then, clean reads were mapped to B73 RefGen_v4.37 using TopHat (version:2.0.13).
The unique reads were normalized as fragments per kilobase of exon per million fragments mapped (FPKM) using Cufflinks (version: 2.2.1) and cuffdiff2 (version: 2.2.1).
Genome_build: Ensembl plants release-37 zea_mays
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Zea mays

source_name: kernel

extract_protocol:
Total RNA was extracted from every biological sample using RNAprep pure plant Kit (Tiangen, R6102, Beijing, China) following the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols. Barcode for WT_rep1: TCACCTCA, for WT_rep2: GCGACTCC, for WT_rep3: GTTAAGCC, for dek15_rep1: ACCTTGCA, for dek15_rep2: TACAGGCC, for dek15_rep3: TAATTACC.

tag: tissue

value: kernel

tag: age

value: 15 DAP

value: dek15 homozygous mutant


title: dek15_rep2

tag: genotype


title: dek15_rep1


title: Donor 1, non-transduced T cells, before co-culture

description:
1A
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.

value: T cells


title: Donor 1, TRuC T cells, before co-culture

description:
1B
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.


title: ChIPseq_TIME1_H3K27ac


title: WT_rep3

value: Wild-type


title: WT_rep2


title: ChIPseq_TIME1_H3K4me3


title: ChIPseq_TIME1_ER1

value: ERα


title: WT_rep1


title: High mutant cells, biological rep3 [MH_3]

city: Roanoke

first: Sarika

last: Srivastava

state: Virginia

address: 2 Riverside Circle

department: Fralin Biomedical Research Institute

institute: Virginia Tech Carilion

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C onGeneChip HG U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed using R/Bioconductor software and normalized using the robust multi-chip average (RMA) method. Statistical significance was analyzed by a two-tailed Student's t-test (p < 0.05).

source_name: Osteosarcoma-derived cybrid cells carrying high level of m.3243A>G mutation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured in DMEM high glucose media supplemented with 1mM pyruvate, 50 mg/ml uridine, and 10% fetal bovine serum, and incubated in a 5% CO2 incubator at 370C.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Invitrogen). RNA cleanup was performed using RNeasy Mini Kit spin columns from Qiagen.

treatment_protocol: No treatment was applied.

value: osteosarcoma cells

tag: genotype/variation

value: cybrid cells harboring 100% mutant mtDNA load


title: dek42-ref_Rep3

first: Yi

last: Zuo

address: No. 50 Road Zhanghua

institute: Beijing Academy of Agriculture and Forestry Science

data_processing:
Illumina Casava1.7 was used for basecalling.
Sequenced reads were trimmed using fastx (version:0.0.13), then mapped to B73 RefGen_v4.37 using TopHat (version:2.1.0).
The unique reads were normalized as Fragments Per Kilobase Million (FPKM) using Cufflinks (version:2.2.1).
Genome_build: Ensembl plants release-37 zea_mays
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

extract_protocol:
RNA was extracted from pooled kernels at 15 DAP with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.
RNA libraries were prepared for sequencing using standard Illumina protocols. Barcode for WT_Rep1: CATCATAA , for WT_Rep2: CACATGAA , for WT_Rep3: ACACGCGG , for dek42-ref_Rep1: ACCTTGCA, for dek42-ref_Rep2: ATACTCCA, for dek42-ref_Rep3: GTTCGACA.

value: dek42 mutant


title: Low mutant cells, biological rep3 [ML_3]

source_name: Osteosarcoma-derived cybrid cells carrying low level of m.3243A>G mutation

value: cybrid cells harboring 33% mutant mtDNA load


title: Low mutant cells, biological rep2 [ML_2]


title: ChIPseq_TIME1_INPUT


title: Low mutant cells, biological rep1 [ML_1]


title: High mutant cells, biological rep2 [MH_2]


title: High mutant cells, biological rep4 [MH_4]


title: dek42-ref_Rep2


title: dek42-ref_Rep1


title: WT_Rep3


title: ChIPseq_TIME0_CTCF

value: untreated


title: ChIPseq_TIME1_H3K4me1


title: WT_Rep2


title: ChIPseq_TIME0_H3K9me3


title: High mutant cells, biological rep1 [MH_1]


title: Donor 1, 28z CAR T cells, before co-culture

description:
1C
T cells were activated and transduced to express TRuC or CARs. After 10 days of expansion, T cells were co-cultured with Raji cells for 4 hours at 1:1 ratio. Raji cells were depleted from the co-culture with CD19-microbeads (Miltenyi). Purified T cells were pelleted and submitted to NanoString.

value: CD19-specific CD28z CAR

value: Before co-culture with Raji cells

value: Healthy


title: ChIPseq_TIME0_ER1

value: immortalized breast epithelial cell line


title: ChIPseq_TIME0_H3K27me3


title: Low mutant cells, biological rep4 [ML_4]


title: ChIPseq_TIME0_H3K4me1


title: NSC shRNA screen (day 12)

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

data_processing:
Sequencing reads were scanned for occurences of perfect matches of 28 bp-long sequences containing shRNA barcodes.
Genome_build: hg38
Supplementary_files_format_and_content: The bigWig files were generated by makeMultiWigHub.pl script from the HOMER package. The peaks file contains a list of genomic coordinates of putative binding sites with corresponding fold change scores and p-values, as reported by findPeaks tool from the HOMER package. Abundance files report transcript expression levels, as reported by kallisto. The shRNA count files are in the tsv format, where each row represents abundance of a single shRNA, and with four columns providing the shRNA target gene symbol, its RefSeq ID, the shRNA barcode ID and the total sequencing read count. The complete list of shRNA barcodes and their sequences is provided in a separate file (shRNA_barcodes.txt.gz)

source_name: Neural stem cells

growth_protocol: PB samples were obtained from G-CSF treated donors. Whole blood was lysed with ACK lysis buffer (Invitrogen), and enriched for CD34 by the CD34 MicroBead Kit (Miltenyi) according to the manufacturer’s instructions. Cells were cultivated in StemSpan SFEM (STEMCELL) medium, supplemented with 1 uM UM729 (STEMCELL), 100 ng/ml FLT3, 100 ng/ml SCF, 50 ng/ml TPO (all R&D Systems), 100 U/ml Penicillin, 100 U/Streptomycin, and 2 mM L-glutamine (both Invitrogen). | iPSCs were cultivated on matrigel coated dishes (Corning) in mTeSR1 supplemented with 100 U/ml Penicillin and 100 U/Streptomycin (both Invitrogen). | NSCs were cultured as previously described (Reinhardt et al., 2013).

extract_protocol:
Cells carrying shRNAs were sorted according to the given sorting criteria and DNA fragments containing the shRNA barcodes were PCR amplified from genomic DNA.
Libraries were prepared for sequencing using standard Illumina protocols for PCR amplicons.

treatment_protocol: Cells were infected with the custom-made pooled shRNA library at an MOI of 0.1.

value: CD34+ HSPC-derived iPSC-differentiated NSC

tag: passage

tag: sorting criteria

value: RFP (shRNA reporter)


title: NSC shRNA screen (day 22)


title: Wild type cells, biological rep3 [WT_3]

source_name: 143B wild type osteosarcoma cells

tag: cell line

value: wild type cells


title: WT_Rep1

value: kernel

value: 15 DAP


title: Wild type cells, biological rep2 [WT_2]


title: HSPC CD34- shRNA screen (day 22)

source_name: Hematopoietic stem and progenitors

treatment_protocol: Cells were infected with the custom-made pooled shRNA library at an MOI of 7.5.

value: CD34- enriched peripheral blood cells

value: primary cells

value: CD34- (BD 340668) and RFP (shRNA reporter)


title: Wild type cells, biological rep1 [WT_1]

value: osteosarcoma cells


title: ChIPseq_TIME0_H3K4me3

tag: cell types

tag: chip antibody


title: Wild type cells, biological rep4 [WT_4]


title: HSPC CD34- shRNA screen (day 12)


title: ChIPseq_TIME0_INPUT

tag: agent


title: HSPC CD34+ shRNA screen (day 22)

value: CD34+ enriched peripheral blood cells

value: CD34+ (BD 340668) and RFP (shRNA reporter)


title: TCC_TIME24

value: treated with E2

tag: time point

value: 24 hours


title: TCC_TIME16

value: 16 hours


title: ChIPseq_TIME0_H3K27ac

value: untreated


title: NSC shRNA screen (day 2)


title: TCC_TIME4

value: 4 hours


title: HSPC CD34+ shRNA screen (day 2)


title: NSC RNA-Seq

data_processing:
Expression levels of individual transcripts were estimated by kallisto (ver. 0.42.5) using Ensembl transcriptome (release 79) as a reference, with sequence bias correction turned on.
Genome_build: hg38
Supplementary_files_format_and_content: The bigWig files were generated by makeMultiWigHub.pl script from the HOMER package. The peaks file contains a list of genomic coordinates of putative binding sites with corresponding fold change scores and p-values, as reported by findPeaks tool from the HOMER package. Abundance files report transcript expression levels, as reported by kallisto. The shRNA count files are in the tsv format, where each row represents abundance of a single shRNA, and with four columns providing the shRNA target gene symbol, its RefSeq ID, the shRNA barcode ID and the total sequencing read count. The complete list of shRNA barcodes and their sequences is provided in a separate file (shRNA_barcodes.txt.gz)

extract_protocol:
For RNA extraction, typically 1-2 million cells were pooled down. Total RNA extraction was performed with the RNeasy Mini kit (Qiagen) according to manufacturer’s instructions. To avoid contamination with genomic DNA an on-column DNase I digest was included as part of the RNase Mini kit protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: growth conditions

value: Adherent, monolayer


title: HSPC CD34+ shRNA screen (day 12)


title: TCC_TIME1

value: immortalized breast epithelial cell line

value: 1 hour


title: HSPC CD34+ day 22 RNA-Seq

value: Suspension


title: iPSC RNA-Seq

source_name: Induced pluripotent stem cells

value: CD34+ HSPC-derived iPSC

value: Adherent


title: TCC_TIME0


title: HSPC CD34+ day 12 RNA-Seq


title: PTE_rep3

city: Oak Ridge

first: Xiaohan

last: Yang

state: TN

address: 1 Bethel Valley Road

department: Biosciences Division

institute: Oak Ridge National Laboratory

data_processing:
Sequenced reads were trimmed for low-quality regions and adaptor sequences using Trimmomatic v0.35 (Bolger et al. 2014) to remove trailing sequences below a phred quality score of 20 and to drop reads which are less than 20 bases long
The trimmed sequencing reads from P. trichocarpa and P. deltoides were mapped to the P. trichocarpa genome v3.0 and P. deltoides WV94 v2.1 (https://phytozome.jgi.doe.gov), respectively, using TopHat2 (Kim et al. 2013).
Novel genes were assembled and transcript abundance in RPKM (Reads Per Kilobase of transcript per Million mapped reads) was estimated using Cufflinks (Trapnell et al. 2012).
Analysis of differential gene expression was performed using Cuffdiff (Trapnell et al. 2012)
For miRNA analysis, the small RNA sequencing reads were filtered to remove adaptors and low-quality bases by FastQC (Andrews 2010). The clean reads were further selected by length between 18-30 bp for miRNA identification process. The miRDP1.3 package (Yang and Li 2011) was used for miRNA precursor prediction with size set at 250 nt. To validate the miRNAs, the secondary structure and reads distribution were evaluated to generate the final set of miRNAs (Yin et al. 2016). The precursors and mature sequences were aligned with the searching toolbox in PNRD database for annotation of miRNAs (Yi et al. 2015). To quantify the abundance of miRNA, transcripts per million value was defined as ‘counts of read mapped to miRNA*1000000’/‘reads mapped to reference genome’ (Fahlgren et al. 2007)
Genome_build: Populus trichocarpa genome v3.0 and Populus deltoides WV94 v2.1 (https://phytozome.jgi.doe.gov)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample; the fasta files include the sequences of differentially-expressed transcripts
isoform_exp_diff_sig_PD.txt: Abundance measurements of differentially-expressed transcripts
isoform_exp_diff_sig_PT.txt: Abundance measurements of differentially-expressed transcripts
isoform_exp_diff_sig_transcript_PD.fa: Sequence of differentially-expressed transcripts
isoform_exp_diff_sig_transcript_PT.fa: Sequence of differentially-expressed transcripts
miRNA_EXP_diff_sig_PD.fa: Sequence of differentially-expressed miRNAs
miRNA_EXP_diff_sig_PD.txt: Abundance measurements of differentially-expressed miRNAs
miRNA_EXP_diff_sig_PT.fa: Sequence of differentially-expressed miRNAs
miRNA_EXP_diff_sig_PT.txt: Abundance measurements of differentially-expressed miRNAs

organism: Populus trichocarpa

source_name: Root

growth_protocol: Inoculated cuttings were grown for three months post inoculation in a greenhouse at 15–28˚C, 12-h photoperiod at INRA-Nancy, France during summer

extract_protocol:
Total RNA was extracted from the root system of three of the eight replicates per genotype per treatment by combining a CTAB extraction method and the Spectrum™ Total Plant RNA extraction kit (Sigma) as reported in Bryan et al. (2016)
Prior to synthesizing sequencing libraries, RNA templates were quantified using a Nanodrop Spectrophotometer (Thermo Scientific) and RNA quality was determined using BioRad Experion™. Samples with a 260/280 reading between 2.0 and 2.2 and a RIN >7 were determined to be of high enough quality and the high-quality RNA samples were used for sRNA-sequencing library preparation with an Illumina TruSeq small RNA sample prep kit (Illumina, CA, USA). As specified in the Illumina protocol, small RNA fragments were selected after PCR amplification by gel purification to capture RNA approximately 20bp-170bp in length.  The Illumina TruSeq small RNA library prep workflow is considered to be stranded because adapters are ligated directionally, facilitating maintenance of strand information during analysis.

treatment_protocol: The rooted cuttings of Populus trichocarpa (genotype 101-74) and Populus deltoides (genotype 73028-62) were individually inoculated with a 1/9 (v/v) mixture of Laccaria bicolor inoculum and calcined clay (Oil Dri US Special, Damolin, Denmark). Eight replicates per genotype and treatment were carried out. L. bicolor S238N inoculum was produced by growing mycelium on an autoclaved peat-vermiculite nutrient mixture in 1-L glass jars for 2 months in the dark at 25°C and kept at 4°C before use (Duponnois and Garbaye 1991). Rhizophagus irregularis inoculum consisted of spores (200 spores per litter of calcinate clay).

value: Root

tag: treatment

value: Laccaria bicolor


title: genomic DNA from oral tissue 24

type: genomic

city: Shillong

first: Srimoyee

last: Ghosh

state: Meghalaya

address: Umshing-Mawkynroh

department: Zoology

country: India

institute: North Eastern Hill University

description:
Sample 24
Normal oral tissue sample.

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

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

data_processing: BeadStudio software v3.2.

label: Cy5 and Cy3

source_name: Oral tissue, normal

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from oral tissue samples using Qiagen DNeasy Kit according to standard instructions.

value: Oral tissue

tag: disease state

value: normal

tag: gender

value: Female


title: OHC-TRECK DT(+)

city: Tokyo

first: Kunie

last: Matsuoka

address: 2-1-6 Kami-kitazawa

institute: Tokyo Metropolitan Institute of Medical Science

description: Gene expression in cochleae from DT-administered OHC-TRECK mice.

hyb_protocol: 1.65 µg of Cy3-labeled cRNA was fragmented and hybridized to Agilent Mouse Gene Expression v2 Microarray (G4846A) using Agilent Gene Expression Hybridization Kit. Hybridization was performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 5µm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters.

source_name: Cochleae, OHC-TRECK, DT(+)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng of total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: Total RNA was isolated from the cochlea using the PureLink RNA Mini Kit (Thermo Fisher Scientific, Grand Island, NY, USA) according to the manufacturer’s protocol. RNA was quantified using a NanoDrop-LITE spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Mice were administered with 50 μg/kg bodyweight of diphtheria toxin 7 days before dissection of cochleae.

tag: strain/background

value: OHC-TRECK

tag: Sex

value: pooled male and female

value: Cochlea

value: Diphtheria toxin (DT)


title: PTE_rep1

tag: tissue


title: PTE_rep2


title: genomic DNA from oral tissue 21

description:
Sample 21
Cancer oral tissue sample.

source_name: Oral tissue, cancer

value: cancer


title: Input ChIP-Seq (NSC)

data_processing:
Alignment of filtered reads to the human genome (hg38 assembly) was performed with Bowtie 2, using the default parameters.
The peak calling and generation of tag density files was performed using tools from the HOMER package.
Genome_build: hg38
Supplementary_files_format_and_content: The bigWig files were generated by makeMultiWigHub.pl script from the HOMER package. The peaks file contains a list of genomic coordinates of putative binding sites with corresponding fold change scores and p-values, as reported by findPeaks tool from the HOMER package. Abundance files report transcript expression levels, as reported by kallisto. The shRNA count files are in the tsv format, where each row represents abundance of a single shRNA, and with four columns providing the shRNA target gene symbol, its RefSeq ID, the shRNA barcode ID and the total sequencing read count. The complete list of shRNA barcodes and their sequences is provided in a separate file (shRNA_barcodes.txt.gz)

extract_protocol:
Total genomic DNA was fragmented to 200-500bp with a Covaris water-bath sonicator. DNA was purified and eluted using a PCR purification kit (Qiagen) in 30 μl HPLC-grade water.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: CD34+ HSPC-derived iPSC-differentiated NSC


title: genomic DNA from oral tissue 22

description:
Sample 22
Normal oral tissue sample.


title: PTC_rep3

tag: genotype

value: Control


title: SMARCA4 ChIP-Seq (NSC)

extract_protocol:
Chromatin immunoprecipitation was done as described previously (Ding et al., 2015) using 20 μl of ChIP-grade SMARCA4 (abcam 110641). DNA was fragmented to 200-500bp with a Covaris water-bath sonicator before the IP. DNA was purified and eluted using a PCR purification kit (Qiagen) in 30 μl HPLC-grade water.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols.

value: SMARCA4 ChIP grade (abcam 110641)


title: genomic DNA from oral tissue 9

description:
Sample 9
Cancer oral tissue sample.


title: genomic DNA from oral tissue 15

description:
Sample 15
Cancer oral tissue sample.


title: OHC-TRECK DT(-)

description: Gene expression in cochleae from OHC-TRECK mice.

source_name: Cochleae, OHC-TRECK, DT(-)

tag: genotype/variation

tag: age


title: genomic DNA from oral tissue 16

description:
Sample 16
Normal oral tissue sample.


title: genomic DNA from oral tissue 23

description:
Sample 23
Cancer oral tissue sample.


title: genomic DNA from oral tissue 18

description:
Sample 18
Normal oral tissue sample.


title: genomic DNA from oral tissue 13

description:
Sample 13
Cancer oral tissue sample.


title: genomic DNA from oral tissue 14

description:
Sample 14
Normal oral tissue sample.


title: genomic DNA from oral tissue 17

description:
Sample 17
Cancer oral tissue sample.


title: genomic DNA from oral tissue 19

description:
Sample 19
Cancer oral tissue sample.


title: genomic DNA from oral tissue 11

description:
Sample 11
Cancer oral tissue sample.


title: PTA_rep3

value: Rhizophagus irregularis


title: PTC_rep1


title: S21_PB

city: Boston

first: Jarrett

last: Morrow

address: 181 Longwood Ave.

department: Channing Division of Network Medicine

institute: Brigham and Women's Hospital

data_processing:
The quality control pipeline included FastQC and RNA-SeQC. Adapter trimming was performed using Skewer.
STAR aligner version 2.4.0h was used to map the reads to the GRCH38 genome reference.
The Python framework HTSeq was used to produce gene-level counts with the Ensembl version 81 gene annotation.
The samples retained for analysis each had more than 7 million total reads, and greater than 70% of reads mapped to the reference genome, with less than 10% of R1 reads in the sense orientation.
Only data for genes mapped to autosomal chromosomes were retained, leaving counts for 54,243 of the 65,988 transcripts available for analysis.
Genome_build: GRCH38
Supplementary_files_format_and_content: Gene-level counts

source_name: peripheral blood

extract_protocol:
Whole blood was collected in a PaxGene RNA tube on the day of bronchoscopy.
Total RNA was extracted using the AllPrep kit (Qiagen, Valenica, CA). RNA quality was assessed on a BioAnalyzer (Agilent, Santa Clara, CA). Extracted RNA samples with RNA integrity number (RIN) greater than six and a concentration greater than or equal to 20 μg/ul were sequenced.
Libraries were QCed by quantification with picogreen, size analysis on an Agilent Bioanalyzer (Agilent, Santa Clara, CA) and qPCR quantitation against a standard curve. Paired end reads with nominal 75 bp length were generated on an Illumina HiSeq 2500 flow cell. Sequencing was performed to an average depth of 20 million reads.

value: whole blood

tag: rin

value: M

tag: race

value: NHW

tag: packyears

tag: smoke

value: Never

tag: copd

value: cont

tag: bmi

tag: pctemph

tag: awt

tag: wallareapct

tag: wbc


title: PTC_rep2

value: Root

tag: treatment


title: genomic DNA from oral tissue 12

description:
Sample 12
Normal oral tissue sample.

value: Oral tissue

tag: disease state

value: normal

tag: gender


title: WT DT(+)

description: Gene expression in cochleae from DT-administered B6J mice.

source_name: Cochleae, WT, DT(+)

tag: strain/background

value: WT

tag: Sex

tag: tissue


title: WT DT(-)

description: Gene expression in cochleae from B6J mice.

source_name: Cochleae, WT, DT(-)

tag: genotype/variation

tag: age

value: pooled male and female


title: WT TFH, biological rep2

city: Chongqing

first: Yifei

address: Gaotanya Street

department: Institute of Immunology

institute: Third Military Medical University

description: Gene expression data from TFH cells in spleen of WT mice at day 8-post LCMV Armstrong infection

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 with constant rotation at the speed of 60 rpm.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and RMA as normalization method.

source_name: WT mice, LCMV Armstrong D8

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

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

value: Spleen

tag: cell type

value: follicular T helper cells

tag: genotype

value: wildtype


title: S21_LA

source_name: large airway

extract_protocol:
Large airway brushings were performed in the right mainstem bronchus and placed in RLT buffer (Qiagen).
Total RNA was extracted using the AllPrep kit (Qiagen, Valenica, CA). RNA quality was assessed on a BioAnalyzer (Agilent, Santa Clara, CA). Extracted RNA samples with RNA integrity number (RIN) greater than six and a concentration greater than or equal to 20 μg/ul were sequenced.
Libraries were QCed by quantification with picogreen, size analysis on an Agilent Bioanalyzer (Agilent, Santa Clara, CA) and qPCR quantitation against a standard curve. Paired end reads with nominal 75 bp length were generated on an Illumina HiSeq 2500 flow cell. Sequencing was performed to an average depth of 20 million reads.

value: bronchial epithelium

tag: rin

tag: race

tag: packyears

tag: smoke


title: genomic DNA from oral tissue 20

description:
Sample 20
Normal oral tissue sample.

value: Female


title: PDE_rep2

organism: Populus deltoides

value: Laccaria bicolor


title: genomic DNA from oral tissue 5

description:
Sample 5
Cancer oral tissue sample.

value: cancer


title: PTA_rep2

value: Rhizophagus irregularis


title: PDC_rep3

value: Control


title: PDC_rep2


title: genomic DNA from oral tissue 10

description:
Sample 10
Normal oral tissue sample.


title: PDE_rep1


title: genomic DNA from oral tissue 1

description:
Sample 1
Cancer oral tissue sample.

value: Male


title: genomic DNA from oral tissue 8

description:
Sample 8
Normal oral tissue sample.


title: S20_LA

value: M

value: NHW

value: Never

tag: copd

tag: bmi

tag: pctemph

tag: awt


title: S21_BAL

source_name: bronchoalveolar lavage

extract_protocol:
Bronchoalveolar lavage (BAL) was performed in two lung segments with 60ml of normal saline in each segment, and the BAL fluid obtained from each subject was pooled.
Total RNA was extracted using the AllPrep kit (Qiagen, Valenica, CA). RNA quality was assessed on a BioAnalyzer (Agilent, Santa Clara, CA). Extracted RNA samples with RNA integrity number (RIN) greater than six and a concentration greater than or equal to 20 μg/ul were sequenced.
Libraries were QCed by quantification with picogreen, size analysis on an Agilent Bioanalyzer (Agilent, Santa Clara, CA) and qPCR quantitation against a standard curve. Paired end reads with nominal 75 bp length were generated on an Illumina HiSeq 2500 flow cell. Sequencing was performed to an average depth of 20 million reads.

value: alveolar macrophage

value: cont

tag: wallareapct

tag: wbc


title: S20_PB

value: whole blood


title: PTA_rep1

value: Root

tag: treatment


title: PDE_rep3


title: PDA_rep3


title: genomic DNA from oral tissue 7

description:
Sample 7
Cancer oral tissue sample.

value: Oral tissue

tag: disease state

tag: gender


title: S20_BAL

tag: Sex


title: X3_3_E_S18

city: Charlestown

first: Alexandra-Chloe

last: Villani

department: Medicine

institute: MGH

data_processing:
BCL2FASTQ conversion using bcl2fastq2-2.17.1.14
Aligmnent using STAR 2.6.0 with default parameters
Read QC using RNASEQC_STAR
Abundance estimation using RSEM v1.2.8
N/A
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited files including raw count and RPKM values for each sample

source_name: Sorted Murine Treg Cells

extract_protocol:
T cells were sorted according  directly in 10μL of lysis buffer consisting of TCL buffer (Qiagen) and 1% of beta-mercaptoethanol. Samples were the flash frozen and kept at -80°C prior to further processing
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sorted Murine Treg Cells

tag: batch

value: FCre x C1fl/fl

tag: treg status

value: Effector


title: PDA_rep2

tag: genotype

tag: tissue


title: X3_3_C_S15

tag: cell type

value: Resting


title: Rictor-null TFH, biological rep2

description: Gene expression data from TFH cells in spleen of Rictor-null mice at day 8-post LCMV Armstrong infection

source_name: Rictor-null mice, LCMV Armstrong D8

value: Spleen

value: follicular T helper cells

value: Rictor-null


title: Rictor-null TFH, biological rep1


title: S19_PB

tag: rin

tag: age

tag: race

tag: packyears


title: PDA_rep1

value: Rhizophagus irregularis


title: X3_2_E_S17