title: Non-malignant lung 07L25_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 07L25_T

status: Public on Oct 23 2019

type: genomic

city: Vancouver

first: Katey

middle: SS

last: Enfield

state: BC

address: 675 West 10th Ave

country: Canada

institute: BC Cancer Research Centre

description: Fresh frozen lung adenocarcinoma sample

hyb_protocol: Standard Illumina hyb protocol

scan_protocol: Standard Illumina scan protocol

data_processing: DNA methylation levels are reported as  Î²-values, calculated from mean non-background corrected methylated (M) and unmethylated (U) signal intensities for each locus for each sample using the formula (Î²=M/(M+U)) and the Illumina BeadStudio software v3.2. Probes with detection p-values of >0.05 as described previously (Noushemehr et al., 2010) were deemed not significantly different from background noise and were labeled NA.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Lung adenocarcinoma

label_protocol: Standard Illumina protocol with Cy3 and Cy5

growth_protocol: Fresh-frozen tissue

extract_protocol: Genomic DNA was extracted after macrodissection and a proteinase K digstion using standard phenol:chloroform methods

treatment_protocol: Bisulfite treatment

tag: tissue

value: Lung adenocarcinoma

tag: patient

tag: age (years)

tag: Sex

value: Female

tag: race

value: Caucasian

value: Current

tag: Stage

value: IB

tag: egfr mutation

value: WT

tag: kras mutation

value: MUT


title: Non-malignant lung 07L51_N

description: Fresh frozen non-malignant lung sample

source_name: Non-malignant lung

value: Non-malignant lung


title: Non-malignant lung 07L36_N

description: Fresh frozen non-malignant lung sample

value: American Indian or Alaska Native


title: Lung adenocarcinoma 07L32_T

description: Fresh frozen lung adenocarcinoma sample

value: IIB


title: Non-malignant lung 07L32_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 07L28_N

description: Fresh frozen non-malignant lung sample

value: Never


title: Lung adenocarcinoma 3013_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 07L5_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 07L31_T

description: Fresh frozen lung adenocarcinoma sample

value: Asian

value: IA


title: Lung adenocarcinoma 07L5_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 07L38_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 07L38_T

description: Fresh frozen lung adenocarcinoma sample

value: IIIB


title: Non-malignant lung 07L24_N

description: Fresh frozen non-malignant lung sample

value: Male


title: Lung adenocarcinoma 07L24_T

description: Fresh frozen lung adenocarcinoma sample

value: IIA


title: Lung adenocarcinoma 07L22_T

description: Fresh frozen lung adenocarcinoma sample


title: Lung adenocarcinoma 07L28_T

description: Fresh frozen lung adenocarcinoma sample

value: IIIA


title: Non-malignant lung 07L22_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 07L16_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 07L19_T

description: Fresh frozen lung adenocarcinoma sample

value: Lung adenocarcinoma


title: Lung adenocarcinoma 07L18_T

description: Fresh frozen lung adenocarcinoma sample

value: Former


title: Lung adenocarcinoma 07L16_T

description: Fresh frozen lung adenocarcinoma sample

value: Caucasian


title: Non-malignant lung 07L18_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 07L21_T

description: Fresh frozen lung adenocarcinoma sample

value: Current


title: Lung adenocarcinoma 07L14_T

description: Fresh frozen lung adenocarcinoma sample

value: IB


title: Non-malignant lung 07L19_N

description: Fresh frozen non-malignant lung sample

value: Female


title: Non-malignant lung 07L14_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 07L21_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 07L13_T

description: Fresh frozen lung adenocarcinoma sample

value: WT

value: MUT


title: Lung adenocarcinoma 06L74_T

description: Fresh frozen lung adenocarcinoma sample

value: asian


title: Lung adenocarcinoma 06L64_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 06L75_N

description: Fresh frozen non-malignant lung sample

value: Non-malignant lung


title: Lung adenocarcinoma 06L71_T

description: Fresh frozen lung adenocarcinoma sample

value: Never


title: Non-malignant lung 07L13_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 06L75_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 06L71_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 06L57_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 06L74_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 06L53_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 06L64_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 06L52_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 06L46_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 06L29_T

description: Fresh frozen lung adenocarcinoma sample

value: Asian


title: Lung adenocarcinoma 06L46_T

description: Fresh frozen lung adenocarcinoma sample


title: Lung adenocarcinoma 06L30_T

description: Fresh frozen lung adenocarcinoma sample

value: IIB


title: Non-malignant lung 06L42_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 06L54_T

description: Fresh frozen lung adenocarcinoma sample

value: IA


title: Non-malignant lung 06L57_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 06L52_N

description: Fresh frozen non-malignant lung sample

value: Male


title: Lung adenocarcinoma 06L50_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 06L53_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 06L54_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 06L29_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 06L50_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 06L20_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 06L20_T

description: Fresh frozen lung adenocarcinoma sample


title: Lung adenocarcinoma 06L42_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 06L14_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 06L11_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 06L10_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 06L14_T

description: Fresh frozen lung adenocarcinoma sample


title: Lung adenocarcinoma 06L10_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 06L30_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 05L9_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 05L54_T

description: Fresh frozen lung adenocarcinoma sample


title: Lung adenocarcinoma 06L11_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 06L3_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 05L9_T

description: Fresh frozen lung adenocarcinoma sample


title: Lung adenocarcinoma 05L6_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 05L7_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 05L7_T

description: Fresh frozen lung adenocarcinoma sample


title: Lung adenocarcinoma 05L49_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 05L45_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 05L47_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 05L46_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 05L45_T

description: Fresh frozen lung adenocarcinoma sample


title: Lung adenocarcinoma 05L47_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 05L49_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 05L43_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 05L43_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 05L6_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 05L40_T

description: Fresh frozen lung adenocarcinoma sample


title: Lung adenocarcinoma 05L39_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 05L40_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 05L34_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 05L54_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 05L39_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 05L38_T

description: Fresh frozen lung adenocarcinoma sample

value: IV


title: Non-malignant lung 05L4_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 06L3_T

description: Fresh frozen lung adenocarcinoma sample


title: Lung adenocarcinoma 05L46_T

description: Fresh frozen lung adenocarcinoma sample


title: Lung adenocarcinoma 05L33_T

description: Fresh frozen lung adenocarcinoma sample


title: Lung adenocarcinoma 05L13_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 05L27_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 05L32_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 05L19_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 05L27_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 05L38_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 05L12_T

description: Fresh frozen lung adenocarcinoma sample

value: IIIA


title: Non-malignant lung 05L33_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 05L32_T

description: Fresh frozen lung adenocarcinoma sample

value: Lung adenocarcinoma


title: Lung adenocarcinoma 05L4_T

description: Fresh frozen lung adenocarcinoma sample


title: Lung adenocarcinoma 05L19_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 05L10_N

description: Fresh frozen non-malignant lung sample

value: Former


title: Non-malignant lung 05L12_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 05L34_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 05L13_N

description: Fresh frozen non-malignant lung sample


title: HO_CD47 treatedreplicate3

type: SRA

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

country: USA

institute: University of Michigan

description:
HO model (30% body surface area dorsal burn and Achilles tenotomy) was used in C57 and LysmCre/Tgfb1fx/fx mice
CD47 treated and harvested at day 7
HO_CD47treated_Markers

library_source: transcriptomic

data_processing:
Cell Ranger Single Cell Software Suite 1.3 was used to perform sample de-multiplexing, barcode processing, and single cell gene counting (Alignment, Barcoding and UMI Count) at the University of Michigan Biomedical Core Facilities DNA Sequencing Core.
Seurat R package was used to perform unsupervised clustering and identification of cell-type specific markers.
Genome_build: GRCh38
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, and matrix.mtx files.

molecule: total RNA

organism: Mus musculus

source_name: Tenotomy site of a burn/tenotomy mouse

extract_protocol: Single-cell 3’ library generation was performed on the 10x Genomics Chromium Controller following the manufacturers protocol for the v2 reagent kit (10X Genomics, Pleasanton, CA, USA). Cell suspensions were loaded onto a Chromium Single-Cell A chip along with reverse transcription (RT) master mix and single cell 3’ gel beads, aiming for 2000-6000 cells per channel. In this experiment, 8700 cells were encapsulated into emulsion droplets at a concentration of 700-1200 cells/ul which targets 5000 single cells with an expected multiplet rate of 3.9%. Following generation of single-cell gel bead-in-emulsions (GEMs), reverse transcription was performed and the resulting Post GEM-RT product was cleaned up using DynaBeads MyOne Silane beads (ThermoFisher Scientific, Waltham, MA, USA).  The cDNA was amplified, SPRIselect (Beckman Coulter, Brea, CA, USA) cleaned and quantified then enzymatically fragmented and size selected using SPRIselect beads to optimize the cDNA amplicon size prior to library construction. An additional round of double-sided SPRI bead cleanup is performed after end repair and A-tailing.  Another single-sided cleanup is done after adapter ligation.  Indexes were added during PCR amplification and a final double-sided SPRI cleanup was performed. Libraries were quantified by Kapa qPCR for Illumina Adapters (Roche) and size was determined by Agilent tapestation D1000 tapes. Read 1 primer sequence are added to the molecules during GEM incubation. P5, P7 and sample index and read 2 primer sequence are added during library construction via end repair, A-tailing, adaptor ligation and PCR. Libraries were generated with unique sample indices (SI) for each sample.

treatment_protocol:
A partial-thickness scald burn injury was administered to animals according to a previously described protocol by a single surgeon.3,57 Briefly, mice were anesthetized with inhaled isoflurane. Dorsal hair was closely clipped, and an aluminum block heated to 60°C was exposed to the dorsal region over 30% of the total body surface area for 18 s to achieve a partial-thickness burn injury. Each mouse then received a concurrent sterile dorsal hind limb tendon transection at the midpoint of the Achilles tendon (Achilles tenotomy) with placement of a single 5-0 vicryl suture to close the skin. Pain management was achieved with subcutaneous injections of buprenorphine (Buprenex, Reckitt Benckiser Pharmaceuticals) every 12 hr for 2 days.
Post injury harvested tissue samples were digested for 45 minutes in 0.3% Type 1 Collagenase and 0.4% Dispase II (Gibco) in Roswell Park Memorial Institute (RPMI) medium at 37°C under constant agitation at 120rpm. Digestions were subsequently quenched with 10% FBS RPMI and filtered through 40μm sterile strainers. Cells were then washed in PBS with 0.04% BSA, counted and resuspended at a concentration of ~1000 cells/ul. Cell viability was assessed with Trypan blue exclusion on a Countess II (Thermo Fisher Scientific) automated counter and only samples with >85% viability were processed for further sequencing.

tag: treatment

value: A partial-thickness scald burn injury was administered to animals; CD47 activating peptide (10mg/kg i.p. daily) treated 3 days prior to injury and 3 days after injury.

tag: timepoint

value: cells recruited to injury site at day 7


title: HODay21replicate3

description:
HO model (30% body surface area dorsal burn and Achilles tenotomy) was used in C57 and LysmCre/Tgfb1fx/fx mice
Day 21
HO_Day21_Markers

value: A partial-thickness scald burn injury was administered to animals

value: cells recruited to injury site at day 21


title: HO_CD47 treatedreplicate1


title: Lung adenocarcinoma 05L10_T

description: Fresh frozen lung adenocarcinoma sample

value: Female

value: Caucasian

value: WT


title: RM3, SIV-, MRS Control

type: RNA

city: Davis

first: Satya

last: Dandekar

state: CA

address: 415 Health Sciences Dr

department: Medical Microbiology and Immunology

institute: University of California, Davis

hyb_protocol: Following fragmentation, cDNA was hybridized to rhesus macaque whole genome GeneChips (Affymetrix).

scan_protocol: GeneChips were scanned according to the Affymetrix Gene Expression Analysis Technical Manual.

data_processing: A minimum fold-change of 50% (p-value ≤ 0.05) was used as inclusion criteria for identifying significant differentially expressed genes between experimental and control groups. These genes were then functionally categorized to identify enriched and depleted biological pathways using Ingenuity Pathway Analysis software (Ingenuity Systems Inc., Redwood City, CA).

label: biotin

organism: Macaca mulatta

source_name: SIV-_MRS control_ileum

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

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions (RNAeasy RNA Isolation Kit, Qiagen)

tag: animal id

value: Rhesus macaque 3

tag: infection

value: SIV-

value: MRS Control

value: ileum


title: HODay21replicate2


title: RM2, SIV+, MRS Control

source_name: SIV+_MRS control_ileum

value: Rhesus macaque 2

value: SIV+


title: HO_CD47 treatedreplicate2


title: HODay0replicate1

description:
HO model (30% body surface area dorsal burn and Achilles tenotomy) was used in C57 and LysmCre/Tgfb1fx/fx mice
Day 0
HO_Day0_Markers

value: cells recruited to injury site at day 0


title: HODay21replicate1


title: RM8, SIV-, MRS Control

value: Rhesus macaque 8


title: RM4, SIV-, MRS Control

value: Rhesus macaque 4


title: HODay0replicate2


title: hiPSC-derived lt-NES cell, AF22_H10

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

state: Tokyo

address: 35 Shinanomachi

department: Department of Physiology

country: Japan

institute: Keio University School of Medicine

data_processing:
Base-calling and chastity ﬁltering were performed using Real-Time Analysis Software version 1.18.61.
The resulting reads were mapped to the UCSC human genome 19 using STAR version 2.6.0c or sailfish version 0.7.6 with default setting.
Reads mapped to exon regions were counted using featureCount version 1.5.1.
Raw count data was loaded to R software and normalized using Seurat version 3.0.0.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each Sample.

source_name: hiPSC-derived lt-NES

extract_protocol:
AF22 NE cells were sorted into 96 well plate with a flow cytometer SH800 (SONY) and dissolved with single cell lysis buffer
Total RNA was amplified as previously described (Hayashi et al, 2018 ). Amplified cDNA from single cell was processed for library preparation using Nextera XT Library Prep Kit (Illumina).

tag: cell line

tag: cell type

value: hiPSC-derived lt-NES cell


title: hiPSC-derived lt-NES cell, AF22_H11


title: HODay3replicate1

description:
HO model (30% body surface area dorsal burn and Achilles tenotomy) was used in C57 and LysmCre/Tgfb1fx/fx mice
Day 3
HO_Day3_Markers

value: cells recruited to injury site at day 3


title: RM7, SIV+, MRS Control

value: Rhesus macaque 7


title: hiPSC-derived lt-NES cell, AF22_H09


title: HODay3replicate2

value: A partial-thickness scald burn injury was administered to animals


title: RM5, SIV-, MRS Control

value: Rhesus macaque 5


title: RM6, SIV+, MRS Control

value: Rhesus macaque 6


title: RM2, SIV+, LP Treatment

source_name: SIV+_LP treatment_ileum

value: LP Treatment


title: RM1, SIV+, MRS Control

value: Rhesus macaque 1


title: RM7, SIV+ LP Treatment


title: RM1, SIV+, LP Treatment


title: hiPSC-derived lt-NES cell, AF22_H08


title: hiPSC-derived lt-NES cell, AF22_H06


title: hiPSC-derived lt-NES cell, AF22_H07


title: HODay0replicate3


title: hiPSC-derived lt-NES cell, AF22_H05


title: hiPSC-derived lt-NES cell, AF22_H04


title: HODay3replicate3


title: hiPSC-derived lt-NES cell, AF22_H01


title: hiPSC-derived lt-NES cell, AF22_H02


title: hiPSC-derived lt-NES cell, AF22_G05


title: hiPSC-derived lt-NES cell, AF22_G07


title: hiPSC-derived lt-NES cell, AF22_G06


title: hiPSC-derived lt-NES cell, AF22_G09


title: hiPSC-derived lt-NES cell, AF22_G04


title: hiPSC-derived lt-NES cell, AF22_F10


title: hiPSC-derived lt-NES cell, AF22_G02


title: hiPSC-derived lt-NES cell, AF22_G10


title: hiPSC-derived lt-NES cell, AF22_G03


title: hiPSC-derived lt-NES cell, AF22_F07


title: hiPSC-derived lt-NES cell, AF22_F08


title: hiPSC-derived lt-NES cell, AF22_F06


title: hiPSC-derived lt-NES cell, AF22_F09


title: hiPSC-derived lt-NES cell, AF22_F04


title: hiPSC-derived lt-NES cell, AF22_F05


title: hiPSC-derived lt-NES cell, AF22_F03


title: hiPSC-derived lt-NES cell, AF22_F02


title: hiPSC-derived lt-NES cell, AF22_E11


title: hiPSC-derived lt-NES cell, AF22_E10


title: hiPSC-derived lt-NES cell, AF22_E08


title: hiPSC-derived lt-NES cell, AF22_H03


title: hiPSC-derived lt-NES cell, AF22_E09


title: hiPSC-derived lt-NES cell, AF22_G08


title: hiPSC-derived lt-NES cell, AF22_F11


title: hiPSC-derived lt-NES cell, AF22_G11


title: hiPSC-derived lt-NES cell, AF22_G01


title: hiPSC-derived lt-NES cell, AF22_E06


title: hiPSC-derived lt-NES cell, AF22_E05


title: hiPSC-derived lt-NES cell, AF22_E03


title: hiPSC-derived lt-NES cell, AF22_D11


title: hiPSC-derived lt-NES cell, AF22_D08


title: hiPSC-derived lt-NES cell, AF22_D05


title: hiPSC-derived lt-NES cell, AF22_D04


title: hiPSC-derived lt-NES cell, AF22_E02


title: hiPSC-derived lt-NES cell, AF22_F01


title: hiPSC-derived lt-NES cell, AF22_D10


title: hiPSC-derived lt-NES cell, AF22_E04


title: hiPSC-derived lt-NES cell, AF22_E01


title: hiPSC-derived lt-NES cell, AF22_D01


title: hiPSC-derived lt-NES cell, AF22_D07


title: hiPSC-derived lt-NES cell, AF22_C10


title: hiPSC-derived lt-NES cell, AF22_C11


title: hiPSC-derived lt-NES cell, AF22_D06


title: hiPSC-derived lt-NES cell, AF22_C09


title: hiPSC-derived lt-NES cell, AF22_D03


title: hiPSC-derived lt-NES cell, AF22_C07


title: hiPSC-derived lt-NES cell, AF22_D02


title: hiPSC-derived lt-NES cell, AF22_C08


title: hiPSC-derived lt-NES cell, AF22_C03


title: hiPSC-derived lt-NES cell, AF22_C05


title: hiPSC-derived lt-NES cell, AF22_C04


title: hiPSC-derived lt-NES cell, AF22_E07


title: hiPSC-derived lt-NES cell, AF22_C02


title: hiPSC-derived lt-NES cell, AF22_C06


title: hiPSC-derived lt-NES cell, AF22_D09


title: hiPSC-derived lt-NES cell, AF22_C01


title: hiPSC-derived lt-NES cell, AF22_B11


title: hiPSC-derived lt-NES cell, AF22_B07


title: hiPSC-derived lt-NES cell, AF22_B10


title: hiPSC-derived lt-NES cell, AF22_B09


title: hiPSC-derived lt-NES cell, AF22_B08


title: hiPSC-derived lt-NES cell, AF22_B04


title: hiPSC-derived lt-NES cell, AF22_B05


title: hiPSC-derived lt-NES cell, AF22_A10


title: hiPSC-derived lt-NES cell, AF22_B06


title: hiPSC-derived lt-NES cell, AF22_B03


title: hiPSC-derived lt-NES cell, AF22_A08


title: hiPSC-derived lt-NES cell, AF22_A09


title: hiPSC-derived lt-NES cell, AF22_A07


title: hiPSC-derived lt-NES cell, AF22_B01


title: hiPSC-derived lt-NES cell, AF22_A11


title: hiPSC-derived lt-NES cell, AF22_A05


title: hiPSC-derived lt-NES cell, AF22_A06


title: hiPSC-derived lt-NES cell, AF22_A03


title: hiPSC-derived lt-NES cell, AF22_A02


title: hiPSC-derived lt-NES cell, AF22_A04


title: 24 hr -Asn ISRIB Replicate 3

city: New Haven

first: Don

last: Nguyen

state: CT

address: 310 Cedar St BML 338

department: Pathology

institute: Yale University

data_processing:
Raw 75-bp R1 single-end reads were mapped to human genome with Bowtie2 in local mode, which allows the reads spanning the exon-exon junctions to get mapped to one of the two exons independent of the transcriptome annotation.
The uniquely mapped reads (cutoff by MAPQ>10) were counted to ENCODE gene annotation (v24) using featureCounts.
Differential gene expression was performed with DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Comma-delimited text files include count of reads mapped to each annotated gene (geneCount.csv), or log2 normalized gene expression measurements (geneExpr.vst.csv).

source_name: PC9 cells

growth_protocol: PC9 cells were routinely passaged every 4-5 days, with refeeding every 2-3 days, in RPMI-1640 medium supplemented with 10% FBS, 1% pen-strep, and 0.2% amphotericin B.

extract_protocol:
Total RNA was isolated using a RNeasy mini kit (Qiagen) with DNase step, following the instructions provided.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 5e5 PC9 cells were plated in 10 cm dishes and allowed to grow for 2 days. Then at either 24 hr or 6 hr prior to endpoint, media was removed, cells rinsed 2x with PBS, indicated media with vehicle or drug replaced, and cells incubated at 37°C with 5% CO2 until harvest.

value: Non-small cell lung cancer

tag: media

value: RPMI 1640 without asparagine

value: 200 nM ISRIB

tag: time

value: 24 hr


title: hiPSC-derived lt-NES cell, AF22_A01


title: 24 hr -Asn DMSO Replicate 3

value: Vehicle (0.004% DMSO)


title: 24 hr +Asn ISRIB Replicate 3

value: RPMI 1640 with asparagine


title: 6 hr -Asn DMSO Replicate 3

value: 6 hr


title: 24 hr +Asn DMSO Replicate 3


title: 6 hr -Asn ISRIB Replicate 3


title: 6 hr +Asn ISRIB Replicate 3


title: hiPSC-derived lt-NES cell, AF22_B02


title: 6 hr +Asn DMSO Replicate 3


title: 24 hr +Asn DMSO Replicate 2


title: 6 hr -Asn ISRIB Replicate 2


title: 6 hr +Asn DMSO Replicate 2


title: 24 hr -Asn ISRIB Replicate 1


title: 24 hr -Asn DMSO Replicate 2


title: 6 hr -Asn DMSO Replicate 2


title: 24 hr +Asn ISRIB Replicate 2


title: 24 hr -Asn DMSO Replicate 1


title: 24 hr -Asn ISRIB Replicate 2


title: 6 hr -Asn DMSO Replicate 1


title: 6 hr +Asn ISRIB Replicate 2


title: 24 hr +Asn DMSO Replicate 1


title: 24 hr +Asn ISRIB Replicate 1


title: 6 hr +Asn ISRIB Replicate 1


title: 6 hr +Asn DMSO Replicate 1


title: ATACseq_3TP_3hr_rep1

city: Berkeley

first: Anat

last: Kreimer

address: 378 Stanley Hall

institute: University of California, Berkeley

library_source: genomic

data_processing:
We used the FASTQC pipeline (Version 0.3.2; Babraham Bioinformatics) on our reads, and aligned them to the reference genome (hg19) with bowtie2 version 2.2.9 (Langmead and Salzberg, 2012), retaining only reads that mapped to a unique position in the genome [“–m 1”].
We marked duplicate reads in the bam files using PICARD and checked for contamination of primer sequences using Trimmomatic (Version 0.3.2; (Bolger et al., 2014)).
After alignment of the reads to the reference genome, reads aligned to the positive strand were moved +4 bp, and reads aligning the negative strand were moved -5bp.
For each of our two replicate pairs per time point, we called peaks using MACS2 version 2.1.0 (Zhang et al., 2008) with default parameters (setting the FDR to 0.05 and default hg19 human genome size).
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak

source_name: Neural progenitor cells

growth_protocol: H1 hESCs were culture in mTeSR1 media on matrigel coated dishes.

extract_protocol:
Cell nuclei were isolated as described previously (Buenrostro et al., 2013). 50,000 cell nuclei were used for library construction.
Chromatin was tagmented using Illumina Nextera kit as described previously (Buenrostro et al., 2013).

treatment_protocol: Neural induction was performed according to dual-Smad inhibition protocol (Chambers et al., 2009) for up to 72 hours.

value: H1 hESC-derived neural progenitor cells


title: ATACseq_3TP_0hr_rep2


title: CY129 Nodule

city: Boston

first: Yuheng

last: Lu

address: 360 Longwood Ave

institute: Dana-Farber Cancer Institute

data_processing:
Alignment, demultiplexing, and generation of cell-gene-count matrices all performed with cellranger 3.0.2 from 10x genomics.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files; matrix.mtx: UMI count matrix in a sparse matrix format; genes.tsv: Gene names; barcodes.tsv: Cell barcodes

source_name: natural killer cells

extract_protocol:
Freshly resected tumor tissue was dissociated using a Tumor Dissociation Kit (Miltenyi Biotec, catalog 130-095-929).  Red blood cells in PBMC samples were lysed using ACK buffer.   NK cells were isolated using a BD Aria flow cytometer (BD Biosciences) from melanoma lesions and corresponding blood samples as lymphocyte-size single viable cells that were CD45+ (Biolegend, catalog numbers 304037 and 304022) , CD56+ (Biolegend, catalog numbers 355504 and 318312), CD3- (Biolegend, catalog numbers 300447, 300330, 317322), CD4- (eBiosciences, catalog number 4345826), CD8a- (Biolegend, catalog number 301038), CD14- (Biolegend, catalog number 301843), CD15- (Biolegend, catalog number 323028), and CD163- (Biolegend, catalog number 333628). Immediately after sorting of NK cells, cell suspensions were washed in 0.05% RNase-free BSA in PBS.
The 10X Genomics 3’ V2 single cell assay (10X Genomics) was used for construction of scRNA-seq libraries.  Reverse transcription, cDNA amplification and library preparation were all performed according to the manufacturer’s instructions.

value: Tumor (nodule)

value: natural killer cells


title: ATACseq_3TP_3hr_rep2


title: CY164 Tumor

value: Tumor


title: ATACseq_3TP_72hr_rep1


title: ATACseq_3TP_0hr_rep1


title: ATACseq_3TP_72hr_rep2


title: CY129 Center

value: Tumor (center)


title: CY129 Cortex

value: Tumor (cortex)


title: 6 hr -Asn ISRIB Replicate 1


title: CY164 Blood

value: Blood


title: CY129 Blood


title: CY155 Tumor


title: CY155 Blood


title: CY160 Tumor


title: ATACseq_7TP_72hr_rep2


title: CY158 Blood


title: CY158 Tumor


title: ATACseq_7TP_6hr_rep2


title: ATACseq_7TP_0hr_rep2


title: ATACseq_7TP_72hr_rep1


title: ATACseq_7TP_3hr_rep2


title: ATACseq_7TP_48hr_rep2


title: ATACseq_7TP_24hr_rep2


title: ATACseq_7TP_24hr_rep1


title: ATACseq_7TP_12hr_rep1


title: input_DNA_rrep2_72hr_Input

data_processing:
We used the FASTQC pipeline (Version 0.3.2; Babraham Bioinformatics) on our reads, and aligned them to the reference genome (hg19) with bowtie version 1.1.1 (Langmead et al., 2009) , retaining only reads that mapped to a unique position in the genome [“–m 1”].
We marked duplicate reads in the bam files using PICARD and checked for contamination of primer sequences using Trimmomatic (Version 0.3.2; (Bolger et al., 2014)).
For each of our H3K27ac and H3K27me3 ChIP-seq replicate pairs per time points peaks were called using MACS2 version 2.1.0 (Zhang et al., 2008), with the relevant control input file with default parameters (setting the FDR to 0.05 and default hg19 human genome size).
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak or broadPeak

extract_protocol:
Cells were crosslinked with 1% formaldehyde. Chromatin was shared with Covaris S2 sonicator. ChIP was performed using LowCell# ChIP kit (Diagenode). H3K27ac (Abcam, ab4729) and H3K27me3 antibodies (EMD Millipore, 07-449) were used.
Library construction was performed using ThruPLEX DNA-seq kit (Rubicon Genomics) accoring to manufacture's protocol.


title: CY160 Blood


title: ATACseq_7TP_0hr_rep1


title: ATACseq_7TP_6hr_rep1


title: input_DNA_rrep2_48hr_Input


title: ATACseq_7TP_3hr_rep1


title: input_DNA_rrep2_12hr_Input


title: input_DNA_rrep2_24hr_Input


title: input_DNA_rrep2_6hr_Input


title: input_DNA_rrep2_3hr_Input


title: input_DNA_rrep2_0hr_Input


title: ATACseq_7TP_12hr_rep2


title: ATACseq_7TP_48hr_rep1


title: SOX17-V118Mday9rep2

city: Guangzhou

first: YOGESH

last: SRIVASTAVA

state: Guangdong

address: 190 Kaiyuan Avenue

department: Biochemistry and Molecular Biology

country: China

institute: Guangzhou Institutes of Biomedicine and Health

data_processing:
fastqc
The mouse transcriptome index was generated by RSEM with bowtie 2 and then the raw reads were aligned to the transcriptome index
Per-gene read counts were calculated using RSEM GC normalized using EDAseq
Genes with mean read counts over all traits and replicates of less than 20 were discarded leading to a final set of 15,130 genes
DESeq2 for differential gene expression
Genome_build: mm10

growth_protocol: OG2MEF cells were transduced twice by pMX-Sox2, Klf4 along with OCT4, SOX17 or SOX17-V118M or GFP retroviruses produced using PlatE cells in DMEM + 10% FBS media supplemented with 1x NEAA and Glutamax. After second viral transduction, the medium was switched to mouse ESC media ((DMEM containing 4.5 g/L D-glucose, 15% FBS, 1% NEAA, 1% GlutaMAX, 1% Sodium Pyruvate, 0.5% penicillin/streptomycin, 1000 U/mL Leukemia inhibiting factor (LIF, prepared by the core facility of GIBH), 0.055 mM β-ME (beta mercaptoethanol) and 50 μg/mL Vitamin C).

extract_protocol:
Total RNA was isolated with TRIzol
TruSeq Nano RNA sample prep kit (Illumina) was used for library constructions.

value: reprogramming cells

tag: day of reprogramming

tag: genotype/variation


title: SOX17day9rep1

value: SOX17 WT


title: SOX17day9rep2


title: H3K27me3_ChIPSeq_rep2_3hr


title: H3K27me3_ChIPSeq_rep2_72hr


title: H3K27me3_ChIPSeq_rep2_48hr


title: H3K27me3_ChIPSeq_rep2_12hr


title: H3K27me3_ChIPSeq_rep2_6hr


title: H3K27me3_ChIPSeq_rep2_24hr


title: H3K27ac_ChIPSeq_rep2_72hr


title: G170D 6h

first: Zlata

last: Gvozdenov

state: MA

address: 240 Longwood Ave

department: BCMP

institute: Harvard Medical School

data_processing:
Quality control: FastQC
Aligning to the reference genome: Bowtie (0.12.8) ( -m 1 -v 2 --sam). Only uniquely mapped reads were retained for further analyses.
DHS peak detection: Hotspot (v4), fdr 0.01
Footprint detection: DNase2TF (Sung et al., 2014) (maxw=30, minw=6, z_threshold =-2, numworker = 10, FDRs=c( 0.01))
Genome_build: sacCer3
Supplementary_files_format_and_content: *mapped_reads.bigWig contain the information about mapped DHS-Seq reads (chromatin cleavage), *dhs.bed are identified DHSs, and *footprints_dnase2tf_fdr001 are detected footprints

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: Yeast were grown in YPD medium from OD 0.25 (WT) and  OD 0.37 (G170D) till 0.65-0.7 at 37˚C (6h).

extract_protocol:
Nuclei were isolated from the yeast and subject to limited DNaseI digestion. Short (>650bp) sequences were size selected and deep sequenced.
The libraries were prepared with Illumina's 'TruSeq DNAseq Sample Prep kit' with one modification: adaptors were diluted 1:20. The libraries were quantitated by qPCR, and sequenced on two lanes for 101 cycles on a HiSeq2000 using a TruSeq SBS sequencing kit version 3 and processed with Casava 1.8.2.

tag: strain

value: Hsp90 temperature-sensitive strain with allele G170D


title: H3K27ac_ChIPSeq_rep2_48hr


title: H3K27ac_ChIPSeq_rep2_24hr


title: H3K27ac_ChIPSeq_rep2_12hr


title: H3K27ac_ChIPSeq_rep2_6hr


title: H3K27ac_ChIPSeq_rep2_3hr


title: WT 6h RNA

data_processing:
Reads trimming: Trimmomatic (TRAILING:20 MINLEN:40)
Aligning to the reference genome: STAR (2.5.2b) (--outFilterType BySJout --outFilterMultimapNmax 1 --alignIntronMin 10 --alignIntronMax 2500 --alignMatesGapMax 2500 --alignSJDBoverhangMin 1)
Differential gene expresion: Gfold (V1.1.0)
Genome_build: sacCer3

molecule: polyA RNA

extract_protocol:
Total RNA was isolated with the Ambion RiboPur RNA Purification Kit
The libraries were prepared with Illumina's 'TruSeq DNAseq Sample Prep kit' with one modification: adaptors were diluted 1:20. The libraries were quantitated by qPCR, and sequenced on two lanes for 101 cycles on a HiSeq2000 using a TruSeq SBS sequencing kit version 3 and processed with Casava 1.8.2.

value: WT


title: SOX17-V118Mday9rep1


title: RM6, SIV+, LP Treatment

value: Rhesus macaque 6

value: SIV+

value: LP Treatment

tag: tissue

value: ileum


title: H3K27ac_ChIPSeq_rep2_0hr


title: input_DNA_rep1_72hr_Input


title: WT 6h


title: H3K27me3_ChIPSeq_rep2_0hr


title: G170D 6h RNA


title: input_DNA_rep1_24hr_Input


title: input_DNA_rep1_12hr_Input


title: input_DNA_rep1_0hr_Input


title: H3K27me3_ChIPSeq_rep1_48hr


title: input_DNA_rep1_3hr_Input


title: H3K27me3_ChIPSeq_rep1_72hr


title: H3K27me3_ChIPSeq_rep1_24hr


title: Traditional serrated adenoma 1

city: Tokyo

first: Kohta

last: Toshimitsu

address: 35, Shinanomachi, Shinjuku-ku

institute: Keio University

description: Gene expression data of traditional serrated adenoma organoid 1

hyb_protocol: Standard Affymetrix procedures

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G

data_processing: Raw expression data were normalized by RMA together with normal and adenomatous organoid data from GSE74843, GSE112369 and GSE127757.

source_name: Traditional serrated adenoma

label_protocol: Standard Affymetrix procedures

growth_protocol: Organoids were maintained in a medium containing Wnt-3A, R-spondin, Noggin, A83-01, EGF, IGF-1 and FGF-2.

extract_protocol: Total RNA was extracted using the Rneasy Plus Mini Kit according to the manufacturer's instructions.

tag: tissue source

value: Colon

tag: tissue/cell type

value: Traditional serrated adenoma


title: H3K27me3_ChIPSeq_rep1_12hr

value: H1 hESC-derived neural progenitor cells


title: H3K27me3_ChIPSeq_rep1_6hr


title: Engineered organoid, BRAFV600E, EIF3E-RSPO2 fusion gene, GREM1 overexpression

description: Gene expression data of genetically engineered normal colon organoid, BRAFV600E, EIF3E-RSPO2, GREM1 overexpression


title: Traditional serrated adenoma 2

description: Gene expression data of traditional serrated adenoma organoid 2


title: H3K27ac_ChIPSeq_rep1_72hr


title: H3K27me3_ChIPSeq_rep1_3hr


title: Normal colon organoid

description: Gene expression data of normal colon organoid

source_name: Normal colon organoid

value: Normal colon organoid


title: H3K27me3_ChIPSeq_rep1_0hr


title: Engineered organoid, BRAFV600E, EIF3E-RSPO2 fusion gene

description: Gene expression data of genetically engineered normal colon organoid, BRAFV600E, EIF3E-RSPO2


title: c114416_rnaseq_uziel_22rv1_22: 22RV1_DHT_ABBV-744 rep2

city: North Chicago

first: Xin

state: IL

address: 1 North Waukegan Rd

department: Oncology Discovery

institute: Abbvie

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned using the OmicSoft aligner and gene expression quantified based on UCSC gene model.
Differentially expressed genes between treatment conditions detected by DESeq2 with a statistical cut-off (FC>2, p<0.01)
Genome_build: B37
Supplementary_files_format_and_content: FPKM value of all samples

source_name: 22RV1 immortalized prostate cancer cell line

growth_protocol: 22RV1 cells were grown for 72 hrs in charcoal stripped (steroid free) serum.

extract_protocol:
RNA was prepared by Qiazol extraction followed by RNeasy mini column (QIAGEN)
10 ug of total RNA was submitted to poly-A selection to remove ribosomal RNA and reverse transcribed to double-stranded cDNA. The cDNA was eblunt ended, adenylated, and ligated with Illumina indexes.

treatment_protocol: Cells were pretreated with indicated inhibitors for 45 minutes followed by 24 hr stimulation with 5 nM DHT or EtOH.

value: prostate adenocarcinoma cancer cell line


title: H3K27ac_ChIPSeq_rep1_24hr


title: H3K27ac_ChIPSeq_rep1_12hr


title: c114416_rnaseq_uziel_22rv1_20: 22RV1_DHT_ABBV-075 rep2


title: c114416_rnaseq_uziel_22rv1_21: 22RV1_DHT_ABBV-744 rep1


title: input_DNA_rep1_6hr_Input


title: input_DNA_rep1_48hr_Input


title: H3K27ac_ChIPSeq_rep1_6hr


title: H3K27ac_ChIPSeq_rep1_3hr


title: c114416_rnaseq_uziel_22rv1_19: 22RV1_DHT_ABBV-075 rep1


title: c114416_rnaseq_uziel_22rv1_16: 22RV1_DHT_DMSO rep2


title: c114416_rnaseq_uziel_22rv1_17: 22RV1_DHT_ENZ rep1


title: c114416_rnaseq_uziel_22rv1_15: 22RV1_DHT_DMSO rep1


title: H3K27ac_ChIPSeq_rep1_0hr


title: c114416_rnaseq_uziel_22rv1_18: 22RV1_DHT ENZ rep2


title: MPRA_rep2

description:
Protocol includes extraction of Total RNA
There are four fastq files per sample. R1 and R2 contain the biological data. The 15 bp barcode is included in both R1 and R2. There is also an Index and UMI file.

data_processing:
Library strategy: MPRA
We used both the forward and reverse reads to sequence the 15-bp reporter barcodes and obtain consensus sequences.
Only correct size barcodes that are observed at least once in both RNA and DNA of the same sample were subsequently used for further analyses.
We summed up the RNA or DNA counts across all associated barcodes for each enhancer observed in a given experiment.
Processing of raw files is described in experimental_design.txt, available on the series record.
For each replicate (1-3) there's an index file that indicates the time point and RNA or DNA:
index_rep1.lst.txt
index_rep2.lst.txt
index_rep3.lst.txt
The barcodes that are being sequenced are 15bp long and each enhancer is 171bp long as described in this fasta file plasmid_library_MPRA.fa.
format:
*230-base sequence in fasta file:*
*First half array:*
AGGACCGGATCAACT*****171base_enhancer*****CCTGCAGGGAATTC*****15base_barcode*****CATTGCGTGAACCGA
*Second half array:*
AATGCTAGCGCATGG*****171base_enhancer*****CCTGCAGGGAATTC*****15base_barcode*****CTGCAACCTACGGAA
Genome_build: hg19
Supplementary_files_format_and_content: text file with 15bp barcode, count of barcode, associated enhancer/barcode combination (as it appears in the FASTA file).  We had two arrays (A1/2) and 45 barcodes per enhancer per array (overall: 90 barcodes were designed per 2664 enhancers = 239760 different 15bp barcodes). Processed data files are included in the archive GSE115042_MPRA.tar.gz on the series page.

extract_protocol:
Cell nuclei were isolated as described previously (Buenrostro et al., 2013), lysed in RLT plus buffer (Qiagen) and stored at -80C. Genomic DNA and RNA were extracted using AllPrep DNA/RNA mini kit (Qiagen).
24ug RNA and reverse-transcribed using SuperscriptII. The cDNA and 8ug genomic DNA were used for PCR. PCR products were size-selected with an agarose gel, purified and pooled.

treatment_protocol: hESCs were infected with the lentiMPRA library and incubated for 2 days, followed by neural induction with dual-Smad inhibition protocol (Chambers et al., 2009) for up to 72 hours.


title: Engineered organoid, BRAFV600E, GREM1 overexpression

description: Gene expression data of genetically engineered normal colon organoid, BRAFV600E, GREM1 overexpression


title: MPRA_rep1


title: H3K27ac_ChIPSeq_rep1_48hr


title: c114416_rnaseq_uziel_22rv1_13: 22RV1_EtOH_DMSO rep1


title: c114416_rnaseq_uziel_22rv1_14: 22RV1_EtOH_DMSO rep2


title: Patients_156_Validation_P_96

city: Daejeon

first: Jin Young

last: Park

address: 24,Techno 11-ro, Yuseong-gu

country: South Korea

institute: CbsBioscience

description: 6 positive controls  and 8 negative controls were contained NanoString panel

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.

data_processing: The raw data were numerical counts of each reporter barcode that hybridized with target RNA. The raw data were normalized through NanoString nSolver software. Training cohort and validation cohort normalization were separately conducted.

source_name: Locally Advanced Rectal Cancer

extract_protocol: Total RNA was extracted from FFPE tissues (n = 156) using the RNeasy FFPE kit (Qiagen, Hilden, Germany) with Deparaffinization Solution (Qiagen) and DNase I treatment (Qiagen).

tag: histology

value: Good-Response


title: MPRA_rep3


title: Patients_155_Validation_P_95


title: Patients_152_Validation_P_92

value: Non-Response


title: Patients_151_Validation_P_91


title: Patients_153_Validation_P_93


title: Patients_150_Validation_P_90


title: Patients_149_Validation_P_89


title: Patients_147_Validation_P_87


title: Patients_148_Validation_P_88


title: Patients_145_Validation_P_85


title: Patients_146_Validation_P_86


title: Patients_144_Validation_P_84


title: Patients_143_Validation_P_83


title: Patients_142_Validation_P_82


title: Patients_140_Validation_P_80


title: Patients_137_Validation_P_77


title: Patients_138_Validation_P_78


title: OVCAR5 PTPRR-DA-2

city: Shanghai

first: Yuetong

last: Wang

address: 320 Yue Yang Road, Room 713

department: Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences

institute: Chinese Academy of Sciences

data_processing:
raw fastq data cleaned by cutadapt with multi steps: trim adapter with cutadapt -a AGATCGGAAGAGCAC -n 3;then cutadapt -u 7 -u -7 -q 20 -m 15 got the clean reads.
sequence mapped to human tRNA & rRNA index for filter: bowtie MT_trRNA -l 16 -v 2 -k 1 -m 100 --best --strata; trRNA unmapped reads next map to hg19: STAR --genomeDir hg19_star_index --outFilterMultimapNmax 10 --outFilterMultimapScoreRange 0 --outFilterMismatchNmax 2 --alignIntronMax 500000 --genomeLoad NoSharedMemory --seedSearchStartLmax 15 --outSJfilterOverhangMin 28 6 6 6 --outReadsUnmapped Fastx.
count mapped bam file by: htseq-count -f bam -s reverse --nonunique none -a 30 Homo_sapiens.GRCh37.75.gtf; then use DESeq2 did the differential expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene counts matrix for each Sample.

source_name: Human ovarian cancer cell line

growth_protocol: Cells were grown in  DMEM medium containing 10% FBS, and supplemented with penicillin (50 units/ml), streptomycin (100 mg/ml). For tumor RNA-seq, cells were grown in  DMEM medium containing 10% FBS, and supplemented with penicillin (50 units/ml), streptomycin (100 mg/ml). Then 1*106 cells were collected and injected into mice subscutaneously. After about 20 days, tumors were collected for RNA extraction.

extract_protocol:
mRNA were extracted using RNA extract Kit (NEB T2010S) and DNA were digested by using RQ1( Promega M6101)
RNA-seq was performed as described (Vagin et al., 2013 RNA and Armour et al., 2009 Nat Methods). Samples were sequenced on Illumina platforms with HiSeq X Ten.

treatment_protocol: All cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before harvested for RNA-seq

value: OVCAR5 PTPRR-DA


title: Patients_139_Validation_P_79


title: Patients_141_Validation_P_81


title: Patients_135_Validation_P_75


title: Patients_136_Validation_P_76


title: OVCAR5 PTPRR-DA-1


title: OVCAR5 PTPRR-WT-2

value: OVCAR5 PTPRR-WT


title: Patients_134_Validation_P_74


title: Patients_154_Validation_P_94


title: Patients_133_Validation_P_73


title: OVCAR5 PTPRR-WT-1


title: Lung adenocarcinoma 3035_T

description: Fresh frozen lung adenocarcinoma sample

hyb_protocol: DNA was hybridized according to manufacturer's instructions

scan_protocol: Arrays were scanned according to manufacturer's instructions

data_processing: Probe intensity files were processed in Partek Genomics Suite (Partek Incorporated, Missouri, USA). Probe sequencing, GC content, fragment length, and background adjustments were applied to correct for biases in signal intensities. DNA copy number profiles were generated in the Copy Number, Paired Analysis Workflow using patient-matched non-malignant lung as a baseline for each lung tumour sample. Segmentation was applied using stringent significance thresholds to identify regions of copy number gain and loss (signal to noise >0.3, minimum of 50 markers per segment, p-value < 10-7). Segments were merged using a 1 Mbp windown. Genomic mapping was based on the hg18 genomic build.

label_protocol: DNA was labeled according to manufacturer's instructions

growth_protocol: Fresh frozen tissue

extract_protocol: DNA was extracted using standard phenol:chloroform procedures

value: Lung adenocarcinoma

tag: patient

tag: sample

value: Tumor

tag: age (years)

tag: Sex

value: Male

tag: race

value: Caucasian

tag: smoking history

value: Never

tag: pack-years

tag: Stage

value: IA

tag: egfr mutation


title: Non-malignant lung 3035_N

description: Fresh frozen lung adenocarcinoma sample

value: Non-malignant lung

value: Normal

tag: kras mutation


title: Non-malignant lung 3036_N

description: Fresh frozen lung adenocarcinoma sample

value: Female

value: Asian


title: Non-malignant lung L12_N

description: Fresh frozen lung adenocarcinoma sample

value: Current


title: Patients_132_Validation_P_72


title: Patients_131_Validation_P_71


title: OVCAR5 Ctrl-2

value: OVCAR5 Ctrl


title: Non-malignant lung L2_N

description: Fresh frozen lung adenocarcinoma sample


title: OVCAR5 Ctrl-1


title: Lung adenocarcinoma L2_T

description: Fresh frozen lung adenocarcinoma sample

value: IIIA

value: MUT

value: WT


title: Lung adenocarcinoma L9_T

description: Fresh frozen lung adenocarcinoma sample

value: Former


title: Patients_130_Validation_P_70

value: Non-Response


title: XENO_OVCAR5 PTPRR-DA-3

value: XENO_OVCAR5 PTPRR-DA


title: Lung adenocarcinoma 3036_T

description: Fresh frozen lung adenocarcinoma sample

value: Lung adenocarcinoma

value: Tumor

value: IIB


title: Patients_129_Validation_P_69

value: Good-Response


title: Lung adenocarcinoma L12_T

description: Fresh frozen lung adenocarcinoma sample

value: Male

value: Caucasian


title: Non-malignant lung L9_N

description: Fresh frozen lung adenocarcinoma sample

value: Non-malignant lung

value: Normal


title: Lung adenocarcinoma 3032_T

description: Fresh frozen lung adenocarcinoma sample

value: Female

value: Never


title: Lung adenocarcinoma L15_T

description: Fresh frozen lung adenocarcinoma sample

value: Asian

value: IB


title: Non-malignant lung 3033_N

description: Fresh frozen lung adenocarcinoma sample


title: XENO_OVCAR5 PTPRR-DA-2


title: Patients_128_Validation_P_68


title: Non-malignant lung 3039_N

description: Fresh frozen lung adenocarcinoma sample


title: Lung adenocarcinoma 3039_T

description: Fresh frozen lung adenocarcinoma sample


title: XENO_OVCAR5 PTPRR-DA-1


title: Non-malignant lung 3032_N

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung L15_N

description: Fresh frozen lung adenocarcinoma sample


title: Lung adenocarcinoma L1_T

description: Fresh frozen lung adenocarcinoma sample

value: Current

value: MUT


title: XENO_OVCAR5 PTPRR-WT-3

value: XENO_OVCAR5 PTPRR-WT


title: Lung adenocarcinoma 3024_T

description: Fresh frozen lung adenocarcinoma sample

value: III

value: WT


title: Non-malignant lung 3030_N

description: Fresh frozen lung adenocarcinoma sample


title: Patients_126_Validation_P_66


title: XENO_OVCAR5 PTPRR-WT-2


title: XENO_OVCAR5 PTPRR-WT-1


title: Patients_125_Validation_P_65


title: Patients_124_Validation_P_64


title: XENO_OVCAR5 Ctrl-3

value: XENO_OVCAR5 Ctrl


title: Lung adenocarcinoma 3030_T

description: Fresh frozen lung adenocarcinoma sample

value: Lung adenocarcinoma

value: Tumor


title: Non-malignant lung L1_N

description: Fresh frozen lung adenocarcinoma sample


title: Patients_123_Validation_P_63

value: Good-Response


title: XENO_OVCAR5 Ctrl-2


title: Patients_127_Validation_P_67


title: Lung adenocarcinoma 3031_T

description: Fresh frozen lung adenocarcinoma sample

value: IIA


title: Patients_122_Validation_P_62


title: XENO_OVCAR5 Ctrl-1


title: Non-malignant lung 3024_N

description: Fresh frozen lung adenocarcinoma sample

value: Male

value: Caucasian


title: Patients_121_Validation_P_61

value: Non-Response


title: Non-malignant lung 3031_N

description: Fresh frozen lung adenocarcinoma sample

value: Non-malignant lung

value: Normal

value: Female


title: PLC/PRF/5 ATRX-KO T21

city: Beijing

first: Xiaoyue

address: 5 Dongdansantiao, Dongcheng District

institute: Chinese Academy of Medical Sciences

description: amplify the sgRNA regions which were integrated into genomic DNA through lentivirus infection

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were filtered against the lentiviruse backbone sequence, then the backbone sequence were trimmed, leaving only the sgRNA sequence
sgRNA sequence were mapped to the Human CRISPR Knockout Pooled Library (GeCKO v2,addgene #1000000048, #1000000049),and the count number of each sgRNA was caculated using an in-house perl script
Genome_build: Human CRISPR Knockout Pooled Library (GeCKO v2,addgene #1000000048, #1000000049)
Supplementary_files_format_and_content: tab-delimited text files include count number for each sgRNA for each Sample

source_name: PLC/PRF/5 cells

growth_protocol: PLC/PRF/5 ATRX-/- cells were cultured in DMEM-high glucose medium (Hyclone) supplemented with 10% heat-inactivated FBS (Hyclone) at 37℃.

extract_protocol:
Genomic DNA (gDNA)were isolated from cell pellets harvested from T21, which was performed with the Blood & Cell Culture DNA Maxi Kit (Qiagen; Hilden, Germany).
Two rounds of PCR were performed for identification of sgRNA inserts. In the first round PCR, we performed 67 separate PCR reactions (3 µg gDNA/50 µL reaction volume) for each sample using NEBNext High-Fidelity 2× PCR Master Mix (NEB; Ipswich, MA, USA) and combined resulting amplicons. The second round PCR was performed to attach Illumina adaptors and index samples. A volume of 2 µL of PCR products from the first round PCR were used as templates for each 50 µL reaction volume.

treatment_protocol: PLC/PRF/5 ATRX knockout cells (200×106) were transduced with lentivirus of the human GeCKO v2 library at an MOI of ~ 0.3 and an average of 500-fold coverage of the library. As the human GeCKO v2 library contains 123,411 sgRNAs, at least 60×106 cells need to be infected to achieve 500-fold coverage. At 48 h post-infection, cells were selected in puromycin (2 μg/mL; Life Technologies) for 2 days. At this time point, 60×106 transduced cells were harvested as reference samples (T0), and the remaining cells were passaged every 3 days. A final pool of cell populations was collected at day 21 (T21), after approximately 14 population doublings.

tag: cell type

value: PLC/PRF/5 cells

tag: genotype

value: ATRX-/-


title: Patients_120_Validation_P_60


title: Lung adenocarcinoma 3033_T

description: Fresh frozen lung adenocarcinoma sample

source_name: Lung adenocarcinoma

value: Never

value: IIB

value: MUT


title: Non-malignant lung 3023_N

description: Fresh frozen lung adenocarcinoma sample

source_name: Non-malignant lung

value: Current


title: Lung adenocarcinoma 3023_T

description: Fresh frozen lung adenocarcinoma sample

value: IA

value: WT


title: Patients_119_Validation_P_59


title: Lung adenocarcinoma 3022_T

description: Fresh frozen lung adenocarcinoma sample

value: Lung adenocarcinoma

value: Tumor


title: Non-malignant lung 3021_N

description: Fresh frozen lung adenocarcinoma sample


title: PLC/PRF/5 WT T21

growth_protocol: PLC/PRF/5 cells were cultured in DMEM-high glucose medium (Hyclone) supplemented with 10% heat-inactivated FBS (Hyclone) at 37℃.

treatment_protocol: PLC/PRF/5 parental cells (200×106) were transduced with lentivirus of the human GeCKO v2 library at an MOI of ~ 0.3 and an average of 500-fold coverage of the library. As the human GeCKO v2 library contains 123,411 sgRNAs, at least 60×106 cells need to be infected to achieve 500-fold coverage. At 48 h post-infection, cells were selected in puromycin (2 μg/mL; Life Technologies) for 2 days. At this time point, 60×106 transduced cells were harvested as reference samples (T0), and the remaining cells were passaged every 3 days. A final pool of cell populations was collected at day 21 (T21), after approximately 14 population doublings.

value: wild type


title: Non-malignant lung 3022_N

description: Fresh frozen lung adenocarcinoma sample

value: Male


title: PLC/PRF/5 WT T0

extract_protocol:
Genomic DNA (gDNA)were isolated from cell pellets harvested from T0, which was performed with the Blood & Cell Culture DNA Maxi Kit (Qiagen; Hilden, Germany).
Two rounds of PCR were performed for identification of sgRNA inserts. In the first round PCR, we performed 67 separate PCR reactions (3 µg gDNA/50 µL reaction volume) for each sample using NEBNext High-Fidelity 2× PCR Master Mix (NEB; Ipswich, MA, USA) and combined resulting amplicons. The second round PCR was performed to attach Illumina adaptors and index samples. A volume of 2 µL of PCR products from the first round PCR were used as templates for each 50 µL reaction volume.


title: Patients_118_Validation_P_58

value: Good-Response


title: PLC/PRF/5 ATRX-KO T0


title: Lung adenocarcinoma 3021_T

description: Fresh frozen lung adenocarcinoma sample

value: Caucasian


title: Patients_117_Validation_P_57

value: Non-Response


title: 8 = empty 4

city: Milano

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

country: Italy

institute: Istituto Italiano di Tecnologia

description: small RNA sequecing Illumina

data_processing:
FASTQ data were trimmed using cutadapt-1.9.1; then trimmed data was aligned to custom sequence libraries listing all isoforms of small RNA molecules by using Bowtie with --best and -v 0 switches and saved in .map output format.
Isomirage software was used to count the number of occurrences in the .map file of each isoform listed in the .genome file
Raw counts were finally normalized using CPM (copies-per-million)
Genome_build: custom genome containing microRNA sequences and isomiRs
Supplementary_files_format_and_content: Excel Spreadsheet containing the raw counts of miRNA, including miRNA isoforms

source_name: HeLa

growth_protocol: HeLa cells were grown in DMEM medium supplemented with 10% FBS, 1% Glutamine and 100 U/mL Penicillin and Streptomycin, according to manufacturer's protocol.

extract_protocol:
Total RNA was isolated through the mirVANA miRNA Isolation kit (Ambion), according to the manufacturer’s specification
1000 nanograms of total RNA were used to prepare Small RNA libraries following the Illumina TruSeqTM Small RNA kit instructions

treatment_protocol: HeLa cells infected with pLKO lentiviral vectors in which specific sh-RNA targeting PRMT1 were cloned. The pLKO-Empty vector was used as control. All the samples were collected 48hs after transduction. Two independent infections were performed.

tag: treatment

value: Empty vector

tag: condition

value: cervical cancer


title: 7 = empty 3

description: small RNA sequecing Illumina


title: Patients_116_Validation_P_56


title: Lung adenocarcinoma 3003_T

description: Fresh frozen lung adenocarcinoma sample

tag: tissue

value: Female

value: IIA


title: Lung adenocarcinoma 3013_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 3013_N

description: Fresh frozen lung adenocarcinoma sample

value: Non-malignant lung

value: Normal


title: 6 = sh-B10 2

description: small RNA sequecing Illumina

value: PRMT1-KD sh #2


title: Non-malignant lung 07L66_N

description: Fresh frozen lung adenocarcinoma sample

value: Current


title: Non-malignant lung 3012_N

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 3003_N

description: Fresh frozen lung adenocarcinoma sample


title: Lung adenocarcinoma 07L6_T

description: Fresh frozen lung adenocarcinoma sample

value: Asian

value: Never

value: IIB

value: MUT


title: 5 = sh-B6 2

description: small RNA sequecing Illumina

value: PRMT1-KD sh #1


title: Patients_114_Validation_P_54


title: Lung adenocarcinoma 3012_T

description: Fresh frozen lung adenocarcinoma sample

value: Lung adenocarcinoma

value: Tumor

value: IIIA

value: WT


title: Non-malignant lung 07L6_N

description: Fresh frozen lung adenocarcinoma sample

value: Male


title: Lung adenocarcinoma 07L59_T

description: Fresh frozen lung adenocarcinoma sample

value: Former

value: IB


title: Patients_115_Validation_P_55

value: Non-Response


title: Lung adenocarcinoma 3014_T

description: Fresh frozen lung adenocarcinoma sample

value: Female

value: Caucasian


title: 4 = empty 2

description: small RNA sequecing Illumina

value: Empty vector

value: cervical cancer


title: Lung adenocarcinoma 07L51_T

description: Fresh frozen lung adenocarcinoma sample

value: Current

value: IA


title: Patients_113_Validation_P_53


title: 3 = sh-B10 1

description: small RNA sequecing Illumina

value: PRMT1-KD sh #2


title: Patients_112_Validation_P_52


title: 2 = sh-B6 1

description: small RNA sequecing Illumina


title: Patients_111_Validation_P_51

value: Good-Response


title: Lung adenocarcinoma 07L38_T

description: Fresh frozen lung adenocarcinoma sample

value: Asian

value: Never

value: IIIB

value: MUT


title: Patients_110_Validation_P_50


title: 1 = empty1

description: small RNA sequecing Illumina


title: Lung adenocarcinoma 07L36_T

description: Fresh frozen lung adenocarcinoma sample

value: Lung adenocarcinoma

value: Tumor

value: American Indian or Alaska Native

value: WT


title: Non-malignant lung 07L38_N

description: Fresh frozen lung adenocarcinoma sample

value: Non-malignant lung

value: Normal


title: Non-malignant lung 07L36_N

description: Fresh frozen lung adenocarcinoma sample

value: Female


title: Wfdc2GG_P1.5lung_R2

city: Yokohama

first: Shin-ichi

last: Tomizawa

state: Kanagawa

address: 3-9 Fukuura, Kanazawa-ku

department: School of Medicine

institute: Yokohama City University

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were quality- and adaptor-trimmed using Trim Galore! version 0.4.0 after 3‘ ends of reads longer than 36 nucleotides were removed using NGS QC Toolkit (version 2.3.1).
RNA-seq reads were aligned to mouse genome using TopHat version 2.1.1 with default parameters except that a gtf reference file was used.
RNA-seq read count (log2 RPKM) was done using SeqMonk version 1.44.1.
Genome_build: mm10
Supplementary_files_format_and_content: Text files generated using SeqMonk contain normalised RNA-seq read count (RPKM) for all genes.

source_name: Lung

extract_protocol:
Total lung RNA was purified using Isogen (Nippon Gene) according to manufacturer’s instructions.
Purified RNA was used for library preparation using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).

value: P1.5 lung

value: Wfdc2 GFP/GFP


title: Lung adenocarcinoma 07L32_T

description: Fresh frozen lung adenocarcinoma sample

value: Caucasian

value: Current

value: IIB


title: Non-malignant lung 07L32_N

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 07L59_N

description: Fresh frozen lung adenocarcinoma sample

value: Former


title: Non-malignant lung 07L31_N

description: Fresh frozen lung adenocarcinoma sample

value: Asian


title: Non-malignant lung 07L51_N

description: Fresh frozen lung adenocarcinoma sample


title: Wfdc2GG_P1.5lung_R1


title: Patients_108_Validation_P_48

value: Non-Response


title: Lung adenocarcinoma 07L31_T

description: Fresh frozen lung adenocarcinoma sample

value: IA


title: Wfdc2GG_E18.5lung_R2

value: E18.5 lung


title: Patients_107_Validation_P_47


title: Wfdc2GG_E18.5lung_R1


title: Patients_106_Validation_P_46

value: Good-Response


title: Patients_105_Validation_P_45


title: Lung adenocarcinoma 07L5_T

description: Fresh frozen lung adenocarcinoma sample

value: Lung adenocarcinoma

value: Tumor

value: IB

value: MUT


title: 121

city: Stockholm

first: Mikael

last: Svensson

state: Stockholm

address: Solnavägen 30

department: Clinical neuroscience

country: Sweden

institute: Karolinska Institutet

data_processing:
FastQC (v0.11.5)
Trim Galore! (v0.4.1)
Star (v2.5.1)
StringTie (v1.3.3)
Preseq (v0.1.0)
featureCounts (v1.5.1)
dupRadar (v1.0.0)
Picard MarkDuplicates (v2.0.1)
Nextflow (v0.25.7)
Genome_build: GRCm38: mouse
Supplementary_files_format_and_content: tab-delimited text file include raw counts for each sample

source_name: Non-injured spinal cord

extract_protocol:
RNA isolation and clean-up was performed using the RNeasy mini kit (Qiagen, 74104). The tissue was mechanically dissociated (IKA®, T8.01) in lysis buffer containing β-mercaptoethanol (1 %). Genomic DNA was digested using DNase I (Qiagen, 79254).
Sequencing libraries for RNA isolated from spinal cords were prepared using TruSeq stranded mRNA library preparation kit implementing polyA selection (Illumina Inc.).

tag: host strain

tag: mouse status

value: Non-injured

value: Spinal cord tissue


title: 120


title: Patients_109_Validation_P_49

tag: histology


title: Patients_104_Validation_P_44


title: Patients_103_Validation_P_43


title: 119


title: 210

source_name: Spinal cord injury+allogeneic MSCs

value: Spinal cord injury

tag: transplanted with

value: allogeneic mesenchymal stem cells (MSCs)


title: Non-malignant lung 07L5_N

first: Katey

address: 675 West 10th Ave

institute: BC Cancer Research Centre

description: Fresh frozen lung adenocarcinoma sample

value: Non-malignant lung

tag: patient

tag: sample

value: Normal

tag: age (years)

value: Female

value: Caucasian


title: 205


title: Non-malignant lung 07L25_N

description: Fresh frozen lung adenocarcinoma sample

tag: Sex

tag: race

tag: smoking history

value: Current


title: Patients_101_Validation_P_41

value: Non-Response


title: Patients_102_Validation_P_42


title: Lung adenocarcinoma 07L66_T

description: Fresh frozen lung adenocarcinoma sample

tag: pack-years

tag: Stage

value: IA

tag: egfr mutation

value: WT


title: Non-malignant lung 07L28_N

description: Fresh frozen lung adenocarcinoma sample

value: Never

tag: kras mutation


title: Non-malignant lung 3014_N

description: Fresh frozen lung adenocarcinoma sample


title: 204


title: Patients_100_Validation_P_40


title: CD248 heterozygote

city: taipei

first: shuwha

last: lin

state: taiwan

address: No.1 santer street taipei, taiwan

country: Taiwan

institute: medical technology

description: Cd248 heterozygote pericytes

data_processing:
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina
The clustering of the index-coded samples was performed on a cBot Cluster Generation System (Illumina) using HiSeq PE Cluster Kit cBot-HS
Index of the reference genome was built using Bowtie v2.2.3
Genome_build: mm8
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: Tumor pericytes

growth_protocol: Pericytes were culture on gelatin coating plates.

extract_protocol:
Tumor pericytes were sorting by FACS, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: tumor derived primary pericytes

tag: passages

tag: strain

tag: genotype

value: hetero type


title: Lung adenocarcinoma 07L25_T

city: Vancouver

description: Fresh frozen lung adenocarcinoma sample

tag: tissue

value: Lung adenocarcinoma

value: Tumor

value: IB


title: CD248 null

description: Cd248 null pericytes

value: knockout type


title: 192

source_name: Spinal cord injury+syngeneic MSCs

tag: host strain

tag: mouse status

value: Spinal cord injury

value: syngeneic mesenchymal stem cells (MSCs)

value: Spinal cord tissue


title: Patients_98_Validation_P_38

tag: histology


title: Patients_97_Validation_P_37


title: Non-malignant lung 07L24_N

description: Fresh frozen lung adenocarcinoma sample

value: Non-malignant lung

tag: patient

tag: sample

value: Normal

value: Male


title: Lung adenocarcinoma 07L19_T

description: Fresh frozen lung adenocarcinoma sample

tag: age (years)

tag: Sex

value: Female

value: Asian

value: MUT


title: Lung adenocarcinoma 07L28_T

description: Fresh frozen lung adenocarcinoma sample

tag: race

value: Caucasian

tag: smoking history

value: IIIA

value: WT


title: Non-malignant lung 07L21_N

description: Fresh frozen lung adenocarcinoma sample

value: Current

tag: pack-years

tag: Stage


title: PP_H3K27ac_ChIPSeq 2

city: chengdu

first: Jue

last: Xu

address: 18# 3rd section, Renmin South Road

institute: Sichuan University

data_processing:
For HA and H3K27ac ChIP-seq, the reads were aligned to the mouse genome assembly version of mm10, using the Bowtie2 program (usegalaxy.com; version 2.3.4.2). Resulting BAM files were processed with BAM to Wiggle (usegalaxy.com; version Version 2.6.4) and Wig/BedGraph-to-bigWig (usegalaxy.com; version Version 1.1.1) converters.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using Wig/BedGraph-to-bigWig (usegalaxy.com; version Version 1.1.1) converters.

source_name: Posterior Palate

extract_protocol:
The anterior and posterior palate tissues were dissected out under a fluorescence dissecting scope from Shox2HA-DsRed embryos. Pooled palatal tissues were subjected to ChIP using anti-HA (Abcam, ab9110) or anti-H3K27ac antibodies (Abcam, ab4729) following the manufacturer’s protocol. Three independent ChIPs were conducted for library generation for each group. The libraries were then sequenced on the Illumina HiSeq 2000 platform using 50-bp single-end configuration. HA-enriched or H3K27ac-enriched genomic regions of the Shox2-expressing anterior palate and the posterior palate were analyzed and intersected comprehensively.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols

tag: antibody

value: anti-H3K27ac (Abcam, ab4729)


title: Lung adenocarcinoma 07L22_T

last: Enfield

description: Fresh frozen lung adenocarcinoma sample

value: Lung adenocarcinoma

value: Tumor

value: Never

value: IA

tag: egfr mutation

tag: kras mutation


title: Patients_99_Validation_P_39

value: Non-Response


title: Non-malignant lung 07L22_N

description: Fresh frozen lung adenocarcinoma sample


title: Lung adenocarcinoma 07L21_T

description: Fresh frozen lung adenocarcinoma sample

value: IB


title: Patients_96_Validation_P_36

value: Good-Response


title: PP_H3K27ac_ChIPSeq 1

tag: strain


title: 126

source_name: Spinal cord injury

value: Spinal cord injury

value: Spinal cord tissue


title: 191

tag: transplanted with

value: syngeneic mesenchymal stem cells (MSCs)


title: AP_H3K27ac_ChIPSeq 2

source_name: Anterior Palate


title: Patients_95_Validation_P_35


title: 193

tag: tissue


title: AP_H3K27ac_ChIPSeq 1


title: Lung adenocarcinoma 07L18_T

description: Fresh frozen lung adenocarcinoma sample

value: Male

value: Former


title: 100

tag: host strain


title: HA_ChIPSeq 2

value: anti-HA (Abcam, ab9110)


title: Non-malignant lung 07L19_N

description: Fresh frozen lung adenocarcinoma sample

value: Non-malignant lung

value: Normal

value: Female

value: Asian


title: Patients_93_Validation_P_33


title: Patients_94_Validation_P_34


title: Patients_92_Validation_P_32


title: HA_ChIPSeq 1


title: NoHelp_62pos_003

city: New York

first: Tomasz

last: Ahrends

state: NY

address: 1230 York Ave

institute: The Rockefellere University

description: Table S2. H vs NH Tcm (193).xlsx

data_processing:
Illumina adapter sequences were trimmed from Fastq files using trimmomatic (v. 0.36) with 4-base wide sliding window, to trim reads when the average quality per base drops below 15. Any reads remaining below ≤ 36 bases long were filtered out.
Adapter-trimmed files were aligned to GRCm38.77 with STAR (v. 2.5.3a). Using the genes (GRCm38.77.gtf), HTSeq-count was used in intersection-strict mode for exon feature type to generate a count matrix for all samples.
Differential expression analysis was performed using Qlucore Omics Explorer (v. 3.4). Genes with less than 5 reads in at least one of the samples were discarded. Mapping quality threshold was set to 10. TNM normalization method was applied. Differential expression with two-group comparison was considered significant at P<0.01.
Genome_build: GRCm38.77.gtf
Supplementary_files_format_and_content: Data files inlcude differentially expressed genes, comparing Tcm (CD62L+) cells (Table1) and Tem (CD62L-) cells (Table 2) in Help and No Help conditions.

source_name: spleen

extract_protocol:
For isolation of TCM and TEM cells, H-2Db/E749-57-specific CD8+ T cells were flow cytometrically sorted based on anti-CD8, anti-CD62L and tetramer staining from 3 mice per experimental group. Cells  were resuspended in Trizol (Ambion Life Technologies) and total RNA was extracted according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cd4 t cell help

value: absence

tag: cell type

value: CD8 T cells


title: NoHelp_62pos_002

description: Table S2. H vs NH Tcm (193).xlsx


title: Non-malignant lung 07L18_N

description: Fresh frozen lung adenocarcinoma sample

tag: patient

value: Caucasian


title: 125

tag: mouse status


title: KO_rep3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 or mm10? whole genome using HISAT2
Gene expression values were calculated as Fragments Per Kilobase of transcript per Million mapped reads (FPKM) using StringTie
Differential gene expression was determined using Ballgown
Genome_build: mm10

source_name: Palate

extract_protocol:
The palatal tissues that would form the future anterior hard palate were dissected out from E14.5 Shox2Cre/+;Nkx2.5F/F and Shox2Cre/-;Nkx2.5F/F mice (N = 3 for each group), respectively. The dissected tissues were subsequently subjected to RNA extraction under the manufacturer’s instructions (RNeasy Micro Kit, Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

tag: developmental stage


title: NoHelp_62pos_001

description: Table S2. H vs NH Tcm (193).xlsx


title: Patients_90_Validation_P_30

tag: histology


title: Non-malignant lung 07L14_N

description: Fresh frozen lung adenocarcinoma sample

tag: sample

tag: age (years)

tag: Sex

tag: race

tag: smoking history


title: NoHelp_62neg_003

description: Table S1. H vs NH Tem (2522).xlsx


title: Patients_91_Validation_P_31


title: Patients_89_Validation_P_29


title: KO_rep1


title: NoHelp_62neg_002

description: Table S1. H vs NH Tem (2522).xlsx


title: Lung adenocarcinoma 07L14_T

description: Fresh frozen lung adenocarcinoma sample

value: Lung adenocarcinoma

value: Tumor

tag: pack-years

tag: Stage

tag: egfr mutation

value: WT

tag: kras mutation

value: MUT


title: Patients_88_Validation_P_28

value: Good-Response


title: WT_rep3

tag: strain


title: NoHelp_62neg_001

description: Table S1. H vs NH Tem (2522).xlsx

tag: cd4 t cell help


title: KO_rep2


title: Non-malignant lung 07L16_N

description: Fresh frozen lung adenocarcinoma sample

tag: tissue

value: Never


title: Lung adenocarcinoma 07L13_T

description: Fresh frozen lung adenocarcinoma sample

tag: patient

value: IB


title: Help_62pos_003

description: Table S2. H vs NH Tcm (193).xlsx

value: presence

tag: cell type


title: Patients_87_Validation_P_27


title: WT_rep2

tag: genotype


title: Help_62pos_002

description: Table S2. H vs NH Tcm (193).xlsx


title: Lung adenocarcinoma 07L16_T

description: Fresh frozen lung adenocarcinoma sample

value: Male

value: IA


title: MT2

data_processing:
ATAC-Seq raw data was processed by atac-seq systematic analysis  pipeline
Genome_build: mm10

extract_protocol:
The GFP-positive palatal mesenchymal cells from E14.5 Shox2Cre/+;Nkx2.5F/F;R26RmTmG and Shox2Cre/-;Nkx2.5F/F;R26RmTmG embryos were sorted by FACS following our published protocol. Sorted cells were counted and pooled (N = 50,000 for each group) and prepared for ATAC-Seq and analysis.
ATAC-Seq libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage


title: Help_62pos_001

description: Table S2. H vs NH Tcm (193).xlsx


title: MT1


title: Patients_84_Validation_P_24

tag: histology


title: Help_62neg_003

description: Table S1. H vs NH Tem (2522).xlsx


title: Lung adenocarcinoma 06L75_T

description: Fresh frozen lung adenocarcinoma sample

tag: sample

value: Current


title: Patients_85_Validation_P_25


title: WT2


title: Patients_83_Validation_P_23

value: Non-Response


title: WT_rep1


title: Patients_86_Validation_P_26


title: Help_62neg_002

description: Table S1. H vs NH Tem (2522).xlsx


title: Patients_82_Validation_P_22


title: Non-malignant lung 06L75_N

description: Fresh frozen lung adenocarcinoma sample

value: Non-malignant lung

value: Normal

tag: age (years)

value: Female


title: Help_62neg_001

description: Table S1. H vs NH Tem (2522).xlsx

value: CD8 T cells


title: WT1


title: Patients_81_Validation_P_21


title: WT_S5: PIASy-WT overexpressed 2-cell embryo -2

city: Kinokawa

first: Chika

last: Higuchi

state: Wakayama

address: 930 Nishimitani

department: Faculty of Biology-Oriented Science and Technology

institute: Kindai University

data_processing:
FASTQ files from Illumina sequencing were filtered for low quality reads (<Q20), and low quality bases were trimmed from the ends of the reads (<Q20).
Adapters were removed from raw illumina reads using trim_galore.
Reads were mapped to the mouse reference genome (mm10) using STAR.
Generation of FPKM values using featureCount.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: A text file include FPKM values for genes.

source_name: A pool of 5 embryos at the 2-cell stage were subjected to cDNA synthesis

growth_protocol: The overexpressed embryos were cultured in potassium simplex optimized medium (KSOM) at 37°C under 5% CO2.

extract_protocol:
A pool of five 2-cell embryos at 28 hpi after the removal of zona pellucida were subjected to RNA purification and cDNA synthesis using a SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio) according to the manufacturer’s instructions. At the cell lysis step, 1 µL of ERCC (External RNA Controls Consortium) RNA Spike-In Control Mixes (1:40,000 dilution; Thermo Fishcer) was added to each of the samples. The cDNA was amplified with 11 cycles of PCR.
For making a library for sequencing, Nextera XT DNA Library Preparation kit (illumina) was used and final PCR amplification was done for 13 cycles using standard Illumina protocols. The obtained library was quality-checked by Kapa Library Quantification kit (Nippon Genetics).

treatment_protocol: Mouse fertilized oocytes were overexpressed with PIASy-WT or PIASy-C335F (SUMO ligase mutant) to investigate the effect of PIASy overexpression on gene expression. Each RNA (100 ng/µL) was injected into the cytoplasm of mouse fertilized oocytes from 1.5 hours post insemination (hpi) to 3 hpi in Chatot-Ziomek-Bavister (CZB)-Hepes medium. The injected zygotes showing fluorescence signal at 9 hpi after microinjection were selected and then cultured until 2-cell stage at 28 hpi. In these experiments, non-injected embryos were used as a control.

value: ICR

value: Mouse 2-cell stage embryos

value: 2-cell stage

tag: injected mrna type

value: PIASy-WT-HA


title: Wfdc2++_P1.5lung_R2

value: P1.5 lung

value: Wfdc2 +/+


title: Non-malignant lung 06L57_N

description: Fresh frozen non-malignant lung sample

tag: Sex

tag: race

value: Caucasian


title: Non-malignant lung 06L71_N

description: Fresh frozen non-malignant lung sample

tag: smoking history

value: Never

tag: pack-years


title: Patients_80_Validation_P_20

source_name: Locally Advanced Rectal Cancer

value: Good-Response


title: WT_S2: PIASy-WT overexpressed 2-cell embryo -1


title: Non-malignant lung 06L74_N

description: Fresh frozen lung adenocarcinoma sample

value: asian

value: Former

tag: Stage

tag: egfr mutation


title: Non-malignant lung 06L64_N

description: Fresh frozen non-malignant lung sample

tag: kras mutation


title: PM_S6: PIASy-Mut overexpressed 2-cell embryo -2

tag: strain

value: PIASy-C335F mutation-HA


title: Patients_79_Validation_P_19


title: Lung adenocarcinoma 07L24_T

description: Fresh frozen lung adenocarcinoma sample

tag: tissue

value: Lung adenocarcinoma

value: Tumor

value: Male

value: Current

value: IIA

value: WT

value: MUT


title: Wfdc2++_E18.5lung_R2

value: E18.5 lung


title: PM_S3: PIASy-Mut overexpressed 2-cell embryo -1

value: ICR

value: Mouse 2-cell stage embryos

value: 2-cell stage


title: Wfdc2++_E18.5lung_R1

value: Wfdc2 +/+


title: Lung adenocarcinoma 06L57_T

description: Fresh frozen non-malignant lung sample

tag: patient

value: Female

value: Caucasian

value: IIIA


title: Patients_78_Validation_P_18

value: Good-Response


title: Patients_77_Validation_P_17


title: Lung adenocarcinoma 06L71_T

description: Fresh frozen lung adenocarcinoma sample

value: Never

value: IA


title: NonInjection_S4: Non-injected 2-cell embryo -2

value: Non-injected


title: Help 3 H3K27me3

data_processing:
Single-end fastq files were aligned to mm10 (GrCm38.77) using bwa (v. 0.7.17)
Resulting alignments were filtered for mapping quality > MQ20 using samtools version 1.5
Peak calling for H3K27me3 ChIP-seq was performed using MACS2 (v. 2.1.1) with detection for broad peaks using input for normalization
For H3K4me3 we performed narrow peak calling using MACS (v. 2.1.1) with input normalization
For differential binding, we used the R package Diffbind (v. 2.2.1) to determine differentially bound peaks found in all replicates for “No help” vs “Help” with the EdgeR method
We annotated the bound regions using BEDTools (v. 2.17.0) closestBed reporting the first feature against a file of genes and locations determined from GRCm38.77 gtf file selecting for ‘gene_name’
Genome_build: GRCm38.77
Supplementary_files_format_and_content: Processed data contain BED files (narrowPeak, broadPeak) with all the called peaks for each experimental sample.

source_name: Help H3K27me3

growth_protocol: Cells isolated from spleens after vaccination.

extract_protocol:
Between 6-9 x 10^4 E7-specific memory CD8+ T cells per sample were subjected to ULI-NChIP procedure
ChIP libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Help or No Help intraepidermal vaccination.

value: spleen

tag: cell type

value: memory CD8 T cells

tag: treatment

value: CD4 T cell help

tag: chip antibody

value: aH3K27me3 mAb (C15410069, Diagenode)


title: Wfdc2++_P1.5lung_R1

value: P1.5 lung

tag: genotype


title: Lung adenocarcinoma 06L74_T

description: Fresh frozen lung adenocarcinoma sample

value: Lung adenocarcinoma

tag: sample

value: Tumor

value: asian

value: Former

value: IIB

value: MUT

value: WT


title: Non-malignant lung 06L54_N

description: Fresh frozen non-malignant lung sample

value: Non-malignant lung

value: Normal

tag: age (years)

value: Male

value: Caucasian

value: Current


title: Patients_76_Validation_P_16

tag: histology

value: Good-Response


title: NonInjection_S1: Non-injected 2-cell embryo -1

value: ICR

value: Mouse 2-cell stage embryos

tag: developmental stage

value: 2-cell stage

tag: injected mrna type

value: Non-injected


title: Help 2 H3K27me3

value: spleen

value: memory CD8 T cells

value: CD4 T cell help

value: aH3K27me3 mAb (C15410069, Diagenode)


title: Lung adenocarcinoma 06L54_T

description: Fresh frozen non-malignant lung sample

value: Lung adenocarcinoma

value: Tumor

tag: Sex

tag: race

tag: smoking history

value: IA


title: Help 1 H3K27me3


title: Patients_75_Validation_P_15


title: RNAseq_dSi rep 2

first: Anat

address: 378 Stanley Hall

institute: University of California, Berkeley

data_processing:
Reads were aligned to the hg19 human genome assembly with Tophat2 (Version 2.1.1; (Kim et al., 2013)), and low quality reads were removed with Trimmomatic (Version 0.3.2; (Bolger et al., 2014)). Reads that aligned to more than one gene as well as chimeric fragments were excluded.
We also removed genes that failed to be quantified in at least one sample by Cufflinks (Trapnell et al., 2010). We implemented a quality control (QC) pipeline that computes an extensive set of quality metrics, relying in part on FASTQC (Version 0.3.2; Babraham Bioinformatics) and the PICARD suite of alignment metrics (Version 2.5.0 with samtools 1.3.1).
Transcript levels were determined using RefSeq transcript annotations, and counting the number of reads aligning to every gene (defined as the union of all splice forms) with featureCounts (Version 1.5.0-p3; (Liao et al., 2014)).
Genome_build: hg19

source_name: H1 hESCs

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen).
mRNA enrichment, cDNA synthesis, and library generation were performed by Novogene (https://en.novogene.com/).

treatment_protocol: H1 hESCs were infected with transcription factor overexpression vectors via lentivirus and incubated for 14 days. As a control, hESC were induced by dual-Smad inhibition for 72 hours followed by further 72h-culture in N2B27 medium supplemented with FGF and EGF.

value: hESC-derived neural progenitors that were induced by dual-Smad inhibition for 72 hours followed by further 72h-culture in N2B27 medium supplemented with FGF and EGF


title: RNAseq_dSi rep 3


title: Non-malignant lung 07L13_N

description: Fresh frozen lung adenocarcinoma sample

value: Non-malignant lung

value: Normal

value: Female

value: Former

tag: pack-years

tag: Stage

tag: egfr mutation


title: No Help 3 H3K27me3

source_name: No Help H3K27me3

tag: strain

tag: tissue

value: No CD4 T cell help


title: No Help 2 H3K27me3

tag: cell type


title: Patients_74_Validation_P_14

value: Good-Response


title: Patients_73_Validation_P_13


title: RNAseq_EGFP rep 3

tag: treatment

value: Overexpressed with EGFP


title: No Help 1 H3K27me3

tag: chip antibody


title: Patients_72_Validation_P_12


title: Patients_71_Validation_P_11


title: Lung adenocarcinoma 06L53_T

description: Fresh frozen non-malignant lung sample

source_name: Lung adenocarcinoma

tag: patient

value: Caucasian

value: IIIA

value: WT

tag: kras mutation

value: MUT


title: RNAseq_EGFP rep 2


title: Help 3 H3K4me3

source_name: Help H3K4me3

value: spleen

value: memory CD8 T cells

value: CD4 T cell help

value: aH3K4me3 mAb (#9272, Cell Singaling Technology)


title: RNAseq_dSi rep 1


title: Help 2 H3K4me3


title: Help 1 H3K4me3


title: Patients_69_Validation_P_9


title: Patients_70_Validation_P_10


title: Patients_68_Validation_P_8


title: RNAseq_PAX6 rep 2

value: Overexpressed with PAX6


title: No Help 3 H3K4me3

source_name: No Help H3K4me3


title: RNAseq_PAX6 rep 3


title: Non-malignant lung 06L50_N

description: Fresh frozen non-malignant lung sample

source_name: Non-malignant lung

tag: sample

tag: age (years)

value: Current


title: Lung adenocarcinoma 06L46_T

description: Fresh frozen non-malignant lung sample

value: Lung adenocarcinoma

value: Tumor

value: IB


title: No Help 2 H3K4me3


title: Non-malignant lung 06L53_N

description: Fresh frozen non-malignant lung sample

value: Non-malignant lung

value: Normal

value: Female

value: Former


title: RNAseq_EGFP rep 1

value: Overexpressed with EGFP


title: Lung adenocarcinoma 06L50_T

description: Fresh frozen non-malignant lung sample

value: Caucasian

value: IA


title: RNAseq_OTX2 rep 3

value: Overexpressed with OTX2


title: RNAseq_PAX6 rep 1


title: Patients_66_Validation_P_6

tag: histology

value: Good-Response


title: Lung adenocarcinoma 06L43_T

description: Fresh frozen non-malignant lung sample

value: WT


title: Lung adenocarcinoma 06L64_T

description: Fresh frozen non-malignant lung sample

value: Never

value: MUT


title: Help 3 input

source_name: Help input

value: spleen

value: memory CD8 T cells

value: CD4 T cell help


title: Lung adenocarcinoma 06L52_T

description: Fresh frozen non-malignant lung sample

value: Lung adenocarcinoma

value: Tumor

value: Male


title: RNAseq_OTX2 rep 2


title: Patients_65_Validation_P_5


title: Lung adenocarcinoma 06L45_T

description: Fresh frozen non-malignant lung sample

value: Current

value: IB


title: RNAseq_OTX2 rep 1


title: Help 2 input


title: Patients_64_Validation_P_4


title: Non-malignant lung 06L45_N

description: Fresh frozen non-malignant lung sample

value: Non-malignant lung

value: Normal

value: Female


title: Patients_63_Validation_P_3


title: RNAseq_OTX1 rep 2

value: Overexpressed with OTX1


title: Patients_67_Validation_P_7


title: Help 1 input


title: No Help 3 input

source_name: No Help input

value: No CD4 T cell help


title: Patients_62_Validation_P_2

value: Good-Response


title: Lung adenocarcinoma 06L42_T

description: Fresh frozen non-malignant lung sample

value: Caucasian

value: Former

value: WT


title: Patients_61_Validation_P_1

value: Non-Response


title: No Help 1 H3K4me3

value: spleen

value: memory CD8 T cells

value: aH3K4me3 mAb (#9272, Cell Singaling Technology)


title: Non-malignant lung 06L52_N

description: Fresh frozen non-malignant lung sample


title: No Help 2 input


title: Patients_60_Training_P_60


title: Patients_59_Training_P_59


title: RNAseq_OTX1 rep 1


title: Non-malignant lung 06L30_N

description: Fresh frozen non-malignant lung sample

value: asian


title: No Help 1 input


title: RNAseq_LHX5 rep 2

value: Overexpressed with LHX5


title: RNAseq_LHX5 rep 3


title: Non-malignant lung 06L42_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 06L43_N

description: Fresh frozen non-malignant lung sample

value: Current


title: Non-malignant lung 06L46_N

description: Fresh frozen non-malignant lung sample


title: RNAseq_IRX3 rep 3

value: Overexpressed with IRX3


title: Patients_57_Training_P_57


title: RNAseq_IRX3 rep 2


title: Lung adenocarcinoma 06L39_T

description: Fresh frozen non-malignant lung sample

value: Lung adenocarcinoma

value: Tumor

value: IB


title: Patients_58_Training_P_58


title: RNAseq_LHX5 rep 1


title: Patients_56_Training_P_56


title: A549_ELF3_knockdown_rep3

description: A549 ELF3 shRNA knock-down clone

hyb_protocol: cDNA was hybridized according to manufacturer's instructions at The Centre for Applied Genomics

scan_protocol: GeneChips were scanned according to manufacturer's instructions at The Centre for Applied Genomics

data_processing: Experssion data was RMA normalized by The Centre for Applied Genomics

source_name: A549 non-small cell lung cancer cell line

label_protocol: 150ng of RNA was converted to cDNA according to manufacturer's instructions and labelled at The Centre for Applied Genomics

growth_protocol: Cells were cultured in RPMI media supplemented with 10% FBS at 37C and 5% CO2

extract_protocol: After homogenization, total RNA was extracted using TRI Reagent (Life Technologies, Grand Island, NY) according to manufacturer's protocol. The nanodrop spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE) was used to estimate the concentration of RNA and the quality of the RNA (RIN number) was assessed on Nano Series II RNA LAB-chips using Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Santa Clara, CA).

tag: cell line

value: non-small cell lung cancer

tag: genotype/variation

value: ELF3 knock-down


title: Lung adenocarcinoma 06L29_T

description: Fresh frozen non-malignant lung sample

tag: Sex

value: Female

tag: race

value: Asian

value: Never


title: A549_ELF3_knockdown_rep2

description: A549 ELF3 shRNA knock-down clone


title: Lung adenocarcinoma 06L3_T

description: Fresh frozen non-malignant lung sample

value: Caucasian

tag: smoking history

tag: pack-years

value: IIB

value: WT


title: RNAseq_IRX3 rep 1


title: A549_empty_vector_control_rep3

description: A549 empty vector control

value: control


title: RNAseq_BARHL1 rep 3

value: Overexpressed with BARHL1


title: Patients_55_Training_P_55

extract_protocol: Total RNA was extracted from FFPE tissues (n = 156) using the RNeasy FFPE kit (Qiagen, Hilden, Germany) with Deparaffinization Solution (Qiagen) and DNase I treatment (Qiagen).

value: Good-Response


title: Patients_54_Training_P_54

value: Non-Response


title: RNAseq_OTX1 rep 3

value: Overexpressed with OTX1


title: A549_empty_vector_control_rep2

description: A549 empty vector control


title: Non-malignant lung 06L3_N

description: Fresh frozen non-malignant lung sample

value: Non-malignant lung

value: Normal

value: Current

tag: Stage

tag: egfr mutation


title: Patients_53_Training_P_53


title: Non-malignant lung 06L39_N

description: Fresh frozen non-malignant lung sample

tag: tissue


title: RNAseq_BARHL1 rep 2


title: A549_empty_vector_control_rep1

description: A549 empty vector control

tag: cell type


title: RNAseq_BARHL1 rep 1

tag: treatment


title: RNAseq_48hr_rep3

data_processing:
Reads were aligned to the hg19 human genome assembly with Tophat2 (Version 2.1.1; (Kim et al., 2013)), and low quality reads were removed with Trimmomatic (Version 0.3.2; (Bolger et al., 2014)). Reads that aligned to more than one gene as well as chimeric fragments were excluded.
We also removed genes that failed to be quantified in at least one sample by Cufflinks (Trapnell et al., 2010). We implemented a quality control (QC) pipeline that computes an extensive set of quality metrics, relying in part on FASTQC (Version 0.3.2; Babraham Bioinformatics) and the PICARD suite of alignment metrics (Version 2.5.0 with samtools 1.3.1).
Transcript levels were determined using RefSeq transcript annotations, and counting the number of reads aligning to every gene (defined as the union of all splice forms) with featureCounts (Version 1.5.0-p3; (Liao et al., 2014)).
Genome_build: hg19
Supplementary_files_format_and_content: featureCountsTable

source_name: Neural progenitor cells

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen).
Library construction was done using Illumina TruSeq Stranded Total RNA Kit.

value: H1 hESC-derived neural progenitor cells


title: Patients_52_Training_P_52

data_processing: The raw data were numerical counts of each reporter barcode that hybridized with target RNA. The raw data were normalized through NanoString nSolver software. Training cohort and validation cohort normalization were separately conducted.


title: Patients_51_Training_P_51


title: Lung adenocarcinoma 06L22_T

description: Fresh frozen non-malignant lung sample

extract_protocol: DNA was extracted using standard phenol:chloroform procedures

value: Lung adenocarcinoma

value: Tumor

value: Male

value: asian

value: IA

value: MUT


title: MED8_0.1_rep3

city: Liverpool

first: Sophie

last: Cowman

address: Crown Street

department: Institute of Integrative Biology

country: United Kingdom

institute: University of Liverpool

hyb_protocol: 20ug of total RNA was used in hybridisation reactions following the manufacturers protocol.

data_processing: Data was processed and analysed usung nSolverTM Analysis Software (3.0) with nCounter® Advanced Analysis plug-in (2.0.115).

source_name: MED-MED8A cells incubated in 0.1% O2 for 5 days

extract_protocol: Total RNA was extracted using a spin column based kit

treatment_protocol: Cells were incubated in 21%, 1% or 0.1% oxygen for 5 days before RNA extraction

tag: tumour type

value: Medulloblastoma

tag: oxygen percentage


title: RNAseq_24hr_rep3

city: Berkeley


title: MED8_0.1_rep2


title: RNAseq_72hr_rep3


title: RNAseq_12hr_rep3


title: Non-malignant lung 06L20_N

description: Fresh frozen non-malignant lung sample

data_processing: Probe intensity files were processed in Partek Genomics Suite (Partek Incorporated, Missouri, USA). Probe sequencing, GC content, fragment length, and background adjustments were applied to correct for biases in signal intensities. DNA copy number profiles were generated in the Copy Number, Paired Analysis Workflow using patient-matched non-malignant lung as a baseline for each lung tumour sample. Segmentation was applied using stringent significance thresholds to identify regions of copy number gain and loss (signal to noise >0.3, minimum of 50 markers per segment, p-value < 10-7). Segments were merged using a 1 Mbp windown. Genomic mapping was based on the hg18 genomic build.

tag: patient

value: Female

value: Caucasian

tag: kras mutation


title: Lung adenocarcinoma 06L30_T

description: Fresh frozen non-malignant lung sample

tag: sample

tag: age (years)

value: Former

value: IIB

value: WT


title: MED8_0.1_rep1


title: Non-malignant lung 06L14_N

description: Fresh frozen non-malignant lung sample


title: Patients_49_Training_P_49

tag: histology

value: Good-Response


title: A549_ELF3_knockdown_rep1

description: A549 ELF3 shRNA knock-down clone

tag: cell line

value: non-small cell lung cancer

tag: genotype/variation

value: ELF3 knock-down


title: RNAseq_6hr_rep3


title: RNAseq_3hr_rep3


title: MED8_1_rep3

source_name: MED-MED8A cells incubated in 1% O2 for 5 days


title: RNAseq_0hr_rep3


title: Lung adenocarcinoma 06L10_T

description: Fresh frozen non-malignant lung sample

tag: Sex

tag: race

value: Current

value: IB


title: Non-malignant lung 06L29_N

description: Fresh frozen non-malignant lung sample

value: Non-malignant lung

value: Normal

value: Asian

tag: smoking history

value: Never

tag: pack-years


title: MED8_1_rep2


title: Lung adenocarcinoma 06L14_T

description: Fresh frozen non-malignant lung sample

value: Lung adenocarcinoma

value: Tumor

tag: Stage

tag: egfr mutation


title: Lung adenocarcinoma 06L11_T

description: Fresh frozen non-malignant lung sample

tag: tissue

value: IA

value: MUT


title: Patients_47_Training_P_47


title: MED8_1_rep1

value: Medulloblastoma


title: Patients_46_Training_P_46


title: Patients_48_Training_P_48


title: RNAseq_72hr_rep2

tag: cell type

value: H1 hESC-derived neural progenitor cells


title: Patients_50_Training_P_50

value: Non-Response


title: Non-malignant lung 06L22_N

description: Fresh frozen non-malignant lung sample

value: Male

value: asian


title: RNAseq_48hr_rep2


title: MED8_21_rep3

source_name: MED-MED8A cells incubated in 21% O2 for 5 days

tag: tumour type


title: Patients_45_Training_P_45

value: Good-Response


title: Lung adenocarcinoma 05L9_T

description: Fresh frozen non-malignant lung sample

value: Female

value: Caucasian

value: WT


title: RNAseq_24hr_rep2


title: MED8_21_rep2

tag: oxygen percentage


title: RNAseq_12hr_rep2


title: Lung adenocarcinoma 06L20_T

description: Fresh frozen non-malignant lung sample

tag: patient

value: Current

value: IB


title: Patients_44_Training_P_44


title: Patients_43_Training_P_43


title: MED8_21_rep1


title: Patients_42_Training_P_42


title: D283_1_rep3

source_name: D283-MED cells incubated in 1% O2 for 5 days


title: Non-malignant lung 06L11_N

description: Fresh frozen non-malignant lung sample

value: Non-malignant lung

value: Normal

tag: kras mutation


title: Patients_41_Training_P_41


title: RNAseq_3hr_rep2


title: Patients_40_Training_P_40


title: D283_1_rep1