title: reg_batch1_rep198


title: reg_batch1_rep200

status: Public on Aug 20 2022

type: SRA

city: Palo Alto

first: Xue

last: Feng

state: CA

address: 1651 Page Mill road

country: USA

institute: Stanford

library_source: transcriptomic single cell

data_processing:
Illumina's bcl2fastq 2.17 software used for basecalling.
Raw data were trimmed by trim-galore (version 0.6.7) to remove adaptor sequences and aligned with Hisat2 (version 2.2.1) to the mouse reference genome (mm10). Transcripts per million reads (TPMs) per gene was calculated by StringTie (version 2.1.7), and genes with TPM > 0 were defined as detected genes.
All the downstream analysis was performed by R, using Seurat (version 4.1.0)5 with modifications.
Assembly: mm10
Supplementary files format and content: Matrix table with gene TPM for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: retina

extract_protocol:
The fresh isolated retinas at one day post retrograde labeling were dissociated with AMES solution. FACS purification with BD Influx System cell sorter was gated as: Alexa Fluor 488 positive but Texas Red negative RGCs were collected as surRGCs; Texas Red positive RGCs were collected as regRGCs. Individual cell was directly sorted into individual well of 96 well plate with 4ul pre-filled cell lysis buffer, containing 1 U/µl of Recombinant RNase inhibitor (Clontech), 0.1% Triton X-100 (Thermo), 2.5mM dNTP (Thermo), 2.5 µM oligodT30VN (5'AAGCAGTGGTATCAACGCAGAGTACT30VN-3', IDT). Cells were immediately spun down after sorting and frozen at -80°C.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For AAV intravitreal injection, a pulled and polished microcapillary was inserted into the peripheral retina of around 4-week-old mice just behind the ora serrata. Approximately 2 µl of the vitreous was removed to allow injection of 2 µl AAV into the vitreous chamber. ONC was performed 2 weeks following AAV injection at about 7-8 weeks of age and crushed with a jeweler’s forceps (Dumont #5; Fine Science Tools, Foster City, California) for 5 seconds approximately 0.5 mm behind the eyeball. For retrograde labeling regenerating RGCs, the ON was exposed intraorbitally ~1.5-2 mm distal to the eyeball. A piece of tissue paper was placed in between the ON trunk and surrounding soft tissue to keep it from moving. A 33g needle was used to pock a hole on the dura at the injection site first, ~1 mm distal to ONC site. Then a glass micropipette connected with 50μL microsyringe (80900, Hamilton) that attached to a Micro4 controller was used to delivery ~60nL dextran into the ON through the pre-made hole, at a speed of 100nL/min. The leaking dye at injection site were removed by the tissue paper.

tag: cell type

value: retinal ganglion cell (RGC)

tag: strain

tag: tissue

value: retina

tag: genotype

value: Pten knock out

tag: cell subtype

value: regenerating RGCs (regRGCs)


title: 1mGyMM/ reference male mouse12

type: genomic

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

country: Japan

institute: Institute for Environmental Science

hyb_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Genomic Workbench Software (v 7.0.) was used.

molecule: genomic DNA

extract_protocol: PI-50a (Kurabo Industries LTD.) tissue DNA extraction protocol.

value: tail

source_name: reference male mouse12


title: reference male mouse12/ 1mGyL6

label_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8


title: reg_batch1_rep196


title: 1mGyL6/ reference male mouse12


title: reg_batch1_rep195


title: reg_batch1_rep194


title: reg_batch1_rep193


title: reg_batch1_rep192


title: reg_batch1_rep197


title: 1mGyL5/ reference male mouse12


title: reference male mouse12/ 1mGyL5


title: reference male mouse12/ 1mGyMF


title: 1mGyNF/ reference male mouse12


title: reg_batch1_rep191


title: 1mGyMF/ reference male mouse12


title: reference male mouse12/ 1mGyL4


title: reg_batch1_rep190


title: reg_batch1_rep189


title: reg_batch1_rep188


title: 1mGyL3/ reference male mouse12


title: reg_batch1_rep187


title: 1mGyL1/ reference male mouse12


title: 1mGyL2/ reference male mouse12


title: reg_batch1_rep186


title: 1mGyLF/ reference male mouse12


title: reference male mouse12/ 1mGyL2


title: reg_batch1_rep183


title: reference male mouse12/ 1mGyL3


title: reference male mouse12/ 1mGyK7


title: reference male mouse12/ 1mGyLF


title: reg_batch1_rep181


title: reference male mouse12/ 1mGyLM


title: reg_batch1_rep185


title: reference male mouse12/ 1mGyK6


title: reg_batch1_rep184


title: reg_batch1_rep180


title: reg_batch1_rep179


title: 1mGyK6/ reference male mouse12


title: 1mGyK7/ reference male mouse12


title: reg_batch1_rep178


title: reference male mouse12/ 1mGyM1


title: reg_batch1_rep177


title: reg_batch1_rep176


title: reference male mouse12/ 1mGyK5


title: reg_batch1_rep175


title: 1mGyK5/ reference male mouse12


title: reg_batch1_rep174


title: reg_batch1_rep182


title: 1mGyK2/ reference male mouse12


title: reg_batch1_rep172


title: reg_batch1_rep173


title: 1mGyLM/ reference male mouse12


title: 1mGyK4/ reference male mouse12


title: reference male mouse12/ 1mGyK4


title: reference male mouse12/ 1mGyK2


title: 1mGyK1/ reference male mouse12


title: 1mGyK3/ reference male mouse12


title: reg_batch1_rep171


title: 1mGyKM/ reference male mouse12


title: reference male mouse12/ 1mGyK1


title: reference male mouse12/ 1mGyKF


title: reference male mouse12/ 1mGyK3


title: reg_batch1_rep167


title: reg_batch1_rep170


title: 1mGyKF/ reference male mouse12


title: reg_batch1_rep165


title: 1mGyL4/ reference male mouse12


title: reference male mouse12/ 1mGyL1


title: reg_batch1_rep163


title: reg_batch1_rep168


title: reg_batch1_rep162


title: reference male mouse12/ 1mGyKM


title: reg_batch1_rep164


title: reference male mouse11/ 1mGyJ5

source_name: reference male mouse11


title: reg_batch1_rep161


title: 1mGyJ5/ reference male mouse11


title: reg_batch1_rep160


title: reg_batch1_rep159


title: 1mGyJ4/ reference male mouse11


title: reg_batch1_rep158


title: reference male mouse11/ 1mGyJ6


title: reg_batch1_rep157


title: reg_batch1_rep169


title: reg_batch1_rep166


title: 1mGyJ6/ reference male mouse11


title: reg_batch1_rep154


title: reg_batch1_rep155


title: reference male mouse11/ 1mGyJ4


title: reg_batch1_rep153


title: reg_batch1_rep152


title: 1mGyJ3/ reference male mouse11


title: reg_batch1_rep156


title: reference male mouse11/ 1mGyJ3


title: reg_batch1_rep151


title: reg_batch1_rep150


title: 1mGyJ1/ reference male mouse11


title: 1mGyJF/ reference male mouse11


title: 1mGyJ2/ reference male mouse11


title: reg_batch1_rep148


title: reg_batch1_rep149


title: reference male mouse11/ 1mGyJF


title: reference male mouse11/ 1mGyI6


title: reg_batch1_rep146


title: reference male mouse11/ 1mGyJ1


title: reference male mouse11/ 1mGyJ2


title: reg_batch1_rep147


title: reference male mouse11/ 1mGyJM


title: reg_batch1_rep144


title: reg_batch1_rep142


title: reg_batch1_rep143


title: reg_batch1_rep145


title: 1mGyJM/ reference male mouse11


title: 1mGyI3/ reference male mouse11


title: reference male mouse11/ 1mGyI2


title: reg_batch1_rep140


title: reg_batch1_rep139


title: reg_batch1_rep141


title: reg_batch1_rep138


title: 1mGyI4/ reference male mouse11


title: 1mGyIF/ reference male mouse11


title: reference male mouse11/ 1mGyI5


title: reg_batch1_rep137


title: reference male mouse11/ 1mGyI1


title: reg_batch1_rep134


title: reg_batch1_rep135


title: reference male mouse11/ 1mGyI3


title: reg_batch1_rep133


title: 1mGyH6/ reference male mouse10

source_name: reference male mouse10


title: 1mGyIM/ reference male mouse11


title: reference male mouse10/ 1mGyH6


title: 1mGyI2/ reference male mouse11


title: reg_batch1_rep132


title: reg_batch1_rep136


title: 1mGyH4/ reference male mouse10


title: 1mGyI1/ reference male mouse11


title: 1mGyI5/ reference male mouse11


title: reference male mouse11/ 1mGyI4


title: reg_batch1_rep129


title: reference male mouse11/ 1mGyIM


title: 1mGyH5/ reference male mouse10


title: reg_batch1_rep128


title: reg_batch1_rep127


title: reg_batch1_rep126


title: 1mGyH3/ reference male mouse10


title: 1mGyI6/ reference male mouse11


title: reg_batch1_rep125


title: reg_batch1_rep130


title: reference male mouse10/ 1mGyH5


title: reg_batch1_rep124


title: reference male mouse10/ 1mGyH3


title: reference male mouse10/ 1mGyH2


title: reg_batch1_rep123


title: reg_batch1_rep121


title: reg_batch1_rep122


title: 1mGyH1/ reference male mouse10


title: reference male mouse10/ 1mGyH4


title: reg_batch1_rep131


title: reg_batch1_rep119


title: reg_batch1_rep120


title: reference male mouse10/ 1mGyH1


title: 1mGyHF/ reference male mouse10


title: reg_batch1_rep117


title: reg_batch1_rep116


title: reg_batch1_rep115


title: reg_batch1_rep118


title: reference male mouse10/ 1mGyHM


title: reg_batch1_rep112


title: reference male mouse10/ 1mGyG8


title: reg_batch1_rep113


title: reg_batch1_rep114


title: 1mGyG8/ reference male mouse10


title: reg_batch1_rep111


title: reference male mouse11/ 1mGyIF


title: 1mGyHM/ reference male mouse10


title: 1mGyH2/ reference male mouse10


title: reg_batch1_rep110


title: reg_batch1_rep109


title: reg_batch1_rep108


title: reg_batch1_rep107


title: reference male mouse10/ 1mGyG7


title: 1mGyG3/ reference male mouse10


title: reference male mouse10/ 1mGyHF


title: reference male mouse10/ 1mGyG5


title: reference male mouse10/ 1mGyG6


title: 1mGyG1/ reference male mouse10


title: reg_batch1_rep104


title: 1mGyG7/ reference male mouse10


title: reference male mouse10/ 1mGyG1


title: reg_batch1_rep103


title: reg_batch1_rep102


title: reg_batch1_rep105


title: reg_batch1_rep101


title: 1mGyG2/ reference male mouse10


title: 1mGyGF/ reference male mouse10


title: reg_batch1_rep106


title: 1mGyG5/ reference male mouse10


title: reference male mouse10/ 1mGyG4


title: 1mGyG6/ reference male mouse10


title: 1mGyGM/ reference male mouse10


title: reference male mouse10/ 1mGyG2


title: IgG_histidinol_rep3_histidinol, 2 millimolar, 6hrs

city: Albany

first: Morgan

middle: A

last: Sammons

state: NY

address: 1400 Washington Ave, Life Sciences 2075

department: Biological Sciences

institute: University at Albany - SUNY

library_source: genomic

data_processing:
Paired end Cut&Run reads were aligned to the hg38 human reference genome using HISAT2 (v.2.2.1) and saved as sorted BAM files
HISAT2 options (-X 700 -I 10 --phred33 --no-spliced-alignment --no-discordant --no-mixed --no-unal)
Aligned reads were processed for visualization and other analyses using the deepTools (v.3.4.1) bamCoverage module
deepTools options (--effectiveGenomeSize 2913022398 --binSize 5 --ignoreDuplicates --normalizeUsing RPKM)
Assembly: hg38
Supplementary files format and content: bigWig files, bin size of 5, unique alignments only, RPKM normalized
Library strategy: CUT&Run

organism: Homo sapiens

source_name: colon

growth_protocol: Cells were grown in McCoy's 5A media supplemented with 10% fetal bovine serum at 37˚C and 5% carbon dioxide in a humidified, water-jacketed incubator.

extract_protocol:
DNA fragments released by ATF4-targeted Mnase were isolated via Cut&Run using standard methods.
Cut&Run-released DNA fragments were used as the template for Illumina-compatible DNA library prep (adapter ligation and multiplexing via NEBNext Ultra 2 DNA Library Prep)

treatment_protocol: Fresh media (McCoy's 5A with 10% fetal bovine serum) was added to cells which were then treated with either DMSO,  etoposide, histidinol, or tunicamycin at the specified concentrations for 6 hrs before RNA was harvested

value: colon

tag: cell line

value: colon carcinoma

tag: treatment

value: histidinol, 2 millimolar, 6hrs


title: reference male mouse10/ 1mGyGM


title: reg_batch1_rep100


title: IgG_histidinol_rep2_histidinol, 2 millimolar, 6hrs


title: reg_batch1_rep99


title: reg_batch1_rep98


title: reference male mouse9/ 1mGyF7

source_name: reference male mouse9


title: reference male mouse10/ 1mGyGF


title: 1mGyG4/ reference male mouse10


title: reg_batch1_rep97


title: reference male mouse10/ 1mGyG3


title: 1mGyF4/ reference male mouse9


title: IgG_tunicamycin_rep3_tunicamycin, 2 micromolar, 6hrs

value: tunicamycin, 2 micromolar, 6hrs


title: IgG_tunicamycin_rep2_tunicamycin, 2 micromolar, 6hrs


title: reference male mouse9/ 1mGyF6


title: 1mGyF6/ reference male mouse9


title: reg_batch1_rep96


title: IgG_tunicamycin_rep1_tunicamycin, 2 micromolar, 6hrs


title: reference male mouse9/ 1mGyF4


title: reg_batch1_rep94


title: reference male mouse9/ 1mGyF5


title: IgG_etoposide_rep3_etoposide, 100 micromolar, 6hrs

value: etoposide, 100 micromolar, 6hrs


title: IgG_etoposide_rep2_etoposide, 100 micromolar, 6hrs


title: 1mGyF7/ reference male mouse9


title: reg_batch1_rep93


title: IgG_histidinol_rep1_histidinol, 2 millimolar, 6hrs


title: reference male mouse9/ 1mGyF3


title: reg_batch1_rep92


title: reg_batch1_rep95


title: IgG_DMSO_rep3_DMSO, 6hrs

value: DMSO, 6hrs


title: reference male mouse9/ 1mGyF2


title: 1mGyF5/ reference male mouse9


title: reg_batch1_rep91


title: 1mGyFF/ reference male mouse9


title: IgG_DMSO_rep2_DMSO, 6hrs


title: IgG_etoposide_rep1_etoposide, 100 micromolar, 6hrs


title: reference male mouse9/ 1mGyFF


title: 1mGyE5/ reference male mouse9


title: 1mGyF2/ reference male mouse9


title: reg_batch1_rep90


title: IgG_DMSO_rep1_DMSO, 6hrs


title: ATF4_histidinol_rep3_histidinol, 2 millimolar, 6hrs


title: reference male mouse9/ 1mGyFM


title: reg_batch1_rep88


title: Sample3: Week12

city: Harbin

first: Hailong

last: Hu

address: No.2 of Yikuang Road, 2E-215

country: China

institute: Harbin Institute of Technology

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v2.1.0 with default parameters
Transcript assembly and FPKM (RPKM) estimated for RNA-Seq data using Cufflinks v2.2.1.0 with default parameters
Genome_build: mm10

source_name: liver

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After ultrasonic wave stirring for 30 min, ZnO NP suspensions (25 mg/kg b.w. per day) were given to mice per day by oral administration with a syringe. Control group mice were given an equal volume of PBS.

value: liver

value: treated with ZnO NPs for 12 weeks


title: 1mGyF1/ reference male mouse9


title: reference male mouse9/ 1mGyE5


title: 1mGyE4/ reference male mouse9


title: 1mGyFM/ reference male mouse9


title: 1mGyE3/ reference male mouse9


title: reg_batch1_rep87


title: Sample1: Control

value: treated with PBS


title: Sample2: Week8

value: treated with ZnO NPs for 8 weeks


title: ATF4_histidinol_rep1_histidinol, 2 millimolar, 6hrs


title: reg_batch1_rep86


title: ATF4_tunicamycin_rep3_tunicamycin, 2 micromolar, 6hrs


title: 1mGyE2/ reference male mouse9


title: CD4 T cells, Nacl 5mM (CTRL), rep3

city: Charlestown

first: Da

last: Teng

state: MA

address: Building 149, 13th Street

institute: Massachusetts General Hospital

data_processing:
Sequencing reads were mapped to the UCSC mm10 reference genome using STAR version 2.7.0f.
The differential expression analysis was performed with rsem version 1.3.0.
Normalized RNA-seq data were analyzed with GSEA v4.0.3. Enrichment analyses were performed using 1,000 gene set permutations, a weighted enrichment statistic, the Signal2Noise ranking metric, and gene set minimum and maximum sizes of 15 and 500, respectively.
Assembly: mm10
Supplementary files format and content: tab-delimited text normalized read counts include count values for each Sample

source_name: spleen

growth_protocol: CD4+ T cells were isolated from spleen of naïve C57/BL6 mice and incubated with 5 µmol CFSE dye (Invitrogen, Cat #. C34554) in pre-warmed 37℃ PBS for 15mins, protected from light.

extract_protocol:
Cells pellets were collected for isolation of RNA with RNeasy mini kit from Qiagen (cat# 74104). RNA quality (RIN > 7) was confirmed using the TapeStation 4200 system (Agilent Technologies).
Preparation of RNA library and transcriptome sequencing was conducted by Novogene Co., LTD (Sacramento, CA).

treatment_protocol: CD4+ T cells were cultured in RPMI medium (in the presence of IL-2, anti-CD28/anti-CD3) with NaCl (5mM) or itaconate (5mM) for 48 hrs.

value: spleen

value: CD4 T cells

value: WT

value: NaCl 5mM for 48h in presenceof anti-CD3/CD28 and 200U IL-2


title: reference male mouse9/ 1mGyE1


title: ATF4_tunicamycin_rep2_tunicamycin, 2 micromolar, 6hrs


title: reg_batch1_rep89

value: retinal ganglion cell (RGC)

value: retina

value: Pten knock out


title: reference male mouse9/ 1mGyE2

value: tail


title: reference male mouse9/ 1mGyE3


title: CD4 T cells, Nacl 5mM (CTRL), rep2


title: reference male mouse9/ 1mGyF1


title: 1mGyE1/ reference male mouse9


title: reference male mouse9/ 1mGyE4


title: CD4 T cells, Nacl 5mM (CTRL), rep1


title: ATF4_tunicamycin_rep1_tunicamycin, 2 micromolar, 6hrs

value: colon

value: colon carcinoma


title: reg_batch1_rep83

value: regenerating RGCs (regRGCs)


title: reference male mouse9/ 1mGyE6


title: reg_batch1_rep84


title: reference male mouse9/ 1mGyEF


title: ATF4_etoposide_rep3_etoposide, 100 micromolar, 6hrs

value: etoposide, 100 micromolar, 6hrs


title: CD4 T cells, ITA 5mM, rep3

value: ITA 5mM for 48h in presenceof anti-CD3/CD28 and 200U IL-2


title: reg_batch1_rep85


title: reg_batch1_rep82


title: ATF4_etoposide_rep2_etoposide, 100 micromolar, 6hrs


title: CD4 T cells, ITA 5mM, rep2


title: ATF4_etoposide_rep1_etoposide, 100 micromolar, 6hrs


title: reg_batch1_rep80


title: ATF4_DMSO_rep3_DMSO, 6hrs

value: DMSO, 6hrs


title: ATF4_histidinol_rep2_histidinol, 2 millimolar, 6hrs

value: histidinol, 2 millimolar, 6hrs


title: reg_batch1_rep79


title: NERCPcast2

city: Glasgow

first: Rachana

middle: Ravindra

last: Patel

state: Outside the United States or Canada

address: Bearsden, Switchback Road

department: Prostate Cancer

country: United Kingdom

institute: Cancer Research UK Beatson Institute

data_processing:
Quality checks on the raw RNA-seq files were done using fastqc version 0.11.4 and fastq_screen version 0.5.2.
RNA-seq paired-end reads were aligned to the GRCm38.p3 version of the mouse genome using Tophat2 version 2.1.0 with Bowtie version 2.2.6.0.
Gene expression levels were determined using htseq-count package version 0.6.0. Expression counts were further processed and analysed in the R environment (version 3.2.3) using packages from the Bioconductor data analysis suite and differential gene expression analysis based on the negative binomial distribution using the DESeq2 version 1.14.1.
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: csv files with RPKM

source_name: prostate tumor

extract_protocol:
RNA was extracted from the frozen prostate tumours or tissues of WT (n=3; 12 months age), Ptenpc-/- (n=3; ~14 months), Ctnnb1pc(ex3)Δ/+ (n=3; ~12 months), Ctnnb1pc(ex3)Δ/+ Ptenpc+/- (n=3; ~6-8 months) and Mock (n=2; ~15 months) and ADT (n=3; ~15 months) treated Ctnnb1Nkx3-1CreERT2(ex3)Δ/+ PtenNkx3-1CreERT2(ex3)Δ+/-. RNA quality of RNA extracted was evaluated by RNA integrity number (RIN>7.3), calculated using an Agilent 2100 Bioanalyzer (Agilent Technologies) with the Agilent RNA 6000 Nano Kit.  The library preparation and sequencing was carried out by BGI (Beijing) using the following steps and reagents according to the manufacturer’s instructions.
The library was pair end sequenced on the Illumina® HiSeq 2000 platform, with 90 nucleotide reads and at least 6 Gb of reads generated per sample.

value: prostate tumor

tag: genotype/variation

tag: age

value: ~15 months


title: 1mGyE6/ reference male mouse9


title: reg_batch1_rep78


title: ATF4_DMSO_rep2_DMSO, 6hrs


title: 1mGyEF/ reference male mouse9


title: 1mGyF3/ reference male mouse9


title: NERCPcast3


title: ATF4_DMSO_rep1_DMSO, 6hrs


title: 1mGyEM/ reference male mouse9


title: NERCPcast1


title: reference male mouse9/ 1mGyD7


title: reg_batch1_rep77


title: reference male mouse9/ 1mGyEM


title: reg_batch1_rep76


title: NERCPctrl1

value: Mock treated Ctnnb1Nkx3-1CreERT2(ex3)delta/+ PtenNkx3-1CreERT2(ex3)delta+/-


title: NERCPctrl2


title: 1mGyD7/ reference male mouse9


title: reg_batch1_rep74


title: Chet15

value: ~12 months


title: 1mGyO8/ reference male mouse12-S


title: Chet14


title: 1mGyD8/ reference male mouse9


title: reg_batch1_rep75


title: reference male mouse12/ 1mGyO8-S


title: reference male mouse12/ 1mGyO7-S


title: reg_batch1_rep73


title: 1mGyD6/ reference male mouse9


title: CD4 T cells, ITA 5mM, rep1

value: spleen

value: CD4 T cells

value: WT


title: CPhet12

value: Ctnnb1pc(ex3)delta/+ Ptenpc+/-

value: ~6-8 months


title: Chet13


title: reg_batch1_rep72

value: retinal ganglion cell (RGC)

value: retina

value: Pten knock out


title: reg_batch1_rep71

value: regenerating RGCs (regRGCs)


title: 1mGyO6/ reference male mouse12-S

value: tail


title: reference male mouse9/ 1mGyD6


title: reference male mouse9/ 1mGyD8


title: CPhet11


title: reg_batch1_rep70


title: reference male mouse12/ 1mGyO6-S


title: reg_batch1_rep81


title: CPhet10


title: reference male mouse9/ 1mGyD5


title: Phom6

value: Ptenpc-/-

value: ~14 months


title: reg_batch1_rep68


title: reference male mouse9/ 1mGyD2


title: 1mGyO5/ reference male mouse12-S


title: reference male mouse9/ 1mGyD3


title: reference male mouse9/ 1mGyD4


title: 1mGyD3/ reference male mouse9


title: 1mGyD5/ reference male mouse9


title: Phom5


title: reg_batch1_rep69


title: 1mGyD2/ reference male mouse9


title: reg_batch1_rep66


title: Phom4


title: Wt2

source_name: prostate

value: prostate

value: wild type

value: 12 months


title: reg_batch1_rep64


title: 1mGyO4/ reference male mouse12-S


title: reg_batch1_rep65


title: 1mGyO3/ reference male mouse12-S


title: 1mGyO7/ reference male mouse12-S


title: reference male mouse12/ 1mGyO5-S


title: Wt3


title: reference male mouse12/1mGyO4-S


title: 1mGyDF/ reference male mouse9


title: 1mGyO2/ reference male mouse12-S


title: Wt1


title: reg_batch1_rep63


title: 1mGyD4/ reference male mouse9


title: 60Gy, long survival, unmethylated MGMT 5

city: Linköping

first: Malgorzata

last: Lysiak

state: Östergötland

country: Sweden

institute: Linköping University

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing:
Unmethylated and methylated signal intensities
Average Beta normalization

label: Cy5 and Cy3

source_name: brain tumor sample

label_protocol: Standard Illumina protocol

extract_protocol: DNA was exctracted with Maxwell FFPE DNA Purification Kit (Promega)

tag: gender

value: Male

tag: surgery type

value: resection

tag: diagnosis

value: GBM WHO IV


title: reference male mouse9/ 1mGyD1


title: reference male mouse12/ 1mGyO3-S


title: reg_batch1_rep61


title: 1mGyD1/ reference male mouse9


title: reg_batch1_rep60


title: reference male mouse9/ 1mGyDF


title: 60Gy, long survival, unmethylated MGMT 3


title: 1mGyO1/ reference male mouse12-S


title: reference male mouse9/ 1mGyDM


title: reg_batch1_rep67


title: 60Gy, long survival, unmethylated MGMT 4


title: 60Gy, long survival, unmethylated MGMT 2

value: Female


title: 1mGyOF/ reference male mouse12-S


title: reg_batch1_rep59


title: reg_batch1_rep62


title: 60Gy, long survival, unmethylated MGMT 1


title: reference male mouse12/ 1mGyOF-S


title: reg_batch1_rep58


title: 60Gy, short survival, unmethylated MGMT 5


title: reference male mouse12/ 1mGyO2-S


title: 60Gy, short survival, unmethylated MGMT 4


title: 1mGyOM/ reference male mouse12-S


title: 60Gy, short survival, unmethylated MGMT 3


title: reg_batch1_rep55


title: 1mGyC5/ reference male mouse8

source_name: reference male mouse7


title: 60Gy, short survival, unmethylated MGMT 2


title: reference male mouse12/ 1mGyOM-S


title: reference male mouse8/ 1mGyC5


title: reg_batch1_rep56


title: 1mGyDM/ reference male mouse9


title: reference male mouse8/ 1mGyC6


title: reg_batch1_rep57


title: reg_batch1_rep54


title: 1mGyC6/ reference male mouse8


title: 1mGyC4/ reference male mouse8


title: reference male mouse12/ 1mGyN6-S


title: 60Gy, short survival, unmethylated MGMT 1


title: reference male mouse8/ 1mGyC3


title: reference male mouse12/ 1mGyO1-S


title: reg_batch1_rep53


title: 1mGyN5/ reference male mouse12-S


title: reg_batch1_rep52


title: 1mGyC3/ reference male mouse8


title: 60Gy, long survival, methylated MGMT 4


title: 60Gy, long survival, methylated MGMT 5


title: reference male mouse8/ 1mGyC4


title: reg_batch1_rep51


title: 60Gy, long survival, methylated MGMT 3


title: 60Gy, long survival, methylated MGMT 2


title: reg_batch1_rep50


title: reg_batch1_rep49


title: 1mGyN6/ reference male mouse12-S


title: 60Gy, long survival, methylated MGMT 1


title: reference male mouse8/ 1mGyC2


title: 1mGyN3/ reference male mouse12-S


title: reg_batch1_rep48


title: 1mGyN4/ reference male mouse12-S


title: 60Gy, short survival, methylated MGMT 4


title: reg_batch1_rep47


title: reference male mouse12/ 1mGyN4-S


title: reference male mouse12/ 1mGyN3-S


title: reg_batch1_rep46


title: 60Gy, short survival, methylated MGMT 3


title: 60Gy, short survival, methylated MGMT 2


title: 1mGyN2/ reference male mouse12-S


title: 1mGyN1/ reference male mouse12-S


title: 1mGyC2/ reference male mouse8


title: reference male mouse12/ 1mGyN2-S


title: reg_batch1_rep45


title: reference male mouse8/ 1mGyC1


title: reference male mouse8/ 1mGyCF


title: reference male mouse12/ 1mGyN1-S


title: 34Gy, long survival, unmethylated MGMT 5


title: 1mGyNF/ reference male mouse12-S


title: 1mGyCM/ reference male mouse8


title: reference male mouse12/ 1mGyN5-S


title: 60Gy, short survival, methylated MGMT 1


title: reg_batch1_rep43


title: reference male mouse8/ 1mGyCM


title: reg_batch1_rep44


title: reference male mouse8/ 1mGyB7

source_name: reference male mouse8


title: 1mGyC1/ reference male mouse8


title: reference male mouse12/ 1mGyNM-S


title: reg_batch1_rep41


title: 1mGyNM/ reference male mouse12-S


title: 34Gy, long survival, unmethylated MGMT 4


title: reg_batch1_rep40


title: reference male mouse12/ 1mGyNF-S


title: 1mGyB7/ reference male mouse8


title: 34Gy, long survival, unmethylated MGMT 1


title: 1mGyCF/ reference male mouse8


title: 1mGyB5/ reference male mouse8


title: reference male mouse8/ 1mGyB5


title: reg_batch1_rep42


title: 34Gy, short survival, unmethylated MGMT 5


title: 1mGyB6/ reference male mouse8


title: 1mGyB4/ reference male mouse8


title: 34Gy, long survival, unmethylated MGMT 3


title: 34Gy, long survival, unmethylated MGMT 2


title: 34Gy, short survival, unmethylated MGMT 3


title: reg_batch1_rep36


title: 1mGyB2/ reference male mouse8


title: reg_batch1_rep38


title: reference male mouse8/ 1mGyB4


title: 1mGyB3/ reference male mouse8


title: reg_batch1_rep39


title: 34Gy, short survival, unmethylated MGMT 1


title: 1mGyM5/ reference male mouse12-S


title: 1mGyM7/ reference male mouse12-S


title: reference male mouse8/ 1mGyB6


title: reference male mouse12/ 1mGyM5-S


title: 34Gy, short survival, unmethylated MGMT 4


title: reference male mouse12/ 1mGyM7-S


title: reg_batch1_rep37


title: 34Gy, long survival, methylated MGMT 4


title: 1mGyM6/ reference male mouse12-S


title: reg_batch1_rep35


title: 1mGyM4/ reference male mouse12-S


title: reg_batch1_rep34


title: reference male mouse8/ 1mGyB1


title: 34Gy, long survival, methylated MGMT 3


title: 34Gy, long survival, methylated MGMT 5

value: AO III


title: reg_batch1_rep33


title: reg_batch1_rep31


title: 1mGyB1/ reference male mouse8


title: reference male mouse8/ 1mGyBF


title: reference male mouse8/ 1mGyB3


title: reg_batch1_rep32


title: reference male mouse8/ 1mGyBM


title: 34Gy, short survival, unmethylated MGMT 2


title: 1mGyBF/ reference male mouse8


title: reference male mouse8/ 1mGyB2


title: 34Gy, long survival, methylated MGMT 2


title: 34Gy, long survival, methylated MGMT 1


title: reference male mouse12/ 1mGyM6-S


title: reg_batch1_rep30


title: reg_batch1_rep29


title: reference male mouse12/ 1mGyM2-S


title: reg_batch1_rep27


title: 1mGyBM/ reference male mouse8


title: reference male mouse12/ 1mGyM1-S


title: 34Gy, short survival, methylated MGMT 3


title: 1mGyM3/ reference male mouse12-S


title: reference male mouse8/ 1mGyA6


title: 34Gy, short survival, methylated MGMT 5


title: 34Gy, short survival, methylated MGMT 4


title: 34Gy, short survival, methylated MGMT 2


title: reg_batch1_rep26


title: 1mGyM1/ reference male mouse12-S


title: 34Gy, short survival, methylated MGMT 1


title: 1mGyM2/ reference male mouse12-S


title: reference male mouse12/ 1mGyM3-S


title: 1mGyMF/ reference male mouse12-S


title: 1mGyA6/ reference male mouse8


title: reg_batch1_rep25


title: reg_batch1_rep24


title: TMZ, long survival, unmethylated MGMT 5


title: reg_batch1_rep28


title: reg_batch1_rep23


title: reference male mouse12/ 1mGyM4-S


title: reg_batch1_rep22


title: 1mGyA5/ reference male mouse8


title: TMZ, long survival, unmethylated MGMT 4


title: reference male mouse12/ 1mGyMF-S


title: reg_batch1_rep21


title: 1mGyA4/ reference male mouse8


title: reference male mouse12/ 1mGyMM-S


title: TMZ, long survival, unmethylated MGMT 1


title: TMZ, long survival, unmethylated MGMT 3


title: reg_batch1_rep19


title: reference male mouse8/ 1mGyA5


title: TMZ, long survival, unmethylated MGMT 2


title: 1mGyMM/ reference male mouse12-S


title: TMZ, short survival, unmethylated MGMT 5


title: reg_batch1_rep20


title: reg_batch1_rep18


title: reference male mouse8/ 1mGyA3


title: 1mGyA2/ reference male mouse8


title: reference male mouse14/ 0.05mGyO7

source_name: reference male mouse14


title: 0.05mGyO6/ reference male mouse14


title: TMZ, short survival, unmethylated MGMT 4


title: reference male mouse8/ 1mGyA2


title: reg_batch1_rep17


title: TMZ, short survival, unmethylated MGMT 3


title: reg_batch1_rep16


title: 0.05mGyO7/ reference male mouse14


title: TMZ, short survival, unmethylated MGMT 2


title: reference male mouse14/ 0.05mGyO6


title: TMZ, short survival, unmethylated MGMT 1


title: reg_batch1_rep15


title: reg_batch1_rep14


title: TMZ, long survival, methylated MGMT 5


title: reference male mouse14/ 0.05mGyO5


title: reference male mouse8/ 1mGyA4


title: 0.05mGyO5/ reference male mouse14


title: TMZ, long survival, methylated MGMT 4


title: reg_batch1_rep13


title: reg_batch1_rep12


title: 1mGyA1/ reference male mouse8


title: reference male mouse14/ 0.05mGyO4


title: 0.05mGyO3/ reference male mouse14


title: 0.05mGyO4/ reference male mouse14


title: TMZ, long survival, methylated MGMT 2


title: TMZ, long survival, methylated MGMT 3


title: reg_batch1_rep11


title: reference male mouse8/ 1mGyA1


title: 1mGyAF/ reference male mouse8


title: 0.05mGyO2/ reference male mouse14


title: TMZ, long survival, methylated MGMT 1


title: reg_batch1_rep9


title: reference male mouse14/ 0.05mGyO7


title: reference male mouse14/ 0.05mGyO2


title: 1mGyA3/ reference male mouse8


title: reference male mouse14/ 0.05mGyO3


title: reference male mouse8/ 1mGyAF


title: 0.05mGyO1/ reference male mouse14


title: reg_batch1_rep8


title: TMZ, short survival, methylated MGMT 4


title: reg_batch1_rep7


title: 0.05mGyOF/ reference male mouse14


title: reference male mouse14/ 0.05mGyO6


title: 1mGyAM/ reference male mouse8


title: TMZ, short survival, methylated MGMT 3


title: reg_batch1_rep10


title: 0.05mGyO7/ reference male mouse14


title: 0.05mGyO5/ reference male mouse14


title: TMZ, short survival, methylated MGMT 2


title: reference male mouse14/ 0.05mGyO1


title: reg_batch1_rep6


title: reg_batch1_rep5


title: 0.05mGyO6/ reference male mouse14


title: TMZ, short survival, methylated MGMT 5


title: 0.05mGyOM/ reference male mouse14


title: reg_batch1_rep4


title: TMZ, short survival, methylated MGMT 1


title: reference male mouse14/ 0.05mGyOF


title: reg_batch1_rep3


title: 0.05mGyO3/ reference male mouse14


title: reg_batch1_rep2


title: 0.05mGyO4/ reference male mouse14


title: reference male mouse14/ 0.05mGyOM


title: reference male mouse14/ 0.05mGyO4


title: reg_batch1_rep1


title: 1mGyL6/ reference male mouse12-S


title: 0.05mGyN6/ reference male mouse14


title: reference male mouse14/ 0.05mGyN6


title: reference male mouse14/ 0.05mGyN7


title: 1mGyL5/ reference male mouse12-S


title: olig2+ cells in zebrafish trunks - 28hpf

city: Nantong City

first: lingyan

last: xing

email: xlyan011@163.com, xlyan@ntu.edu.cn

address: Xincheng Bridge Street

institute: Nantong University

description: fluorescent cells from Tg(olig2:dsred) trunks

data_processing:
Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters.
Genes detectable in more than two cells were defined as “expressed”. Cells with <1000 genes detected were removed. Counts were normalized to 10000 and transformed into logarithmic scales.
A neighborhood graph was embedded using UMAP displaying the top 4000 highly variable genes across cells. Cells were clustered by the Louvain Algorithm. The trajectory interface of all cell clusters was done using the layout 'fa'. These analyses were performed by the Python-based SCANPY package
Genome_build: GRCz11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Danio rerio

source_name: Tg(olig2:dsred) trunks

extract_protocol:
Tg(olig2:dsred) trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol.
cDNAs were amplified and libraries were generated with the Single Cell 3’ Library and Gel Bead kit V3

tag: Stage

value: 28 hour post fertilization (hpf)

value: Tg (olig2:dsred)

value: trunk


title: 0.05mGyN7/ reference male mouse14


title: reference male mouse14/ 0.05mGyO2


title: reference male mouse8/ 1mGyAM


title: olig2+ cells in zebrafish trunks - 60hpf

value: 60 hour post fertilization (hpf)


title: 0.05mGyO2/ reference male mouse14


title: reference male mouse12/ 1mGyL6-S


title: reference male mouse14/ 0.05mGyO5


title: reference male mouse14/ 0.05mGyO3


title: 0.05mGyOF/ reference male mouse14


title: reference male mouse14/ 0.05mGyO1


title: 0.05mGyO1/ reference male mouse14


title: 0.05mGyOM/ reference male mouse14


title: 0.05mGyN5/ reference male mouse14


title: 0.05mGyN4/ reference male mouse14


title: 0.05mGyN3/ reference male mouse14


title: reference male mouse14/ 0.05mGyN5


title: reference male mouse14/ 0.05mGyOF


title: olig2+ cells in zebrafish trunks

tag: developmental stage

value: 42 hour post fertilization (hpf)

value: fluorescent cells from Tg(olig2:dsred) trunks


title: 0.05mGyN2/ reference male mouse14

value: tail


title: reference male mouse12/ 1mGyL4-S


title: reference male mouse14/ 0.05mGyN4


title: 1mGyL2/ reference male mouse12-S


title: HREC-overexpressing_overexpression positive control group [Lenti-EGIP-2]

type: RNA

city: shanghai

first: zichang

last: zhao

address: 168 changhai road

department: Ophthalmology

institute: Changhai Hospital

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US). Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA,Agilent technologies, Santa Clara, CA, US)and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings.

source_name: HREC cells -overexpressing_overexpression positive control group

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Quantitative PCR uses Trizol (ThermoFisher, scientific, Shanghai, China) to extract total RNA. The total RNA was then reverse transcribed using the PrimeScript RT Kit (TaKaRa Biotechnology, Dalian, China) according to the manufacturer's protocol. Total RNA was extracted using Trizol according to the manufacturer's instructions. Equal amounts of RNA were transcribed into cDNA using the PrimeScript RT kit (TaKaRa Biotechnology, Dalian, China).

treatment_protocol: HRECs (ScienCell, San Diego, USA) were cultured in Endothelial Cell Medium (ECM; ScienCell, San Diego, USA). The cell line was kept in an incubator humidified at 37 ℃ with 5% CO2.

value: human retinal vascular endothelial cells (HREC)

value: overexpression positive control group

tag: time point


title: 0.05mGyN1/ reference male mouse14


title: reference male mouse12/ 1mGyL1-S


title: reference male mouse14/ 0.05mGyN3


title: 1mGyL4/ reference male mouse12-S


title: reference male mouse12/ 1mGyL5-S


title: HREC-overexpressing_negative control group [Lenti-A2-1]

source_name: HREC cells -overexpressing_negative control group

value: negative control group


title: HREC-overexpressing_negative control group [Lenti-A2-2]


title: HREC-overexpressing_overexpression positive control group [Lenti-EGIP-1]


title: HREC-overexpressing_overexpression positive control group [Lenti-EGIP-3]


title: reference male mouse14/ 0.05mGyN2


title: reference male mouse12/ 1mGyL3-S


title: 1mGyL1/ reference male mouse12-S


title: reference male mouse12/ 1mGyL2-S


title: 1mGyL3/ reference male mouse12-S


title: HREC-overexpressing_negative control group [Lenti-A2-3]


title: 1mGyLF/ reference male mouse12-S


title: reference male mouse14/ 0.05mGyN1


title: reference male mouse14/ 0.05mGyOM


title: reference male mouse12/ 1mGyLF-S


title: 1mGyLM/ reference male mouse12-S


title: HREC-interfering_positive interference group [Sh-A2-3]

source_name: HREC cells-interfering_positive interference group

value: positive interference group


title: HREC-interfering_positive interference group [Sh-A2-1]


title: reference male mouse12/ 1mGyLM-S

source_name: reference male mouse12


title: 0.05mGyN4/ reference male mouse14


title: 0.05mGyN5/ reference male mouse14


title: reference male mouse14/ 0.05mGyNM


title: 0.05mGyNF/ reference male mouse14


title: 0.05mGyNM/ reference male mouse14


title: reference male mouse14/ 0.05mGyN3


title: HREC-interfering_negative control group [Sh-NC-2]

source_name: HREC cells-interfering_negative control group


title: HREC-interfering_positive interference group [Sh-A2-2]


title: reference male mouse14/ 0.05mGyN5


title: 1mGyJ6/ reference male mouse12-S


title: reference male mouse14/ 0.05mGyN7


title: 0.05mGyN7/ reference male mouse14


title: reference male mouse14/ 0.05mGyNF


title: reference male mouse12/ 1mGyJ6-S


title: 0.05mGyM7/ reference male mouse14


title: HREC-interfering_negative control group [Sh-NC-1]


title: 0.05mGyN2/ reference male mouse14


title: reference male mouse14/ 0.05mGyN6


title: HREC-interfering_negative control group [Sh-NC-3]


title: Sample 46

city: Raleigh

first: Heather

last: Patisaul

state: North Carolina

institute: North Carolina State University

data_processing:
FastQC
StarAlignment
featurecounts
DESeq2 Bioconductor

organism: Rattus norvegicus

source_name: PND1 prefrontal cortex

extract_protocol:
Qiagen RNEasy Miniprep (Qiagen, Cat. 74134)
NEBNext Ultra Directional RNA Library Prep kit and NEBNext Poly(A) mRNA Magnetic Isolation Module (catalogs E7420 and E7490; New England Biolabs, Ipswich, MA, USA)

treatment_protocol: Gestational exposure once daily to one of three flame retardants; 1000 µg BFR (2-ethylhexyl-2,3,4,5-tetrabromobenzoate (EH-TBB) and bis (2-ethylhexyl)-2,3,4,5-tetrabromophthalate (BEH-TEBP), 1000µg OPFR (triphenyl phosphate and isopropylated triphenyl phosphate) or 2000 µg FireMaster 550 (FM 550).

value: Brain

tag: Sex

value: F


title: Sample 45

value: M


title: Sample 47


title: 1mGyJ5/ reference male mouse12-S


title: Sample 44


title: reference male mouse12/ 1mGyJ5-S


title: 0.05mGyN3/ reference male mouse14


title: 0.05mGyN6/ reference male mouse14


title: reference male mouse14/ 0.05mGyN2


title: 1mGyJ4/ reference male mouse12-S


title: reference male mouse14/ 0.05mGyN4


title: Sample 43


title: reference male mouse12/ 1mGyJ4-S


title: 0.05mGyM6/ reference male mouse14


title: reference male mouse14/ 0.05mGyM6


title: Sample 41


title: 0.05mGyM5/ reference male mouse14


title: Sample 42


title: reference male mouse12/ 1mGyJ3-S


title: 1mGyJ3/ reference male mouse12-S


title: 0.05mGyNF/ reference male mouse14


title: 1mGyJ2/ reference male mouse12-S


title: reference male mouse14/ 0.05mGyM5


title: 1mGyJ1/ reference male mouse12-S


title: Sample 39


title: 0.05mGyM4/ reference male mouse14


title: 0.05mGyN1/ reference male mouse14


title: reference male mouse14/ 0.05mGyM3


title: reference male mouse12/ 1mGyJ2-S


title: 0.05mGyM3/ reference male mouse14


title: reference male mouse14/ 0.05mGyN1


title: 0.05mGyNM/ reference male mouse14


title: Sample 40


title: reference male mouse14/ 0.05mGyNF


title: Sample 38


title: 0.05mGyM2/ reference male mouse14


title: reference male mouse14/ 0.05mGyNM


title: Sample 36


title: reference male mouse14/ 0.05mGyM7


title: reference male mouse12/ 1mGyJF-S


title: reference male mouse14/ 0.05mGyM4


title: Sample 35

value: OPFR


title: reference male mouse12/ 1mGyJ1-S


title: 0.05mGyM6/ reference male mouse13


title: Sample 37


title: Sample 34


title: reference male mouse13/ 0.05mGyM7


title: reference male mouse12/ 1mGyJM-S


title: reference male mouse13/ 0.05mGyM6


title: reference male mouse14/ 0.05mGyM2


title: Sample 33


title: reference male mouse14/ 0.05mGyM1


title: 1mGyJF/ reference male mouse12-S


title: 0.05mGyMF/ reference male mouse14


title: Sample 32


title: 0.05mGyM1/ reference male mouse14


title: Sample 31


title: reference male mouse14/ 0.05mGyMF


title: 0.05mGyM5/ reference male mouse13


title: Sample 30


title: 1mGyC6/ reference male mouse9-S


title: Sample 29


title: 0.05mGyM3/ reference male mouse13


title: 0.05mGyMM/ reference male mouse14


title: reference male mouse13/ 0.05mGyM5


title: 1mGyC5/ reference male mouse9-S


title: 0.05mGyM4/ reference male mouse13


title: reference male mouse9/ 1mGyC5-S


title: Sample 28


title: reference male mouse14/ 0.05mGyMM


title: reference male mouse9/ 1mGyC6-S


title: Sample 27


title: 0.05mGyM2/ reference male mouse13


title: 1mGyJM/ reference male mouse12-S


title: 0.05mGyL5/ reference male mouse14


title: Sample 26


title: reference male mouse14/ 0.05mGyL6


title: 0.05mGyL6/ reference male mouse14


title: Sample 25


title: reference male mouse14/ 0.05mGyL5


title: reference male mouse13/ 0.05mGyM4


title: 1mGyC4/ reference male mouse9-S


title: 0.05mGyL4/ reference male mouse14


title: Sample 24

value: BFR


title: 0.05mGyM7/ reference male mouse13


title: 0.05mGyL3/ reference male mouse14


title: reference male mouse13/ 0.05mGyM2


title: 0.05mGyM1/ reference male mouse13


title: 1mGyC2/ reference male mouse9-S


title: reference male mouse14/ 0.05mGyL4


title: reference male mouse9/ 1mGyC2-S


title: reference male mouse9/ 1mGyC3-S


title: reference male mouse13/ 0.05mGyM1


title: Sample 23


title: reference male mouse9/ 1mGyC4-S


title: Sample 22


title: reference male mouse13/ 0.05mGyM3


title: 1mGyC3/ reference male mouse9-S


title: 1mGyC1/ reference male mouse9-S


title: Sample 21


title: 0.05mGyMF/ reference male mouse13


title: Sample 20


title: Sample 19


title: reference male mouse9/ 1mGyC1-S


title: Sample 18


title: reference male mouse14/ 0.05mGyL1


title: 0.05mGyL2/ reference male mouse14


title: 0.05mGyL1/ reference male mouse14


title: reference male mouse14/ 0.05mGyL3


title: 1mGyH6/ reference male mouse11-S

source_name: reference male mouse11


title: reference male mouse14/ 0.05mGyL2


title: 0.05mGyMM/ reference male mouse13


title: reference male mouse11/ 1mGyH6-S


title: 1mGyCM/ reference male mouse9-S

source_name: reference male mouse9


title: reference male mouse9/ 1mGyCF-S


title: 1mGyCF/ reference male mouse9-S


title: reference male mouse14/ 0.05mGyLF


title: Sample 17


title: 0.05mGyL5/ reference male mouse13

source_name: reference male mouse13


title: reference male mouse9/ 1mGyCM-S


title: reference male mouse11/ 1mGyH5-S


title: reference male mouse13/ 0.05mGyMM


title: Sample 14


title: 0.05mGyL6/ reference male mouse13


title: reference male mouse13/ 0.05mGyL5


title: reference male mouse13/ 0.05mGyMF


title: reference male mouse14/ 0.05mGyLM


title: Sample 15


title: reference male mouse11/ 1mGyH4-S


title: 0.05mGyLM/ reference male mouse14


title: reference male mouse8/ 1mGyA6-S


title: reference male mouse13/ 0.05mGyL6


title: Sample 13


title: reference male mouse13/ 0.05mGyL4


title: reference male mouse8/ 1mGyA5-S


title: 1mGyA5/ reference male mouse8-S


title: 2_10_APAP

city: Chapel Hill

first: Merrie

last: Mosedale

address: 301 Pharmacy Lane, Kerr Hall CB#7569

department: Division of Pharmacotherapy and Experimental Therapeutics

institute: UNC Eshelman School of Pharmacy

description: human hepatocyte RNA

hyb_protocol: Labeled cRNA was fragmented and prepared for hybridization.

scan_protocol: The Affymetrix Gene Titan system was used to perform the hybridization, washing and scanning of the arrays.

data_processing: Affymetrix CEL files were normalized using Robust Multi-array Average method with a log base 2 transformation (Irizarry et al., 2003). Data summarization and QC was performed using the Transcriptome Analysis Console software version 4.0 (ThermoFisher). A filtering step was performed to remove low expression probe sets using Partek Genomics Suite version 7.0 (Partek Inc.).

label: biotin

source_name: primary human hepatocytes_donor 2

label_protocol: Double-stranded cDNA was synthesized using the GeneChip WT PLUS Reagent Kit (Affymetrix).

growth_protocol: Hepatocytes were cultured in a sandwich configuration using previously described methods (LeCluyse et al., 2005). Once established, sandwich-cultured human hepatocyte plates were maintained in a 37°C humidified incubator at 5% CO2.

extract_protocol: Total cellular RNA was isolated using an RNeasy total RNA isolation kit. The quantity and integrity of the RNA was evaluated spectrophotometrically and with an Agilent 2200 TapeStation.

treatment_protocol: Cultures were exposed to chemicals or vehicle alone for 24 h.

tag: donor (id)

value: WWQ

tag: donor (#)

tag: concentration (microm)

tag: treatment (compound)

value: APAP

value: hepatocytes


title: 1mGyH5/ reference male mouse11-S

tag: strain

tag: tissue


title: Sample 12

value: Control


title: 1mGyA6/ reference male mouse8-S


title: 1mGyH3/ reference male mouse11-S


title: 0.05mGyL3/ reference male mouse13


title: 3_10_APAP

description: human hepatocyte RNA

source_name: primary human hepatocytes_donor 3

tag: cell type


title: Sample 11

tag: treatment


title: 0.05mGyL2/ reference male mouse13


title: Sample 10


title: 1_10_APAP

description: human hepatocyte RNA

source_name: primary human hepatocytes_donor 1


title: Sample 9


title: 1mGyH2/ reference male mouse11-S


title: 0.05mGyL4/ reference male mouse13


title: reference male mouse8/ 1mGyA4-S


title: 1mGyA3/ reference male mouse8-S


title: Sample 8


title: reference male mouse8/ 1mGyA3-S


title: Sample 7


title: 3_0_APAP

description: human hepatocyte RNA


title: 1mGyH1/ reference male mouse11-S


title: reference male mouse11/ 1mGyH2-S


title: 1_0_APAP

description: human hepatocyte RNA


title: 1mGyA2/ reference male mouse8-S


title: 3_180 uM_Idela

description: human hepatocyte RNA

value: Idelalisib


title: reference male mouse11/ 1mGyH1-S


title: 0.05mGyLF/ reference male mouse14


title: 1mGyA4/ reference male mouse8-S


title: reference male mouse8/ 1mGyA2-S


title: 1mGyHF/ reference male mouse11-S


title: 1mGyA1/ reference male mouse8-S


title: Sample 6


title: reference male mouse13/ 0.05mGyL3


title: Sample 5


title: reference male mouse11/ 1mGyHF-S


title: reference male mouse11/ 1mGyH3-S


title: Sample 4


title: Sample 16


title: Sample 3


title: 1_180 uM_Idela

description: human hepatocyte RNA


title: Sample 2


title: 3_60 uM_Idela

description: human hepatocyte RNA


title: 1mGyHM/ reference male mouse11-S


title: 2_180 uM_Idela

description: human hepatocyte RNA


title: 1mGyH4/ reference male mouse11-S


title: reference male mouse8/ 1mGyA1 -S


title: 2_60 uM_Idela

description: human hepatocyte RNA


title: reference male mouse11/ 1mGyHM-S


title: Sample 1


title: 1_60 uM_Idela

description: human hepatocyte RNA


title: 1mGyAF/ reference male mouse8-S


title: 1mGyG8/ reference male mouse10-S

source_name: reference male mouse10


title: 1mGyAM/ reference male mouse8-S


title: Skn3

city: Sapporo

first: Masato

last: Hara

state: Hokkaido

address: Kita-15 Nishi-7

department: Orthopaedic Surgery

institute: Hokkaido University

data_processing:
Quality was checked with FastQC v 0.11.7
Sequence reads were trimmed with Trimmomatic v 0.38
Trimmed sequence reads were mapped with HISAT2 v 2.1.0
Read count extraction and normalization were performed using featureCounts v 1.6.3
Assembly: rn6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Skin

growth_protocol: Epineurium and parenchyma were manually separated from dissected sciatic nerves with a micro-forceps. Abdominal skin (1 cm2) was dissected, followed by the removal of subcutaneous adipose tissue. These tissues were cut into 1-2 mm pieces using micro-scissors, transferred to enzymatic digestion medium containing 2% collagenaseⅠ (Sigma-Aldrich, St. Louis, MO) and 0.125% trypsin in Dulbecco’s modified Eagle Medium (DMEM)/Ham’s F-12 (Wako, Osaka, Japan). After enzymatic incubation for 1 hour at 37℃, 10% fetal bovine serum (FBS, Sigma-Aldrich) in DMEM was added to stop the enzymatic digestion. After centrifugation and removal of the supernatant, the pieces were mechanically dissociated by 30 cycles of pipetting in a Fb culture medium consisting of DMEM/Ham’s F-12 with 10% FBS, 1% GlutaMAX (Thermo Fisher Scientific, Waltham, MA, USA), and 1% penicillin–streptomycin (Thermo Fisher Scientific). The cell suspension was then filtered through a 40 µm cell strainer (Greiner Bio-One, Kremsmünster, Austria) to remove tissue pieces. The cell viability of the dissociated cells was assessed by Trypan Blue (Thermo Fisher Scientific) and was within the range of 92 - 96%. Dissociated cells were seeded onto a non-coated 75-cm2 flask, followed by the replacement of the culture medium 30 minutes later. After a single passaging 3 to 4 days later, the cells were subjected to RNA sequence.

extract_protocol:
RNA was extracted from a total of 9 samples (3 samples per each Fb) using a RNeasy plus mini kit (Qiagen, Netherlands) according to the manufacturer's instructions.
Each library was prepared using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat No. E7490), NEBNext® UltraTMII Directional RNA Library Prep Kit (Cat No. E7760), and Paired-end reads (150 bp) were obtained on an Illumina NovaSeq 6000 (Illumina, Inc.).

value: Skin

value: fibroblasts

tag: genotype

value: WT


title: reference male mouse10/ 1mGyG8-S

value: tail


title: 1_18 uM_Idela

description: human hepatocyte RNA


title: 1mGyG7/ reference male mouse10-S


title: 3_18 uM_Idela

description: human hepatocyte RNA


title: Skn1


title: reference male mouse8/ 1mGyAM-S

source_name: reference male mouse8


title: Par3

source_name: Parenchyma

value: Parenchyma


title: 2_18 uM_Idela

description: human hepatocyte RNA


title: 3_6 uM_Idela

description: human hepatocyte RNA


title: Skn2


title: 0.05mGyG6/ reference male mouse6

source_name: reference male mouse6


title: reference male mouse10/ 1mGyG7-S


title: 2_6 uM_Idela

description: human hepatocyte RNA


title: 1_6 uM_Idela

description: human hepatocyte RNA


title: reference male mouse10/ 1mGyG6-S


title: reference male mouse6/ 0.05mGyG6


title: 1mGyG6/ reference male mouse10-S


title: 1mGyG5/ reference male mouse10-S


title: Par1


title: reference male mouse6/ 0.05mGyG4


title: reference male mouse6/ 0.05mGyG5


title: 3_1.8 uM_Idela

description: human hepatocyte RNA


title: 0.05mGyG5/ reference male mouse6


title: 2_1.8 uM_Idela

description: human hepatocyte RNA


title: Par2


title: 0.05mGyG4/ reference male mouse6


title: Epn3

source_name: Epineurium

value: Epineurium


title: reference male mouse10/ 1mGyG5-S


title: Epn1


title: reference male mouse10/ 1mGyG4-S


title: Epn2


title: 2_0_APAP

description: human hepatocyte RNA


title: 1_1.8 uM_Idela

description: human hepatocyte RNA


title: 1mGyG4/ reference male mouse10-S


title: 3_0-Idela

description: human hepatocyte RNA


title: 2_0-Idela

description: human hepatocyte RNA


title: 0.05mGyG3/ reference male mouse6


title: reference male mouse10/ 1mGyG3-S


title: reference male mouse6/ 0.05mGyG3


title: reference male mouse6/ 0.05mGyG2


title: 1mGyG2/ reference male mouse10-S


title: 1mGyG3/ reference male mouse10-S


title: reference male mouse10/ 1mGyG2-S


title: 0.05mGyG1/ reference male mouse6


title: 0.05mGyG2/ reference male mouse6


title: 1mGyK7/ reference male mouse12-S


title: 1mGyK3/ reference male mouse12-S


title: reference male mouse12/ 1mGyK4-S


title: reference male mouse6/ 0.05mGyG1


title: 1mGyK4/ reference male mouse12-S


title: reference male mouse12/ 1mGyK6-S


title: 1mGyK5/ reference male mouse12-S


title: 1mGyG1/ reference male mouse10-S


title: reference male mouse5/ 0.05mGyE5

source_name: reference male mouse5


title: 0.05mGyE6/ reference male mouse5


title: 1_0-Idela

description: human hepatocyte RNA


title: 1mGyK6/ reference male mouse12-S


title: reference male mouse12/ 1mGyK3-S


title: reference male mouse12/ 1mGyK7-S


title: 1mGyGM/ reference male mouse10-S


title: reference male mouse8/ 1mGyAF-S


title: reference male mouse10/ 1mGyGF-S


title: 1mGyF7/ reference male mouse10-S


title: 1mGyGF/ reference male mouse10-S


title: reference male mouse6/ 0.05mGyGF


title: 0.05mGyGF/ reference male mouse6


title: 0.05mGyGM/ reference male mouse6


title: reference male mouse6/ 0.05mGyGM


title: reference male mouse5/ 0.05mGyE6


title: 1mGyF6/ reference male mouse10-S


title: 0.05mGyE4/ reference male mouse5


title: reference male mouse10/ 1mGyGM-S


title: reference male mouse10/ 1mGyF6-S


title: reference male mouse10/ 1mGyF7-S


title: reference male mouse10/ 1mGyG1-S


title: 0.05mGyE5/ reference male mouse5


title: reference male mouse12/ 1mGyK5-S


title: 1mGyK2/ reference male mouse12-S


title: 0.05mGyE3/ reference male mouse5


title: reference male mouse5/ 0.05mGyE4


title: 1mGyK1/ reference male mouse12-S


title: 1mGyF5/ reference male mouse10-S


title: reference male mouse5/ 0.05mGyE3


title: reference male mouse5/ 0.05mGyE2


title: reference male mouse12/ 1mGyK2-S


title: 0.05mGyE2/ reference male mouse5


title: reference male mouse12/ 1mGyK1-S


title: 1mGyKF/ reference male mouse12-S


title: 0.05mGyE1/ reference male mouse5


title: 1mGyF4/ reference male mouse10-S


title: 0.05mGyEF/ reference male mouse5


title: 1mGyF3/ reference male mouse10-S


title: reference male mouse10/ 1mGyF2-S


title: reference male mouse5/ 0.05mGyEF


title: reference male mouse10/ 1mGyF4-S


title: reference male mouse12/ 1mGyKF-S


title: 1mGyF1/ reference male mouse10-S


title: 1mGyF2/ reference male mouse10-S


title: reference male mouse10/ 1mGyF1-S


title: reference male mouse11/ 1mGyI6-S


title: reference male mouse12/ 1mGyKM-S


title: reference male mouse5/ 0.05mGyE1


title: 1mGyKM/ reference male mouse12-S


title: 0.05mGyEM/ reference male mouse5


title: 1mGyFF/ reference male mouse10-S


title: 1mGyI5/ reference male mouse11-S


title: 1mGyI6/ reference male mouse11-S


title: 1mGyFM/ reference male mouse10-S


title: reference male mouse10/ 1mGyF3-S


title: 0.05mGyC6/ reference male mouse5-S


title: reference male mouse11/ 1mGyI5-S


title: 0.05mGyC4/ reference male mouse5-S


title: reference male mouse5/ 0.05mGyEM


title: reference male mouse10/ 1mGyFF-S


title: 0.05mGyC5/ reference male mouse5-S


title: reference male mouse5/ 0.05mGyC6-S


title: reference male mouse5/ 0.05mGyC4-S


title: 1mGyI4/ reference male mouse11-S


title: reference male mouse10/ 1mGyFM-S


title: 1mGyI3/ reference male mouse11-S


title: reference male mouse11/ 1mGyI4-S


title: reference male mouse11/ 1mGyI3-S


title: reference male mouse5/ 0.05mGyC5-S


title: 1mGyI2/ reference male mouse11-S


title: reference male mouse9/ 1mGyE6-S


title: 1mGyE6/ reference male mouse9-S


title: KO-OLA-WWE (ChAP-seq)

city: Baltimore

first: Jong-Hyuk

last: Lee

state: Maryland

address: 251 Bayview BLVD

institute: National Institute of Health

data_processing:
Library strategy: ChAP-seq
The sequencing data were uploaded to the Galaxy web platform, and we used the public server at usegalaxy.org to analyze the data.
Sequencing reads were mapped against the human genome (GRCh37/hg19) using Bowtie for Illumina with default parameters
The SAM format outputs were sorted by genomic coordinates and uniquely mapped reliable reads were used in subsequent steps. SAM files were preprocessed using SAMtools
We used the MACS tool to select regions that were enriched for H3K9me3 and PAR. We applied the default settings and found significant regions (P-value ≤ 10-5), using non-IP chromatin as a control to eliminate unspecific signals.
Genome_build: hg19
Supplementary_files_format_and_content: BIGWIG

molecule: other

source_name: Mitochondria isolated from HeLa PARP1 knockout cells

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10 % fetal bovine serum (FBS), 1 % pen-strep and grown in 20 % O2/5 % CO2 at 37° C.

extract_protocol:
isolated mitochondria were cross-linked in a solution of 4 % formaldehyde in PBS for 10 min on ice The cross-linking reaction was stopped by adding glycine to a final concentration of 0.125 M. Mitochondrial pellets were resuspended in buffer B (100 mM Tris–Cl (pH 8.1), 1 % sodium dodecyl sulfate (SDS), 10 mM ethylenediaminetetraacetic acid (EDTA), and protease inhibitor cocktail) and the chromatin was sheared with S-450 sonicator (Branson, Danbury, CT USA) or Bioruptor Pico (Diagenode, Denville, NJ USA). Sonication conditions were optimized by analyzing purified DNA samples on the BIOANALYZER (Agilent, DNA1000 Kit). The prepared mtDNA fraction was diluted 1/10 in IP buffer (0.01 % SDS, 1.1 % Triton X-100, 1.2 mM EDTA, 16.7 mM Tris–Cl (pH 8.1), 167 mM NaCl and a protease inhibitor cocktail) and incubated with PARP1 (39559, Active Motif, Carlsbad, CA USA) or TFAM (ABE483, Millipore-Sigma) antibodies, overnight at 4 °C. Samples were incubated for 1 h at 4 °C with protein A or G beads. Then the beads were washed with TSE150 (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris–Cl (pH 8.1), 150 mM NaCl), TSE500 (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris–Cl (pH 8.1), 500 mM NaCl), Buffer III (0.25 M LiCl, 1 % NP-40, 1 % sodium deoxycholate, 1 mM EDTA, 10 mM Tris-Cl (pH 8.1)) and two times with TE (pH 8.0) for 10 min in each solution. Bead-bound chromatin was eluted with elution buffer (1 % SDS, 0.1 M NaHCO3 (pH 8.0)) for 30 min at 65 °C. The supernatant containing the chromatin, without the beads, was isolated and incubated overnight at 65 °C with 200 mM NaCl to reverse the cross-links. Five hundred microliters of the sample were incubated at 50 °C after adding 10 μl of 0.5 M EDTA, 20 μl of 1 M Tris (pH 6.5) and 4 μl of Proteinase K (20 mg ml-1) and then purified with phenol/chloroform/isoamyl alcohol. Nucleic acids were precipitated by centrifugation for 30 min at 4 °C after mixing the sample with 1 μl of glycogen solution (20 mg ml-1), 20 μl 5 M NaCl and 500 μl isopropanol. Purified nucleic acid pellets were washed with 70 % ethanol, dried and dissolved in nuclease-free water.
According to the manufacturer's protocol

treatment_protocol: Mitochondrial aliquots were treated with 100 µM NAD+ with 5 µM olaparib or vehicle (DMSO) and incubated at 37 °C for 30 min with gentle shaking.

tag: cell line

value: HeLa

value: Fibroblast

value: PARP1 knockout

value: OLA

tag: subcellular organelle

value: Mitochondria

tag: affinity purification reagent

value: WWE affinity resin


title: 1mGyI1/ reference male mouse11-S


title: 1mGyE5/ reference male mouse9-S


title: reference male mouse11/ 1mGyI2-S


title: KO-ctrl-WWE (ChAP-seq)

value: ctrl


title: reference male mouse9/ 1mGyE5-S


title: KO-OLA-input (ChAP-seq)

value: none (input)


title: 0.05mGyC2/ reference male mouse5-S


title: 1mGyE4/ reference male mouse9-S


title: reference male mouse5/ 0.05mGyC3-S


title: KO-NAD-WWE (ChAP-seq)

value: NAD


title: 0.05mGyC3/ reference male mouse5-S


title: reference male mouse5/ 0.05mGyC2-S


title: reference male mouse9/ 1mGyE4-S


title: reference male mouse11/ 1mGyIF-S


title: KO-NAD-input (ChAP-seq)


title: reference male mouse11/ 1mGyI1-S


title: reference male mouse9/ 1mGyE3-S


title: 1mGyIF/ reference male mouse11-S


title: 1mGyIM/ reference male mouse11-S


title: 0.05mGyC1/ reference male mouse5-S


title: reference male mouse5/ 0.05mGyC1-S


title: reference male mouse10/ 1mGyF5-S


title: 1mGyD8/ reference male mouse9-S


title: 0.05mGyCF/ reference male mouse5-S


title: KO-ctrl-input (ChAP-seq)


title: 1mGyE3/ reference male mouse9-S


title: 1mGyE2/ reference male mouse9-S


title: reference male mouse11/ 1mGyIM-S


title: WT-ctrl-WWE (ChAP-seq)

source_name: Mitochondria isolated from HeLa wildtype cells

value: wildtype


title: WT-NAD-WWE (ChAP-seq)


title: WT-ctrl-Tfam (ChIP-seq)

data_processing:
The sequencing data were uploaded to the Galaxy web platform, and we used the public server at usegalaxy.org to analyze the data.
Sequencing reads were mapped against the human genome (GRCh37/hg19) using Bowtie for Illumina with default parameters
The SAM format outputs were sorted by genomic coordinates and uniquely mapped reliable reads were used in subsequent steps. SAM files were preprocessed using SAMtools
We used the MACS tool to select regions that were enriched for H3K9me3 and PAR. We applied the default settings and found significant regions (P-value ≤ 10-5), using non-IP chromatin as a control to eliminate unspecific signals.
Genome_build: hg19
Supplementary_files_format_and_content: BIGWIG

tag: chip antibody

value: anti-TFAM (ABE483)


title: WT-NAD-input (ChIP-seq)


title: WT-OLA-input (ChIP-seq)


title: reference male mouse5/ 0.05mGyCF-S


title: 1mGyEF/ reference male mouse9-S


title: reference male mouse9/ 1mGyE1-S


title: 0.05mGyI7/ reference male mouse5

source_name: reference male mouse14


title: reference male mouse5/ 0.05mGyI7


title: reference male mouse9/ 1mGyEF-S


title: reference male mouse5/ 0.05mGyCM-S


title: WT-ctrl-input (ChIP-seq)


title: reference male mouse9/ 1mGyD8-S


title: reference male mouse9/ 1mGyD6-S


title: UACC257_etop_r2

city: Pittsburgh

first: Jacob

last: Stewart-Ornstein

state: PA

address: UPMC Hillman Cancer Center, 5117 Centre Avenue

department: computational and systems biology

institute: University of Pittsburgh, School of Medicine

data_processing:
Fastq files were aligned and quantified using Salmon on Hg19 Refseq transcript annotations
Reads were summed across transcripts to obtain a total per gene count
Genome_build: Hg19
Supplementary_files_format_and_content: Count data by gene, tab delimited files

molecule: polyA RNA

growth_protocol: The UACC62, UACC257, LOXIMVI, and SKMel5 lines were grown in RPMI media (Gibco or VWR) + 10% FBS (Hyclone) + 1% PFS (Gibco) at 5% CO2 at 37 °C.  The hTert immortalized melanocytes were obtained from ATCC and were grown in the Human Melanocyte Cell Culture System (GIBCO – Medium 254 supplemented with Human melanocyte growth supplement) at 5% CO2 at 37 °C.

extract_protocol:
total RNA was extracted from each cell line by Trizol (thermo) and directZol miniprep kit (Zymo)
RNAseq librares were constructed using the NEB Ultra ii kit with a PolyA selection module
mRNA libraries from treated and untreated sampes, generated on duplicate samples

treatment_protocol: Cells were treated with Etoposide (25uM) by direct addition to media from a 50mM DMSO stock.  Nutlin was added to media (5uM) from a 10mM DMSO stock.  Cells were treated with UV by first changing the media to DPBS, followed by direct exposure to UV (256nM)

value: Etoposide(25uM, 3hrs)


title: 1mGyD7/ reference male mouse9-S


title: UACC62_etop_r2


title: 1mGyE1/ reference male mouse9-S


title: 1mGyD4/ reference male mouse9-S


title: reference male mouse5/ 0.05mGyB8-S


title: reference male mouse9/ 1mGyD7-S


title: reference male mouse9/ 1mGyE2-S


title: 1mGyD6/ reference male mouse9-S


title: reference male mouse5/ 0.05mGyI5


title: 1mGyD5/ reference male mouse9-S


title: reference male mouse9/ 1mGyD5-S


title: 0.05mGyB8/ reference male mouse5-S


title: SKMEL5_etop_r2


title: reference male mouse5/ 0.05mGyI6


title: 0.05mGyI6/ reference male mouse5


title: 1mGyEM/ reference male mouse9-S


title: 0.05mGyB7/ reference male mouse5-S


title: 0.05mGyI4/ reference male mouse5


title: 0.05mGyCM/ reference male mouse5-S


title: 0.05mGyI5/ reference male mouse5


title: reference male mouse5/ 0.05mGyB7-S


title: reference male mouse9/ 1mGyD4-S


title: 1mGyD3/ reference male mouse9-S


title: reference male mouse9/ 1mGyEM-S


title: WT-OLA-WWE (ChAP-seq)


title: LOXIMVI_etop_r2

source_name: LOX-IMVI


title: UACC257_nut_r2


title: UACC62_nut_r2


title: SKMEL5_nut_r2


title: LOXIMVI_nut_r2


title: UACC257_UV_r2


title: UACC62_UV_r2


title: 1mGyD2/ reference male mouse9-S


title: reference male mouse9/ 1mGyD3-S


title: SKMEL5_UV_r2


title: reference male mouse9/ 1mGyDF-S


title: reference male mouse9/ 1mGyD1-S


title: 0.05mGyI3/ reference male mouse5


title: 0.05mGyI1/ reference male mouse5


title: 1mGyDM/ reference male mouse9-S


title: reference male mouse5/ 0.05mGyI1


title: reference male mouse9/ 1mGyD2-S


title: reference male mouse5/ 0.05mGyB6-S


title: 1mGyDF/ reference male mouse9-S


title: reference male mouse5/ 0.05mGyI2


title: reference male mouse5/ 0.05mGyI3


title: 0.05mGyI2/ reference male mouse5


title: 1mGyD1/ reference male mouse9-S


title: LOXIMVI_UV_r2


title: 0.05mGyB2/ reference male mouse5-S


title: reference male mouse5/ 0.05mGyB5-S


title: reference male mouse5/ 0.05mGyB4-S


title: reference male mouse5/ 0.05mGyIF


title: reference male mouse5/ 0.05mGyB3-S


title: 0.05mGyIM/ reference male mouse5


title: UACC257_nt_r2

value: NT


title: 0.05mGyIF/ reference male mouse5


title: reference male mouse9/ 1mGyDM-S


title: 0.05mGyB4/ reference male mouse5-S


title: 0.05mGyB6/ reference male mouse5-S


title: 0.05mGyB3/ reference male mouse5-S


title: 0.05mGyB5/ reference male mouse5-S


title: CFI-1, Input

city: Chicago

first: Paschalis

last: Kratsios

state: IL

department: Department of Neurobiology

institute: University of Chicago

data_processing:
ChIP-Seq reads were alligned to the ce10 genome with bowtie2
Peak calling was performed with MACS2
Assembly: ce10
Supplementary files format and content: The bigWig files were generated by normalizing read counts to 1x genome coverage

organism: Caenorhabditis elegans

source_name: Whole worms

extract_protocol:
Lysates were clarified from sonicated worm tissue and CFI-1-DNA complexes were isolated with FLAG antibody.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: Whole worms

value: cfi-1::3xflag (syb1778)

tag: antibody


title: UACC62_nt_r2


title: SKMEL5_nt_r2


title: reference male mouse5/ 0.05mGyI4

value: tail


title: CFI-1, ChIP

description: ChIP DNA was isolated with FLAG antibody from whole worm lysates

tag: developmental stage

value: Monoclonal ANTI-FLAG M2 antibody (sigma F3165)


title: 1mGyB7/ reference male mouse8-S


title: HBMEC_cells_P.falciparum_infected_RBC_lysate_rep3_lane2 [I3_S18_L002]

city: New York City

first: Ze

last: Chen

state: New York

address: 430 East 29th Street

institute: NYU Grossman School of Medicine

data_processing:
Libraries were sequenced on the Illumina Novaseq. For the bioinformatic pipeline of RNA-seq data, the Seq-N-Slide workflow (source code available at:https://github.com/igordot/sns) was employed. Raw paired-end reads were trimmed via Trimmomatic v0.36, and quality control was performed by using FastQC v0.11.7 and fastQ-Screen v0.13.0. Trimmed reads were mapped to GRCh38/hg38 via STAR v2.7.3a. We used subread v1.6.3 to generate the RNA count table. The R package DESeq2 was used for the differential expression analysis. The significant differentially expressed genes were determined with the cutoff of log2 fold change of 1 or -1 and a false discovery rate (FDR) of ,0.05. The pathway analysis was performed by using R package goseq. We used the principal-component analysis (PCA) and Z-score heat map to visualize DEGs. the visualization was performed by using R packages ggplot2, ComplexHeatmap, and ggVennDiagram.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized count values

source_name: brain

growth_protocol: HBMECs were immortalized as previously described (7). HBMECs were grown in endothelial cell basal medium (ECM) (Sciencell) supplemented with 5% fetal bovine serum (FBS) (Sciencell), 1% endothelial cell growth factor supplement (ECGS) (Sciencell), and 1% penicillin-streptomycin solution (PS) (Sciencell). They were incubated at 37°C in 5% CO2. HBMECs were seeded for experiments until they reached 90% to 95% confluence. All experimental conditions were performed in ECM supplemented with only 1% penicillin-streptomycin solution.

extract_protocol: Total RNA was extracted with the RNeasy Plus microkit(Qiagen) as per the manufacturer’s instructions.

treatment_protocol: Monolayers of HBMEC were incubated for 6 hours with the different conditions: media control, TNF-alpha (1 ng/mL), RBCLs (8 x 10exp6/cm2), or P. falciparum-iRBCLs (8 x 10exp6/cm2)

value: brain

value: HBMEC

value: endothelial

value: WT

value: iRBCL


title: HBMEC_cells_P.falciparum_infected_RBC_lysate_rep3_lane1 [I3_S18_L001]


title: UACC257_etop_r1


title: HBMEC_cells_P.falciparum_infected_RBC_lysate_rep2_lane2 [I2_S10_L002]


title: HBMEC_cells_P.falciparum_infected_RBC_lysate_rep2_lane1 [I2_S10_L001]


title: UACC62_etop_r1


title: reference male mouse5/ 0.05mGyB2-S


title: SKMEL5_etop_r1


title: HBMEC_cells_P.falciparum_infected_RBC_lysate_rep1_lane2 [I1_S2_L002]


title: LOXIMVI_nt_r2


title: reference male mouse5/ 0.05mGyIM


title: HBMEC_cells_P.falciparum_infected_RBC_lysate_rep1_lane1 [I1_S2_L001]


title: reference male mouse5/ 0.05mGyBF-S


title: 0.05mGyB1/ reference male mouse5-S


title: 1mGyB5/ reference male mouse8-S


title: LOXIMVI_etop_r1


title: UACC257_nut_r1


title: 0.05mGyBM/ reference male mouse5-S


title: reference male mouse8/ 1mGyB6-S


title: 0.05mGyBF/ reference male mouse5-S


title: reference male mouse5/ 0.05mGyB1-S


title: UACC62_nut_r1


title: 0.05mGyA6/ reference male mouse5-S


title: 1mGyB4/ reference male mouse8-S


title: HBMEC_cells_RBC lysate_rep3_lane2 [R3_S17_L002]

value: RBCL


title: HBMEC_cells_RBC lysate_rep3_lane1 [R3_S17_L001]


title: HBMEC_cells_RBC lysate_rep2_lane2 [R2_S9_L002]


title: SKMEL5_nut_r1


title: reference male mouse8/ 1mGyB4-S


title: 1mGyB6/ reference male mouse8-S


title: reference male mouse8/ 1mGyB7-S


title: 1mGyB3/ reference male mouse8-S


title: reference male mouse5/ 0.05mGyBM-S


title: reference male mouse5/ 0.05mGyA6-S


title: reference male mouse8/ 1mGyB3-S


title: 0.05mGyA5/ reference male mouse5-S


title: LOXIMVI_nut_r1


title: HBMEC_cells_RBC lysate_rep2_lane1 [R2_S9_L001]


title: UACC257_UV_r1


title: HBMEC_cells_RBC lysate_rep1_lane2 [R1_S1_L002]


title: 1mGyB2/ reference male mouse8-S


title: reference male mouse5/ 0.05mGyA5-S


title: 0.05mGyA4/ reference male mouse5-S


title: HBMEC_cells_RBC lysate_rep1_lane1 [R1_S1_L001]


title: reference male mouse8/ 1mGyB2-S


title: SKMEL5_UV_r1


title: HBMEC_cells_TNF-alpha_rep3_lane1 [T3_S24_L001]

value: TNF-alpha


title: 1mGyB1/ reference male mouse8-S


title: LOXIMVI_UV_r1


title: reference male mouse8/ 1mGyB5-S


title: reference male mouse8/ 1mGyB1-S


title: HBMEC_cells_TNF-alpha_rep2_lane2 [T2_S16_L002]


title: reference male mouse5/ 0.05mGyA3-S


title: reference male mouse5/ 0.05mGyA4-S


title: UACC257_nt_r1


title: 0.05mGyA3/ reference male mouse5-S


title: HBMEC_cells_TNF-alpha_rep3_lane2 [T3_S24_L002]


title: 1mGyBF/ reference male mouse8-S


title: UACC62_UV_r1


title: reference male mouse8/ 1mGyBF-S


title: UACC62_nt_r1


title: 0.05mGyA2/ reference male mouse5-S


title: SKMEL5_nt_r1


title: HBMEC_cells_TNF-alpha_rep2_lane1 [T2_S16_L001]


title: HBMEC_cells_TNF-alpha_rep1_lane1 [T1_S8_L001]


title: reference male mouse5/ 0.05mGyA2-S


title: LOXIMVI_nt_r1


title: 1mGyBM/ reference male mouse8-S


title: reference male mouse5/ 0.05mGyA1-S


title: reference male mouse8/ 1mGyBM-S


title: SKMEL5_dp53_c3_R2


title: reference male mouse5/ 0.05mGyF6


title: 0.05mGyA1/ reference male mouse5-S


title: HBMEC_cells_control_rep3_lane2 [M3_S23_L002]

value: Media control


title: 0.05mGyF6/ reference male mouse5


title: SKMEL5_dp53_c3_R1


title: HBMEC_cells_control_rep2_lane2 [M2_S15_L002]


title: HBMEC_cells_control_rep3_lane1 [M3_S23_L001]


title: SKMEL5_dp53_c2_R2


title: reference male mouse5/ 0.05mGyF5


title: HBMEC_cells_control_rep2_lane1 [M2_S15_L001]


title: SKMEL5_dp53_c2_R1


title: 0.05mGyAF/ reference male mouse5-S


title: reference male mouse5/ 0.05mGyAF-S


title: SKMEL5_dp53_c1_R2


title: HBMEC_cells_control_rep1_lane2 [M1_S7_L002]


title: SKMEL5_dp53_c1_R1


title: 0.05mGyAM/ reference male mouse5-S


title: HBMEC_cells_control_rep1_lane1 [M1_S7_L001]


title: SKMEL5_wt_R2


title: 0.05mGyF4/ reference male mouse5


title: reference male mouse5/ 0.05mGyAM-S


title: 0.05mGyF3/ reference male mouse5


title: LOXIMVI_dp53_c3_R2


title: reference male mouse5/ 0.05mGyF3


title: SKMEL5_wt_R1


title: 0.05mGyK7/ reference male mouse14


title: PDAC-04

city: Essen

first: Laura

last: Godfrey

address: Hufelandstraße 55

country: Germany

institute: DKTK Partner Site Essen/Düsseldorf

data_processing:
Adapter and low-quality base trimming was carried out with Trimmomatic (v0.38).
Trimmed reads were mapped against the GRCh38/hg38 human reference genome using the Bowtie2 (v2.3.4.1) aligner.
The aligned reads were assembled with Cufflinks (v2.2.1).
After assembly the abundance of gene was calculated in read counts per gene. Lowly expressed genes with lower read count as 0.5 transcripts per million reads and that were missing in more than one sample per group were excluded.
The filtered raw count matrix was normalized and batch-corrected using the DESeq2 package (v3.14).
Assembly: hg38
Supplementary files format and content: csv file of normalized and batch corrected read counts

source_name: Pancreatic tissue

extract_protocol:
For RNA-isolation 5-8 8-µm-thick tissue sections were prepared, and lesions were dissected manually or by laser-capture microdissection (LMD), depending on their size to ensure adequate cellularity (>80%). In some samples containing larger lesions, manual microdissection was used. RNA was isolated using the RNeasy FFPE Kit for RNA (Qiagen, Hilden, Germany) following the manufacturer’s instructions.
Illumina TruSeqTM Stranded mRNA Library Prep kit

value: Pancreas

tag: type

value: PDAC

tag: grade


title: reference male mouse5/ 0.05mGyF4

data_processing: Agilent Genomic Workbench Software (v 7.0.) was used.


title: PDAC-06


title: PDAC-05


title: 0.05mGyK6/ reference male mouse14


title: 0.05mGyF2/ reference male mouse5


title: reference male mouse5/ 0.05mGyF2


title: LOXIMVI_dp53_c3_R1


title: reference male mouse14/ 0.05mGyK6


title: reference male mouse14/ 0.05mGyK7


title: reference male mouse14/ 0.05mGyK5


title: 0.05mGyK5/ reference male mouse14


title: LOXIMVI_dp53_c2_R2


title: PDAC-03


title: LOXIMVI_dp53_c2_R1


title: LOXIMVI_dp53_c1_R2


title: LOXIMVI_dp53_c1_R1


title: LOXIMVI_wt_R2


title: reference male mouse5/ 0.05mGyF1


title: iIPMN-H05

value: iIPMN

value: high


title: iIPMN-H06


title: iIPMN-H04


title: iIPMN-H01


title: 0.05mGyFF/ reference male mouse5


title: reference male mouse5/ 0.05mGyFF


title: iIPMN-H02


title: iIPMN-H03


title: 0.05mGyFM/ reference male mouse5


title: 0.05mGyF1/ reference male mouse5


title: 0.05mGyK4/ reference male mouse14


title: LOXIMVI_wt_R1

value: NT


title: reference male mouse14/ 0.05mGyK4


title: 0.05mGyK3/ reference male mouse14


title: 0.05mGyK2/ reference male mouse14


title: Melanocytes_Nutlin_r2

source_name: Melanocyte hTERT


title: iIPMN-06

value: low


title: 0.05mGyK1/ reference male mouse14


title: reference male mouse14/ 0.05mGyK2


title: reference male mouse14/ 0.05mGyK3


title: reference male mouse5/ 0.05mGyFM


title: 0.05mGyD7/ reference male mouse5-S


title: reference male mouse14/ 0.05mGyK1


title: reference male mouse5/ 0.05mGyD7-S


title: reference male mouse5/ 0.05mGyD8-S


title: Melanocytes_Nutlin_r1


title: 0.05mGyD8/ reference male mouse5-S


title: 0.05mGyKF/ reference male mouse14


title: iIPMN-05


title: iIPMN-04


title: iIPMN-03


title: Melanocytes_NT_r1


title: reference male mouse14/ 0.05mGyKF


title: iIPMN-02


title: Gastric organoid 3D (A1)

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

description: mRNA

data_processing:
Data were analyzed using Cell Ranger™ pipelines which is available in 10x Genomics website.
Genome_build: GRCh38
Supplementary_files_format_and_content: h5; contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis.
Supplementary_files_format_and_content: tar.gz; gene barcode matrices and feature barcode matrix.

source_name: gastric organoids

growth_protocol: Generation and culture of stomach gastric organoids was performed as described before (Bartfeld et al. 2015, Kayisoglu et al. 2020). Monolayers were allowed to grow using the culture media described above (ENRWFGTi_) and differentiate for 14 days to reach 90-100% confluency. Six days prior infection, primocin was exchange for H. pylori compatible antibiotics.

extract_protocol:
Ex vivo gastric units were isolated from gastric biopsies as described before (Bartfeld et al. 2015). Ex vivo gastric units, 3D organoids and 2D organoid-derived monolayers were made single cells by incubation with TripLE Express. Ex vivo units were stained for EpCam before sorting. Cells were then subjected to FACS sorting. Total RNA was isolated using 10x Chromium kit.
Cells were loaded in the 10X Genomics Chromium at a concentration of 200 cells/µl with the aim of recovering 3000 cells. Libraries were generated with the Chromium Single Cell 3’ Reagents Kit v2 Chemistry.
Chromium single cell 3'v2 (10X Genomics).

treatment_protocol: Infection: Organoid-derived monolayers were infected with Helicobacter pylori by adding the bacteria apically onto monolayers with a MOI of 1 for 6 h.

value: 3D gastric organoid

value: Epithelial gastric cells

value: untreated

tag: disease state

value: Healthy


title: gIPMN-H06

value: gIPMN


title: gIPMN-H05


title: reference male mouse5/ 0.05mGyD6-S

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

institute: Institute for Environmental Science

extract_protocol: PI-50a (Kurabo Industries LTD.) tissue DNA extraction protocol.

value: tail


title: Melanocytes_NT_r2


title: HBMEC_cells_TNF-alpha_rep1_lane2 [T1_S8_L002]

value: brain

value: HBMEC

value: endothelial

value: WT


title: gIPMN-H04


title: gIPMN-H03


title: iIPMN-01


title: reference male mouse5/ 0.05mGyD5-S


title: 0.05mGyD4/ reference male mouse5-S


title: 0.05mGyD5/ reference male mouse5-S


title: reference male mouse14/ 0.05mGyKM


title: 0.05mGyD6/ reference male mouse5-S


title: 0.05mGyKM/ reference male mouse14


title: 0.05mGyD3/ reference male mouse5-S


title: 0.05mGyF5/ reference male mouse5


title: reference male mouse5/ 0.05mGyD4-S


title: reference male mouse5/ 0.05mGyD3-S


title: gIPMN-H02


title: gIPMN-H01


title: reference male mouse14/ 0.05mGyJ6


title: 0.05mGyJ6/ reference male mouse14


title: reference male mouse14/ 0.05mGyJ5


title: 0.05mGyJ5/ reference male mouse14


title: reference male mouse14/ 0.05mGyJ4


title: 0.05mGyJ4/ reference male mouse14


title: gIPMN-05


title: gIPMN-06


title: gIPMN-03


title: S21CP2

description: prostate orthograft tumour

data_processing:
Quality checks on the raw RNA-seq files were done using fastqc version 0.11.4 and fastq_screen version 0.5.2. RNA-seq paired-end reads were aligned to the GRCm38.p3 version of the mouse genome using Tophat2 version 2.1.0 with Bowtie version 2.2.6.0.  Gene expression levels were determined using htseq-count package version 0.6.0. Expression counts were further processed and analysed in the R environment (version 3.2.3) using packages from the Bioconductor data analysis suite and differential gene expression analysis based on the negative binomial distribution using the DESeq2 version 1.14.1.
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: .csv files with RPKM values

source_name: CP2 cells (RRID:CVCL_VQ85) generated from prostate tumour from Ctnnb1pcex3(Δ)/+Ptenpc-/+

growth_protocol: P1 and P2 cell lines (RRID:CVCL_VQ82; RRID:CVCL_VQ83) were derived from prostate tumours from Ptenpc-/- mice at 14 and 13 months, respectively. CP1 and CP2 cell lines (RRID:CVCL_VQ84; RRID:CVCL_VQ85) were derived from prostate tumours from Ctnnb1pc(ex3)Δ/+ Ptenpc+/- mice at 6 and 8 months, respectively. P1, P2, CP1 and CP2 cell lines were derived using following the following:- Briefly, the tumour fragments were collected and finely chopped before incubation with collagenase (1mg/ml) in antibiotic and glutamine containing DMEM medium with 20% serum for up to 2 hrs at 370C water bath with intermittent shaking. Following centrifugation, the tumour tissues were suspended in 2 ml Trypsin/0.5% EDTA for 5 minutes at 37°C. Trypsin was inactivated following the addition of 3 ml DMEM containing 500 U DNase I and the cell suspension passed through an 18G followed by 20G needle, five times each followed by filtration. The washed and pelleted cells were mixed with Matrigel in a 2:3 (cells: Matrigel) ratio.  Tumour spheroids were cultured at 37°C for 7-10 days in penicillin, streptomycin, gentamycin and glutamine containing DMEM medium with 20% FBS with Matrigel before passaging and expanding. To obtained stable cell lines for further genetic manipulations and in vivo transplantation experiments, the cells were expanded in 3D culture until passage 4 and then expanded in 2D culture for use in experiments. In 2D, the cells were maintained in glutamine containing DMEM with 10 % FBS without antibiotics.

extract_protocol:
Qiagen RNA kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For orthograft experiments, approximately 5 million murine prostate cancer cells were injected in one of the anterior prostate lobes of male CD-1 Nude mice

value: CD-1 Nude

value: prostate orthograft generated from CP2 cells (RRID:CVCL_VQ85)


title: gIPMN-04

value: Pancreas


title: S19CP2

description: prostate orthograft tumour


title: S16CP2

description: prostate orthograft tumour


title: gIPMN-01


title: PanIN-H04

value: PanIN


title: S13CP1

description: prostate orthograft tumour


title: gIPMN-02


title: 0.05mGyD1/ reference male mouse5-S


title: PanIN-H03

value: high


title: reference male mouse5/ 0.05mGyD2-S


title: 0.05mGyJ3/ reference male mouse14


title: 0.05mGyDF/ reference male mouse5-S


title: reference male mouse14/ 0.05mGyJ3


title: reference male mouse14/ 0.05mGyJF


title: 0.05mGyD2/ reference male mouse5-S


title: reference male mouse5/ 0.05mGyD1-S


title: reference male mouse5/ 0.05mGyDM-S


title: PanIN-H02


title: reference male mouse14/ 0.05mGyJ2


title: 0.05mGyJ2/ reference male mouse14


title: reference male mouse5/ 0.05mGyDF-S


title: 0.05mGyJ1/ reference male mouse14


title: S3CP1

description: prostate orthograft tumour

source_name: CP1 cells (RRID:CVCL_VQ84) generated from prostate tumour from Ctnnb1pcex3(Δ)/+ Ptenpc-/+

value: prostate orthograft generated from CP1 cells (RRID:CVCL_VQ84)


title: reference male mouse5/ 0.05mGyH7


title: reference male mouse14/ 0.05mGyJ1


title: 0.05mGyJF/ reference male mouse14


title: 0.05mGyDM/ reference male mouse5-S


title: 9- KO lit 26 emb 1

city: Irvine

first: Jamison

last: Nourse

state: California

address: 845 Health Sciences Rd.

department: Physiology and Biophysics

institute: University of California, Irvine

data_processing:
Open source software will be used including FASTQC, Trimmomatic, Hisat2, Samtools and featureCounts.
Raw reads were trimmed using quality threshold of 15 and Truseq adapter sequence, trimmed reads shorter than 20-bp were discarded.
Reference genome sequence mm10 and its transcriptome annotation were collected and indexed for mapping.
Gene expression level was quantified using featureCount for raw counts.
Statistical comparison was made using DESeq2 to obtain Differential gene expression data
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample, Differential Gene Expression analysis (csv file), Sample Sequence variance graph (PNG file)

source_name: E10.5 brain

extract_protocol:
Brains were removed, flash frozen on dry ice, and total RNA was harvested using Biorad Aurum RNA isolation kit.
RNA libraries were prepared for sequencing using Illumina TruSeq mRNA stranded protocol. The input quantity for total RNA within the recommended range and mRNA was enriched using oligo dT magnetic beads.Sequenced using paired end 150 cycles chemistry on the NovaSeq 6000

tag: age

value: Piezo1 KO


title: 0.05mGyH7/ reference male mouse5


title: 0.05mGyJM/ reference male mouse14


title: 0.05mGyH6/ reference male mouse5


title: PanIN-H01


title: S1CP1

description: prostate orthograft tumour


title: 10- KO lit 26 emb 5


title: S2CP1

description: prostate orthograft tumour


title: reference male mouse14/ 0.05mGyJM


title: reference male mouse5/ 0.05mGyH6


title: PanIN-08

value: low


title: 8- KO lit 15 emb 4


title: PanIN-07


title: 6-KO lit 15 emb 2


title: S20P1

description: prostate orthograft tumour

source_name: P1 cells (RRID:CVCL_VQ82) generate from prostate tumour from Ptenpc-/- mouse

value: prostate orthograft generated from P1 cells (RRID:CVCL_VQ82)


title: 5-KO lit 15 emb 1


title: 0.05mGyH5/ reference male mouse5


title: PanIN-06


title: 7- KO lit 15 emb 3


title: S19P1

description: prostate orthograft tumour


title: S21P1

description: prostate orthograft tumour


title: PanIN-05


title: 4-KO lit 14 emb 3


title: reference male mouse5/ 0.05mGyH5


title: S8

source_name: Distal metastases (diaphragm metastases)

growth_protocol: RNA was extracted from the frozen localised prostate tumour (primary prostate tumours), proximal (epididymal fat) and distal (lung) metastases from Ctnnb1pc(ex3)Δ/+ Ptenpc+/- (n=3 matched; ~9-10 months)

value: Ctnnb1pc(ex3)delta/+ Ptenpc+/-


title: S7

value: Distal metastases (diaphragm metastases)


title: 0.05mGyH4/ reference male mouse5


title: 3-KO lit 14 emb 2


title: PanIN-04


title: S6

source_name: Proximal metastases (epididymal fat metastases)


title: NG-03

value: bulk acinus


title: 6-WT Lit 27 emb 3


title: S9


title: S5

value: Proximal metastases (epididymal fat metastases)


title: PanIN-03


title: NG-02


title: NG-01


title: 4-WT Lit 16 emb 5

value: brain


title: 2 KO lit14 emb 1


title: 5-WT Lit 26 emb 6


title: S3

source_name: Primary prostate tumour

value: Primary prostate tumour


title: S4


title: reference male mouse5/ 0.05mGyH3

value: tail


title: 0.05mGyH1/ reference male mouse5


title: Gastric organoid-derived monolayer infected (C10)

description: mRNA

value: 2D gastric organoid-derived monolayer

value: Epithelial gastric cells

value: infected with H. pylori

value: Healthy


title: 3 -WT Lit 15 emb 5

value: WT


title: reference male mouse5/ 0.05mGyH2


title: 0.05mGyH3/ reference male mouse5


title: S2


title: 2-WT Lit 13 WT 5


title: S1


title: reference male mouse5/ 0.05mGyH1


title: 1-WT Lit 13 WT 1


title: 0.05mGyH2/ reference male mouse5


title: co_ment_3

status: Public on Aug 19 2022

city: Beijing

first: Yubo

last: Ma

address: Xicheng street

institute: peking university first hospital

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep  (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default  parameters.
 Clean reads were separately aligned to reference genome with orientation mode  using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml)[1] software. The mapped reads of  each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml?  t=example) in a reference-based approach

organism: Trichophyton mentagrophytes

source_name: fungi

growth_protocol: The experiment was carried out for 24 h in a humidified incubator maintained at 37 ºC .

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent  for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was  removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser  (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA  sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to  construct sequencing library
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit  from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated  according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation  buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript  double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina).Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition  according to Illumina’s library construction protocol. Libraries were size selected for cDNA target  fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion  DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq  sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 ×  150bp read length).

treatment_protocol: For co-culture assays, a ratio of 2.5×105 cells/mL of keratinocytes to 2.5×105 conidia/mL of T. mentagrophytes, T. interdigitale, and T. tonsurans solution were used (MOI=1).

value: co-culture with HaCat cell for 24h

tag: moi


title: ment_3


title: reference male mouse5/ 0.05mGyHF


title: 0.05mGyHF/ reference male mouse5


title: co_ment_2


title: co_ton_3

organism: Trichophyton tonsurans


title: ment_2


title: ment_1


title: co_ton_2


title: co_ment_1


title: co_ton_1


title: ton_2


title: ton_1


title: Gastric organoid-derived monolayer naïve (C8)

description: mRNA

value: untreated (naive)


title: 0.05mGyHM/ reference male mouse5


title: co_int_2

organism: Trichophyton interdigitale


title: co_int_1


title: co_int_3


title: reference male mouse5/ 0.05mGyHM


title: int_2


title: int_1


title: int_3


title: S17

city: Grange, Dunsany

first: Stephanie

last: O'Donoghue

state: Meath

address: Animal Bioscience Research Centre

department: Animal & Bioscience Research Department

country: Ireland

institute: Teagasc

data_processing:
The 3' end of the sequence reads were trimmed for Illumina adapters, low quality reads (quality score <  20), ambiguous nucleotides, and poly-G artefacts resulting from the NextSeq’s two-colour chemistry, using CutAdapt (version 1.18).
The cleaned sequence reads were evaluated for quality using FastQC.
Reads were aligned to the ARS-UCD1.2 bovine reference genome and read counts were generated by converting aligned reads into counts per gene using the Spliced Transcripts Alignment to a Reference (STAR) aligner (version 2.6.1b)
Assembly: ARS-UCD1.2
Supplementary files format and content: TXT file of raw counts table of sequenced reads

organism: Bos taurus

source_name: whole blood

extract_protocol:
Total RNA was extracted using the Tempus™ Spin RNA Isolation Kit (Bio-Sciences LTD, Dublin, Ireland), according to the manufacturer's instructions.
RNA-Seq library preparation was performed using the TruSeq stranded mRNA Kit (Illumina, San Diego, California, USA).

value: BoHV1 challenged

tag: breed

value: Holstein-Friesian

tag: shed

value: C


title: S14


title: S18


title: S13


title: S15


title: ton_3


title: S9

value: B


title: S12


title: S5

value: control

value: A


title: S6


title: S2


title: S1


title: S7


title: HaCat_T_tonsurans_3

source_name: cell

value: HaCat cell

value: co-culture with T. tonsurans for 24 h


title: S8


title: S16


title: S4


title: S3


title: HaCat_T_tonsurans_2


title: HaCat_1

value: untreated


title: HaCat_T_tonsurans_1

value: co-culture with T. tonsurans for 24h


title: HaCat_T_inter_2

value: co-culture with T. interdigitale for 24h


title: HaCat_T_ment_1

value: co-culture with T. mentagrohpytes for 24h


title: HaCat_T_inter_1


title: HaCat_T_inter_3


title: S11


title: PD1 Knock Out NK cells_384

city: Solna

first: Chris

middle: Andrew

last: Tibbitt

state: non-US

address: Biomedicum C7,, Tomtebodavägen 16

institute: KI

description:
SMART-SEQ2
SS2_20_019_expression_rpkms.tab
P9

data_processing:
RNA-seq reads were aligned to the NCBI Build 37 (UCSC mm9) of the mouse genome using TopHat (Trapnell et al., 2009). The resulting alignments were processed by Cufflinks to evaluate the expression of transcripts from RefSeq.
Assembly: mm10

source_name: MTAP1A tumor

extract_protocol:
The tumors were isolated, rapidly processed, stained for a panel of surface markers and single cell sorted within approximately 90 minutes of organ harvest. In total 382 NK cells were sorted directly into 2 ml lysis buffer using a BD Influx from pooled tumors from either 3 WT and 3 PD-1-/- KO mouse respectively.
SMART-Seq2 libraries were prepared using the method described in Picelli et al. (Picelli et al., 2013)

tag: tissue

value: MTAP1A tumor

tag: strain

value: tumor-infiltrating NK cells


title: S10

tag: treatment


title: HaCat_T_ment_2

value: co-culture with T. mentagrohpytes for 24 h


title: PD1 Knock Out NK cells_382

description:
SMART-SEQ2
SS2_20_019_expression_rpkms.tab
P7

tag: cell type

tag: genotype


title: PD1 Knock Out NK cells_381

description:
SMART-SEQ2
SS2_20_019_expression_rpkms.tab
P6