title: P8_UN14_P2759_N711.S503

description:
processed data file: P2759.tsv
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title: P8_UN14_P2759_N710.S502

status: Public on Nov 16 2021

type: SRA

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

description:
processed data file: P2759.tsv
CD2ALANXX_4_N710-S502-NX-xt

library_source: transcriptomic

data_processing:
Reads were then demultiplexed according to the cell barcodes
Sequenced reads were filtered for low-complexity or low-quality sequence.
High quality reads were mapped according to the GEM pipeline
Genome_build: Human:  GRCh38
Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing gene expression values as read counts

molecule: total RNA

organism: Homo sapiens

growth_protocol: SCC-25 (ATCCR CRL-168TM) were grown in keratinocyte serum-free media (KSFM, Gibco) supplemented with 5 μg ml–1 penicillin/streptomycin, 0.025 mg ml–1 bovine pituitary extract and 0.2 μg ml–1 hEGF.

extract_protocol:
Live SCC-25 sorted cells were lysed using lysis buffer (0.2% Triton-100, 1U/ul RNase inhibitor). Reverse transcription was performed using SuperScript II (ThermoFisher Scientific) in the presence of 1 μM oligo-dT30VN (IDT), 1 μM template-switching oligonucleotides (QIAGEN), and 1 M betaine.
Libraries were prepared according to the Nextera XT (Illumina) instructions.

treatment_protocol: Cells growing in serum–free media were treated in vitro with 300 μM palmitic acid for 96 h (4 days) and after palmitic acid withdrawal cells were passaged normally (when reaching 80% confluence) for 14 days and collected for sorting of live SCC-25 cells into 96 well sorting plates.

tag: cell line

tag: cell type

value: oral squamous cell carcinoma (OSCC) cell line

tag: shRNA

value: control pLKO.1

tag: protocol

value: Smart-seq2; full-length RNA-seq


title: P8_UN14_P2759_N710.S507

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title: Empty_P2759_N707.S502

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source_name: Empty


title: P8_PA4_P2759_N706.S511

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title: P8_PA4_P2759_N706.S510

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title: P8_PA4_P2759_N706.S507

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title: P7_PA14_P2725_N729.S510

description:
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title: P7_PA14_P2725_N729.S511

description:
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description:
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description:
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description:
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description:
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description:
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description:
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title: P4_UN4_P2669_N702.S516

description:
processed data file: P2669.tsv
CD2WGANXX_1_N702-S516-NX-xt


title: P4_UN4_P2669_N701.S517

description:
processed data file: P2669.tsv
CD2WGANXX_1_N701-S517-NX-xt


title: P4_UN4_P2669_N702.S513

description:
processed data file: P2669.tsv
CD2WGANXX_1_N702-S513-NX-xt


title: P4_UN4_P2669_N701.S515

description:
processed data file: P2669.tsv
CD2WGANXX_1_N701-S515-NX-xt


title: P4_UN4_P2669_N701.S516

description:
processed data file: P2669.tsv
CD2WGANXX_1_N701-S516-NX-xt


title: P4_UN4_P2669_N701.S513

description:
processed data file: P2669.tsv
CD2WGANXX_1_N701-S513-NX-xt


title: P4_UN4_P2669_N701.S521

description:
processed data file: P2669.tsv
CD2WGANXX_1_N701-S521-NX-xt


title: P4_UN4_P2669_N701.S522

description:
processed data file: P2669.tsv
CD2WGANXX_1_N701-S522-NX-xt


title: P4_UN4_P2669_N701.S520

description:
processed data file: P2669.tsv
CD2WGANXX_1_N701-S520-NX-xt


title: P4_UN4_P2669_N701.S518

description:
processed data file: P2669.tsv
CD2WGANXX_1_N701-S518-NX-xt


title: P4_UN4_P2669_N702.S515

description:
processed data file: P2669.tsv
CD2WGANXX_1_N702-S515-NX-xt


title: 25-shGAL #73_4 PALM- #3

type: RNA

description: CD36-dim FACS sorted cells from shGAL orthotopic VDH15 oral carcinoma cell line xenografts exposed to PA-rich diet

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays were scanned with GeneChip scanner GSC3000 (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization method as implemented in affy Bioconductor R package

label: biotin

source_name: CD36-dim cells / shGAL / VDH15 oral carcinoma cell line / PA-rich diet

label_protocol: 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Cells were grown in an orthotopic xenograft model in NOD-SCIDγ mice (NSG)

extract_protocol: RNA was isolated using magnetic beads. Library preparation and amplification were performed as described by Gonzalez et al., 2010.

tag: sample id

tag: scan batch

tag: biological replicate

tag: technical replicate

tag: diet

value: PA-rich diet

tag: sh

value: shGAL

value: VDH15 oral carcinoma cell line


title: P3_PA14_P2655_N715.S521

description:
processed data file: P2655.tsv
CCYYKANXX_8_N715-S521-NX-xt


title: P3_PA14_P2655_N715.S522

description:
processed data file: P2655.tsv
CCYYKANXX_8_N715-S522-NX-xt


title: P3_PA14_P2655_N715.S520

description:
processed data file: P2655.tsv
CCYYKANXX_8_N715-S520-NX-xt


title: P3_PA14_P2655_N715.S518

description:
processed data file: P2655.tsv
CCYYKANXX_8_N715-S518-NX-xt


title: 25-shEGR2 #38_9 PALM+ #3

description: CD36-bright FACS sorted cells from shEGR2_38.9 orthotopic VDH15 oral carcinoma cell line xenografts exposed to PA-rich diet

source_name: CD36-bright cells / shEGR2_38.9 / VDH15 oral carcinoma cell line / PA-rich diet


title: 25-shGAL #73_4  PALM-   #2


title: 25-shGAL #73_4  CT- #1

description: CD36-dim FACS sorted cells from shGAL orthotopic VDH15 oral carcinoma cell line xenografts exposed to control diet

source_name: CD36-dim cells / shGAL / VDH15 oral carcinoma cell line / control diet

value: control diet


title: 25-shEGR2 #38_9 PALM- #3

description: CD36-dim FACS sorted cells from shEGR2_38.9 orthotopic VDH15 oral carcinoma cell line xenografts exposed to PA-rich diet

source_name: CD36-dim cells / shEGR2_38.9 / VDH15 oral carcinoma cell line / PA-rich diet


title: 25-shEGR2 #38_9 PALM- #1


title: 25-shEGR2 #38_9 CT- #3

description: CD36-dim FACS sorted cells from shEGR2_38.9 orthotopic VDH15 oral carcinoma cell line xenografts exposed to control diet

source_name: CD36-dim cells / shEGR2_38.9 / VDH15 oral carcinoma cell line / control diet


title: 25-shGAL #73_4 CT+ #1

description: CD36-bright FACS sorted cells from shGAL orthotopic VDH15 oral carcinoma cell line xenografts exposed to control diet

source_name: CD36-bright cells / shGAL / VDH15 oral carcinoma cell line / control diet


title: 25-shEGR2 #38_9 PALM+ #1


title: 25-shGAL #73_4 CT- #3


title: 25-shGAL #73_4  PALM+ #3

description: CD36-bright FACS sorted cells from shGAL orthotopic VDH15 oral carcinoma cell line xenografts exposed to PA-rich diet

source_name: CD36-bright cells / shGAL / VDH15 oral carcinoma cell line / PA-rich diet


title: 25-shGAL #73_4  CT-   #2


title: 25-shEGR2 #38_9 PALM-   #2


title: P3_PA14_P2655_N715.S515

description:
processed data file: P2655.tsv
CCYYKANXX_8_N715-S515-NX-xt


title: P3_PA14_P2655_N715.S516

description:
processed data file: P2655.tsv
CCYYKANXX_8_N715-S516-NX-xt


title: P3_PA14_P2655_N715.S517

description:
processed data file: P2655.tsv
CCYYKANXX_8_N715-S517-NX-xt


title: P3_PA14_P2655_N715.S513

description:
processed data file: P2655.tsv
CCYYKANXX_8_N715-S513-NX-xt


title: 25-shGAL #73_4  PALM+ #2


title: 25-shGAL #73_4  CT+ #2


title: P3_PA14_P2655_N714.S522

description:
processed data file: P2655.tsv
CCYYKANXX_8_N714-S522-NX-xt


title: P3_PA14_P2655_N714.S521

description:
processed data file: P2655.tsv
CCYYKANXX_8_N714-S521-NX-xt


title: 25-PLKO PALM+ #6

description: CD36-bright FACS sorted cells from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to PA-rich diet

source_name: CD36-bright cells / PLKO / VDH15 oral carcinoma cell line / PA-rich diet

value: PLKO


title: 25-shEGR2 #38_9 PALM+ #2


title: 25-shEGR2 #38_9 CT-   #2


title: 25-shEGR2 #38_9 CT+ #2

description: CD36-bright FACS sorted cells from shEGR2_38.9 orthotopic VDH15 oral carcinoma cell line xenografts exposed to control diet

source_name: CD36-bright cells / shEGR2_38.9 / VDH15 oral carcinoma cell line / control diet


title: 25-shGAL #73_4 PALM+ #1


title: 25-shGAL #73_4  PALM- #1

description: CD36-dim FACS sorted cells from shGAL orthotopic VDH15 oral carcinoma cell line xenografts exposed to PA-rich diet


title: P3_PA14_P2655_N714.S516

description:
processed data file: P2655.tsv
CCYYKANXX_8_N714-S516-NX-xt


title: P3_PA14_P2655_N712.S522

description:
processed data file: P2655.tsv
CCYYKANXX_8_N712-S522-NX-xt


title: P3_PA14_P2655_N714.S515

description:
processed data file: P2655.tsv
CCYYKANXX_8_N714-S515-NX-xt


title: P3_PA14_P2655_N714.S517

description:
processed data file: P2655.tsv
CCYYKANXX_8_N714-S517-NX-xt


title: P3_PA14_P2655_N714.S520

description:
processed data file: P2655.tsv
CCYYKANXX_8_N714-S520-NX-xt


title: P3_PA14_P2655_N714.S518

description:
processed data file: P2655.tsv
CCYYKANXX_8_N714-S518-NX-xt


title: 25-shGAL #73_4  CT+ #3

description: CD36-bright FACS sorted cells from shGAL orthotopic VDH15 oral carcinoma cell line xenografts exposed to control diet


title: uninfected with control rep 3

city: San Francisco

first: Xinyue

last: Chen

state: California

address: 1650 Owens St

country: USA

institute: Gladstone Institutes

data_processing:
Read quality was checked via FASTQC, followed by mapping to MesAur1.0 (GCA_000349665.1) reference genome using STAR (STAR-2.7.9a) with default parameters.
Transcript level quantification was performed using featureCounts (subread-2.0.2) with default parameters.
Genome_build: MesAur1.0
Supplementary_files_format_and_content: Text files for raw gene counts for each individual samples.
Supplementary_files_format_and_content: Excel file for a matrix table containing normalized gene counts across all samples.

organism: Mesocricetus auratus

source_name: lung tissue

extract_protocol:
Lungs were homogenized, RNA was extracted from the lung lysates using Direct-zol RNA extraction kit.
RNA libraries were prepared using Illumina Stranded total RNA library prep kit (cat# 20040525, Illumina inc.) and sequencing performed on a NextSeq 500 sequencer (cat# SY-415-1001, Illumina Inc).

treatment_protocol: Samples 1-10: 8-week old syrian golden hamsters were infected through intranasal installation of 10^6 total PFU per animal of SARS-CoV-2 (USA-WA1/2020) 100 ml of DMEM, as described (Rogers et al., 2020).  6 hours pre-infection and 18 hours post infection animals were given an intranasal dose of 100 ml  of LNP solution containing 60 mg of either TIP RNA (hamsters n=5; samples 1-5) or control RNA (hamsters n=5; samples 6-10). For uninfected samples; 8-week old syrian golden hamsters were intranasally treated with TIP (hamsters n=3; samples 11-13) or control RNA LNPs (hamsters n=3; samples 14-16). At day-5 post-infection, animals were sacrificed and lungs were harvested.

tag: agent

value: uninfected

tag: treatment

value: LNPs containing control RNA


title: 25-PLKO PALM- #6

description: CD36-dim FACS sorted cells from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to PA-rich diet

source_name: CD36-dim cells / PLKO / VDH15 oral carcinoma cell line / PA-rich diet


title: 25-shEGR2 #38_9 CT- #1

description: CD36-dim FACS sorted cells from shEGR2_38.9 orthotopic VDH15 oral carcinoma cell line xenografts exposed to control diet


title: P3_PA14_P2655_N712.S521

description:
processed data file: P2655.tsv
CCYYKANXX_8_N712-S521-NX-xt


title: 25-PLKO PALM- #4


title: uninfected with control rep 2


title: 25-PLKO CT+#6

description: CD36-bright FACS sorted cells from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to control diet

source_name: CD36-bright cells / PLKO / VDH15 oral carcinoma cell line / control diet


title: 25-PLKO CT- #5

description: CD36-dim FACS sorted cells from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to control diet

source_name: CD36-dim cells / PLKO / VDH15 oral carcinoma cell line / control diet


title: 25-PLKO PALM+ #5


title: 25-PLKO PALM+ #4


title: P3_PA14_P2655_N712.S518

description:
processed data file: P2655.tsv
CCYYKANXX_8_N712-S518-NX-xt


title: uninfected with TIP rep 3

value: LNPs containing TIP RNA


title: P3_PA14_P2655_N712.S517

description:
processed data file: P2655.tsv
CCYYKANXX_8_N712-S517-NX-xt


title: uninfected with TIP rep 2


title: P3_PA14_P2655_N712.S520

description:
processed data file: P2655.tsv
CCYYKANXX_8_N712-S520-NX-xt


title: P3_PA14_P2655_N712.S516

description:
processed data file: P2655.tsv
CCYYKANXX_8_N712-S516-NX-xt


title: 25-PLKO CT- #4


title: 25-PLKO PALM- #5


title: uninfected with control rep 1


title: 25-PLKO CT+ #5


title: P3_PA14_P2655_N714.S513

description:
processed data file: P2655.tsv
CCYYKANXX_8_N714-S513-NX-xt


title: 25-shEGR2 #40_9 PALM- #1

description: CD36-dim FACS sorted cells from shEGR2_40.9 orthotopic VDH15 oral carcinoma cell line xenografts exposed to PA-rich diet

source_name: CD36-dim cells / shEGR2_40.9 / VDH15 oral carcinoma cell line / PA-rich diet


title: uninfected with TIP rep 1


title: P3_PA14_P2655_N712.S515

description:
processed data file: P2655.tsv
CCYYKANXX_8_N712-S515-NX-xt


title: P3_Empty_P2655_N712.S513

description:
processed data file: P2655.tsv
CCYYKANXX_8_N712-S513-NX-xt


title: 25-shEGR2 #40_9 CT- #2

description: CD36-dim FACS sorted cells from shEGR2_40.9 orthotopic VDH15 oral carcinoma cell line xenografts exposed to control diet

source_name: CD36-dim cells / shEGR2_40.9 / VDH15 oral carcinoma cell line / control diet


title: infected with control pre-treat rep 4

value: infected with SARS-CoV-2


title: 25-shEGR2 #40_9 CT- #3


title: infected with control pre-treat rep 5


title: 25-PLKO CT+ #4


title: 25-shEGR2 #40_9 PALM- #3


title: 25-shEGR2 #40_9 PALM- #2


title: 25-shEGR2 #40_9 CT+ #2

description: CD36-bright FACS sorted cells from shEGR2_40.9 orthotopic VDH15 oral carcinoma cell line xenografts exposed to control diet

source_name: CD36-bright cells / shEGR2_40.9 / VDH15 oral carcinoma cell line / control diet


title: infected with control pre-treat rep 3


title: 25-PLKO CT- #6


title: 25-shEGR2 #40_9 CT+ #1


title: 25-shEGR2 #40_9 CT- #1


title: 25-shEGR2 #40_9 PALM+ #1

description: CD36-bright FACS sorted cells from shEGR2_40.9 orthotopic VDH15 oral carcinoma cell line xenografts exposed to PA-rich diet

source_name: CD36-bright cells / shEGR2_40.9 / VDH15 oral carcinoma cell line / PA-rich diet


title: infected with control pre-treat rep 2


title: 25-shEGR2 #40_9 PALM+ #3


title: P3_UN14_P2655_N711.S521

description:
processed data file: P2655.tsv
CCYYKANXX_8_N711-S521-NX-xt


title: P3_UN14_P2655_N711.S520

description:
processed data file: P2655.tsv
CCYYKANXX_8_N711-S520-NX-xt


title: 25-PLKO PALM- #3

description: CD36-dim FACS sorted cells from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to PA-rich diet


title: 25-shEGR2 #40_9 CT+ #3


title: 25-PLKO PALM+#3

description: CD36-bright FACS sorted cells from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to PA-rich diet


title: P3_UN14_P2655_N711.S522

description:
processed data file: P2655.tsv
CCYYKANXX_8_N711-S522-NX-xt


title: 25-PLKO PALM- #1


title: P3_UN14_P2655_N711.S518

description:
processed data file: P2655.tsv
CCYYKANXX_8_N711-S518-NX-xt


title: infected with TIP pre-treat rep 5


title: P3_UN14_P2655_N711.S517

description:
processed data file: P2655.tsv
CCYYKANXX_8_N711-S517-NX-xt


title: infected with TIP pre-treat rep 4


title: infected with control pre-treat rep 1


title: 25-PLKO PALM- #2


title: P3_UN14_P2655_N711.S515

description:
processed data file: P2655.tsv
CCYYKANXX_8_N711-S515-NX-xt


title: 25-PLKO CT- #3

description: CD36-dim FACS sorted cells from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to control diet


title: 25-PLKO PALM+ #1


title: 25-PLKO PALM+ #2


title: infected with TIP pre-treat rep 2


title: infected with TIP pre-treat rep 3


title: 25-PLKO CT+#3

description: CD36-bright FACS sorted cells from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to control diet


title: 25-PLKO CT+ #2


title: P3_UN14_P2655_N710.S522

description:
processed data file: P2655.tsv
CCYYKANXX_8_N710-S522-NX-xt


title: 15-shCD36PALM-nb.2

description: CD36-dim FACS sorted cells from shCD36 orthotopic VDH15 oral carcinoma cell line xenografts exposed to PA-rich diet

source_name: CD36-dim cells / shCD36 / VDH15 oral carcinoma cell line / PA-rich diet

tag: hybridization batch


title: infected with TIP pre-treat rep 1


title: P3_UN14_P2655_N711.S516

description:
processed data file: P2655.tsv
CCYYKANXX_8_N711-S516-NX-xt


title: 15-shCD36PALM-nb.1


title: P3_UN14_P2655_N710.S521

description:
processed data file: P2655.tsv
CCYYKANXX_8_N710-S521-NX-xt


title: 15-shCD36PALM-nb.3


title: 25-PLKO CT+ #1


title: P3_UN14_P2655_N710.S518

description:
processed data file: P2655.tsv
CCYYKANXX_8_N710-S518-NX-xt


title: 15-shCD36CT-nb.2

description: CD36-dim FACS sorted cells from shCD36 orthotopic VDH15 oral carcinoma cell line xenografts exposed to control diet

source_name: CD36-dim cells / shCD36 / VDH15 oral carcinoma cell line / control diet


title: P3_UN14_P2655_N711.S513

description:
processed data file: P2655.tsv
CCYYKANXX_8_N711-S513-NX-xt


title: 15-PLKOPALM-nb.3


title: P3_UN14_P2655_N710.S517

description:
processed data file: P2655.tsv
CCYYKANXX_8_N710-S517-NX-xt


title: P3_UN14_P2655_N710.S516

description:
processed data file: P2655.tsv
CCYYKANXX_8_N710-S516-NX-xt


title: 15-shCD36CT-nb.3


title: 25-PLKO CT- #1


title: P3_UN14_P2655_N707.S521

description:
processed data file: P2655.tsv
CCYYKANXX_8_N707-S521-NX-xt


title: P3_UN14_P2655_N710.S513

description:
processed data file: P2655.tsv
CCYYKANXX_8_N710-S513-NX-xt


title: P3_UN14_P2655_N710.S515

description:
processed data file: P2655.tsv
CCYYKANXX_8_N710-S515-NX-xt


title: 15-PLKOCT+nb.3


title: 15-PLKOPALM-nb.2

description: CD36-dim FACS sorted cells from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to PA-rich diet


title: P3_UN14_P2655_N707.S522

description:
processed data file: P2655.tsv
CCYYKANXX_8_N707-S522-NX-xt


title: 15-PLKOCT+nb.1


title: 15-PLKOPALM+nb.1

description: CD36-bright FACS sorted cells from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to PA-rich diet


title: 15-shCD36CT-nb.1


title: 15-PLKOCT-nb.3

description: CD36-dim FACS sorted cells from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to control diet


title: 15-PLKOPALM-nb.1


title: 25-shCD36 PALM- nb.3

description: CD36-dim FACS sorted cells from shCD36 orthotopic SCC25 oral carcinoma cell line xenografts exposed to PA-rich diet

source_name: CD36-dim cells / shCD36 / SCC25 oral carcinoma cell line / PA-rich diet

value: SCC25 oral carcinoma cell line


title: 15-PLKOPALM+nb.3


title: 25-PLKO PALM+ nb.1

description: CD36-bright FACS sorted cells from PLKO orthotopic SCC25 oral carcinoma cell line xenografts exposed to PA-rich diet

source_name: CD36-bright cells / PLKO / SCC25 oral carcinoma cell line / PA-rich diet


title: P3_UN14_P2655_N710.S520

description:
processed data file: P2655.tsv
CCYYKANXX_8_N710-S520-NX-xt


title: 25-PLKO PALM- nb.2

description: CD36-dim FACS sorted cells from PLKO orthotopic SCC25 oral carcinoma cell line xenografts exposed to PA-rich diet

source_name: CD36-dim cells / PLKO / SCC25 oral carcinoma cell line / PA-rich diet


title: 15-PLKOCT+nb.2

description: CD36-bright FACS sorted cells from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to control diet


title: 15-PLKOCT-nb.1


title: 25-PLKO PALM- nb.3


title: 25-PLKO PALM+nb.3


title: P3_UN14_P2655_N707.S520

description:
processed data file: P2655.tsv
CCYYKANXX_8_N707-S520-NX-xt


title: 25-PLKO PALM- nb.1


title: 15-PLKOCT-nb.2


title: 15-PLKOPALM+nb.2


title: P3_UN14_P2655_N707.S518

description:
processed data file: P2655.tsv
CCYYKANXX_8_N707-S518-NX-xt


title: 25-shCD36 PALM- nb.1


title: P3_UN14_P2655_N707.S517

description:
processed data file: P2655.tsv
CCYYKANXX_8_N707-S517-NX-xt


title: 25-shCD36 PALM- nb.2


title: 2276-Mut

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

data_processing:
Image processing, base calling, quality scoring (Phred), and sample demultiplexing were executed by HiSeq Control Software (HCS) HD 3.4.0 and Real-Time Analysis (RTA) v2.7.7 software. The bcl2fastq conversion software was used for sample demultiplexing and FASTQ conversion.
RNA-seq data was analyzed using a TopHat-Cufflinks pipeline. De-multiplexed raw sequence reads (FASTQ format) were mapped to the reference mouse genome assembly (GRCm38/mm10) using TopHat. Mapped reads were then passed onto Cufflinks for transcript assembly and quantitation of gene- and transcript isoform expression as FPKM (Fragments Per Kilobase of transcript per Million mapped reads). Subsequently, FPKM expression values were normalized with Cufflinks tools (e.g., Cuffquant, Cuffnorm).
Processed data are Cufflinks-Cufffnorm output files and contain Gene_Symbol, FPKM values, and FPKM status.
Genome_build: Dec. 2011, GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text files include Gene Symbol, FPKM values, and FPKM status for each transcript and were prepared from the Cufflinks-Cuffnorm gene-level output files.

organism: Mus musculus

source_name: gastrocnemius muscle

extract_protocol:
Total cellular RNA was isolated from mouse gastrocnemius muscle samples using the the RNeasy Universal Kit (Qiagen).
Indexed, directional RNA-Seq libraries were prepared from total RNA using the KAPA Stranded mRNA-Seq Kit (Roche) according to the manufacturer’s standard protocol.

treatment_protocol: Wild type and heterozygous Hras G12V mice were untreated prior to collection of gastrocnemius muscle tissue. All animal procedures were reviewed and approved by the UC Davis Institutional Animal Care and Use Committee (IACUC).

tag: mouse model

value: Hras G12V

tag: hras genotype

value: heterozygous

tag: genotype

tag: mouse strain

value: Caggs-Cre+/HrasG12V/+ (HrasG12V)


title: 2279-Mut


title: P3_UN14_P2655_N707.S516

description:
processed data file: P2655.tsv
CCYYKANXX_8_N707-S516-NX-xt

tag: cell line


title: 2278-Mut


title: 2281-WT

value: wild type

value: Hras+/+

value: Caggs-Cre-/HrasflG12V/+ (WT)


title: 25-PLKO PALM+ nb.2


title: 2280-WT


title: 2277-WT


title: P3_UN14_P2655_N707.S515

description:
processed data file: P2655.tsv
CCYYKANXX_8_N707-S515-NX-xt

tag: cell type

value: oral squamous cell carcinoma (OSCC) cell line

value: control pLKO.1

value: Smart-seq2; full-length RNA-seq


title: P3_Empty_P2655_N707.S513

description:
processed data file: P2655.tsv
CCYYKANXX_8_N707-S513-NX-xt

tag: shRNA


title: P3_PA4_P2655_N706.S522

description:
processed data file: P2655.tsv
CCYYKANXX_8_N706-S522-NX-xt

tag: protocol


title: 25-PLKO CT+nb.3

description: CD36-bright FACS sorted cells from PLKO orthotopic SCC25 oral carcinoma cell line xenografts exposed to control diet

source_name: CD36-bright cells / PLKO / SCC25 oral carcinoma cell line / control diet

tag: sample id


title: P3_PA4_P2655_N706.S521

description:
processed data file: P2655.tsv
CCYYKANXX_8_N706-S521-NX-xt


title: E11_NSC_rep2_H3K27ChIP-seq

city: Fukuoka

first: Sayako

last: Katada

address: Higashiku Maidashi

country: Japan

institute: Kyushu University

library_source: genomic

data_processing:
Obtained reads were assessed with FastQC, and mapped to the mouse mm10 genome using Bowtie2.
Genome_build: mm10

molecule: genomic DNA

source_name: E11 NS/PCs primary culture

growth_protocol: Telencephalons of E11 or E14 fetal mice were tritutated in Hank's balanced salt solution by mild pippetting. After centifugation, the cell pellet was resuspended in N2-supplemented Dulbecco's Modified Eagle Medium /F-12, containing 10 ng/mL basic fibloblast growth factor and plated on dishes precoated with poly-L-ornithine/fibronectin.

extract_protocol:
Cells were fixed with 1% formaldehyde and then suspended in lysis buffer. The lysates were sonicated with a sonicator.
Libraries were made according to instructions in the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, Cat# E7645S).

treatment_protocol: Not applicable.

tag: strain

tag: developmental stage

value: Neural stem/precursor cells (primary culture)

tag: chip antibody

value: Ab:H3K27me3 (MBL, Cat# MAB10323)


title: P3_PA4_P2655_N706.S520

description:
processed data file: P2655.tsv
CCYYKANXX_8_N706-S520-NX-xt


title: P3_PA4_P2655_N706.S518

description:
processed data file: P2655.tsv
CCYYKANXX_8_N706-S518-NX-xt


title: E11_NSC_rep1_H3K27ChIP-seq


title: M421_Primary

city: Washington

first: Zhenhua

last: Xu

state: District of Columbia

address: 111 Michigan Ave NW

institute: Children's National Hospital

data_processing:
FASTQ files were mapped to human reference (GRCh38) using STAR software with default settings. Gene counts were obtained using the function featureCounts from the R package Rsubread using the NCBI human RefSeq annotation. Diferentyally expressed genes (DEG) were obtained with the R package DESeq2. The genes with an p-adjusted < 0.001 and Fold change > 2 were consider as significant differentially expressed genes.
Genome_build: GRCh38
Supplementary_files_format_and_content: Total raw counts for RNA-seq

source_name: patient-derived xenograft MB002

growth_protocol: Tumor cells were transplanted into the cerebella of R2G2 mice and monitored for growth weekly by bioluminescent imaging with an IVIS imager.

extract_protocol:
Tumor tissue was digested into single cell fraction using papain (10U/mL PBS) and Dnase I (250U/mL).  Following tissue digestion, RNA was extracted from tumor cell pellets using the QIAGEN RNAeasy prep kit (Cat #74134)  and reverse transcribed into cDNA using the Bio-Rad Reverse Transcriptase kit.
RNA libraries were prepared for sequencing using standard DBNseq protocols

treatment_protocol: Once tumors reached a luminescence signal of 10^7, animals in the treatment group were administered radiotherapy with a RS 2000 Biological System Irradiator.  Animals were treated with 2Gy per dose at a rate of approximately 120 rads/minute every other day for a total cumulative dose of 18Gy.  For spontaneous recurrent tumors, animals were maintained following radiotherapy until they relapsed.  For transplanted recurrent tumors, the radioresistant tumor cells were collected from irradiated tumor-bearing animals, cultured and passaged in stem cell medium until they grew neurospheres.  The neurospheres were then transplanted into the cerebella of R2G2 mice and all animals were monitored weekly by bioluminescent imaging to track the growth of relapsed tumors.

tag: tumor cells

value: patient-derived xenograft MB002

value: Rag2-Il2rg double Knockout mice

value: untreated


title: M413_Primary


title: M426_Primary

value: Rag2-Il2rg double Knockout mice (R2G2)


title: M297_Spontanous_recurrent_tumor

value: radiation for 18 Gy


title: E14_NSC_rep2_H3K27ChIP-seq

source_name: E14 NS/PCs primary culture


title: E11/14NSC IgG

source_name: E11/14 NS/PCs primary culture

value: Ab:IgG (SantaCruz, sc-2025)


title: P3_PA4_P2655_N706.S517

description:
processed data file: P2655.tsv
CCYYKANXX_8_N706-S517-NX-xt


title: 25-PLKO CT- nb.2

description: CD36-dim FACS sorted cells from PLKO orthotopic SCC25 oral carcinoma cell line xenografts exposed to control diet

source_name: CD36-dim cells / PLKO / SCC25 oral carcinoma cell line / control diet

tag: scan batch

tag: biological replicate

tag: technical replicate

tag: diet

value: control diet

value: PLKO

value: SCC25 oral carcinoma cell line


title: P3_PA4_P2655_N706.S516

description:
processed data file: P2655.tsv
CCYYKANXX_8_N706-S516-NX-xt


title: M295_Spontanous_recurrent_tumor

tag: treatment


title: 25-PLKO CT- #2

description: CD36-dim FACS sorted cells from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to control diet

source_name: CD36-dim cells / PLKO / VDH15 oral carcinoma cell line / control diet

tag: sh

value: VDH15 oral carcinoma cell line


title: M1029_Transplanted_recurrent_tumor

value: Residual cells after 18 Gy of radiation, then cultere in vitro for 3 weeks, the cells from the neurosphere were transplanted into R2G2 mice


title: 25-PLKO CT+ nb.2

tag: hybridization batch


title: 25-PLKO CT+ nb.1


title: Retina E14.5 SE WT RNA-seq

city: Memphis

first: Victoria

last: Honnell

state: Tennessee

address: 262 Danny Thomas

institute: St. Jude Children's Research Hospital

description:
Retina E14.5 Vsx2SE WT bulk RNA-seq
DE_single_subject_protein_coding_ko_vs_wt.txt

data_processing:
scRNA-sequencing data was processed individually then aggregated using cellranger v3.0.2
scATAC-sequencing data was processed using cellranger-atac v1.0.1
Genome_build: mm10
Supplementary_files_format_and_content: For scRNA-seq tab delimited features(genes) and barcodes file and matrix file.
Supplementary_files_format_and_content: For scATAC-seq tab delimited fragments and barcodes file, matrix file, peaks bed file, and tab delimited peak_annotation

source_name: retina

extract_protocol:
Retinas were removed, dissociated with papain, and run through a 4% BSA cushion. Cells were processed using the 10x genomics protocols. For bulk RNA, RNA was extracted from retina through trizol method. For ChIP, retina were removed and immediately place on dry ice.
Library construction was completed using the 10x RNA(v3) and ATAC-seq(v1) single cell kits

value: retina

tag: age

tag: genotype

value: Wildtype

tag: molecule type

value: RNA


title: P3_PA4_P2655_N706.S515

description:
processed data file: P2655.tsv
CCYYKANXX_8_N706-S515-NX-xt

tag: cell line

tag: cell type

value: oral squamous cell carcinoma (OSCC) cell line

tag: shRNA

value: control pLKO.1

value: Smart-seq2; full-length RNA-seq


title: PB.GSKJ4.rep3

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm9 version of the mouse genome using Tophat2 and the UCSC mm9 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Genome_build: mm9
Supplementary_files_format_and_content: Annotation file containing RPKM normalized read counts for all detected genes.

molecule: polyA RNA

source_name: ex vivo cultured B cells

extract_protocol:
After 3 days of culture, total RNA was extracted using the Zymo Quick-RNA MicroPrep Kit
500ng  of total RNA was used as input for the KAPA Biosystems mRNA HyperPrep Kit.

treatment_protocol: CD43- B cells were isolated from wild-type mice and cultured ex vivo in the presence of LPS, IL-2, and IL-5 with either DMSO or GSK-J4

tag: Sex

value: female

tag: sorting markers

value: magnetically enriched CD138+ cells

tag: strain

tag: mouse id

value: mouse 3

tag: stimulation

value: LPS, IL-2, IL-5

tag: drug treatment

value: 250nM GSK-J4

value: B cells


title: 25-PLKO CT- nb.1

tag: sample id

tag: scan batch

tag: biological replicate

tag: technical replicate

value: control diet


title: M1028_Transplanted_recurrent_tumor

tag: tumor cells

value: patient-derived xenograft MB002

tag: mouse strain

value: Rag2-Il2rg double Knockout mice

tag: treatment


title: M1027_Transplanted_recurrent_tumor


title: PB.DMSO.rep3

value: DMSO


title: M296_Spontanous_recurrent_tumor

value: radiation for 18 Gy


title: E14_NSC_rep1_H3K27ChIP-seq

tag: developmental stage

value: Neural stem/precursor cells (primary culture)

tag: chip antibody

value: Ab:H3K27me3 (MBL, Cat# MAB10323)


title: P3_PA4_P2655_N706.S513

description:
processed data file: P2655.tsv
CCYYKANXX_8_N706-S513-NX-xt

tag: cell line

tag: cell type

tag: protocol


title: 501mel shCD36-PALM Diet nb.3

description: CD36-dim FACS sorted cells from shCD36 orthotopic melanoma cell line xenografts exposed to PA-rich diet

source_name: CD36-dim cells / shCD36 / melanoma cell line / PA-rich diet

tag: hybridization batch

tag: diet

value: PA-rich diet

value: melanoma cell line


title: P3_PA4_P2655_N705.S522

description:
processed data file: P2655.tsv
CCYYKANXX_8_N705-S522-NX-xt

value: oral squamous cell carcinoma (OSCC) cell line

tag: shRNA

value: control pLKO.1


title: ActB.GSKJ4.rep3

tag: Sex

value: female

tag: sorting markers

value: magnetically enriched GL7+ B cells

tag: strain

tag: mouse id

tag: stimulation


title: 25-PLKO CT- nb.3

tag: sample id

tag: scan batch

tag: biological replicate

tag: technical replicate

value: PLKO

value: SCC25 oral carcinoma cell line


title: 501mel shCD36-CONTROL Diet nb.4

description: CD36-dim FACS sorted cells from shCD36 orthotopic melanoma cell line xenografts exposed to control diet

source_name: CD36-dim cells / shCD36 / melanoma cell line / control diet


title: 501mel shCD36-PALM Diet nb.4


title: 501mel shCD36-PALM Diet nb.2


title: ActB.DMSO.rep3

value: mouse 3

value: LPS, IL-2, IL-5

tag: drug treatment


title: P3_PA4_P2655_N705.S520

description:
processed data file: P2655.tsv
CCYYKANXX_8_N705-S520-NX-xt

value: Smart-seq2; full-length RNA-seq


title: PB.GSKJ4.rep2

value: magnetically enriched CD138+ cells

value: mouse 2

value: 250nM GSK-J4

value: B cells


title: PB.DMSO.rep2

value: DMSO


title: ActB.GSKJ4.rep2


title: P3_PA4_P2655_N705.S518

description:
processed data file: P2655.tsv
CCYYKANXX_8_N705-S518-NX-xt


title: 501mel shCD36-CONTROL  Diet nb.2

value: control diet


title: P3_PA4_P2655_N705.S517

description:
processed data file: P2655.tsv
CCYYKANXX_8_N705-S517-NX-xt


title: P3_PA4_P2655_N705.S516

description:
processed data file: P2655.tsv
CCYYKANXX_8_N705-S516-NX-xt


title: 501mel shCD36-CONTROL Diet nb.1


title: P3_PA4_P2655_N705.S521

description:
processed data file: P2655.tsv
CCYYKANXX_8_N705-S521-NX-xt


title: ActB.DMSO.rep2


title: 501mel PLKO-PALM Diet nb.2

description: CD36-dim FACS sorted cells from PLKO orthotopic melanoma cell line xenografts exposed to PA-rich diet

source_name: CD36-dim cells / PLKO / melanoma cell line / PA-rich diet

value: PA-rich diet


title: P3_PA4_P2655_N705.S515

description:
processed data file: P2655.tsv
CCYYKANXX_8_N705-S515-NX-xt


title: 501mel shCD36-PALM Diet nb.1

value: melanoma cell line


title: QC-034682

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

hyb_protocol: Labeled cDNA was hybridized at 48°C to Affymetrix Human Gene ST 2.1 array plates, which were then washed, stained and scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515) with the assistance of the University of Michigan DNA Sequencing Core.

data_processing: R bioconduct was used to process the data, and RMA was used to summarize and normalize the expression values

source_name: Skin

label_protocol: Complementary DNA was prepared and biotinylated using the NuGEN Encore Biotin Module (Encore Biotin Module Manual, P/N M01111 v6).

extract_protocol: RNA was isolated from 10μm sections of formalin-fixed paraffin embedded blocks of identified skin biopsies. RNA was extracted using the E.N.Z.A. FFPE RNA Kit (Omega Bio-tek).

tag: disease state

value: DLE


title: PB.GSKJ4.rep1

value: mouse 1


title: 501mel shCD36-CONTROL Diet nb.3

tag: cell line


title: P3_PA4_P2655_N705.S513

description:
processed data file: P2655.tsv
CCYYKANXX_8_N705-S513-NX-xt

tag: cell type

value: oral squamous cell carcinoma (OSCC) cell line

value: control pLKO.1


title: PB.DMSO.rep1

value: female


title: 501mel PLKOCONTROL Diet nb.4

description: CD36-dim FACS sorted cells from PLKO orthotopic melanoma cell line xenografts exposed to control diet

source_name: CD36-dim cells / PLKO / melanoma cell line / control diet

value: PLKO


title: P3_PA4_P2655_N704.S522

description:
processed data file: P2655.tsv
CCYYKANXX_8_N704-S522-NX-xt

tag: protocol


title: ActB.GSKJ4.rep1

value: magnetically enriched GL7+ B cells


title: P3_PA4_P2655_N704.S521

description:
processed data file: P2655.tsv
CCYYKANXX_8_N704-S521-NX-xt


title: P3_PA4_P2655_N704.S520

description:
processed data file: P2655.tsv
CCYYKANXX_8_N704-S520-NX-xt


title: naïve.rep3

source_name: splenic mouse B cells

value: mouse 3

value: no stimulation

value: no treatment


title: QC-034679

scan_protocol: Labeled cDNA was hybridized at 48°C to Affymetrix Human Gene ST 2.1 array plates, which were then washed, stained and scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515) with the assistance of the University of Michigan DNA Sequencing Core.


title: 501mel PLKO-PALM Diet nb.4

tag: hybridization batch


title: 501mel PLKOCONTROL Diet nb.3

tag: diet


title: QC-034678


title: P3_PA4_P2655_N704.S518

description:
processed data file: P2655.tsv
CCYYKANXX_8_N704-S518-NX-xt

tag: shRNA

value: Smart-seq2; full-length RNA-seq


title: QC-034681


title: 501mel PLKOCONTROL Diet nb.2


title: QC-034680


title: 501mel PLKOCONTROL Diet nb.1


title: 501mel PLKO-PALM Diet nb.3


title: naïve.rep2

tag: Sex

value: mouse 2


title: ActB.DMSO.rep1

tag: sorting markers

value: LPS, IL-2, IL-5

value: B cells


title: P3_PA4_P2655_N704.S516

description:
processed data file: P2655.tsv
CCYYKANXX_8_N704-S516-NX-xt


title: QC-034676


title: P3_PA4_P2655_N704.S517

description:
processed data file: P2655.tsv
CCYYKANXX_8_N704-S517-NX-xt


title: QC-034677


title: 14- PLKO PALM- nb.2

description: CD36-dim FACS sorted cells from PLKO orthotopic SCC25 oral carcinoma cell line xenografts exposed to PA-rich diet

source_name: CD36-dim cells / PLKO / SCC25 oral carcinoma cell line / PA-rich diet

value: SCC25 oral carcinoma cell line


title: P3_PA4_P2655_N704.S515

description:
processed data file: P2655.tsv
CCYYKANXX_8_N704-S515-NX-xt


title: 13- PLKO PALM- nb.1

value: PA-rich diet


title: 15- PLKO PALM- nb.3


title: Mouse liver THRB ChAP-Seq HAB hypo bio-rep 1

city: new york

first: arturo

last: mendoza

state: ny

address: 1 east loop 15a

department: Division of Endocrinology, Diabetes and Metabolism

institute: weill cornell medicine

description: ChAP-Seq_THRB_Mm_liver_HAB_hypo_001_001_001.bw

data_processing:
Library strategy: ChAP-Seq
ChAP-seq data were aligned to the mm10 mouse genome using Bowtie2 (Langmead and Salzberg, 2012).
Duplicates and low quality reads were removed by Picard (http://picard.sourceforge.net)
Reads were processed using samtools (Li et al., 2009)
Peaks were called by MACS2 (Zhang et al., 2008), and low peaks (4<fold higher coverage than control) were removed.
Reads were assigned to peaks, normalized and quantified using EdgeR. Low signal peaks (log2 CPM<2) were removed, and differential peaks were defined at log2 FC≥1 and log2 FDR≤0.05.
For ChAP-seq track visualization, reads were processed to the BigWig file format using bedtools (Quinlan and Hall, 2010) and bedGraphToBigWig (Kent et al., 2010).
Processed Bigwig files were viewed in WashU Epigenome Browser (Zhou and Wang, 2012).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Liver

growth_protocol: Mice expressing a TRB1 attached to HA/Biotynilation peptide sequence

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with Dynabeads MyOne Streptavidin T1
Affinity-bound chromatin fragments were reverse-crosslinked, purified and used to construct DNA libraries for sequencing using the Illumina TruSeq ChIP Library Preparation Kit (Illumina)

treatment_protocol: hypothyroidisn was induced  by 0.05% methimazole and 1% potassium percholrate in drinking water for 5 weeks, hyperthyroid mice were treated similarly but T3 1mg/dl was aded to drinking water on the 5th week. Then, livers were collected and frozen in liquid nitrogen

tag: strain

tag: tissue

value: liver

tag: genotype

value: expressing a TRB1 attached to HA/Biotinylation peptide sequence

tag: condition

value: hypothyroidism

tag: chip antibody

value: Dynabeads MyOne Streptavidin T1, Thermo Fisher Scientific


title: Mouse liver THRB ChAP-Seq HAB hypo bio-rep 2

description: ChAP-Seq_THRB_Mm_liver_HAB_hypo_002_001_001.bw


title: QC-034675

value: DLE


title: Mouse liver THRB ChAP-Seq HAB hyper bio-rep 2

description: ChAP-Seq_THRB_Mm_liver_HAB_hyper_002_001_001.bw

value: hyperthyroidism


title: 11- PLKO PALM+ nb.3

description: CD36-bright FACS sorted cells from PLKO orthotopic SCC25 oral carcinoma cell line xenografts exposed to PA-rich diet

source_name: CD36-bright cells / PLKO / SCC25 oral carcinoma cell line / PA-rich diet

tag: sample id

tag: scan batch

tag: biological replicate

value: PLKO


title: QC-034673

tag: disease state


title: naïve.rep1

value: female

tag: mouse id

value: mouse 1

tag: stimulation

tag: drug treatment


title: QC-034672


title: Mouse liver THRB ChAP-Seq HAB hyper bio-rep 1

description: ChAP-Seq_THRB_Mm_liver_HAB_hyper_001_001_001.bw


title: P3_UN4_P2655_N703.S521

description:
processed data file: P2655.tsv
CCYYKANXX_8_N703-S521-NX-xt

tag: cell line

tag: cell type

value: oral squamous cell carcinoma (OSCC) cell line

value: control pLKO.1

tag: protocol


title: Mouse liver THRB ChAP-Seq BirA hypo bio-rep 2

description: ChAP-Seq_THRB_Mm_liver_BirA_hypo_002_001_001.bw


title: P3_PA4_P2655_N704.S513

description:
processed data file: P2655.tsv
CCYYKANXX_8_N704-S513-NX-xt

tag: shRNA

value: Smart-seq2; full-length RNA-seq


title: Mouse liver THRB ChAP-Seq BirA hypo bio-rep 1

description: ChAP-Seq_THRB_Mm_liver_BirA_hypo_001_001_001.bw


title: 9- PLKO PALM+ nb.1

tag: hybridization batch

tag: technical replicate

tag: diet


title: P3_UN4_P2655_N703.S518

description:
processed data file: P2655.tsv
CCYYKANXX_8_N703-S518-NX-xt


title: QC-034670


title: 10- PLKO PALM+ nb.2


title: QC-034671


title: P3_UN4_P2655_N703.S517

description:
processed data file: P2655.tsv
CCYYKANXX_8_N703-S517-NX-xt


title: Mouse liver THRB ChAP-Seq BirA hyper bio-rep 1

description: ChAP-Seq_THRB_Mm_liver_BirA_hyper_001_001_001.bw

tag: strain

tag: tissue

tag: genotype


title: QC-034674


title: 3- PLKO CT+ nb.3

description: CD36-bright FACS sorted cells from PLKO orthotopic SCC25 oral carcinoma cell line xenografts exposed to control diet

source_name: CD36-bright cells / PLKO / SCC25 oral carcinoma cell line / control diet

tag: sample id

value: control diet


title: P3_UN4_P2655_N703.S516

description:
processed data file: P2655.tsv
CCYYKANXX_8_N703-S516-NX-xt


title: 5- PLKO CT- nb.1

description: CD36-dim FACS sorted cells from PLKO orthotopic SCC25 oral carcinoma cell line xenografts exposed to control diet

tag: scan batch


title: P3_UN4_P2655_N703.S515

description:
processed data file: P2655.tsv
CCYYKANXX_8_N703-S515-NX-xt


title: QC-034665

value: ACLE


title: 1- PLKO CT+ nb.1

tag: biological replicate


title: Mouse liver THRB ChAP-Seq BirA hyper bio-rep 2

description: ChAP-Seq_THRB_Mm_liver_BirA_hyper_002_001_001.bw

tag: condition

tag: chip antibody


title: 7- PLKO CT- nb.3


title: QC-034657

tag: disease state


title: QC-034659


title: QC-034668


title: QC-034666


title: OL-4

description: CD36-dim FACS sorted cells from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to OA-rich diet

source_name: CD36-dim cells / PLKO / VDH15 oral carcinoma cell line / OA-rich diet

value: OA-rich diet

value: VDH15 oral carcinoma cell line


title: 2- PLKO CT+ nb.2

value: SCC25 oral carcinoma cell line


title: QC-034658


title: iNOS_inf_M3

city: Rehoboth

first: Dotan

last: Hoffman

address: Herzel St 234, Biological regulation

department: Biological regulation

country: Israel

institute: Weizmann institute of science

data_processing:
The cel-seq pipeline (https://github.com/yanailab/CEL-Seq-pipeline) was used for sample demultiplexing, alignment to the genome (mm9), and gene counting.
Gene normalization to the samples median
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include normalized number of reads.

source_name: Splenocytes

extract_protocol:
24 hours post infection spleens were removed squashed against 70 um strainer followed by red blood lysis and stained with antibodies. 1000 cells of CD9 Mf (Cd3e-Cd19-Ly6g-NK1.1-CD11B+F4/80+Ly6C-CD9+) and iNOS Mf (Cd3e-Cd19-Ly6g-NK1.1-CD11B+F4/80+Ly6C+CD9-) were sorted to lysis buffer (0.1% Triton-100, 0.5U/Ml RNasin+ (promega).
RNA-seq libraries were prepared according to Cel-seq2 libraries protocol (Hashimshony, T. et al Genome Biology 2016)

treatment_protocol: 8 weeks old female mice were intravenously inculated with 1X10^7 S.Tm

value: iNOS Mf

value: Spleen

tag: replicate


title: QC-034654

value: SCLE


title: iNOS_inf_M4


title: OL-1

tag: cell line


title: QC-034653


title: P3_UN4_P2655_N703.S513

description:
processed data file: P2655.tsv
CCYYKANXX_8_N703-S513-NX-xt

tag: cell type


title: QC-034655


title: OL-3


title: OL+4

description: CD36-bright FACS sorted cells from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to OA-rich diet

source_name: CD36-bright cells / PLKO / VDH15 oral carcinoma cell line / OA-rich diet


title: OL-2


title: iNOS_inf_M2


title: P3_UN4_P2655_N702.S521

description:
processed data file: P2655.tsv
CCYYKANXX_8_N702-S521-NX-xt

tag: protocol


title: iNOS_M3


title: QC-034652


title: P3_UN4_P2655_N702.S522

description:
processed data file: P2655.tsv
CCYYKANXX_8_N702-S522-NX-xt

tag: shRNA


title: P3_UN4_P2655_N702.S520

description:
processed data file: P2655.tsv
CCYYKANXX_8_N702-S520-NX-xt


title: OL+2

tag: hybridization batch


title: iNOS_M2


title: P3_UN4_P2655_N702.S518

description:
processed data file: P2655.tsv
CCYYKANXX_8_N702-S518-NX-xt


title: iNOS_M4


title: iNOS_M1


title: CM_M5

value: Classical monocytes


title: P3_UN4_P2655_N702.S517

description:
processed data file: P2655.tsv
CCYYKANXX_8_N702-S517-NX-xt


title: OL+1

tag: technical replicate


title: P3_UN4_P2655_N702.S516

description:
processed data file: P2655.tsv
CCYYKANXX_8_N702-S516-NX-xt


title: QC-034651


title: P3_UN4_P2655_N702.S515

description:
processed data file: P2655.tsv
CCYYKANXX_8_N702-S515-NX-xt


title: CM_M3


title: QC-034649


title: PLM-4

description: CD36-dim FACS sorted cells from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to PA-rich diet

source_name: CD36-dim cells / PLKO / VDH15 oral carcinoma cell line / PA-rich diet

tag: diet

value: PA-rich diet


title: CM_M2

tag: strain


title: P3_UN4_P2655_N702.S513

description:
processed data file: P2655.tsv
CCYYKANXX_8_N702-S513-NX-xt


title: CM_M4

tag: tissue


title: P3_UN4_P2655_N701.S522

description:
processed data file: P2655.tsv
CCYYKANXX_8_N701-S522-NX-xt


title: CM_M1


title: P3_UN4_P2655_N701.S520

description:
processed data file: P2655.tsv
CCYYKANXX_8_N701-S520-NX-xt


title: QC-034647


title: P3_UN4_P2655_N701.S518

description:
processed data file: P2655.tsv
CCYYKANXX_8_N701-S518-NX-xt


title: QC-034650


title: PLM-1


title: Cd9_inf_M3

value: CD9 Mf


title: PLM-2

value: PLKO


title: QC-034648


title: P3_UN4_P2655_N701.S521

description:
processed data file: P2655.tsv
CCYYKANXX_8_N701-S521-NX-xt


title: Cd9_inf_M4


title: QC-034646


title: PLM+4

description: CD36-bright FACS sorted cells from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to PA-rich diet

source_name: CD36-bright cells / PLKO / VDH15 oral carcinoma cell line / PA-rich diet


title: PLM-3


title: PLM+2


title: P3_UN4_P2655_N701.S517

description:
processed data file: P2655.tsv
CCYYKANXX_8_N701-S517-NX-xt


title: PLM+3


title: Cd9_inf_M2


title: PLM+1


title: P3_UN4_P2655_N703.S522

description:
processed data file: P2655.tsv
CCYYKANXX_8_N703-S522-NX-xt


title: Cd9_M3


title: Cd9_M4


title: P3_UN4_P2655_N703.S520

description:
processed data file: P2655.tsv
CCYYKANXX_8_N703-S520-NX-xt


title: QC-034643


title: 501mel PLKO-PALM Diet nb.1

description: CD36-dim FACS sorted cells from PLKO orthotopic melanoma cell line xenografts exposed to PA-rich diet

value: melanoma cell line


title: CT-3

description: CD36-dim FACS sorted cells from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to control diet

source_name: CD36-dim cells / PLKO / VDH15 oral carcinoma cell line / control diet


title: P3_UN4_P2655_N701.S516

description:
processed data file: P2655.tsv
CCYYKANXX_8_N701-S516-NX-xt


title: Cd9_M2


title: P3_UN4_P2655_N701.S515

description:
processed data file: P2655.tsv
CCYYKANXX_8_N701-S515-NX-xt


title: P3_UN4_P2655_N701.S513

description:
processed data file: P2655.tsv
CCYYKANXX_8_N701-S513-NX-xt


title: P2_PA14_P2644_N729.S522

description:
processed data file: P2644.tsv
CCYYKANXX_8_N729-S522-NX-xt


title: Cd9_M1


title: Cd9_inf_M1


title: QC-034645


title: P2_PA14_P2644_N729.S521

description:
processed data file: P2644.tsv
CCYYKANXX_8_N729-S521-NX-xt


title: QC-034640


title: CT-4


title: 6- PLKO CT- nb.2

description: CD36-dim FACS sorted cells from PLKO orthotopic SCC25 oral carcinoma cell line xenografts exposed to control diet

source_name: CD36-dim cells / PLKO / SCC25 oral carcinoma cell line / control diet


title: sample.m1_cre_1 [RNA-seq]

city: St Louis

first: Joshua

middle: B

last: Rubin

state: Missouri

address: 660 South Euclid Ave

department: Pediatrics

institute: Washington University In St Louis

data_processing:
The resulting sequencing reads were demultiplexed by index with a custom Python demultiplexing script and further demultiplexed by barcode with a custom Perl demultiplexing script.
The RNA-Seq reads were then aligned to the Mus musculus Ensembl release 76 top-level assembly with STAR version 2.5.1a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount vsersion 1.4.6-p5.
Genome_build: Ensemble R76
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Primary cortical astrocytes_m1_cre

growth_protocol: Cells were grown in DMEM/F12 supplemented with 10% FBS.

extract_protocol:
Qiagen RNAeasy mini kit
Clontech SMRTr

tag: strain background

tag: genotype

value: Trp53 Knockout

tag: passages

tag: Sex

value: male

value: Primary postnatal day 1 cortical astorcytes


title: sample.m1_cre_2 [RNA-seq]


title: QC-034641


title: P2_PA14_P2644_N729.S520

description:
processed data file: P2644.tsv
CCYYKANXX_8_N729-S520-NX-xt

value: oral squamous cell carcinoma (OSCC) cell line

value: control pLKO.1

value: Smart-seq2; full-length RNA-seq


title: sample.m1_cre_3 [RNA-seq]


title: QC-034642


title: NC_M4

value: Non-calssical monocytes


title: QC-034644


title: P2_PA14_P2644_N729.S518

description:
processed data file: P2644.tsv
CCYYKANXX_8_N729-S518-NX-xt


title: NC_M3


title: QC-034635


title: CT-2

tag: sample id

tag: scan batch

tag: biological replicate

value: control diet

value: VDH15 oral carcinoma cell line


title: sample.f1_cre_1 [RNA-seq]

source_name: Primary cortical astrocytes_f1_cre

value: female


title: P2_PA14_P2644_N729.S517

description:
processed data file: P2644.tsv
CCYYKANXX_8_N729-S517-NX-xt


title: NC_M5

value: Spleen

tag: replicate


title: NC_M2


title: sample.f1_cre_2 [RNA-seq]


title: QC-034633

tag: disease state

value: SCLE


title: sample.f1_cre_3 [RNA-seq]

tag: cell type


title: P2_PA14_P2644_N729.S516

description:
processed data file: P2644.tsv
CCYYKANXX_8_N729-S516-NX-xt

tag: cell line

tag: protocol


title: NC_M1


title: QC-034630

value: DLE


title: QC-034632

value: ACLE


title: P2_PA14_P2644_N729.S515

description:
processed data file: P2644.tsv
CCYYKANXX_8_N729-S515-NX-xt

tag: shRNA


title: sample.m1_r172h_1 [RNA-seq]

source_name: Primary cortical astrocytes_m1_r172h

value: Trp53:R172H Overexpression


title: sample.m1_r172h_2 [RNA-seq]


title: CT+4

description: CD36-bright FACS sorted cells from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to control diet

source_name: CD36-bright cells / PLKO / VDH15 oral carcinoma cell line / control diet

tag: hybridization batch

tag: technical replicate

value: PLKO


title: P2_PA14_P2644_N729.S513

description:
processed data file: P2644.tsv
CCYYKANXX_8_N729-S513-NX-xt


title: QC-034631

source_name: Skin