title: HSD male rat liver tissue S3P1_H07

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_H09

status: Public on May 12 2020

type: SRA

city: Research Triangle Park

first: Will

last: Gwinn

state: NC

address: 111 Alexander Dr.

department: National Toxicology Program

country: USA

institute: National Institute of Health Sciences

description: HSD male rat liver tissue

library_source: transcriptomic

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing  language R. The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains  the reads and quality scores for one sample. Each FASTQ file is aligned using the Bowtie algorithm to a pseudotranscriptome  input by the user. The output for TempO-Seq data analysis is a table of counts with each column  representing a sample and each row representing a gene.
Data normalization was not done
Supplementary_files_format_and_content: Raw data matrix all smaples

molecule: total RNA

organism: Rattus norvegicus

extract_protocol: The liver and left and right kidneys were collected, weighed, and the left liver lobe and right kidney were preserved in RNAlater (Qiagen, Valencia, CA) and stored at 4°C for RNA extraction. Total RNA was extracted from liver and kidney within 1 week of harvest using the RNeasy Mini Kit (Qiagen) with a DNA digestion step. RNA was sent frozen to BioSpyder (Carlsbad, CA) for HTT analysis using the rat S1500+ TempO-Seq platform.

treatment_protocol: Eight to ten concentrations plus vehicle control were tested for each of the eighteen selected chemicals with n = 4 rats per exposure concentration. Exposure concentrations for each chemical were selected based on those used in the chronic or sub-chronic toxicity study and included concentrations that were both higher and lower than those previously tested. Whenever possible, the gavage vehicle was matched to that used in the chronic or sub-chronic study; however, multiple chemicals were orally administered in feed (MTE, DEHP, PFOA, EE2, and TCPP) or drinking water (BDCA and ACR) in the chronic or sub-chronic study. On day 5, the rats were weighed and euthanized via exsanguination.

tag: strain

value: Sprague Dawley

tag: gender

value: male

tag: age

value: 8-10 weeks

tag: animal id

tag: tissue

value: liver

tag: chemical

value: PFOA

tag: dose(mg/kg)


title: HSD male rat liver tissue S3P1_H11

description: HSD male rat liver tissue

value: HCB


title: HSD male rat liver tissue S3P1_H06

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_H03

description: HSD male rat liver tissue

value: BPAF


title: HSD male rat liver tissue S3P1_H02

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_H04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_G12

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_H08

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_G11

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_H01

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_G09

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_G10

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P2_B05

description: HSD male rat liver tissue

value: EE


title: HSD male rat liver tissue S3P1_G08

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_G05

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_F12

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_G07

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_G06

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_G03

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_G02

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_G01

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_F09

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_F11

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_H05

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_F08

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_F10

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_F06

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_F07

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_F02

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_F03

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_F04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_F01

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_E11

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_E10

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_E12

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_E09

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_E07

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_E04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_E06

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_G04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_E08

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_F05

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_E03

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_E01

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_D09

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_D12

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_E02

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_D11

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_D04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_D05

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_D08

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_D03

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_D02

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_E05

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_D06

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_C12

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_C10

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_C09

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_D01

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_C11

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_C08

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_C04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_C07

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_C03

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_D10

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_B12

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_C06

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_B11

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_D07

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_B09

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_B07

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_B05

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_B06

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_A12

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_B10

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_B04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_A09

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_A10

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_A08

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_A06

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_A05

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_C05

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P1_A04

description: HSD male rat liver tissue


title: HSD male rat kidney tissue S2P4_H05

description: HSD male rat kidney tissue

value: kidney

value: TCPP


title: HSD male rat kidney tissue S2P4_H03

description: HSD male rat kidney tissue


title: HSD male rat liver tissue S3P1_A07

description: HSD male rat liver tissue


title: HSD male rat kidney tissue S2P4_H02

description: HSD male rat kidney tissue

value: Fenofibrate


title: HSD male rat kidney tissue S2P4_H04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_H01

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_G06

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_G05

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_G03

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_G02

description: HSD male rat kidney tissue


title: HSD male rat liver tissue S3P1_B03

description: HSD male rat liver tissue


title: HSD male rat kidney tissue S2P4_F06

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_G01

description: HSD male rat kidney tissue


title: HSD male rat liver tissue S3P1_A11

description: HSD male rat liver tissue


title: HSD male rat kidney tissue S2P4_F03

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_F01

description: HSD male rat kidney tissue


title: HSD male rat liver tissue S3P1_B08

description: HSD male rat liver tissue


title: HSD male rat kidney tissue S2P4_E07

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_E06

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_E05

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_E04

description: HSD male rat kidney tissue


title: HSD male rat liver tissue S3P1_A03

description: HSD male rat liver tissue


title: HSD male rat liver tissue S3P2_C03

description: HSD male rat liver tissue


title: HSD male rat kidney tissue S2P4_E03

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_F04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_E01

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_D07

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_G04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_D03

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_D04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_D06

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_D02

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_F07

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_F02

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_C05

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_D05

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_C07

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_F05

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_D01

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_C06

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_B06

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_C03

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_B07

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_C04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_E02

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_B05

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_B03

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_A07

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_B04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_H06

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_A05

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_A04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_A06

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P4_A03

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_H11

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_H12

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_H09

description: HSD male rat kidney tissue

value: DEHP


title: HSD male rat kidney tissue S2P3_H08

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_H05

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_H07

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_H10

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_H04

description: HSD male rat kidney tissue

value: Pulegone


title: HSD male rat kidney tissue S2P3_H03

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_G10

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_G09

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_H01

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_G12

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_G11

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_G08

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_G02

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_G05

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_G03

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_G06

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_G01

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_F12

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_F11

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_F10

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_F09

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_F08

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_F07

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_F05

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_H06

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_F04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_H02

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_F01

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_F03

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_E12

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_E08

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_E10

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_E09

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_E07

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_G07

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_G04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_F02

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_E11

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_E05

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_D11

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_E01

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_E03

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_D12

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_D09

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_D10

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_F06

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_D08

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_D06

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_D07

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_D05

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_D04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_D03

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_C12

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_E06

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_D01

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_D02

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_C10

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_C11

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_C08

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_C09

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_C03

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_B12

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_C05

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_C06

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_C07

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_E02

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_E04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_C04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_B09

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_B11

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_B10

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_B07

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_B08

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_B06

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_B05

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_B04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_A12

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_B03

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_A11

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_A09

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_A08

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_A06

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_A07

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_A04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_A05

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S2P3_A03

description: HSD male rat kidney tissue


title: HSD male rat liver tissue S2P2_H06

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_H04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_H05

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_H02

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_H01

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_G05

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_G03

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_G06

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_G02

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_G04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_G01

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_F07

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_F06

description: HSD male rat liver tissue


title: HSD male rat kidney tissue S2P3_A10

description: HSD male rat kidney tissue


title: HSD male rat liver tissue S2P2_F04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_F05

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_F01

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_E07

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_F02

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_E04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_E05

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_E06

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_E03

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_E02

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_H03

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_D07

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_E01

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_D05

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_D04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_D02

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_D06

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_D03

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_C06

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_D01

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_C07

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_C04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_F03

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_B07

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_C03

description: HSD male rat liver tissue


title: PR_CLAMP_Rep2

city: Carrboro

first: Ashlesha

last: Chaubal

address: 3342 Genome Sciences Building

department: Integrative Biological and Genome Sciences

institute: University of North Carolina at Chapel Hill

library_source: genomic

data_processing:
Illumina adapter sequences were trimmed using the BBDuk tool in the Bbmap package (version 38.82) and quality check was performed using Fastqc (version 0.11.8)
Due to the presence of contaminating reads, the Bbsplit tool in the Bbmap package (version 38.82) was used to obtain reads that mapped only to the Drosophila genome. These cleaned up fastq files have been provided.
Custom genome builds were generated using the Drosophila genome version dm3, by removing all replication-dependent histone gene repeat sequences and by adding back a single 5kb histone gene repeat unit with DWT or PR sequences as a separate chromosome (Mckay et al., 2015).
The paired-end sequencing reads were mapped to the custom genomes using Bowtie2 (version 2.3.4.1) using default parameters.
MACS2 (version 2.1.2) was used to call peaks using the following options: -g dm --keep-dup all -B
Genome_build: custom_dm3
Supplementary_files_format_and_content: Bedgraph files were generated using MACS2 (version 2.1.2)

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: 0-2 hr old embryos were collected on grape juice plates at 25C

extract_protocol:
Embryos were collected, fixed in formaldehyde, and stored at -80 according to Blythe and Wieschaus, 2015, Chromatin immunoprecipitation was performed using Rabbit anti CLAMP or Rabbit IgG as described in Reider et al., 2017
Libraries were synthesized using 4ul of inputs and 36ul of each ChIP sample (Rabbit anti CLAMP or Rabbit IgG; Millipore-Sigma, 12-370) according to Blythe and Wieschaus (2015). Briefly, libraries were made using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs), 12 samples pooled per lane, and sequenced on an Illumina HiSeq 2500 in 2×150-bp mode (Genewiz).

treatment_protocol: Aged for 2 hr at 25C

tag: developmental stage

value: 2-4 hr old embryos

tag: genotype

value: +; HisC deletion; 12xPR (VK33)

tag: chip antibody

value: Rabbit anti-CLAMP (Rieder et al. 2017)


title: HSD male rat liver tissue S2P2_B06

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_B05

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_C05

description: HSD male rat liver tissue


title: PR_CLAMP_Rep1


title: HSD male rat liver tissue S2P2_A07

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_A06

description: HSD male rat liver tissue


title: PR_IgG_Rep2

value: Rabbit IgG (Millipore-Sigma, 12-370)


title: PR_Input2_Rep2


title: HSD male rat liver tissue S2P2_A05

description: HSD male rat liver tissue

value: Sprague Dawley


title: PR_IgG_Rep1


title: HSD male rat liver tissue S2P2_A04

description: HSD male rat liver tissue

value: male


title: HSD male rat liver tissue S2P2_A03

description: HSD male rat liver tissue

value: 8-10 weeks


title: DWT_CLAMP_Rep2

value: +; HisC deletion; 12xDWT (VK33)


title: HSD male rat liver tissue S2P1_H12

description: HSD male rat liver tissue

value: liver


title: DWT_CLAMP_Rep1


title: HSD male rat liver tissue S2P1_H11

description: HSD male rat liver tissue


title: DWT_IgG_Rep2


title: PR_Input1_Rep1


title: HSD male rat liver tissue S2P1_H09

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_B04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P2_B03

description: HSD male rat liver tissue


title: DWT_IgG_Rep1


title: TC71_cnr_Rb_rep2

city: Columbus

first: Emily

middle: Rose

last: Theisen

state: OH

address: 700 Childrens Drive

department: Center For Childhood Cancer and Blood Diseases

institute: Nationwide Children's Hospital

description:
TC71-Rb-rep_S3.bw
TC71_FLI_sml_FE.bw
TC71_LSD1_comb_FE.bw

data_processing:
Library strategy: CUT&RUN
Illumina’s Bcl2fastq conversion software
FastQC
Quality and adapter trimming: TrimGalore!
Alignment to hg19 with bowtie2
SAM to BAM conversion with samtools
Peak calling with MACS2 and csaw
Track building with MACS2 using fold enrichment calculations over input
BAM to BED and BED to spike-in normalized bedgraph with Pybedtools (H3K27ac and Rb CUT&RUN bigwigs)
Bedgraph to bigwig with bedGraphToBig UCSC util (H3K27ac and Rb CUT&RUN bigwigs)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, genome tracks for each sample
Supplementary_files_format_and_content: bed, peak calling output for H3K27ac from csaw package in R and peak calling output for CUT&Tag using pileups from MACS2 call peak + bdgdiff
Supplementary_files_format_and_content: xls, peak calling output from MACS2

organism: Homo sapiens

source_name: TC71 cells

growth_protocol: A673 and SKNMC cells were grown in DMEM supplemented with FBS and PSQ. A673 cells were also supplemented with NaPyruvate. EWS502 and TC71 cells were grown in RPMI supplemented with FBS and PSQ.

extract_protocol:
KAPA Hyper Prep
KAPA Hyper Prep

treatment_protocol: Cell were untreated

tag: cell type

tag: replicate


title: HSD male rat liver tissue S2P1_H10

description: HSD male rat liver tissue


title: DWT_Input2_Rep2


title: HSD male rat liver tissue S2P1_H08

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_H07

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_H06

description: HSD male rat liver tissue


title: TC71_cnr_Rb_rep1

description:
TC71_Rb_S5.bw
TC71_FLI_sml_FE.bw
TC71_LSD1_comb_FE.bw


title: TC71_cnr_LSD1_rep2

description:
TC71_LSD1_comb_FE.bw
TC71_LSD1_peaks.xls


title: TC71_cnr_H3K27ac_rep2

description:
TC71_K27ac_rep2_S20.bw
k27ac_TC71_peaks.bed


title: HSD male rat liver tissue S2P1_H03

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_H04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_H05

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_G12

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_H02

description: HSD male rat liver tissue


title: TC71_cnr_EWS/FLI_rep2

description:
TC71_FLI_sml_FE.bw
TC71_sml_peaks.xls


title: TC71_cnr_H3K27ac_rep1

description:
TC71_K27ac_rep1_S8.bw
k27ac_TC71_peaks.bed


title: SK-N-MC_cnr_Rb_rep2

description:
SK-N-MC-Rb-rep_S7.bw
SKNMC_FLI_sml_FE.bw
SKNMC_LSD1_comb_FE.bw

source_name: SK-N-MC cells

value: SK-N-MC


title: HSD male rat liver tissue S2P1_G10

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_G11

description: HSD male rat liver tissue


title: TC71_cnr_EWS/FLI_rep1

description:
TC71_FLI_sml_FE.bw
TC71_sml_peaks.xls


title: SK-N-MC_cnr_Rb_rep1

description:
SK-N-MC_Rb_S7.bw
SKNMC_FLI_sml_FE.bw
SKNMC_LSD1_comb_FE.bw


title: DWT_Input1_Rep1


title: HSD male rat liver tissue S2P1_G09

description: HSD male rat liver tissue


title: SK-N-MC_cnr_LSD1_rep2

description:
SKNMC_LSD1_comb_FE.bw
SKNMC_LSD1_peaks.xls


title: SK-N-MC_cnr_LSD1_rep1


title: HSD male rat liver tissue S2P1_G08

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_G07

description: HSD male rat liver tissue


title: SK-N-MC_cnr_H3K27ac_rep2

description:
SKNMC_K27ac_rep2_S17.bw
k27ac_SKNMC_peaks.bed


title: HSD male rat liver tissue S2P1_G05

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_G06

description: HSD male rat liver tissue


title: SK-N-MC_cnr_H3K27ac_rep1

description:
SKNMC_K27ac_rep1_S6.bw
k27ac_SKNMC_peaks.bed


title: SK-N-MC_cnr_EWS/FLI_rep1

description:
SKNMC_FLI_sml_FE.bw
SKNMC_sml_peaks.xls


title: SK-N-MC_cnr_EWS/FLI_rep2

description:
SKNMC_FLI_sml_FE.bw
SKNMC_sml_peaks.xls


title: HSD male rat liver tissue S2P1_G04

description: HSD male rat liver tissue


title: TC71_cnr_LSD1_rep1


title: HSD male rat liver tissue S2P1_G03

description: HSD male rat liver tissue


title: EWS-502_cnr_Rb_rep2

description:
EWS-502-Rb-rep_S5.bw
EWS502_FLI_sml_FE.bw
EWS502_LSD1_comb_FE.bw

source_name: EWS-502 cells


title: EWS-502_cnr_LSD1_rep1

description:
EWS502_LSD1_comb_FE.bw
EWS502_LSD1_peaks.xls


title: HSD male rat liver tissue S2P1_H01

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_G01

description: HSD male rat liver tissue


title: EWS-502_cnr_Rb_rep1

description:
EWS-502_Rb_S9.bw
EWS502_FLI_sml_FE.bw
EWS502_LSD1_comb_FE.bw


title: HSD male rat liver tissue S2P1_F12

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_F11

description: HSD male rat liver tissue


title: EWS-502_cnr_H3K27ac_rep2

description:
EWS502_K27ac_rep2_S14.bw
k27ac_EWS502_peaks.bed


title: EWS-502_cnr_EWS/FLI_rep2

description:
EWS502_FLI_sml_FE.bw
EWS502_sml_peaks.xls


title: A673_cnr_Rb_rep2

description:
A673-Rb-rep_S1.bw
A673_FLI_sml_FE.bw
A673_LSD1_comb_FE.bw

source_name: A673 cells


title: HSD male rat liver tissue S2P1_F07

description: HSD male rat liver tissue


title: EWS-502_cnr_EWS/FLI_rep1


title: HSD male rat liver tissue S2P1_F06

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_F05

description: HSD male rat liver tissue


title: A673_cnr_Rb_rep1

description:
A673_Rb_S1.bw
A673_FLI_sml_FE.bw
A673_LSD1_comb_FE.bw


title: A673_cnr_LSD1_rep2

description:
A673_LSD1_comb_FE.bw
A673_LSD1_peaks.xls


title: A673_cnr_LSD1_rep1


title: HSD male rat liver tissue S2P1_G02

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_F04

description: HSD male rat liver tissue


title: EWS-502_cnr_LSD1_rep2


title: HSD male rat liver tissue S2P1_F03

description: HSD male rat liver tissue


title: A673_cnr_H3K27ac_rep2

description:
A673_K27ac_rep2_S11.bw
k27ac_A673_peaks.bed


title: HSD male rat liver tissue S2P1_F10

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_F02

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_F01

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_E12

description: HSD male rat liver tissue


title: A673_cnr_EWS/FLI_rep1

description:
A673_FLI_sml_FE.bw
A673_sml_peaks.xls


title: EWS-502_cnr_H3K27ac_rep1

description:
EWS502_K27ac_rep1_S4.bw
k27ac_EWS502_peaks.bed


title: A673_cnr_EWS/FLI_rep2

description:
A673_FLI_sml_FE.bw
A673_sml_peaks.xls


title: HSD male rat liver tissue S2P1_E09

description: HSD male rat liver tissue


title: A673_cnr_H3K27ac_rep1

description:
A673_K27ac_rep1_S2.bw
k27ac_A673_peaks.bed


title: HSD male rat liver tissue S2P1_E11

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_E10

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_F08

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_F09

description: HSD male rat liver tissue


title: wtEF_cnt_LSD1_rep1

description:
CUT&Tag
714_LSD1_cutoff_peaks.bed

data_processing:
Library strategy: CUT&Tag
Illumina’s Bcl2fastq conversion software
FastQC
Quality and adapter trimming: TrimGalore!
Alignment to hg19 with bowtie2
SAM to BAM conversion with samtools
Peak calling with MACS2: first call peaks using both replicates of each condition pooled using "callpeak". Then use "bdgdiff" to call peaks up in test conditions as compared to Rb IgG. Peaks were included only if the summit in the spike-in normalized bigwig exceeded 10000.
BAM to BED and BED to spike-in normalized bedgraph with Pybedtools; spike-in normalization first normalized all samples to the same total number of reads and then to the number of spike-in reads.
Bedgraph to bigwig with bedGraphToBig UCSC util
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, genome tracks for each sample
Supplementary_files_format_and_content: bed, peak calling output from MACS2 callpeak + bdgdiff

growth_protocol: A673 cells were cultured in DMEM supplemented with FBS, PSQ, and NaPyruvate.

extract_protocol:
NEBNext
For KD-rescue samples cells were seeded at 50% confluency and left to adhere overnight (day 0). shRNAs were retrovirally delivered on day 1. Selection in 2 µg/mL puromycin (Sigma P8833)until days 5, and then rescue or mock-rescue was performed. Cells were then double selected in puro and hygro for 7 days before collection for CUT&Tag.

treatment_protocol: Cells were retrovirally transduced with either control shRNA (iLuc) or shRNA targeting EWS/FLI (iEF) on day 0. Cells were selected in 2 ug/mL puromycin and transduced with either empty vector or cDNA encoding 3XFLAG-wtEWS/FLI on day 4. Cells were then double selected in puro and 100 ug/mL hygromycin B for 7 days before collection for CUT&Tag

tag: transduced shrna

value: iEF + 3XFLAG-EWS/FLI


title: wtEF_cnt_LSD1_rep2

description:
CUT&Tag
714_LSD1_cutoff_peaks.bed


title: HSD male rat liver tissue S2P1_E07

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_E06

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_E04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_E03

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_E05

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_D12

description: HSD male rat liver tissue


title: EFKD_cnt_LSD1_rep1

description:
CUT&Tag
iEF_LSD1_cutoff_peaks.bed

value: iEF + empty cDNA


title: HSD male rat liver tissue S2P1_D11

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_D10

description: HSD male rat liver tissue


title: EFKD_cnt_LSD1_rep2

description:
CUT&Tag
iEF_LSD1_cutoff_peaks.bed


title: HSD male rat liver tissue S2P1_E08

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_D06

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_D07

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_D03

description: HSD male rat liver tissue


title: A673_cnt_LSD1_rep2

description:
CUT&Tag
iLuc_LSD1_cutoff_peaks.bed

value: iLuc + empty cDNA


title: HSD male rat liver tissue S2P1_D04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_D02

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_C11

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_D09

description: HSD male rat liver tissue


title: A673_cnt_LSD1_rep1

description:
CUT&Tag
iLuc_LSD1_cutoff_peaks.bed


title: HSD male rat liver tissue S2P1_C09

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_D01

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_C06

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_C07

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_C10

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_C12

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_C08

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_E02

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_C05

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_C04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_C03

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_D08

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_B12

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_B11

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_B09

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_B08

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_D05

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_B07

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_B05

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_A12

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_B06

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_B04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_B03

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_A11

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_A10

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_A07

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_A08

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_A03

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_A06

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_A04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_A05

description: HSD male rat liver tissue


title: HSD male rat liver tissue S2P1_A09

description: HSD male rat liver tissue


title: HSD male rat kidney tissue S1P4_H03

description: HSD male rat kidney tissue

value: kidney

value: TCAB


title: HSD male rat kidney tissue S1P4_G04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P4_H02

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P4_G03

description: HSD male rat kidney tissue


title: HSD male rat liver tissue S2P1_B10

description: HSD male rat liver tissue

value: Fenofibrate


title: HSD male rat kidney tissue S1P4_G02

description: HSD male rat kidney tissue


title: HSD male rat liver tissue S2P1_E01

description: HSD male rat liver tissue

value: Pulegone


title: HSD male rat kidney tissue S1P4_F04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P4_F02

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P4_E03

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P4_E02

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P4_D04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P4_D03

description: HSD male rat kidney tissue


title: N2 oma-1 RNAi (pAS74) F4

city: Boston

first: Aditi

last: Shukla

state: MA

address: 77 Avenue Louis Pasteur, NRB 266

department: Genetics

institute: Harvard Medical School

data_processing:
Remove unique molecular identifiers (UMIs) from each read pair and append to the end of the read name using UMI-tools
Trim low-quality bases (quality score < 20) from 3' ends of reads using cutadapt
Trim the 5' adapter (AACAACGAGAAGATCGATGA) from Read 1 using cutadapt
Trim the 3' adapter (GGCGTCGCCATATTCTACTTACACACACACACACACAC) from Read 2 using cutadapt
Trim any 5' adapter sequence (if present) from Read 2 using cutadapt
Discard read pairs that do not contain additional pACs at the 5' end of Read 2
Trim pACs from the 5' end of Read 2 using cutadapt
Discard Read 2 sequences shorter than 5 nucleotides using cutadapt
Align Read 2 sequences to the C. elegans genome using STAR
Generate SAM file of unique alignments using SAMtools
Generate BED file of unique alignments using BEDtools
Deduplicate alignments based on the combination of the UMI and end coordinate
Discard alignments that mapped to the "+" strand and/or to coordinates outside of the oma-1 gene
Split pre-pAC-trimmed version of each remaining read into the aligned portion ("oma-1") and any remaining downstream sequence ("pUG")
If first 1-6 nucleotides of the "pUG" portion have the potential to be templated in oma-1, reassign those nucleotides to the "oma-1" portion
Discard reads with "pUG" portions starting with bases other than "U" or "G" and/or containing 2 or more bases other than "U" or "G"
Genome_build: WS260
Supplementary_files_format_and_content: Excel files listing reads that were called as "oma-1 pUG RNAs" (reads that mapped uniquely to oma-1 and had pUG tails that were longer than the 18nt RT oligo) and the chromosome coordinates of oma-1 pUGylations sites.

organism: Caenorhabditis elegans

source_name: population - whole animal

extract_protocol:
Adult animals were harvested and RNA was extracted using TRIzol Reagent.
Custom library prep.

value: whole animal


title: HSD male rat kidney tissue S1P4_D01

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P4_H01

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P4_C03

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P4_C04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P4_D02

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P4_A03

description: HSD male rat kidney tissue


title: N2 oma-1 RNAi (pAS74) F3


title: HSD male rat kidney tissue S1P3_H12

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P4_A04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P4_B04

description: HSD male rat kidney tissue


title: YY1449 oma-1 RNAi (Ahringer clone)


title: HSD male rat kidney tissue S1P3_H11

description: HSD male rat kidney tissue


title: YY1449 L4440


title: HSD male rat kidney tissue S1P4_F01

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P4_F03

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_H09

description: HSD male rat kidney tissue

value: Triclosan


title: HSD male rat kidney tissue S1P3_H08

description: HSD male rat kidney tissue


title: N2 oma-1 RNAi (Ahringer clone)


title: HSD male rat kidney tissue S1P4_E04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P4_G01

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_H07

description: HSD male rat kidney tissue


title: N2 oma-1 RNAi (pAS74) F1


title: HSD male rat kidney tissue S1P4_E01

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_H06

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P4_B03

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_H10

description: HSD male rat kidney tissue


title: N2 oma-1 RNAi (pAS74)


title: HSD male rat kidney tissue S1P3_H05

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_H03

description: HSD male rat kidney tissue


title: N2 oma-1 RNAi (pAS74) F2


title: HSD male rat kidney tissue S1P3_H04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_H02

description: HSD male rat kidney tissue


title: N2 L4440


title: HSD male rat kidney tissue S1P3_G11

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_H01

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_G12

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_G09

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_G10

description: HSD male rat kidney tissue


title: H3K27ac_ChIPSeq_COMBO

first: Ryan

middle: P

last: Kuzmickas

address: 77 Avenue Louis Pasteur, NRB458B

institute: Brigham and Women's Hospital

data_processing:
reads were aligned using BWA alignment software using the BWA-MEM algorithm and the hg19 build of the human genome
peaks were called using the Homer peak-calling software package with the “histone” peak-detection option

source_name: PC3 prostate cancer cells

growth_protocol: 4x10^7 cells per IP (8 total) were grown in incubators at 37 degrees C, 5% CO2 in RPMI media supplemented with 10%FBS and 1% penicillin/streptomycin

extract_protocol:
Cells were cross-linked for 12 min at room temperature by the addition of one-tenth of the volume of 11% formaldehyde solution to the growth media. DNA was prepared using Agilent Chip-on-chip protocol (G4481-90010). Each immunoprecipitation was performed by incubating 10ug of the corresponding antibody with sheared DNA overnight at 4 degrees C, followed by 2 hour incubation with protein A/G (50/50) dynabeads and magnetic isolation of beads. Cross-links were reversed, and purified DNA was sent to the Dana Farber Center for Computation Cancer Biology (CCCB) core for library construction and sequencing.
Performed by Dana Farber CCCB using NEBNext ChIP Master Mix Kit for Illumina following manufacturers instructions.

treatment_protocol: Sub-confluent cells were treated for 48 hours with vehicle (DMSO), 2uM Vorinostat (HDAC inhibitor), 5uM GSK126 (EZH2 inhibitor), or combined HDAC/EZH2 inhibition.

tag: sample type

value: cell line derived from prostate cancer metastasis

tag: antibody

value: H3K27ac (Abcam, AB4729)

tag: treatment

value: combined HDAC/EZH2


title: H3K27me3_ChIPSeq_COMBO

value: H3K27me3 (Millipore, 07-449)


title: H3K27me3_ChIPSeq_DMSO

value: vehicle (DMSO)


title: H3K27me3_ChIPSeq_GSK126

value: 5uM GSK126


title: HSD male rat kidney tissue S1P3_G07

description: HSD male rat kidney tissue

value: Sprague Dawley

value: male

value: 8-10 weeks


title: HSD male rat kidney tissue S1P3_G04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_G08

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_G06

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_G01

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_G05

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_F12

description: HSD male rat kidney tissue


title: H3K27ac_ChIPSeq_GSK126


title: HSD male rat kidney tissue S1P3_G03

description: HSD male rat kidney tissue


title: H3K27ac_ChIPSeq_DMSO


title: HSD male rat kidney tissue S1P3_G02

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_F11

description: HSD male rat kidney tissue


title: H3K27ac_ChIPSeq_VOR

value: 2uM Vorinostat


title: INPUT_DNA_GSK126


title: INPUT_DNA_VOR


title: HSD male rat kidney tissue S1P3_F08

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_F04

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_F09

description: HSD male rat kidney tissue


title: INPUT_DNA_COMBO


title: H3K27me3_ChIPSeq_VOR


title: HSD male rat kidney tissue S1P3_F05

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_F10

description: HSD male rat kidney tissue


title: INPUT_DNA_DMSO


title: HSD male rat kidney tissue S1P3_F02

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_E11

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_F01

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_F03

description: HSD male rat kidney tissue


title: CIA1-1_L4.D701

city: houston

first: Ming-Jer

last: Tsai

state: Texas

address: One Baylor Plaza

institute: baylor college of medicine

data_processing:
Read preparation and QC through EA | Q² Solutions developed tool, fastq-mcf
Alignment and Quantification using STAR version 2.4 and RNA-Seq quantification software RSEM, version 1.2.14
Post-quantification analysis using the SAMPLE.star.bam
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: LNCaP cells were cultured in PRMI1640 medium supplemented with 10% FBS

extract_protocol:
Cells wer flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA sample preparation kit (Illumina # RS-122-2103) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cells were transfected with siRNA for 72 hours or treated with 1uM CIA1 for 18 hours.

tag: cell line

value: LNCaP

value: prostate cancer cell line

value: CIA1 18 hours


title: DMSO-2_L5.D712

value: DMSO 18 hours


title: HSD male rat kidney tissue S1P3_E06

description: HSD male rat kidney tissue

tag: strain

value: kidney


title: DMSO-1_L5.D711


title: HSD male rat kidney tissue S1P3_E08

description: HSD male rat kidney tissue

tag: gender


title: 2siCII-2_L1.D708

value: siCOUP-TFII 72 hours


title: HSD male rat kidney tissue S1P3_E07

description: HSD male rat kidney tissue

tag: age

value: Triclosan


title: HSD male rat kidney tissue S1P3_E04

description: HSD male rat kidney tissue

tag: animal id


title: HSD male rat kidney tissue S1P3_E05

description: HSD male rat kidney tissue

tag: tissue


title: HSD male rat kidney tissue S1P3_F06

description: HSD male rat kidney tissue

tag: chemical


title: HSD male rat kidney tissue S1P3_E09

description: HSD male rat kidney tissue

tag: dose(mg/kg)


title: 2siCII-1_L1.D707


title: HSD male rat kidney tissue S1P3_E03

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_E02

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_F07

description: HSD male rat kidney tissue


title: 1siNC-2_L1.D706

value: negative control siRNA 72 hours


title: 1siNC-1_L1.D705


title: HSD male rat kidney tissue S1P3_E01

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_D12

description: HSD male rat kidney tissue

value: TCAB


title: HSD male rat kidney tissue S1P3_D11

description: HSD male rat kidney tissue


title: CIA1-2_L4.D702


title: Control input

city: Stanford

first: Min

last: Huang

state: CA

address: 265 Campus Drive

department: Internal Medicine

institute: Stanford Cancer Institute

data_processing:
using FASTQ in Galaxy online platform for quality control
Sequencing reads were aligned using Bowtie aligner with default parameters using Galaxy
Peaks were called by MACS version 2.1.0. Peaks were defined as significant with a q value cut-off of 5.00e-02 using Galaxy
ChIP-input samples with or without Dinaciclib treatment were used to construct a peak matrix using Galaxy
ChIP-seq density heat map and genome-wide occupancy histogram plots were generated using Galaxy.
Genome_build: Human reference genome (hg38)
Supplementary_files_format_and_content: Bigwig files generated by Galaxy

source_name: CLB-GA

growth_protocol: CLB-GA cells were cultured in RPMI 1640 w/ HEPES, supplemented with 5% FBS, 2 mM glutamine, 1X Insulin-Transferrin-Selenium (ITS -G), 100 U ml−1 penicillin and 100 μg/ml streptomycin

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as described previously (Lee TI, Johnstone SE, Young RA. Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc. 2006;1(2):729-748)
ChIP-seq libraries were prepared according to the Illumina protocol for ChIP-seq

treatment_protocol: CLB-GA cells were treated with 10 nM Dinaciclib for 8 h

value: CLB-GA

value: Neuroblastoma

value: Control No Treatment


title: HSD male rat kidney tissue S1P3_E12

description: HSD male rat kidney tissue


title: Dinaciclib Input

value: Dinaciclib, 10 nM, 8 h


title: HSD male rat kidney tissue S1P3_E10

description: HSD male rat kidney tissue

value: Sprague Dawley


title: HSD male rat kidney tissue S1P3_D09

description: HSD male rat kidney tissue

value: male


title: H3K36me3-CHIP-control

value: Histone H3 (tri methyl K36) (ab9050, Abcam)


title: HSD male rat kidney tissue S1P3_D10

description: HSD male rat kidney tissue

value: 8-10 weeks


title: HSD male rat kidney tissue S1P3_D08

description: HSD male rat kidney tissue


title: H3K36me3-CHIP-Dinaciclib


title: HSD male rat kidney tissue S1P3_D07

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_D06

description: HSD male rat kidney tissue


title: H3K27Ac-CHIP-control

value: Acetyl Histone H3 (K27) (ab4729, Abcam)


title: HSD male rat kidney tissue S1P3_D04

description: HSD male rat kidney tissue


title: A673_histone_input_rep3

description:
processed data file: K4me1_A673_broad_FE.bw
processed data file: K4me2_A673_FE.bw
processed data file: K4me3_A673_FE.bw

data_processing:
Illumina’s Bcl2fastq conversion software.
FastQC
Quality and adapter trimming: TrimGalore!
Alignment to hg19 with bowtie2.
SAM to BAM conversion with samtools.
Peak calling with MACS2 and csaw.
Track building with MACS2 using fold enrichment calculations over input.
BAM to BED and BED to spike-in normalized bedgraph with Pybedtools (H3K27ac and Rb CUT&RUN bigwigs).
Bedgraph to bigwig with bedGraphToBig UCSC util (H3K27ac and Rb CUT&RUN bigwigs).
Differential H3K27ac was calculated with csaw.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig, genome tracks for each sample.
Supplementary_files_format_and_content: txt, peak calling output for H3K27ac from csaw package in R.
Supplementary_files_format_and_content: xls, peak calling output from MACS2.

extract_protocol:
Histone ChIP
NEBNext

treatment_protocol: A673 cells were seeded at 50% confluency and left to adhere overnight (day 0). shRNAs were retrovirally delivered on day 1. Selection in 2 µg/mL puromycin (Sigma P8833) occurred on days 7. Cells were then collected for ChIP or CUT&RUN.

value: iLuc


title: EFKD_H3K4me3_rep3

description: processed data file: K4me3_EFKD_FE.bw

value: iEF


title: H3K27Ac-CHIP-Dinaciclib


title: EFKD_histone_input_rep3

description:
processed data file: K4me1_EFKD_broad_FE.bw
processed data file: K4me2_EFKD_FE.bw
processed data file: K4me3_EFKD_FE.bw


title: HSD male rat kidney tissue S1P3_D03

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_D05

description: HSD male rat kidney tissue


title: A673_H3K4me3_rep3

description: processed data file: K4me3_A673_FE.bw


title: HSD male rat kidney tissue S1P3_D01

description: HSD male rat kidney tissue


title: EFKD_H3K4me2_rep3

description: processed data file: K4me2_EFKD_FE.bw


title: Brd4-CHIP control

value: Brd4 (A301-985A50,Lot # 6,  BETHYL Laboratories)


title: HSD male rat kidney tissue S1P3_C12

description: HSD male rat kidney tissue

value: kidney


title: HSD male rat kidney tissue S1P3_C11

description: HSD male rat kidney tissue


title: A673_H3K4me2_rep3

description: processed data file: K4me2_A673_FE.bw


title: HSD male rat kidney tissue S1P3_C10

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_C09

description: HSD male rat kidney tissue


title: EFKD_H3K4me1_rep3

description:
processed data file: K4me1_EFKD_broad_FE.bw
processed data file: K4me1_EFKD_broad_peaks.xls


title: HSD male rat kidney tissue S1P3_C08

description: HSD male rat kidney tissue


title: 11dpi_i_2

first: Michelle

last: Lissner

address: 299 Campus Drive Fairchild D333

institute: Stanford University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Supplementary_files_format_and_content: FPKM

organism: Mus musculus

source_name: liver

extract_protocol:
Livers were dissect and flash-frozen in liquid nitrogen before being frozen at -80C. RNA was isolated using TRIzol reagent.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Library Prep Kit v2 (RS-122-2001) using 500 ng RNA as input.

treatment_protocol: 8-12 week-old female C57BL/6-Crl mice were infected with 100,000 red blood cells infected with Plasmodium chabaudi AJ

tag: agent

value: Plasmodium chabaudi AJ

tag: day post infection

tag: Sex

value: female


title: 11dpi_i_1


title: HSD male rat kidney tissue S1P3_C07

description: HSD male rat kidney tissue

value: Triclosan


title: HSD male rat kidney tissue S1P3_C06

description: HSD male rat kidney tissue


title: EFKD_histone_input_rep2


title: A673_H3K4me1_rep3

description:
processed data file: K4me1_A673_broad_FE.bw
processed data file: K4me1_A673_broad_peaks.xls


title: HSD male rat kidney tissue S1P3_C05

description: HSD male rat kidney tissue


title: Brd4-CHIP Dinaciclib

tag: cell type

tag: chip antibody

value: Brd4 (A301-985A50, Lot # 6, BETHYL Laboratories)


title: 10dpi_ui_1

value: uninfected


title: HSD male rat kidney tissue S1P3_D02

description: HSD male rat kidney tissue


title: EFKD_H3K4me3_rep2

description: processed data file: K4me3_EFKD_FE.bw

tag: transduced shrna

tag: replicate


title: HSD male rat kidney tissue S1P3_B12

description: HSD male rat kidney tissue

value: TCAB


title: HSD male rat kidney tissue S1P3_B10

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_C03

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_C04

description: HSD male rat kidney tissue


title: A673_H3K4me3_rep2

description: processed data file: K4me3_A673_FE.bw

tag: antibody


title: A673_histone_input_rep2


title: 10dpi_i_4


title: HSD male rat kidney tissue S1P3_B08

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_B11

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_B09

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_B07

description: HSD male rat kidney tissue


title: 10dpi_i_3


title: EFKD_H3K4me2_rep2

description: processed data file: K4me2_EFKD_FE.bw


title: 10dpi_i_2


title: 10dpi_ui_2


title: A673_H3K4me2_rep2

description: processed data file: K4me2_A673_FE.bw


title: HSD male rat kidney tissue S1P3_B05

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_B04

description: HSD male rat kidney tissue


title: 10dpi_i_1


title: HSD male rat kidney tissue S1P3_B03

description: HSD male rat kidney tissue


title: 9dpi_i_2


title: HSD male rat kidney tissue S1P3_A12

description: HSD male rat kidney tissue


title: 10dpi_i_5


title: A673_H3K4me1_rep2


title: HSD male rat kidney tissue S1P3_B06

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_A11

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_A10

description: HSD male rat kidney tissue


title: 9dpi_i_1


title: 8dpi_ui_2


title: HSD male rat kidney tissue S1P3_A07

description: HSD male rat kidney tissue


title: EFKD_histone_input_rep1


title: 8dpi_ui_1


title: HSD male rat kidney tissue S1P3_A08

description: HSD male rat kidney tissue


title: A673_histone_input_rep1


title: HSD male rat kidney tissue S1P3_A05

description: HSD male rat kidney tissue


title: A673_H3K4me3_rep1

description: processed data file: K4me3_A673_FE.bw


title: HSD male rat kidney tissue S1P3_A06

description: HSD male rat kidney tissue


title: 8dpi_i_5


title: 8dpi_i_4


title: HSD male rat kidney tissue S1P3_A03

description: HSD male rat kidney tissue


title: HSD male rat kidney tissue S1P3_A04

description: HSD male rat kidney tissue


title: EFKD_H3K4me2_rep1

description: processed data file: K4me2_EFKD_FE.bw


title: HSD male rat liver tissue S1P2_H01

description: HSD male rat liver tissue

value: liver


title: 8dpi_i_3


title: HSD male rat liver tissue S1P2_H02

description: HSD male rat liver tissue


title: EFKD_H3K4me3_rep1

description: processed data file: K4me3_EFKD_FE.bw


title: HSD male rat liver tissue S1P2_G03

description: HSD male rat liver tissue


title: EFKD_H3K4me1_rep2


title: HSD male rat kidney tissue S1P3_A09

description: HSD male rat kidney tissue


title: HSD male rat liver tissue S1P2_G04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S1P2_G02

description: HSD male rat liver tissue


title: A673_H3K4me2_rep1

description: processed data file: K4me2_A673_FE.bw


title: HSD male rat liver tissue S1P2_G01

description: HSD male rat liver tissue


title: 8dpi_i_1


title: A673_H3K4me1_rep1


title: 7dpi_i_2


title: HSD male rat liver tissue S1P2_F04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S1P2_F03

description: HSD male rat liver tissue


title: BPA-plus-KRG_uterus

city: seoul

first: Jeonggeun

last: Lee

address: Kwangjin-gu, Seoul

country: South Korea

institute: sejong univ

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: CD-1 mouse uterus, exposed to BPA 200mg/kg/day and KRG 1.2g/kg/day

growth_protocol: The animals kept at a temperature of 23±2°C with 12 hours dark and light cycle and allowed free access to food and water.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: the BPA dose of 200 mg/kg/day and the KRG dose of 1.2g/kg/day were determined and treated daily for 7 days by oral administration.

value: uterus

tag: treatment


title: HSD male rat liver tissue S1P2_F02

description: HSD male rat liver tissue

value: Sprague Dawley


title: 7dpi_i_1


title: HSD male rat liver tissue S1P2_E04

description: HSD male rat liver tissue

value: male


title: KRG_uterus

source_name: CD-1 mouse uterus, exposed to KRG 1.2g/kg/day

value: exposed to KRG 1.2g/kg/day


title: HSD male rat liver tissue S1P2_E02

description: HSD male rat liver tissue

value: 8-10 weeks


title: HSD male rat liver tissue S1P2_E03

description: HSD male rat liver tissue


title: OVX-Con_uterus

source_name: CD-1 mouse uterus, OVX-control

value: OVX-control


title: HSD male rat liver tissue S1P2_E01

description: HSD male rat liver tissue


title: BPA_uterus

source_name: CD-1 mouse uterus, exposed to BPA 200mg/kg/day

value: exposed to BPA 200mg/kg/day


title: 0dpi_3_ui


title: HSD male rat liver tissue S1P2_D04

description: HSD male rat liver tissue


title: EFKD_H3K4me1_rep1

tag: cell line

value: iEF


title: HSD male rat liver tissue S1P2_H03

description: HSD male rat liver tissue

tag: strain


title: 8dpi_i_2


title: HSD male rat liver tissue S1P2_D02

description: HSD male rat liver tissue

tag: gender


title: HSD male rat liver tissue S1P2_D03

description: HSD male rat liver tissue

tag: age


title: BPA-plus-KRG_liver

source_name: CD-1 mouse liver, exposed to BPA 200mg/kg/day and KRG 1.2g/kg/day


title: HSD male rat liver tissue S1P2_D01

description: HSD male rat liver tissue

tag: animal id


title: HSD male rat liver tissue S1P2_C04

description: HSD male rat liver tissue

tag: tissue


title: KRG_liver

source_name: CD-1 mouse liver, exposed to KRG 1.2g/kg/day


title: BL4: NETs neg rep 3

city: New York

last: Brown

state: NY

address: 435 E 30th St

department: Medicine

institute: NYU Langone

data_processing:
Align reads to m10 using STAR
counts reads per gene for all samples using FeatCounts module of SubRead
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file, output of FeatCounts, with unnormalized reads per gene

source_name: Atherosclerotic CD68 positive cells

growth_protocol: RNA from CD68 positive cells from NET positive and NET negative areas were collected from sectioned atherosclerotic roots using laser capture microdissection

extract_protocol:
RNA was isolated using the PicoPure Kit (Molecular Devices, Inc., Sunnyvale, CA), treated with DNase and the quality and quantity determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). RNA was amplified (Automated Nugen Ovation Trio Low Input RNA (500pg)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Atherosclerotic Plaque (Root)

tag: genotype

value: Ldlr-/-

value: Atherosclerotic CD68 positive cells


title: HSD male rat liver tissue S1P2_C03

description: HSD male rat liver tissue

tag: chemical

tag: dose(mg/kg)


title: HSD male rat liver tissue S1P2_B04

description: HSD male rat liver tissue


title: BPA_liver

source_name: CD-1 mouse liver, exposed to BPA 200mg/kg/day


title: HSD male rat liver tissue S1P2_B03

description: HSD male rat liver tissue


title: OVX-Con_liver

source_name: CD-1 mouse liver, OVX-control


title: BL2: NETs neg rep 2


title: HSD male rat liver tissue S1P2_A04

description: HSD male rat liver tissue


title: 0dpi_2_ui

tag: agent

tag: day post infection

value: female


title: Cebpa-/p30; Asxl1G643W/G643W #3 (90MUT)

city: Copenhagen

first: Bo

last: Porse

address: Ole Maaløes Vej 5, 4

department: Finsen Laboratory and BRIC

country: Denmark

institute: University of Copenhagen

data_processing:
The Illumina bcl2fastq2 Conversion Software (v2.20.0.422) was used to demultiplex and to convert base call files into FASTQ files (bcl2fastq --no-lane-splitting).
Salmon 0.12.0 was used to quantify expression of transcripts from RNA-seq experiments using mm10/GRCm38_94 Ensembl transcriptome (salmon quant -l U --seqBias --numBootstraps 30)
Genome_build: GRCm38.p6 (Ensembl release 94)
Supplementary_files_format_and_content: Tab-delimited text file including estimated number of reads mapping to each transcript and relative abundance of transcript in TPM.

source_name: AML BM cells

extract_protocol:
sorted into RLT lysis buffer (Qiagen) and RNA was extracted using the microRNA Mini kit (Qiagen)
TruSeq V2 kit (Illumina)

treatment_protocol: FACS sorting of blast cells from Bone Marrow of leukemic mice (Ter119-, B220-, CD3-, Mac1low, Gr1low, CD45.2+ )

tag: cell type

value: leukemic blast cells

value: Cebpa-/p30; Asxl1G643W/G643W

tag: mouse strain


title: BL1: NETs neg


title: BL2: NETs pos rep 2


title: Cebpa-/p30; Asxl1G643W/G643W #2 (89MUT)


title: HSD male rat liver tissue S1P1_H10

description: HSD male rat liver tissue

value: Triclosan


title: HSD male rat liver tissue S1P1_H12

description: HSD male rat liver tissue

value: TCAB


title: 0dpi_1_ui

value: uninfected

tag: Sex


title: HSD male rat liver tissue S1P1_H08

description: HSD male rat liver tissue

value: liver


title: HSD male rat liver tissue S1P1_H09

description: HSD male rat liver tissue

value: Sprague Dawley


title: BL1: NETs pos


title: Cebpa-/p30; Asxl1WT #3 (67WT)

value: Cebpa-/p30; Asxl1WT


title: BL4: NETs pos rep 3


title: Cebpa-/p30; Asxl1G643W/G643W #1 (87MUT)


title: Cebpa-/p30; Asxl1WT #2 (64WT)


title: Foxp3-GFP+Treg_WT_Rep3_scRNA-seq

city: Cambridge

first: Mohammed-Firas

last: Sadiyah

address: The Old Schools, Trinity Ln

country: United Kingdom

institute: University of Cambridge

data_processing:
Raw 10X sequencing data files underwent quality control with FastQC, adaptor trimming with Cutadapt and alignment to the mm10 Mus musculus genome annotation with hisat2 using ClusterFlow pipelines
Each library was down-sampled to equivalent sequencing depth and were merged with cell ranger aggr (v2.0.2)
Merged data were transferred to the R statistical environment for analysis using the package Seurat
Only cells expressing between 200 to 2500 genes, less than 5% mitochondrial-associated transcripts and genes expressed in at least 3 cells were included in the analysis
The data were then lognormalized and scaled per cell, and variable genes were detected using Findvariablegenes function in Seurat, as per default settings
The transcriptomic data from each cell were then further normalized by the number of genes quantified, UMI-detected and mitochondrial genes to account for technical variation
Genome_build: mm10
Supplementary_files_format_and_content: Genes exhibiting enrichment in at least one cluster seurat find cluster.xlsx
Supplementary_files_format_and_content: rawdata.csv: contains raw counts, all cells, all genes (14098 genes,  10685 cells)
Supplementary_files_format_and_content: data.csv: processed normalised counts, from the filtered cells and filtered genes (i.e. cells with high mitochondrial % - dead / too many genes - enriched for doublets)  (14098 genes  10464 cells).

source_name: Treg cells

extract_protocol:
Single-cell suspensions were purified by total CD4+ T cell enrichment followed by FACS-sorting
stored in 40 µl RNAlater™ Stabilization Solution at -80 °C
Samples were processed using the QIAshredder Kit (Qiagen) according to the manufacturer’s protocol
RNA was extracted from samples using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol
RNA libraries were prepared for single-cell RNA sequencing (scRNA-seq) using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 (10x Genomics), processed with the Chromium (10x Genomics) and sequenced using the HiSeq 4000 System (Illumina)

value: spleen

value: post natal 18–21 weeks

value: Bach2+/+ Foxp3EGFP-Cre-ERT2


title: HSD male rat liver tissue S1P1_H06

description: HSD male rat liver tissue

value: male

value: 8-10 weeks


title: HSD male rat liver tissue S1P1_H07

description: HSD male rat liver tissue


title: Foxp3-GFP+Treg_WT_Rep2_scRNA-seq


title: Cebpa-/p30; Asxl1WT #1 (63WT)


title: Foxp3-GFP+Treg_WT_Rep1_scRNA-seq


title: HSD male rat liver tissue S1P2_A03

description: HSD male rat liver tissue


title: HSD male rat liver tissue S1P1_H05

description: HSD male rat liver tissue


title: HSD male rat liver tissue S1P1_H11

description: HSD male rat liver tissue


title: TAZ2_YAP1_HepG2#3

type: RNA

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: Gene expression of TAZ2/TAZ3 and YAP1/YAP2 specific siRNA transfected HepG2 cells

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 19 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

source_name: liver cancer cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: HepG2 cells were cultured in RPMI medium supplemented with 10% FCS and 1% penicillin/streptomycin.

extract_protocol: For isolation of total RNA, the NucleoSpin RNA II kit was used according to the manufacturer's instructions (Machery-Nagel, Düren, Germany).

treatment_protocol: For siRNA inhibition assays cells were seeded one day before transfection. Untreated and nonsense siRNA-treated cells served as controls. SiRNAs (final concentration 20 nM) and the transfection reagent Oligofectamine (Life Technologies, Darmstadt, Germany) were diluted in Opti-MEM (Gibco/Life Technologies), mixed and incubated at room temperature, before being distributed onto the cells, which were covered with Opti-MEM. Four hours later fresh medium was added and 24 hours later the medium was replaced.

value: liver cancer cell line

tag: vector

value: siTAZ+YAP


title: HSD male rat liver tissue S1P1_H04

description: HSD male rat liver tissue


title: NegControl5

first: David

middle: T

last: Ting

address: 149 E 13th street

department: Cancer Center

institute: Massachusetts General Hospital

data_processing:
Reads aligned to HG38
Deduplicated BAM files used with HTSeq-Count to create count tables
Data was analyzed with DESeq2 for differential expresison analysis
Genome_build: GRCH38
Supplementary_files_format_and_content: Text file with raw counts
Supplementary_files_format_and_content: Text file with DESeq2 Normalized counts

molecule: polyA RNA

source_name: lung

growth_protocol: Rapid autopsy was performed for samples collection.

extract_protocol:
RNA extraction from FFPE slides was done using the FormaPure Total nucleic acid extraction kit (C16675, Beckman Coulter) according to manufacturer instructions. Three 5 um thin tissue sections from areas devoid of acute inflammation were used per sample
The Smarter Stranded Total RNA-Seq kit v2 (634413, Illumina) was used with 10 ng RNA input, according to the manufacturer instructions to generate libraries.
Dual-indexed pooled libraries were sequenced on the Illumina NextSeq 500 platform using a 150 cycles kit with paired end read mode.

treatment_protocol: Samples were formalin fixed for 3 days prior to embedding in paraffin and sectioning.

tag: sample case

value: Control

tag: tissue type

value: Formalin fixed paraffin embedded tissue

tag: pool no

tag: infection


title: Foxp3-GFP+Treg_cKO_Rep3_scRNA-seq

tag: strain

value: Bach2fl/fl Foxp3EGFP-Cre-ERT2


title: NegControl4


title: NegControl3


title: Foxp3-GFP+Treg_cKO_Rep2_scRNA-seq

tag: age


title: Foxp3-GFP+Treg_cKO_Rep1_scRNA-seq


title: HSD male rat liver tissue S1P1_H02

description: HSD male rat liver tissue

tag: gender

tag: animal id


title: TAZ3_YAP2_HepG2#2

tag: cell line


title: 0dpi_4_ui

value: female


title: NegControl2


title: TAZ2_HepG2#3

description: Gene expression of TAZ2/TAZ3 specific siRNA transfected HepG2 cells

value: siTAZ


title: HSD male rat liver tissue S1P1_H01

description: HSD male rat liver tissue

tag: tissue

tag: chemical


title: TAZ2_YAP1_HepG2#2


title: TAZ2_HepG2#2


title: HSD male rat liver tissue S1P1_G12

description: HSD male rat liver tissue

value: TCAB

tag: dose(mg/kg)


title: HSD male rat liver tissue S1P1_G11

description: HSD male rat liver tissue


title: case5-marrow1

source_name: marrow


title: HSD male rat liver tissue S1P1_H03

description: HSD male rat liver tissue


title: case5-heart1

source_name: heart


title: TAZ3_YAP2_HepG2#1


title: HSD male rat liver tissue S1P1_G10

description: HSD male rat liver tissue

value: Triclosan


title: HSD male rat liver tissue S1P1_G09

description: HSD male rat liver tissue

value: liver


title: END-seq ZCWPW1-KO (Adult)

city: Bethesda

first: Mohamed

last: Mahgoub

state: MD

address: 6 Center Dr

department: Division of Developmental Biology

institute: NICHD

data_processing:
Mapping: reads were aligned to the mouse (GRCm38p2/mm10) genome using Bowtie version 1.1.2 and 3 mismatches were allowed and the best strata for reads were kept with multiple alignments (-n 3 -k 1 -l 50). Functions ‘‘view’’ and ‘‘sort’’ of samtools (version 1.6) were used to convert and sort the mapping output to sorted bam file.  Peaks Calling: peaks were called using MACS 1.4.3. END-seq peaks were called using the parameters: --shiftsize=1000, --nolambda, --nomodel and --keep-dup = all. Peaks with >2.5 fold-enrichment are kept and those within blacklisted regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were filtered.   Estimation of total breaks and comparison between genotypes: we added a spike-in control into END-seq samples which consists of a G1-arrested Ableson-transformed pre-B cell line (Lig4-/-) carrying a single zinc-finger-induced DSB at the TCRβ enhancer. This site is expected to break in all spike-in cells, which were mixed in at a 5% frequency with bulk testicular cells. END-seq signal was calculated, as RPKM, within ±3kb window around all hotspot centers. Total intensity was divided by the signal around the spiked-in breaks and then divided by 20 since the spiked-in was added at a 1:20 ratio (5%).
Genome_build: mm10

source_name: Testis

extract_protocol:
Testes were dissected, tunica removed, and tubules were gently dissociated with forceps and enzymatic digestion to make single cell suspension. Cells were then embeded into agarose plugs to perform END-seq
END-seq (Canela et al., 2017, 2019)

tag: genotype

value: Zcwpw1 KO

value: Adult

value: whole testis

tag: assay

value: END-seq

tag: anitbody used

tag: library layout

value: single-end


title: case5-kidney1

source_name: kidney


title: HSD male rat liver tissue S1P1_G08

description: HSD male rat liver tissue

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing  language R. The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains  the reads and quality scores for one sample. Each FASTQ file is aligned using the Bowtie algorithm to a pseudotranscriptome  input by the user. The output for TempO-Seq data analysis is a table of counts with each column  representing a sample and each row representing a gene.
Data normalization was not done
Supplementary_files_format_and_content: Raw data matrix all smaples

extract_protocol: The liver and left and right kidneys were collected, weighed, and the left liver lobe and right kidney were preserved in RNAlater (Qiagen, Valencia, CA) and stored at 4°C for RNA extraction. Total RNA was extracted from liver and kidney within 1 week of harvest using the RNeasy Mini Kit (Qiagen) with a DNA digestion step. RNA was sent frozen to BioSpyder (Carlsbad, CA) for HTT analysis using the rat S1500+ TempO-Seq platform.

value: Sprague Dawley

value: male


title: OligoPrecursorCell_OGD-4

city: Kobe

first: Yuichi

last: Ono

state: Hyogo

address: 6-8-2 Minatojima-minamimachi, Chuo-ku

department: Developmental Neurobiology

country: Japan

institute: KAN Research Institute Inc.

description: processed data file: OPC-OGD.txt

data_processing:
All raw sequencing reads were trimmed using Trimmomatic software.
Bases and QC were generated by FastQC.
The abundance of transcripts was then estimated using an Expectation-Maximization algorithm implicated in the software package Cufflink v2.2.1.
Genome_build: rn6 (Rnor_6.0)
Supplementary_files_format_and_content: OPC-OGD.txt: Tab-delimited text file includes FPKM values for all samples.

source_name: Cerebral cortex

growth_protocol: Mixed glial culture cells was prepared from 1-2 day old rat and maintained in DMEM containing 20% FBS. Then oligodendrocyte precursor cells were collected as non-adherent cells and cultured in Neurobasal medium containing 2 mM glutamine, 1% penicillin/streptomycin, 10 ng/ml PDGF, 10 ng/ml FGF, and 2% B27 supplement on poly-DL-ornithine-coated plates for 4-5 days.

extract_protocol:
Total RNA was harvested using RNeasy kit (QIAGEN).
RNA libraries were prepared for sequencing using Agilent SureSelect Strand Specific RNA prep kit (G9691A).

treatment_protocol: Cultured oligodendrocyte precursor cells were shifted to oxygen glucose deprivation condition for 6 hours.

tag: strain/background

tag: cell type

value: Primary cultured oligodendrocyte precursor cells

tag: treatment

value: Cultured under oxygen glucose deprivation condition


title: case5-liver1

source_name: liver

tag: sample case

tag: tissue type

tag: pool no


title: OligoPrecursorCell_OGD-3

description: processed data file: OPC-OGD.txt


title: END-seq WT (Adult)

tag: strain

value: wild type

tag: age

tag: Sex


title: NegControl1

value: Control

value: Formalin fixed paraffin embedded tissue

tag: infection


title: HSD male rat liver tissue S1P1_G07

description: HSD male rat liver tissue

tag: gender

value: 8-10 weeks

tag: animal id

tag: tissue


title: OligoPrecursorCell_OGD-2

description: processed data file: OPC-OGD.txt


title: OligoPrecursorCell_OGD-1

description: processed data file: OPC-OGD.txt


title: END-seq ZCWPW1-KO (Juvenile)

tag: genotype

value: Juvenile (14 days)


title: TAZ2_YAP1_HepG2#1

value: liver cancer cell line

tag: cell line

tag: vector

value: siTAZ+YAP


title: case5-bowel1

source_name: bowel


title: TAZ3_HepG2#2

value: siTAZ


title: PC3_miR26

city: Chuo-ku

first: Yusuke

last: Yamamoto

state: Tokyo

address: 5-1-1, Tsukiji, Chuo-ku

institute: National cancer center research institute

description: Total RNA extracted from prosate cancer cells, and 100 ng of RNA for analysis

hyb_protocol: Gene Expression Hybridization Kit and Gene Expression Wash Pack (Agilent)

scan_protocol: Agilent SureScan G4900DA

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: miR-26a-overexpressing prostate cancer cell

label_protocol: Low Input Quick Amp Labeling Kit (Agilent Technologies)

growth_protocol: The human prostate cancer epithelial metastatic cell line PC3 (ATCC CRL-1435) were purchased from ATCC. PC3 and PC-3M-luc-C6 (PC3M) (Xenogen, Alameda, CA) were cultured in RPMI 1640 medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS) and an antibiotic-antimycotic (Gibco) solution at 37℃. For routine maintenance, each cell line was grown as a monolayer at 37℃ with 5% carbon dioxide and 95% relative humidity.

extract_protocol: Total RNA was extracted using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA was quantified using a NanoDrop-1000 spectrophotometer and a Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, Calif.).

treatment_protocol: Transfections of 10 nM microRNA mimics or negative control miRNA were accomplished with the DharmaFECT Transfection Reagent 1 according to the manufacturer’s protocol. The miR-26a mimic or negative control miRNA  was used at a final concentration of 10 nM. After 24 hours, the conditioned medium was changed to Advanced RPMI medium containing an antibiotic-antimyotic and 2mM L-glutamine and cultured for 2 days.

value: prostate cancer cell line

tag: genotype/variation

value: miR-26a mimic


title: case5-skin1

source_name: skin


title: PC3M_miR26


title: HSD male rat liver tissue S1P1_G06

last: Gwinn

address: 111 Alexander Dr.

institute: National Institute of Health Sciences

description: HSD male rat liver tissue

value: liver

tag: chemical

value: Triclosan

tag: dose(mg/kg)


title: END-seq WT (Juvenile)

value: whole testis

tag: assay

value: END-seq

tag: anitbody used

tag: library layout

value: single-end


title: TAZ2_HepG2#1

tag: cell type


title: PC3_NC1

source_name: control prostate cancer cell

value: negative control miRNA


title: PC3M_NC1


title: case5-lung5

tag: sample case

tag: tissue type

tag: pool no


title: OligoPrecursorCell_Control-4

description: processed data file: OPC-OGD.txt

tag: strain/background

value: Sprague Dawley

value: Primary cultured oligodendrocyte precursor cells

tag: treatment


title: HSD male rat liver tissue S1P1_G05

description: HSD male rat liver tissue

tag: strain

tag: gender

value: male

tag: age

tag: animal id


title: TAZ3_HepG2#1

tag: cell line

tag: vector


title: OligoPrecursorCell_Control-3

description: processed data file: OPC-OGD.txt

value: Control


title: HSD male rat liver tissue S1P1_G04

description: HSD male rat liver tissue

value: 8-10 weeks

tag: tissue

tag: chemical


title: case5-fat1

source_name: fat

value: Formalin fixed paraffin embedded tissue

tag: infection


title: OligoPrecursorCell_Control-2

description: processed data file: OPC-OGD.txt


title: HSD male rat liver tissue S1P1_G03

description: HSD male rat liver tissue

tag: dose(mg/kg)


title: case5-lung3


title: OligoPrecursorCell_Control-1

description: processed data file: OPC-OGD.txt


title: case5-lung4


title: HSD male rat liver tissue S1P1_G01

description: HSD male rat liver tissue


title: case5-lung2


title: HSD male rat liver tissue S1P1_F12

description: HSD male rat liver tissue

value: TCAB


title: HSD male rat liver tissue S1P1_G02

description: HSD male rat liver tissue


title: HSD male rat liver tissue S1P1_F11

description: HSD male rat liver tissue


title: case5-lung1


title: case4-bowel1


title: HSD male rat liver tissue S1P1_F10

description: HSD male rat liver tissue


title: case4-heart2


title: HSD male rat liver tissue S1P2_F01

description: HSD male rat liver tissue


title: HSD male rat liver tissue S1P1_F09

description: HSD male rat liver tissue


title: case4-kidney1


title: SAFB2-OE-ChIP

city: Beijing

first: Hai

last: Qi

address: Zhongguancun North Street

department: School of Medicine

country: China

institute: Tsinghua University

data_processing:
Basecalls performed using CASAVA version
Reads obtained from ChIP-seq/ATAC-seq library sequencing were aligned to the mm9 genome assembly using bowtie2 program with default parameters.
Reads obtained from RNA-seq library sequencing were aligned to the mm9 genome assembly using tophat with uniq mapping parameters.
Peaks were called using the MACS program (p < 10e-3).
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing peaks called from ChIP-seq,  bedgraph files containing the sequencing signals of ChIP-seq or ATAC-seq
Supplementary_files_format_and_content: bedgraph files containing the sequencing signals of TT-seq

source_name: FB(OE)-SAFB2 mESC (constructed from BirA J1 mES cells)

growth_protocol:
ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1009 U/ml recombinant leukemia inhibitory factor (LIF, millipore).
ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore). 293T cells  were maintained in medium supplemented with 10% heat-inactivated FCS, Penicillin-Streptomycin Solution (100 × stock, Life Technologies).

extract_protocol:
ChIP was done following previously protocol with modifications (Shen, 2008). Cells were crosslinked by 2 mM DSP (dithiobis succinimidyl propionate) for 30 minutes, followed by a 10-minute 1% formaldehyde crosslinking. The crosslinked cells were first partially fragmented by 12 U/ml DNase I at 37 °C for 10 minutes, then sonicated at 25% amplitude for 30 seconds. The lysate were further sonicated into average DNA size 200-500 bp. spin at 14000rpm for 15 min, transferred the supernatant into a new tube and diluted by adding 5 × volume of ChIP dilution buffer. Added 5 μg FLAG antibody, end to end rotate overnight at 4℃. The target were further captured by adding 20 ul Protein A/G UltraLink Resin, further rotated for 4 hours at 4℃. After thoroughly washing, these samples were subjected to a second purification step using 30 μl M-280 Streptavidin Dynabeads (Invitrogen 11205D). The rest of the steps were performed as previously described (Shen et al., 2008)
Libraries were prepared by NEBNext Ultra II DNA library preparation kit according to the standard protocols provided by the manufacturer.

value: embryonic stem cells

tag: chip antibody

value: FLAG (Sigma-Aldrich, F3167)

tag: affinity purification

value: M280 Streptavidin Dynabeads (Invitrogen, 11205D)


title: SAFB-OE-ChIP-input

source_name: FB(OE)-SAFB mESC (constructed from BirA J1 mES cells)

growth_protocol:
ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1008 U/ml recombinant leukemia inhibitory factor (LIF, millipore).
ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore). 293T cells  were maintained in medium supplemented with 10% heat-inactivated FCS, Penicillin-Streptomycin Solution (100 × stock, Life Technologies).

tag: cell type


title: case4-lung2

tag: sample case

tag: tissue type


title: UTP6-OE-ChIP

source_name: FB(OE)-UTP6 mESC (constructed from BirA J1 mES cells)

growth_protocol:
ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1012 U/ml recombinant leukemia inhibitory factor (LIF, millipore).
ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore). 293T cells  were maintained in medium supplemented with 10% heat-inactivated FCS, Penicillin-Streptomycin Solution (100 × stock, Life Technologies).

extract_protocol:
ChIP was done following previously protocol with modifications (Shen, 2008). Briefly, cells were crosslinked on plate with 3% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. The lysate were further sonicated into average DNA size 200-500 bp. spin at 14000rpm for 15 min, transferred the supernatant into a new tube and diluted by adding 5 × volume of ChIP dilution buffer. Added 5 μg FLAG antibody, end to end rotate overnight at 4℃. The target were further captured by adding 20 ul Protein A/G UltraLink Resin, further rotated for 4 hours at 4℃. After thoroughly washing, the targeted DNA was eluted by elution buffer with protease K at 67℃.
Libraries were prepared by NEBNext Ultra II DNA library preparation kit according to the standard protocols provided by the manufacturer.

value: FLAG (Sigma-Aldrich, F3170)


title: CIRH1A-OE-ChIP

source_name: FB(OE)-CIRH1A mESC (constructed from BirA J1 mES cells)

growth_protocol:
ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1010 U/ml recombinant leukemia inhibitory factor (LIF, millipore).
ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore). 293T cells  were maintained in medium supplemented with 10% heat-inactivated FCS, Penicillin-Streptomycin Solution (100 × stock, Life Technologies).

extract_protocol:
ChIP was done following previously protocol with modifications (Shen, 2008). Briefly, cells were crosslinked on plate with 3% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. The lysate were further sonicated into average DNA size 200-500 bp. spin at 14000rpm for 15 min, transferred the supernatant into a new tube and diluted by adding 5 × volume of ChIP dilution buffer. Added 5 μg FLAG antibody, end to end rotate overnight at 4℃. The target were further captured by adding 20 ul Protein A/G UltraLink Resin, further rotated for 4 hours at 4℃. After thoroughly washing, the targeted DNA was eluted by elution buffer with protease K at 65℃.
Libraries were prepared by NEBNext Ultra II DNA library preparation kit according to the standard protocols provided by the manufacturer.

value: FLAG (Sigma-Aldrich, F3168)


title: HSD male rat liver tissue S1P1_F08

first: Will

description: HSD male rat liver tissue

value: liver

value: Triclosan


title: SAFB-OE-ChIP

value: FLAG (Sigma-Aldrich, F3166)


title: 12-0358p15Ctrl

city: Durham

first: Landon

middle: J

last: Hansen

address: 203 Research Drive, MSRB1 Rm 171

institute: Duke University School of Medicine

description: Control

hyb_protocol: Product generated from the label protocol was hybridized onto the Affymetrix GeneChip Human Genome 2.0 plus array in Affymetrix GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450 according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).

scan_protocol: Arrays were scanned with Affymetrix GeneChip® Scanner 7G according to Affymetrix GeneChip protocols

data_processing: Data was initially processed using the Affymetrix Expresson Console and Affymetrix Transcriptome Analysis Console v3.0 software

source_name: Patient-derived GBM cell line_MTAP WT

label_protocol: Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE). Hybridization targets were prepared with the affymetrix GeneChip 3' IVT Plus Kit from total RNA.

growth_protocol: Patient derived GBM cell lines were grown in human Neural Stem Cell media following the NeuroCult NS-A Proliferation Protocol

extract_protocol: Total RNA was extracted using the Zymo Quick RNA prep kit

value: patient-derived primary glioblastoma cell line

tag: genotype/variation

value: MTAP WT

tag: treated with

value: vehicle control NaOH (1:1000 dilution)


title: 12-0008p19Ctrl

description: Control


title: 13-0302p18Ctrl

description: Control

source_name: Patient-derived GBM cell line_MTAP deleted

value: MTAP Deleted