title: patient HC4290 monocyte

description: Gene expression data from patient HC4290 monocyte

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.

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

value: PBMC

value: uHC - unrelated healthy control


title: Her2/Neu mouse model cells,Day7,Bio4,run4

status: Public on Jan 01 2024

type: SRA

city: Philadelphia

first: Lewis

last: Chodosh

state: Pennsylvania

address: 421 Curie Blvd

department: Cancer Biology

country: USA

institute: University of Pennsylvania

library_source: transcriptomic

data_processing:
Bcl2fastq (Illumina output to fastq format)
Fastqc (Quality control)
STAR aligner (To align to mm10 genome)
FeatureCounts (For read counting)
DESeq2 (Differential expression analysis)
Assembly: mm10
Supplementary files format and content: Tab delimited text file with raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Her2-dependent cells derived from theMTB/TANmouse model

extract_protocol:
RNA extraction using Rneasy mini kit (Qiagen)
Illumina TruSeq Stranded mRNA library prep for NeoPrep kit

tag: cell line

tag: timepoint

value: Day 7


title: MGG4-Nes-high-1

city: Orsay

first: Giorgio

last: Seano

address: Bâtiment 110, Rue Henri Becquerel

department: INSERM U1021 - CNRS UMR3347

country: France

institute: Institut Curie

description:
MGG4_tpm.csv
D348-D347T26

data_processing:
The reads obtained were processed using the Curie Institute Nextflow RNA-seq analysis pipeline
reads quality was assessed using FastQC and mapped to the reference genome (hg19/GRCh37 or mm10/GRCm38 for GL261) using STAR software
raw reads count tables were generated using STAR
Software versions and full pipelines are available at https://github.com/bioinfo-pf-curie/RNA-seq/
Assembly: hg19, mm10
Supplementary files format and content: Matrix table with TPM gene counts for every gene and every sample (.csv)

organism: Homo sapiens

source_name: brain

growth_protocol: cells were maintained in neurospheres using NeuroCult basal medium with NeuroCult proliferation supplement (STEMCELL technologies, #05751), 20ng/ml EGF, 20ng/ml bFGF, 5ug/ml heparin (STEMCELL Technologies, #07980) and gentamycin (Sigma) (NC complete media) in low attachment flasks (Corning, #3814)

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen)
RNA-seq libraries were constructed using 100ng to 1ug of RNA using Illumina library structure (Stranded mRNA Library preparation, Illumina), according to the manufacturer’s instructions. For MGG4-BV samples only, SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian protocol was used. Samples were sequenced as 100bp paired-end runs on the Novaseq 6000 (Illumina).

treatment_protocol: In-vitro MGG4 cells were treated with 25uM of temozolomide for 3 days before RNA extraction. For in-vivo MGG4 samples, mouse were irradiated with 10 Gy using a X-ray irradiator, or treated with 10mg/kg of temozolomide. Tissue was harvested 7 days after treatment. MGG4-Nes, MGG18-Nes and GL261-Nes samples were FACS-sorted based on reporter expression before RNA extraction with no additional treatment. For co-culture experiment, MGG4 cells were co-cultured 3 days with brain blood vessels before isolation of tumor cells for RNA extraction.

tag: tissue

value: brain

tag: cell type

value: patient-derived glioblastoma cell line

tag: group

value: Nes-high


title: CSBKD, 43

city: Copenhagen N

first: Morten

last: Scheibye-Knudsen

state: Copenhagen N

address: Blegdamsvej 3B

country: Denmark

institute: University of Copenhagen

data_processing:
Python
Paired-end reads from 44 RNA-Seq samples were aligned to mm9 using bowtie2
Differential expression analysis was performed using a Salmon → tximeta → DESeq2
GSEA was performed directly on DESeq2 normalized counts
Assembly: mm9
Supplementary files format and content: DESeq2 normalized counts

source_name: cerebellum

extract_protocol:
RNA extraction with trizol-chloroform
Total RNA, rRNA depleted
libraries were prepared using the DNBseq protocol from BGI.

value: cerebellum

tag: Sex

value: M

tag: strain

tag: genotype

value: CSB

tag: treatment

value: KD


title: EC, MEF2C ChIP, A , bio rep 1

city: Sacramento

first: Julian

last: Halmai

state: CA

address: 2921 Stockton Blvd

department: Department of Neurology

institute: UC Davis

library_source: genomic

data_processing:
bowtie2/2.4.2 (Aligner)
samtools/1.15.1 (SAM to BAM)
sambamba0.6.7 (duplicate, unmapped removal)
macs3/3.0.0a6 (peak caller)
deeptools/3.5.1 (data visualization)
Assembly: Ensembl GRCh38
Supplementary files format and content: narrowPeak
Supplementary files format and content: bigWig

molecule: genomic DNA

extract_protocol:
These ECs were cross-linked in 1% formaldehyde for 10 min at room temperature and the reaction was stopped with 0.125 M glycine. Cross-linked cells were lysed with ChIP lysis buffer (5 mM PIPES pH8, 85 mM KCl, 1% Igepal) with a protease inhibitor (PI) cocktail (Millipore Sigma, #11697498001). Nuclei were collected by centrifugation at 2000 rpm for 5 min at 4 °C and lysed in nuclei lysis buffer (50 mM Tris pH8, 10 mM EDTA, 1% SDS) supplemented with the PI cocktail. Chromatin was fragmented using the Bioruptor Pico (Diagenode, Denville, NJ) and diluted with 5 volumes RIPA buffer (50 mM Tris pH 7.6, 150 mM NaCl, 1 mM EDTA pH8, 1% Igepal, 0.25% deoxycholic acid). ChIP enrichment was performed by incubation with 3 µg MEF2C antibody (Abcam, #ab211493) or 2 µg normal rabbit IgG (ab46540, Abcam) for 16 h at 4 °C. Immune complexes were bound to 20 µl magnetic protein A/G beads (Biorad, Hercules, CA) for 2 h at 4 °C. Beads were washed 2 × with RIPA (Thermo Fisher Scientific, #J62524.AE) and 3 × with ChIP wash buffer (100 mM Tris pH8, 500 mM LiCl, 1% deoxycholic acid). The final wash was performed in ChIP wash buffer with 150 mM NaCl. Cross-links were then reversed by heating beads in 100 µl ChIP elution buffer (50 mM NaHCO3, 1% SDS) overnight at 65 °C. DNA was purified using the QIAquick PCR Purification Kit (Qiagen, Hilden, Germany).
Libraries were prepared by Novogene.

value: Dura6.9 iPSC derivatives

value: endothelial cells

tag: chip antibody

value: Control


title: Her2/Neu mouse model cells,Day7,Bio2,run5

value: Her2-dependent cells derived from theMTB/TANmouse model


title: patient HC4224 monocyte

type: RNA

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Gene expression data from patient HC4224 monocyte

hyb_protocol: The Affymetrix GeneChip Human Genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

label: biotin

source_name: monocytes

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: RNA was extracted from monocytes negatively selected from PBMC and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

tag: sampletype


title: patient HC3971 monocyte

description: Gene expression data from patient HC3971 monocyte


title: Her2/Neu mouse model cells,Day7,plusDox,Bio3,run2

value: Doxycycline


title: WTSD, 42

value: WT

value: SD


title: patient HC4007 monocyte

description: Gene expression data from patient HC4007 monocyte

value: PBMC


title: patient HC4140 monocyte

description: Gene expression data from patient HC4140 monocyte

value: uHC - unrelated healthy control


title: MGG4-Nes-low-1

description:
MGG4_tpm.csv
D348-D347T25

value: Nes-low


title: patient HC3946 monocyte

description: Gene expression data from patient HC3946 monocyte


title: Her2/Neu mouse model cells,Day7,Bio2,run3

value: Day 7


title: patient HC4075 monocyte

description: Gene expression data from patient HC4075 monocyte


title: Her2/Neu mouse model cells,Day3,Bio5,run5

value: Day 3


title: WTSD, 41


title: MGG4-BV-CTL-2

description:
MGG4_BV_tpm.csv
D487T16

value: brain

value: patient-derived glioblastoma cell line

value: CTL

value: BV


title: Her2/Neu mouse model cells,Day3,Bio4,run4


title: WTSD, 40

value: cerebellum

value: M


title: WTSD, 39


title: MGG4-Nes-high-3

description:
MGG4_tpm.csv
D348-D347T30

value: Nes-high


title: DKOSD, 36

value: DKO


title: MGG4-BV-2

description:
MGG4_BV_tpm.csv
D487T15

value: Blood vessels co-culture


title: Her2/Neu mouse model cells,Day3,Bio3,run2

value: Her2-dependent cells derived from theMTB/TANmouse model


title: patient HC4077 monocyte

description: Gene expression data from patient HC4077 monocyte


title: Her2/Neu mouse model cells,Day3,Bio2,run3


title: patient HC3882 monocyte

description: Gene expression data from patient HC3882 monocyte


title: DKOKD, 47

value: KD


title: DKOSD, 35

value: SD


title: MGG4-BV-1

description:
MGG4_BV_tpm.csv
D487T13


title: MGG4-BV-3

description:
MGG4_BV_tpm.csv
D487T17


title: male_thorax_rep3

city: Moscow

first: Sergei

last: Funikov

state: Moscow

address: Vavilov str. 32

country: Russia

institute: Engelhardt Insitute of Molecular Biology

description:
small RNAs (18-32 nt)
Gel extraction of small RNAs

data_processing:
3’-adapter cropping, filtration of reads by length filtration (>18 nt) and quality (80% of nt have ≥ 20 Phred quality) using Trim Galore.
Pre-processed reads were further subjected to subtraction of reads matching to rRNA, tRNA, snoRNA, snRNA, SRP_RNA, RNase_MRP_RNA, microRNAs and tracers (M19:CGTACGGTTTAAACTTCGA and M30:CCATCGATAAAAGTTTAAACGAGCTTCCCG)
The selected reads were mapped separately to the A. coluzzii genome by Bowtie with the following settings: “--all --tryhard -v 3 --best --strata --quiet”.
The number of reads mapped to repeats, lncRNAs and protein-coding genes was calculated using custom script written by Python.
Assembly: Anopheles coluzzii MOPTI VectorBase rel. 56
Supplementary files format and content: counts text files

organism: Anopheles coluzzii

source_name: thorax

extract_protocol:
Total RNA was isolated from heads and thoraxes of adult males and females of the An. coluzzii MOPTI (MRA-763) laboratory colony using TRIzol Reagent (Invitrogen) extraction in three biological replicates.  Thirty individual mosquitoes were used per each replicate. Small RNAs (18-30 nt) were cloned as previously described (Olovnikov et al. 2013). Sequencing was performed in the Duke Center for Genomics and Computational Biology on the Illumina HiSeq4000 to obtain 50-bp single reads. About 18.1 Gb of total data or ~1.5 Gg of data on average for each replicate were obtained.
Cloning of small RNA libraries was performed by Illumina TruSeq Small RNA prep kit (Illumina, USA) according to the manufacturer’s protocol.

value: thorax

tag: gender

value: male

value: MOPTI


title: Her2/Neu mouse model cells,Day3,Bio1,run4


title: patient HC2368 monocyte

description: Gene expression data from patient HC2368 monocyte

value: PBMC

value: uHC - unrelated healthy control


title: DKOSD, 34


title: male_thorax_rep2


title: MGG4-BV-CTL-3

description:
MGG4_BV_tpm.csv
D487T18

value: brain


title: patient HC3878 monocyte

description: Gene expression data from patient HC3878 monocyte


title: patient HC1730 monocyte

description: Gene expression data from patient HC1730 monocyte


title: Her2/Neu mouse model cells,Day28plusDox,Bio5,run5

value: Doxycycline

value: Day 28


title: male_thorax_rep1


title: INDYSD, 33

value: INDY


title: MGG4-BV-CTL-1

description:
MGG4_BV_tpm.csv
D487T14

value: patient-derived glioblastoma cell line

value: CTL

value: BV


title: MGG4-vitro-TMZ-3

description:
MGG4_vitro_TMZ_tpm.csv
D622T74

value: temozolomide, 25uM

value: in vitro


title: male_head_rep3

source_name: head

value: head


title: MGG4-vitro-DMSO-2

description:
MGG4_vitro_TMZ_tpm.csv
D622T71

value: DMSO


title: MGG4-vitro-DMSO-3

description:
MGG4_vitro_TMZ_tpm.csv
D622T73


title: INDYSD, 32

value: cerebellum

value: M

value: SD


title: Her2/Neu mouse model cells,Day28plusDox,Bio4,run4

value: Her2-dependent cells derived from theMTB/TANmouse model


title: Her2/Neu mouse model cells,Day28plusDox,Bio2,run3


title: hu_PBMC_CD14+CD34+

city: Kumamoto

first: Naofumi

last: Takahashi

address: 2-2-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45˚C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChip array was washed and stained in the GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: GeneChip array was scanned using GeneChip Scanner 3000 7G.

data_processing: Single Array Analysis was calculated by Microarray Suite version 5.0 (MAS5.0) with Thermo Fisher Scientific default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: CD34+ monocyte fraction sorted form PBMC

label_protocol: Biotinylated cRNA was synthesized by GeneChip 3' IVT PLUS Reagent Kit Thermo Fisher Scientific) from 100 ng total RNA according to the manufacturer's instructions. Biotinylated cRNA yield was checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy kit according to the manufacturer's instructions.

value: PBMC


title: CSBSD, 31

value: CSB


title: male_head_rep2

value: male

value: MOPTI


title: hu_PBMC_CD14+CD34-

source_name: CD34- monocyte fraction sorted form PBMC


title: Her2/Neu mouse model cells,Day28,plusDox,Bio3,run2

value: Doxycycline

value: Day 28


title: MGG4-vitro-DMSO-1

description:
MGG4_vitro_TMZ_tpm.csv
D622T69

value: brain

value: patient-derived glioblastoma cell line


title: CSBSD, 30


title: male_head_rep1


title: MGG4-vitro-TMZ-1

description:
MGG4_vitro_TMZ_tpm.csv
D622T70


title: Her2/Neu mouse model cells,Day28,Bio3,run2


title: bladder cancer specimen, 16877

city: New York

first: Li

last: Wang

address: 1 Gustave L. Levy Pl

institute: Icahn school of medicine at Mount Sinai

data_processing:
TPM value was quantified by kallisto program
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: Bladder cancer specimen

extract_protocol:
Total RNA from UC tissue stored in RNAlater or embedded in OCT was isolated with the Qiagen miRNeasy Mini Kit (217084, Qiagen, Germantown, MD, USA), eluted in water and treated with DNAse, at The Biorepository and Pathology Core Facility at the Icahn School of Medicine at Mount Sinai.
Total RNA was sequenced at the Genomics Core Facility at Icahn School of Medicine at Mount Sinai. Agilent RNA Direct SureSelect XT V6 kit was used for library prep and NovaSeq 6000 S2 Reagent Kit v1.5 (300 cycles) was used for sequencing.

tag: age

value: Bladder cancer specimen

tag: disease state

value: Bladder cancer


title: female_thorax_rep3

value: thorax

value: female


title: MGG4-vitro-TMZ-2

description:
MGG4_vitro_TMZ_tpm.csv
D622T72

value: temozolomide, 25uM

value: in vitro


title: female_thorax_rep2


title: Her2/Neu mouse model cells,Day28,Bio5,run3


title: MGG4-vivo-DMSO-2

description:
Mice were sacrificed using the standard method of cervical dislocation, following which the brain was immediately harvested. Dissect pieces of tumor were immediately immersed in RNAlater solution (Invitrogen). After 2-3 hours of incubation at RT, the tumor pieces in RNAlater were stored at 4°C for 1 week before initiating RNA extraction. Tumor tissues were homogenized using precellys CK28 Hard tissue homogenizing columns with ceramic beads and evolution homogenizer (Bertin Corp). Samples were then processed as described for the other samples.
MGG4_vivo_tpm.csv
D759T29

value: DMSO

value: in vivo


title: Her2/Neu mouse model cells,Day28,Bio5,run5

value: Her2-dependent cells derived from theMTB/TANmouse model


title: female_thorax_rep1


title: CSBSD, 26

value: cerebellum

value: M

value: SD


title: MGG4-vivo-DMSO-1

description:
Mice were sacrificed using the standard method of cervical dislocation, following which the brain was immediately harvested. Dissect pieces of tumor were immediately immersed in RNAlater solution (Invitrogen). After 2-3 hours of incubation at RT, the tumor pieces in RNAlater were stored at 4°C for 1 week before initiating RNA extraction. Tumor tissues were homogenized using precellys CK28 Hard tissue homogenizing columns with ceramic beads and evolution homogenizer (Bertin Corp). Samples were then processed as described for the other samples.
MGG4_vivo_tpm.csv
D759T30


title: DKOKD, 24

value: DKO

value: KD


title: patient HRS_PRO017 monocyte

description: Gene expression data from patient HRS_PRO017 monocyte

value: PBMC

value: HRS - high risk healthy sibling


title: Her2/Neu mouse model cells,Day28,Bio2,run3

value: Day 28


title: female_head_rep3

value: head

value: MOPTI


title: Her2/Neu mouse model cells,Day28,Bio4,run4


title: DKOKD, 23


title: Her2/Neu mouse model cells,Day1,Bio5,run2

value: Day 1


title: female_head_rep1

value: female


title: MGG4-vivo-TMZ-1

description:
Mice were sacrificed using the standard method of cervical dislocation, following which the brain was immediately harvested. Dissect pieces of tumor were immediately immersed in RNAlater solution (Invitrogen). After 2-3 hours of incubation at RT, the tumor pieces in RNAlater were stored at 4°C for 1 week before initiating RNA extraction. Tumor tissues were homogenized using precellys CK28 Hard tissue homogenizing columns with ceramic beads and evolution homogenizer (Bertin Corp). Samples were then processed as described for the other samples.
MGG4_vivo_tpm.csv
D759T32

value: brain

value: patient-derived glioblastoma cell line

value: temozolomide, 10mg/kg


title: Her2/Neu mouse model cells,Day1,Bio5,run5


title: INDYKD, 22

value: INDY


title: MGG4-vivo-IR-2

description:
Mice were sacrificed using the standard method of cervical dislocation, following which the brain was immediately harvested. Dissect pieces of tumor were immediately immersed in RNAlater solution (Invitrogen). After 2-3 hours of incubation at RT, the tumor pieces in RNAlater were stored at 4°C for 1 week before initiating RNA extraction. Tumor tissues were homogenized using precellys CK28 Hard tissue homogenizing columns with ceramic beads and evolution homogenizer (Bertin Corp). Samples were then processed as described for the other samples.
MGG4_vivo_tpm.csv
D773T207

value: irradiation, 10Gy

value: in vivo


title: MGG4-vivo-IR-1

description:
Mice were sacrificed using the standard method of cervical dislocation, following which the brain was immediately harvested. Dissect pieces of tumor were immediately immersed in RNAlater solution (Invitrogen). After 2-3 hours of incubation at RT, the tumor pieces in RNAlater were stored at 4°C for 1 week before initiating RNA extraction. Tumor tissues were homogenized using precellys CK28 Hard tissue homogenizing columns with ceramic beads and evolution homogenizer (Bertin Corp). Samples were then processed as described for the other samples.
MGG4_vivo_tpm.csv
D759T37


title: INDYKD, 21

value: cerebellum

value: M


title: WTKD, 28

value: WT


title: Her2/Neu mouse model cells,Day1,Bio4,run4

value: Her2-dependent cells derived from theMTB/TANmouse model


title: INDYKD, 20

value: KD


title: MGG4-vivo-TMZ-2

description:
Mice were sacrificed using the standard method of cervical dislocation, following which the brain was immediately harvested. Dissect pieces of tumor were immediately immersed in RNAlater solution (Invitrogen). After 2-3 hours of incubation at RT, the tumor pieces in RNAlater were stored at 4°C for 1 week before initiating RNA extraction. Tumor tissues were homogenized using precellys CK28 Hard tissue homogenizing columns with ceramic beads and evolution homogenizer (Bertin Corp). Samples were then processed as described for the other samples.
MGG4_vivo_tpm.csv
D759T33


title: mouse submandibular gland, 24h after IR, replicate2

city: shenzhen

first: yang

last: kaibin

address: No.1066 Xueyuan Road, Nanshan District

country: China

institute: shenzhen university

description:
IR24h rep2
The submandibular gland of  mice after IR

data_processing:
bowtie2
hisat2
samtools
cufflinks
bowtie2
Assembly: mm10
Supplementary files format and content: text files include FPKM values for each sample
Supplementary files format and content: bigWig files were generated from bed files using bamCoerage tool
Supplementary files format and content: BED (Browser Extensible Data)

source_name: submandibular gland

extract_protocol:
For RNA-seq, we euthanized mice aged 6-8 weeks using the neck dislocation method, cut the skin along the neck to expose the submandibular gland, and then remove the gland tissue. Total RNAs were extracted using the Trizol method. Library construction and sequencing were performed on the DNBSEQ-T7 platform at the Geneplus Co, Shenzhen, China. Final data were presented as FPKM value for each gene. Tissue samples were collected at ZT3, ZT9 and ZT15 (10:00 am, 4:00 pm, and 10:00 pm).
For Cut-taq, the mouse submandibular gland was minced and digested with Worthington Collagenase I at 0.2% concentration for 25-30 minutes at 37°C. The sample was filtered through a Falcon 40um filter, and the remaining tissue was incubated with 1x Gibco Trypsin/EDTA at 37°C for 20 minutes. After filtration, the sample was resuspended in PBS and centrifuged at 500 g for 5 minutes to obtain the supernatant. Standard operations were performed according to the instructions ofTD901-TD902 from Hyperactive In-Situ Chip Library Prep Kit for IIIumina. The 150 bp paired-end DNA sequencing was performed on the Illumina NovaSeq 6000 system (Haplox Genomics Center, Jiangxi, China).
RNA libraries for RNA-seq were prepared using Hieff NGS Ultima Dual-mode mRNA Library Prep Kitfor Illumina following manufacturer's protocols.
The 150 bp paired-end DNA sequencing was performed on the Illumina NovaSeq 6000 system (HaploX Genomics Center, Jiangxi, China) according to the manufacturer's instructions.
Library was performed according to the manufacter’s instructions (Single Cell RNA Library Kit Cell/Tissue for Matrix V2 protocol GEXSCOPE). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: submandibular gland

value: 24hr after IR 5Gy


title: Her2/Neu mouse model cells,Day1,Bio3,run2


title: mouse submandibular gland, 6h after IR, replicate2

description:
IR6h rep2
The submandibular gland of  mice after IR

value: 6hr after IR 5Gy


title: MGG4-vivo-CTL-2

description:
Mice were sacrificed using the standard method of cervical dislocation, following which the brain was immediately harvested. Dissect pieces of tumor were immediately immersed in RNAlater solution (Invitrogen). After 2-3 hours of incubation at RT, the tumor pieces in RNAlater were stored at 4°C for 1 week before initiating RNA extraction. Tumor tissues were homogenized using precellys CK28 Hard tissue homogenizing columns with ceramic beads and evolution homogenizer (Bertin Corp). Samples were then processed as described for the other samples.
MGG4_vivo_tpm.csv
D759T35

value: CTL


title: CSBKD, 19

value: CSB


title: WTKD, 25


title: MGG4-vivo-CTL-1

description:
Mice were sacrificed using the standard method of cervical dislocation, following which the brain was immediately harvested. Dissect pieces of tumor were immediately immersed in RNAlater solution (Invitrogen). After 2-3 hours of incubation at RT, the tumor pieces in RNAlater were stored at 4°C for 1 week before initiating RNA extraction. Tumor tissues were homogenized using precellys CK28 Hard tissue homogenizing columns with ceramic beads and evolution homogenizer (Bertin Corp). Samples were then processed as described for the other samples.
MGG4_vivo_tpm.csv
D759T34


title: Her2/Neu mouse model cells,Day1,Bio2,run3

value: Day 1


title: female_head_rep2

value: head

value: female

value: MOPTI


title: CSBKD, 18


title: mouse submandibular gland, 6h after IR, replicate1

description:
IR6h rep1
The submandibular gland of  mice after IR


title: control mouse submandibular gland, ZT15, replicate2

description:
ZT15 rep2
The submandibular gland of  control mice

tag: time


title: CSBSD, 16

value: SD


title: MGG18-Nes-low-3

description:
MGG18_tpm.csv
D773T205

value: brain

value: patient-derived glioblastoma cell line

value: Nes-low


title: control mouse submandibular gland, ZT15, replicate1

description:
ZT15 rep1
The submandibular gland of  control mice


title: Her2/Neu mouse model cells,Day14plusDox,Bio4,run4

value: Doxycycline

value: Day 14


title: Her2/Neu mouse model cells,Day14plusDox,Bio2,run3

value: Her2-dependent cells derived from theMTB/TANmouse model


title: INDYKD, 15

value: cerebellum

value: M

value: INDY

value: KD


title: mouse submandibular gland, 24h after IR, replicate1

description:
IR24h rep1
The submandibular gland of  mice after IR

value: submandibular gland

value: WT

value: 24hr after IR 5Gy


title: MGG18-Nes-low-1

description:
MGG18_tpm.csv
D773T201


title: INDYSD, 14


title: control mouse submandibular gland, ZT9, replicate1

description:
ZT9 rep1
The submandibular gland of  control mice


title: CSBKD, 13

value: CSB


title: MGG18-Nes-high-2

description:
MGG18_tpm.csv
D773T204

value: Nes-high


title: MGG18-Nes-high-3

description:
MGG18_tpm.csv
D773T206


title: Her2/Neu mouse model cells,Day14,plusDox,Bio1,run2


title: control mouse submandibular gland, ZT9, replicate2

description:
ZT9 rep2
The submandibular gland of  control mice


title: Her2/Neu mouse model cells,Day14plusDox,Bio5,run5


title: Her2/Neu mouse model cells,Day14,plusDox,Bio3,run2


title: control mouse submandibular gland, ZT3, replicate1

description:
T0ZT3rep1
The submandibular gland of  control mice


title: Her2/Neu mouse model cells,Day14,Bio3,run2


title: INDYSD, 11


title: WTKD, 12


title: MGG18-Nes-high-1

description:
MGG18_tpm.csv
D773T202


title: Her2/Neu mouse model cells,Day14,Bio5,run5


title: MGG18-Nes-low-2

description:
MGG18_tpm.csv
D773T203


title: ET6_CKDL210011621-1a_HC5FKDSX2_L3 [ATAC-seq]

city: Bronx

first: Taylor

last: Thompson

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

data_processing:
paired end reads were sequenceed using the Novaseq platform
raw 100 bp paired-end reads were trimmed to remove low quality base calls and Illumina universal adapters using Trim Galore! (version 0.6.5) with default parameters and then assessed using fastQC
The cleaned paired-end reads were aligned with   Burrows  -  Wheeler Aligner  (BWA) version 0.7.13 and then converted to SAM files to remove low qulity reades with mapq <20
PCR duplicates removed using samtools and reads mapping to bias areas from ENCODE blacklist were removed
Reads then run using MACS2 Peak caller -BSPMR for paired end peack aclling with a quality cutoff were identified. And IDR threshold fo 0.05 assigned to form final consensus narrow peaks files
Assembly: hg38
Supplementary files format and content: feature counts text file
Supplementary files format and content: tab delineated TPM file

growth_protocol: Samples were differntitated into adipocytes utilizeing StemXVivo Adipogenic Supplement

extract_protocol:
DNA for the ATAC library was isolated  following the OMNI-ATAC-seq protocol with modification suggested by the Claussnitzer group for hig lipid concentration cells
ATAC-library was constructed following Omni-ATAC protocol with Nextra primers

treatment_protocol: Chemicals were added at nM concentrtions dexcribed in the paper using a DMSO vector

value: treatment

value: HTERT-immortalized  Adipose Derived Mesencymal stem cell

value: Adipogenic differentiation

tag: condition replicate

tag: condition

value: TBT


title: control mouse submandibular gland, ZT3, replicate2

description:
T0ZT3rep2
The submandibular gland of  control mice


title: INDYSD, 10

value: SD


title: Her2/Neu mouse model cells,Day14,Bio4,run4

tag: cell line


title: non-targeting shRNA,Tumor non-necrotic rim, Rat4834

city: Seattle

first: Kevin

middle: J

last: Cheung

state: WA

address: 1100 Fairview Ave N

department: Public Health Sciences

institute: Fred Hutchinson Cancer Center

description: processed data are matrices of normalized abundances (“CPM”) for each gene/sample in tidy format. Columns: "ensembl_gene_id","external_gene_name","Sample","RatID","Treatment","Region","Condition","Label","CPM"  . Separate files are provided for genes mapped to the mouse genome (mm) and the rat genome (rn), respectively. Regions: in/out correspond to inside the necrotic core and outside the necrotic core (i.e. in the non-necrotic rim), respectively

data_processing:
Reads trimmed with TrimGalore
Trimmed reads aligned to catenated mouse-rat genome using STAR, and reads mapping uniquely to mouse or rat segregated into separate BAM files.
Aligned reads mapped to genomic features using FeatureCounts
TMM library normalization and differential expression analysis performed with limma/voom pipeline
Assembly: GRCm38, Rnor_6.0
Supplementary files format and content: Processed data files “cpm_voom_tidy_mm.csv” and “cpm_voom_tidy_rn.csv”  are files with a matrix of normalized gene-wise abundance values (CPM) for expression of rat(rn) or mouse (mm) genes. Tumor region column: in, out, lung corresponds to necrotic region (in), non-necrotic rim (out)

molecule: polyA RNA

organism: Rattus norvegicus

source_name: mammary tumor

growth_protocol: 4T1 cells transplanted into SRG host mammary fat pads and tissue collected after 27 days.

extract_protocol:
The primary tumors were cut in half to expose the cross-section, and the tumors were dissected to isolate the necrotic core region and the non-necrotic rim region. Samples were snap frozen and sent to Genewiz-Azenta for RNA extraction, library prep, and next-gen sequencing.
Library was constructed by Genewiz-Azenta using PolyA selection.

value: mammary tumor

value: breast cancer

value: nontargeting shRNA


title: non-targeting shRNA,Tumor non-necrotic rim, Rat4833


title: ET4_CKDL210011619-1a_HC5FKDSX2_L3 [ATAC-seq]


title: INDYSD, 9

value: cerebellum


title: Her2/Neu mouse model cells,Day14,Bio2,run4

value: Her2-dependent cells derived from theMTB/TANmouse model

tag: timepoint

value: Day 14


title: non-targeting shRNA,Tumor non-necrotic rim, Rat4832

tag: tissue


title: non-targeting shRNA,Tumor non-necrotic rim, Rat4831

tag: cell type


title: CSBSD, 8

value: M


title: ET2_CKDL210011618-1a_HC5FKDSX2_L3 [ATAC-seq]

tag: group


title: Her2/Neu mouse model cells,Day14,Bio2,run3


title: WTKD, 7

tag: Sex

value: KD


title: ET5_CKDL210011620-1a_HC5FKDSX2_L3 [ATAC-seq]


title: ER5_CKDL210011624-1a_HC5FKDSX2_L3 [ATAC-seq]

value: ROSI


title: CSBSD, 6

tag: strain


title: Her2/Neu mouse model cells,Day0,Bio5,run5

value: Day 0


title: non-targeting shRNA,Tumor necrotic core, Rat4834

tag: genotype


title: non-targeting shRNA,Tumor necrotic core, Rat4833

tag: treatment


title: ER4_CKDL210011623-1a_HC5FKDSX2_L3 [ATAC-seq]


title: Her2/Neu mouse model cells,Day0,Bio4,run4


title: DKOKD, 2

value: DKO


title: non-targeting shRNA,Tumor necrotic core, Rat4832


title: ER1_CKDL210011622-1a_HC5FKDSX2_L3 [ATAC-seq]


title: ED6_CKDL210011617-1a_HC5FKDSX2_L3 [ATAC-seq]

value: control

value: DMSO


title: Her2/Neu mouse model cells,8hr,Bio1,run1

value: 8 Hr


title: ED5_CKDL210011616-1a_HC5FKDSX2_L3 [ATAC-seq]

value: HTERT-immortalized  Adipose Derived Mesencymal stem cell

value: Adipogenic differentiation


title: Angptl7 knockdown,Tumor non-necrotic rim, Rat4823

value: Angptl7 knockdown shRNA #3


title: Her2/Neu mouse model cells,Day0,Bio2,run3


title: DKOKD, 3


title: DKOSD, 1

value: SD


title: Her2/Neu mouse model cells,8hr,Bio3,run2


title: ED3_CKDL210011615-1a_HC5FKDSX2_L3 [ATAC-seq]


title: Angptl7 knockdown,Tumor non-necrotic rim, Rat4822

value: mammary tumor

value: breast cancer


title: ED1_CKDL210011614-1a_HC5FKDSX2_L3 [ATAC-seq]


title: DT6_CKDL210011609-1a_HC5FKDSX2_L3 [ATAC-seq]

value: treatment

value: TBT


title: Angptl7 knockdown,Tumor necrotic core, Rat4823


title: Her2/Neu mouse model cells,8Hr,Bio4,run4

value: Her2-dependent cells derived from theMTB/TANmouse model


title: Her2/Neu mouse model cells,Day0,Bio3,run2


title: Her2/Neu mouse model cells,8Hr,Bio5,run5


title: Her2/Neu mouse model cells,8Hr,Bio4,run3


title: Angptl7 knockdown,Tumor non-necrotic rim, Rat4821


title: Angptl7 knockdown,Tumor necrotic core, Rat4822


title: Her2/Neu mouse model cells,8Hr,Bio2,run3


title: non-targeting shRNA,Tumor necrotic core, Rat4831

value: nontargeting shRNA


title: DT5_CKDL210011608-1a_HC5FKDSX2_L3 [ATAC-seq]


title: DT4_CKDL210011607-1a_HC5FKDSX2_L3 [ATAC-seq]


title: Angptl7 knockdown,Tumor necrotic core, Rat4821


title: DT1_CKDL210011606-1a_HC5FKDSX2_L3 [ATAC-seq]


title: TPN16  rat

city: Shanghai

first: Siyang

last: Cheng

address: KongJiang Rd.1665

institute: Xinhua hospital

data_processing:
Randfold tools soft (v2.0) was used for novel miRNA secondary structure prediction.
DEGs were identified using the DESeq2 package in R . P values were adjusted using the Benjamini and Hochberg’s approach to control for false discovery rate.
MiRNA with |log2(FC) | ≥ 0.58 and P value ≤ 0.05 were subjected for functional analysis.
GO enrichment analysis of DEGs was implemented by the GOseq R packages based Wallenius non-central hyper-geometric distribution .
KOBAS software  was used to test the statistical enrichment of DEGs in KEGG pathways.
Supplementary files format and content: All_miRNA expression.xlsx

source_name: liver

extract_protocol:
Total RNA from livers and cells were extracted using TRIzol reagent according to the manufacturer’s instruction.
libraries were constructed and sequenced on Illumina HiSeq 4000 platform

treatment_protocol: Male Sprague-Dawley rats (Sippurbec Laboratory Animal Co, Ltd, Shanghai, China) at the age of 4 weeks were subjected to 0.9% saline with standard chow diet or TPN for 7 days

value: liver

value: Sprague-Dawley

value: male

value: total parenteral nutrition 7days


title: TPN15  rat


title: 12 Nonbeta_Week8

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
The reads were trimmed for adapters and filtered by sequencing Phred quality (>= Q15) using fastp.
The gene count table was generated by aligning reads to the mouse transcriptome (Ensembl version 98) using kallisto and converting transcript counts to gene counts using tximport.
Assembly: GRCm38
Supplementary files format and content: CSV file includes gene counts for each Sample

source_name: Islets

extract_protocol:
High-quality total RNA (>200nt) was extracted using standard Trizol reagent (Invitrogen) according to manufacturer instructions and the resultant aqueous phase was mixed (1:1) with 70% RNA-free ethanol and added to Qiagen Rneasy mini kit columns (Qiagen) and the kit protocol was followed with DNA digestion on column step performed.
RNA libraries for RNA-seq were prepared Takara Pico-Input Strand-Specific Total RNA-seq for Illumina v2 Kit following manufacturer's protocols.

value: Islets

value: nonbeta cells

value: NOD

value: Week 8


title: DR6_CKDL210011613-1a_HC5FKDSX2_L3 [ATAC-seq]

value: HTERT-immortalized  Adipose Derived Mesencymal stem cell

value: Adipogenic differentiation

value: ROSI


title: Condition 4: non-producer 96h stationary C

city: Saarbruecken

first: Michael

last: Kohlstedt

address: Campus A1.5

country: Germany

institute: Saarland University

hyb_protocol: Agilent hybridization kit

scan_protocol: Agilent SureScan S2600D Microarray Scanner

data_processing: GeneSpring 14.9 GC, Feature extraction, Statistical analysis (moderated t-test, p_corr < 0.05 (Benjamini-Hochberg), 2fold change). Reference: T1 for each condition; custom probes averaged.

organism: Yarrowia lipolytica

source_name: cell biomass

label_protocol: Agilent: Low Input Quick Amp WT Labeling Kit, One-Color, WT primers

growth_protocol: baffled 500 mL shake flask, 50 mL yeast nitrogen base (YNB) minimal medium with different nutrient concentrations (20-40 g L-1 glycerol, 5 g L-1 ammonium sulfate, MES buffer pH = 6.8), 28°C, 230 rpm, initial OD600 = 0.1

extract_protocol: mRNA extracted from harvested cell pellets using RiboPure Yeast RNA extraction kit

treatment_protocol: Cells (2 mL) were harvested via centrifugation (30 sec, 4°C, 13.000 x g) and snap-frozen in liquid nitrogen

tag: dha production

value: No DHA production

tag: growth phase

value: late production phase

value: yeast cells


title: 10 Nonbeta_Week8


title: TPN11  rat


title: DR5_CKDL210011612-1a_HC5FKDSX2_L3 [ATAC-seq]

value: treatment


title: 9 Nonbeta_Week4

value: Week 4


title: Condition 4: non-producer 72h stationary B

value: middle production phase


title: DR3_CKDL210011611-1a_HC5FKDSX2_L3 [ATAC-seq]


title: TPN8  rat

value: liver


title: Condition 4: non-producer 96h stationary A


title: TPN6  rat

value: Sprague-Dawley


title: 7 Nonbeta_Week4


title: Condition 4: non-producer 72h stationary C


title: DD6_CKDL210011605-1a_HC5FKDSX2_L3 [ATAC-seq]

value: control

value: DMSO


title: Control19 rat

value: male

value: chow+intravenous saline 7 days


title: DR1_CKDL210011610-1a_HC5FKDSX2_L3 [ATAC-seq]


title: Condition 4: non-producer 96h stationary B


title: 11 Nonbeta_Week8

value: Islets

value: nonbeta cells

value: NOD


title: 6 Beta_Week8

value: beta cells

value: Week 8


title: 8 Nonbeta_Week4


title: Control18 rat


title: Condition 4: non-producer 48h stationary C

value: No DHA production


title: DD3_CKDL210011603-1a_HC5FKDSX2_L3 [ATAC-seq]

value: HTERT-immortalized  Adipose Derived Mesencymal stem cell

value: Adipogenic differentiation


title: Control16 rat


title: DD5_CKDL210011604-1a_HC5FKDSX2_L3 [ATAC-seq]


title: Condition 4: non-producer 48h stationary A

value: yeast cells


title: 4 Beta_Week8


title: DD1_CKDL210011602-1a_HC5FKDSX2_L3 [ATAC-seq]


title: Condition 4: non-producer 72h stationary A


title: Control12 rat


title: Condition 4: non-producer 24h stationary C

value: early stationary phase


title: Condition 4: non-producer 48h stationary B

value: middle production phase


title: 3 Beta_Week4

value: Week 4


title: CT6_CKDL210011597-1a_HC5FKDSX2_L3 [ATAC-seq]

value: treatment

value: TBT


title: 5 Beta_Week8


title: Control5 rat

value: liver

value: Sprague-Dawley


title: Condition 4: non-producer 6h exponential C

value: exponential growth


title: 1 Beta_Week4

value: Islets


title: Rat normal mammary gland (no xenograft); replicate 3

description: RNA-seq of control normal rat mammary gland

data_processing:
Reads trimmed with TrimGalore
Trimmed reads aligned to catenated mouse-rat genome using STAR.
Aligned reads mapped to genomic features using FeatureCounts
TMM library normalization and differential expression analysis performed with limma/voom pipeline
Assembly: GRCm38, Rnor_6.0
Supplementary files format and content: Processed data files “cpm_voom_tidy_mm.csv” and “cpm_voom_tidy_rn.csv”  are files with a matrix of normalized gene-wise abundance values (CPM) for expression of rat(rn) or mouse (mm) genes. Tumor region column: in, out, lung corresponds to necrotic region (in), non-necrotic rim (out), or lung (lung).
Supplementary files format and content: Processed files ‘crossmap_gene_counts_mm.csv’ and “crossmap_gene_counts_rn.csv’ are unnormalized read counts mapped to the mouse (mm) or rat (rn) genomes using the disambiguation procedure. Columns correspond to samples

source_name: mammary gland

value: mammary gland

value: primary mammary tissue

value: wildtype

value: no treatment


title: 2 Beta_Week4

value: beta cells

value: NOD


title: Condition 4: non-producer 24h stationary B

value: No DHA production


title: CT1_CKDL210011594-1a_HC5FKDSX2_L3 [ATAC-seq]

value: HTERT-immortalized  Adipose Derived Mesencymal stem cell

value: Adipogenic differentiation


title: Mouse ovary DKO LXR TG-AMH-LXRb 3

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

institute: igred

data_processing:
Quality score trimming and filtering were performed with Cutadapt.
Trimmed reads were aligned to the annotated mouse genome (mm10) using Hisat2 (v2.1.0)
Per gene read counts were calculated from the Hisat2 output using htseq-count (v0.5.4p5)
RPKM (Reads Per Kilobase of exon per Megabase of library size)  were caclulated
Differential gene expression was analyzed using the R package DESeq2 (v1.2.8)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include ENS id and gene and RPKM values for each sample.

source_name: Mouse ovary DKO LXR TG-AMH-LXRb

extract_protocol: RNA were extracted with Nacherey-Nagel RNA L extraction kit.

treatment_protocol: Ovary samples post 40h PMSG induction

value: DKO LXR TG-AMH-LXRb

value: Ovary

value: Adult


title: Rat normal mammary gland (no xenograft); replicate 1


title: Mouse ovary DKO LXR TG-AMH-LXRb 2


title: CT3_CKDL210011595-1a_HC5FKDSX2_L3 [ATAC-seq]

value: treatment

value: TBT


title: CR6_CKDL210011601-1a_HC5FKDSX2_L3 [ATAC-seq]

value: ROSI


title: Condition 4: non-producer 24h stationary A

value: early stationary phase

value: yeast cells


title: Iwat, NRG4-AKO, cold, rep3

city: Ann Arbor

first: Jiandie

last: Lin

state: MI

address: 210 Washtenaw Ave

department: Life Sciences Institute

institute: University of Michigan

data_processing:
FastQC was used to asses the sequencing qualtiy on fastq files; STAR was used for alignment to generate bam files; The reads aligned to each gene feature were counted by Rsubread package (version 2.0.1); DESeq2 pacakge was used for differential gene expression analysis
Assembly: mm10
Supplementary files format and content: DEseq2 normalized reads counts for bulk RNA-seq data

source_name: inguinal white adipose tissue

extract_protocol:
Total inguinal white adipose tissue RNA was extracted from frozen tissues using RNA extract kit (Invitrogen, Cat: 12183025)
Bulk RNA libraries were prepared using high-throughput sequenicng set following the user manual

value: inguinal white adipose tissue

value: cold, 10days


title: Mouse ovary DKO LXR TG-AMH-LXRb 1


title: Condition 4: non-producer 6h exponential B

value: exponential growth


title: CR5_CKDL210011600-1a_HC5FKDSX2_L3 [ATAC-seq]


title: Control7 rat

value: liver

value: Sprague-Dawley

value: male

value: chow+intravenous saline 7 days


title: Iwat, NRG4-AKO, cold, rep2


title: Mouse ovary DKO LXR 3

source_name: Mouse ovary DKO LXR

value: DKO LXR


title: CT5_CKDL210011596-1a_HC5FKDSX2_L3 [ATAC-seq]

value: HTERT-immortalized  Adipose Derived Mesencymal stem cell

value: Adipogenic differentiation


title: Condition 4: non-producer 6h exponential A

value: No DHA production


title: CR3_CKDL210011599-1a_HC5FKDSX2_L3 [ATAC-seq]


title: Iwat, NRG4-AKO, cold, rep1


title: Condition 3: DHA producer 120h stationary B

value: Plateau of DHA production

value: late production phase


title: Mouse ovary DKO LXR 2

value: Ovary

value: Adult


title: Condition 3: DHA producer 120h stationary C


title: CR1_CKDL210011598-1a_HC5FKDSX2_L3 [ATAC-seq]

value: treatment

value: ROSI


title: CD6_CKDL210011593-1a_HC5FKDSX2_L3 [ATAC-seq]

value: control

value: DMSO


title: Iwat, wt, cold, rep2

value: inguinal white adipose tissue

value: wt

value: cold, 10days


title: Mouse ovary WT 3

source_name: Mouse ovary WT

value: WT


title: Condition 3: DHA producer 96h stationary A

value: Highest DHA production rate

value: middle production phase

value: yeast cells


title: Iwat, wt, cold, rep1


title: Mouse ovary WT 2


title: CD4_CKDL210011592-1a_HC5FKDSX2_L3 [ATAC-seq]

value: HTERT-immortalized  Adipose Derived Mesencymal stem cell

value: Adipogenic differentiation


title: Condition 3: DHA producer 96h stationary B


title: CD2_CKDL210011591-1a_HC5FKDSX2_L3 [ATAC-seq]


title: Condition 3: DHA producer 120h stationary A

value: Plateau of DHA production


title: Adult_Mouse_14dpi_4

city: Fukuoka

first: Hirotaka

last: Iura

address: 3-1-1 Maedashi

department: Orthopedic Surgery

institute: Kyushu University

data_processing:
Quality trimming and adapter clipping of the read data were performed using Trimmomatic version 0.36.
Trimmed reads were mapped to the transcript in the human  reference sequence mm10 using Bowtie2 aligner within RSEM.
Read count extraction and normalization were performed using edgeR program.
Assembly: mm10
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

source_name: Posterior knee joint capsule

extract_protocol:
Posterior joint capsules were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. The sequencing libraries were prepared from 200 ng of total RNA with an MGIEasy rRNA Depletion Kit and MGIEasy RNA Directional Library Prep Set (MGI Tech Co., Ltd., Shenzhen, China) according to the manufacturer's instructions.
The libraries were sequenced on the DNBSEQ-G400 FAST Sequencer (MGI Tech Co., Ltd.) with a paired-end 150-nt strategy. Quality trimming and adapter clipping of the read data were performed using a Trimmomatic, version 0.38. Trimmed reads were mapped to the transcript in the reference human genome (hg38) using the Bowtie2 aligner within RSEM.

treatment_protocol: The knee joints of adult male mice were immobilized at 140° with a cast for 2 weeks.

value: Posterior knee joint capsule

value: ten-week-old

value: wild type

value: Immobilized in casting for 2 weeks


title: Mouse ovary WT 1

value: Ovary

value: Adult


title: CD1_CKDL210011590-1a_HC5FKDSX2_L3 [ATAC-seq]

value: control

value: DMSO


title: Condition 3: DHA producer 72h stationary C


title: Iwat, wt, cold, rep3

value: inguinal white adipose tissue

value: wt


title: Adult_Mouse_14dpi_2


title: Adult_Mouse_14dpi_3


title: Corona radiata DKO LXR TG-AMH-LXRb 3

data_processing:
Quality score trimming and filtering were performed with Cutadapt.
Trimmed reads were aligned to the annotated mouse genome (mm10) using Hisat2 (v2.1.0)
Per gene read counts were calculated from the Hisat2 output using htseq-count (v0.5.4p5)
RPKM (Reads Per Kilobase of exon per Megabase of library size)  were caclulated
Differential gene expression was analyzed using the R package DESeq2 (v1.2.8)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include ENS id gene symbol and RPKM values for each sample.

source_name: Cumulus DKO LXR TG-AMH-LXRb

treatment_protocol: Granulosa cell samples post J4 PMSG/hCG induction

value: DKO LXR TG-AMH-LXRb

value: Corona radiata - granulosa


title: Corona radiata DKO LXR TG-AMH-LXRb 2


title: BT5_CKDL210011584-1a_HC5FKDSX2_L3 [ATAC-seq]

value: treatment

value: TBT


title: Condition 3: DHA producer 96h stationary C

value: Highest DHA production rate

value: middle production phase

value: yeast cells


title: Adult_Mouse_14dpi_1

value: Posterior knee joint capsule


title: Mouse ovary DKO LXR 1

value: DKO LXR


title: Condition 3: DHA producer 72h stationary A


title: Condition 3: DHA producer 72h stationary B


title: Corona radiata DKO LXR TG-AMH-LXRb 1


title: Condition 3: DHA producer 48h stationary C

value: Start of DHA production

value: early stationary phase


title: BT6_CKDL210011585-1a_HC5FKDSX2_L3 [ATAC-seq]

value: HTERT-immortalized  Adipose Derived Mesencymal stem cell

value: Adipogenic differentiation


title: Adult_Mouse_naive_4

value: ten-week-old

value: wild type

value: naive


title: BT2_CKDL210011582-1a_HC5FKDSX2_L3 [ATAC-seq]


title: Corona radiata DKO LXR 2

source_name: Cumulus DKO LXR

value: Adult


title: Adult_Mouse_naive_2


title: BT1_CKDL210011581-1a_HC5FKDSX2_L3 [ATAC-seq]


title: Corona radiata DKO LXR 1


title: BT3_CKDL210011583-1a_HC5FKDSX2_L3 [ATAC-seq]


title: BR6_CKDL210011589-1a_HC5FKDSX2_L3 [ATAC-seq]

value: ROSI


title: Corona radiata WT 3

source_name: Cumulus WT

value: WT

value: Corona radiata - granulosa


title: Adult_Mouse_naive_1


title: Condition 3: DHA producer 48h stationary B


title: BR4_CKDL210011588-1a_HC5FKDSX2_L3 [ATAC-seq]

value: treatment


title: Corona radiata WT 2


title: Adult_Mouse_naive_3


title: HCC tumor from patient MDA_113

type: protein

city: Houston

first: Ju-Seog

last: Lee

state: Texas

address: 6565 MD Anderson Blvd

institute: UT MD Anderson Cancer Ctr.

hyb_protocol: Protein lysate from each sample was spotted to nitrocellulose-coated slides and probed with over 200  antibodies.  Printed proteins in slides were probed with 201 validated primary antibodies followed by corresponding secondary antibodies (goat anti-rabbit IgG, goat anti-mouse IgG, or rabbit anti-goat IgG)

scan_protocol: Slides were scanned on a flatbed scanner to produce 16-bit tiff images. Spots from tiff images were identified and their densities were quantified by MicroVigene. Relative protein levels for each sample were determined by interpolation of each dilution curve from the standard curve (supercurve) of the slide (antibody). Supercurve is constructed from a script in R written by the informatics department. These values are given as Normalized values.

data_processing: Expression data was normalized for possible unequal protein loading, taking into account the signal intensity for each sample for all antibodies tested. Log2 values were media-centered by protein to account for variability in signal intensity by time and were calculated using the formula log2 signal to  log2 median. Principal component analysis was used to check for a batch effect and feature-by-feature two-sample t-tests were used to assess differences between treatment and control groups. We also used feature-by-feature one-way analysis of variance (ANOVA) followed by the Tukey test to perform pair comparisons for all groups. Beta-uniform mixture models were used to fit the resulting p value distributions to adjust for multiple comparisons. The cutoff p values and number of significant proteins were computed for several different false discovery rates (FDRs).

molecule: protein

source_name: primary HCC tumor

growth_protocol: Collected primary tumors

extract_protocol: protein was extracted from tumors using an RPPA lysis buffer (1% Triton X-100, 50 nmol/L HEPES, pH 7.4, 150 nmol/L NaCl, 1.5 nmol/L MgCl2, 1 mmol/L EGTA, 100 nmol/L NaF, 10 nmol/L sodium pyrophosphate, 10% glycerol, 1 nmol/L phenylmethylsulfonyl fluoride, 1 nmol/L Na3VO4, 10 µg/mL aprotinin). Lysis buffer was used to lyse frozen tumors with a Precellys homogenizer (Bertin Instruments). Tumor lysates were adjusted to a concentration of 1 g/L as determined using a bicinchoninic acid assay and boiled with 1% sodium dodecyl sulfate.

treatment_protocol: Not treated

tag: organ

value: liver

tag: age (years)

value: M

tag: death

value: alive

tag: follow-up (month)


title: BR2_CKDL210011587-1a_HC5FKDSX2_L3 [ATAC-seq]

tag: time

tag: condition replicate


title: Corona radiata WT 1

tag: age


title: Condition 3: DHA producer 48h stationary A

tag: condition

value: yeast cells


title: Corona radiata DKO LXR 3

value: DKO LXR

tag: tissue


title: Condition 3: DHA producer 6h exponential C

value: No DHA production

value: exponential growth

tag: cell type


title: Condition 3: DHA producer 20h exponential A

value: late exponential growth


title: HCC tumor from patient MDA_111

label_protocol: Protein lysate from each sample was spotted to nitrocellulose-coated slides and probed with over 200  antibodies.  Printed proteins in slides were probed with 201 validated primary antibodies followed by corresponding secondary antibodies (goat anti-rabbit IgG, goat anti-mouse IgG, or rabbit anti-goat IgG)


title: HCC tumor from patient MDA_112

description: Protein lysate from each sample was spotted to nitrocellulose-coated slides and probed with over 200  antibodies.

value: dead


title: BD5_CKDL210011580-1a_HC5FKDSX2_L3 [ATAC-seq]

tag: group

value: control

tag: cell line

value: HTERT-immortalized  Adipose Derived Mesencymal stem cell

value: Adipogenic differentiation

value: DMSO


title: MitfNdrg1, replicate 5 [E8_MitfNdrg1_5]

city: La Jolla

first: Samuel

middle: L

last: Pfaff

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Prior to quantification RNA-seq reads were filtered to discard reads with average base quality less than 15 and any detected adapter sequences were trimmed.
Single and paired-end RNA-Seq reads were quantified using Kallisto against the Gencode (M17) transcript database based on the mm10 mouse genome.
Prior to further analysis the expression and count values for transcripts were summed into gene level values.
Estimated counts and TPM values for genes were imported into R for downstream analysis.
Assembly: mm10
Supplementary files format and content: CSV formatted unnormalized gene level read counts.

source_name: sciatic nerve

extract_protocol:
Total RNA was isolated using Qiagen RNAeasy Plus Micro kit (# 74034). The Agilent Bioanalyzer (Tape Station) was used to determine RNA integrity (RIN) prior to library preparation.
Stranded mRNA sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit according to manufacturer’s instructions (Illumina).

treatment_protocol: Sciatic nerves were rapidly dissected after euthanasia, and quick-frozen on dry ice. Sciatic nerves were lysed with a pellet pestle in RLT buffer (Qiagen) with β-mercaptoethanol.

value: sciatic nerve


title: Condition 3: DHA producer 6h exponential B

tag: strain


title: Condition 2: DHA producer 96h stationary C

value: Plateau of DHA production

value: late production phase


title: Condition 3: DHA producer 20h exponential B


title: Condition 3: DHA producer 20h exponential C


title: HCC tumor from patient MDA_110

tag: Sex


title: Condition 3: DHA producer 6h exponential A


title: BD1_CKDL210011578-1a_HC5FKDSX2_L3 [ATAC-seq]

tag: treatment


title: MitfNdrg1, replicate 3 [E8_MitfNdrg1_3]

tag: genotype


title: BR1_CKDL210011586-1a_HC5FKDSX2_L3 [ATAC-seq]

value: treatment

value: ROSI


title: Condition 2: DHA producer 96h stationary B

tag: dha production

tag: growth phase


title: HCC tumor from patient MDA_108

tag: organ

value: liver

tag: age (years)

value: F


title: Condition 2: DHA producer 72h stationary C

value: Highest DHA production rate

value: middle production phase

value: yeast cells


title: AO4_CKDL210011577-1a_HC5FKDSX2_L3 [ATAC-seq]

value: No Adipogenic differentiation


title: HCC tumor from patient MDA_107

value: M

tag: death

value: alive

tag: follow-up (month)


title: Ndrg1, replicate 5 [E8_Ndrg1_5]


title: MitfNdrg1, replicate 4 [E8_MitfNdrg1_4]


title: AO1_CKDL210011575-1a_HC5FKDSX2_L3 [ATAC-seq]

value: control

tag: time

tag: condition replicate


title: Condition 2: DHA producer 72h stationary B

tag: condition


title: BD4_CKDL210011579-1a_HC5FKDSX2_L3 [ATAC-seq]

value: HTERT-immortalized  Adipose Derived Mesencymal stem cell


title: AO3_CKDL210011576-1a_HC5FKDSX2_L3 [ATAC-seq]


title: HCC tumor from patient MDA_105


title: HCC tumor from patient MDA_106


title: MitfNdrg1, replicate 1 [E8_MitfNdrg1_1]

tag: tissue


title: MitfNdrg1, replicate 2 [E8_MitfNdrg1_2]


title: HCC tumor from patient MDA_104


title: ET3_GCGCAAGC-CGGCGTGA_H3FL7DSX2_L004_001 [RNA-seq]

description:
ET3_GCGCAAGC-CGGCGTGA_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

data_processing:
paired end reads were sequenceed using the Novaseq platform
raw 100 bp paired-end reads were trimmed to remove low quality base calls and Illumina universal adapters using Trim Galore! (version 0.6.5) with default parameters and then assessed using fastQC
The cleaned paired-end reads were aligned with STAR (version 2.5.2a) to GRCh38 genome, with Gencode v25 annotation.
RNA abundance was measured by mapping with Bowtie2 to GRCh38 genome, with Gencode v25 annotation.
Quality control was performed using Picard and RSeQC, and reads passing QC filters were annotated genes were quantified with featureCounts (v1.4.3-p1
Assembly: hg38
Supplementary files format and content: feature counts text file
Supplementary files format and content: tab delineated TPM file

extract_protocol:
RNA was harvested using Rneasy micro plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using  KAPA Stranded RNA-seq Kit by the New york genome center following

tag: cell type

value: Adipogenic differentiation

value: TBT


title: ET2_ATATGGAT-TAATACAG_HJLL5DSX2_L004_001 [RNA-seq]

description:
ET2_ATATGGAT-TAATACAG_HJLL5DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

tag: group


title: Ndrg1, replicate 2 [E8_Ndrg1_2]

value: sciatic nerve


title: ET1_CGGACAAC-AATCCGGA_H3FL7DSX2_L004_001 [RNA-seq]

description:
ET1_CGGACAAC-AATCCGGA_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

tag: cell line


title: Ndrg1, replicate 3 [E8_Ndrg1_3]


title: Condition 2: DHA producer 72h stationary A

tag: strain


title: HCC tumor from patient MDA_103

tag: Sex


title: Ndrg1, replicate 1 [E8_Ndrg1_1]


title: Ndrg1, replicate 4 [E8_Ndrg1_4]


title: ER3_ACCTTGGC-ATGAGGCC_HLY3GDSX2_L001_001 [RNA-seq]

description:
ER3_ACCTTGGC-ATGAGGCC_HLY3GDSX2_L001_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

tag: treatment


title: Condition 2: DHA producer 24h stationary C

value: No DHA production

value: early stationary phase


title: Condition 2: DHA producer 48h stationary A

value: Start of DHA production


title: ER3_ACCTTGGC-ATGAGGCC_HJLL5DSX2_L004_001 [RNA-seq]

description:
ER3_ACCTTGGC-ATGAGGCC_HJLL5DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

value: treatment

value: ROSI


title: ER2_GTTCCAAT-GCAGAATT_H3FL7DSX2_L004_001 [RNA-seq]

description:
ER2_GTTCCAAT-GCAGAATT_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: Mitf, replicate 5 [E8_Mitf_5]

tag: genotype

value: Mitf


title: ER1_GCAATGCA-AACGTTCC_H3FL7DSX2_L004_001 [RNA-seq]

description:
ER1_GCAATGCA-AACGTTCC_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: HCC tumor from patient MDA_099

value: liver


title: HCC tumor from patient MDA_102

value: dead


title: HCC tumor from patient MDA_101


title: HCC tumor from patient MDA_100


title: Condition 2: DHA producer 48h stationary C

tag: dha production

value: middle production phase

value: yeast cells


title: Mitf, replicate 6 [E8_Mitf_6]


title: ED3_ATGGCATG-GGTACCTT_H3FL7DSX2_L004_001 [RNA-seq]

description:
ED3_ATGGCATG-GGTACCTT_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: Mitf, replicate 4 [E8_Mitf_4]


title: ED2_GGAGCGTC-GCACGGAC_H3FL7DSX2_L004_001 [RNA-seq]

description:
ED2_GGAGCGTC-GCACGGAC_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

value: DMSO


title: Mitf, replicate 2 [E8_Mitf_2]


title: Mitf, replicate 1 [E8_Mitf_1]


title: ED1_AAGATACT-ATGTAAGT_H3FL7DSX2_L004_001 [RNA-seq]

description:
ED1_AAGATACT-ATGTAAGT_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: Condition 2: DHA producer 6h exponential B

tag: growth phase

value: exponential growth


title: HCC tumor from patient MDA_098

tag: organ

value: M

value: alive


title: Control, replicate 6 [E8_control_6]

value: control


title: Condition 2: DHA producer 48h stationary B


title: HCC tumor from patient MDA_095

tag: age (years)


title: HCC tumor from patient MDA_096

value: F

tag: death


title: Mitf, replicate 3 [E8_Mitf_3]

value: sciatic nerve


title: DT4_TACCGAGG-AGTTCAGG_H3FL7DSX2_L004_001 [RNA-seq]

description:
DT4_TACCGAGG-AGTTCAGG_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

value: HTERT-immortalized  Adipose Derived Mesencymal stem cell

value: Adipogenic differentiation


title: Control, replicate 5 [E8_control_5]


title: DT3_AATGCCTC-TGGATCGA_H3FL7DSX2_L004_001 [RNA-seq]

description:
DT3_AATGCCTC-TGGATCGA_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: Condition 2: DHA producer 96h stationary A

value: Plateau of DHA production

value: late production phase


title: HCC tumor from patient MDA_097

tag: follow-up (month)


title: HCC tumor from patient MDA_094


title: Condition 2: DHA producer 24h stationary A

value: No DHA production

tag: time

value: early stationary phase


title: Control, replicate 4 [E8_control_4]


title: HCC tumor from patient MDA_093

value: liver


title: DT2_GGCATTCT-CAAGCTAG_H3FL7DSX2_L004_001 [RNA-seq]

description:
DT2_GGCATTCT-CAAGCTAG_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

value: treatment

tag: condition replicate

value: TBT


title: Condition 2: DHA producer 6h exponential C

tag: condition

value: yeast cells


title: HCC tumor from patient MDA_092


title: DT1_TTACAGGA-GCTTGTCA_H3FL7DSX2_L004_001 [RNA-seq]

description:
DT1_TTACAGGA-GCTTGTCA_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: DR3_TAAGTGGT-GGCTTAAG_H3FL7DSX2_L004_001 [RNA-seq]

description:
DR3_TAAGTGGT-GGCTTAAG_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: Control, replicate 2 [E8_control_2]

tag: tissue


title: Control, replicate 1 [E8_control_1]


title: DR2_CTACGACA-TTGGACTC_H3FL7DSX2_L004_001 [RNA-seq]

description:
DR2_CTACGACA-TTGGACTC_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

tag: cell type


title: Mitf, replicate 3 [E7_Mitf_3]

value: Mitf


title: HCC tumor from patient MDA_091

description: Protein lysate from each sample was spotted to nitrocellulose-coated slides and probed with over 200  antibodies.


title: DR1_TCGTAGTG-CCAAGTCT_H3FL7DSX2_L004_001 [RNA-seq]

description:
DR1_TCGTAGTG-CCAAGTCT_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

tag: group

value: ROSI


title: Control, replicate 3 [E8_control_3]


title: DD3_GATTCTGC-CTCTCGTC_H3FL7DSX2_L004_001 [RNA-seq]

description:
DD3_GATTCTGC-CTCTCGTC_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

tag: cell line


title: Mitf, replicate 2 [E7_Mitf_2]


title: Condition 2: DHA producer 6h exponential A

tag: strain

value: exponential growth


title: Mitf, replicate 1 [E7_Mitf_1]


title: Egr2Cre Mitf, replicate 3 [E7_Egr2Cre_Mitf_3]

value: Egr2Cre Mitf


title: DD2_AGCCTCAT-TCTCTACT_H3FL7DSX2_L004_001 [RNA-seq]

description:
DD2_AGCCTCAT-TCTCTACT_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

value: control


title: Egr2Cre Mitf, replicate 2 [E7_Egr2Cre_Mitf_2]


title: DD1_CGTTAGAA-GACCTGAA_HLY3GDSX2_L002_001 [RNA-seq]

description:
DD1_CGTTAGAA-GACCTGAA_HLY3GDSX2_L002_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

value: DMSO


title: Egr2Cre Mitf, replicate 1 [E7_Egr2Cre_Mitf_1]

value: sciatic nerve


title: DD2_AGCCTCAT-TCTCTACT_HLY3GDSX2_L003_001 [RNA-seq]

description:
DD2_AGCCTCAT-TCTCTACT_HLY3GDSX2_L003_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

value: HTERT-immortalized  Adipose Derived Mesencymal stem cell


title: DD1_CGTTAGAA-GACCTGAA_H3FL7DSX2_L004_001 [RNA-seq]

description:
DD1_CGTTAGAA-GACCTGAA_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

value: Adipogenic differentiation


title: HCC tumor from patient MDA_087

tag: Sex

value: F

value: dead


title: HCC tumor from patient MDA_083

value: M


title: HCC tumor from patient MDA_085


title: HCC tumor from patient MDA_086


title: Mutant, 14 days post injury, replicate 3 [E6_Inj_14dp_MUT_3]

value: Mutant 14 days post injury


title: BLANK2_OR, spleen

city: hangzhou

first: bo

last: zhong

state: zhejiang

address: No. 928, 2nd Street, Xiasha Higher Education Park, Qiantang District, Hangzhou City, Zhejiang Province

institute: Zhejiang Sci-Tech University

description: BLANK2_OR, PE250

data_processing:
the raw reads were analyzed using fastqc to assess the sequencing quality. Adapters were then removed using trim-galore in paired mode.The resulting read pairs were merged using bbmerge with default parameters. If necessary, primers could be removed using cutadpt with paramater --revcomp.
In our case, the binding regions for IgNAR_NR and IgNAR_OR were different. To generate the same VNAR sequences, the modified primer IgNAR_NR (5’- CTGGCCGCGGTGGCCAAGYTGMAGAAATCCRTTTGCYCTCTKTTCTT -3’) and IgNAR_OR (5’- CTGGCCGCGGTGGCCAASAAATCCRTTTRCYCTCTKTTCTT -3’) needed to be removed from the merged sequences.
DNA sequences were counted using the R package dplyr and then translated into amino acid sequences using Biostrings in six different frames. Only the longest amino acid sequences were kept for each DNA sequence.
Differential expression of VNARs was identified using DESeq2 with the following cutoff values: q ≤ 0.05 and abs(log2(foldChange)) ≥ 1.
Assembly: Chiloscyllium_plagiosum_GCF_004010195.1_ASM401019v2
Supplementary files format and content: txt file reports protein_count (DNA sequences were counted using the R package dplyr and then translated into amino acid sequences using Biostrings in six different frames.At the same time, count the generated amino acid sequences and finally generate a processed file (*. protoin_count. txt. gz). The four columns in the file are the processed DNA sequence, the count of VNAR DNA sequences, and the translated amino acid sequence and the count of VNAR protein sequences.)

organism: Chiloscyllium plagiosum

source_name: spleen

growth_protocol: The sharks were maintained in a controlled environment with a water temperature of 25 °C and a salt concentration ranging between 1.020 and 1.025.

extract_protocol:
Two weeks after the final vaccination, the sharks were sacrificed using humanitarian execution methods and the spleen was then carefully isolated and stored at -80 °C for future study.Total RNA from the spleen was isolated using TRIzol (Thermo Fisher Scientific) according to the manual. cDNA synthesis was carried out using the SuperScript III First-Strand Synthesis System (Thermo Fisher Scientific).
VNAR libraries for next-generation sequencing were prepared, utilizing the primers provided.The PCR products ranging from 300 to 500 bp were recovered. In our assay, the PCR cycles ranged between 25 and 30 cycles. Sequencing libraries were prepared with the NEBNext® Ultra™ II DNA Library Prep Kit (NEB, USA) as the manufacturer's recommendations. Indexes were added to attribute sequences to each sample.

treatment_protocol: For vaccination, the antigen was diluted to a concentration of 2 μg/μl using 1x PBS and thoroughly mixed with Freund’s Adjuvant (Sigma) in an equal volume. Each shark received a subcutaneous injection of 100 μg of antigen every two weeks, with a total of 6 consecutive vaccinations.

value: spleen

tag: treatment


title: HCC tumor from patient MDA_090

value: liver

value: alive


title: HCC tumor from patient MDA_089


title: HCC tumor from patient MDA_084


title: HCC tumor from patient MDA_109


title: CT4_GGTACCTT-GACGTCTT_H3FL7DSX2_L004_001 [RNA-seq]

description:
CT4_GGTACCTT-GACGTCTT_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

value: treatment

value: TBT


title: BLANK2_NR, spleen

description: BLANK2_NR, PE250


title: CT3_GCACGGAC-TGCGAGAC_H3FL7DSX2_L004_001 [RNA-seq]

description:
CT3_GCACGGAC-TGCGAGAC_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: Mutant, 14 days post injury, replicate 2 [E6_Inj_14dp_MUT_2]

tag: genotype


title: BLANK1_OR, spleen

description: BLANK1_OR, PE250


title: CT2_ATGTAAGT-CATAGAGT_HLY3GDSX2_L003_001 [RNA-seq]

description:
CT2_ATGTAAGT-CATAGAGT_HLY3GDSX2_L003_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: Mutant, 14 days post injury, replicate 1 [E6_Inj_14dp_MUT_1]


title: BLANK1_NR, spleen

description: BLANK1_NR, PE250


title: Condition 1: DHA producer 96h stationary A

tag: dha production

value: Plateau of DHA production

value: late production phase

value: yeast cells


title: Wild type, 14 days post injury, replicate 3 [E6_Inj_14dp_WT_3]

value: Wild type 14 days post injury


title: CT2_ATGTAAGT-CATAGAGT_H3FL7DSX2_L004_001 [RNA-seq]

description:
CT2_ATGTAAGT-CATAGAGT_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: BAFF_OR, spleen

description: BAFF_OR, PE250

value: immune BAFF antigen


title: Wild type, 14 days post injury, replicate 2 [E6_Inj_14dp_WT_2]

value: sciatic nerve


title: CT1_CGGCGTGA-ACAGGCGC_H3FL7DSX2_L004_001 [RNA-seq]

description:
CT1_CGGCGTGA-ACAGGCGC_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

value: HTERT-immortalized  Adipose Derived Mesencymal stem cell


title: HCC tumor from patient MDA_081


title: HCC tumor from patient MDA_082


title: Condition 1: DHA producer 24h stationary B

value: No DHA production

tag: growth phase

value: early stationary phase


title: Condition 1: DHA producer 72h stationary A

value: Highest DHA production rate

value: middle production phase


title: Wild type, 14 days post injury, replicate 1 [E6_Inj_14dp_WT_1]


title: BAFF_NR, spleen

description: BAFF_NR, PE250


title: CR4_CCGTGAAG-ATCCACTG_H3FL7DSX2_L004_001 [RNA-seq]

description:
CR4_CCGTGAAG-ATCCACTG_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

value: Adipogenic differentiation

value: ROSI


title: HCC tumor from patient MDA_079

tag: organ

value: liver

value: M

value: dead


title: HCC tumor from patient MDA_080

tag: age (years)

value: alive


title: HCC tumor from patient MDA_078

tag: death


title: 26695 ΔrdxA-ΔhsdM1, pH 5

city: Williamsburg

first: Mark

last: Forsyth

state: Virginia

address: 540 Landrum Dr

department: Biology

institute: William & Mary

description: del-hsdM1 pH5

data_processing:
Azenta Life Sciences mapped subreads to the H.pylori reference genome GCF_000307795.1, GenBank accession CP003904.1.
Azenta Life Sciences performed Base Modification and Motif Analysis using PacBio SMRTLink v6.0
Assembly: GCF_000307795.1
Supplementary files format and content: comma-delimited file contains motif information for each sample
Supplementary files format and content: gff file contains base modification information for each sample

organism: Helicobacter pylori

growth_protocol: H. pylori strains were grown on Trypticase Soy Agar II plates with 5% sheep blood then SFBB-cholesterol-vancomycin broth at 37°C in 5% CO2/ 95% ambient air.

extract_protocol:
Samples were prepared via genomic DNA extraction using the Bio-Rad genomic DNA extraction kit via the manufacturer’s suggested protocol including the optional RNA elimination step. The extracted DNA was quantified for concentration and purity using a Nanodrop (Thermo Fisher). As an additional quality check, we performed agarose gel electrophoresis to ensure all extracted DNA was above 5kB and had not been fragmented.
SMRT-seq; PacBio SMRTbell libraries were prepared by Azenta Life Sciences

treatment_protocol: Each strain underwent a 72 hour growth in either pH 5 or pH 7 SFBB-cholesterol-vancomycin broth culture conditions.  Every 24 hours during this 72 hour growth period, each culture was subcultured by taking 0.2 OD600 units of each culture into 6 mL of fresh media. To collect samples, 4 mL of each culture was harvested by centrifugation at 4,500 rpm, 20°C, for 10 min. The supernatant was decanted, and the pellets were stored at -20°C.

value: H. pylori 26695 mutant strain

value: hsdM1 deletion

value: acidic pH


title: HCC tumor from patient MDA_077

tag: follow-up (month)


title: Mutant, 7 days post injury, replicate 3 [E6_Inj_7dp_MUT_3]

value: Mutant 7 days post injury


title: Condition 2: DHA producer 24h stationary B

tag: time

value: yeast cells


title: Condition 1: DHA producer 96h stationary C

value: Plateau of DHA production

value: late production phase


title: Condition 1: DHA producer 48h stationary A

value: Start of DHA production


title: CR3_TCCAACGC-AAGTCCAA_H3FL7DSX2_L004_001 [RNA-seq]

description:
CR3_TCCAACGC-AAGTCCAA_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

value: treatment

value: HTERT-immortalized  Adipose Derived Mesencymal stem cell

tag: condition replicate


title: CR2_CTTGGTAT-GGACTTGG_HMHWVDSX2_L001_001 [RNA-seq]

description:
CR2_CTTGGTAT-GGACTTGG_HMHWVDSX2_L001_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

tag: condition


title: 26695 ΔrdxA-ΔhsdM1, pH 7

description: del-hsdM1 pH7

value: neutral pH


title: Mutant, 7 days post injury, replicate 1 [E6_Inj_7dp_MUT_1]

tag: tissue

value: sciatic nerve


title: 26695 ΔrdxA-ΔarsS, pH 5

description: del-arsS pH5

tag: cell type

value: arsS deletion


title: CR2_CTTGGTAT-GGACTTGG_H3FL7DSX2_L004_001 [RNA-seq]

description:
CR2_CTTGGTAT-GGACTTGG_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

tag: group

value: Adipogenic differentiation

value: ROSI


title: Wild type, 7 days post injury, replicate 3 [E6_Inj_7dp_WT_3]

value: Wild type 7 days post injury


title: Condition 1: DHA producer 72h stationary C

value: Highest DHA production rate

value: middle production phase


title: 26695 ΔrdxA, pH 5, acidic control

value: H. pylori 26695 mutant strain

value: WT


title: 26695 ΔrdxA-ΔarsS, pH 7

description: del-arsS pH7


title: CR1_GTCGGAGC-TTATAACC_HLY3GDSX2_L002_001 [RNA-seq]

description:
CR1_GTCGGAGC-TTATAACC_HLY3GDSX2_L002_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

tag: cell line


title: CR1_GTCGGAGC-TTATAACC_H3FL7DSX2_L004_001 [RNA-seq]

description:
CR1_GTCGGAGC-TTATAACC_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: Wild type, 7 days post injury, replicate 2 [E6_Inj_7dp_WT_2]


title: 26695 ΔrdxA, pH 7, neutral control


title: Mutant, 7 days post injury, replicate 2 [E6_Inj_7dp_MUT_2]

value: Mutant 7 days post injury


title: Wild type, 7 days post injury, replicate 1 [E6_Inj_7dp_WT_1]


title: CD4_AACAGGTT-CTTGGTAT_H3FL7DSX2_L004_001 [RNA-seq]

description:
CD4_AACAGGTT-CTTGGTAT_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

value: control

value: DMSO


title: Mutant, 3 days post injury, replicate 3 [E6_Inj_3dp_MUT_3]

value: Mutant 3 days post injury


title: Condition 1: DHA producer 24h stationary C

tag: strain

value: No DHA production

value: early stationary phase

value: yeast cells


title: M. avium, BMDMs, clarithromycin, 24 hours, biol rep 3

city: Nijmegen

first: Jodie

last: Schildkraut

address: Geert Grooteplein Zuid 10

country: Netherlands

institute: Radboudumc

description:
Column G
Bc3

data_processing:
Base calling (Illumina automated Real-time analysis software 3)
Demultiplexing and fastq generation (Illumina automated bcl2fastq Conversion Software)
Mapping using STAR
Count table generation using R
Assembly: CP029332.1
Supplementary files format and content: Count table (.xlsx)

organism: Mycobacterium avium subsp. hominissuis

source_name: bacterial cell

extract_protocol:
NucleoSpin RNA
Illumina TruSeq RNA Library Prep Kit v2

value: bacterial cell

tag: host cell type

value: human monocyte-derived macrophages

value: Clarithromycin

value: 24 hours


title: CD3_ATGAGGCC-CAATTAAC_H3FL7DSX2_L004_001 [RNA-seq]

description:
CD3_ATGAGGCC-CAATTAAC_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

value: HTERT-immortalized  Adipose Derived Mesencymal stem cell

tag: treatment

value: Adipogenic differentiation


title: Mutant, 3 days post injury, replicate 2 [E6_Inj_3dp_MUT_2]

value: sciatic nerve

tag: genotype


title: CD2_GCAGAATT-TGGCCGGT_H3FL7DSX2_L004_001 [RNA-seq]

description:
CD2_GCAGAATT-TGGCCGGT_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: M. avium, BMDMs, clarithromycin, 24 hours, biol rep 2

description:
Column F
Bc2


title: HCC tumor from patient MDA_088

description: Protein lysate from each sample was spotted to nitrocellulose-coated slides and probed with over 200  antibodies.

value: liver

tag: Sex

value: M

value: dead


title: M. avium, BMDMs, clarithromycin, 24 hours, biol rep 1

description:
Column E
Bc1


title: Mutant, 3 days post injury, replicate 1 [E6_Inj_3dp_MUT_1]


title: CD1_AACGTTCC-AGTACTCC_H3FL7DSX2_L004_001 [RNA-seq]

description:
CD1_AACGTTCC-AGTACTCC_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: M. avium, BMDMs, growth control, 24 hours, biol rep 3

description:
Column D
B3


title: Wild type, 3 days post injury, replicate 3 [E6_Inj_3dp_WT_3]

value: Wild type 3 days post injury


title: BT4_GACCTGAA-CTCACCAA_H3FL7DSX2_L004_001 [RNA-seq]

description:
BT4_GACCTGAA-CTCACCAA_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

value: treatment

value: TBT


title: Condition 1: DHA producer 72h stationary B

tag: dha production

value: Highest DHA production rate

tag: growth phase

value: middle production phase


title: M. avium, BMDMs, growth control, 24 hours, biol rep 2

description:
Column C
B2


title: Wild type, 3 days post injury, replicate 2 [E6_Inj_3dp_WT_2]


title: BT3_AGTTCAGG-TCTGTTGG_H3FL7DSX2_L004_001 [RNA-seq]

description:
BT3_AGTTCAGG-TCTGTTGG_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: Wild type, 3 days post injury, replicate 1 [E6_Inj_3dp_WT_1]


title: M. avium, BMDMs, growth control, 24 hours, biol rep 1

description:
Column B
B1


title: BT2_TGGATCGA-TATCGCAC_HJLL5DSX2_L004_001 [RNA-seq]

description:
BT2_TGGATCGA-TATCGCAC_HJLL5DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: BT1_CAAGCTAG-CGCTATGT_HJLL5DSX2_L004_001 [RNA-seq]

description:
BT1_CAAGCTAG-CGCTATGT_HJLL5DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: HCC tumor from patient MDA_067

tag: organ

tag: age (years)

value: alive


title: HCC tumor from patient MDA_069

value: F

tag: death

tag: follow-up (month)


title: HCC tumor from patient MDA_072


title: HCC tumor from patient MDA_070


title: HCC tumor from patient MDA_068


title: HCC tumor from patient MDA_071


title: M. avium, rifampicin, 72 hours, biol rep 3

description:
Column P
3v5_R1

data_processing:
Base calling (Illumina automated Real-time analysis software 2.0)
Demultiplexing and fastq generation (Illumina automated bcl2fastq Conversion Software)
Mapping using STAR
Count table generation using R
Assembly: NC_008595.1
Supplementary files format and content: Count table 24h (.xlsx)
Supplementary files format and content: Count table 72h (.xlsx)

value: bacterial cell

value: Rifampicin

tag: time

value: 72 hours


title: BR4_TAATACAG-GTGAATAT_H3FL7DSX2_L004_001 [RNA-seq]

description:
BR4_TAATACAG-GTGAATAT_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

tag: condition replicate

tag: condition

value: ROSI


title: Condition 1: DHA producer 6h exponential C

value: No DHA production

value: exponential growth

tag: cell type

value: yeast cells


title: M. avium, rifampicin, 72 hours, biol rep 2

description:
Column K
2v5_R1


title: M. avium, rifampicin, 72 hours, biol rep 1

description:
Column F
1v5_R1


title: Mitf, 3 days post injury, replicate 3 [E5_Inj3dp_Mitf_3]

tag: tissue

value: sciatic nerve

value: Mitf 3 days post injury


title: Mitf, 3 days post injury, replicate 4 [E5_Inj3dp_Mitf_4]


title: HCC tumor from patient MDA_075

value: liver

value: M


title: HCC tumor from patient MDA_076


title: HCC tumor from patient MDA_073


title: BR3_AATCCGGA-AACTGTAG_H3FL7DSX2_L004_001 [RNA-seq]

description:
BR3_AATCCGGA-AACTGTAG_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

tag: group

value: treatment

tag: cell line

value: HTERT-immortalized  Adipose Derived Mesencymal stem cell

value: Adipogenic differentiation


title: Condition 1: DHA producer 6h exponential A

tag: strain


title: Condition 1: DHA producer 48h stationary C

value: Start of DHA production

value: middle production phase


title: Mitf, Uninjured, replicate 4 [E5_UI_MItf_4]

value: Mitf uninjured


title: Mitf, Uninjured, replicate 3 [E5_UI_MItf_3]


title: Mitf, 3 days post injury, replicate 2 [E5_Inj3dp_Mitf_2]


title: Condition 1: DHA producer 48h stationary B


title: M. avium, ethambutol, 72 hours, biol rep 2

description:
Column J
2v4_R1

value: bacterial cell

tag: treatment

value: Ethambutol


title: Condition 1: DHA producer 96h stationary B

value: Plateau of DHA production

value: late production phase


title: BR1_TTGGACTC-CTGCTTCC_H3FL7DSX2_L004_001 [RNA-seq]

description:
BR1_TTGGACTC-CTGCTTCC_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

value: ROSI


title: Condition 1: DHA producer 24h stationary A

value: No DHA production

value: early stationary phase


title: BR2_GGCTTAAG-GGTCACGA_H3FL7DSX2_L004_001 [RNA-seq]

description:
BR2_GGCTTAAG-GGTCACGA_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: BD4_CCAAGTCT-TCATCCTT_H3FL7DSX2_L004_001 [RNA-seq]

description:
BD4_CCAAGTCT-TCATCCTT_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

value: control

value: DMSO


title: Condition 1: DHA producer 6h exponential B

value: exponential growth

value: yeast cells


title: M. avium, ethambutol, 72 hours, biol rep 1

description:
Column E
1v4_R1

value: 72 hours


title: M. avium, amikacin, 72 hours, biol rep 3

description:
Column N
3v3_R1

value: Amikacin


title: M. avium, amikacin, 72 hours, biol rep 2

description:
Column I
2v3_R1


title: BD3_CTCTCGTC-AGGTTATA_H3FL7DSX2_L004_001 [RNA-seq]

description:
BD3_CTCTCGTC-AGGTTATA_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

value: HTERT-immortalized  Adipose Derived Mesencymal stem cell

value: Adipogenic differentiation


title: Mitf, Uninjured, replicate 1 [E5_UI_MItf_1]

value: sciatic nerve

tag: genotype


title: HCC tumor from patient MDA_061

value: liver

tag: Sex

value: M

value: alive


title: HCC tumor from patient MDA_065


title: HCC tumor from patient MDA_063


title: HCC tumor from patient MDA_066


title: HCC tumor from patient MDA_060


title: HCC tumor from patient MDA_062


title: Mitf, 3 days post injury, replicate 1 [E5_Inj3dp_Mitf_1]

value: Mitf 3 days post injury


title: HCC tumor from patient MDA_064


title: HCC tumor from patient MDA_059


title: M. avium, ethambutol, 72 hours, biol rep 3

description:
Column O
3v4_R1

value: bacterial cell

value: Ethambutol


title: HCC tumor from patient MDA_058


title: M. avium, amikacin, 72 hours, biol rep 1

description:
Column D
1v3_R1


title: BD1_TCTCTACT-GAACCGCG_HLY3GDSX2_L003_001 [RNA-seq]

description:
BD1_TCTCTACT-GAACCGCG_HLY3GDSX2_L003_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: BD1_TCTCTACT-GAACCGCG_H3FL7DSX2_L004_001 [RNA-seq]

description:
BD1_TCTCTACT-GAACCGCG_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: Egr2Cre, P12, replicate 3 [E4_Egr2Cre_P12_3]


title: HCC tumor from patient MDA_057


title: Mitf, P12, replicate 3 [E4_MItf_P12_3]

value: Mitf


title: M. avium, clarithromycin, 72 hours, biol rep 3

description:
Column M
3v2_R1

value: Clarithromycin


title: Mitf, Uninjured, replicate 2 [E5_UI_MItf_2]

value: Mitf uninjured


title: AO3_GCTTGTCA-GTATGTTC_HJLL5DSX2_L004_001 [RNA-seq]

description:
AO3_GCTTGTCA-GTATGTTC_HJLL5DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

value: control

value: No Adipogenic differentiation

value: DMSO


title: M. avium, clarithromycin, 72 hours, biol rep 2

description:
Column H
2v2_R1

value: 72 hours


title: Mitf, P12, replicate 2 [E4_MItf_P12_2]


title: AO2_ATCCACTG-ACGCACCT_H3FL7DSX2_L004_001 [RNA-seq]

description:
AO2_ATCCACTG-ACGCACCT_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: HCC tumor from patient MDA_055


title: HCC tumor from patient MDA_056


title: AO1_AAGTCCAA-TACTCATA_H3FL7DSX2_L004_001 [RNA-seq]

description:
AO1_AAGTCCAA-TACTCATA_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: M. avium, growth control, 72 hours, biol rep 3

description:
Column L
3v1_R1


title: Egr2Cre, P12, replicate 2 [E4_Egr2Cre_P12_2]


title: Mitf, P12, replicate 1 [E4_MItf_P12_1]


title: Egr2Cre, P12, replicate 1 [E4_Egr2Cre_P12_1]


title: M. avium, growth control, 72 hours, biol rep 1

description:
Column B
1v1_R1


title: M. avium, growth control, 72 hours, biol rep 2

description:
Column G
2v1_R1


title: Mitf, P21, replicate 5 [E3_Mitf_P21_5]


title: HCC tumor from patient MDA_053

description: Protein lysate from each sample was spotted to nitrocellulose-coated slides and probed with over 200  antibodies.


title: HCC tumor from patient MDA_054


title: AA3_GGACTTGG-CGTCTGCG_HLY3GDSX2_L003_001 [RNA-seq]

description:
AA3_GGACTTGG-CGTCTGCG_HLY3GDSX2_L003_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: M. avium, rifampicin, 24 hours, biol rep 4

description:
Column T
5-3_R1

value: Rifampicin

value: 24 hours


title: AA3_GGACTTGG-CGTCTGCG_HJLL5DSX2_L004_001 [RNA-seq]

description:
AA3_GGACTTGG-CGTCTGCG_HJLL5DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

value: HTERT-immortalized  Adipose Derived Mesencymal stem cell


title: DhhCre, P21, replicate 5 [E3_DhhCre_P21_5]

value: sciatic nerve

value: DhhCre


title: HCC tumor from patient MDA_052

value: liver

value: F


title: HCC tumor from patient MDA_051

value: M

value: alive


title: DhhCre, P21, replicate 4 [E3_DhhCre_P21_4]


title: M. avium, rifampicin, 24 hours, biol rep 3

description:
Column Q
4-5_R1

value: bacterial cell


title: HCC tumor from patient MDA_049


title: HCC tumor from patient MDA_050


title: M. avium, rifampicin, 24 hours, biol rep 2

description:
Column F
2-2_R1


title: AA1_CCGCGGTT-CTAGCGCT_H3FL7DSX2_L004_001 [RNA-seq]

description:
AA1_CCGCGGTT-CTAGCGCT_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: DhhCre, P21, replicate 3 [E3_DhhCre_P21_3]


title: HCC tumor from patient MDA_048


title: AET2_GCGCTCTA-GTCGGAGC_HJLL5DSX2_L004_001 [RNA-seq]

description:
AET2_GCGCTCTA-GTCGGAGC_HJLL5DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

value: treatment

value: Adipogenic differentiation

value: TBT


title: AET1_ATATCTCG-ACTAAGAT_H3FL7DSX2_L004_001 [RNA-seq]

description:
AET1_ATATCTCG-ACTAAGAT_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt


title: HCC tumor from patient MDA_047


title: M. avium, rifampicin, 24 hours, biol rep 1

description:
Column K
3-2_R1


title: Mitf, P21, replicate 4 [E3_Mitf_P21_4]

value: Mitf


title: M. avium, ethambutol, 24 hours, biol rep 5

description:
Column S
5-1_R1

value: Ethambutol


title: Sarcoma tumor tissue, Sample 64

first: Jennifer

state: TX

address: 1515 Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

data_processing:
Raw RNA sequencing reads of the samples were mapped to the hg19 reference genome using the STAR aligner.
RSEM was used to quantify aligned reads and produce raw counts of known transcripts
The raw count of transcripts in the samples were then converted to transcripts per million that normalize counts for library size and gene length.
Assembly: hg19
Supplementary files format and content: rawcounts and TPMs

source_name: Sarcoma tumor tissue

extract_protocol:
RNA was extracted by NORGEN Total RNA Purification Kit (Cat. 37500) (NORGEN BIOTEK CORP). The extracted RNA was treated with DNase I. The treated RNA then was cleaned-up using the AMPure XP beads (Beckman Coulter Life Sciences) and eluted into 1x TE buffer. The purified RNA was quantified using Quant-iT™ RiboGreen™ RNA Assay Kit (ThermoFisher SCIENTIFIC) and the RNA quality was accessed using Agilent RNA 6000 Nano Kit and the 2100 Bioanalyzer Instrument (Agilent Technologies).
Up to 200 ng of each cDNA sample based on the PicoGreen quantification was sheared (mechanically fragmented) using the E220 Focused-ultrasonicator Covaris (Covaris). The sonication was performed under the following conditions: Peak Incident Power 200, Duty Cycle 25%, Cycles per Burst 50, and duration 10 seconds for 120 iterations. To ensure the proper fragment size, samples were examined on TapeStation 4200 using the DNA High Sensitivity kit (Agilent Technologies). The sheared cDNA was proceeded to library preparation using SureSelect XT Low Input Reagent Kit with indexes 1-96 (Agilent Technologies) as automated method on the Sciclone G3 NGSx Workstation (PerkinElmer, Inc.).This protocol consists of 3 enzymatic reactions for end repair, A-tailing and Adaptor ligation, followed by barcode insertion by PCR using Herculase II Fusion DNA Polymerase (8 to 14 cycles, based on input DNA quality and quantity). PCR primers were removed by using 1x volume of Agencourt AMPure PCR Purification kit (Agencourt Bioscience Corporation). The quality and quantity of the prepared libraries were evaluated using TapeStation 4200 and the DNA High Sensitivity kit (Agilent Technologies) to verify correct fragment size and to ensure complete removal of primer dimers.

value: Sarcoma tumor tissue

tag: disease state

value: Soft-Tissue Sarcoma

value: Immune checkpoint blockade

tag: collected date

tag: collected

value: Surgery

tag: age

tag: outcome

value: SD

tag: grade

value: High Grade


title: Mitf, P21, replicate 3 [E3_Mitf_P21_3]

value: sciatic nerve


title: M. avium, clarithromycin, 72 hours, biol rep 1

description:
Column C
1v2_R1

value: Clarithromycin

tag: time

value: 72 hours


title: Sarcoma tumor tissue, Sample 63

value: M

value: PD


title: M. avium, ethambutol, 24 hours, biol rep 3

description:
Column J
3-1_R1

value: bacterial cell

value: 24 hours


title: Mitf, P21, replicate 2 [E3_Mitf_P21_2]


title: Mitf, P21, replicate 1 [E3_Mitf_P21_1]


title: AA2_TTATAACC-TCGATATC_H3FL7DSX2_L004_001 [RNA-seq]

description:
AA2_TTATAACC-TCGATATC_H3FL7DSX2_L004_001
TPM_from_featureCounts.txt
featureCounts_count_matrix.txt

value: control

value: HTERT-immortalized  Adipose Derived Mesencymal stem cell

value: No Adipogenic differentiation

tag: condition replicate

value: DMSO


title: M. avium, ethambutol, 24 hours, biol rep 2

description:
Column H
2-4_R1

value: Ethambutol


title: Sarcoma tumor tissue, Sample 60

value: Sarcoma tumor tissue

value: Soft-Tissue Sarcoma

value: baseline

value: F


title: HCC tumor from patient MDA_045

tag: organ

value: liver

tag: age (years)

tag: death

value: alive

tag: follow-up (month)


title: HCC tumor from patient MDA_044

value: dead


title: HCC tumor from patient MDA_046


title: M. avium, ethambutol, 24 hours, biol rep 1

description:
Column C
1-3_R1

tag: cell type


title: Sarcoma tumor tissue, Sample 59

tag: tissue

value: Immune checkpoint blockade

value: SD

value: High Grade


title: Sarcoma tumor tissue, Sample 62

tag: treatment


title: DhhCre, P21, replicate 1 [E3_DhhCre_P21_1]

value: sciatic nerve

tag: genotype

value: DhhCre


title: M. avium, amikacin, 24 hours, biol rep 5

description:
Column U
5-4_R1

tag: strain

value: bacterial cell

value: Amikacin

value: 24 hours


title: Sarcoma tumor tissue, Sample 58

tag: disease state

tag: Sex

value: M

value: PD


title: HCC tumor from patient MDA_042


title: Fig4 double negative, P4, replicate 3 [E2_Fig4nn_P4_3]


title: HCC tumor from patient MDA_041


title: M. avium, ethambutol, 24 hours, biol rep 4

description:
Column N
4-2_R1

value: Ethambutol


title: HCC tumor from patient MDA_074


title: M. avium, amikacin, 24 hours, biol rep 4

description:
Column R
4-6_R1


title: Fig4 double negative, P4, replicate 2 [E2_Fig4nn_P4_2]


title: M. avium, amikacin, 24 hours, biol rep 3

description:
Column M
3-5_R1


title: HCC tumor from patient MDA_040


title: Sarcoma tumor tissue, Sample 61

value: Sarcoma tumor tissue

value: Soft-Tissue Sarcoma

tag: collected date

tag: collected

value: Surgery


title: HCC tumor from patient MDA_039

value: liver


title: Fig4 double positive, P4, replicate 3 [E2_Fig4pp_P4_3]


title: Fig4 double positive, P4, replicate 2 [E2_Fig4pp_P4_2]


title: HCC tumor from patient MDA_043

value: alive


title: DhhCre, P21, replicate 2 [E3_DhhCre_P21_2]


title: HCC tumor from patient MDA_038


title: Sarcoma tumor tissue, Sample 55

tag: age

tag: outcome


title: Fig4 double positive, P4, replicate 1 [E2_Fig4pp_P4_1]


title: Sarcoma tumor tissue, Sample 54

tag: grade


title: Sarcoma tumor tissue, Sample 53

value: baseline


title: M. avium, amikacin, 24 hours, biol rep 1

description:
Column D
1-5_R1

tag: time


title: HCC tumor from patient MDA_037

tag: organ

value: F

value: dead


title: HCC tumor from patient MDA_036

tag: age (years)


title: Sarcoma tumor tissue, Sample 52

value: Immune checkpoint blockade

value: High Grade


title: M. avium, clarithromycin, 24 hours, biol rep 4

description:
Column P
4-4_R1

value: Clarithromycin


title: M. avium, clarithromycin, 24 hours, biol rep 3

description:
Column L
3-4_R1

value: bacterial cell


title: HCC tumor from patient MDA_035

tag: death


title: Fig4 double negative, P12, replicate 2 [E1_Fig4nn_P12_2]

value: sciatic nerve


title: Sarcoma tumor tissue, Sample 57


title: M. avium, amikacin, 24 hours, biol rep 2

description:
Column G
2-3_R1

value: Amikacin

value: 24 hours


title: M. avium, clarithromycin, 24 hours, biol rep 2

description:
Column E
2-1_R1


title: Fig4 double negative, P12, replicate 1 [E1_Fig4nn_P12_1]


title: Sarcoma tumor tissue, Sample 50

value: M

value: PD


title: M. avium, clarithromycin, 24 hours, biol rep 1

description:
Column B
1-2_R1


title: Fig4 double positive, P12, replicate 3 [E1_Fig4pp_P12_3]


title: Sarcoma tumor tissue, Sample 49

value: Sarcoma tumor tissue

value: SD


title: M. avium, growth control, 24 hours, biol rep 2

description:
Column I
2-6_R1


title: HCC tumor from patient MDA_032

tag: follow-up (month)


title: Fig4 double positive, P12, replicate 2 [E1_Fig4pp_P12_2]


title: HCC tumor from patient MDA_031


title: Fig4 double negative, P4, replicate 1 [E2_Fig4nn_P4_1]


title: M. avium, clarithromycin, 24 hours, biol rep 5

description:
Column V
5-6_R1

tag: cell type


title: M. avium, growth control, 24 hours, biol rep 1

description:
Column O
4-3_R1


title: HCC tumor from patient MDA_033


title: HCC tumor from patient MDA_034


title: Sarcoma tumor tissue, Sample 47

tag: tissue

value: Soft-Tissue Sarcoma

value: Surgery


title: Sarcoma tumor tissue, Sample 48

tag: treatment


title: Fig4 double negative, P12, replicate 3 [E1_Fig4nn_P12_3]

tag: genotype


title: UPFL6

city: Chapel Hill

first: William

last: Kim

state: NC

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

institute: UNC Chapel Hill

description: bulk RNA

data_processing:
75b paired-end reads were sequenced on a NextSeq 500 Desktop Sequencer using a high output flow cell kit (Illumina), yielding an average of over 28M reads per sample.
QC-passed reads were aligned to the mouse reference genome using STAR
Transcript abundance estimates for each sample were performed using SALMON
Raw SALMON read counts for all RNAseq samples were normalized by DESeq2
Illumina Novaseq_6000 for scRNAseq base calling
Transcript abundance estimates for cell were performed using cell ranger
Supplementary files format and content: Tab-delimited text files include Normalized count values for each sample
Supplementary files format and content: H5 format files of cell ranger output for each scRNAseq samples
Assembly: mm10

source_name: bladder tumor

extract_protocol:
RNA was extracted with Qiagen RNeasy Plus Mini kit
Libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina)
scRNAseq libraries were prepared using Chromium Single Cell 3' Reagent Kits (v3.1 Chemistry)

tag: strain

value: bladder tumor

tag: tissue type

value: primary UPFL tumor

value: untreated


title: UPFL7

description: bulk RNA


title: Sarcoma tumor tissue, Sample 46

tag: disease state

value: baseline

tag: Sex


title: Sarcoma tumor tissue, Sample 45

value: Immune checkpoint blockade

tag: collected date

tag: collected


title: Tumor tissue from patient with Ovarian cancer [P29]

type: genomic

city: Athens

first: Georgios

last: Tsaousis

state: Attiki

address: Spaton 52, Ave., Gerakas

department: Bioinformatics

country: Greece

institute: Genekor Medical SA

hyb_protocol: After amplification, the fragments are subjected to HAEIII endonuclease digestion and hybridized to OncoScan® CNV  assay on Affymetrix Genechip® Hybridization Oven 645 (Thermo Fisher Scientific, Waltham, MA, USA) set at 49, 60rpm for 16-18h (overnight)

scan_protocol: The Arrays were  scanned using a GeneChip Scanner 3000 7 G (cat no. 00-0218 Thermo Fisher Scientific Inc.)

data_processing: Scanning results from both arrays (AT/GC) are combined and subjected to further analysis in Chromosome Analysis Suite (Thermo Fisher Scientific, Waltham, MA, USA).

label_protocol: Biotin

growth_protocol: All samples were collected from the second Department of Surgery, Aretaieion Hospital, Medical School, National and Kapodistrian University of Athens.

extract_protocol: Genomic DNA was extracted from the FFPE tumor biopsies using the MagMAX™ Total Nucleic Acid Isolation Kit (cat no. AM1840; Thermo Fisher Scientific Inc.)

tag: disease

value: ovarian cancer


title: HCC tumor from patient MDA_029

value: liver

value: dead


title: Sarcoma tumor tissue, Sample 51

last: Wang

tag: age

tag: outcome

tag: grade

value: High Grade


title: Sarcoma tumor tissue, Sample 56


title: Tumor tissue from patient with Ovarian cancer [P30]


title: UPFL5

description: bulk RNA


title: Tumor tissue from patient with Ovarian cancer [P28]


title: Tumor tissue from patient with Ovarian cancer [P26]


title: HCC tumor from patient MDA_027

tag: organ

tag: age (years)


title: HCC tumor from patient MDA_028

tag: death

value: alive

tag: follow-up (month)


title: UPFL4

description: bulk RNA

tag: tissue


title: Tumor tissue from patient with Ovarian cancer [P25]


title: UPFL3

description: bulk RNA

tag: treatment


title: Sarcoma tumor tissue, Sample 42