title: Tet1_WT_Cdh1_BS_V4

city: Babraham

first: Myriam

last: Hemberger

state: Cambridgeshire

address: Babraham Hall

department: Epigenetics

country: United Kingdom

institute: Babraham Institute

description:
lane5946_TGACCACT_V4
DNA from TS cells was bisulfite-converted using the EpiTect kit (Qiagen). The Cdh1 locus was amplified with KAPA HiFi Hotstart Uracil+ ReadyMix (Roche Diagnostics Ltd KK2801). Libraries were amplified and indexed using KAPA HiFi HotStart ReadyMix (Roche Diagnostic Ltd KK2602). Libraries were quantified as above by Bioanalyzer 2100 system (Agilent) and using the KAPA Library Quantification Kit (KAPA Biosystems KK4824, and sequenced with a 150bp paired-end protocol on a MiSeq sequencer (Illumina), with 10% PhIX spike-in

data_processing:
Reads trimmed with Trim Galore using standard protocols.
RNA-Seq reads mapped to GRCm38/mm10 using hisat
RNA-Seq cpm generated by edgeR
ChIP-Seq reads mapped to GRCm38/mm10 using Bowtie
ChIP-Seq peaks called using MACS2 and standard parameters
Bisulfite sequencing data was mapped to the Mus musculus GRCm38 genome assembly and processed using Bismark to find the percent methylation for each CpG
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bed file contains MACS2 peak calls for Tet1 WT; csv files contain normalised cpm data per gene for each sample generated using edgeR; cov files are tab delimited files containing CpG coverage per genomic region.

growth_protocol: TS-Rs26 trophoblast stem cells were routinely cultured in complete TS medium, consisting of 30% TS base medium (RPMI 1640 w/ glutamine (invitrogen 21875-0910) + 20% FBS + Na-pyruvate + 2ME + antibiotics) and 70% MEF conditioned TS base + bFGF + Heparin. Differentiation was induced by withdrawal of bFGF, heparin and conditioned medium.

extract_protocol:
Total RNA was extracted using TRI reagent (Sigma T9424), followed by DNase treatment using the TURBO-DNA-free kit (Life Technologies AM1907). For ChIP-seq, cells (1-2x108) were fixed in 2 mM DSG (Sigma 80424) for 45min and 1% formaldehyde in TS base media for 12 min, both at room temperature (RT). Fixation was stopped by 0.125M glycine. Cells were washed in buffer 1 (10 mM Hepes pH 7. 5, 10 mM EDTA, 0.5 mM EGTA, 0.75% Triton X-100), buffer 2 (10 mM Hepes pH 7.5, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and lysed in the lysis/sonication buffer (150 mM NaCl, 25 mM Tris pH 7.5, 5 mM EDTA, 0.1% Triton, 1% SDS, 0.5% sodium deoxycholate on ice for 30min. Chromatin was sonicated 30sec on/30off for 25-30 cycles using the BioRuptor (Diagenode), diluted 1/10 with the dilution buffer (150 mM NaCl, 25 mM Tris pH 7.5, 5 mM EDTA, 1% Triton-X 100, 0.1% SDS, 0.5% sodium deoxycholate) and pre-cleared with protein G magnetic Dynabeads (Invitrogen 10004D) pre-blocked with BSA and tRNA. Immunoprecipitation was performed with 350 μg chromatin and 10 μg of antibody over night at 4oC and pre- blocked magnetic beads were added next morning for 7-8h. Beads were washed three times each with buffer A (150 mM NaCl, 25 mM Tris pH 7.5, 5 mM EDTA, 1% Triton-X 100, 0.1% SDS, 0.5% Sodium Deoxycolate), buffer B (50 mM Tris pH8.0, 500 mM NaCl, 0.1% SDS, 0.5% sodium deoxycholate, 1% NP40, 1 mM EDTA), buffer C (50 mM Tris pH8.0, 250 mM LiCl, 0.5% sodium deoxycholate, 1% NP40, 1 mM EDTA). DNA was eluted (1%SDS, 0.1M NaHCO3), reverse cross-linked overnight at 65oC and purified on PCR purification columns (Qiagen). For BS-seq, DNA from vector control (WT) and Tet1 KO cells was bisulfite-converted using the EpiTect kit (Qiagen). The Cdh1 locus was amplified with KAPA HiFi Hotstart Uracil+ ReadyMix (Roche Diagnostics Ltd KK2801).
To generate RNA libraries, mRNA was isolated using the Dynabeads mRNA purification kit (Life Technologies 61006) and processed into indexed, strand-specific libraries using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre SSV21106). Libraries were quantified and assessed using the KAPA Library Quantification Kit (KAPA Biosystems KK4824) and Bioanalyzer 2100 system (Agilent). Indexed libraries were sequenced with a 100bp single-end protocol on an Illumina HiSeq2500 sequencer. ChIP sequencing libraries were quantified as above by Bioanalyzer 2100 system (Agilent) and using the KAPA Library Quantification Kit (KAPA Biosystems KK4824). Indexed libraries from ChIP and Input samples were sequenced with a 50bp paired-end protocol on an Illumina HiSeq2500 sequencer. For BS-seq, libraries were amplified and indexed using KAPA HiFi HotStart ReadyMix (Roche Diagnostic Ltd KK2602). Libraries were quantified as above by Bioanalyzer 2100 system (Agilent) and using the KAPA Library Quantification Kit (KAPA Biosystems KK4824, and sequenced with a 150bp paired-end protocol on a MiSeq sequencer (Illumina), with 10% PhIX spike-in.

value: Mouse trophoblast stem cells

value: WT


title: Tet1_KO_Cdh1_BS_7c

status: Public on May 02 2018

type: SRA

description:
lane5946_GCCAATGT_7c
DNA from TS cells was bisulfite-converted using the EpiTect kit (Qiagen). The Cdh1 locus was amplified with KAPA HiFi Hotstart Uracil+ ReadyMix (Roche Diagnostics Ltd KK2801). Libraries were amplified and indexed using KAPA HiFi HotStart ReadyMix (Roche Diagnostic Ltd KK2602). Libraries were quantified as above by Bioanalyzer 2100 system (Agilent) and using the KAPA Library Quantification Kit (KAPA Biosystems KK4824, and sequenced with a 150bp paired-end protocol on a MiSeq sequencer (Illumina), with 10% PhIX spike-in

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell line

tag: cell type

tag: genotype


title: Treated-HSF16,Sensitive 1431005387_84

type: RNA

city: Rochester

first: Michael

middle: K

last: Asiedu

state: MN

address: 200 Fisrt ST SW

department: Surgery

country: USA

institute: Mayo Foundation for Medical Education and Research

description:
Gene expression data from patient derived fibroblast cell lines
Technical replicates 2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 and performed by the Mayo Clinic Genomic Core

data_processing: The data were analyzed with using Partek Genomic Suite Ver. 6.6 (Partek Inc, St. Louis, MO) Partek Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Patient-derived Fibroblast cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA was purified with the RNeasy Mini-kit (Qiagen, CA).

value: Fibroblast cell line


title: H3K27me3, rep2

type: genomic

city: Madison

first: Youngsook

last: Lee

state: WI

address: 1111 Highland Ave

department: CRB

institute: University of Wisconsin-Madison

description: Wild type E17.5 hearts

hyb_protocol: Hybridized onto the Roche NimbleGen 3X720K RefSeq promoter arrays

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol

data_processing:
Global and local normalization and data soothing in R (version, 2.10.1) was performed
Peaks were detected using ChIPOlte and in-house algorithms, Correct P-value 0.001

source_name: H3K27me3 ChIP DNA form E17.5 hearts

label_protocol: ChIP DNA was labeled with fluorescence per manufacturer's protocol

extract_protocol: 20 embryonic hearts were fixed with 1% formaldehyde and lysed in lysis buffer (50mM Tris pH8.0, 10mM EDTA, 1% SDS, protease inhibitors). The crosslinked chromatin was sheared by sonication, and chromatin was diluted in dilution buffer (20mM Tris pH8.0, 2mM EDTA, 150mM NaCl, 1% Triton, 0.01% SDS, protease inhibitors). The samples were incubated with protein A agarose beads and H3K27me3 antibody ( (EMD Millipore, 07-449). The beads were washed with the following buffers; Wash buffer 1 (20mM Tris pH8.0, 2mM EDTA, 50mM NaCl, 1% triton, 0.1% SDS), Wash buffer 2 (10mM Tris pH8.0, 1mM EDTA, 250mM LiCl, 1% NP40, 1% Deoxycholic acid), TE buffer (10mM Tris pH8.0, 1mM EDTA). The protein-DNA complexes were eluted with elution buffer (100mM NaHCO3, 1% SDS) followed by the addition of proteinase K. Genomic DNA was isolated by phenol extraction and precipitation.

value: Wild type

tag: strain

value: Mixed 129/Svj and C57BL/6

tag: tissue

value: Embryonic heart

tag: developmental stage

tag: chip antibody

source_name: Input DNA from E17.5 hearts

value: none, input DNA


title: Treated-HSF16,Sensitive 1431005386_83

description:
Gene expression data from patient derived fibroblast cell lines
Technical replicates 1


title: WT Macrophages CMA rep2

city: Lausanne

first: Muhammet

middle: Fatih

last: Gulen

state: VD

address: Station 19

department: GHI

country: Switzerland

institute: EPFL

library_source: transcriptomic

data_processing:
Mapping: software Bowtie2 v.2.2.1, assembly: mm10; web-based HTSstation was used to process the data (David, et al. 2014)
RNA counter: HTSstation; web-based HTSstation was used to process the data (David, et al. 2014)
Differential expression analysis: Bioconductor limma (v. 3.18.13)
the computations were performed at the Vital-IT (http://www.vital-it.ch) Center for high-performance computing of the SIB Swiss Institute of Bioinformatics.
Supplementary_files_format_and_content: tab-delimited text files include counts and RPKM values for each sample.

source_name: Primary Bone Marrow Derived Macrophages

extract_protocol:
Total RNA from bulk MEF populations was extracted using the RNeasy mini kit (Qiagen). 1.5 and 3 ug of total RNA was used for the preparation of the library using the TruSeq mRNA stranded LT (Illumina kit)
TruSeq mRNA stranded LT (Illumina kit), with qubit quantification and QC with  tapestation 4200 and Fragment analyzer.

tag: treatment

value: Sting agonist (CMA)

value: Primary Bone Marrow Derived Macrophages

tag: passages


title: WT Macrophages C-178+CMA rep2

value: Sting inhibitor + Sting agonist (CMA)


title: WT Macrophages C-178+CMA rep1


title: WT Macrophages CMA rep3


title: WT Macrophages C-178+CMA rep3


title: ENDO 6.1 Treated

description:
Gene expression data from patient derived fibroblast cell lines
ENDO 6.1 ENDO 6.1 Treated

source_name: Patient-derived iPS differentiated cells

value: epithelial cells

value: ENDO 6.1


title: Control-HSF11,Resistant 1431005380_69


title: Control-HSF16,Sensitive 1431005384_81


title: Control-HSF16,Sensitive 1431005385_82


title: WT Macrophages CMA rep1


title: Control-HSF20,Sensitive 1431005404_161


title: Control-HSF11,Resistant 1431005381_70


title: Control-HSF15,Sensitive 1431005388_93


title: Treated-HSF20,Sensitive 1431005407_164


title: Treated-HSF11,Resistant 1431005382_71


title: Control-HSF20,Sensitive 1431005405_162


title: Treated-HSF11,Resistant 1431005383_72


title: H3K27me3, rep3

description: Wild type E17.5 hearts


title: Treated-HSF12,Resistant 1431005374_19


title: Treated-HSF20,Sensitive 1431005406_163


title: WT Macrophages C-178 rep3

value: Sting inhibitor


title: WT Macrophages C-178 rep2


title: H3K27me3, rep1

description: Wild type E17.5 hearts


title: WT Macrophages no stim. rep3

value: no stimulation


title: 5C_Lucio5C-A2-HB-20-30-Combined

city: Worcester

first: Lucio

last: Castilla

state: MA

address: 364 Plantation Street

department: MCCB

institute: University of Massachusetts

data_processing:
Library strategy: 5C
The files are processed as described in the github repository https://github.com/dekkerlab/5C-CBFb-SMMHC-Inhib
The source code of all scripts are provided in the provided github repository.
Genome_build: Custom built based on 5C primers PRIMERPOOL_6217_KelliherMyc.fa . This file is available at https://github.com/dekkerlab/5C-CBFb-SMMHC-Inhib/blob/master/PRIMERPOOL_6217_KelliherMyc.fa
Supplementary_files_format_and_content: tab separated text files

source_name: ME-1 cells

growth_protocol: ME-1 cells were cultured in RPMI 1640 with 20%fetal bovine serum, 25mM HEPES, 100 U/ml Pencillin/ Streptomycin and 1 μl/ml Plasmocin

extract_protocol:
3 ml of 16% formaldehyde solution was added to the 50  ml tube to obtain a  final  concentration of 1%. The content was quickly mixed by inverting the tube twice and left at RT for 10 min for cross-linking.  2.5  ml  of  2.5  M  glycine  was  then  added  to  the  tube to  stop  cross-linking.  The content was quickly mixed by inverting the tube twice and left at RT for 5 min, and then on ice for at least 15 min.  Subsequently, cells were collected by centrifugation (2000 rpm, 10 min), and the cell pellet was frozen on dry ice and then stored at -80°C.
5C was performed as in Maria A. Ferraiuolo et. al, 2012, http://www.sciencedirect.com/science/article/pii/S1046202312002769?via%3Dihub

treatment_protocol: ME-1 cells were treated with DMSO/ AI-10-49 (1uM) for six hours.

value: Human inv(16) leukemia cell line

tag: agent


title: 5C_Lucio5C-D2-HB-20-30-Combined

value: DMSO


title: 5C_Lucio5C-D1-HB-20-30-Combined


title: WT Macrophages no stim. rep1


title: WT Macrophages no stim. rep2


title: Treated-HSF12,Resistant 1431005375_20


title: Control-HSF12,Resistant 1431005373_18


title: Control-HSF12,Resistant 1431005372_17


title: SIRNA-TTR-RVR replicate 2

city: Cambridge

first: Joseph

last: Barry

address: 300 Third Street #3

institute: Alnylam Pharmaceuticals

data_processing:
fastq-mcf filtering, minimal quality 25, minimal length 36
STAR alignment to NCBIM37
Differential gene expression analysis using DESeq2
Genome_build: NCBIM37
Supplementary_files_format_and_content: DESeq2 output tables, tab separated fields, log2FoldChange and padj (adjusted p-value) fields used to create volcano plots in paper. Counts files containing unnormalized gene counts are also supplied for each sample.

source_name: Plateable cryopreserved CD-1 male mouse hepatocytes (ThermoFisher Cat# MSCP10)

extract_protocol: none provided by the submitter

value: REVERSIR targeting TTR-siRNA


title: Control 2

city: Columbia

first: Yuanyuan

middle: R

last: Li

state: MO

address: University of Missouri School of Medicine, One Hospital Dr., Medical Sciences Building, NW508, Medical Sciences Building, NW508, Medical Sciences Building, M659

department: Ob&Gyn

institute: University of Missouri

description: Control replicate 1

data_processing:
The raw RNA-Seq fastq reads were imported into CLC Genomics Workbench for normalization and alignment to the mouse GRCm38/mm10 reference sequence.
Read Quality Assessment was performed by using FASTQC framework to compare read QC metrics across all samples and samples representing different treatment conditions.
Sequenced reads were trimmed for adaptor sequence. We used a Phred threshold of 20 which corresponds to a base call error of 1 in 100 reads. Also, removal of adaptor sequences increases the probability of a read binding to 1 unique genomic location rather than multiple sites. Trimgalore, a wrapper tool around cutadapt to automatically determine adapter sequences and trim low-quality bases, was employed to retain high-quality, non-adapter bases within each read. Calibrated reads were catalogued in separate FASTQ files.
Read Alignment and quality control were conducted by STAR (Boblin et al. 2013). Raw read counts were normalized using DESeq framework.
We utilized the R/Bioconductor package DESeq to evaluate differential gene expression for sequence count data by the use of negative binomial distribution
Genome_build: mm10
Supplementary_files_format_and_content: Quantile Normlized file include values for each Sample. Significant differential expressed gene file was included.

source_name: Mammary tumor

growth_protocol: Dams were treated with control or 26% BSp diets from conception until weaning, all offspring remained untreated.

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 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols. A RNA Integrity Number (RIN) of 7.0 or above was used for sequencing library preparation and Agilent SureSelect Strand Specific mRNA library kit was used as per the manufacturer’s instruction.

value: FVB

tag: age

value: 20 weeks


title: B 2

description: BSp replicate 2

value: Maternal 26percent BSp diet


title: B 1

description: BSp replicate 1


title: B 3

description: BSp replicate 3


title: Control 3

description: Control replicate 2


title: SIRNA-SCRA-RVR replicate 3

value: scrambled control REVERSIR for TTR-siRNA


title: SIRNA-TTR-RVR replicate 1


title: WT Macrophages C-178 rep1


title: SIRNA-SCRA-RVR replicate 2


title: 5C_Lucio5C-A1-HB-20-30-Combined


title: TTR-RVR replicate 2

description:
R-35
groupTTR-RVR.vsPBS.DESeq2.txt

value: TTR-REVERSIR


title: SIRNA-TTR-RVR replicate 3


title: SCRA-RVR replicate 3

description:
R-61
groupSCRA-RVR.vsPBS.DESeq2.txt

value: scrambled REVERSIR


title: SCRA-RVR replicate 1

description:
R-61
groupSCRA-RVR.vsPBS.DESeq2.txt


title: SIRNA replicate 2

value: TTR-siRNA


title: SCRA-RVR replicate 2

description:
R-61
groupSCRA-RVR.vsPBS.DESeq2.txt


title: SIRNA replicate 1


title: SIRNA-SCRA-RVR replicate 1


title: SIRNA replicate 3


title: PBS control replicate 3

value: PBS


title: ORR3

status: Public on May 04 2018

city: BeiJing

first: Xiong

last: Yao

address: No. 17, Tsinghua East Road, Haidian District

country: China

institute: China Agriculture University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house  perl scripts. In this step, clean data (clean reads) were obtained by removing  reads containing adapter, reads containing ploy-N and low quality reads from  raw data. At the same time, Q20, Q30 and GC content sequence of the clean  data were calculated. All the downstream analyses were based on the clean data  with high quality.
Reference genome and gene model annotation files were downloaded from  genome website directly (NC_014656.1). Both building index of reference genome and aligning  clean reads to reference genome were used Bowtie2-2.2.3. (Langmead, B. and S.  L. Salzberg, 2012)
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And  then FPKM of each gene was calculated based on the length of the gene and  reads count mapped to this gene.
(For DESeq with biological replicates) Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using  the DESeq R package (1.18.0). DESeq provide statistical routines for  determining differential expression in digital gene expression data using a  model based on the negative binomial distribution. The resulting P-values were  adjusted using the Benjamini and Hochberg’s approach for controlling the false  discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were  assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was  implemented by the GOseq R package, in which gene length bias was corrected.  GO terms with corrected Pvalue less than 0.05 were considered significantly  enriched by differential expressed genes.
Genome_build: NC_014656.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Bifidobacterium longum subsp. longum BBMN68

source_name: B. longum BBMN68

growth_protocol: Bifidobacterium longum BBMN68 was cultured in de Man-Rogosa-Sharpe (MRS) medium supplemented with L-cysteine (0.05% w/v) anaerobically at 37℃ with or without 0.075% (w/v) oxgall for 24h

extract_protocol:
Total RNA isolation was carried out using TRIzol reagent (Invitrogen, Carlsbad, CA) as the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: medium

value: MRSc with 0.075 percent oxgall

tag: growth phase

value: late-stationary-phase,about 24h


title: TTR-RVR replicate 3

description:
R-35
groupTTR-RVR.vsPBS.DESeq2.txt


title: Progeny of TQ4_225_20, line #2

city: Nagakute

first: Nobuhiko

last: Muramoto

state: Aichi

address: 41-1, Yokomichi

country: Japan

institute: TOYOTA Central R&D Labs., Inc.

description:
TAQing treated tetraploid strain TQ4_225_20_2. Leaves from progeny of TAQing treated plant
TQ4_225_20_2

hyb_protocol: Oligo aCGH/ChIP-on-chip Hybridization Kit and Oligo aCGH/ChIP Wash Buffer Kit

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 11.0.1.1).
Background normalization and dye normalization (linear) using Feature Extraction Software was performed. After that, log10 ratio (Cy5/Cy3) representing test/reference was calculated.

organism: Arabidopsis thaliana

source_name: leaves from progeny of TAQing treated plant

label_protocol: 100 ng of genomic DNA was fluorescently labeled using SureTag DNA Labeling Kit according to the manufaturer instructions (Agilent).  Initially, the DNA was denaturede in the presence of the random primer at 95 ºC for 10 minutes in a heatblock, and then quickly cooled on ice. Labeling occurred with the addition of dNTP, Cy5-dUTP(sample) or Cy3-dUTP(control) and Klenow. Incubation took place 2 hours at 37ºC in a heatblock. The unincorporated nucleotides were removed using a Microcon YM-30 ultra-fltration column (Millipore) and the labeled probe was concentrated to 25 µL.

growth_protocol: Plants were grown in corner dishes on germinaton medium (MS medium containing 1% sucrose and 0.8% agar) for 3 weeks under a 16 h light/8 h dark regime.

extract_protocol: Genomic DNA was isolated using DNeasy plant Mini Kit according to the manufacturer instructions (Quiagen).

treatment_protocol: Arabidopsis plant was introduced of Taq I reatriction enzyme gene with strong constitutive CaMV35S promoter. For the activation of Taq I, 1-week-old plants were incubated at 37ºC for 24 h under a 16-h light/8-h dark regime.

value: progeny of TAQing treated plant

value: leaves

source_name: Wild type (Col-0)

tag: ecotype background

tag: genotype/variation

value: wild type


title: Progeny of TQ4_79_04, line #10

description:
TAQing treated tetraploid strain TQ4_79_04_10. Leaves from progeny of TAQing treated plant
TQ4_79_04_10


title: Progeny of TQ4_79_04, line #5

description:
TAQing treated tetraploid strain TQ4_79_04_5. Leaves from progeny of TAQing treated plant
TQ4_79_04_5


title: Progeny of TQ4_79_04, line #4

description:
TAQing treated tetraploid strain TQ4_79_04_4. Leaves from progeny of TAQing treated plant
TQ4_79_04_4


title: Progeny of TQ4_79_04, line #3

description:
TAQing treated tetraploid strain TQ4_79_04_3. Leaves from progeny of TAQing treated plant
TQ4_79_04_3


title: TAQing treated diploid strain TQ2_44_8

description:
TAQing treated diploid strain TQ2_44_8. Leaves from progeny of TAQing treated plant
TQ2_44_8


title: TTR-RVR replicate 1

description:
R-35
groupTTR-RVR.vsPBS.DESeq2.txt


title: PBS control replicate 2


title: TAQing treated diploid strain TQ2_44_13

description:
TAQing treated diploid strain TQ2_44_13. Leaves from progeny of TAQing treated plant
TQ2_44_13


title: Progeny of TQ4_225_20, line #1

description:
TAQing treated tetraploid strain TQ4_225_20_1. Leaves from progeny of TAQing treated plant
TQ4_225_20_1


title: PBS control replicate 1


title: TAQing treated diploid strain TQ2_43_1

description:
TAQing treated diploid strain TQ2_43_1. Leaves from progeny of TAQing treated plant
TQ2_43_1


title: TAQing treated diploid strain TQ2_19_4

description:
TAQing treated diploid strain TQ2_19_4. Leaves from progeny of TAQing treated plant
TQ2_19_4


title: TAQing treated diploid strain TQ2_39_2

description:
TAQing treated diploid strain TQ2_39_2. Leaves from progeny of TAQing treated plant
TQ2_39_2


title: TAQing treated diploid strain TQ2_41_1

description:
TAQing treated diploid strain TQ2_41_1. Leaves from progeny of TAQing treated plant
TQ2_41_1


title: ChIP_NPC_Mkl1OE_H3K27ac_rep2

city: Kyoto

first: Takashi

last: Ikeda

address: 53 Shogoin Kawahara-cho Sakyo-ku

institute: Kyoto Univ.

description: Mkl1 overexpression

data_processing:
The low-quality bases at the 3' read ends and the adaptors were trimmed using cutadapt-1.9.1.
Untrimmed and trimmed reads of 20 bp or longer were mapped to mouse genome (mm9) with BWA 0.7.12 using the default parameters.
The reads with high mapping quality (MAPQ>=20) were used for further analysis. The duplicate reads were removed with the Picard tool. The reads mapping to the mitochondrial DNA (chrM) were excluded for further analysis.
Peak detection was performed using MACS ver. 1.3.7.1, with parameters --mfold=8 --gsize=2.43e+09 --pvalue 1e-5.
Peaks falling within blacklisted regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were excluded from further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bw (bigwig) *The data were normalized as RPM (reads per million)

source_name: Neural progenitor cells

growth_protocol: Neural progenitor cells were maintained on a gelatin-coated culture plate in a NPC medium consisting of RHB basal (StemCells) containing epidermal growth factor (EGF) (Peprotech) at 10 ng/ml and human basic fibroblast growth factor (bFGF) (Peprotech) at 10 ng/ml. Hepatoblasts were maintained on a type IV collagen-coated culture plate in a medium consisting of a 1:1 mixture of DMEM/Ham’s F-12 with L-glutamine, HEPES and sodium pyruvate (Wako) supplemented with 10% fetal bovine serum (vol/vol) (Nichirei Bioscience), 1 µg/ml insulin (Wako), 100 nM dexamethasone (Sigma-Aldrich), 10 mM nicotinamide (Sigma-Aldrich), 50 µM β-mercaptoethanol (Nacalai Tesque), 50 ng/ml human recombinant hepatocyte growth factor (HGF) (Peprotech) and 20 ng/ml EGF.

extract_protocol:
Cells were fixed in 1% paraformaldehyde at room temperature for 10 min followed by quenching with 125 mM glycine at room temperature for 5 min. Fixed cells were washed with cold PBS twice. Cells were harvested by scraper and centrifuged at 700 × g for 3 min and then resuspended in nucleic lysis buffer (10 mM Tris-HCl, 10mM EDTA, 1% SDS, 200 mM NaCl, pH 7.5). The genomic DNA was fragmented with Bioruptor (Cosmo Bio) at 4 °C to a size range between 300 and 600 bp. Cell contaminants were removed by centrifugation. A part of cleared solution was used as the input sample. An anti-SRF antibody (clone D71A9; Cell Signaling Technology) or anti- Histone H3 acetyl Lys27 antibody (Active Motif, #39133) were prebound by incubating with Protein-G Dynabeads (Thermo Fisher Scientific) in IP dilution buffer (16.7 mM Tris-HCl, 1.2 mM EDTA, 1.1% (vol/vol) Triton X-100, 167 mM NaCl, 0.01% SDS, pH 8.0) and then incubated at 4 °C overnight with constant rotation. Samples were washed twice with IP dilution buffer, twice with low NaCl buffer (20 mM Tris-HCl, 2 mM EDTA, 1% Trion X-100, 150 mM NaCl, 0.1% SDS, pH 8.0), twice with high NaCl buffer (20 mM Tris-HCl, 2 mM EDTA, 1% Trion X-100, 500 mM NaCl, 0.1% SDS, pH 8.0), twice with LiCl buffer (10 mM Tris-HCl, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, pH 8.0) and twice with TE (10 mM Tris-HCl, 1 mM EDTA, pH 8.0). The DNA-protein complex was finally eluted with elution buffer (25 mM Tris-HCl, 5 mM EDTA, 0.5% SDS, pH 7.5). Eluates and input samples were treated with Pronase (Roche) at 42 °C for 2 h followed by 65 °C overnight with constant shaking. DNA was purified with MinElute Reaction Cleanup Kit (Qiagen).
Immunoprecipitated DNA was ligated with adaptors of Illumina TruSeq using TruSeq ChIP Sample Prep Kit (Illumina). Libraries were assessed for quality and quantity using Agilent Bioanalyzer 2000 and the KAPA Library Quantification Kit for Illumina (KAPA Biosystems).

treatment_protocol: For establishing OE cells, the transgene of Mkl1 was introduced retrovirally.

value: In vitro differentiated neural progenitor cells

tag: antibody


title: TAQing treated diploid strain TQ2_41_10

description:
TAQing treated diploid strain TQ2_41_10. Leaves from progeny of TAQing treated plant
TQ2_41_10


title: ChIP_NPC_Mkl1OE_H3K27ac_rep1

description: Mkl1 overexpression

value: nti- Histone H3 acetyl Lys27 antibody (Active Motif, #39133)


title: ChIP_NPC_Mkl1OE_input


title: OMC-2_Prex2a_induction_1

city: Nagoya

first: Shinya

last: Toyokuni

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

institute: Nagoya University

hyb_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Version 6.5, May 2010).

scan_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Version 6.5, May 2010, Agilent C Scanner Settings).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities. The data set from the scanned microarrays were analyzed with GeneSpring software 13.1 (Agilent). The parameter settings for importing the data into GeneSpring were as follows: Threshold, 1.0; Logbase, 2; Technology, Agilent.SingleColor.72363; Normalization, Shift to 75 percentile; Baseline Transformation, None.
Signal intensity after normalization by GeneSpring GX11.5 software (Agilent). [Threshold: 1.0, Logbase: 2, Normalization: Shift to 75 percentile, Baseline Transformation: None]

source_name: OMC-2, Prex2a induction, sample 1

growth_protocol: JHUEM-14 were cultured in DMEM/ Ham F12 (Sigma) + 20% FBS (EQUITECH-BIO) + MEM NEAA (gibco). OMC-2 were cultured in Ham’s F-12 (Sigma) + 20% FBS.

extract_protocol: Total RNA was extracted using RNeasy Mini(QIAGEN).

treatment_protocol: We performed retroviral gene transduction for cells expressing short hairpin (sh) RNAs  and  lentiviral induction of  Prex2a.

value: endometrium

tag: diagnosis

value: endometrioid adenocarcinoma


title: TAQing treated diploid strain TQ2_39_1

description:
TAQing treated diploid strain TQ2_39_1. Leaves from progeny of TAQing treated plant
TQ2_39_1


title: TAQing treated diploid strain TQ2_36_13

description:
TAQing treated diploid strain TQ2_36_13. Leaves from progeny of TAQing treated plant
TQ2_36_13


title: TAQing treated diploid strain TQ2_36_5

description:
TAQing treated diploid strain TQ2_36_5. Leaves from progeny of TAQing treated plant
TQ2_36_5


title: TAQing treated diploid strain TQ2_36_3

description:
TAQing treated diploid strain TQ2_36_3. Leaves from progeny of TAQing treated plant
TQ2_36_3


description:
TAQing treated tetraploid strain TQ4_225_20. Leaves from progeny of TAQing treated plant
TQ4_225_20


description:
TAQing treated tetraploid strain TQ4_105_07. Leaves from progeny of TAQing treated plant
TQ4_105_07


description:
TAQing treated tetraploid strain TQ4_79_08. Leaves from progeny of TAQing treated plant
TQ4_79_08


description:
TAQing treated tetraploid strain TQ4_225_14. Leaves from progeny of TAQing treated plant
TQ4_225_14


description:
TAQing treated tetraploid strain TQ4_105_17. Leaves from progeny of TAQing treated plant
TQ4_105_17


title: TAQing treated diploid strain TQ2_36_1

description:
TAQing treated diploid strain TQ2_36_1. Leaves from progeny of TAQing treated plant
TQ2_36_1


description:
TAQing treated tetraploid strain TQ4_105_01. Leaves from progeny of TAQing treated plant
TQ4_105_01


title: control_diploid strain_1406

description:
control_diploid strain_1406. Leaves from control dipoid plant.
WT_1406

source_name: leaves from control diploid plant

value: control diploid plant


description:
TAQing treated tetraploid strain TQ4_20_22. Leaves from progeny of TAQing treated plant
TQ4_20_22


description:
TAQing treated tetraploid strain TQ4_105_08. Leaves from progeny of TAQing treated plant
TQ4_105_08


description:
TAQing treated tetraploid strain TQ4_79_04. Leaves from progeny of TAQing treated plant
TQ4_79_04


description:
TAQing treated tetraploid strain TQ4_60_4. Leaves from progeny of TAQing treated plant
TQ4_60_4


description:
TAQing treated tetraploid strain TQ4_79_01. Leaves from progeny of TAQing treated plant
TQ4_79_01


description:
TAQing treated tetraploid strain TQ4_20_19. Leaves from progeny of TAQing treated plant
TQ4_20_19


description:
TAQing treated tetraploid strain TQ4_60_09. Leaves from progeny of TAQing treated plant
TQ4_60_09


description:
TAQing treated tetraploid strain TQ4_63_1. Leaves from progeny of TAQing treated plant
TQ4_63_1


description:
TAQing treated tetraploid strain TQ4_63_2. Leaves from progeny of TAQing treated plant
TQ4_63_2


description:
TAQing treated tetraploid strain TQ4_60_2. Leaves from progeny of TAQing treated plant
TQ4_60_2


description:
TAQing treated tetraploid strain TQ4_20_11. Leaves from progeny of TAQing treated plant
TQ4_20_11


description:
TAQing treated tetraploid strain TQ4_60_05. Leaves from progeny of TAQing treated plant
TQ4_60_05


description:
TAQing treated tetraploid strain TQ4_63_4. Leaves from progeny of TAQing treated plant
TQ4_63_4


description:
TAQing treated tetraploid strain TQ4_63_3. Leaves from progeny of TAQing treated plant
TQ4_63_3


description:
TAQing treated tetraploid strain TQ4_20_02. Leaves from progeny of TAQing treated plant
TQ4_20_02


description:
TAQing treated tetraploid strain TQ4_24_3. Leaves from progeny of TAQing treated plant
TQ4_24_3


description:
TAQing treated tetraploid strain TQ4_60_1. Leaves from progeny of TAQing treated plant
TQ4_60_1


description:
TAQing treated tetraploid strain TQ4_24_4. Leaves from progeny of TAQing treated plant
TQ4_24_4


description:
TAQing treated tetraploid strain TQ4_25_2. Leaves from progeny of TAQing treated plant
TQ4_25_2


description:
TAQing treated tetraploid strain TQ4_24_2. Leaves from progeny of TAQing treated plant
TQ4_24_2


description:
TAQing treated tetraploid strain TQ4_25_1. Leaves from progeny of TAQing treated plant
TQ4_25_1


description:
TAQing treated tetraploid strain TQ4_20_4. Leaves from progeny of TAQing treated plant
TQ4_20_4


description:
TAQing treated tetraploid strain TQ4_25_4. Leaves from progeny of TAQing treated plant
TQ4_25_4


description:
TAQing treated tetraploid strain TQ4_20_08. Leaves from progeny of TAQing treated plant
TQ4_20_08


description:
TAQing treated tetraploid strain TQ4_22_1. Leaves from progeny of TAQing treated plant
TQ4_22_1


description:
TAQing treated tetraploid strain TQ4_60_3. Leaves from progeny of TAQing treated plant
TQ4_60_3


description:
TAQing treated tetraploid strain TQ4_22_2. Leaves from progeny of TAQing treated plant
TQ4_22_2


title: Tet1_WT_ChIP-seq_R26_2

description:
lane5037_CGATGTTT_R26_2
Chromatin immunoprecipitation (ChIP) and sequencing library generation was carried out as described previously (Latos et al., 2015b). 150mg chromatin and 5mg Tet1 antibody (GeneTex GTX125888) were used for each ChIP. ChIP as well as Input libraries were generated in biological triplicates. Sequencing libraries were quantified as above by Bioanalyzer 2100 system (Agilent) and using the KAPA Library Quantification Kit (KAPA Biosystems KK4824).

tag: cell line

value: Mouse trophoblast stem cells

value: WT


description:
TAQing treated tetraploid strain TQ4_22_4. Leaves from progeny of TAQing treated plant
TQ4_22_4


description:
TAQing treated tetraploid strain TQ4_24_1. Leaves from progeny of TAQing treated plant
TQ4_24_1


description:
TAQing treated tetraploid strain TQ4_233_02. Leaves from progeny of TAQing treated plant
TQ4_233_02


title: input_DNA

description:
lane4458_TTAGGCAT_R26_input
Chromatin immunoprecipitation (ChIP) and sequencing library generation was carried out as described previously (Latos et al., 2015b). 150mg chromatin and 5mg Tet1 antibody (GeneTex GTX125888) were used for each ChIP. ChIP as well as Input libraries were generated in biological triplicates. Sequencing libraries were quantified as above by Bioanalyzer 2100 system (Agilent) and using the KAPA Library Quantification Kit (KAPA Biosystems KK4824).

tag: cell type


title: Tet1_WT_ChIP-seq_R26_1

description:
lane5037_ATCACGTT_R26_1
Chromatin immunoprecipitation (ChIP) and sequencing library generation was carried out as described previously (Latos et al., 2015b). 150mg chromatin and 5mg Tet1 antibody (GeneTex GTX125888) were used for each ChIP. ChIP as well as Input libraries were generated in biological triplicates. Sequencing libraries were quantified as above by Bioanalyzer 2100 system (Agilent) and using the KAPA Library Quantification Kit (KAPA Biosystems KK4824).

tag: genotype


description:
TAQing treated tetraploid strain TQ4_20_1. Leaves from progeny of TAQing treated plant
TQ4_20_1

tag: strain


title: Tet1_WT_ChIP-seq_R26_Tet1

description:
lane4458_ATCACGTT_R26_Tet1
Chromatin immunoprecipitation (ChIP) and sequencing library generation was carried out as described previously (Latos et al., 2015b). 150mg chromatin and 5mg Tet1 antibody (GeneTex GTX125888) were used for each ChIP. ChIP as well as Input libraries were generated in biological triplicates. Sequencing libraries were quantified as above by Bioanalyzer 2100 system (Agilent) and using the KAPA Library Quantification Kit (KAPA Biosystems KK4824).


description:
TAQing treated tetraploid strain TQ4_20_2. Leaves from progeny of TAQing treated plant
TQ4_20_2

tag: tissue


description:
TAQing treated tetraploid strain TQ4_20_3. Leaves from progeny of TAQing treated plant
TQ4_20_3


description:
TAQing treated tetraploid strain TQ4_233_18. Leaves from progeny of TAQing treated plant
TQ4_233_18


description:
TAQing treated tetraploid strain TQ4_233_12. Leaves from progeny of TAQing treated plant
TQ4_233_12


description:
TAQing treated tetraploid strain TQ4_22_3. Leaves from progeny of TAQing treated plant
TQ4_22_3


title: Tet1/2_DKO_RNA-seq_G8

description:
lane4654_GTGGCC_20_G8
Total RNA was extracted using TRI reagent (Sigma T9424), followed by DNase treatment using the TURBO-DNA-free kit (Life Technologies AM1907). mRNA was isolated using the Dynabeads mRNA purification kit (Life Technologies 61006) and processed into indexed, strand-specific libraries using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre SSV21106). Libraries were quantified and assessed using the KAPA Library Quantification Kit (KAPA Biosystems KK4824) and Bioanalyzer 2100 system (Agilent).


description:
TAQing treated tetraploid strain TQ4_225_28. Leaves from progeny of TAQing treated plant
TQ4_225_28


description:
TAQing treated tetraploid strain TQ4_225_27. Leaves from progeny of TAQing treated plant
TQ4_225_27


description:
TAQing treated tetraploid strain TQ4_225_10. Leaves from progeny of TAQing treated plant
TQ4_225_10


description:
TAQing treated tetraploid strain TQ4_225_06. Leaves from progeny of TAQing treated plant
TQ4_225_06


title: Tet1/2_DKO_RNA-seq_F2

description:
lane4654_GTCCGC_20_F2
Total RNA was extracted using TRI reagent (Sigma T9424), followed by DNase treatment using the TURBO-DNA-free kit (Life Technologies AM1907). mRNA was isolated using the Dynabeads mRNA purification kit (Life Technologies 61006) and processed into indexed, strand-specific libraries using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre SSV21106). Libraries were quantified and assessed using the KAPA Library Quantification Kit (KAPA Biosystems KK4824) and Bioanalyzer 2100 system (Agilent).


description:
TAQing treated tetraploid strain TQ4_167_38. Leaves from progeny of TAQing treated plant
TQ4_167_38


description:
TAQing treated tetraploid strain TQ4_167_08. Leaves from progeny of TAQing treated plant
TQ4_167_08


description:
TAQing treated tetraploid strain TQ4_167_03. Leaves from progeny of TAQing treated plant
TQ4_167_03


description:
TAQing treated tetraploid strain TQ4_167_05. Leaves from progeny of TAQing treated plant
TQ4_167_05


title: Tet1_WT_RNA-seq_V5

description:
lane4654_CACCGG_20_v5
Total RNA was extracted using TRI reagent (Sigma T9424), followed by DNase treatment using the TURBO-DNA-free kit (Life Technologies AM1907). mRNA was isolated using the Dynabeads mRNA purification kit (Life Technologies 61006) and processed into indexed, strand-specific libraries using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre SSV21106). Libraries were quantified and assessed using the KAPA Library Quantification Kit (KAPA Biosystems KK4824) and Bioanalyzer 2100 system (Agilent).


title: Tet1_KO_RNA-seq_8a

description:
lane4654_TCATTC_20_8a
Total RNA was extracted using TRI reagent (Sigma T9424), followed by DNase treatment using the TURBO-DNA-free kit (Life Technologies AM1907). mRNA was isolated using the Dynabeads mRNA purification kit (Life Technologies 61006) and processed into indexed, strand-specific libraries using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre SSV21106). Libraries were quantified and assessed using the KAPA Library Quantification Kit (KAPA Biosystems KK4824) and Bioanalyzer 2100 system (Agilent).


title: Tet1_WT_RNA-seq_V1

description:
lane4654_ATTCCT_20_v1
Total RNA was extracted using TRI reagent (Sigma T9424), followed by DNase treatment using the TURBO-DNA-free kit (Life Technologies AM1907). mRNA was isolated using the Dynabeads mRNA purification kit (Life Technologies 61006) and processed into indexed, strand-specific libraries using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre SSV21106). Libraries were quantified and assessed using the KAPA Library Quantification Kit (KAPA Biosystems KK4824) and Bioanalyzer 2100 system (Agilent).


title: Tet1_KO_RNA-seq_7c

description:
lane4654_TCGAAG_20_7c
Total RNA was extracted using TRI reagent (Sigma T9424), followed by DNase treatment using the TURBO-DNA-free kit (Life Technologies AM1907). mRNA was isolated using the Dynabeads mRNA purification kit (Life Technologies 61006) and processed into indexed, strand-specific libraries using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre SSV21106). Libraries were quantified and assessed using the KAPA Library Quantification Kit (KAPA Biosystems KK4824) and Bioanalyzer 2100 system (Agilent).


title: Tet1_KO_RNA-seq_2a

description:
lane4654_GACGAC_20_2a
Total RNA was extracted using TRI reagent (Sigma T9424), followed by DNase treatment using the TURBO-DNA-free kit (Life Technologies AM1907). mRNA was isolated using the Dynabeads mRNA purification kit (Life Technologies 61006) and processed into indexed, strand-specific libraries using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre SSV21106). Libraries were quantified and assessed using the KAPA Library Quantification Kit (KAPA Biosystems KK4824) and Bioanalyzer 2100 system (Agilent).


description:
TAQing treated tetraploid strain TQ4_163_35. Leaves from progeny of TAQing treated plant
TQ4_163_35


description:
TAQing treated tetraploid strain TQ4_163_29. Leaves from progeny of TAQing treated plant
TQ4_163_29


title: Tet1_WT_RNA-seq_V4

description:
lane4654_CAACTA_20_v4
Total RNA was extracted using TRI reagent (Sigma T9424), followed by DNase treatment using the TURBO-DNA-free kit (Life Technologies AM1907). mRNA was isolated using the Dynabeads mRNA purification kit (Life Technologies 61006) and processed into indexed, strand-specific libraries using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre SSV21106). Libraries were quantified and assessed using the KAPA Library Quantification Kit (KAPA Biosystems KK4824) and Bioanalyzer 2100 system (Agilent).


description:
TAQing treated tetraploid strain TQ4_163_33. Leaves from progeny of TAQing treated plant
TQ4_163_33


description:
TAQing treated tetraploid strain TQ4_163_21. Leaves from progeny of TAQing treated plant
TQ4_163_21


description:
TAQing treated tetraploid strain TQ4_92_37. Leaves from progeny of TAQing treated plant
TQ4_92_37


description:
TAQing treated tetraploid strain TQ4_97_16. Leaves from progeny of TAQing treated plant
TQ4_97_16


description:
TAQing treated tetraploid strain TQ4_25_3. Leaves from progeny of TAQing treated plant
TQ4_25_3


description:
TAQing treated tetraploid strain TQ4_92_08. Leaves from progeny of TAQing treated plant
TQ4_92_08


description:
TAQing treated tetraploid strain TQ4_97_09. Leaves from progeny of TAQing treated plant
TQ4_97_09


description:
TAQing treated tetraploid strain TQ4_92_14. Leaves from progeny of TAQing treated plant
TQ4_92_14


title: Raji cells_24h_biological rep3

city: Bandar Sungai Long

first: Wai

middle: Meng

last: Lau

state: Selangor

address: Lot PT 21144

department: Faculty of Medicine and Health Sciences

country: Malaysia

institute: Universiti Tunku Abdul Rahman

hyb_protocol: 12.5 µL of the biotin-labeled cDNA was hybridized for 14 hours on the Affymetrix GeneChip™ according to the manufacturer’s instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Genespring GX12 using Exon Expression default analysis settings and normalized with RMA16.

label: Biotin

source_name: Maslinic acid treated Raji cells at 24h

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA

growth_protocol: RPMI medium supplemented with 10% FBS

extract_protocol: As per instructed in the manual of Total RNA and protein isolation kit from Macherey-Nagel (column binding method)

treatment_protocol: 1 ml of RPMI complete growth medium containing 3 mM of sodium n-butyrate, 0.05 µM phorbol ester and 19 µM maslinic acid.

value: Raji

tag: first induced with

value: 3 mM sodium n-butyrate and  0.05 µM phorbol ester

tag: treated with

value: 19 µM maslinic acid

tag: harvested at


title: Raji cells_12h_biological rep2

source_name: Maslinic acid treated Raji cells at 12h


title: Raji cells_12h_biological rep1


title: Raji cells_48h_biological rep2

source_name: Maslinic acid treated Raji cells at 48h


title: Raji cells_8h_biological rep3

source_name: Maslinic acid treated Raji cells at 8h


description:
TAQing treated tetraploid strain TQ4_97_07. Leaves from progeny of TAQing treated plant
TQ4_97_07


title: Raji cells_24h_biological rep1


title: Raji cells_48h_biological rep3


title: Raji cells_48h_biological rep1


title: Raji cells_24h_biological rep2


description:
TAQing treated tetraploid strain TQ4_92_15. Leaves from progeny of TAQing treated plant
TQ4_92_15


title: Raji cells_12h_biological rep3


title: Tet1/2_DKO_RNA-seq_A10

description:
lane4654_GTAGAG_20_A10
Total RNA was extracted using TRI reagent (Sigma T9424), followed by DNase treatment using the TURBO-DNA-free kit (Life Technologies AM1907). mRNA was isolated using the Dynabeads mRNA purification kit (Life Technologies 61006) and processed into indexed, strand-specific libraries using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre SSV21106). Libraries were quantified and assessed using the KAPA Library Quantification Kit (KAPA Biosystems KK4824) and Bioanalyzer 2100 system (Agilent).


description:
TAQing treated tetraploid strain TQ4_89_23. Leaves from progeny of TAQing treated plant
TQ4_89_23


description:
TAQing treated tetraploid strain TQ4_97_25. Leaves from progeny of TAQing treated plant
TQ4_97_25


description:
TAQing treated tetraploid strain TQ4_89_07. Leaves from progeny of TAQing treated plant
TQ4_89_07


description:
TAQing treated tetraploid strain TQ4_233_34. Leaves from progeny of TAQing treated plant
TQ4_233_34


description:
TAQing treated tetraploid strain TQ4_89_30. Leaves from progeny of TAQing treated plant
TQ4_89_30


description:
TAQing treated tetraploid strain TQ4_79_31. Leaves from progeny of TAQing treated plant
TQ4_79_31


title: Raji cells_8h_biological rep1


description:
TAQing treated tetraploid strain TQ4_79_16. Leaves from progeny of TAQing treated plant
TQ4_79_16


title: Raji cells_8h_biological rep2


title: Raji cells_4h_biological rep3

source_name: Maslinic acid treated Raji cells at 4h


description:
TAQing treated tetraploid strain TQ4_79_09. Leaves from progeny of TAQing treated plant
TQ4_79_09


title: RORgt-WT, biological rep2

city: Seattle

first: Raymond

last: Doty

state: WA

department: Division of Hematology

institute: University of Washington

description: Gene expression data from Th17 cells.

hyb_protocol: Samples were hybridized according to Affymetrix protocol. The chips were washed and stained using fluidics protocol FS450_0007.

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 7G Scanner. Images were processed into CEL files with the Affymetrix GCOS software.

data_processing: Raw CEL intensity data was RMA normalized using Expression Console from Affymetrix.

source_name: RORgt WT mice, Th17 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: Both WT and SRC-3 deficient naive CD4+ T cells stimulated with anti-CD3 and anti-CD28 antibodies in the absence of exogenous cytokines (Th 0 cells), or differentiated with IL-1, IL-6 plus IL-23 (pathogenic Th17 cells).

value: Th17 cells

value: wild-type


description:
TAQing treated tetraploid strain TQ4_74_40. Leaves from progeny of TAQing treated plant
TQ4_74_40


title: RORgt-deficient, biological rep2

description: Gene expression data from Th17 cells.

source_name: RORgt (-/-) mice, Th17 cells

value: RORgt deficient


title: SRC3-deficient, biological rep2

description: Gene expression data from Th17 cells.

source_name: SRC-3 (f/f) mice, Th17 cells

value: SRC-3 deficient


title: RORgt-deficient, biological rep1

description: Gene expression data from Th17 cells.


title: SRC3-WT, biological rep1

description: Gene expression data from Th17 cells.

source_name: SRC-3 WT mice, Th17 cells


title: RORgt-WT, biological rep1

description: Gene expression data from Th17 cells.


title: Raji cells_4h_biological rep2


title: SRC3-deficient, biological rep1

description: Gene expression data from Th17 cells.


title: Raji cells_4h_biological rep1


title: SRC3-WT, biological rep2

description: Gene expression data from Th17 cells.


description:
TAQing treated tetraploid strain TQ4_74_36. Leaves from progeny of TAQing treated plant
TQ4_74_36

value: progeny of TAQing treated plant


description:
TAQing treated tetraploid strain TQ4_74_35. Leaves from progeny of TAQing treated plant
TQ4_74_35

value: leaves


title: Raji cells_0h_biological rep3

source_name: Maslinic acid treated Raji cells at 0h


description:
TAQing treated tetraploid strain TQ4_74_01. Leaves from progeny of TAQing treated plant
TQ4_74_01

value: wild type


description:
TAQing treated tetraploid strain TQ4_105_37. Leaves from progeny of TAQing treated plant
TQ4_105_37


description:
TAQing treated tetraploid strain TQ4_79_10. Leaves from progeny of TAQing treated plant
TQ4_79_10


title: NRDE3_IP_small_RNA_eri1(mg366)_susi3(ust51)_GFPNRDE3

city: Hefei

first: Shouhong

last: Guang

state: Anhui

address: 443 HuangShan Road

department: School of Life Sciences

institute: University of Science & Technology of China

description: IPed small RNA

data_processing:
The Illumina-generated raw reads were first filtered to remove adaptors, low quality tags as well as contaminants to get clean reads at BGI Shenzhen. Clean reads ranging from 17 to 30 nt were mapped to the C. elegans genome and the transcriptome assembly WS243, respectively, using Bowtie2 with default parameters (Langmead and Salzberg Nat Methods 9: 357-359. (2012)). The number of reads targeting each gene was counted by custom Perl scripts and displayed by IGV (Thorvaldsdottir et al. Brief Bioinform 14: 178-192. (2013)). Total mappable reads excluding sense rRNA were used for normalization.
Genome_build: WS243
Supplementary_files_format_and_content: .txt files.located in /count content. Basically, the reads were aligned to C. elegans transcriptome WS243 version by Bowtie2 and counted the number of reads targeting each transcript by Perl script.

organism: Caenorhabditis elegans

source_name: L3 stage

growth_protocol: C. elegans strains were cultured on NGM plates with E. coli OP50 as the food source in a temperature controlled incubator. Worms were maintained at 20°C prior to the experiment. Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10 cm NGM concentrated OP50 plate (approximately 3000 L1s per plate).

extract_protocol:
NRDE-3-associated siRNAs were isolated from L3 stage worm lysates as described (Zhou, X et al, Genetics 197, 121-32 (2014)). Briefly, the animals were sonicated in lysis buffer (20 mM Tris-HCl [pH 7.5], 200 mM NaCl, 2.5 mM MgCl2, and 0.5% NP-40); the lysate was pre-cleared with protein G-agarose beads (Roche), and incubated with anti-FLAG M2 agarose (Sigma) beads. The beads were washed extensively, and FLAG::GFP::NRDE-3 and associated RNA were eluted with 100 μg/ml 3xFLAG peptide (Sigma). The eluates were incubated with TRIzol reagent (Invitrogen), followed by isopropanol precipitation. The precipitates were treated with calf intestinal alkaline phosphatase (CIAP, Invitrogen), re-extracted with TRIzol, and treated with T4 polynucleotide kinase (T4 PNK, New England Biolabs) in the presence of 1 mM ATP.
Small RNAs were cloned and deep sequenced using an Illumina platform, according to the manufacturer's instructions, by the Beijing Genomics Institute (BGI Shenzhen). sRNAs ranging from 17 to 30 nt were gel-purified and ligated to a 3’ adaptor (5’-pUCGUAUGCCGUCUUCUGCUUGidT-3’; p, phosphate; idT, inverted deoxythymidine) and a 5’ adaptor (5’-GUUCAGAGUUCUACAGUCCGACGAUC-3’). The ligation products were gel-purified, reverse transcribed, and amplified using Illumina’s sRNA primer set (5’-CAAGCAGAAGACG GCATACGA-3’; 5’-AATGATACGGCGACCACCGA-3’). The samples were sequenced using an Illumina Hiseq platform.

tag: developmental stage

value: L3 stage

tag: temperature

value: 15oC on OP50

value: anti-FLAG M2 antibody (Sigma)


title: Raji cells_0h_biological rep1


title: TRIM33-deficient, biological rep2

city: Osaka

last: Tanaka

state: Osaka

address: 2nd Fl. IFReC Research Building, Osaka University 3-1 Yamadaoka, Suita

department: Immunology Frontier Research Center

institute: Osaka University

description: Gene expression data from Th17 cells.

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 7G Scanner. Images were processed into CEL files with the Affymetrix Command Console software.

source_name: TRIM33 (f/f) mice, Th17 cells

growth_protocol: culture condition: WT and Trim33 KO CD4+ T cells were cultured under Th17-skewing condition.

value: TRIM33 deficient


title: Total_small_RNA_eri1(mg366)_susi3(ust51)_GFPNRDE3

description: total small RNA

extract_protocol:
Total small RNAs were isolated from L3 stage worms. Briefly, worms were harvested and dounced on ice with pestle B in TRIzol reagent (Invitrogen) followed by isopropanol precipitation. The precipitates were treated with calf intestinal alkaline phosphatase (CIAP, Invitrogen), re-extracted with TRIzol, and treated with T4 polynucleotide kinase (T4 PNK, New England Biolabs) in the presence of 1 mM ATP.
Small RNAs were cloned and deep sequenced using an Illumina platform, according to the manufacturer's instructions, by the Beijing Genomics Institute (BGI Shenzhen). sRNAs ranging from 17 to 30 nt were gel-purified and ligated to a 3’ adaptor (5’-pUCGUAUGCCGUCUUCUGCUUGidT-3’; p, phosphate; idT, inverted deoxythymidine) and a 5’ adaptor (5’-GUUCAGAGUUCUACAGUCCGACGAUC-3’). The ligation products were gel-purified, reverse transcribed, and amplified using Illumina’s sRNA primer set (5’-CAAGCAGAAGACG GCATACGA-3’; 5’-AATGATACGGCGACCACCGA-3’). The samples were sequenced using an Illumina Hiseq platform.


title: NRDE3_IP_small_RNA_ eri1(mg366)_GFPNRDE3

description: IPed small RNA


title: TRIM33-deficient, biological rep1

description: Gene expression data from Th17 cells.


title: TRIM33-WT, biological rep1

description: Gene expression data from Th17 cells.

source_name: TRIM33 WT mice, Th17 cells


description:
TAQing treated tetraploid strain TQ4_89_02. Leaves from progeny of TAQing treated plant
TQ4_89_02

source_name: leaves from progeny of TAQing treated plant

source_name: Wild type (Col-0)


title: Total_small_RNA_eri1(mg366)_GFPNRDE3

description: total small RNA


title: TRIM33-WT, biological rep2

description: Gene expression data from Th17 cells.


title: NRDE3_IP_small_RNA_eri1(mg366)_susi2(ust49)_GFPNRDE3

description: IPed small RNA


title: Total_ small_RNA_eri1(mg366)_susi2(ust49)_GFPNRDE3

description: total small RNA


title: Raji cells_0h_biological rep2


description:
TAQing treated tetraploid strain TQ4_105_32. Leaves from progeny of TAQing treated plant
TQ4_105_32


title: Uhrf1 KO mESC

city: New Haven

first: Kun-Yong

last: Kim

state: CT

address: 10 Amistad Street

department: Genetics

institute: Yale University

description: Gene expression in ESC

data_processing:
Illumina Casava1.8 software used for basecalling.
All RNA-seq reads were mapped into mm9 mouse genome using Tophat (v1.1.4), Samtools (v0.1.18), and Bowtie (v0.12.7) with default parameters
Normalized expression value (Reads Per Kilobase per Million mapped reads (RPKM)) was calculated by Cufflinks (v1.1.0) using RefSeq genes as reference annotation by “--GTF” option
Genome_build: mm9
Supplementary_files_format_and_content: xlsx file including RPKM value

source_name: Uhrf1 KO E14 mESC

growth_protocol: ESCs were maintained in mES medium (DMEM supplemented with 15% FBS, 1% nonessential amino acids, 2 mM glutamine, 100 U/mL penicillin/streptomycin, 0.1 mM β-mercaptoethanol, and 1,000 U/mL ESGRO leukemia inhibitory factor) on 0.1% gelatin or MEF coated plates, incubated at 37°C and passaged every second or third day.

extract_protocol:
Total RNA was isolated using an RNeasy mini kit (Qiagen). mRNA was isolated from 5 μg total RNA using Dynabeads mRNA DIRECT (Invitrogen) and was fragmented with RNA fragmentation reagent (Ambion). First strand cDNA synthesis was done using the SuperScript III First-Strand Synthesis System and 3 μg μl−1 random hexamers (Invitrogen), followed by second strand synthesis with DNA Polymerase I and RNase H.
NEBNext DNA Sample Prep Reagent Set 1

value: E14 mESC

tag: status

value: Undifferentiated

value: Uhrf1 KO


title: Uhrf1 KO EB week3

description: Gene expression in EB

source_name: Uhrf1 KO E14 mESC-derived EB

value: E14 mESC-derived EB

value: Differentiated at week3


title: Uhrf1 KO EB week2

description: Gene expression in EB

value: Differentiated at week2


title: Uhrf1 KO EB week1

description: Gene expression in EB

value: Differentiated at week1


title: WT EB week1

description: Gene expression in EB

source_name: E14 mESC-derived EB

value: WT


title: Uhrf1 KO EB week3 input

description: Gene expression in EB

data_processing:
Illumina Casava1.8 software used for basecalling.
ChIP-seq reads were mapped to mm9 genome by Bowtie2 (v2.1.0) with options "--local -D 15 -R 3 -N 1 -L 20 -i S,1,0.50 -k 1".
For histone modifications, peak regions were identified by the rseg-diff program in RSEG software (v0.4.8) with parameters “-i 20 –v –mode 2” and the 50bp-deadzone correction file
Uhrf1 enriched and depleted regions were assigned when there was more than 2-fold difference between ChIP and input and less than a 0.05 adjusted p-value within 10k-bp sliding window. The p-value was estimated by Poisson distribution from the ChIP-seq read counts compared to the normalized input counts
Oct4, Nanog and Sox2 binding sites were identified by MACS peak caller (v1.4.2) with “-g mm” option.
Genome_build: mm9
Supplementary_files_format_and_content: Bed format file of ChIP peaks

extract_protocol:
Histone-DNA and TF-DNA complexes were isolated with antibody
Illumina TrueSeq ChIP Sample Preparation Kit


title: Uhrf1 KO EB week2 input

description: Gene expression in EB


title: WT mESC

description: Gene expression in ESC

source_name: E14 mESC


title: Uhrf1 KO EB week1 input

description: Gene expression in EB


title: Uhrf1 KO mESC Oct4

description: Gene expression in ESC

value: anti-Oct4 (#5677, Cell Signaling Technology)


title: Uhrf1 KO mESC Sox2

description: Gene expression in ESC

value: anti-Sox2 (#23064, Cell Signaling Technology)


title: Uhrf1 KO mESC input

description: Gene expression in ESC


title: WT EB week3

description: Gene expression in EB


title: control tetraploid strain WT4_142_20

description:
control tetraploid strain WT4_142_20. Leaves from progeny of tetraploid wild type plant.
WT4_142_20

source_name: leaves from progeny of tetraploid wild type plant

value: progeny of tetraploid wild type plant


title: control tetraploid strain WT4_142_19

description:
control tetraploid strain WT4_142_19. Leaves from progeny of tetraploid wild type plant.
WT4_142_19

value: leaves


title: Uhrf1 KO mESC Nanog

description: Gene expression in ESC

value: anti-Nanog (#8785, Cell Signaling Technology)


title: control tetraploid strain WT4_142_07

description:
control tetraploid strain WT4_142_07. Leaves from progeny of tetraploid wild type plant.
WT4_142_07

value: wild type


title: Uhrf1 KO mESC H3K9me3

description: Gene expression in ESC

value: anti-H3K9me3 (ab8898, abcam)


description:
TAQing treated tetraploid strain TQ4_105_10. Leaves from progeny of TAQing treated plant
TQ4_105_10

value: progeny of TAQing treated plant


title: WT EB week2

description: Gene expression in EB


title: Uhrf1 KO EB week3 H3K27me3

description: Gene expression in EB

value: anti-H3K27me3 (07-499, Millipore)


title: control tetraploid strain WT4_142_03

description:
control tetraploid strain WT4_142_03. Leaves from progeny of tetraploid wild type plant.
WT4_142_03


title: control tetraploid strain WT4_23_15

description:
control tetraploid strain WT4_23_15. Leaves from progeny of tetraploid wild type plant.
WT4_23_15


title: Uhrf1 KO EB week2 H3K27me3

description: Gene expression in EB


title: Uhrf1 KO EB week3 H3K4me3

description: Gene expression in EB

value: anti-H3K4me3 (07-473, Millipore)


title: Uhrf1 KO EB week2 H3K4me3

description: Gene expression in EB


title: Uhrf1 KO EB week1 H3K27me3

description: Gene expression in EB


title: Uhrf1 KO mESC H3K4me3

description: Gene expression in ESC

value: E14 mESC

value: Undifferentiated


title: Uhrf1 KO EB week1 H3K4me3

description: Gene expression in EB

value: E14 mESC-derived EB

value: Uhrf1 KO


title: control tetraploid strain WT4_142_17

description:
control tetraploid strain WT4_142_17. Leaves from progeny of tetraploid wild type plant.
WT4_142_17


title: control tetraploid strain WT4_23_12

description:
control tetraploid strain WT4_23_12. Leaves from progeny of tetraploid wild type plant.
WT4_23_12


title: Uhrf1 KO mESC H3K27me3

description: Gene expression in ESC


title: WT EB week3 input

description: Gene expression in EB

value: Differentiated at week3


title: control tetraploid strain WT4_142_16

description:
control tetraploid strain WT4_142_16. Leaves from progeny of tetraploid wild type plant.
WT4_142_16


title: WT EB week2 input

description: Gene expression in EB

value: Differentiated at week2


title: WT mESC input

description: Gene expression in ESC

value: WT


title: control tetraploid strain WT4_23_18

description:
control tetraploid strain WT4_23_18. Leaves from progeny of tetraploid wild type plant.
WT4_23_18


title: control tetraploid strain WT4_23_20

description:
control tetraploid strain WT4_23_20. Leaves from progeny of tetraploid wild type plant.
WT4_23_20


title: control tetraploid strain WT4_142_08

description:
control tetraploid strain WT4_142_08. Leaves from progeny of tetraploid wild type plant.
WT4_142_08


title: control tetraploid strain WT4_142_02

description:
control tetraploid strain WT4_142_02. Leaves from progeny of tetraploid wild type plant.
WT4_142_02


title: control tetraploid strain WT4_23_11

description:
control tetraploid strain WT4_23_11. Leaves from progeny of tetraploid wild type plant.
WT4_23_11


title: WT mESC Sox2

description: Gene expression in ESC


title: WT mESC Oct4

description: Gene expression in ESC

value: anti-Oct4 (#5677, Cell Signaling Technology)


title: WT EB week3 H3K27me3

description: Gene expression in EB


title: WT EB week2 H3K27me3

description: Gene expression in EB


title: WT EB week1 H3K27me3

description: Gene expression in EB

value: Differentiated at week1


title: WT mESC H3K9me3

description: Gene expression in ESC


title: control tetraploid strain WT4_23_14

description:
control tetraploid strain WT4_23_14. Leaves from progeny of tetraploid wild type plant.
WT4_23_14

value: progeny of tetraploid wild type plant


title: WT EB week1 input

description: Gene expression in EB


title: WT mESC Uhrf1

description: Gene expression in ESC

value: anti-Uhrf1 (sc98817, Santa Cruz)


title: WT EB week3 H3K4me3

description: Gene expression in EB


title: WT EB week2 H3K4me3

description: Gene expression in EB


title: TAQing treated strain #107

description: TAQing treated strain #107. Yeast strain having change of genome structure derived from heat treated of TaqI expressed WT14.

organism: Saccharomyces cerevisiae

source_name: TAQing treated strain

growth_protocol: Cells were grown in YPD (1% yeast extract, 2% peptone, 2% glucose), incubated for 24 h at 30ºC.

extract_protocol: Genomic DNA was isolated using columns (Quiagen, Genomic DNA Buffer Set No. 19060, Genomic tip 500/G No.10262) according to the manufacturer instructions.

treatment_protocol: Cell-fused strain WT14 was introduced Taq I gene, and then induction of expression treated by culture with Cu2+ ion, and heat activation of Taq I for 30 min at 42ºC.

value: cell culture

value: Mutant strain from TAQing treated WT14

tag: strain id

value: TAQing treated strain #107

source_name: control strain WT14

value: fusant strain of S288C and SK1


title: WT mESC Nanog

description: Gene expression in ESC

value: anti-Nanog (#8785, Cell Signaling Technology)


title: TAQing treated strain #113

description: TAQing treated strain #113. Yeast strain having change of genome structure derived from heat treated of TaqI expressed WT14.

value: TAQing treated strain #113


title: WT EB week1 H3K4me3

description: Gene expression in EB

value: anti-H3K4me3 (07-473, Millipore)


title: WT mESC H3K27me3

description: Gene expression in ESC

value: E14 mESC

value: Undifferentiated

value: anti-H3K27me3 (07-499, Millipore)


title: TAQing treated strain #119

description: TAQing treated strain #119. Yeast strain having change of genome structure derived from heat treated of TaqI expressed WT14.

value: TAQing treated strain #119


title: TAQing treated strain #117

description: TAQing treated strain #117. Yeast strain having change of genome structure derived from heat treated of TaqI expressed WT14.

value: TAQing treated strain #117


title: TAQing treated strain #106

description: TAQing treated strain #106. Yeast strain having change of genome structure derived from heat treated of TaqI expressed WT14.

value: TAQing treated strain #106


title: control tetraploid strain WT4_23_09

description:
control tetraploid strain WT4_23_09. Leaves from progeny of tetraploid wild type plant.
WT4_23_09

value: leaves

value: wild type


title: control tetraploid strain WT4_23_04

description:
control tetraploid strain WT4_23_04. Leaves from progeny of tetraploid wild type plant.
WT4_23_04

value: progeny of tetraploid wild type plant


title: Uhrf1 KO mESC [ATAC-Seq]

description: Open chromatin in ESC

data_processing:
Illumina Casava1.8 software used for basecalling.
ATAC-seq reads were mapped to mm9 genome by Bowtie2 (v2.1.0) with options "--local -D 15 -R 3 -N 1 -L 20 -i S,1,0.50 -k 1"
Peaks were detected by findPeak script in HOMER software (v4.9.1) with "-localSize 50000 -size 100 -minDist 50 -fragLength 0"
Genome_build: mm9
Supplementary_files_format_and_content: BED format file of ATAC peaks

extract_protocol:
50,000 cells were lysed in cold lysis buffer (10mM Tris-HCl, pH7.4, 10mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630)
After spinning at 500g for 5 minutes, the pellet was used for transposition reaction by Nextera® DNA Library Prep Kit. Following purification by Qiagen EinElute kit, ATAC-seq library was constructed and amplified by NEB High Fidelity 2xPCR master mix. Finally, the library was purified by AxyPrepTM Mag PCR Clean-up kit.

value: Uhrf1 KO


title: WT mESC  [ATAC-Seq]

description: Open chromatin in ESC

value: WT


title: WT mESC H3K4me3

description: Gene expression in ESC


description:
TAQing treated tetraploid strain TQ4_105_25. Leaves from progeny of TAQing treated plant
TQ4_105_25

value: progeny of TAQing treated plant


title: Cartilage_control_27 days_rep3

city: Uppsala

first: Maria

last: Löfgren

department: Department of Biomedical Sciences and Veterinary Public Health

country: Sweden

institute: Swedish University of Agricultural Sciences

hyb_protocol: GeneChip Equine Gene 1.0 ST Arrays (Affymetrix Inc.) were hybridized for 16 h in a 45°C incubator, with agitation at 60 rpm. In line with the GeneChip Expression Wash, Stain and Scan Manual (P/N 702731 Rev 3, Affymetrix Inc.), the arrays were washed and stained using the Fluidics Station 450 (Affymetrix Inc.).

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix Inc.).

data_processing: The raw data were normalized in an Expression Console (Affymetrix Inc.), using the robust multi-array average method first suggested by Li and Wong. Subsequent analysis of the gene expression data was carried out in the statistical computing language R, (www.r-project.org) using packages available from the Bioconductor project (www.bioconductor.org). To search for the genes expressed differentially between the IL-1β stimulated and unstimulated explants, a paired empirical Bayes moderated t-test was applied using the ‘limma’ package. To address the problem with multiple testing, the p-values were adjusted using the method of Benjamini and Hochberg.

organism: Equus caballus

source_name: Cartilage_control_27 days

label_protocol: Two nanograms of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome, according to the GeneChip® WT Pico Reagent Kit User Manual (P/N 703262 Rev 1, Affymetrix Inc.; Santa Clara, CA, USA)

growth_protocol: Equine cartilage explants were incubated in cell culture media for 48 h.

extract_protocol: Cartilage explants (two explants from each treatment group and time point) were minced into small pieces before digestion of matrix via incubation trypsin followed by digestion with collagenase type II. After filtration, centrifugation and wash, cells were lysed with TRIzol® reagent. RNA was extracted using TRIzol® and 1-bromo-3-chloropropane, followed by purification using RNeasy Mini Kit according to the manufacturer’s instructions. Genomic DNA was removed using Qiagen RNase-Free DNase Set, and the samples were cleaned using Qiagen RNeasy MinElute Cleanup Kit.

treatment_protocol: 10 ng/mL recombinant equine IL-1β was added to 5 wells containing 3 explants each. Medium without IL-1β was added to 5 wells as wells containing unstimulated controls. Cartilage explants from one well containing medium with IL-1β and one well without IL-1β were then harvested at days 3, 9, 15, 21, and 27 post-stimulation.

value: Cartilage

tag: treatment

value: Control


title: Extrafloral nectary gut contents applied sample 2

city: Duluth

first: Marshall

last: Hampton

address: 1117 University Drive

institute: University of Minnesota Duluth

data_processing:
Contigs assembled with Trinity v.2.3
Reads aligned to contigs using NCBI blastn
Read counts by contig normalized by upper-quartile normalization.
Contigs aligned to Arabidopsis thaliana genes (Araport 11 build 201606).
Genome_build: Reference is Araport 11 build 201606.
Supplementary_files_format_and_content: Acacia_to_Athaliana_normalized_counts.xls, contains individual upper-quartile normalized counts and averages.

organism: Vachellia cornigera

source_name: Extrafloral nectary tissue

extract_protocol: Illumina’s Truseq RNA Preparation v2 kit (RS-122-2001)

tag: sample type

value: Gut


title: Cartilage_IL.1b_21 days_rep3

source_name: Cartilage_IL.1b_21 days


title: Extrafloral nectary ants replaced after 2 days sample 1

value: 2d Replaced 9 AM


title: Cartilage_IL.1b_15 days_rep3

source_name: Cartilage_IL.1b_15 days


title: Cartilage_control_15 days_rep3

source_name: Cartilage_control_15 days


title: Extrafloral nectary gut contents applied sample 1


title: Cartilage_control_9 days_rep3

source_name: Cartilage_control_9 days


title: Extrafloral nectary Gracilis replacement sample 3

value: Gracilis


title: TAQing treated strain #84

description: TAQing treated strain #84. Yeast strain having change of genome structure derived from heat treated of TaqI expressed WT14.

value: cell culture

value: Mutant strain from TAQing treated WT14

value: TAQing treated strain #84

value: fusant strain of S288C and SK1


title: TAQing treated strain #73

description: TAQing treated strain #73. Yeast strain having change of genome structure derived from heat treated of TaqI expressed WT14.

value: TAQing treated strain #73


title: Cartilage_control_21 days_rep3

source_name: Cartilage_control_21 days


title: TAQing treated strain #83

description: TAQing treated strain #83. Yeast strain having change of genome structure derived from heat treated of TaqI expressed WT14.

value: TAQing treated strain #83


title: TAQing treated strain #1

description: TAQing treated strain #1. Yeast strain having change of genome structure derived from heat treated of TaqI expressed WT14.

value: TAQing treated strain #1


title: TAQing treated strain #76

description: TAQing treated strain #76. Yeast strain having change of genome structure derived from heat treated of TaqI expressed WT14.

value: TAQing treated strain #76


title: Cartilage_IL.1b_27 days_rep3

source_name: Cartilage_IL.1b_27 days


title: TAQing treated strain #81

description: TAQing treated strain #81. Yeast strain having change of genome structure derived from heat treated of TaqI expressed WT14.

value: TAQing treated strain #81


title: Extrafloral nectary Gracilis replacement sample 2


title: Cartilage_control_3 days_rep3

source_name: Cartilage_control_3 days


title: control strain WT14

description: Yeast diploid strain derived from cell fusion of S288C and SK1 wild type.

value: control strain WT14


title: TAQing treated strain #97

description: TAQing treated strain #97. Yeast strain having change of genome structure derived from heat treated of TaqI expressed WT14.

value: TAQing treated strain #97


title: Cartilage_IL.1b_9 days_rep3

source_name: Cartilage_IL.1b_9 days


title: Cartilage_IL.1b_3 days_rep3

source_name: Cartilage_IL.1b_3 days


title: Cartilage_IL.1b_27 days_rep2


title: Cartilage_control_27 days_rep2


title: Extrafloral nectary Gracilis replacement sample 1


title: Cartilage_control_21 days_rep2


title: Extrafloral nectary ants removed 2 days sample 3

value: No ant 2d


title: Extrafloral nectary ants removed 2 days sample 2


title: Extrafloral nectary ants removed 2 days sample 1


title: Cartilage_control_0 days_rep3

source_name: Cartilage_control_0 days

value: Cartilage


title: Extrafloral nectary 8 am control sample 3


title: Extrafloral nectary 8 am control sample 2


title: Extrafloral nectary 3 am, day 2, sample 1


title: Extrafloral nectary 3 pm sample 3


title: Extrafloral nectary 3 am, day 2, sample 2


title: Cartilage_control_15 days_rep2

value: Control


title: Extrafloral nectary 8 am control sample 1


title: Extrafloral nectary 3 pm sample 2


title: Extrafloral nectary 2 pm sample 1


title: Cartilage_control_3 days_rep2


title: Cartilage_IL.1b_3 days_rep2


title: Extrafloral nectary 3 pm sample 1


title: Cartilage_IL.1b_15 days_rep2


title: Extrafloral nectary noon sample 3


title: Cartilage_control_0 days_rep2


title: scrambled_rep3

city: Beijing

first: Wen

last: Zhong

address: Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
Trimmomatic v0.36 was used to trim/filter sequenced reads with default parameters
Sequencing reads were mapped to the rat genome (version Rn5) using Tophat (version 2.0.9) and the default options(Kim et al., 2013). Mapped reads were used with Cufflinks software suite (Trapnell et al., 2012) in combination with rat transcripts annotations from Ensembl database(Aken et al., 2016) version 79 for transcripts assembly.
Genome_build: rn5
Supplementary_files_format_and_content: bigwig files were generated using UCSC bedGraphToBigWig

organism: Rattus norvegicus

extract_protocol:
Total RNA was prepared directly from the scrambled and shDDX1 INS1 cells using Trizol (Invitrogen, Carlsbad, CA, USA) as per the manufacturer's instructions.
The mRNA was purified by Dynabeads mRNA DIRECT kit (Invitrogen, Carlsbad, CA, USA) from total RNA, fragmented, converted to cDNA.

value: pancreatic beta cell line

tag: shRNA

value: scarmble


title: scrambled_rep2


title: Extrafloral nectary noon sample 2


title: Cartilage_control_9 days_rep2


title: Cartilage_IL.1b_9 days_rep2


title: scrambled_rep1


title: Cartilage_control_27 days_rep1


title: Cartilage_control_21 days_rep1


title: Cartilage_control_15 days_rep1


title: Cartilage_IL.1b_21 days_rep1


title: Extrafloral nectary noon sample 1


title: Cartilage_IL.1b_27 days_rep1


title: Cartilage_IL.1b_21 days_rep2


title: Extrafloral nectary 9 am sample 3


title: Extrafloral nectary 9 am sample 2


title: Extrafloral nectary 9 am sample 1


title: shDDX1_rep3


title: shDDX1_rep2


title: shDDX1_rep1


title: T7134_SAd_chromRNA_rep2

status: Public on May 01 2018

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

data_processing:
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
Gro-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50 --trim5 2
Gro-Seq_density: filtering (uniquely aligned reads): samtools-1.2/samtools view -S -b -F4
Gro-Seq_density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor -strand, ucsc-314/bedGraphToBigWig
mRNA-Seq_density:alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-Seq_density: filtering: samtools-1.2/samtools view -S -b -F132 -q 20
mRNA-Seq density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor, ucsc-314/bedGraphToBigWig
HiC-Seq: alignment: bwa-sw with default parameter (map each read separately)
HiC-Seq: filter: remove duplicates and near duplicates, removes reads that map to the same fragemnt and low quality reads (MAPQ <30)
HiC-Seq: generate contact matrix: juicer runnning with default parameter
4C-Seq: filtering: each read pair was tested for the presence of a perfect match to the respective bait primer as well as the bait spacer  between the  end of the primer and the restriction sites  used  in  the  corresponding  experiment.
4C-Seq: mapping: bowtie-1.1.1/bowite -X 500 -p 3 -v2 -k2 -m1 --phred64-quals -sam
4C-Seq: frequency: assign to DPNII/CSP6i fragment to calculate fraction of restriction fragments for which 4C reads were found
ChIAPET: followed the process described in Li et al.,2010
ChIAPET: interaction call by chiapettool v2 program with default parameter
ChIA-PET: Chia-PET processing pipeline is described in greater detail in Li et al., 2010 (PMCID: PMC2872882)
local HiC: preprocess & normalization: juicer.sh using default parameter
local HiC: 5kb resolution matrices extraction: juicebox dump obsevered NONE .hic BP 5000
local HiC: R & custom script: generate genome wide contact matrix as in Sanborn et al. PNAS 2015
local HiC: estimation of number of in silico spike-ins: median of the genome-wide per-bin coverage of the local HiC matrix at the targeted region
local HiC: reconstruct HiC matrix: combine the targeted region local HiC with the global CH12 wt matrix which matched to spike-ins
local HiC: re-normalization: Knight-Ruiz balancing algorithm with the juicebox pre -r 5000
ChromRNA_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChromRNA_density: filtering (uniquely aligned reads): samtools-1.2/samtools view -S -b -F4
ChromRNA_density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor -strand, ucsc-314/bedGraphToBigWig
Genome_build: mm9
Supplementary_files_format_and_content:
ChIP-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
Gro-Seq: .wig files tag density divided by library size in millions to obtain normalized read density (rpkm)
HiC-Seq: .hic format including contact matrix, normalization information generated by juicer.sh
ChIAPET: bed12 format by editting the result of chiapettool by restricting to show only interactions having more than or equal to 3 PETs
4C-Seq: bed file showing read frequency in 100K window normalized by the number of fragments in each window
mRNA-Seq:.wig files tag density divided by library size in millions to obtain normalized read density (rpkm)
ChromRNA: strand-specific density tracks are generated by using bedtools genomecov program divided by library size in millions to obtain normalized read density (rpm)

extract_protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 1 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. For native chip, chromatin was digested with Mnase (Sigma) in digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, butyrate 5 mM) for 5’ at 37°C and dialyzed against RIPA buffer for 2hrs at 4°C. Five micrograms of antibody were incubated with 40 μl of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μl of sonicated or Mnase-digested chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation. MNase-Seq: 4x107 resting and activated B cells were digested with 24 different concentrations of MnaseI. After an initial RT-qPCR analysis and curve-fitting, the MnaseI concentrations for the most representative nucleosomal fraction was determined. The lowest three nucleosomal fractions (which corresponded to MnaseI concentrations of 0U, 0U, and 0.0026U) were pooled together and used as input control. Nucleosomal fractions 16-18 (which corresponded to enzyme concentrations of 0.068U, 0.045U, and 0.03U) were also pooled for further processing. Input samples were sonicated to obtain similar fragment sizes as the MnaseI-digested samples. DNA was then concentrated and each sample was spiked with 0.055mg of l DNA (also sonicated to match the sample size as was input DNA).
HiC-Seq: we used the same protocol for in situ HiC libraries at Rao et al., (Cell, 2014 Dec; 159:1-16)
Gro-seq: Nuclei was extracted from 8-12 million cells grown on 10 cm plates and after run-on reaction the RNA was extracted with Trizol LS Reagent (Invitrogen, Carlsbad, CA, USA). RNA was treated with TURBO DNase (Ambion), fragmented using RNA Fragmentation Reagents (Ambion) and purified by running through P-30 column (Bio-Rad, Hercules, CA, USA). Fragmented RNA was dephosphorylated with PNK (New England Biolabs, Ipswich, MA, USA) followed by heatinactivation. Dephosphorylation reactions were purified using anti-BrdU beads (SantaCruz Biotech, Santa Cruz, CA, USA) and precipitated overnight. Poly(A)-tailing and cDNA synthesis was performed the next day as described in (Wang et al., 2011). However, for reverse transcription oligos with custom barcodes (underlined) were used : 5’-Phos CA/TG/AC/GT GATCGTCGGACTGTAGAACTCT /idSp/CAAGCAGAAGACGGCATACGA TTTTTTTTTTTTTTTTTTTTVN-3'. After cDNA synthesis, Exonuclease I (New England Biolabs; 30 min) was used to catalyze the removal of excess oligo. Enzyme was inactivated and RNA hydrolyzed by alkaline treatment (100 mM NaOH) and heat (25 min, 95°C). The cDNA fragments of were purified on a denaturing Novex 10% polyacrylamide TBE-urea gel (Invitrogen). The recovered cDNA was circularized, linearized, amplified for 10-14 cycles. The final product was ran on Novex 10%TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit (Zymo Research Corporation, Irvine, CA, USA).
4C-seq: The 4C assay was performed as previously described van de Werken et al. (2012) with minor modifications. Ten million of CH12 B cell line were crosslinked in 2% formaldehyde at 37°C for 10 min. The reaction was quenched by the addition of glycine (final concentration of 0.125 M). Cells were then washed with cold PBS and lysed (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% NP-40, 1× complete protease inhibitors [Roche]) at 4°C for 1 hr. Nuclei were incubated at 65°C for 30 min, 37°C for 30 min in 500 μl of restriction buffer (New England BioLabs DpnII buffer) containing 0.3% SDS. To sequester SDS, Triton X-100 was then added to a final concentration of 1.8%. DNA digestion was performed with 400 U of DpnII (New England Biolabs) at 37°C overnight. After heat inactivation (65°C for 30 min), the reaction was diluted to a final volume of 7 ml with ligation buffer containing 100 U T4 DNA Ligase (Roche) and incubated at 16°C overnight. Samples were then treated with 500 μg Proteinase K (Ambion) and incubated overnight at 65°C to reverse formaldehyde crosslinking. DNA was then purified by phenol extraction and ethanol precipitation. For circularization, the ligation junctions were digested with Csp6I (Fermentas) at 37°C overnight. After enzyme inactivation and phenol extraction, the DNA  was  religated  in  a  7 ml  volume  (1,000 U  T4  DNA  Ligase,  Roche).  Three micrograms of 4C library DNA was amplified with Expand Long template PCR System (Roche). Thermal cycle conditions were DNA denaturing for 2 min at 94°C, followed by 30 cycles of 15 s at 94°C, 1 min at 58°C, 3 min at 68°C, and a final step of 7 min at 68°C.  Bait was amplified with inverse PCR primers as follows: 3RR with DpnII:_4C 5'-GCTTATCTGTAAAGAATGGGTC-3', 3RR_Csp6i 5'-GGCCTTAGAAGGCTCTGTAC-3'. 4C-amplified DNA was microsequenced with the Illumina platform.
mRNA-seq: Total RNA from 106 of WT or ZF9-11 CH12 cells was isolated by Trizol extraction. mRNA was then isolated .
local Hi-C: 500ng of Hi-C library (8 cycles of amplification) was mixed with 2.5 µg of mouse Cot-1 DNA and 10µg of salomon sperm DNA in a total volume of 25µl. The sample was heated to 95℃ for 5 minutes. Next the temperature was diminished to 65℃ and the samples incubated for at least 5 minutes at 65℃. In the meantime 6µl of a RNA probe mixture (500ng of RNA probes, 20U of supreRNAseIn) and 33µl of hybridization buffer (10xSSPE, 10xDenhardt buffer, 10mM EDTA, 0.2% SDS) were incubated at 65℃. Next, the hybridization buffer and the RNA probe mixture were added to the sample. The final mix was incubated at 65℃ for 24 hours. Following the hybridization, 50 µl of MyOne Streptavidin T1 beads were washed 3 times with Bind-and-Wash buffer (1M NaCl, 10 mM Tris-HCl, pH=7.5, 1mM EDTA) and then resuspended in 134 µl of Bind-and-Wash buffer and added to the sample. The mixture was incubated for 30 minutes at room temperature with occasional swirling. Next, beads were separated using a magnet and the supernatant discarded. Beads were then washed once with 200µl of low-stringency buffer (1xSSC, 0.1%SDS) and incubated for 15 minutes at RT. Beads were separated and washed 3 times with high stringency.
ChromRNA-seq: chromatin RNA fraction was prepared from 3*10^6 cells following the method previously described (Pandya-Jones & Black, RNA, 2009) with some modifications. The pellet was lysed in a cytoplasm lysis buffer (20mM Hepes-KOH pH 7.6, 2mM MgCl2, 10% glycerol, 0.1% NP40, 0.5mM DTT with protease inhibitor, phosphatase inhibitor and RNase inhibitor). The lysate was then layered on top of a sucrose buffer in order to isolate the nuclei fraction from the cytoplasmic one (10mM Hepes-KOH pH7.6, 10mM NaCl, 1.5mM MgCl2, 10% glycerol, 0.5mM EDTA, 0.5mM DTT, 34% sucrose w/v with protease inhibitor, phosphatase inhibitor and RNase inhibitor).
ChromRNA-seq: The nuclei fraction was resuspended and lysed in a nuclear lysis buffer (10mM Hepes-KOH pH 7.6, 100mM NaCl, 0.5mM EDTA, 50% glycerol, 0.5mM DTT with protease inhibitor, phosphatase inhibitor and RNase inhibitor). Chromatin was precipitated by adding a Urea c

value: Tumor 7134 cell

tag: genotype/variation

value: SA deletion

value: lymphoma cell line

tag: molecule subtype

value: nacent RNA


title: ch12a_12h_wt_mRNA_rep4

tag: cell line

value: CH12 B

value: WT

tag: activation time

value: activated, 12h


title: ch12a_12h_FSA_mRNA_rep2

tag: cell type


title: T7134_wt_chromRNA_rep1


title: ch12a_12h_HSA_mRNA_rep1

value: half SA deletion


title: ch12a_12h_FSA_mRNA_rep3


title: ch12a_12h_HSA_mRNA_rep2


title: ch12a_12h_wt_mRNA_rep3


title: aB30h_wt_Rad21_HU_treated_rep1

value: spleen

value: activated B cell

tag: chip antibody

value: abcam; ab992

value: activated, 30h, HU


title: ch12a_12h_wt_mRNA_rep2


title: ch12a_12h_wt_mRNA_rep1


title: aB24h_wt_Rad21_flavopiridol

description: flavopiridol treated

tag: tissue

value: activated, 24h, flavopiridol 2h treatement


title: aB30h_wt_Rad21_HU_treated_rep2


title: aB30h_wt_Rad21_untreated_rep1

description: control

value: activated, 30h


title: ch12a_12h_HSA_mRNA_rep4


title: ch12a_12h_HSA_mRNA_rep3


title: T7134_SAd_chromRNA_rep1


title: T7134_wt_chromRNA_rep2


title: ch12a_12h_FSA_mRNA_rep1


title: aB30h_wt_Rad21_untreated_rep2

description: control


title: aB30h_wt_Nipbl_HU_treated_rep2

value: Bethyl Laboratories; A301-779A


title: aB30h_wt_Nipbl_untreated_rep1

description: control


title: aB30h_wt_Nipbl_untreated_rep2

description: control


title: esc_wt_Nipbl

value: blastocyst

value: ES cell


title: Cartilage_IL.1b_3 days_rep1

value: Cartilage


title: aB30h_wt_CTCF_untreated_rep2

description: control

value: Millipore; 07-729


title: TAQing treated strain #101

description: TAQing treated strain #101. Yeast strain having change of genome structure derived from heat treated of TaqI expressed WT14.

value: cell culture

tag: strain

value: Mutant strain from TAQing treated WT14

value: TAQing treated strain #101

value: fusant strain of S288C and SK1


title: aB30h_wt_Nipbl_HU_treated_rep1

value: WT


title: aB24h_wt_CTCF_rep1

value: activated, 24h


title: aB24h_wt_CTCF_rep2

value: spleen


title: Cartilage_control_0 days_rep1

value: Control


title: ch12_SAhalfd_CTCF_rep2

value: CH12 B

value: half SA deletion

value: lymphoma cell line


title: aB30h_wt_CTCF_HU_treated_rep2

value: activated B cell

value: activated, 30h, HU


title: aB30h_wt_CTCF_untreated_rep1

description: control

value: activated, 30h


title: ch12_SAhalfd_CTCF_rep1


title: Cartilage_control_3 days_rep1


title: aB24h_wt_PolII_flavopiridol

description: flavopiridol treated

value: abcam; ab817

value: activated, 24h, flavopiridol 2h treatement


title: ch12_SAd_CTCF_rep2

value: SA deletion

value: Millipore; 07-729


title: Cartilage_IL.1b_9 days_rep1

value: Cartilage


title: Cartilage_control_9 days_rep1


title: Cartilage_IL.1b_15 days_rep1


title: aB72h_smc3KAbiot_rep2

description: KA mutant

value: streptavidin pull down

value: activated, 72h


title: aB72h_smc3EQbiot_rep2

description: EQ mutant

value: WT


title: aB72h_smc3EQbiot_rep1

description: EQ mutant


title: aB24h_wt_PolII

description: control

value: activated, 24h


title: aB72h_smc3KAbiot_rep1

description: KA mutant

value: spleen


title: X1481.T

city: Smithville

first: Bin

last: Liu

state: TX

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: University of Texas MD Anderson Cancer Center

data_processing:
fastq reads were mapped to mouse genome NCBIM37
read count was generated by HT-seq count
The differential expression analysis was performed by DESeq
Genome_build: NCBIM37
Supplementary_files_format_and_content: raw count in text file

extract_protocol:
Tumors from tamoxifen-treated p53neo/R172H;R26CreER/GNZ mice were harvested right after the final MRI in which a response (growth vs shrinkage) was observed and flash frozen on dry ice. Total RNA was isolated using using TRIzol reagent (Life Technologies) following standard manufacturers protocol
Total RNA was submitted to the M.D. Anderson sequencing core facility and barcoded illumina compatible libaries wre prepared using the Illumina TruSeq mRNA seq Kit, per the manufacturer's protocol. The libraries were multiplexed 4 per lane and sequenced on the HiSeq3000 sequencer using the 75 bp paired end format. the raw RNA seq readouts were mapped to the mouse mm10 assembly reference

treatment_protocol: Mice were monitored by MRI for spontaneous tumor development. To genetically reactivate WT p53, tumor-bearing mice were administered weekly intraperitoneal tamoxifen treatments to activate Cre recombinase

tag: strain background

tag: tumor type

value: thymic lymphoma

tag: response to p53 restoration

value: non-responder


title: ch12_SAd_CTCF_rep1

value: CH12 B


title: X1488.T


title: aB30h_wt_CTCF_HU_treated_rep1


title: X1533.T

value: responder


title: X1538.T


title: X1537.T


title: X1397.T


title: X1442.T


title: X1534.T


title: aB72h_smc3biot_rep2

description: control

value: activated B cell


title: aB72h_smc3biot_rep1

description: control


title: X1516.T


title: X1485.T


title: T7134_SAd_mRNA_c2

source_name: Tumor 7134 cell

treatment_protocol: Myc floxed allele was obtained from Douglas Green (St. Jude Children’s research hospital). Myc flox/flox mice (WT) or RosaCreERTam/Myc flox/flox mice (KO) were treated with tamoxifen (three times of i.p. 1mg/mouse at 4, 3 and 1 day before sacrifice). The deletion of floxed allele was checked by PCR or intracellular staining of Myc protein.

tag: genotype

value: lymphoma cell line


title: T7134_SAd_mRNA_c1


title: T7134_SAd_mRNA_c3_rep1


title: T7134_wt_mRNA_rep1


title: T7134_SAd_mRNA_c3_rep3


title: aB24h_wt_input_ATPd_rep1

source_name: activated B cell

tag: activation treatment

value: input, 24h, Oligomycin


title: aB24h_wt_input_rep2

value: input, 24h


title: rB_wt_input

source_name: resting B cell

value: input, 0h


title: aB24h_wt_input_rep1


title: aB24h_wt_Rad21_rep2

value: Anti-Rad21 (abcam; ab992)


title: rB_wt_Rad21


title: aB24h_wt_Rad21_rep1


title: X1499.T


title: X1493.T


title: T7134_wt_mRNA_rep3


title: aB24h_wt_Nipbl_rep2

value: Anti-NIPBL (Bethy Laboratories; catalog# A301-779A, lot# A301-779A-3)


title: T7134_SAd_mRNA_c3_rep2

value: SA deletion


title: T7134_wt_mRNA_rep2


title: aB24h_wt_Rad21_ATPd

value: 24h, Oligomycin


title: aB24h_wt_Nipbl_rep1