title: LNCaP_10uMEnza_6GyIR_rep4_batch2

city: Charlottesville

first: Thomas

middle: G

last: Scott

state: VA

address: 1340 Jefferson Park Ave, Pinn Hall 6225

department: Biochemistry and Molecular Genetics

institute: University of Virginia

library_source: other

data_processing:
Adapter trimming: cutadapt v1.8.1
UMI trimming and reverse complementing: seqtk v1.3
FASTQ deduplication: https://github.com/guertinlab/fqdedup v1.0.0
FASTQ pairing: fastq_pair v1.0
Alignment: bowtie2 v2.4.4
File manipulation: samtools v1.9
File manipulation: https://github.com/guertinlab/seqOutBias v1.3.1
All details and code: https://gioeli-lab.github.io/AR_IR_PRO-seq_analysis/Vignette.html
Assembly: hg38
Supplementary files format and content: Stranded bigWig counts files
Supplementary files format and content: Gene counts files
Library strategy: PRO-Seq

molecule: other

source_name: LNCaP

growth_protocol: LNCaP (RRID:CVCL_0395) cells (gift from Dr. L. W. K. Chung) were grown in DMEM:F12 (Invitrogen) with 5% non-heat inactivated serum (Gemini) and 1% Insulin-Transferrin-SeleniumEthanolamine (ITS) (ThermoFisher).

treatment_protocol: LNCaP cells were plated into 150 mm tissue-culture dishes at 4.2 x 10^6 cells, grown two days in the whole medium under standard growth conditions (37°C, 5% CO2) and then 1) DMSO (control) vehicle treated for 90 min; 2) DMSO vehicle treated for 30 min plus 6 Gy IR followed by 60 min incubation; 3) 10 µM Enzalutamide for 90 min; and 4) 10 µM Enzalutamide for 30 min followed by 6 Gy IR and incubated for 60 min.

value: LNCaP

value: 10uM Enzalutamide + 6Gy IR


title: LNCaP_10uMEnza_rep4_batch2

status: Public on Sep 18 2023

type: SRA

country: USA

organism: Homo sapiens

tag: cell line

tag: treatment

value: 10uM Enzalutamide + Mock


title: LNCaP_10uMEnza_6GyIR_rep3_batch2


title: Prj169-L3-31

city: East Lansing

first: Tim

last: Zacharewski

state: Michigan

address: 1129 Farm Ln

department: Biochemistry and Molecular Biology, Integrative Toxicological Sciences

institute: Michigan State University

description:
Adult male mouse dosed every 4 days for 28 days
31

library_source: transcriptomic

data_processing:
Read quality was assessed using FastQC v0.11.7 and adapter trimming was performed using Trimmomatic v0.39.
Alignment was performed with STAR v2.7.3a. Genome indices were created using Mus_musculus.GRCm39.dna.chromosome.fa and Mus_musculus.GRCm39.104.gtf.
Gene counts were determined using STAR v2.7.3a.
Assembly: mm10 (build 39)
Supplementary files format and content: Transformed counts were normalized using a semi-parametric approach (Eckel et al., 2004) and analyzed using an empirical Bayes method (Eckel et al., 2005).
Supplementary files format and content: Tab-delimited text files represent the number of aligned PE reads to each gene.

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Frozen liver (~100 mg) was homogenized in 1 mL of TriZOL with chrome-steel beads using a Mixer Mill 300 (Life Sciences, Carlsbad, CA) for 4 minutes. Following, total RNA was extracted per the manufacturer’s instructions with an additional 5:1 phenol:chloroform extraction step (Sigma Aldrich, St. Louis, MO). RNA purity (260/280 ratio) and concentration (ng/µL) were assessed with a NanoDrop 1000 spectrophotometer. RNA quality was determined using an Agilent 2100 Bioanalyzer. All RNA samples had RNA integrity numbers (RINs) ≥7.
Library preparation was performed using a Ultra2 NEB RNA kit.

treatment_protocol: Mice were orally gavaged with TCDD in sesame oil vehicle every 4 days for 28 days at 28°C.

tag: tissue

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

tag: Sex

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

tag: vehicle substance

value: sesame oil

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

value: milliliter

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

value: oral gavage

tag: administration route ontology

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

value: Carbon dioxide euthanasia

tag: euthaniasia method ontology

tag: library kit

value: NEBNext Ultra II


title: GC, no light, +NU-7441, +antibody, rep2

city: Austin

first: Tanya

middle: T.

last: Paull

state: TX

address: 2500 Speedway MBB 2.448

department: Molecular Biosciences

institute: Univ. of Texas at Austin

library_source: genomic

data_processing:
DNA-PKcs GLASS-ChIP and pellet-ChIP :Raw data was pre-processed with BedTools fastp, mapped with BWA-MEM, duplicates were removed with SAMTools RmDup, and peaks called with MACS2. AsiSI-associated data was processed using genome build Hg19; Cas9-associated data was processed using genome build Hg38. Mre11 ChIP data:
For Glass-ChIP, no-antibody sample libraries were used as controls whereas for pellet-ChIP, input DNA libraries were used as controls. body sample libraries were used as controls whereas for pellet-ChIP, input DNA libraries were used as controls.
Bedgraph output files from MACS2 were converted to bigwig files using ucsc-wigtobigwig (Version 357)
Assembly: all processed data files are Hg19 except files with 'light' in the name which are Hg38

molecule: genomic DNA

extract_protocol:
GLASS-ChIP assay   Human U2OS cells with inducible AsiSI15 were grown to 50-60% confluency in 150 mm dishes and treated with 600 nM 4-OHT for 4 h at 37°C. When used, 10 µM NU7441 was added 30 min. prior to 4-OHT addition. After 4-OHT treatment, cells were fixed with 1% formaldehyde for 7 min at RT with gentle rotation. Crosslinking was stopped by addition of 125 mM glycine for 5 min, washed twice with cold PBS, harvested, flash frozen in liquid nitrogen and stored at -80°C.   For the GLASS-ChIP assay, we modified a standard protocol (Abcam) with a gentle lysis procedure and minimal, low-level sonication to rupture cells without extensive DNA damage as previously described16. The formaldehyde fixed cells were thawed at RT for 5 min, resuspended in RIPA buffer (50 mM Tris-HCl pH8.0, 150 mM NaCl, 2 mM EDTA pH8.0, 1% NP-40, 0.5% Sodium Deoxycholate, 0.1% SDS) with 1x protease inhibitors (Pierce #A32955) and sonicated using a Cell Ruptor at low power, for 10 sec followed by 10 pulses after a 20 sec interval. Cell lysates were then centrifuged at 3000 rpm for 3 min at RT to remove the bulk of chromatin. The supernatant was then incubated with 1.6 µg of anti-DNA-PKcs pS2056 antibodies (abcam 124918) overnight at 4°C, followed by incubation with 25 µl Protein A/G magnetic beads (Pierce) at RT for 2 h. Beads were then washed sequentially  once in low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), once in high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl), once in LiCl wash buffer (0.25 M LiCl, 1% NP-40, 1% Sodium Deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0).  Beads were then resuspended in TE buffer (10 mM Tris pH 8.0, 0.1 mM EDTA) and transferred to a fresh tube and finally eluted with 100 µl elution buffer (1% SDS, 100mM NaHCO3). Crosslinks were reverted for the elutions (65°C for 24 h) and DNA was purified with a Qiagen Nucleotide Clean up kit. DNA fragments <300 bp from ChIP elutions were separated by pulling down larger fragments using paramagnetic Ampure XP beads: 65 µl of Ampure XP beads were added to the uncrosslinked ChIP elution and mixed thoroughly. After 10 min incubation at RT, beads were isolated using a magnet. The supernatant was collected and 25 µl of fresh Ampure XP beads were added and mixed thoroughly. After 10 min at RT, beads were separated and the supernatant was purified using Qiagen Nucleotide Clean up kit. At the final step DNA was eluted in 60 µl of elution buffer (TE). To monitor the Mre11 nuclease dependence, we treated the human U2OS cells expressing inducible AsiSI with 10 µM NU7441, 100 µM PFM01 or PFM39 and 600 nM 4-OHT simultaneously for 1 hour at 37°C before harvesting cells.   Pellet ChIP  For DNA-PKcs pellet ChIP, the protocol for GLASS-ChIP was followed through the step where chromatin is isolated. The chromatin fraction was then resuspended in 2.2 ml RIPA buffer and was fragmented using a Diagenode Bioruptor on high setting for 30 min. with 10 sec on, 10 sec off. After removal of debris by centrifuging at 800 g for 3 min., the supernatant was incubated with 1.6 µg of anti-DNA-PKcs pS2056 antibodies (abcam 124918) overnight at 4°C, followed by incubation with 25 µl Protein A/G magnetic beads (Pierce) at RT for 2 h. The rest of the procedure was identical to GLASS-ChIP above except that the AMPure bead size selection was not performed.
For DNA-PKcs GLASS-ChIP and pellet-ChIP  sequencing libraries, the eluted DNA was used to make sequencing libraries using the NEBNext Ultra or Ultra II DNA Library Prep Kit for Illumina (NEB) with NEBNext Multiplex dual index primers.
DNA-PKcs GLASS-ChIP and pellet-ChIP: NovaSeq SP platform with PE150

tag: cell line

tag: cell type

value: embryonic kidney

tag: chip antibody

value: phospho-DNA-PKcs(S2056)(Abcam ab124918)

tag: treatment

value: no light, +antibody


title: LNCaP_10uMEnza_rep3_batch2

value: LNCaP

value: 10uM Enzalutamide + Mock


title: GC, no light, +NU-7441, +antibody, rep1


title: NAA35.T18B.br3

city: Toronto

first: Jason

last: Moffat

state: Ontario

address: 686 Bay Street

department: Genetics and Genome Biology

country: Canada

institute: Hospital for Sick Children

description: gDNA amplicon

data_processing:
FASTQ files were pre-processed to extract Cas9 guide sequence using a bespoke Perl script.
The Cas9 guide sequence was extracted from read1 files as the 20 bases preceeding 'CGGTGTTT'.
Trimmed FASTQ files were then aligned to the TKOv3 FASTA file using bowtie v0.12.1 using the following command line parameters:   -p 16 -v 3 -l 18 --chunkmbs 256 -t <library_file> --un unmapped.fastq --al mapped.fastq -1 <trimmed_read1.fastq> aligned.sam
The number of reads aligning to each guide sequence was enumerated for each aligned .sam file, and alignment statistics were recorded.  Guide IDs and counts were written to individual count files.
All individual count files were merged along with library annotations in R.
Supplementary files format and content: tab-delimited read count matrix

source_name: haematopoeitic

growth_protocol: Cells were cultured in IMDM media supplemented with 10% FBS and 1% Penicillin/Streptomycin and serially passaged for up to 18 days (propagated in biological triplicates).  Aliquots were pelleted at indicated timepoints for gDNA extraction and quantification by next-generation sequencing.

extract_protocol:
Genomic DNA was extracted using the Wizard Genomic DNA Purification kit (Promega) according to manufacturer’s instructions
For each sample, the gRNA cassette was amplified directly from genomic DNA using primers harboring Illumina TruSeq adaptors with i5 and i7 barcodes. The resulting sequencing libraries were pooled and gel-purified.
CRISPRseq

tag: tissue

value: haematopoeitic

value: chronic myelogenous leukemia-derived

tag: genotype

value: NAA35 1bp del (HAP1) (HZGHC006636c011)

value: TKOv3 (lentiCRISPRv2)


title: Prj169-L3-30

description:
Adult male mouse dosed every 4 days for 28 days
30

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

tag: Sex

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

tag: vehicle substance

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route


title: Prj169-L3-29

description:
Adult male mouse dosed every 4 days for 28 days
29

tag: tissue

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

tag: Sex

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

tag: administration route ontology

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

value: Carbon dioxide euthanasia

tag: euthaniasia method ontology

tag: library kit

value: NEBNext Ultra II


title: LNCaP_6GyIR_rep4_batch2

tag: cell line

value: LNCaP

tag: treatment

value: 6Gy IR + Vehicle


title: Prj169-L3-28

description:
Adult male mouse dosed every 4 days for 28 days
28

tag: tissue

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

tag: Sex

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

tag: vehicle substance

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route


title: PC, plus 4-OHT, input

description: All processed data files are Hg19 except files with 'light' in the name which are Hg38

tag: cell line

tag: cell type

value: osteosarcoma

tag: chip antibody

tag: treatment

value: plus 4-OHT, input


title: LNCaP_6GyIR_rep3_batch2


title: PC, plus 4-OHT, +antibody

value: phospho-DNA-PKcs(S2056)(Abcam ab124918)

value: plus 4-OHT, +antibody


title: NAA35.T0.br3

description: gDNA amplicon

tag: tissue

value: haematopoeitic

value: chronic myelogenous leukemia-derived

tag: genotype

value: NAA35 1bp del (HAP1) (HZGHC006636c011)

value: TKOv3 (lentiCRISPRv2)


title: NAA35.T18C.br2

description: gDNA amplicon


title: GSC-040815-C2

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: GSCs cultures in neurobasal medium

data_processing:
Illumina bcl2fastq v2.20.0.422 used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC hg19) using HiSAT2 default settings. The aligned BAM files sorted (SAMTools) and then processed using FatureCounts to obtain the counts per gene
gene count measurements were obtained using FeatureCounts
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format generated by FeatureCounts. Seven (7) columns are: Geneid; Chr; Start; End; Strand; Length; bamFileName

source_name: Patient derived Glioma stem cells (GSC)- 040815

growth_protocol: GSC-040815  were cultured  as neurospheres in neurobasal medium supplemented with B27 serum-free supplement, EGF (20 ng/mL), bFGF (20 ng/mL), LIF (10 ng/mL) and heparin (5 µg/mL).

extract_protocol:
Total RNA from  vehicle (0.1% DMSO v/v) and  CIDD-0149897 treated cells were isolated using RNeasy mini kit (Qiagen). Illumina TruSeq RNA Sample preparation and sequencing was done using UT Health San Antonio sequencing core protocol.
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide

treatment_protocol: GSC-040815  were treated with vehicle (0.1% DMSO v/v) or  ERβ agonist (CIDD-0149897-20 µM) syntesized by Center for Innovative Drug Discovery-UTSA. GSCs were cultured as neurospheres in neurobasal medium supplemented with B27 serum-free supplement, EGF (20 ng/mL), bFGF (20 ng/mL), LIF (10 ng/mL) and heparin (5 µg/mL) for 48 hrs. After 48 hrs of treatment cell pellet were collected and used for RNA isolation.

value: Control


title: Prj169-L3-26

description:
Adult male mouse dosed every 4 days for 28 days
26

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

tag: Sex

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

tag: administration route ontology

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

value: Carbon dioxide euthanasia

tag: euthaniasia method ontology

tag: library kit

value: NEBNext Ultra II


title: LNCaP_rep4_batch2

tag: cell line

value: LNCaP

tag: treatment

value: Mock + Vehicle


title: PC, no 4-OHT, input

tag: cell type

value: osteosarcoma

tag: chip antibody

value: no 4-OHT, input


title: LNCaP_rep3_batch2


title: NAA35.T18C.br3

description: gDNA amplicon

tag: tissue

value: haematopoeitic

value: chronic myelogenous leukemia-derived

tag: genotype

value: NAA35 1bp del (HAP1) (HZGHC006636c011)

value: TKOv3 (lentiCRISPRv2)


title: NAA35.T18B.br2

description: gDNA amplicon


title: PC, no 4-OHT, +antibody

value: phospho-DNA-PKcs(S2056)(Abcam ab124918)

value: no 4-OHT, +antibody


title: Prj169-L3-24

description:
Adult male mouse dosed every 4 days for 28 days
24

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

tag: Sex

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

tag: vehicle substance

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route


title: PC, plus 4-OHT, +NU-7441, input

tag: cell line

tag: cell type

value: osteosarcoma

tag: chip antibody

tag: treatment

value: plus 4-OHT, +NU7441, input


title: Prj169-L3-23

description:
Adult male mouse dosed every 4 days for 28 days
23

tag: tissue

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

tag: Sex

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance purity

value: sesame oil

value: milliliter

value: oral gavage

tag: administration route ontology

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

value: Carbon dioxide euthanasia

tag: euthaniasia method ontology

tag: library kit

value: NEBNext Ultra II


title: NAA35.T0.br2

description: gDNA amplicon

tag: tissue

value: haematopoeitic

tag: cell line

tag: cell type

value: chronic myelogenous leukemia-derived

tag: genotype

value: NAA35 1bp del (HAP1) (HZGHC006636c011)

tag: treatment

value: TKOv3 (lentiCRISPRv2)


title: Prj169-L3-21

description:
Adult male mouse dosed every 4 days for 28 days
21

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

tag: Sex

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance lot

tag: toxic substance storage

tag: vehicle substance

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route


title: NAA35.T18A.br3

description: gDNA amplicon

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: LNCaP_6GyIR_rep1t2_batch1

value: LNCaP

value: 6Gy IR


title: PC, plus 4-OHT, +NU-7441, +antibody

value: osteosarcoma

tag: chip antibody

value: phospho-DNA-PKcs(S2056)(Abcam ab124918)

value: plus 4-OHT, +NU7441, +antibody


title: NAA35.T18C.br1

description: gDNA amplicon

value: haematopoeitic

value: chronic myelogenous leukemia-derived

value: NAA35 1bp del (HAP1) (HZGHC006636c011)


title: PC, no 4-OHT, +NU-7441, input

value: no 4-OHT, +NU7441, input


title: NAA35.T18B.br1

description: gDNA amplicon

value: TKOv3 (lentiCRISPRv2)


title: Prj169-L3-19

description:
Adult male mouse dosed every 4 days for 28 days
19

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

tag: Sex

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: feed name

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

tag: administration route ontology

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

value: Carbon dioxide euthanasia

tag: euthaniasia method ontology

tag: library kit

value: NEBNext Ultra II


title: Prj169-L3-27

description:
Adult male mouse dosed every 4 days for 28 days
27

tag: tissue

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

tag: Sex

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: vehicle substance

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route


title: Prj169-L3-18

description:
Adult male mouse dosed every 4 days for 28 days
18

tag: tissue

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

tag: Sex

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

tag: administration route ontology

tag: dose

tag: dose unit

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

tag: euthaniasia method ontology

tag: library kit


title: NAA35.T18A.br1

description: gDNA amplicon

tag: tissue

value: haematopoeitic

tag: cell line

tag: cell type

value: chronic myelogenous leukemia-derived

tag: genotype

value: NAA35 1bp del (HAP1) (HZGHC006636c011)

tag: treatment

value: TKOv3 (lentiCRISPRv2)


title: NAA35.T18A.br2

description: gDNA amplicon


title: NAA35.T0.br1

description: gDNA amplicon


title: LNCaP_rep2t2_batch1

value: LNCaP

value: Mock


title: Prj169-L3-17

description:
Adult male mouse dosed every 4 days for 28 days
17

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

tag: Sex

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: feed name

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

value: Room temperature

tag: vehicle substance

value: sesame oil

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

value: milliliter

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

value: oral gavage

value: microgram per kilogram

value: Carbon dioxide euthanasia

value: NEBNext Ultra II


title: LNCaP_rep2t1_batch1

tag: cell line

tag: treatment


title: GC, plus 4-OHT, -antibody, rep2

tag: cell type

value: osteosarcoma

tag: chip antibody

value: plus 4-OHT, -antibody


title: LNCaP_6GyIR_rep2t1_batch1

value: 6Gy IR


title: LNCaP_rep1t2_batch1


title: Prj169-L3-16

description:
Adult male mouse dosed every 4 days for 28 days
16

tag: tissue

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

tag: Sex

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance storage

tag: administration route ontology

tag: dose

tag: dose unit

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

tag: euthaniasia method ontology

tag: library kit


title: LNCaP_rep1t1_batch1

tag: cell line

value: LNCaP

tag: treatment

value: Mock


title: cKO14 hypothalamus, control, week 5

city: Safed

first: Evan

last: Elliott

address: Henrietta Szold Street, P.O. Box 1589

department: The Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

data_processing:
Base-calling done with the bcl2fastq software using default parameters.
Data filtering included using 'fastqc' (0.11.9) for base quality evaluation and 'fastq-screen' (0.14.0) for contamination evaluation. Additionally, Trimming was also done automatically by the sequencing machine.
read alignment was made with the 'STAR' aligner tool v.2.7.9a using the "--outFilterMultimapNmax 10"  flag
for general statistics samtools and qualimap used
for counting used by the Subread 'featurecounts'

source_name: hypothalamus

growth_protocol: 8 week old mice

extract_protocol:
RNA havrasted using Qiagen mini kit (cat# 74104), purification of total RNA from animal tissues according to manufaturer's
RNA libraries were made using mRNS isolation (NEB protocol E7490), than NEBNext Ultra II RNA Library prep (E7770L) according manufacturer's protocol

treatment_protocol: wild type and knockout

tag: tissue

value: hypothalamus

tag: Sex

value: male

tag: time

value: 5 weeks after tamoxifen treatment

tag: genotype

value: floxed Smc3 and Camk2a-cre/ERT2+ (Cre+)

value: Tamoxifen


title: GC, plus 4-OHT, +antibody, rep2

tag: cell type

value: osteosarcoma

tag: chip antibody

value: phospho-DNA-PKcs(S2056)(Abcam ab124918)

value: plus 4-OHT, +antibody


title: cKO13 hypothalamus, control, week 5


title: LNCaP_6GyIR_rep1t1_batch1

value: 6Gy IR


title: GC, plus 4-OHT, +antibody, rep1


title: LNCaP_6GyIR_rep2t2_batch1


title: PC, no 4-OHT, +NU-7441, +antibody

value: no 4-OHT, +NU7441, +antibody


title: Prj169-L3-14

description:
Adult male mouse dosed every 4 days for 28 days
14

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: feed name

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

tag: vehicle substance

value: sesame oil

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

value: milliliter

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

value: oral gavage

tag: administration route ontology

tag: dose

value: microgram per kilogram

value: Carbon dioxide euthanasia

value: NEBNext Ultra II


title: cKO12 hypothalamus, control, week 5

tag: tissue

value: hypothalamus

tag: Sex

value: male

tag: time

value: 5 weeks after tamoxifen treatment

tag: genotype

value: floxed Smc3 and Camk2a-cre/ERT2+ (Cre+)

tag: treatment

value: Tamoxifen


title: Prj169-L3-15

description:
Adult male mouse dosed every 4 days for 28 days
15

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

tag: vehicle substance

tag: dose unit

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

tag: euthaniasia method ontology

tag: library kit


title: Prj169-L3-13

description:
Adult male mouse dosed every 4 days for 28 days
13

tag: tissue

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

tag: Sex

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: feed name

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

value: Accustandard

value: Room temperature

value: sesame oil

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

value: milliliter

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

value: oral gavage

tag: administration route ontology

tag: dose

value: microgram per kilogram


title: cKO9 hypothalamus, control, week 5

tag: tissue

value: hypothalamus

tag: Sex

value: male

tag: time

value: 5 weeks after tamoxifen treatment

tag: genotype

value: floxed Smc3 and Camk2a-cre/ERT2+ (Cre+)

tag: treatment

value: Tamoxifen


title: Parental_rep2

city: Kumamoto

first: Mitsuhiro

last: Endoh

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

department: Institute of Molecular Embryology and Genetics (IMEG)

country: Japan

institute: Kumamoto University

data_processing:
Adaptor trimming and QC were done using Trim galore (v0.6.6).
Mapping of the trimmed reads on the reference genome was done using STAR (v2.7.8a).
Expression quantification was done using rsem-calculate-expression (RSEM v1.3.3).
Differentially expressed gene (DEG) analysis was done using RNAseqChef (Etoh K et al., 2023)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: tab-delimited text file includes TPM values for each sample.

growth_protocol: ES cells were cultured in GMEM (Wako) supplemented with  10% FCS, 1× sodium pyruvate (Nacalai), 1× NEAA (Nacalai), 10–4 M 2-mercaptoethanol (Nacalai), and leukemia inhibitory factor (homemade) on a gelatin-coated dish.

extract_protocol:
Total RNA was extracted using the QuickGene RNA cultured cell kit S (Kurabo).
Sequencing libraries were prepared using the TruSeq® Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: In the EB5 cell line used as the parental line, only the Zfp352 gene or both Zfp352/353 genes were deleted using the CRISPR-Cas9 method.

tag: cell line

tag: cell type

value: embryonic stem cells

value: Parental


title: Parental_rep3


title: cKO8 hypothalamus, control, week 5


title: GC, no 4-OHT, +antibody, rep2

value: osteosarcoma

tag: chip antibody

value: phospho-DNA-PKcs(S2056)(Abcam ab124918)

value: no 4-OHT, +antibody


title: Prj169-L3-11

description:
Adult male mouse dosed every 4 days for 28 days
11

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

tag: vehicle substance

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

tag: dose unit

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

value: Carbon dioxide euthanasia

tag: euthaniasia method ontology

tag: library kit

value: NEBNext Ultra II


title: GC, no 4-OHT, +antibody, rep1

tag: cell line

tag: cell type

value: osteosarcoma

tag: chip antibody

tag: treatment


title: Prj169-L3-12

description:
Adult male mouse dosed every 4 days for 28 days
12

tag: tissue

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

tag: Sex

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

value: sesame oil

value: milliliter

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

value: oral gavage

tag: administration route ontology

tag: dose

value: microgram per kilogram


title: Zfp352-KO_rep3

tag: cell line

tag: cell type

value: embryonic stem cells

tag: genotype


title: GC, no 4-OHT, -antibody, rep1

tag: chip antibody

tag: treatment

value: no 4-OHT, -antibody


title: Prj169-L3-10

description:
Adult male mouse dosed every 4 days for 28 days
10

tag: tissue

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

tag: Sex

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: vehicle substance

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

tag: dose unit

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

tag: euthaniasia method ontology

tag: library kit


title: Wt15 hypothalamus, control, week 5

tag: tissue

value: hypothalamus

tag: Sex

value: male

tag: time

value: 5 weeks after tamoxifen treatment

tag: genotype

value: floxed Smc3 and Camk2a-cre/ERT2- (Cre-)

tag: treatment

value: Tamoxifen


title: Zfp352-KO_rep2

tag: cell line

tag: cell type


title: GC, plus 4-OHT, -antibody, rep1

value: osteosarcoma

tag: chip antibody

value: plus 4-OHT, -antibody


title: Zfp352-KO_rep1


title: Prj169-L3-09

description: Adult male mouse dosed every 4 days for 28 days

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

tag: vehicle substance

value: sesame oil

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

value: milliliter

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

value: oral gavage

tag: administration route ontology

tag: dose

value: microgram per kilogram

value: Carbon dioxide euthanasia

value: NEBNext Ultra II


title: Parental_rep1

tag: cell line

tag: cell type

value: embryonic stem cells

tag: genotype

value: Parental


title: GC, plus 4-OHT, +NU-7441, -antibody, rep1

description: All processed data files are Hg19 except files with 'light' in the name which are Hg38

value: osteosarcoma

tag: chip antibody

tag: treatment

value: plus 4-OHT, + NU7441, -antibody


title: Wt7 hypothalamus, control, week 5

tag: tissue

value: hypothalamus

tag: Sex

value: male

tag: time

value: 5 weeks after tamoxifen treatment

value: floxed Smc3 and Camk2a-cre/ERT2- (Cre-)

value: Tamoxifen


title: Zfp352/Zfp353-DKO_rep3


title: Prj169-L3-08

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

tag: vehicle substance

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

tag: dose unit

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

tag: euthaniasia method ontology

tag: library kit


title: GC, no 4-OHT, -antibody, rep2

tag: cell line

tag: cell type

value: osteosarcoma

tag: chip antibody

tag: treatment

value: no 4-OHT, -antibody


title: Zfp352/Zfp353-DKO_rep2

value: embryonic stem cells

tag: genotype


title: Wt6 hypothalamus, control, week 5

tag: tissue

value: hypothalamus

tag: Sex

value: male

tag: time

value: 5 weeks after tamoxifen treatment

value: floxed Smc3 and Camk2a-cre/ERT2- (Cre-)

value: Tamoxifen


title: GC, plus 4-OHT, +NU-7441, +antibody, rep1

value: phospho-DNA-PKcs(S2056)(Abcam ab124918)

value: plus 4-OHT, + NU7441, +antibody


title: Wt5 hypothalamus, control, week 5


title: Zfp352/Zfp353-DKO_rep1


title: GC, no 4-OHT, +NU-7441, +antibody, rep2

value: no 4-OHT, +NU7441, +antibody


title: Prj169-L3-07

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

tag: vehicle substance

value: sesame oil

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

value: milliliter

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

value: oral gavage

tag: administration route ontology

tag: dose

value: microgram per kilogram

value: Carbon dioxide euthanasia

value: NEBNext Ultra II


title: Wt11 hypothalamus, control, week 5

tag: tissue

value: hypothalamus

tag: Sex

value: male

tag: time

value: 5 weeks after tamoxifen treatment

tag: genotype

value: floxed Smc3 and Camk2a-cre/ERT2- (Cre-)

tag: treatment

value: Tamoxifen


title: Input_H3K27me3_rep2

city: Durham

first: Bradley

last: Goldstein

state: NC

address: 203 Research Dr

department: Head and Neck Surgery & Communication Sciences

institute: Duke University

data_processing:
ChIP-Seq data was processed using the fastp toolkit to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads and reserving reads 20nt or longer for further analysis
Reads were mapped to the GRCm38 mouse genome assembly (mm10) using the bowtie alignment tool, keeping those alignments mapping to a single genomic location in. Amplification artifacts were removed using the Picard toolkit.
Regions of enrichment were called using the MACS2 peak calling algorithm with a q value cutoff of 0.1 for broad regions marked by histone markers. Input files were used as ChIP-seq control files correspondingly: H3K27me3_rep1: Input_6632-S1; H3K27me3_rep2: Input_6632-S6; H3K27ac_rep1; Input; and H3K27ac_rep2: Input_6632-S1
Assembly: GRCm38 mouse assembly
Supplementary files format and content: bigwig
Supplementary files format and content: bed

source_name: Olfactory epithelium

extract_protocol:
Olfactory tissue was obtained from adult wild-type mice euthanized 7-10 days following methimazole lesion by decapitation after deep anesthesia, and olfactory mucosa was dissociated in an enzyme cocktail (collagenase, Dispase and DNase I in HBSS for 15 min, followed by 3 min with 0.125% trypsin with gentle trituration. Cells from 3 mice were pooled per ChIP replicate, and GBCs were purified from the cell suspension using APC-conjugated antibody to c-Kit for 15 minutes and then APC magnetic selection. Cells were crosslinked in 1% formaldehyde for 10 minutes at room temperature.Cells were lylsed and homogenized, and a Bioruptor PIco was used to shear chromatin. Chromatin was incubated with antibodies (30 μg chromatin and 4 μg of antibody) at 4°C overnight.
NEBNext Ultra II DNA Library Prep Kit for Illumina with at least 1 ng of ChIP genomic DNA was used as starting material for library prep following manufacturer instructions.

value: Olfactory epithelium

tag: cell type

value: Globose basal cell

tag: chip antibody

value: Methimazole


title: GC, no 4-OHT, +NU-7441, -antibody, rep1

tag: cell line

value: osteosarcoma

value: no 4-OHT, + NU7441, -antibody


title: Prj169-L3-06

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

tag: vehicle substance

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

tag: dose unit

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

tag: euthaniasia method ontology

tag: library kit


title: Wt1 hypothalamus, control, week 5

tag: tissue

value: hypothalamus

tag: Sex

value: male

tag: time

value: 5 weeks after tamoxifen treatment

tag: genotype

value: floxed Smc3 and Camk2a-cre/ERT2- (Cre-)

tag: treatment

value: Tamoxifen


title: GC, plus 4-OHT, +NU-7441, +antibody, rep2

tag: cell line

tag: cell type

value: osteosarcoma

tag: chip antibody

value: phospho-DNA-PKcs(S2056)(Abcam ab124918)

value: plus 4-OHT, + NU7441, +antibody


title: GC, no 4-OHT, +NU-7441, +antibody, rep1

value: no 4-OHT, +NU7441, +antibody


title: Prj169-L3-04

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

tag: vehicle substance

value: sesame oil

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

value: milliliter

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

value: oral gavage

tag: administration route ontology

tag: dose

value: microgram per kilogram

value: Carbon dioxide euthanasia

value: NEBNext Ultra II


title: Prj169-L3-03

tag: tissue

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

tag: Sex

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

value: Room temperature

tag: dose unit

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

tag: euthaniasia method ontology

tag: library kit


title: MYC_RIPseq_INPUT

city: Guangzhou

first: shuang

last: deng

state: Guangdong

address: 651 Dongfeng East Road

country: China

institute: Sun Yat-sen University Cancer Center

data_processing:
Basecalls performed using CASAVA
Sequenced reads were cleaned for adaptor and low-quality sequence, then CLIP-seq reads were mapped to hg38 using Bowtie2, RNA-seq and RIP-seq reads using STAR.
Piranha was used for CLIP-seq peak calling,  RSEM was used for quantification.
bam file were transform into bigwig format using deepTools.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: PANC-1 cells

growth_protocol: PANC-1 cells were cultured in DMEM medium (Invitrogen) supplemented with 10% fetal bovine serum

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen).
Sequencing libraries for RNA-sesq were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB) and the library preparations were sequenced on an Illumina Hiseq platform. For c-Myc RIP-seq assays, the RNA from controls and RIPs was converted to cDNA for sequencing library construction and sequenced on Illumina NovaSeq 6000. SNIP1 CLIP-sequencing was performed on Illumina Hiseq4000.

treatment_protocol: We used the CRISPR interference system to construct MSAR-silencing PDAC cells named ‘MSAR-KD-1’ and ‘MSAR-KD-2’. For CRISPR interference, pLV-CMV-NLS-3× flag-dCas9-NLS-KRAB-T2A-Puro plasmid was used. Small guide RNA (sgRNA) targeting the transcription start site of MSAR or non-targeting control sgRNA was designed and subcloned into the pLV-hU6-sgRNA-hef1a-mNeongreen vector. Stable knockdown cells were generated by lentiviral infection and selection.

tag: cell line

tag: cell type

value: pancreas ductal adenocarcinoma cells

tag: treatment

value: input


title: Input_H3K26ac_rep1

tag: tissue

value: Olfactory epithelium

value: Globose basal cell

tag: chip antibody

value: Methimazole


title: Input_H3K27me3_rep1_H3K27ac_rep2


title: TaH24T

city: Nanjing

first: Xiaoxin

last: Duan

address: No.1 Weigang, Xuanwu District

institute: Nanjing Agricultural University

description: LiangXing66,China, winter wheat

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using HISAT2 v2.0.4 and paired-end clean reads were aligned to the reference genome using HISAT2(Langmead, B.et al) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set as default.
The mapped reads of each sample were assembled by StringTie (v1.3.3) (Mihaela Pertea.et al. 2016) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.
Genome_build: IWGSC 1.0, FASTA provided for TUCP and lncRNA on series record.
Supplementary_files_format_and_content: fpkm expression values

organism: Triticum aestivum

source_name: inoculated with water for 24 hours

growth_protocol: T. aestivum seeds were grown in a light incubator at 25 °C for two and a half days, under a photoperiod of 16 h light and 8 h dark, then the tips of the coleoptile were cut off quickly with aseptic scissors for F. graminearum inoculation.

extract_protocol:
RNA was extracted using Trizol reagent.
A total amount of 20 ng RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37° C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Coleoptiles were inoculated with 3 µL of conidia suspension (1.0 x 106 spores/mL) and then were returned into the incubator. After 12 and 24 hpi, the coleoptile inoculation sites about 3 mm were harvested. At the same time, coleoptiles treated with distilled water were collected as mock treatments. Once harvested, all samples were frozen in liquid nitrogen as quickly as possible and stored at -80 °C for RNA-Seq.

tag: cultivar

value: coleoptile

tag: inoculation status

value: inoculated with water

tag: time

value: 24 hours


title: Prj169-L3-02

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

tag: Sex

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

tag: vehicle substance

value: sesame oil

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

value: milliliter

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

value: oral gavage

tag: administration route ontology

tag: dose

value: microgram per kilogram

value: Carbon dioxide euthanasia


title: MYC_RIPseq_IP_rep1

tag: cell line

tag: cell type

value: pancreas ductal adenocarcinoma cells

tag: treatment

value: myc RIP-seq


title: TaF24T

description: LiangXing66,China, winter wheat

source_name: inoculated with Fusarium graminearum for 24 hours

tag: cultivar

tag: tissue

value: coleoptile

tag: inoculation status

value: inoculated with Fusarium graminearum

tag: time


title: TaH12T

description: LiangXing66,China, winter wheat

source_name: inoculated with water for 12 hours

value: inoculated with water

value: 12 hours


title: MYC_RIPseq_IP_rep2


title: Prj169-L3-01

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

tag: Sex

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

tag: vehicle substance

tag: vehicle substance ontology

tag: administration volume

tag: dose unit

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

tag: euthaniasia method ontology

tag: library kit

value: NEBNext Ultra II


title: H3K27ac_rep2

tag: tissue

value: Olfactory epithelium

tag: cell type

value: Globose basal cell

tag: chip antibody

value: H3K27ac (Abcam, ab4729)

tag: treatment

value: Methimazole


title: H3K27ac_rep1


title: TaF12T

description: LiangXing66,China, winter wheat

source_name: inoculated with Fusarium graminearum for 12 hours

tag: cultivar

value: coleoptile

tag: inoculation status

value: inoculated with Fusarium graminearum

tag: time


title: NC_RNAseq_rep2

molecule: polyA RNA

tag: cell line

value: pancreas ductal adenocarcinoma cells

value: non-targeting control


title: H3K27me3_rep2


title: SC78_10

city: Houston

first: Dhiraj

last: Kumar

address: 1881 East Road

department: Cancer Biology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
10X Genomics Cell Ranger v6.1.
Molecule info for each sample were generated using cell ranger pipeline.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: .h5: molecule info for each sample.

growth_protocol: 4T07-TGL cells and 4T1-TGL cells either with/without Malat1 were grown in DMEM/F12 medium.

extract_protocol:
4T1-TGL cells either with/without Malat1 were tail vein injected and CD45+ cells isolated by FACS for scRNA-seq. Additionally, 4T07-TGL WT or TBK1 KD cells were injected into BALBC mice through tail vein and lung CD45+ cells isolated by FACS for scRNA-seq.
Libraries were prepared according to Illumina's instructions for NovaSeq6000.
10X 3' next gem.

value: Breast Cancer Cell line

tag: strain

value: BALBC

tag: type

tag: isolated cell type

value: lung CD45+ cells


title: SC78_9


title: Rat Islets INGAP-PP 3

city: Autonomous CIty of Buenos Aires

first: Santiago

middle: Andres

last: Rodriguez Segui

address: Intendente Guiraldes s/n

country: Argentina

institute: IFIBYNE-UBA-CONICET

description: INGAP-PP treated rat pancreatic islets. Replicate 3.

data_processing:
RNA sequencing analyses were carried out following standard procedures with default parameters (Pertea et al., 2016).
Reads were aligned to the reference Rattus norvegicus genome Rn6 with HISAT2 version 2.1.0.
Sorting and convertion of SAM files to BAM: with SAMtools 1.9
Assemble and quantification expressed genes and transcripts to the curated rat reference genome annotation: with StringTie v2.0.4
Merging transcripts from all samples: with StrinTie –merge
Assembly: Transcript abundances estimation: with StringTie -eB
Supplementary files format and content: Gene abundance table in transcripts per million (TPM): with PyRanges
Supplementary files format and content: excel file with TPM quantification of all bulk RNA-seq samples
Supplementary files format and content: Curated rat reference de novo genome annotation used for Bulk RNAseq processing pipeline

organism: Rattus norvegicus

source_name: INGAP-PP treated rat islets

growth_protocol: For the bulk RNA-seq experiments, rat pancreatic islets were isolated and cultured in vitro in biological triplicates.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen, #74106) and eluted in 30 μl of RNase free water.
RNA-seq library construction and sequencing was carried out by following the manufacturer instructions (for HiSeq4000 pipeline) at the core facility of BGI.
RNA from triplicate INGAP-PP and untreated samples (10µg at concentration ≥80 ng/µl) was assessed for quality by Agilent bioanalyzer prior to library generation and sequencing.  All samples had RNA integrity number (RIN) > 9. Paired-end RNA-seq libraries were sequenced on Illumina HiSeq4000, obtaining >92 million 100bp reads.

treatment_protocol: Freshly isolated islets were cultured in RPMI-1640 media (Gibco BRL, Carlsbad, CA) pH 7.4, containing 2 g/L NaHCO3, 5% (v/v) fetal bovine serum, 1% penicillin/streptomycin, and 10 mM glucose at 37°C in a humid atmosphere (5% CO2/95% O2). Islets were cultured for 4 days in the absence (C, control) or presence of 50 μg/mL INGAP-PP.

value: INGAP-PP

value: islets


title: Wt4 hypothalamus, control, week 5

value: hypothalamus

tag: Sex

value: male

value: 5 weeks after tamoxifen treatment

tag: genotype

value: floxed Smc3 and Camk2a-cre/ERT2- (Cre-)

value: Tamoxifen


title: Sample_NGS257-4-WT_Even_Input

description: Input

data_processing:
Library strategy: ChIRP-seq
ChIRP-seq data was analyzed based on Chu C, Qu K, Zhong FL, Artandi SE, Chang HY. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell. 2011;44(4):667-678. doi:10.1016/j.molcel.2011.08.027
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig, wig, bedGraph, bed, txt

growth_protocol: Cells were grown in DMEM/F12 medium.

extract_protocol:
Lysates were clarified from sonicated nuclei and DNA-RNA complexes were isolated with Malat1 biotin labeled ASO.
Libraries were prepared according to Illumina's instructions for NextSeq500, 76nt SR.

value: Breast cancer cell line

value: WT


title: Rat Islets INGAP-PP 1

description: INGAP-PP treated rat pancreatic islets. Replicate 1.


title: SC78_6


title: Rat Islets INGAP-PP 2

description: INGAP-PP treated rat pancreatic islets. Replicate 2.


title: MSAR_KD2_rep2

value: MSAR silenced


title: NC_RNAseq_rep1


title: H3K27me3_rep1

value: Olfactory epithelium

value: Globose basal cell

value: Methimazole


title: MSAR_KD2_rep1

value: pancreas ductal adenocarcinoma cells


title: SC78_7

value: Breast Cancer Cell line


title: SC78_3

value: BALBC


title: Sample_NGS257-3-WT_Lacz_ChIRP


title: Rat Islets Control 3

description: Control rat pancreatic islets. Replicate 3.

source_name: Ctrl rat islets

value: Control


title: MSAR_KD1_rep2


title: SC78_2

value: lung CD45+ cells


title: Sample_NGS257-1-WT_Even_ChIRP


title: Sample_NGS257-2-WT_Odd_ChIRP


title: SC78_1

value: Lung

value: Naive CD45+ cells


title: Rat Islets Control 1

description: Control rat pancreatic islets. Replicate 1.

value: islets


title: MSAR_KD1_rep1


title: T3

status: Public on Sep 17 2023

city: Beijing

first: Bo

last: Gao

address: No.11 Xizhenmen South Street

department: General Surgery

institute: Peking University People's Hospital

description: miRNA&tRNA

data_processing:
Basecalls were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8).
Sequencing quality was examined by FastQC software and trimmed reads (pass Illumina quality filter, trimmed 3’-adaptor bases by cutadapt) were aligned to mature-tRNA and pre-tRNA sequences from GtRNAdb using NovoAlign software (v2.07.11). The remaining reads are aligned to the transcriptome sequences (miRNA).
The expression profiling and differential expression of tsRNAs & known miRNAs were calculated based on normalized TPM.
Genome_build: Reference sequence
Supplementary_files_format_and_content: tab-delimited text files include TPM values and gene information of tRNA and premiRNA for each Sample.

source_name: AR42J cells

growth_protocol: The AR42J cell was cultured in F12K medium (Sigma Aldrich; Merck KGaA) supplemented with 10% fetal bovine serum (Gibco; Thermo Fisher Scientific, Inc.) and 100 U/ml penicillin/streptomycin (Beyotime Institute of Biotechnology) in a 5% CO2 environment at 37˚C.

extract_protocol:
Total RNA from each sample was obtained by using Trizol and then was quantified using a NanoDrop ND-1000 instrument. tsRNAs are heavily decorated by RNA modifications that interfere with small RNA-seq library construction. We do the following treatments before library preparation for total RNA samples:  3’-aminoacyl (charged) deacylation to 3’-OH for 3’ adaptor ligation, 3’-cP (2’,3’-cyclic phosphate) removal to 3’-OH for 3’ adaptor ligation, 5’-OH (hydroxyl group) phosphorylation to 5’-P for 5’-adaptor ligation, m1A and m3C demethylation for efficient reverse transcription.
Sequencing libraries are size-selected for the RNA biotypes to be sequenced using an automated gel cutter. The libraries are qualified and absolutely quantified using Agilent BioAnalyzer 2100.  For standard small RNA sequencing on Illumina NextSeq instrument, the sequencing type is 50-bp single-read at 10M reads.
miRNA-seq&tRNA-seq

treatment_protocol: Three replicates were 200 μM sodium taurocholate for 30 min

value: AR42J cells

value: cells of the rat exocrine pancreas

value: treated with  200 μM sodium taurocholate for 30 min


title: T2

description: miRNA&tRNA


title: T1

description: miRNA&tRNA


title: Rat Islets Control 2

description: Control rat pancreatic islets. Replicate 2.


title: C1

description: miRNA&tRNA

value: untreated


title: D11-3

city: Harbin

first: Yu Jie

last: Chi

state: Heilongjiang

address: Hexing road, No.26; Xiangfang district

department: School of Forestry

institute: Northeast Forestry University

data_processing:
Clean reads were obtained after quality control by removing reads containing an adapter and ploy-N, and low-quality reads from raw data through in-house Perl scripts. Q30, GC-content, and sequence duplication level of the clean data were calculated.
Hisat2 (https://daehwankimlab.github.io/hisat2/main/) was used to map the clean reads to the reference genome sequence of Trametes gibbosa (http://genome.jgi.doe.gov/Tragib1/Tragib1.home.html, Hage et al., 2021), then the mapped data were obtained. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome.
StringTie assembled transcripts of each sample according to the GFF files of the reference genome by using the mapped data reads. StringTie-merge merged all the transcripts from 15 samples, and a complete set of transcriptome information was obtained.
Quantification of gene expression levels was estimated by fragments per kilobase of transcript per million fragments mapped. Then, the transcriptome library qualities were assessed by the inserting segment length test, mRNA fragment randomness test, and sequencing data saturation test.
All the transcripts and genes were annotated as much as possible in eight databases, COG, KOG, eggNOG, GO, KEGG, NR, Pfam, and SwissProt, by using BLAST software to perform homologous sequence alignment to determine their function (Altschul et al., 1997).
Getorf software (v2.0, https://international.biocloud.net/zh/software/tools/detail/small/364) was used to predict Open Reading Frames (ORFs) in the predicted new transcripts (Yao et al., 2012). For known genes, the CDS region is directly extracted using GFF files. Based on the ORF length, log-likelihood score, and the alignment between the amino acid sequence and protein domain sequences in Pfam database, Getorf can identify the reliable and potential coding sequence (CDS) from transcripts.
Blastx software was used to annotate the genes in the databases of COG, KOG, eggNOG, KEGG, NR, and SwissProt, Hmmscan software was used in Pfam. And gene annotation in GO database was implemented by using Blast2GO software to associate with the annotation results in NR. The information of all of these genes is available on BMKCloud (https://international.biocloud.net/), and the gene retrieval and mining can be done on BMKCloud.
The screening and differential expression analysis of the DEGs between different two groups (including CK vs D3, D5, D7, and D11; D3 vs D5, D7, and D11; D5 vs D7, D11 d; and D7 vs D11) were also performed using BMKCloud by means of the DESeq R package (1.10.1) (Anders S et al.,2010; Wang et al., 2010) according to gene expression counts in the control group and the four poplar chip treatment groups.
The DESeq R package provides a statistical routine for determining differential gene expression using a model based on the negative binomial distribution, and can show that the counts of gene reads are different between different two groups. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate (FDR). Fold Change≥2 and FDR <0.01 found by DEseq2 were used as screening criteria to select DEGs.
GO function enrichment and significantly enriched pathways of DEGs were analyzed by statistical methods. GO enrichment analysis of the DEGs can screen out the GO terms and DEGs that are significantly related to specific biological functions, it was implemented by the GOseq R packages based Wallenius non-central hypergeometric distribution (Young et al, 2010), which can adjust for gene length bias in DEGs. KOBAS (Mao et al., 2005) software was used to test the statistical enrichment of DEGs in KEGG pathways. GO and KEGG annotation were performed on DEGs to obtain all GO terms and pathways participated by these DEGs.
The P-value of significance level of each GO term and pathway was calculated by using Fisher exact test of hypergeometric distribution. The FDR was obtained by correcting the results of multiple hypothesis tests, so as to select the GO terms and pathways significantly enriched by DEGs. In this study, the screening criteria both for significantly enriched GO terms and KEGG pathways were adjusted adjusted P-value <0.01 for Fisher exact test.
Genome_build: http://genome.jgi.doe.gov/Tragib1/Tragib1.home.html
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each gene and each sample
Supplementary_files_format_and_content: tab-delimited text file includes counts for each gene and each sample

organism: Trametes gibbosa

source_name: Cultural mycelia

growth_protocol: The white-rot fungus L. gibbosa strain CB-1 was isolated from its fruiting body collected from Changbai Mountains in the province of Jilin, China, and maintained on potato dextrose agar (PDA) slants at 4℃ at Northeast Forestry University. For the inoculation of liquid cultures, the preserved strain was pregrown on PDA plates (9 cm) at 25℃ for 7–10 d. Five marginal inoculum plugs were taken using a 5-mm2 perforator and placed on 70 ml of Low-Nitrogen-Asparagine-Succinate (LNAS) medium supplemented with 5 ml of 15% sterilized glucose solution in a 250-ml Erlenmeyer flask.

extract_protocol:
The samples of frozen mycelia were sent to Beijing Biomarker Biotechnology Co., Ltd. The total RNA was extracted using the RNA extraction kit of Beijing Tiangen Biotech Co., Ltd., and corresponding methods.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was conducted using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First-strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After the adenylation of 3' ends of DNA fragments, NEBNext Adaptor with a hairpin loop structure was ligated to prepare for hybridization. To select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then, 3 μl USER Enzyme (NEB, USA) was used with size-selection. Subsequently, PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) Primer. Finally, PCR products were purified (AMPure XP system), and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina HiSeq Xten platform, and paired-end reads were generated.

treatment_protocol: After stationary cultures were incubated at 25℃ for 10 d, 75 bottles were divided into 5 groups，each group had 15 bottles, which were used as 3 biological replicates. In the first group, 15 bottles were randomly selected as the non-woody treated control group. In the other four groups, 60 bottles were supplemented with 2 g of lesser black poplar (Populus simonii × P. nigra) chips and were continuously incubated at 25℃ for 3, 5, 7, and 11 d. The mycelia of all bottles were harvested in the same way.

value: Cultural mycelia

value: woody treatment 11d


title: C3

description: miRNA&tRNA


title: D11-2


title: D11-1


title: D5-2

value: woody treatment 5d


title: D7-3

value: woody treatment 7d


title: D5-3


title: D7-2


title: D1491T18_RNA-seq_p50_AH_rep1

city: Paris

first: Héloïse

last: Muller

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description:
RNA-seq
RNA-seq_p50_PD-D2-24h_AH_TPM.xlsx

data_processing:
Library were sequenced on Novaseq.
Adapter sequences were trimmedfrom reads using trimgalore.
RNA-seq reads were aligned to our custom Bmori_v4 genome assembly using STAR_2.7.8a.
Assembly: Bmori_v4
Supplementary files format and content: Excel table file
Supplementary files format and content: bigWig

organism: Bombyx mori

source_name: full embryo

growth_protocol: ~200 p50 diapaused eggs harvest after release 24h at 25°C

extract_protocol:
Eggs or adult head and thorax were placed in TRIzol™ Reagent from ThermoFisher Scientific before mechanically broken with a piston pellet to allow total RNA extraction.
Sequencing libraries have been obtained using the Illumina stranded mRNA prep ligation protocol.

value: full embryo


title: D1491T19_RNA-seq_p50_AH_rep2


title: D3-3

value: woody treatment 3d


title: D5-1


title: D7-1


title: D429F01_Hi-C p50_PD-D1-2h

description: Hi-C

data_processing:
Library were sequenced on Novaseq.
Adapter sequences were trimmedfrom reads using trimgalore.
Hi-C reads were processed and filtered using the HiCPro suite.
Matrices files have been generated using the cooler suite and format.
Assembly: Bmori_v3 or Bmori_4
Supplementary files format and content: multi-resolution cooler

growth_protocol: 20-30 p50 diapaused eggs harvest after release at 25°C

extract_protocol:
Eggs were glued in a Petri dish filled with 3% formaldehyde before chorions were poked with a fine needle to allow embryos fixation for 30 min. After quenching, embryos were dissected out of chorion with fine forceps before frozen at -80°C and processed with Arima-HiC+ kit from Arima genomics.
Sequencing libraries were prepared using the KAPA HyperPrep Library Preparation Kit complemented with Illumina TruSeq DNA UD Indexes. Libraries were amplified using 8-14 cycles on the thermocycler. Post amplification libraries were size selected at 250-600bp in length using SPRIselect beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity screenTapes.


title: D988F03_D1355F01_Hi-C p50_Adult-Heads

description: Hi-C

source_name: head and thorax

growth_protocol: Bombyx mori moths were grown to adult stage at 25°C fed with Morus alba leaves and heads and thorax were cut using a scalpel

extract_protocol:
The head of one moth was dipped and ground with a piston pellet in 3% formaldehyde and incubated for 30 min. After quenching, the head was frozen at -80°C and processed with Arima-HiC+ kit from Arima genomics.
Sequencing libraries were prepared using the KAPA HyperPrep Library Preparation Kit complemented with Illumina TruSeq DNA UD Indexes. Libraries were amplified using 8-14 cycles on the thermocycler. Post amplification libraries were size selected at 250-600bp in length using SPRIselect beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity screenTapes.

value: head and thorax


title: CK3

value: non-woody control (Cultural mycelia were extracted directly from the cultures on LNAS liquid medium for 10 days)


title: D429F03_D920C05_Hi-C p50_PD-D3-48h

description: Hi-C


title: D3-1

value: woody treatment  3d


title: D710T27_RNA-seq_p50_PD-D2-24h

extract_protocol:
Eggs were placed in TRIzol™ Reagent from ThermoFisher Scientific before chorions were broken with a piston pellet to allow total RNA extraction.
Sequencing libraries have been obtained using the Illumina stranded mRNA prep ligation protocol.


title: D1221C24_ChIP_p50_D2-24h_Bmori-v4_H2A.z_IP

description: ChIP IP

data_processing:
Library were sequenced on Novaseq.
Adapter sequences were trimmedfrom reads using trimgalore.
ChIP-seq reads were aligned to our custom Bmori_v4 genome assembly using Bowtie2 v2.3.5.1. Only uniquely mapping reads with a mapping quality higher than 10 were retained.
To create ChIP-seq coverage plots, log2 IP/Input ratio files have been generated at 25pb resolution using bamCompare from deepTools and reformatted in the bigWig file format.
Assembly: Bmori_v4
Supplementary files format and content: bigWig

extract_protocol:
Eggs were placed in 1% formaldehyde before chorions were broken with a piston pellet to allow embryos fixation for 10 min. After quenching and cell lysis, embyo tissus were ruptured and chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HyperPrep  Library Preparation Kit complemented with Illumina TruSeq DNA UD Indexes. Libraries were amplified using 8-14 cycles on the thermocycler. Post amplification libraries were size selected at 250-600bp in length using SPRIselect beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity screenTapes.


title: CK2


title: D1221C23_ChIP_p50_D2-24h_Bmori-v4_H2A.z_Input

description: ChIP Input

value: none (input)


title: D1221C19_ChIP_p50_D2-24h_Bmori-v4_H4K20me1_rep2_Input

description: ChIP Input


title: cell,exercised,rep3

city: Fuzhou, Fujian, China

first: Jie

last: Liu

address: Shengli Clinical Medical College of Fujian Medical University, Department of Endoscopy, Fujian Provincial Hospital, Fuzhou, China

institute: Fujian Medical University

data_processing:
The mRNA is fragmented using a Fragmentation Buffer, and then the first strand of cDNA is synthesized using six base random primers.
Buffer, dNTPs, RNase H, and DNA polymerase I are added to synthesize the second strand of cDNA. Next, the resulting cDNA is then purified using a QiaQuick PCR kit and eluted with EB buffer.
End-repair is done and base A is added to the cDNA fragments, followed by sequencing connector ligation.
The target size fragments are recovered by agarose gel electrophoresis, and PCR amplification is carried out to complete the preparation of the entire library.
the constructed library is sequenced using the Illumina HiSeq2000 platform to obtain high-throughput sequencing data that can be used for downstream analysis.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: cell line

growth_protocol: cells maintained in a 37℃ incubator with 5% CO2

extract_protocol:
Total RNA is first extracted from the sample, and mRNA is enriched using magnetic beads with Oligo (dT).
RNA libraries for RNA-seg were usind SWARTER mRNASed ibrary prepared Prepkit fol owina manufacturer's protocols

treatment_protocol: Transfection plasmid

value: cell line

value: tumor cell

value: mutant p53


title: D1221C20_ChIP_p50_D2-24h_Bmori-v4_H4K20me1_rep2_IP

description: ChIP IP


title: cell,exercised,rep2


title: C2

description: miRNA&tRNA

value: AR42J cells


title: cell,exercised,rep1


title: cell,control,rep3