title: Mix pool CATE-seq

first: Xu

last: Xinhui

address: Sipailou 2#

institute: SEU

data_processing:
The raw reads data were separated according to the barcode using a homemade Python scripts.
All reads were cut 25 bp at 5' by a homemade Python scripts.
The trimmed reads were aligned to the human genome (hg19) using Bowtie program (version 1.1.2)
The sorted bam files were convert to bedgraph files using genomeCoverageBed.
The bedgraph files were convert to bigwig using the program wigToBigWig.
Genome_build: hg19

growth_protocol: 293T, HepG2, HeLa, SiHa, and C-33A cells were cultivated with the DMEM medium (HyClone) supplemented with 10% fetal bovine serum (HyClone), 100 U/mL penicillin, and 100 μg/mL streptomycin (Biosharp). The HL7702 cell was cultivated with the RPMI-1640 medium (HyClone) supplemented with 10% fetal bovine serum (HyClone), 100 U/mL penicillin, and 100 μg/mL streptomycin (Biosharp). Cells were incubated at 37°C in a 5% CO2 incubator.

extract_protocol:
Cells were inoculated into a 25 cm2 culture flask and cultured in complete medium for 24 h (degree of fusion greater than 80%). Cells were then washed twice with pre-chilled PBS and collected by trypsinization. The genomic DNA (gDNA) was extracted from cells by using the TIANamp Genomic DNA Kit (Tiangen).
The extracted gDNAs of 293T, HepG2, HL7702, C-33a, SiHa, and HeLa cells were tagmented by the Tn5 transposomes T-B-1 to T-B-6, respectively. Additionally, the 293T gDNA was also tagmented by the Tn5 transposome T-B-7, which was called as 293Tm. The tagmentation reaction (30 μL) contained 200 ng gDNA, 5 μL transposome, 6 μL 5× LM buffer, and certain volume of ddH2O that supplemented the total reaction to 30 μL. The reaction was incubated at 55°C for 15 min. The reaction contained no transposome was used as control. The tagmentation products were run with agarose gel and the fragments of 200–1000 bp were recovered, which were used as the input DNA for enriching target sequences.The dCas9 protein was diluted to 0.3 μM with stock solution and stored at -20° C. The csgRNAs were mixed into four groups according to their numbering. In each mixing, about 7.5 ng of each csgRNA was used. Five μL of magnetic beads with streptavidin was added to 50 μL of PBS containing 0.5% BSA and placed on a magnetic stand for 15 s. The supernatant was aspirated. After washing three times with 50 μL of PBS-BSA solution, the beads were added with 50 μL of 1×dCas9 buffer and 2 μL of capture oligonucleotide (10 μM). The sequence of capture oligonucleotide was 5′-Biotin-TTTTTTTGCA TCTGGTATTC GTAAGGTTCC G-3′. The beads were mixing by rotation for 1 hour. The beads were washed three times with 50 μL of 1×dCas9 buffer.

tag: fragment method

value: Tagmentation

tag: barcode


title: HL7702_CATE

status: Public on Sep 15 2018

type: SRA

city: Nanjing

country: China

description: The extracted gDNAs of 293T, HepG2, HL7702, C-33a, SiHa, and HeLa cells were tagmented by the Tn5 transposomes T-B-1 to T-B-6, respectively.

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens


title: 1213411_01G_WT_AT_3_S49 (bulk RNA-seq)

city: Memphis

first: Doug

last: Green

state: Tn

address: 262 Danny Thomas Pl

department: Immunology

country: USA

institute: St. Jude Children's Research Hospital

library_source: transcriptomic

data_processing:
For bulk RNA-seq data, reads were aligned with STAR v2.5.3a using splice junctions inferred from Gencode M15 gene annotations. Unmapped reads were then re-aligned with BWA.
For aligned bulk RNA-seq data, gene counts were calculated using FeatureCounts v1.5.1.
Genome_build: mm10
Supplementary_files_format_and_content: For single-cell RNA-seeq data, processed data contain counts of transcripts for each gene in each cell after removal of read duplicates using UMIs. For bulk RNA-seq data, the processed data file includes counts for each gene per sample.

molecule: total RNA

organism: Mus musculus

source_name: bone marrow-derived macrophages

growth_protocol:
Bone marrow cells were harvested from the femur and differentiated for 6 days in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS), 20 ng/ml recombinant M-CSF (Biolegend cat #574806) 200 mM L-glutamine and 100 units/ml penicillin-streptomycin.
6 mice an maintained in DMEM 10% FBS.

extract_protocol: TruSeq Stranded RNA

treatment_protocol:
10^6 BMDM were fed with apoptotic thymocytes (1 mM staurosporine for 3h, washed in phosphate-buffered saline) in DMEM 10% FBS for 16 hours
1 million BMDM were untreated (NS) or fed with apoptotic thymocytes (1 mM staurosporine for 3h, washed in phosphate-buffered saline) in DMEM 10% FBS for 16 hours

tag: genotype

tag: treatment

value: Stimulated

tag: cell type

value: bone marrow-derived macrophages


title: 1213414_02B_KO_NS_2_S52 (bulk RNA-seq)

treatment_protocol:
10^6 BMDM were left untreated in DMEM 10% FBS for 16 hours
1 million BMDM were untreated (NS) or fed with apoptotic thymocytes (1 mM staurosporine for 3h, washed in phosphate-buffered saline) in DMEM 10% FBS for 16 hours

value: Non-stimulated


title: 1213418_02F_KO_AT_2_S56 (bulk RNA-seq)


title: 1213410_01F_WT_AT_2_S48 (bulk RNA-seq)


title: C-33A_CATE


title: SiHa_CATE

source_name: SiHa


title: 1213407_01C_WT_NS_3_S45 (bulk RNA-seq)


title: 1213409_01E_WT_AT_1_S47 (bulk RNA-seq)


title: 1213406_01B_WT_NS_2_S44 (bulk RNA-seq)


title: 1213408_01D_WT_NS_4_S46 (bulk RNA-seq)


title: RNAleaf_rep2

city: Fuzhou

first: Haifeng

last: Wang

state: Fujian

address: Shangxia dian

institute: Fujian Agriculture and Forestry University

description:
RNA-seq
FPKM_Matrix.txt

data_processing:
For mRNA-seq, total clean reads were aligned to the tea tree reference genome (Camellia sinensis var. assamica) by using Tophat 2.1.0 using default paramters, then quantified by using CufflinksV2.2.1. Expression values were expressed in FPKM.
Genome_build: http://www.plantkingdomgdb.com/tea_tree/
Supplementary_files_format_and_content: For mRNA-seq, the format is "gene name, rep1_FPKM, rep2_FPKM, ave_FPKM".

organism: Camellia sinensis var. assamica

source_name: Leaf

extract_protocol: Total RNA was extracted from young leaf of tea tree following the cetyltrimethylammonium bromide (CTAB) protocol (Doyl and Doyl 1990). Genomic DNA was removed by TURBO DNA-free™ Kit (Ambion) and RNA quality and quantity was assessed, respectively, by Agilent 2100 BioAnalyzer (Agilent Technologies Inc. Santa Clara, CA) and NanoDrop2000c (Thermo Scientific). One microgram of total RNA per sample was utilized for library preparation using the Illumina TruSeq sample preparation kit (v2) with polyA mRNA selection as per manufacturer’s instructions (Illumina, San Diego, CA). three libraries were pooled and sequenced using an Illumina HiSeqX-ten with paired end reads of 150 bp at Biomarker technologies company.

tag: tissue

value: young leaf


title: BSleaf_rep2

description:
BS-seq
Tea_merge.C_coverage.wig.gz
Tea_merge.CG.wig.gz
Tea_merge.CHG.wig.gz
Tea_merge.CHH.wig.gz

data_processing:
For BS-seq, reads were aligned to tea tree reference genome (Camellia sinensis var. assamica) by using BSmap2.9. Only unique mapping reads were used to estimate methylation ratio. . Methylation ratios were calculated as the number of Cs divided by Cs plus Ts (#C/(#C+#T)).
Genome_build: http://www.plantkingdomgdb.com/tea_tree/
Supplementary_files_format_and_content: For BS-seq, the format is cytosine location and corresponding methyaltion as data process step.

extract_protocol: BS-seq libraries were prepared using the TruSeq DNA LT kit (Illumina), except that EZ DNA Methylation-Lightning Kit (Qiagen) was used for bisulfite conversion of the DNA. BS-Seq libraries were sequenced on a HiSeqX-ten system (Illumina) to obtain paired-end 150bp reads per manufacture instructions.


title: salt-48h

city: Wuhan

first: Erick

last: Amombo

state: China

address: Wuhan Botanical Garden

institute: Wuhan Botanical Garden Chinese Academy of Science

description: treated  with 200 mM salt stress and sampled at 48h

data_processing:
The raw data sequenced contained low-quality, linker contaminants, and reads with too high and unknown base content. Therefore, to ensure the reliability of results internally developed software was used for filtering out the reads. The filtered data was designated ‘clean reads’ which were candidates of de novo assembly. ‘Trinity’ program [31] was used to remove PCR duplicates in order to improve the assembly efficiency of clean reads. The assembled transcripts were then clustered and unigenes were obtained. The unigenes were divided into two parts; the first were clusters, which was the result of further redundancy. (Beginning with CL, denotes cluster, followed by the number of the gene family). The remaining were singletons (beginning with Unigene).
The assembled unigenes were annotated by aligning them with the other seven public databases, including Nucleotide sequences databases (Nt and Nr) [32] Eukaryotic Ortholog Groups (KOG) [33] for functional prediction, while blastGO (https://www.blast2go.com) database was used to annotate all the unigene results from the Nr database against Gene Ontology (GO) [34]. For pathway annotation enrichment analysis, the Kyoto Encyclopedia for Genes and Genomes database (KEGG) (version 58) was used while InterProscan database (http://www.ebi.ac.uk/interpro) was used to identify family members based on protein domains. Finally, SwissProt database [35] was used to check for better quality annotation results. Furthermore, a Transdecoder software (version 3.0.1) recommended by ‘Trinity’ was used to identify candidate coding regions (CDS) in Unigene. Briefly, the reading frame was opened by searching for unigene families. The homologous sequence of the protein family was then searched by Blast against the SwissProt database.
Genome_build: denovo assembly
Supplementary_files_format_and_content: FPKM

organism: Lolium arundinaceum

source_name: Festuca arundinacea leaves

extract_protocol:
Total RNA from the leaves of each sample was isolated using Trizol reagent (Invitrogen, Carlsbad, CA) and purified using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA) following the manufacturer's protocol. The RNA was analyzed using the Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit). Total RNA concentration with a fragment size of 28S/18S and purity was measured using a UV spectrophotometer NanoDropTM and processed by enriching the mRNA of polyA tails with magnetic beads containing Oligo(dT) followed by the fragmentation of the obtained RNA using an interrupting buffer. Random primers were used for reverse transcription, and cDNA duplex was synthesized to form double-stranded DNA. Subsequently, the synthetic double-stranded DNA was filled at the 5’ and 3’ ends followed by ligation. The ligation product was amplified by PCR using specific primers. Briefly, the material was heat-denatured into single-stranded chains, and a single-stranded circular DNA library was cyclized with a bridging primer to obtain a single-stranded circular DNA library followed by sequencing on a computer.
The raw data sequenced contained low-quality, linker contaminants, and reads with too high and unknown base content. Therefore, to ensure the reliability of results internally developed software was used for filtering out the reads. The filtered data was designated ‘clean reads’ which were candidates of de novo assembly. ‘Trinity’ program [31] was used to remove PCR duplicates in order to improve the assembly efficiency of clean reads. The assembled transcripts were then clustered and unigenes were obtained. The unigenes were divided into two parts; the first were clusters, which was the result of further redundancy. (Beginning with CL, denotes cluster, followed by the number of the gene family). The remaining were singletons (beginning with Unigene).

tag: cultivar

value: Puregold' cultivar tall fescue

tag: agent

value: 200 mM salt stress

tag: time point


title: BSleaf_rep1


title: salt-24h

description: treated with 200 mM salt stress and sampled at 24h


title: HepG2_CATE


title: 1213405_01A_WT_NS_1_S43 (bulk RNA-seq)


title: 293T_CATE


title: CK

description: treated without 200 mM salt stress

value: control


title: T24_rep1

status: Public on Sep 14 2018

city: Bethesda

first: Samer

last: Hattar

state: MD

address: 35 Convent Drive, Bldg 35A

institute: National Institute of Mental Health

data_processing:
Reads were demultiplexed and mapped to the mouse reference genome (mm10) using STAR v2.4 with default parameters
Aligned reads were counted using HTSeq-count (v0.9.1) with parameters --mode=union --stranded=no --idattr=gene_name, and the mm10 GTF annotation
Genome_build: mm10
Supplementary_files_format_and_content: htseq-count output .txt files for each sample with feature counts mapped to gene_name

source_name: Suprachiasmatic nucleus

extract_protocol:
Mice housed under T24 or T7 cycles were kept in darkness for 1 day, and a light pulse was applied (15 min) at CT14. An hour later, brains were isolated in constant darkness and placed ventral side up on an ice-cold coronal slice brain matrix (Kent Scientific). A 1 mm coronal slice of the brain was made with ice-cold razor blades positioned surrounding the optic chiasm. The slice was laid flat on one of the blades and the SCN was collected using a 1mm diameter sample corer (FST) and immediately placed in Qiazol chilled on ice and stored at -80C. SCN tissue samples from 3 mice were pooled for each biological replicate in all conditions. Following dissection, RNA was extracted using a Qiagen RNeasy lipid tissue mini kit and processed with an Illumina RiboZero Gold kit.
Sequencing libraries were prepared with the Illumina TrueSeq RNA-v2 kit. Libraries were multiplexed and sequenced on a Hiseq4000 using 75bp paired-end reads

tag: strain

value: Brain

tag: age

tag: light cycle treatment


title: T24_rep3


title: T7_rep4


title: T7_rep1


title: T7_rep3


title: T7_rep2


title: HeLa_CATE

source_name: HeLa


title: RNAleaf_rep1

description:
RNA-seq
FPKM_Matrix.txt


title: T24_rep2


title: GST-HALO DAP-seq

city: Piscataway

first: Andrea

last: Gallavotti

state: New Jersey

address: 190 Frelinghuysen Rd

department: Waksman Institute

institute: Rutgers University

data_processing:
Library strategy: DAP-seq
Illumina software used for base calling
Sequenced reads were trimmed for adaptor sequence, then mapped to ZmB73v3 whole genome using bowtie2 v2.2.8 with default parameters. Reads were filtered using samtools with the following parameters -b -q 30 to give MAPQ > 30.
Peaks were called using GEM v2.5 with the following parameters: --d Read_Distribution_default.txt --k_min 6 --k_max 20 --outNP --q 5. Blacklisted peaks were subtracted to created to create final narrowPeak file.
Genome_build: ZmB73v3.31
Supplementary_files_format_and_content: bigwig files were generated using deeptools with a bin size of 10bp and RPKM normalization. NarrowPeak files were generated by GEM v2.5.

organism: Zea mays

source_name: 1-3cm maize ear

growth_protocol: genomic DNA was extracted from 1-3cm field grown ears

extract_protocol:
Genomic DNA was purified using a standard phenol:chloroform extraction protocol. GST-ARF fusion proteins were purified from Ecoli using GSH-sepharose. GST-HALO negative control protein was expressed using Promega's TNT wheatgerm expression system.
DAP-seq is a transcription factor binding site discovery assay that couples affinity-purified transcription factors with next-generation sequencing of a genomic DNA library (O'Malley et al. Cell 2015, Bartlett et al. Nature methods 2017). Please let me know if you need further information. The O'Malley reference is the first publication of DAP-seq.

tag: background

value: negative control


title: AITL_Patient_Sample_TAITL101NA

type: RNA

city: Singapore

first: Weng Khong

last: Lim

state: Singapore

address: 11 Hospital Drive

department: Department of Medical Sciences

country: Singapore

institute: National Cancer Centre Singapore

description: Gene expression profiling of AITL tumors

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G

data_processing: CEL files were loaded into R and then preprocessed and normalized using RMA. A custom CDF was used to reannotate the probes (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/16.0.0/entrezg.asp). The samples were normalized in RMA together with some normal T cell samples from GEO (GSM146182-GSM146196).

label: biotin

source_name: Tumor tissue from AITL patient

label_protocol: Standard Affymetrix protocol, 10ug of RNAeasy-purified total RNA

extract_protocol: Trizol extraction of total RNA was performed according to manufacturer's instructions, followed by purification using the Qiagen RNAeasy kit.

tag: tet2 status

value: Angioimmunoblastic T-Cell lymphoma (AITL)

tag: diagnosis

tag: rhoa status


title: AITL_Patient_Sample_TAITL47

value: Mutant


title: ZmARF10 DAP-seq


title: ZmARF29 DAP-seq


title: ZmARF39 DAP-seq


title: ZmARF14 DAP-seq


title: ZmARF13 DAP-seq


title: ZmARF7 DAP-seq


title: ZmARF36 DAP-seq


title: AITL_Patient_Sample_TAITL32

value: Wild-Type


title: AITL_Patient_Sample_TAITL35


title: AITL_Patient_Sample_TAITL30


title: AITL_Patient_Sample_TAITL33


title: AITL_Patient_Sample_TAITL26


title: AITL_Patient_Sample_TAITL27


title: AITL_Patient_Sample_TAITL38


title: AITL_Patient_Sample_TAITL39


title: AITL_Patient_Sample_TAITL49


title: AITL_Patient_Sample_TAITL100NA


title: AITL_Patient_Sample_TAITL31


title: AITL_Patient_Sample_TAITL28


title: AITL_Patient_Sample_TAITL40


title: AITL_Patient_Sample_TAITL37


title: AITL_Patient_Sample_TAITL41


title: AITL_Patient_Sample_TAITL48


title: AITL_Patient_Sample_TAITL50


title: ZmARF4 DAP-seq


title: AITL_Patient_Sample_TAITL21


title: ZmARF27 DAP-seq

tag: notes

value: dataset was reduced to 20 million reads after mapping


title: ZmARF25 DAP-seq


title: ZmARF35 DAP-seq


title: ZmARF18 DAP-seq


title: seedlingB73_noIAA_30min_rep1

data_processing:
Illumina software used for base calling
Sequenced reads were trimmed for adaptor sequence, then mapped to ZmB73v3 whole genome using Tophat v2.1.1
Differentially expressed genes were identified using Cuffdiff v2.2.1
Genome_build: ZmB73v3.31

extract_protocol:
samples were snap frozen in liquid nitrogen and total RNA was extracted using RNeasy kit (Qiagen) with DNAse treatment
Stranded Illumina RNA sequencing libraries were generated using the TruSeqv3 kit (Illumina)

treatment_protocol: aerial portions of seven day-old maize B73 greenhouse-grown seedlings (three plants per sample) were harvested and incubated in a solution of 100mM IAA in 1% DMSO or 1% DMSO for 30min

value: 30min 1% DMSO


title: ZmARF16 DAP-seq


title: seedlingB73_plusIAA_30min_rep1

source_name: aerial portions of seven day-old maize B73 greenhouse-grown seedlings

value: 30 min in 100mM IAA in 1% DMSO


title: seedlingB73_noIAA_30min_rep2

growth_protocol: seven day-old maize B73 greenhouse-grown seedlings


title: ZmARF34 DAP-seq

value: dataset was reduced to 15 million reads after mapping


title: HEK293_TFIIS_DN_H2O_Trip_15_PolII_170714_R1

city: Aurora

first: David

last: Bentley

state: Colorado

department: BMG

institute: UCD AMC

data_processing:
Single-end 50 base reads (after removing barcodes) or 151 base reads (after removing barcodes) were mapped to the hg19 UCSC human genome with Bowtie2 version 2.3.2 (trim from 3 prime to 50 base pairs)
Genome_build: GRCh37/hg19 assembly

source_name: HEK 293 TFIISDN

growth_protocol: HCT116 cells were grown in McCoy's medium 10% FCS and pen/strep

extract_protocol:
cross-linked Chromatin was sonicated with a Bioruptor
1-2 mg of cross-linked extract was immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, gel purification of ~200bp fragments, and amplification (18cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.

treatment_protocol: In some experiments  HCT116  were treated with 10mM NM-PP1 for 24 hr before cross-linking and harvesting for ChIP-seq, this drug treament should have no effect on these cells.

tag: cell line/genotype

value: HEK 293 TFIISDN

tag: spike in

tag: growth conditions

value: DMEM 10% FCS minus doxycycline triptolide 10 mM 15 min.  (note dominant negative TFIIS is not induced)

tag: antibody

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)

tag: experiment

value: Chromatin IP against RNA pol II


title: Hap1_NELFA_deg_TMP_NaCl_5_PolII_151203_R1

source_name: Hap1 NELFA-degron (Sheridan and Bentley Biotechniques 60:69-74, 2016)

value: IMDM 10% FCS, 10mM trimethoprim  (note NELFA degron not induced) NaCl 350mM 5 min.


title: Hap1_NELFA_deg_TMP_control_PolII_151203_R1

value: Hap1 NELFA-degron (Sheridan and Bentley Biotechniques 60:69-74, 2016)

value: IMDM 10% FCS, 10mM trimethoprim  (note NELFA degron not induced)


title: HEK293_TFIIS_DN_H2O_Trip_10_PolII_170714_R1

value: DMEM 10% FCS minus doxycycline triptolide 10 mM 10 min.  (note dominant negative TFIIS is not induced)


title: seedlingB73_plusIAA_30min_rep3

tag: treatment


title: seedlingB73_noIAA_30min_rep3


title: HCT116_M12_Trip_2_Spt5_170914_R1

value: mouse M12

value: McCoy's 10% FCS triptolide 10 mM 2 min.

value: rabbit anti Spt5 (Glover-Cutter et al NSMB 15:71-78, 2008)

value: Chromatin IP against Spt5


title: seedlingB73_plusIAA_30min_rep2


title: HEK293_TFIIS_DN_H2O_Trip_5_PolII_170714_R1

value: DMEM 10% FCS minus doxycycline triptolide 10 mM 5 min.  (note dominant negative TFIIS is not induced)


title: HCT116_M12_Trip_10_Spt5_170914_R1

value: McCoy's 10% FCS triptolide 10 mM 10 min.


title: HEK293_TFIIS_DN_H2O_control_PolII_170714_R1

value: DMEM 10% FCS minus doxycycline  (note dominant negative TFIIS is not induced)


title: HCT116_M12_Trip_5_Spt5_170914_R1

value: McCoy's 10% FCS triptolide 10 mM 5 min.


title: HCT116_Trip_10_PolII_160809_R1

value: McCoy's 10% FCS triptolide 10 mM 10min.


title: HCT116_Trip_5_PolII_160809_R1

value: McCoy's 10% FCS triptolide 10 mM 5min.


title: HCT116_M12_Trip_20_Spt5_170914_R1

value: McCoy's 10% FCS triptolide 10 mM 20 min.


title: HCT116_Trip_30_PolII_160809_R1

value: McCoy's 10% FCS triptolide 10 mM 30 min.

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)


title: HCT116_W303_Sucrose_10_PolII_160108_R1

value: yeast W303

value: McCoy's 10% FCS  add sucrose 0.63M 10 min.

value: Chromatin IP against RNA pol II


title: HCT116_W303_DRB_PolII_150822_R1

value: McCoy's 10% FCS  DRB 100mM 60min.


title: HCT116_Trip_2_PolII_160809_R1


title: HCT116_W303_DRB_NaCl_10_PolII_150822_R2

value: McCoy's 10% FCS  DRB 100mM 60min. add NaCl 230mM 10 min.


title: HCT116_control_PolII_160809_R4

value: McCoy's 10% FCS 0.1%DMSO


title: HCT116_W303_control_PolII_160108_R5

value: McCoy's 10% FCS


title: HCT116_Trip_NaCl_10_PolII_160615_R2

value: McCoy's 10% FCS triptolide 10 mM 60min. add NaCl 230mM 10 min.


title: HCT116_Trip_NaCl_10_recovery_PolII_160615_R2

value: McCoy's 10% FCS triptolide 10 mM 60min. add NaCl 230mM 10 min. washout out NaCl 15min.+triptolide 10 mM


title: HCT116_M12_control_Spt5_170914_R1

value: mouse M12

value: rabbit anti Spt5 (Glover-Cutter et al NSMB 15:71-78, 2008)

value: Chromatin IP against Spt5


title: HCT116_Trip_control_PolII_160615_R2

value: McCoy's 10% FCS triptolide 10 mM 60min.


title: HCT116_M12_Trip_NaCl_10_PolII_cat_170914_170804_R1

value: McCoy's 10% FCS triptolide 10 mM 15min. add NaCl 230mM 10 min.


title: HCT116_M12_Trip_NaCl_10_recovery_15_PolII_cat_170914_170804_R1

value: McCoy's 10% FCS triptolide 10 mM 15min. add NaCl 230mM 10 min. washout out NaCl +triptolide 10 mM 15min.


title: HCT116_3MB_NaCl_10_Recovery_15_PolII_160615_R1

source_name: HCT116 cdk7 wt/wt neo1-E2R (Larochelle et al Mol. Cell 25:839, 2007)

value: McCoy's 10% FCS 10mM NM-PP1 (note NM-PP1 has no effect on WT cdk7 cells), 24hr  add NaCl 230mM 10 min.washout out NaCl 15min.


title: HCT116_DRB_NaCl_10_PolII_160809_R2

value: McCoy's 10% FCS DRB 100mM 60min. add NaCl 230mM 10 min.

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)


title: HCT116_DRB_NaCl_2_PolII_160809_R2

value: McCoy's 10% FCS DRB 100mM 60min. add NaCl 230mM 2 min.


title: HCT116_M12_AMT_24hr_control_PolII_170914_R1

value: McCoy's 10% FCS a-amanitin 5mg/ml 24hr.

value: Chromatin IP against RNA pol II


title: HCT116_DRB_NaCl_5_PolII_160809_R2

value: McCoy's 10% FCS DRB 100mM 60min. add NaCl 230mM 5 min.


title: WTE17.5_3

city: Turku

first: Kati

last: Elima

address: Tykistökatu 6

department: MediCity

country: Finland

institute: University of Turku

data_processing:
Basecalls performed using the instrument manufacturer’s (Illumina HiSeq2000 ) Pipeline v1.5+ base calling software
Data filtering was as follows: the adaptor sequences were removed, the reads in which the precentage of unkonown bases is greater that 10% were removed, low quality reads were removed (the percentage of the low quality base (base with quality value ≤ 5) is greater than 50% in a read, we define this read as low quality)
the reads were aligned against the mouse reference genome and/or reference gene set using SOAPaligner/SOAP2. No more than 2 mismatches were allowed in the alignment.
gene expression level is calculated by using RPKM method
The strict algorithm used in identifying differentially expressed genes between two samples is described in Audic, S. and J. M. Claverie (1997). The significance of digital gene expression profiles. Genome Res 7(10): 986-95.
NOIseq method was used to screen differentially expressed genes between groups (Tarazano et al 2011 Genome Res 21: 2213)
Filtering of differentially expressed genes was done using the following thresholds: FDR ≤0.001 and the absolute value of log2Ratio ≥1 as the threshold
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values with annotations for each sample

source_name: wild type_E17.5 _liver

extract_protocol:
RNA was extracted from mouse liver tissue using the Nucleo-Spin RNA RNA Isolation Kit (Macherey-Nagel), and the quality of the isolated RNA was checked with the Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols at BGI

tag: strain background

tag: genotype/variation

value: wild type

tag: tissue

value: liver


title: WTE17.5_4


title: WTE17.5_2


title: HCT116_W303_NaCl_10_PolII_150822_R2

value: yeast W303

value: McCoy's 10% FCS   add NaCl 230mM 10 min.


title: HCT116_W303_NaCl_30_PolII_150822_R1

value: McCoy's 10% FCS   add NaCl 230mM 30 min.


title: HCT116_W303_3MB_control_PolII_150622_R1

value: HCT116 cdk7 wt/wt neo1-E2R (Larochelle et al Mol. Cell 25:839, 2007)

value: McCoy's 10% FCS 10mM NM-PP1, 24hr (note NM-PP1 has no effect on WT cdk7 cells)


title: HCT116_NaCl_10_H3_Cterm_170620_R1

value: McCoy's 10% FCS  add NaCl 230mM 10 min.

value: rabbit anti  H3 Cter (Zhang et al EMBO J, 24:2379, 2005 )

value: Chromatin IP against histone H3


title: HCT116_W303_3MB_NaCl_10_PolII_150622_R1

value: McCoy's 10% FCS 10mM NM-PP1, 24hr, (note NM-PP1 has no effect on WT cdk7 cells)  add NaCl 350mM 10 min.


title: HCT116_control_H3_Cterm_170620_R1

value: McCoy's 10% FCS


title: WTE17.5_1


title: KOE17.5_2

source_name: Stab1 knock-out_E17.5 _liver

value: Stab1 knock-out


title: WT2w3

source_name: wild type_2 week old_liver

value: 2 week old


title: HCT116_W303_control_PolII_150822_R2

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)


title: KOE17.5_1


title: WT2w4


title: KOE17.5_3


title: KO2w4

source_name: Stab1 knock-out_2 week old_liver


title: WT2w1


title: WT2w2


title: HCT116_M12_Trip_PolII_cat_170914_170804_R1

value: mouse M12

value: McCoy's 10% FCS triptolide 10 mM 15min.

value: Chromatin IP against RNA pol II


title: HCT116_3MB_control_PolII_160615_R3


title: HCT116_M12_AMT_24hr_NaCl_10_PolII_170914_R1

value: McCoy's 10% FCS a-amanitin 5mg/ml 24hr.  add  NaCl 230mM 10 min.


title: KO2w3

value: liver


title: KO2w1


title: KO2w2


title: Patient T cells, techn. rep3

first: Mehdi

last: Pirooznia

address: 12 SOUTH DR

institute: National Institutes of Health

hyb_protocol: Illumina HT12.v4 arrays were hybridized using standard Illumina protocols at 48 C

scan_protocol: Standard Illumina scanning

data_processing: data was quantile normalized within Illumina Genome Studio

source_name: CD46-deficient patient 1 (CD46-1) CD8+ T cells, 6 hrs activated

label_protocol: cDNA was labelled  usin NuGen Encore Biotin IL kits

extract_protocol: Genomic DNA and RNA was isolated using Qiagen Allprep. 5pg total RNA was amplified using  NuGen Ovation Pico WTA System V2

treatment_protocol: Cells were treated with anti-CD3 and anti-CD46 for 6 h

tag: disease state

value: CD46-deficient patient


title: rat_hepatocyte_T0_rep29

city: Dortmund

first: Jan

middle: G.

last: Hengstler

address: Ardeystrasse 67

country: Germany

institute: Leibniz Research Centre for Working Environment and Human Factors at the TU Dortmund University (IfADo)

hyb_protocol: After amplification, aRNA was purified with magnetic beads and 15 μg of aRNA was fragmented with the fragmentation buffer as per the manufacturer’s instructions. Then, 12.5 μg fragmented aRNA was hybridizd with Affymetrix Rat Genome 230 2.0 Arrays as per the manufacturer’s instructions. The chips were placed in a GeneChip Hybridization Oven-645 for 16 h at 60 rpm and 45 °C. For staining and washing, Affymetrix HWS kits were used on a Genechip Fluidics Station-450.

scan_protocol: For scanning, the Affymetrix Gene-Chip Scanner-3000-7G was used, and the image and quality control assessments were performed with Affymetrix software.

data_processing: Summarized probe set data were generated using R/Bioconductor and the RMA algorithm.

organism: Rattus norvegicus

source_name: cultivated hepatocytes from male Wistar rats

label_protocol: The RNA was quantified using a NanoDrop N-1000 spectrophotometer. First-strand cDNA was synthesised from 100 ng total RNA using an oligo-dT primer with an attached T7 promoter sequence, followed by the complementary second strand. The double-stranded cDNA molecule was used for in vitro transcription (IVT, standard Affymetrix procedure) using Genechip 3′ IVT Express Kit. During synthesis of the aRNA (amplified RNA, also commonly referred to as cRNA), a biotinylated nucleotide analogue was incorporated, which serves as a label for the message.

growth_protocol: Rat hepatocytes were cultivated as sandwich cultures. Cultivation was performed using 6-well dishes. The protocols of hepatocyte isolation and cultivation are described in Grinberg et al., 2018.

extract_protocol: RNA isolation was performed according to the manufacturer’s instruction (details: Grinberg et al., 2018).

treatment_protocol: Incubation of the cultivated rat hepatocytes with the test compounds was performed for 24h. Cultivation was performed using 6-well dishes where three wells were incubated with the same concentration of the test compound and the remaining remaining three wells were used for solvent controls. Details about the test compounds, full names, abbrevations and concentrations are given in Grinberg et al., 2018. and are available in a file on the series record.

tag: strain

value: Wistar

value: hepatocytes

tag: Sex

value: male

tag: compound

tag: phenotype

tag: concentration

tag: sample type


title: rat_hepatocyte_T0_rep32


title: rat_hepatocyte_T0_rep31


title: rat_hepatocyte_T0_rep27


title: rat_hepatocyte_T0_rep34


title: Patient T cells, techn. rep2


title: rat_hepatocyte_3-MC_low_Expr_rep3

value: NC

value: low

value: 0.64 microM

value: Expr


title: HD T Cell, activated, techn. rep1

source_name: Healthy Donor CD8+ T Cell, 6 hrs activated

value: healthy


title: HD T Cell, activated, techn. rep2


title: rat_hepatocyte_T0_rep28


title: rat_hepatocyte_T0_rep26


title: rat_hepatocyte_T0_rep33


title: rat_hepatocyte_3-MC_low_Ctrl_rep3

value: Ctrl


title: rat_hepatocyte_T0_rep25


title: rat_hepatocyte_3-MC_low_Ctrl_rep2


title: rat_hepatocyte_3-MC_low_Expr_rep1


title: rat_hepatocyte_T0_rep24


title: rat_hepatocyte_3-MC_middle_Expr_rep1

value: middle

value: 1.92 microM


title: HD T Cell, activated, techn. rep3


title: rat_hepatocyte_T0_rep30


title: rat_hepatocyte_3-MC_low_Expr_rep2


title: WT spleen NK, replicate 2

city: Hefei

first: Shu

last: Zhu

address: 443 Huangshan Road, Hefei, Anhui, China

institute: University of Science and Technology of China

description: SAMPLE 8

hyb_protocol: Indocarbocyanine-labeled cDNA was assessed with the NanoDrop ND-2000 (Thermo Scientific), and equal amounts of indocarbocyanine-labeled target were hybridized to Agilent SurePrint G3 Mouse Gene Expression (8x60K) microarrays（Design ID：74809）.

scan_protocol: Arrays were scanned with the Agilent Scanner G2505C(Agilent Technologies).

data_processing: Raw signal intensities were extracted and quantile normalized with Feature Extraction v10.7.1.1 software(Agilent Technologies).

label: indocarbocyanine

source_name: WT spleen NK

label_protocol: RNA was amplified and abeling of CTP with indocarbocyanine was done with Agilent one-color labeling kits (Agilent Technologies).

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit and RNase-Free Dnase Set.Total RNA quality was assessed with a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: NK cells were isolated from spleens and lungs of WT and Stage 3 Kras mice, and we lysed the cells in TRIzol (Invitrogen) and freezed them in refrigerator (-80°C).

value: wild type

tag: age

value: 6-8 weeks

tag: infected with

value: Lenti-Cre for induction of lung cancer

tag: time point

value: Stage 3 (16 weeks after Lenti-Cre delivery)

value: spleen

tag: cell type

value: Natural killer (NK)


title: Patient T cells, techn. rep1

value: CD46-deficient patient


title: WT spleen NK, replicate 1

description: SAMPLE 7


title: rat_hepatocyte_3-MC_middle_Expr_rep2

value: Wistar

value: hepatocytes


title: rat_hepatocyte_3-MC_middle_Expr_rep3

value: male

value: NC


title: rat_hepatocyte_3-MC_middle_Ctrl_rep2


title: rat_hepatocyte_3-MC_middle_Ctrl_rep3


title: rat_hepatocyte_3-MC_low_Ctrl_rep1

value: low

value: 0.64 microM


title: rat_hepatocyte_3-MC_high_Expr_rep2

value: high

value: 5.76 microM

value: Expr


title: rat_hepatocyte_3-MC_high_Expr_rep1


title: rat_hepatocyte_3-MC_middle_Ctrl_rep1

value: middle

value: 1.92 microM

value: Ctrl


title: rat_hepatocyte_DCB_low_Expr_rep3

value: DCB

value: 111 microM


title: WT lung NK, replicate 2

description: SAMPLE 4

source_name: WT lung NK

value: wild type

value: 6-8 weeks

value: Lenti-Cre for induction of lung cancer

value: Stage 3 (16 weeks after Lenti-Cre delivery)

value: lung


title: rat_hepatocyte_DCB_low_Expr_rep1

value: Wistar

value: hepatocytes

value: male


title: Kras spleen NK, replicate 2

description: SAMPLE 6

source_name: Kras spleen NK

value: Kras

value: spleen

value: Natural killer (NK)


title: rat_hepatocyte_DCB_low_Expr_rep2

value: NC

value: low

value: Expr


title: WT lung NK, replicate 1

description: SAMPLE 3


title: Kras lung NK, replicate 1

description: SAMPLE 1

source_name: Kras lung NK


title: rat_hepatocyte_3-MC_high_Ctrl_rep2

value: high

value: 5.76 microM

value: Ctrl


title: rat_hepatocyte_DCB_middle_Expr_rep3

value: DCB

value: middle

value: 333 microM


title: rat_hepatocyte_DCB_middle_Ctrl_rep3


title: rat_hepatocyte_DCB_high_Expr_rep1

value: 1000 microM


title: rat_hepatocyte_DCB_high_Ctrl_rep1


title: rat_hepatocyte_AlAl_low_Expr_rep3

value: AlAl

value: 3.08 microM


title: rat_hepatocyte_3-MC_high_Ctrl_rep1

value: Wistar

value: hepatocytes


title: rat_hepatocyte_DCB_middle_Expr_rep1

value: male


title: rat_hepatocyte_DCB_high_Ctrl_rep2


title: rat_hepatocyte_DCB_high_Ctrl_rep3


title: rat_hepatocyte_DCB_middle_Ctrl_rep2


title: Kras spleen NK, replicate 1

description: SAMPLE 5

value: Kras

value: 6-8 weeks

value: Lenti-Cre for induction of lung cancer

value: Stage 3 (16 weeks after Lenti-Cre delivery)

value: spleen


title: Kras lung NK, replicate 2

description: SAMPLE 2

value: lung

value: Natural killer (NK)


title: rat_hepatocyte_DCB_middle_Expr_rep2

value: NC

value: Expr


title: rat_hepatocyte_DCB_high_Expr_rep3

value: DCB

value: high


title: rat_hepatocyte_DCB_high_Expr_rep2

value: 1000 microM


title: rat_hepatocyte_DCB_low_Ctrl_rep1

value: low

value: 111 microM

value: Ctrl


title: rat_hepatocyte_DCB_low_Ctrl_rep2

value: Wistar

value: hepatocytes


title: rat_hepatocyte_DCB_middle_Ctrl_rep1

value: male

value: middle

value: 333 microM


title: DBA splice mutant LCL 9

city: Cambridge

first: Vijay

middle: G

last: Sankaran

state: MA

address: 7 Cambridge Center

institute: Broad Institute

description:
DBA_9
processed data file: DBA_TPMs.txt

data_processing:
Fastq files were aligned to the Ensembl GRCh37 r75 genome assembly (hg19) using 2-Pass STAR alignment. Based on the general approach previously described in Cummings et al., STAR first pass parameters were adjusted as follows in order to more inclusively detect novel splice junctions: -“-outSJfilterCountTotalMin 10 10 10 10 --outSJfilterCountUniqueMin -1 -1 -1 -1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 3 --outSJfilterOverhangMin 0 0 0 0 --outSJfilterDistToOtherSJmin 0 0 0 0 --scoreGenomicLengthLog2scale 0”. Novel junctions detected in the first pass alignment were combined and included as candidate junctions in the second pass. Candidate genes were investigated for splicing using both IGV and the Gviz package. Sashimi plots were created using Gviz. Gene expression was quantified using RSEM, and expression differences were determined by the log2 fold change in transcripts per million (TPM).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: DBA_TPMs.txt: Tab-delimited text file includes TPM files for each individual.

source_name: lymphoblastoid cell line

growth_protocol: LCLs were derived from peripheral blood.

extract_protocol:
RNeasy
Smart-seq2

value: Lymphoblastoid cell line

tag: disease

value: Diamond-Blackfan anemia (DBA)

tag: mutation type

value: splice site


title: DBA splice mutant LCL 7

description:
DBA_7
processed data file: DBA_TPMs.txt


title: DBA splice mutant LCL 8

description:
DBA_8
processed data file: DBA_TPMs.txt


title: rat_hepatocyte_AlAl_low_Expr_rep2

value: AlAl

value: 3.08 microM


title: rat_hepatocyte_AlAl_low_Expr_rep1

value: NC

value: Expr


title: rat_hepatocyte_AlAl_low_Ctrl_rep1


title: rat_hepatocyte_AlAl_low_Ctrl_rep3


title: DBA splice mutant LCL 5

description:
DBA_5
processed data file: DBA_TPMs.txt


title: rat_hepatocyte_AlAl_low_Ctrl_rep2


title: rat_hepatocyte_AlAl_middle_Ctrl_rep3

value: 9.23 microM


title: rat_hepatocyte_AlAl_middle_Expr_rep3


title: DBA splice mutant LCL 4

description:
DBA_4
processed data file: DBA_TPMs.txt


title: rat_hepatocyte_AlAl_middle_Ctrl_rep2


title: DBA splice mutant LCL 2

description:
DBA_2
processed data file: DBA_TPMs.txt


title: DBA splice mutant LCL 3

description:
DBA_3
processed data file: DBA_TPMs.txt


title: rat_hepatocyte_DCB_low_Ctrl_rep3

value: DCB


title: DBA splice mutant LCL 6

description:
DBA_6
processed data file: DBA_TPMs.txt


title: rat_hepatocyte_AlAl_middle_Expr_rep2


title: rat_hepatocyte_AlAl_middle_Ctrl_rep1


title: Control LCL 5

description:
Control_5
processed data file: DBA_TPMs.txt

value: Control


title: rat_hepatocyte_AlAl_high_Expr_rep3

value: high

value: 27.69 microM


title: rat_hepatocyte_AlAl_high_Expr_rep1

value: Wistar


title: rat_hepatocyte_AlAl_high_Ctrl_rep3

value: hepatocytes

value: Ctrl


title: rat_hepatocyte_Ibup_low_Expr_rep3

value: male

value: Ibup

value: low

value: 102 microM


title: rat_hepatocyte_Ibup_low_Expr_rep2


title: rat_hepatocyte_AlAl_high_Ctrl_rep2


title: rat_hepatocyte_Ibup_low_Expr_rep1


title: rat_hepatocyte_AlAl_high_Expr_rep2


title: rat_hepatocyte_Ibup_low_Ctrl_rep3


title: rat_hepatocyte_AlAl_middle_Expr_rep1

value: middle


title: rat_hepatocyte_AlAl_high_Ctrl_rep1

value: AlAl


title: Control LCL 4

description:
Control_4
processed data file: DBA_TPMs.txt

value: Lymphoblastoid cell line


title: rat_hepatocyte_Ibup_low_Ctrl_rep2

value: NC


title: rat_hepatocyte_Ibup_low_Ctrl_rep1


title: Control LCL 3

description:
Control_3
processed data file: DBA_TPMs.txt


title: Control LCL 2

description:
Control_2
processed data file: DBA_TPMs.txt


title: rat_hepatocyte_Ibup_middle_Ctrl_rep3

value: 306.67 microM


title: Control LCL 1

description:
Control_1
processed data file: DBA_TPMs.txt


title: rat_hepatocyte_Ibup_middle_Expr_rep3

value: Expr


title: rat_hepatocyte_Ibup_middle_Expr_rep1


title: rat_hepatocyte_Ibup_middle_Expr_rep2


title: rat_hepatocyte_Ibup_high_Expr_rep3

value: 920 microM


title: rat_hepatocyte_Ibup_high_Expr_rep2


title: 2-ChIP-exo of HCC1806 cells: modification H3K9ac

city: Nashville

last: Perreault

state: TN

address: 746 Robinson Research Building

institute: Vanderbilt University

description: H3K9Ac_1727-3194_ChIP-exo_merge.b20s100dt.bw

data_processing:
To estimate variance across biological replicates, the Pearson correlation coefficient for pairwise gene RPKM was computed using the HOMER suite (Hypergeometric Optimization of Motif EnRichment)
Biological replicates were then merged and converted to bigWig files
Genome_build: hg19
Supplementary_files_format_and_content: each bigWig file is built from merged biological replicates for PRO-seq or ChIP-exo of Pol II, H2A.Z, H3K4me3, H3K4me2, H3K4me1, H3K27ac, H3K9ac, H3K27me3, H4K20me1, or CTCF

source_name: HCC1806 cell line

extract_protocol:
Cells are lysed, the nuclear fraction retained, and the chromatin is fragmented by sonication to 100-500bp.
In vivo protein-DNA interactions are preserved through formaldehyde crosslinking. Cells are lysed, the nuclear fraction retained, and the chromatin is fragmented by sonication to 100-500bp. DNA fragments interacting with the protein of interest are enriched by ChIP, the important lambda exonuclease digestion effectively footprinting the left and right 5' DNA borders of the protein-DNA crosslink site, and a library is prepared by adding sequencing adapters according to manufacturer’s instructions. ChIP-exo enriched DNA fragments are sequenced from the left and right 5' DNA borders of the protein-DNA crosslink site.

tag: antibody

tag: antibody vendor/catalog

value: Abcam ab4441

tag: cell line


title: rat_hepatocyte_Ibup_middle_Ctrl_rep1

tag: tissue


title: 2-ChIP-exo of HCC1806 cells: modification H4K20me1

value: Abcam ab9051


title: 2-ChIP-exo of HCC1806 cells: modification H3K27me3

value: EMD Millipore 07-449


title: rat_hepatocyte_Ibup_high_Expr_rep1

value: Wistar

value: high


title: 2-ChIP-exo of HCC1806 cells: modification H3K4me1

value: Abcam ab8895


title: 2-ChIP-exo of HCC1806 cells: modification H3K27ac

value: Abcam ab4729


title: rat_hepatocyte_Praz_low_Expr_rep2

value: hepatocytes

value: male

value: Praz


title: 2-ChIP-exo of HCC1806 cells: modification H3K4me3

value: Abcam ab8580


title: 2-ChIP-exo of HCC1806 cells: CTCF

value: CTCF

value: EMD Millipore 07-729


title: 2-ChIP-exo of HCC1806 cells: modification H3K4me2

value: Abcam ab7766


title: rat_hepatocyte_Ibup_high_Ctrl_rep1

value: Ibup

value: NC

value: Ctrl


title: rat_hepatocyte_Ibup_high_Ctrl_rep2

value: 920 microM


title: rat_hepatocyte_Praz_low_Ctrl_rep3

value: low


title: rat_hepatocyte_Praz_middle_Expr_rep1

value: middle

value: Expr


title: 2-ChIP-exo of HCC1806 cells: RNA polymerase II

value: RNA polymerase II

value: Santa Cruz sc899


title: rat_hepatocyte_Ibup_middle_Ctrl_rep2

value: Wistar

value: 306.67 microM


title: rat_hepatocyte_Praz_middle_Expr_rep3

value: hepatocytes

value: male


title: 2-ChIP-exo of HCC1806 cells: histone H2AZ

value: histone H2AZ

value: EMD Millipore 07-594


title: rat_hepatocyte_Praz_low_Expr_rep1

value: Praz


title: rat_hepatocyte_Praz_low_Ctrl_rep1


title: rat_hepatocyte_Praz_middle_Ctrl_rep2


title: rat_hepatocyte_Praz_middle_Ctrl_rep3


title: rat_hepatocyte_Praz_middle_Expr_rep2


title: rat_hepatocyte_Praz_middle_Ctrl_rep1


title: rat_hepatocyte_Praz_high_Expr_rep2

value: high

value: 0.0077 microM


title: 2-PRO-seq of HCC1806 cells

data_processing:
Library strategy: PRO-seq
To estimate variance across biological replicates, the Pearson correlation coefficient for pairwise gene RPKM was computed using the HOMER suite (Hypergeometric Optimization of Motif EnRichment)
Biological replicates were then merged and converted to bigWig files
Genome_build: hg19
Supplementary_files_format_and_content: each bigWig file is built from merged biological replicates for PRO-seq or ChIP-exo of Pol II, H2A.Z, H3K4me3, H3K4me2, H3K4me1, H3K27ac, H3K9ac, H3K27me3, H4K20me1, or CTCF

extract_protocol:
Cells are lysed and the nuclear fraction retained.
Precision Run On sequencing measures nascent transcription. This is done by isolating nuclei, incorporating biotin-NTP into the transcription bubble, selecting for biotin labeled transcripts, and sequenced from the 3' end.


title: rat_hepatocyte_Praz_low_Expr_rep3

value: NC


title: rat_hepatocyte_Praz_high_Ctrl_rep2

value: Ctrl


title: rat_hepatocyte_Clon_low_Expr_rep2

value: Clon

value: 0.17 microM


title: rat_hepatocyte_Praz_low_Ctrl_rep2

value: low


title: rat_hepatocyte_Praz_high_Expr_rep1

value: Expr


title: rat_hepatocyte_Praz_high_Ctrl_rep1


title: rat_hepatocyte_Clon_low_Expr_rep3


title: 1-ChIP-exo of HCC1806 cells: modification H3K9ac

value: Abcam ab4441


title: 1-ChIP-exo of HCC1806 cells: modification H3K27me3

value: EMD Millipore 07-449


title: rat_hepatocyte_Praz_high_Expr_rep3

value: Wistar


title: 1-ChIP-exo of HCC1806 cells: modification H3K27ac

value: Abcam ab4729


title: rat_hepatocyte_Clon_low_Expr_rep1

value: hepatocytes


title: rat_hepatocyte_Clon_low_Ctrl_rep3

value: male


title: 1-ChIP-exo of HCC1806 cells: modification H4K20me1

value: Abcam ab9051


title: 1-ChIP-exo of HCC1806 cells: modification H3K4me1

value: Abcam ab8895


title: 1-ChIP-exo of HCC1806 cells: modification H3K4me2

value: Abcam ab7766


title: rat_hepatocyte_Ibup_high_Ctrl_rep3

value: Ibup

value: high

value: 920 microM


title: 1-ChIP-exo of HCC1806 cells: CTCF

value: CTCF

value: EMD Millipore 07-729


title: 1-ChIP-exo of HCC1806 cells: histone H2AZ

value: histone H2AZ

value: EMD Millipore 07-594


title: rat_hepatocyte_Clon_middle_Expr_rep2

value: Clon

value: NC

value: middle

value: 303 microM

value: Expr


title: rat_hepatocyte_Clon_low_Ctrl_rep2

value: Wistar

value: hepatocytes

value: low

value: 0.17 microM

value: Ctrl


title: rat_hepatocyte_Clon_middle_Ctrl_rep3

value: male


title: rat_hepatocyte_Clon_middle_Expr_rep1


title: rat_hepatocyte_Clon_low_Ctrl_rep1


title: rat_hepatocyte_Clon_high_Expr_rep3

value: high

value: 909 microM


title: 1-ChIP-exo of HCC1806 cells: RNA polymerase II

value: RNA polymerase II

value: Santa Cruz sc899


title: rat_hepatocyte_Clon_middle_Expr_rep3


title: rat_hepatocyte_Clon_middle_Ctrl_rep2


title: 1-PRO-seq of HCC1806 cells


title: rat_hepatocyte_Clon_middle_Ctrl_rep1


title: rat_hepatocyte_Clon_high_Ctrl_rep2


title: rat_hepatocyte_CPA_low_Expr_rep3

value: CPA

value: NG

value: 1.11 microM


title: rat_hepatocyte_CPA_low_Expr_rep2


title: 1-ChIP-exo of HCC1806 cells: modification H3K4me3

value: Abcam ab8580


title: rat_hepatocyte_Clon_high_Expr_rep1

value: Clon

value: NC


title: rat_hepatocyte_Clon_high_Ctrl_rep3


title: rat_hepatocyte_Clon_high_Ctrl_rep1


title: rat_hepatocyte_CPA_low_Expr_rep1

value: Expr


title: rat_hepatocyte_CPA_low_Ctrl_rep3

value: Wistar


title: rat_hepatocyte_Clon_high_Expr_rep2

value: hepatocytes


title: dummy (HeLa control 16h rep2)

city: Ako

first: Hiderou

last: Yoshida

state: Hyogo

address: Kamigori, Koto 3-2-1

department: Life Science

country: Japan

institute: University of Hyogo

description:
Gene expression after 16hr in DMSO-treated HeLa cells
xyloside_003-006+Dummy011-014.absolute_read_matrix.txt
IonXpress_013

data_processing:
Torrent Suite software v5.4.0 (Thermo Fisher Scientific) software used for basecalling.
The raw reads were aligned to the mouse reference genome (hg19) using Torrent Suite software v5.4.0 (AmpliSeq RNA plugin).
The raw read counts were calculated by Torrent Suite software v5.4.0 (AmpliSeq RNA plugin).
Calculation of RPM was performed by Torrent Suite software v5.4.0 (AmpliSeq RNA plugin).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol and gene expression (RPM) for each sample.

source_name: HeLa cells treated with DMSO, 16h

growth_protocol: HeLa cells were cultured in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol:
RNA was prepared using Sepasol-RNAⅠSuper G (Nacalai, Japan) and purified through the RNeasy mini kit (QIAGEN, Valencia, CA) following the manufacturers' recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Ion Proton protocols

treatment_protocol: HeLa cells were treated with DMSO or 4MU-xyloside for 16 h in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

value: HeLa

value: cervical cancer

tag: gender

value: female

tag: treatment

value: DMSO


title: dummy (HeLa Benzyl GalNAc 16h rep2)

description:
Gene expression after 16hr in BenzylGalNAc-treated HeLa cells
xyloside_003-006+Dummy011-014.absolute_read_matrix.txt
IonXpress_014

source_name: HeLa cells treated with 10 μM BenzylGalNAc, 16h

value: 10 μM BenzylGalNAc


title: rat_hepatocyte_CPA_middle_Expr_rep3

tag: strain

tag: Sex

value: male

value: middle

value: 33 microM


title: dummy (HeLa Benzyl GalNAc 16h rep1)

description:
Gene expression after 16hr in BenzylGalNAc-treated HeLa cells
xyloside_003-006+Dummy011-014.absolute_read_matrix.txt
IonXpress_012


title: rat_hepatocyte_CPA_low_Ctrl_rep2

tag: compound

value: CPA

tag: phenotype

value: low

value: Ctrl


title: rat_hepatocyte_CPA_middle_Expr_rep1

value: NG

tag: concentration

tag: sample type


title: dummy (HeLa control 16h rep1)

description:
Gene expression after 16hr in DMSO-treated HeLa cells
xyloside_003-006+Dummy011-014.absolute_read_matrix.txt
IonXpress_011


title: rat_hepatocyte_CPA_middle_Expr_rep2


title: rat_hepatocyte_CPA_middle_Ctrl_rep2


title: HeLa 4MU-xyloside 16h rep3

description:
Gene expression after 16hr in 4MU-xyloside-treated HeLa cells
xyloside_003-006+Dummy011-014.absolute_read_matrix.txt
IonXpress_006

source_name: HeLa cells treated with 7.5mM 4MU-xyloside, 16h


title: HeLa 4MU-xyloside 16h rep2

description:
Gene expression after 16hr in 4MU-xyloside-treated HeLa cells
xyloside_003-006+Dummy011-014.absolute_read_matrix.txt
IonXpress_004


title: HeLa control 16h rep3

description:
Gene expression after 16hr in DMSO-treated HeLa cells
xyloside_003-006+Dummy011-014.absolute_read_matrix.txt
IonXpress_005

value: control


title: HeLa control 16h rep2

description:
Gene expression after 16hr in DMSO-treated HeLa cells
xyloside_003-006+Dummy011-014.absolute_read_matrix.txt
IonXpress_003


title: HeLa 4MU-xyloside 16h rep1

description:
Gene expression after 16hr in 4MU-xyloside-treated HeLa cells
xyloside_001-002.absolute_read_matrix.txt
IonXpress_002


title: rat_hepatocyte_CPA_high_Expr_rep3

value: high

value: 100 microM


title: rat_hepatocyte_CPA_high_Ctrl_rep2

value: Wistar


title: rat_hepatocyte_CPA_middle_Ctrl_rep1

value: hepatocytes


title: rat_hepatocyte_Aap_low_Expr_rep1

value: Aap

value: 111 microM

value: Expr


title: rat_hepatocyte_Aap_low_Ctrl_rep3


title: rat_hepatocyte_CPA_high_Ctrl_rep1


title: rat_hepatocyte_CPA_low_Ctrl_rep1

value: 1.11 microM


title: rat_hepatocyte_Aap_low_Expr_rep3


title: rat_hepatocyte_CPA_high_Ctrl_rep3


title: rat_hepatocyte_CPA_high_Expr_rep1


title: rat_hepatocyte_Aap_low_Expr_rep2


title: HeLa control 16h rep1

description:
Gene expression after 16hr in DMSO-treated HeLa cells
xyloside_001-002.absolute_read_matrix.txt
IonXpress_001

value: HeLa

value: cervical cancer

value: female


title: rat_hepatocyte_CPA_middle_Ctrl_rep3

value: male

value: middle

value: 33 microM


title: #42 DDC+EtOH

city: College Station

first: Ivan

last: Rusyn

state: TX

address: 4458 TAMU

institute: TEXAS A&M UNIVERSITY

data_processing:
Pair-end (100bp) sequencing was carried out using the Illumina HiSeq 2500 platform.
RNA-seq reads were aligned to appropriate reference genomes (NCBI mm10) using the “SNP-tolerant” GSNAP software
Differential gene expression analysis was then performed on the complete list of 18,965 genes using R package DESeq2 (v 1.12.3) [20].
Log2 fold-change (compared to Control group) and false discovery rate (FDR)-adjusted p-value (q-value) cut off at ±0.58 and <0.1, respectively, were applied
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample.

source_name: liver

extract_protocol:
Tissues were excised and snap-frozen in liquid nitrogen.
Libraries for RNA-seq were prepared from total liver RNA using the Illumina TruSeq mRNA Sample Prep Kit (Illumina, San Diego, USA).

treatment_protocol: adult male C57BL6/J mice were treated with 3,5-diethoxycarbonyl-1,4-dihydrocolidine (DDC) contain diet (0.05% w/w) to induce chronic liver fibrosis. Following DDC-induced fibrogenesis, ethyl alcohol (EtOH) (up to 27 g/ kg/day, up to 28 days) was administered continuously to mice via a gastric feeding tube (Tsukamoto-French surgery)

tag: treatment 1

value: DDC

tag: treatment 2

value: HFD/EtOH

value: liver


title: rat_hepatocyte_CPA_high_Expr_rep2

value: CPA

value: NG

value: high


title: #41 DDC+EtOH


title: DBA splice mutant LCL 1

description:
DBA_1
processed data file: DBA_TPMs.txt

tag: cell type

value: Lymphoblastoid cell line

value: Diamond-Blackfan anemia (DBA)

value: splice site


title: #43 DDC+EtOH


title: #40 DDC+EtOH


title: #39 DDC+EtOH


title: #37 DDC+HFD

value: HFD


title: #36 DDC+HFD


title: #35 DDC+HFD


title: #33 DDC+HFD


title: rat_hepatocyte_Aap_middle_Expr_rep2

value: Wistar

value: hepatocytes

value: Aap

value: 333 microM

value: Expr


title: rat_hepatocyte_Aap_middle_Ctrl_rep1

value: male

value: middle

value: Ctrl


title: rat_hepatocyte_ETH_low_Ctrl_rep1

value: ETH

value: low

value: 11.1 microM


title: rat_hepatocyte_ETH_low_Expr_rep2

value: NG


title: rat_hepatocyte_Aap_high_Ctrl_rep3

value: high

value: 1000 microM


title: rat_hepatocyte_Aap_high_Expr_rep3


title: rat_hepatocyte_ETH_low_Expr_rep3


title: rat_hepatocyte_Aap_middle_Expr_rep1


title: rat_hepatocyte_Aap_middle_Ctrl_rep3


title: rat_hepatocyte_Aap_middle_Expr_rep3


title: rat_hepatocyte_Aap_low_Ctrl_rep2

value: 111 microM


title: rat_hepatocyte_Aap_high_Expr_rep1


title: rat_hepatocyte_Aap_middle_Ctrl_rep2


title: rat_hepatocyte_Aap_low_Ctrl_rep1


title: rat_hepatocyte_Aap_high_Expr_rep2


title: rat_hepatocyte_Aap_high_Ctrl_rep1


title: rat_hepatocyte_ETH_low_Expr_rep1


title: rat_hepatocyte_Aap_high_Ctrl_rep2


title: rat_hepatocyte_ETH_low_Ctrl_rep2


title: rat_hepatocyte_ETH_middle_Expr_rep1

value: 33.3 microM


title: #38 DDC+EtOH

value: DDC

value: HFD/EtOH

value: liver


title: rat_hepatocyte_ETH_middle_Expr_rep2

value: Wistar

value: hepatocytes


title: #30 DDC+HFD

value: HFD


title: #32 DDC+HFD

value: male


title: rat_hepatocyte_ETH_low_Ctrl_rep3


title: rat_hepatocyte_ETH_middle_Ctrl_rep2

value: middle


title: rat_hepatocyte_ETH_middle_Ctrl_rep3

value: Ctrl


title: #28 DDC+Cont

value: BD


title: #25 DDC+Cont


title: #29 DDC+Cont


title: #23 EtOH


title: #24 DDC+Cont


title: #22 EtOH


title: #21 EtOH


title: rat_hepatocyte_ETH_middle_Ctrl_rep1

value: ETH


title: rat_hepatocyte_ETH_high_Expr_rep2

value: 100 microM

value: Expr


title: #20 EtOH


title: rat_hepatocyte_ETH_high_Expr_rep3

value: NG

value: high


title: rat_hepatocyte_DEHA_low_Ctrl_rep1

value: DEHA

value: low

value: 48.5 microM


title: rat_hepatocyte_DEHA_low_Ctrl_rep3


title: rat_hepatocyte_ETH_high_Ctrl_rep2


title: rat_hepatocyte_DEHA_low_Expr_rep3


title: rat_hepatocyte_ETH_high_Ctrl_rep3


title: rat_hepatocyte_DEHA_low_Expr_rep2


title: rat_hepatocyte_DEHA_middle_Expr_rep2

value: 88.9 microM


title: rat_hepatocyte_DEHA_low_Ctrl_rep2


title: rat_hepatocyte_ETH_high_Expr_rep1


title: rat_hepatocyte_ETH_high_Ctrl_rep1


title: #19 HFD

value: liver


title: rat_hepatocyte_DEHA_low_Expr_rep1

value: Wistar


title: rat_hepatocyte_DEHA_middle_Expr_rep3

value: hepatocytes


title: #26 DDC+Cont

value: DDC


title: #18 HFD

value: male

value: HFD


title: rat_hepatocyte_DEHA_middle_Ctrl_rep3

value: middle

value: Ctrl


title: rat_hepatocyte_DEHA_middle_Ctrl_rep1


title: rat_hepatocyte_DEHA_middle_Ctrl_rep2


title: #17 HFD

value: BD


title: rat_hepatocyte_AA_low_Expr_rep3

value: AA

value: 111.1 microM


title: #14 HFD


title: rat_hepatocyte_AA_low_Ctrl_rep3

value: NG


title: rat_hepatocyte_AA_middle_Expr_rep3

value: 333.3 microM

value: Expr


title: rat_hepatocyte_AA_middle_Expr_rep2


title: rat_hepatocyte_AA_low_Ctrl_rep1

value: low


title: rat_hepatocyte_AA_low_Expr_rep1


title: rat_hepatocyte_DEHA_middle_Expr_rep1

value: DEHA


title: rat_hepatocyte_AA_middle_Ctrl_rep2


title: rat_hepatocyte_AA_middle_Expr_rep1


title: rat_hepatocyte_AA_low_Ctrl_rep2


title: #15 HFD


title: #13 Control 28D


title: #12 Control 28D


title: #16 HFD


title: #10 Control 28D


title: #11 Control 28D


title: rat_hepatocyte_AA_high_Ctrl_rep3

value: high

value: 1000 microM


title: rat_hepatocyte_AA_middle_Ctrl_rep1

value: Wistar


title: #9 Control 28D

value: liver


title: rat_hepatocyte_AA_high_Expr_rep1

value: hepatocytes


title: rat_hepatocyte_ETH_middle_Expr_rep3

value: male

value: ETH

value: 33.3 microM


title: rat_hepatocyte_AA_high_Expr_rep3


title: rat_hepatocyte_AA_high_Expr_rep2


title: rat_hepatocyte_Mcarb_low_Expr_rep3

value: Mcarb


title: rat_hepatocyte_AA_middle_Ctrl_rep3

value: middle

value: Ctrl


title: rat_hepatocyte_AA_high_Ctrl_rep2

value: AA


title: #8 DDC 0D

value: DDC


title: #7 DDC 0D


title: rat_hepatocyte_Mcarb_low_Expr_rep1

value: NG

value: 111.1 microM


title: #6 DDC 0D


title: rat_hepatocyte_Mcarb_low_Expr_rep2

value: low

value: Expr


title: rat_hepatocyte_Mcarb_low_Ctrl_rep2


title: rat_hepatocyte_Mcarb_low_Ctrl_rep1


title: #5 DDC 0D


title: rat_hepatocyte_AA_low_Expr_rep2


title: rat_hepatocyte_Mcarb_middle_Expr_rep2

value: 333.3 microM


title: #2 Control 0D

value: BD


title: #1 Control 0D


title: rat_hepatocyte_Mcarb_low_Ctrl_rep3

value: Wistar


title: rat_hepatocyte_Mcarb_middle_Ctrl_rep1


title: rat_hepatocyte_Mcarb_middle_Ctrl_rep2


title: rat_hepatocyte_Mcarb_middle_Ctrl_rep3


title: rat_hepatocyte_Mcarb_middle_Expr_rep1


title: e37

city: Stanford

first: Mark

middle: Emile

last: Pepin

state: CA

address: 870 Quarry Road

department: Cardiovascular Medicine

institute: Stanford University

description: Results_Diff.Exp for HFD-Drug vs. HFD-Veh.csv

data_processing:
Illumina bcl2fastq version 1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using TrimGalore version 0.4.0 with parameters: --paired, --trim1
Trimmed reads were then aligned with TopHat version 2.0.12 (Bowtie2 version 2.2.3) to UCSC hg19 reference genome with parameters: -r 150, --library-type fr-firststrand, --keep-fasta-order, --transcriptome-index, --rg-id, --rg-sample, --rg-library, --rg-platform-unit, --rg-platform, -o
Cufflinks version 2.2.1 estimated transcript abundances with parameters: --library-type fr-firststrand, -o, -g, -L, -b, -u
Cuffmerge, Cuffquant, Cuffdiff, and Cuffquant were then run to get to final differential expression results
Genome_build: mm10
Supplementary_files_format_and_content: .xlsx

source_name: epididymal white adipose tissue - whole tissue

extract_protocol:
eWAT was removed at time of sacrifice, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: epidydymal white adipose tissue taken from high fat-fed or standard chow-fed mice after 80-day treatment with Atripla or Vehicle

value: Veh

tag: diet

value: HFD


title: rat_hepatocyte_Mcarb_middle_Expr_rep3

value: hepatocytes

value: male


title: e36


title: e28

value: Atripla


title: #4 Control 0D

value: liver


title: rat_hepatocyte_MDA_low_Expr_rep3

value: MDA

value: GT

value: 1.09 microM


title: #3 Control 0D


title: rat_hepatocyte_MDA_low_Expr_rep1


title: rat_hepatocyte_Mcarb_high_Ctrl_rep3

value: Mcarb

value: high

value: 1000 microM

value: Ctrl


title: rat_hepatocyte_Mcarb_high_Expr_rep2

value: NG

value: Expr


title: rat_hepatocyte_MDA_low_Ctrl_rep3

value: low


title: rat_hepatocyte_MDA_low_Ctrl_rep2

value: Wistar


title: rat_hepatocyte_Mcarb_high_Expr_rep3


title: rat_hepatocyte_Mcarb_high_Ctrl_rep1


title: rat_hepatocyte_Mcarb_high_Expr_rep1


title: rat_hepatocyte_MDA_low_Expr_rep2


title: rat_hepatocyte_MDA_middle_Expr_rep3

value: middle

value: 3.27 microM


title: rat_hepatocyte_MDA_low_Ctrl_rep1

value: hepatocytes


title: rat_hepatocyte_MDA_middle_Ctrl_rep3

value: male


title: rat_hepatocyte_MDA_middle_Expr_rep2


title: rat_hepatocyte_MDA_middle_Expr_rep1


title: rat_hepatocyte_Mcarb_high_Ctrl_rep2


title: rat_hepatocyte_AA_high_Ctrl_rep1

value: AA


title: e27

value: Atripla

value: HFD


title: e25

value: Chow


title: e30

value: Veh


title: e24


title: e26


title: rat_hepatocyte_MDA_middle_Ctrl_rep1

value: MDA

value: GT


title: rat_hepatocyte_MDA_high_Expr_rep2

value: high

value: 9.81 microM


title: rat_hepatocyte_MDA_high_Expr_rep1


title: rat_hepatocyte_MDA_middle_Ctrl_rep2

value: Ctrl


title: rat_hepatocyte_MDA_high_Ctrl_rep2


title: rat_hepatocyte_MDA_high_Ctrl_rep3


title: rat_hepatocyte_NPip_middle_Ctrl_rep3

value: NPip

value: 333 microM


title: rat_hepatocyte_NPip_middle_Expr_rep3

value: Wistar

value: Expr


title: rat_hepatocyte_NPip_low_Expr_rep1

value: low

value: 49 microM


title: rat_hepatocyte_NPip_low_Expr_rep2

value: hepatocytes

value: male


title: rat_hepatocyte_NPip_low_Ctrl_rep2


title: rat_hepatocyte_NPip_middle_Ctrl_rep2

value: middle


title: rat_hepatocyte_MDA_high_Ctrl_rep1


title: rat_hepatocyte_NPip_high_Expr_rep1

value: 1000 microM


title: rat_hepatocyte_NPip_high_Expr_rep2


title: rat_hepatocyte_NPip_high_Ctrl_rep3


title: rat_hepatocyte_2AAF_low_Expr_rep3

value: 0.11 microM


title: rat_hepatocyte_NPip_middle_Expr_rep1


title: rat_hepatocyte_NPip_low_Ctrl_rep3


title: rat_hepatocyte_NPip_high_Ctrl_rep2


title: rat_hepatocyte_NPip_middle_Ctrl_rep1


title: rat_hepatocyte_NPip_middle_Expr_rep2


title: rat_hepatocyte_MDA_high_Expr_rep3


title: rat_hepatocyte_NPip_high_Ctrl_rep1


title: rat_hepatocyte_NPip_low_Expr_rep3


title: rat_hepatocyte_2AAF_low_Expr_rep2


title: rat_hepatocyte_NPip_low_Ctrl_rep1


title: rat_hepatocyte_2AAF_low_Ctrl_rep1


title: rat_hepatocyte_2AAF_low_Ctrl_rep2


title: rat_hepatocyte_2AAF_low_Ctrl_rep3


title: knockout back skin at E15.5, biological rep 3

city: Madison

first: Hao

last: Chang

state: WI

address: 1300 University Ave

department: Dermatology

institute: University of Wisconsin-Madison

description: Gene expression data from mutant embryonic skins

hyb_protocol: Johns Hopkins Microarray Core Facility, http://www.microarray.jhmi.edu/

data_processing: Raw data was processed in R2.4.1 using the affy and rma packages from the Bioconductor Project (www.bioconductor.org).

source_name: back skin

growth_protocol: Timed-pregnant females were euthanized and embryonic back skins were collected at E15.5.

extract_protocol: Trizol and Rneasy according to the manufacturer's instructions.

treatment_protocol: Embryonic skins were dissected and kept in Trizol.

value: back skin

tag: genotype

tag: developmental stage

value: C57BL6/129 mixed


title: knockout back skin at E15.5, biological rep 1

scan_protocol: Johns Hopkins Microarray Core Facility, http://www.microarray.jhmi.edu/


title: rat_hepatocyte_2AAF_middle_Ctrl_rep3

value: GT

value: 0.33 microM


title: rat_hepatocyte_2AAF_middle_Expr_rep2


title: knockout back skin at E15.5, biological rep 2

label_protocol: Johns Hopkins Microarray Core Facility, http://www.microarray.jhmi.edu/


title: rat_hepatocyte_2AAF_low_Expr_rep1


title: rat_hepatocyte_2AAF_middle_Expr_rep3


title: rat_hepatocyte_NPip_high_Expr_rep3

value: high


title: control back skin at E15.5, biological rep 1

description: Gene expression data from control embryonic skins


title: control back skin at E15.5, biological rep 3


title: rat_hepatocyte_2AAF_middle_Expr_rep1


title: control back skin at E15.5, biological rep 2


title: rat_hepatocyte_2AAF_middle_Ctrl_rep2

value: Ctrl


title: rat_hepatocyte_2AAF_high_Expr_rep1

value: 0.99 microM


title: rat_hepatocyte_2AAF_high_Expr_rep3


title: rat_hepatocyte_2AAF_high_Ctrl_rep2


title: rat_hepatocyte_2AAF_high_Ctrl_rep3


title: rat_hepatocyte_2AAF_middle_Ctrl_rep1


title: NP2,brain

city: Shanghai

first: Hu

last: Meng

address: 160 Pujian Road, Pudong New Area, Shanghai

institute: Department of Pharmacy, Ren Ji Hospital, School of Medicine，Shanghai Jiaotong University

description:
female mice (9–month old) were used
NP(α-M)
NP_2_pi_NS

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software12.6.1 (Agilent technologies, Santa Clara, CA, US). The normalized data with probe set annotation is also availble on the series record.

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip  3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: APP/PS1 transgenic mice were purchased from Model Animal Research Center of Nanjing University.

treatment_protocol: APP/PS1 transgenic mice were randomly divided into five groups, and intravenously administered with  Blank-NP, NP(α-M) (0.2 ml) daily at the α-M dose of 1 mg/kg for 4 weeks.

value: female

value: brain

tag: age

value: 9 months


title: NP1,brain

description:
female mice (9–month old) were used
NP(α-M)
NP_1_pi_NS

extract_protocol: Total RNA were amplified, labeled and purified by using GeneChip  3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.


title: NP4,brain

description:
female mice (9–month old) were used
NP(α-M)
NP_4_pi_NS


title: NP3,brain

description:
female mice (9–month old) were used
NP(α-M)
NP_3_pi_NS


title: rat_hepatocyte_2AAF_high_Expr_rep2

value: Wistar

value: Expr


title: BP4,brain

description:
female mice (9–month old) were used
Blank-NP
B_4_pi_NS


title: rat_hepatocyte_NNK_low_Expr_rep1

value: hepatocytes

value: NNK

value: low

value: 88 microM


title: rat_hepatocyte_NNK_low_Expr_rep3

value: male


title: rat_hepatocyte_NNK_low_Expr_rep2


title: BP3,brain

description:
female mice (9–month old) were used
Blank-NP
B_3_pi_NS


title: rat_hepatocyte_NNK_low_Ctrl_rep1


title: Dlx3-K14cKO #13

first: Hong-wei

last: Sun

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
Chips were scanned using Affymetrix GeneChip
(GeneChip Operating Software) GCOS 1.4 version software.
To access the efficiency of cDNA synthesis and labeling Poly-A RNAwas spiked to the samples and hybridization controls were added according to the manufacturer’s instructions. Wild type
samples were averaged and used as a baseline to mutant samples.
The significantly affected genes (p   0.05 and fold change   1.5) were selected based on ANOVA analysis by Partek Pro software (Partek, St. Charles, MO, USA).

source_name: Enamel organ at P10

label_protocol: standard Affymetrix protocol

extract_protocol: none provided by the submitter

value: mixed background

value: Enamel organ

value: Post-natal day 10


title: Dlx3-WT #7910


title: Dlx3-K14cKO #11


title: rat_hepatocyte_NNK_middle_Expr_rep2

value: GT

value: middle

value: 333 microM


title: rat_hepatocyte_NNK_low_Ctrl_rep3

value: Ctrl


title: rat_hepatocyte_NNK_low_Ctrl_rep2


title: Dlx3-K14cKO #12


title: BP2,brain

description:
female mice (9–month old) were used
Blank-NP
B_2_pi_NS

value: female


title: rat_hepatocyte_2AAF_high_Ctrl_rep1

value: high

value: 0.99 microM


title: rat_hepatocyte_NNK_middle_Expr_rep1

value: Wistar


title: rat_hepatocyte_NNK_high_Expr_rep2

value: 1000 microM

value: Expr


title: rat_hepatocyte_NNK_high_Ctrl_rep3

value: hepatocytes

value: NNK


title: rat_hepatocyte_NNK_high_Ctrl_rep1


title: BP1,brain

description:
female mice (9–month old) were used
Blank-NP
B_1_pi_NS

value: brain

value: 9 months


title: rat_hepatocyte_NNK_middle_Ctrl_rep2

value: male


title: rat_hepatocyte_NNK_high_Expr_rep1


title: rat_hepatocyte_NNK_middle_Ctrl_rep1


title: rat_hepatocyte_NNK_high_Expr_rep3


title: rat_hepatocyte_NNK_high_Ctrl_rep2


title: rat_hepatocyte_NNK_middle_Ctrl_rep3


title: rat_hepatocyte_T0_rep23


title: rat_hepatocyte_T0_rep22


title: rat_hepatocyte_T0_rep21


title: rat_hepatocyte_T0_rep9


title: rat_hepatocyte_NNK_middle_Expr_rep3


title: rat_hepatocyte_T0_rep12


title: rat_hepatocyte_T0_rep20


title: rat_hepatocyte_T0_rep18


title: rat_hepatocyte_T0_rep14


title: rat_hepatocyte_T0_rep17


title: rat_hepatocyte_Prop_middle_Expr_rep2

value: Prop

value: NC

value: 14.29 microM


title: rat_hepatocyte_T0_rep7


title: rat_hepatocyte_Prop_low_Expr_rep1

value: low

value: 4.76 microM


title: rat_hepatocyte_Prop_middle_Expr_rep3

value: middle


title: rat_hepatocyte_T0_rep15


title: rat_hepatocyte_Prop_middle_Ctrl_rep1

value: Ctrl


title: rat_hepatocyte_T0_rep13


title: rat_hepatocyte_Prop_low_Ctrl_rep2


title: rat_hepatocyte_Prop_low_Ctrl_rep1


title: rat_hepatocyte_Prop_high_Expr_rep2

value: high

value: 42.86 microM


title: rat_hepatocyte_T0_rep16

value: Wistar


title: rat_hepatocyte_Prop_middle_Ctrl_rep3


title: rat_hepatocyte_Prop_low_Ctrl_rep3


title: rat_hepatocyte_T0_rep19


title: rat_hepatocyte_Prop_low_Expr_rep2


title: rat_hepatocyte_T0_rep11


title: rat_hepatocyte_Prop_middle_Expr_rep1


title: rat_hepatocyte_T0_rep8


title: rat_hepatocyte_T0_rep10


title: rat_hepatocyte_Prop_low_Expr_rep3


title: rat_hepatocyte_Prop_high_Expr_rep1


title: rat_hepatocyte_Prop_middle_Ctrl_rep2


title: rat_hepatocyte_Prop_high_Expr_rep3


title: rat_hepatocyte_Prop_high_Ctrl_rep2


title: rat_hepatocyte_Prop_high_Ctrl_rep3


title: rat_hepatocyte_Nif_low_Ctrl_rep2

value: Nif

value: 6.94 microM


title: rat_hepatocyte_Nif_low_Expr_rep3

value: hepatocytes

value: Expr


title: rat_hepatocyte_Nif_high_Expr_rep2

value: 600 microM


title: rat_hepatocyte_Nif_high_Expr_rep3


title: rat_hepatocyte_Nif_middle_Ctrl_rep3

value: 200 microM


title: rat_hepatocyte_Nif_high_Ctrl_rep2

value: male


title: rat_hepatocyte_Nif_middle_Ctrl_rep2


title: rat_hepatocyte_Nif_middle_Expr_rep3


title: rat_hepatocyte_Nif_low_Expr_rep2


title: rat_hepatocyte_Nif_high_Ctrl_rep1


title: rat_hepatocyte_Nif_high_Ctrl_rep3


title: rat_hepatocyte_Nif_low_Expr_rep1


title: rat_hepatocyte_CFX_low_Expr_rep3

value: CFX

value: 75.45 microM


title: rat_hepatocyte_Nif_low_Ctrl_rep3

value: NC


title: rat_hepatocyte_Nif_middle_Ctrl_rep1


title: rat_hepatocyte_CFX_low_Ctrl_rep2

value: low


title: rat_hepatocyte_CFX_middle_Expr_rep3

value: 226.36 microM


title: rat_hepatocyte_Nif_middle_Expr_rep1

value: middle


title: rat_hepatocyte_Nif_high_Expr_rep1


title: rat_hepatocyte_CFX_low_Expr_rep1


title: rat_hepatocyte_CFX_middle_Expr_rep1


title: rat_hepatocyte_Nif_low_Ctrl_rep1

value: Ctrl


title: rat_hepatocyte_CFX_low_Expr_rep2


title: rat_hepatocyte_CFX_low_Ctrl_rep1


title: rat_hepatocyte_CFX_middle_Expr_rep2


title: rat_hepatocyte_CFX_middle_Ctrl_rep3


title: rat_hepatocyte_Prop_high_Ctrl_rep1

value: Prop

value: high


title: rat_hepatocyte_Nif_middle_Expr_rep2

value: Wistar


title: rat_hepatocyte_CFX_low_Ctrl_rep3


title: rat_hepatocyte_CFX_middle_Ctrl_rep1


title: rat_hepatocyte_PBO_low_Expr_rep3

value: PBO

value: NG

value: 3.52 microM


title: rat_hepatocyte_PBO_low_Ctrl_rep2

value: hepatocytes


title: rat_hepatocyte_CFX_high_Ctrl_rep3

value: 679.09 microM


title: rat_hepatocyte_PBO_low_Expr_rep1

value: Expr


title: rat_hepatocyte_CFX_high_Ctrl_rep2

value: male


title: rat_hepatocyte_PBO_high_Ctrl_rep3

value: 31.69 microM


title: rat_hepatocyte_CFX_middle_Ctrl_rep2

value: CFX


title: rat_hepatocyte_PBO_middle_Expr_rep2

value: 10.56 microM


title: rat_hepatocyte_PBO_middle_Expr_rep1


title: rat_hepatocyte_PBO_middle_Ctrl_rep3


title: rat_hepatocyte_CFX_high_Ctrl_rep1

value: NC


title: rat_hepatocyte_CFX_high_Expr_rep3


title: rat_hepatocyte_PBO_middle_Expr_rep3


title: rat_hepatocyte_PBO_low_Ctrl_rep1

value: low


title: rat_hepatocyte_CFX_high_Expr_rep2


title: rat_hepatocyte_PBO_low_Expr_rep2


title: rat_hepatocyte_PBO_high_Ctrl_rep2


title: rat_hepatocyte_PBO_middle_Ctrl_rep1

value: middle


title: rat_hepatocyte_PBO_high_Expr_rep2


title: rat_hepatocyte_PBO_middle_Ctrl_rep2

value: Ctrl


title: rat_hepatocyte_PBO_high_Ctrl_rep1


title: rat_hepatocyte_PBO_low_Ctrl_rep3


title: rat_hepatocyte_PBO_high_Expr_rep3


title: rat_hepatocyte_Wy_low_Expr_rep2

value: Wy

value: 60.05 microM


title: rat_hepatocyte_Wy_low_Expr_rep3

value: Wistar


title: rat_hepatocyte_Wy_low_Ctrl_rep3


title: rat_hepatocyte_PBO_high_Expr_rep1

value: PBO

value: high


title: rat_hepatocyte_Wy_low_Expr_rep1

value: NG


title: rat_hepatocyte_CFX_high_Expr_rep1

value: hepatocytes


title: rat_hepatocyte_Wy_middle_Expr_rep2

value: 180.14 microM


title: rat_hepatocyte_Wy_high_Expr_rep2

value: 540.43 microM

value: Expr


title: rat_hepatocyte_Wy_high_Ctrl_rep3

value: male


title: rat_hepatocyte_Wy_high_Ctrl_rep2


title: rat_hepatocyte_Wy_middle_Expr_rep1


title: rat_hepatocyte_Wy_low_Ctrl_rep2


title: rat_hepatocyte_Wy_low_Ctrl_rep1


title: rat_hepatocyte_Wy_middle_Expr_rep3


title: rat_hepatocyte_Wy_high_Expr_rep3


title: rat_hepatocyte_Wy_high_Expr_rep1


title: rat_hepatocyte_Wy_middle_Ctrl_rep1


title: rat_hepatocyte_Wy_high_Ctrl_rep1


title: rat_hepatocyte_DES_low_Expr_rep2

value: DES

value: 1.35 microM


title: rat_hepatocyte_DES_low_Ctrl_rep1


title: rat_hepatocyte_Wy_middle_Ctrl_rep3


title: rat_hepatocyte_Wy_middle_Ctrl_rep2


title: rat_hepatocyte_DES_middle_Expr_rep1

value: 4.05 microM


title: rat_hepatocyte_DES_high_Expr_rep3

value: 12.15 microM


title: rat_hepatocyte_DES_middle_Ctrl_rep2

value: middle


title: rat_hepatocyte_DES_low_Ctrl_rep3

value: low

value: Ctrl


title: rat_hepatocyte_DES_low_Expr_rep1


title: rat_hepatocyte_DES_middle_Expr_rep2


title: rat_hepatocyte_DES_middle_Expr_rep3


title: rat_hepatocyte_DES_middle_Ctrl_rep3


title: rat_hepatocyte_DES_low_Expr_rep3


title: rat_hepatocyte_DES_low_Ctrl_rep2


title: rat_hepatocyte_DES_high_Ctrl_rep3


title: rat_hepatocyte_DES_high_Expr_rep1


title: rat_hepatocyte_DES_high_Expr_rep2


title: rat_hepatocyte_DES_middle_Ctrl_rep1


title: rat_hepatocyte_TAA_low_Ctrl_rep2

value: TAA

value: 8.74 microM


title: rat_hepatocyte_TAA_low_Expr_rep3

value: Wistar


title: rat_hepatocyte_TAA_middle_Expr_rep2

value: 26.22 microM


title: rat_hepatocyte_TAA_high_Ctrl_rep3

value: NG

value: high

value: 78.67 microM


title: rat_hepatocyte_TAA_high_Expr_rep1

value: hepatocytes


title: rat_hepatocyte_TAA_low_Ctrl_rep3


title: rat_hepatocyte_TAA_low_Expr_rep1

value: Expr


title: rat_hepatocyte_DES_high_Ctrl_rep2

value: male


title: rat_hepatocyte_TAA_middle_Expr_rep3


title: rat_hepatocyte_DES_high_Ctrl_rep1

value: DES


title: rat_hepatocyte_TAA_low_Expr_rep2


title: rat_hepatocyte_TAA_high_Expr_rep3


title: rat_hepatocyte_TAA_middle_Ctrl_rep3


title: rat_hepatocyte_TAA_middle_Ctrl_rep2


title: rat_hepatocyte_TAA_high_Ctrl_rep1


title: rat_hepatocyte_TAA_high_Expr_rep2


title: rat_hepatocyte_MPy_low_Ctrl_rep3

value: MPy

value: 1.92 microM


title: rat_hepatocyte_TAA_high_Ctrl_rep2


title: rat_hepatocyte_MPy_low_Expr_rep3


title: rat_hepatocyte_MPy_low_Expr_rep2


title: rat_hepatocyte_MPy_low_Ctrl_rep2


title: rat_hepatocyte_TAA_middle_Ctrl_rep1


title: rat_hepatocyte_MPy_low_Ctrl_rep1


title: rat_hepatocyte_MPy_middle_Ctrl_rep3

value: 14.78 microM


title: rat_hepatocyte_TAA_low_Ctrl_rep1


title: rat_hepatocyte_MPy_middle_Expr_rep2

value: middle


title: rat_hepatocyte_MPy_low_Expr_rep1

value: low


title: rat_hepatocyte_MPy_middle_Expr_rep3


title: rat_hepatocyte_TAA_middle_Expr_rep1


title: rat_hepatocyte_MPy_middle_Expr_rep1


title: rat_hepatocyte_CIDB_low_Ctrl_rep3

value: CIDB

value: GT

value: Ctrl


title: rat_hepatocyte_CIDB_low_Expr_rep3

value: Wistar


title: rat_hepatocyte_CIDB_middle_Expr_rep3

value: 5.76 microM


title: rat_hepatocyte_MPy_high_Ctrl_rep3

value: NG

value: 44.39 microM


title: rat_hepatocyte_MPy_high_Expr_rep3

value: high


title: rat_hepatocyte_MPy_high_Expr_rep1

value: hepatocytes


title: rat_hepatocyte_CIDB_high_Expr_rep3

value: 17.28 microM

value: Expr


title: rat_hepatocyte_CIDB_middle_Expr_rep2

value: male


title: rat_hepatocyte_CIDB_low_Ctrl_rep2


title: rat_hepatocyte_CIDB_low_Expr_rep1


title: rat_hepatocyte_MPy_high_Ctrl_rep2

value: MPy


title: rat_hepatocyte_CIDB_middle_Ctrl_rep2


title: rat_hepatocyte_NNM_low_Expr_rep3

value: NNM

value: 16.93 microM


title: rat_hepatocyte_CIDB_low_Expr_rep2

value: 1.92 microM


title: rat_hepatocyte_CIDB_high_Expr_rep1


title: rat_hepatocyte_CIDB_middle_Ctrl_rep1

value: middle


title: rat_hepatocyte_CIDB_middle_Expr_rep1

value: CIDB


title: rat_hepatocyte_MPy_high_Ctrl_rep1


title: rat_hepatocyte_CIDB_high_Ctrl_rep2

value: GT


title: rat_hepatocyte_MPy_middle_Ctrl_rep1

value: 14.78 microM

value: Ctrl


title: rat_hepatocyte_CIDB_middle_Ctrl_rep3

value: Wistar

value: 5.76 microM


title: rat_hepatocyte_MPy_high_Expr_rep2

value: NG

value: 44.39 microM


title: rat_hepatocyte_CIDB_high_Ctrl_rep3

value: hepatocytes

value: high


title: rat_hepatocyte_MPy_middle_Ctrl_rep2


title: rat_hepatocyte_CIDB_high_Expr_rep2

value: 17.28 microM

value: Expr


title: rat_hepatocyte_CIDB_high_Ctrl_rep1

value: male


title: rat_hepatocyte_NNM_low_Ctrl_rep3

value: NNM

value: low


title: rat_hepatocyte_NNM_low_Expr_rep1

value: 16.93 microM


title: rat_hepatocyte_NNM_low_Expr_rep2


title: rat_hepatocyte_NNM_low_Ctrl_rep2


title: rat_hepatocyte_NNM_low_Ctrl_rep1


title: rat_hepatocyte_NNM_middle_Expr_rep1

value: middle

value: 50.78 microM


title: rat_hepatocyte_CIDB_low_Ctrl_rep1

value: CIDB

value: GT

value: 1.92 microM


title: rat_hepatocyte_NNM_middle_Expr_rep3

value: Wistar


title: rat_hepatocyte_NNM_middle_Ctrl_rep3

value: Ctrl


title: rat_hepatocyte_NNM_middle_Ctrl_rep1


title: rat_hepatocyte_NNM_middle_Ctrl_rep2


title: rat_hepatocyte_NNM_high_Expr_rep2

value: 152.33 microM


title: rat_hepatocyte_NNM_high_Ctrl_rep3


title: rat_hepatocyte_NNM_high_Expr_rep3


title: rat_hepatocyte_NNM_high_Ctrl_rep2


title: rat_hepatocyte_AfB1_low_Ctrl_rep3


title: rat_hepatocyte_AfB1_middle_Expr_rep2


title: rat_hepatocyte_AfB1_low_Expr_rep1


title: rat_hepatocyte_AfB1_low_Ctrl_rep1


title: rat_hepatocyte_AfB1_middle_Expr_rep3


title: rat_hepatocyte_AfB1_low_Expr_rep3


title: rat_hepatocyte_AfB1_middle_Ctrl_rep1


title: rat_hepatocyte_AfB1_low_Ctrl_rep2


title: rat_hepatocyte_AfB1_middle_Ctrl_rep2


title: rat_hepatocyte_AfB1_high_Expr_rep3

value: 0.0028 microM


title: rat_hepatocyte_NNM_high_Ctrl_rep1

value: hepatocytes


title: rat_hepatocyte_NNM_high_Expr_rep1

value: high


title: rat_hepatocyte_AfB1_middle_Ctrl_rep3


title: rat_hepatocyte_AfB1_low_Expr_rep2


title: rat_hepatocyte_AfB1_middle_Expr_rep1


title: rat_hepatocyte_AfB1_high_Ctrl_rep3


title: rat_hepatocyte_NNM_middle_Expr_rep2


title: rat_hepatocyte_AfB1_high_Expr_rep2


title: rat_hepatocyte_AfB1_high_Ctrl_rep2


title: rat_hepatocyte_DMN_low_Expr_rep1

value: DMN

value: 39.19 microM


title: rat_hepatocyte_DMN_low_Expr_rep3

value: male

value: Expr


title: rat_hepatocyte_AfB1_high_Ctrl_rep1


title: rat_hepatocyte_DMN_low_Expr_rep2

value: low


title: rat_hepatocyte_DMN_middle_Expr_rep3

value: 333 microM


title: rat_hepatocyte_DMN_middle_Ctrl_rep2

value: middle


title: rat_hepatocyte_DMN_low_Ctrl_rep2


title: rat_hepatocyte_DMN_middle_Expr_rep2


title: rat_hepatocyte_DMN_low_Ctrl_rep1


title: rat_hepatocyte_DMN_low_Ctrl_rep3


title: rat_hepatocyte_DMN_middle_Expr_rep1


title: rat_hepatocyte_DMN_middle_Ctrl_rep3


title: rat_hepatocyte_DMN_high_Expr_rep3

value: 1000 microM


title: rat_hepatocyte_DMN_high_Ctrl_rep1


title: rat_hepatocyte_DMN_high_Expr_rep2


title: rat_hepatocyte_2-NF_low_Expr_rep3

value: 4.76 microM


title: rat_hepatocyte_DMN_high_Ctrl_rep2

value: GT


title: rat_hepatocyte_DMN_middle_Ctrl_rep1


title: rat_hepatocyte_DMN_high_Ctrl_rep3


title: rat_hepatocyte_DMN_high_Expr_rep1


title: rat_hepatocyte_2-NF_low_Expr_rep2


title: rat_hepatocyte_2-NF_low_Expr_rep1


title: rat_hepatocyte_2-NF_low_Ctrl_rep2


title: 15_CD46-deficienct Patient 1

description: RNA-seq

data_processing:
Sequencing reads were trimmed for adaptor contamination with Cutadapt (v1.16)
then aligned to human genome with STAR (v2.5.3a)
read counts were produced by using featureCounts(v.1.5.2)
Genome_build: GENCODE release 26

source_name: CD46-deficienct Patient 1 CD8+ T cells activated with anti-CD3+anti-CD46 6hrs

extract_protocol:
CD8+ T cells were isolated from peripheral blood. RNA was extracted using RNeasy Mini kit with on-column DNAse digestion
The sequencing libraries were constructed from 10 pg – 10 ng of total RNA using the Takara Bio USA’s SMART-Seq V4 Ultra Low Input RNA Kit for Sequencing (Cat # 634888) following the manufacturer instruction.

tag: file name

tag: activation state


title: 14_Healthy Donor 1

description: RNA-seq

source_name: Healthy Donor 1 CD8+ T cells activated with anti-CD3+anti-CD46 6hrs


title: rat_hepatocyte_AfB1_high_Expr_rep1

source_name: cultivated hepatocytes from male Wistar rats

tag: tissue


title: rat_hepatocyte_2-NF_low_Ctrl_rep3


title: 11_Healthy Donor 2

description: RNA-seq

source_name: Healthy Donor 2 CD8+ T cells unactivated

value: Unactivated


title: 13_Healthy Donor 1

description: RNA-seq

source_name: Healthy Donor 1 CD8+ T cells unactivated


title: 12_Healthy Donor 2

description: RNA-seq

source_name: Healthy Donor 2 CD8+ T cells activated with anti-CD3+anti-CD46 6hrs


title: rat_hepatocyte_2-NF_low_Ctrl_rep1

value: Wistar


title: rat_hepatocyte_2-NF_high_Expr_rep3

value: 43.13 microM


title: rat_hepatocyte_2-NF_middle_Expr_rep2

value: 14.38 microM


title: rat_hepatocyte_2-NF_middle_Expr_rep1


title: rat_hepatocyte_2-NF_high_Expr_rep2


title: rat_hepatocyte_2-NF_high_Ctrl_rep2

value: Ctrl


title: rat_hepatocyte_T0_rep5

value: hepatocytes


title: rat_hepatocyte_2-NF_high_Ctrl_rep1

value: high


title: rat_hepatocyte_2-NF_middle_Ctrl_rep1


title: rat_hepatocyte_2-NF_high_Expr_rep1


title: RNASeq shZZZ3-2 rescue_D824A Rep2

city: Grand Rapids

first: Hong

last: Wen

state: Michigan

address: 333 Bostwick Ave. N.E.

department: Center for Epigenetics

institute: Van Andel Research Institute

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie2 v2.1.0; RNA-seq reads were aligned to hg19 genome using tophat v2.0.10
Genome_build: hg19
ChIP-seq wig files were generated using MACS-1.3.6+B102; Scores represent the ChIP-seq tag numbers; RNA-seq htseq file include differential significance across treatment and control and the tag numbers in all samples
Supplementary_files_format_and_content: RNA-seq read counts were calculated using HTSeq 0.6.1p1

growth_protocol: Human H1299 cells (ATCC) were cultured in RPMI 1640 with 10% FBS (Cellgro) supplemented with 10% fetal bovine serum (Sigma), 5% CO2, 37 oC.

extract_protocol:
mRNA was prepared using the RNeasy Plus kit (Qiagen) and reverse-transcribed using the First Strand Synthesis kit (Invitrogen). Libraries were prepared using the Illumina TruSeq RNA Library Prep kit following the manufactory manual.
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.   mRNA was prepared using the RNeasy Plus kit (Qiagen) and reverse-transcribed using the iScript™ cDNA Synthesis Kit (Bio-Rad).
For ChIP-seq, sequencing libraries were prepared using the Illumina TruSeq DNA Sample Preparation Kit according to the manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor) were band isolated from an agarose gel. DNA fragments were sequenced using paired-end sequencing technology on Illumina HiSeq 2000 platform.  For RNA-seq, samples were prepared as instructed using the TruSeq mRNA Sample Preparation Kit v2 (Illumina, San Diego, CA) in accordance with the manufacturer's instructions. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles, DNA fragments were sequenced using single-end sequencing technology on Illumina paried-end on Illumina HiSeq2000 .

treatment_protocol: For shRNA knockdown, 293T cells were co-transfected with pMD2.G and pPAX2 (Addgene) together with pLKO-shRNA constructs or a non-targeting pLKO-shRNA (pLKO-shNT). Viral supernatants were harvested after 48 hrs. For infections, H1299 cells were incubated with viral supernatants in the presence of 8 µg/ml polybrene. After 48 hrs, puromycin (2 µg/ml) was added to the medium. Cells were grown with selection for 4-7 days to select for stable knockdown cells.

tag: cell line

value: H1299 cells

tag: treatment

value: ATAC1 Knock Down + D824A rescue


title: rat_hepatocyte_2-NF_middle_Ctrl_rep2

tag: strain

tag: Sex

value: male


title: rat_hepatocyte_T0_rep6

tag: compound

tag: phenotype


title: rat_hepatocyte_T0_rep4

tag: concentration

tag: sample type


title: rat_hepatocyte_T0_rep3


title: rat_hepatocyte_T0_rep1


title: rat_hepatocyte_2-NF_high_Ctrl_rep3


title: rat_hepatocyte_2-NF_middle_Ctrl_rep3


title: rat_hepatocyte_T0_rep2


title: RNASeq shZZZ3-2 rescue_D824A Rep1


title: 10_CD46-deficienct Patient 2

description: RNA-seq

source_name: CD46-deficienct Patient 2 CD8+ T cells activated with anti-CD3+anti-CD46 6hrs


title: RNASeq shZZZ3-2 rescue_F821A Rep2

value: ATAC1 Knock Down + F821A rescue


title: 09_CD46-deficienct Patient 2

description: RNA-seq

source_name: CD46-deficienct Patient 2 CD8+ T cells unactivated


title: 08_Healthy Donor 3

description: RNA-seq

source_name: Healthy Donor 3 CD8+ T cells activated with anti-CD3+anti-CD46 6hrs


title: RNASeq shZZZ3-2 rescue_F821A Rep1


title: 06_CD46-deficienct Patient 3

description: RNA-seq

source_name: CD46-deficienct Patient 3 CD8+ T cells activated with anti-CD3+anti-CD46 6hrs


title: RNASeq shZZZ3-2 rescue_Rep2

value: ATAC1 Knock Down + WT ATAC1 rescue


title: RNASeq shZZZ3-2 rescue_Rep1


title: 05_CD46-deficienct Patient 3

description: RNA-seq

source_name: CD46-deficienct Patient 3 CD8+ T cells unactivated


title: 02_CD46-deficienct Patient 4

description: RNA-seq

source_name: CD46-deficienct Patient 4 CD8+ T cells activated with anti-CD3+anti-CD46 6hrs


title: RNASeq shZZZ3-2 Rep2

value: ATAC1 Knock Down


title: 03_Healthy Donor 4

description: RNA-seq

source_name: Healthy Donor 4 CD8+ T cells unactivated


title: rat_hepatocyte_2-NF_middle_Expr_rep3

value: middle

value: Expr


title: 10 dpl non-vascular niche replicate 6

city: Gdansk

first: Jakub

last: Mieczkowski

address: Debinki 12

country: Poland

institute: Medical University of Gdansk

description:
SAMPLE 24
replicate 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: 10 dpl non-vascular niche

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Demyelination in rats was induced bilaterally by stereotaxic injection of 4 μL of 0.01% ethidium bromide  into the CCP as previously described (Woodruff and Franklin, 1999).

tag: gender

value: female

value: Rat cerebellar white matter (caudal cerebellar peduncle, CCP)

tag: niche

value: non-vascular niche

tag: time

value: 10 dpl


title: 04_Healthy Donor 4

description: RNA-seq

source_name: Healthy Donor 4 CD8+ T cells activated with anti-CD3+anti-CD46 6hrs


title: RNASeq shZZZ3-2 Rep1


title: RNASeq shCtrl-2 Rep2

value: shNT control vector


title: RNASeq shCtrl-2 Rep1


title: 01_CD46-deficienct Patient 4

description: RNA-seq

source_name: CD46-deficienct Patient 4 CD8+ T cells unactivated

value: Unactivated


title: RNASeq shZZZ3-1 rescue_Rep2

description:
H1299.shZZZ3-1.all.edgeR.txt
2R_W_rep2_R1

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie2 v2.1.0; RNA-seq reads were aligned to hg19 genome using tophat v2.0.10
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq htseq file include differential significance across treatment and control and the tag numbers in all samples
Supplementary_files_format_and_content: RNA-seq read counts were calculated using HTSeq 0.6.1p1

tag: cell

tag: antibody


title: 10 dpl vascular niche replicate 5

description:
SAMPLE 21
replicate 5

source_name: 10 dpl vascular niche

value: vascular niche


title: RNASeq shZZZ3-1 rescue_Rep1

description:
H1299.shZZZ3-1.all.edgeR.txt
2R_W_rep1_R1


title: 10 dpl vascular niche replicate 4

description:
SAMPLE 19
replicate 4


title: 10 dpl non-vascular niche replicate 4

description:
SAMPLE 20
replicate 4


title: 10 dpl non-vascular niche replicate 2

description:
SAMPLE 16
replicate 2


title: 10 dpl vascular niche replicate 6

description:
SAMPLE 23
replicate 6


title: 10 dpl vascular niche replicate 3

description:
SAMPLE 17
replicate 3


title: 10 dpl non-vascular niche replicate 5

description:
SAMPLE 22
replicate 5


title: 07_Healthy Donor 3

description: RNA-seq

source_name: Healthy Donor 3 CD8+ T cells unactivated


title: 10 dpl vascular niche replicate 2

description:
SAMPLE 15
replicate 2


title: 10 dpl non-vascular niche replicate 3

description:
SAMPLE 18
replicate 3


title: 10 dpl non-vascular niche replicate 1

description:
SAMPLE 14
replicate 1


title: o2 ChIP rep2

city: Tucson

first: Ramin

last: Yadegari

state: Arizona

address: 1140 E. South Campus Dr.

department: Plant Sciences

institute: University of Arizona

description:
chromatin DNA
O2_peaks.txt.gz

data_processing:
Illumina HiSeq 2500
Raw reads from RNA-Seq and ChIP-Seq were trimmed to remove adapter sequences and low-quality bases using the Trimmomatic program with the parameter TRAILING set to three. The resulting RNA-Seq reads were mapped to the maize reference genome using Tophat v2.0.9. Reads mapped to each gene were counted using the multicov function of BEDTools v2.17.0 and normalized using the R package edgeR v3.2.4 with the trimmed mean of M-values method. The genes with raw counts per million (CPM) > 1 in at least 3 samples were tested for differential expression analysis using edgeR with an exact test analogous to Fisher’s exact test. FDR < 0.05 was used as the cutoff to call DEGs. The trimmed ChIP-Seq reads were mapped to the reference genome using Bowtie v2.1.0 with the following parameters: --score-Min L, -0.6, -0.18 --end-to-end --very-sensitive --no-discordant. Mapped reads for duplicates of the B73 samples and the B73o2 samples (control) were merged, respectively, and were used for peak-calling using MACS v2.1.0.20140616 with the following parameters: -g 2.06e9 -q 0.01 -mfold 10 30.
Genome_build: B73 RefGen_v3
Supplementary_files_format_and_content: A tab-delimited text file containing RPKM normalized using edgeR, and a tab-delimited text file containing O2 peaks identified using MACS.

source_name: Kernel

growth_protocol: Plants were grown under greenhouse conditions (16-h day) at the University of Arizona during June to October 2012, and self-pollinated to obtain 15-DAP kernels.

extract_protocol:
RNA was isolated from dissected endosperms using an SDS-phenol method. ChIP was performed using the ChIP Assay Kit (Millipore Corporation, Billerica, MA) by following the manufacturer’s instruction with modifications.
Using a TruSeq DNA Sample Preparation Kit v2 (Illumina), poly(A)-containing mRNAs were purified, fragmented, and reverse-transcribed by the Univ. Arizona Genetics Core facility to construct multiplexed RNA-Seq libraries. Using an Illumina Pico DNA Seq Library Preparation Kit (Gnomegen Inc.), nearly 10 ng of purified ChIPed DNA from each endosperm sample (2 genotypes × 2 replicates) was used by the Univ. Arizona Genetics Core facility to generate a set of multiplexed ChIP-Seq libraries by following the manufacturer’s instruction.

value: Endosperm

tag: age

value: 15 DAP


title: RNASeq shZZZ3-1 rescue_D824A Rep2

description:
H1299.shZZZ3-1.all.edgeR.txt
2R_D_rep2_R1

value: H1299 cells


title: o2 RNA rep3

molecule: polyA RNA


title: WT ChIP rep2

description:
chromatin DNA
O2_peaks.txt.gz


title: RNASeq shZZZ3-1 rescue_F821A Rep2

description:
H1299.shZZZ3-1.all.edgeR.txt
2R_F_rep2_R1


title: RNASeq shZZZ3-1 rescue_F821A Rep1

description:
H1299.shZZZ3-1.all.edgeR.txt
2R_F_rep1_R1


title: RNASeq shZZZ3-1 Rep2

description:
H1299.shZZZ3-1.all.edgeR.txt
2R_KD_rep2_R1


title: 10 dpl vascular niche replicate 1

description:
SAMPLE 13
replicate 1


title: o2 ChIP rep1

description:
chromatin DNA
O2_peaks.txt.gz


title: RNASeq shZZZ3-1 rescue_D824A Rep1

description:
H1299.shZZZ3-1.all.edgeR.txt
2R_D_rep1_R1

value: ATAC1 Knock Down + D824A rescue


title: o2 RNA rep2


title: RNASeq shZZZ3-1 Rep1

description:
H1299.shZZZ3-1.all.edgeR.txt
2R_KD_rep1_R1


title: o2 RNA rep1


title: WT ChIP rep1

description:
chromatin DNA
O2_peaks.txt.gz


title: RNASeq shCtrl-1 Rep2

description:
H1299.shZZZ3-1.all.edgeR.txt
2R_V_rep2_R1


title: RNASeq shCtrl-1 Rep1

description:
H1299.shZZZ3-1.all.edgeR.txt
2R_V_rep1_R1


title: WT RNA rep3


title: WT RNA rep2


title: WT RNA rep1


title: 6 dpl non-vascular niche replicate 6

description:
SAMPLE 12
replicate 6

source_name: 6 dpl non-vascular niche

value: 6 dpl


title: ChIPSeq_Input

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie2 v2.1.0; RNA-seq reads were aligned to hg19 genome using tophat v2.0.10
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS-1.3.6+B102; Scores represent the ChIP-seq tag numbers; RNA-seq htseq file include differential significance across treatment and control and the tag numbers in all samples
Supplementary_files_format_and_content: RNA-seq read counts were calculated using HTSeq 0.6.1p1

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.   mRNA was prepared using the RNeasy Plus kit (Qiagen) and reverse-transcribed using the iScript™ cDNA Synthesis Kit (Bio-Rad).
For ChIP-seq, sequencing libraries were prepared using the Illumina TruSeq DNA Sample Preparation Kit according to the manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor) were band isolated from an agarose gel. DNA fragments were sequenced using paired-end sequencing technology on Illumina HiSeq 2000 platform.  For RNA-seq, samples were prepared as instructed using the TruSeq mRNA Sample Preparation Kit v2 (Illumina, San Diego, CA) in accordance with the manufacturer's instructions. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles, DNA fragments were sequenced using single-end sequencing technology on Illumina paried-end on Illumina HiSeq2000 .

value: Input


title: 6 dpl vascular niche replicate 6

description:
SAMPLE 11
replicate 6

source_name: 6 dpl vascular niche


title: ChIPSeq_Flag_ATAC1_WT

value: ATAC1 Knock Down + WT ATAC1 rescue

value: Sigma, Flag-M2 F1804


title: 6 dpl non-vascular niche replicate 4

description:
SAMPLE 8
replicate 4


title: ChIPSeq_Flag_ATAC1_V


title: 6 dpl non-vascular niche replicate 5

description:
SAMPLE 10
replicate 5


title: 6 dpl vascular niche replicate 5

description:
SAMPLE 9
replicate 5


title: ChIPSeq_Flag_ATAC1_F821

value: ATAC1 Knock Down + F821A rescue


title: ChIPSeq_ATAC1_vector

value: Rabbit 2616, Laszlo Tora lab


title: ChIPSeq_ATAC1_WT


title: 6 dpl vascular niche replicate 3

description:
SAMPLE 5
replicate 3

value: female


title: ChIPSeq_Flag_ATAC1_D824


title: ChIPSeq_ATAC1_KD

value: ATAC1 Knock Down