title: 1911_Controls uninflamed terminal ileum

source_name: Controls uninflamed terminal ileum

value: Ileum


title: LW_25

status: Public on Jul 26 2021

type: SRA

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

country: USA

institute: National Cancer Institute, NIH

description:
RNA-seq data from  flash frozen tissue
LW_RNASeq39.anno_rpkm

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the mouse mm10 genome assembly using TopHat Software
differentially expressed genes were determined using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: 4T1 Mammary tumor

extract_protocol:
Tumors were resected, flash frozen on dry ice and RNA was harvested using the RNeasy Kit (QIAGEN).
RNA libraries were prepared for sequencing using Illumina TruSeq® Stranded Total RNA LT, RS-122-2201 protocol

treatment_protocol: Mice orthotopically implanted with 4T1 tumor cells were treated with vehicle, control antibodies or therapeutic antibodies (5mg/Kg ip 3x q wk) for 12 days starting on day+1 after tumor cell implantation.

tag: mouse strain

value: BALB/c

tag: tissue

value: Mammary tumor

tag: in vivo timepoint

value: 12 day treatment

tag: treatment

value: Anti-KLH control human MoAb


title: 1911_Controls uninflamed ascending/descending colon

type: RNA

city: South San Francisco

first: Jason

middle: A

last: Hackney

state: CA

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

institute: Genentech, Inc.

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.

scan_protocol: Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 10.7.

data_processing: Raw intensity data were background subtracted using the normal + exponential method from the limma Bioconductor package. The test/reference ratio was log2 transformed and normalized using loess normalization for each array. Loess normalized log2 ratios were then subjected to quantiles normalization across all arrays in the dataset.

organism: Homo sapiens

label_protocol: Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Quick Amp Labeling Kit (Agilent). For all samples, 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal human reference (Stratagene, La Jolla, CA).

extract_protocol: RNA was extracted with Qiagen RNeasy Plus kit with removal of genomic DNA.

tag: Sex

value: not determined

tag: diagnosis

value: Healthy control

tag: inflammation

value: Uninflamed

value: Colon

tag: batch

source_name: Universal human reference (UHR) from Stratagene

tag: sample type

value: pooled human reference RNA


title: LW_28


title: Control Annapurna 7-day-old seedling, Biological replicate 1

city: New Delhi

first: Jitendra

middle: Paul

last: Khurana

address: Benito Juarez Road

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi South Campus

description: Gene expression data of control unstressed 7-day-old Annapurna seedling

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 h at 450C on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3300.

data_processing: First-order analysis was performed using Affymetrix Gene Chip Operating (GCOS) software 1.2.1. Normalization of data and differential expression analysis was done using ArrayAssist ver 5.5  (Stratagene, CA, USA).

label: Biotin

organism: Oryza sativa Indica Group

source_name: 7-day-old seedling

label_protocol: Biotinylated aRNA were prepared according to the revised 3' IVT Affymetrix protocol from 500ng total RNA.

growth_protocol: Seeds of each variety were surface sterilized with 70% ethanol followed by 0.1 % HgCl2 with repeated rinses with Mili-Q water, and were allowed to imbibe in water for 16 h. The seedlings were grown hydroponically for seven days on rice growth medium (RGM), pH 4.8.

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

treatment_protocol: The seven-day-old seedings of each variety were subjected to heat stress by first pre-treating them at 37 oC for 1 h followed by 42 oC for 2 h at approximately 40 % relative humidity, respectively. Control tissues were maintained on RGM for 3 h at 28±1oC.

tag: cultivar

value: Annapurna

tag: stress

value: control unstressed

tag: time

value: control

value: seedling


title: S_b09_2mo_b3_3

city: New York

first: Alison

last: Goate

state: NY

address: Icahn (East) Building Floor 10 Room 10-70C, 1425 Madison Ave

department: Department of Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Paired end reads were trimmed for Illumina TruSeq adapters
Reads were aligned to the hg38 genome, and samples were counted for reads, both using the STAR aligner (v2.5.2b).
Genes were filtered by expression abundance (Counts per million (CPM) >0.1 in 5 or more samples)
Library sizes were estimated by the trimmed mean of M-values normalization (TMM) using edgeR (v3.26.8)
Differential gene expression was predicted by linear mixed model analysis using the variancePartition package (v1.14.1)
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files of raw read counts

source_name: iPSC-derived cerebral organoid

growth_protocol: Cerebral organoids were generated as per previously published protocol - see Yoon et al. Nature Methods, 2019.

extract_protocol:
Total RNA was extracted from individual organoids in a single batch using the KingFisher Flex (ThermoFisher Scientific) automated system and MagMAX mirVana Total RNA isolation kit (ThermoFisher Scientific).
Libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina, and sequenced as paired-end 150bp reads on the Illumina HiSeq 4000.

treatment_protocol: No treatment

value: iPSC-derived cerebral organoid

tag: cell line

tag: age

tag: technical replicate

tag: genotype


title: 1917_Controls uninflamed ascending/descending colon


title: LW_23


title: S_b09_2mo_b3_4


title: 1903_Controls uninflamed sigmoid colon

source_name: Controls uninflamed sigmoid colon


title: LW_24


title: 1917_Controls uninflamed sigmoid colon


title: LW_22


title: 1903_Controls uninflamed ascending/descending colon


title: LW_19

value: 1D11 mouse pan isoform anti-TGFbeta MoAb


title: LW_18


title: S_b09_2mo_b2_4


title: S_b09_2mo_b2_2


title: 1903_Controls uninflamed terminal ileum


title: S_b09_2mo_b2_3


title: S_b09_2mo_b3_2


title: 1902_Controls uninflamed sigmoid colon


title: 1902_Controls uninflamed ascending/descending colon


title: S_b09_2mo_b3_1


title: 1910_Controls uninflamed sigmoid colon


title: LW_20


title: 1693_Controls uninflamed sigmoid colon


title: S_b09_2mo_b2_1


title: LW_15


title: S_b09_2mo_b1_4


title: 1910_Controls uninflamed ascending/descending colon


title: 1902_Controls uninflamed terminal ileum


title: LW_17


title: 1910_Controls uninflamed terminal ileum


title: 1901_Controls uninflamed ascending/descending colon


title: 1693_Controls uninflamed terminal ileum


title: LW_12

value: 13C4 control mouse MoAb


title: 1905_Controls uninflamed ascending/descending colon


title: LW_11


title: S_b09_2mo_b1_1


title: LW_14


title: 1905_Controls uninflamed sigmoid colon


title: S_b06_6mo_b3_4


title: 1693_Controls uninflamed ascending/descending colon


title: S_b09_2mo_b1_2


title: S_b09_2mo_b1_3


title: 1915_Controls uninflamed sigmoid colon


title: 1914_Controls uninflamed ascending/descending colon


title: LW_13


title: 1905_Controls uninflamed terminal ileum

value: Ileum


title: LW_9

value: BALB/c


title: LW_10

value: Mammary tumor


title: S_b06_6mo_b3_2


title: LW_8

value: 12 day treatment


title: LW_7

value: Antibody vehicle


title: S_b06_6mo_b3_3


title: S_b06_6mo_b3_1


title: 1915_Controls uninflamed ascending/descending colon

value: not determined


title: LW_5


title: S_b06_6mo_b2_3


title: S_b06_6mo_b2_4


title: LW_6


title: 2102_Controls uninflamed sigmoid colon

value: Healthy control


title: 2102_Controls uninflamed ascending/descending colon

value: Uninflamed


title: 1677_Crohn's uninflamed terminal ileum

source_name: Crohn's uninflamed terminal ileum

value: Female

value: Crohn's disease


title: LW_4


title: 1503_Crohn's uninflamed terminal ileum

value: Male

value: pooled human reference RNA


title: 1677_Crohn's uninflamed ascending/descending colon

value: Colon


title: S_b06_6mo_b2_2


title: 1712_Crohn's uninflamed terminal ileum


title: LW_3


title: 1712_Crohn's uninflamed ascending/descending colon


title: 1716_Crohn's uninflamed terminal ileum


title: 1330_Crohn's uninflamed terminal ileum


title: 1712_Crohn's inflamed ascending/descending colon

value: Inflamed


title: 1901_Controls uninflamed sigmoid colon


title: S_b06_6mo_b2_1

value: iPSC-derived cerebral organoid


title: S_b06_6mo_b1_3


title: 2102_Controls uninflamed terminal ileum


title: 1915_Controls uninflamed terminal ileum


title: 1682_Crohn's uninflamed terminal ileum


title: 1503_Crohn's uninflamed ascending/descending colon


title: 1716_Crohn's uninflamed ascending/descending colon


title: 1682_Crohn's uninflamed ascending/descending colon


title: 1330_Crohn's uninflamed ascending/descending colon


title: LW_1


title: 1503_Crohn's inflamed terminal ileum

source_name: Crohn's inflamed terminal ileum


title: 1713_Crohn's inflamed terminal ileum


title: 1715_Crohn's uninflamed ascending/descending colon


title: S_b06_6mo_b1_4


title: 1713_Crohn's uninflamed ascending/descending colon


title: 1716_Crohn's inflamed ascending/descending colon


title: 1715_Crohn's uninflamed terminal ileum


title: LW_2


title: S_b06_6mo_b1_2


title: 1678_Crohn's uninflamed terminal ileum


title: S_b06_4mo_b3_4


title: S_b06_6mo_b1_1


title: S_b06_4mo_b3_3


title: GFP knockdown control day2 #4

city: Heidelberg

first: Nina

last: Papavasiliou

address: Im Neuenheimer Feld 280

department: Division of Immune Diversity (D150) Deutsches Krebsforschungszentrum

country: Germany

institute: German Cancer Research Center (DKFZ)

description: bisulfitute converted

library_source: genomic

data_processing:
eRRBS library preparation, sequencing, read alignment and methylation calls were performed by the Epigenomics Core Facility of Weill Cornell Medicine as previously described (Akalin et al., 2012a; Garrett-Bakelman et al., 2015).
Genome_build: mm10
Supplementary_files_format_and_content: Extensive description of data files format and content found in the Epigenomics Core Facility of Weill Cornell Medicine  http://epicore.med.cornell.edu/
methyl call files (.mincov10.txt) contain the locations of C's in either CpG, CHG, or CHH, context and their methylation levels. Sites with greater than or equal to 10x coverage for CpG, CHG, and CHH contexts are included in this file.
wig file, a file that allows the display of the methylation levels at their location in the genome in a track format for uploading into a genome browser such as the UCSC genome browser or Broad Institute's IGV.

molecule: genomic DNA

growth_protocol: C2C12 cells (CRL-1772, ATCC) were maintained in DMEM (30-2002, ATCC) with 10% fetal bovine serum (FBS) and feed every two days. To differentiate equal number of cells (0.25 x 10^6) were seeded in 6-well plates followed by media change to DMEM with 2% horse serum after 12 hours. For generating single cell clones for RNA- seq experiment C2C12s were sorted using fluorescence-activated cell sorting (FACS) and seeded into a 96 well plate. Each clone was expanded and tested for successful knockdown through immunoblotting. Genomic DNA was extracted at these timepoints following differentiation: Day0 (no differentiation), Day1 (one day after inducing differentiation, Day2 (two days after inducing differentiation).

extract_protocol:
Genomic DNA was extracted using isopropanol precipitation and RNA digestion following cell lysis
eRRBS library preparation was performed by the Epigenomics Core Facility of Weill Cornell Medicine as previously described (Akalin et al., 2012a; Garrett-Bakelman et al., 2015). The procedure includes bisulfite conversion of the DNA

treatment_protocol: For consitutive APOBEC2 knockdown C2C12s were infected with lentiviruses carrying shRNAs, targeting APOBEC2 (or GFP as a control). Lentiviruses were produced by co-transfection of pLKO.1-puro short hairpins containing construct, packaging plasmid psPAX2 (Addgene, #12260) and envelope plasmid pMD2.g (Addgene, #12259) in HEK 293T cells. Transfections were done using Lipofectamine 2000 Reagent (Lifetechnologies) as per manufacturer instructions. Supernatants with lentiviral particles were collected at 24 and 48 hours after transfection, passed through a 0.45 mm filter and applied to C2C12s. For APOBEC2 constitutive knockdown 30% confluent cells were infected with pLKO.1 containing lentivirus in growth media containing 8ug/mL polybrene for 12 hours. Two days after lentiviral infection cells were cultured with 4ug/ml virus-free puromycin containing media for two more days to select cells stably expressing the shRNAs. All APOBEC2 shRNAs were obtained from The Broad Institute’s Mission TRC-1 mouse library and are present in pLKO.1-puro construct, which carries the puromycin-resistance gene and drives shRNA transcription from a human U6 promoter. Plasmids used: pLKO.1 - TRC cloning vector (Addgene, # 10878) (Moffat et al., 2006); pLKO.1 puro GFP siRNA (Addgene, # 12273) (Orimo et al., 2005). The design of shRNAs and cloning in pLKO.1-TRC, were done according to the Addgene protocol. The following siRNAs sequences were used: for Apobec2 knockdown GCTACCAGTCAACTTCTTCAA; for GFP knockdown control GCAAGCTGACCCTGAAGTTCAT

tag: days after inducing differentiation

tag: knockdown target

value: GFP (control)


title: GFP knockdown control day2 #5

description: bisulfitute converted


title: GFP knockdown control day2 #3

description: bisulfitute converted


title: GFP knockdown control day2 #1

description: bisulfitute converted


title: S_b06_4mo_b3_2

tag: tissue


title: 1683_Crohn's inflamed terminal ileum

value: re


title: 1805_Crohn's inflamed terminal ileum

value: Ileum


title: 1683_Crohn's uninflamed ascending/descending colon


title: 1678_Crohn's uninflamed ascending/descending colon


title: 1683_Crohn's uninflamed terminal ileum


title: S_b06_4mo_b3_1


title: 1684_Crohn's uninflamed terminal ileum


title: 1684_Crohn's uninflamed ascending/descending colon


title: 1805_Crohn's uninflamed terminal ileum


title: S_b06_4mo_b2_4


title: 1805_Crohn's uninflamed ascending/descending colon


title: 1333_Crohn's uninflamed ascending/descending colon


title: 1717_Crohn's uninflamed terminal ileum


title: GFP knockdown control day1 #2

description: bisulfitute converted


title: GFP knockdown control day1 #3

description: bisulfitute converted


title: S_b06_4mo_b2_1


title: GFP knockdown control day1 #5

description: bisulfitute converted


title: S_b06_4mo_b1_4


title: GFP knockdown control day1 #1

description: bisulfitute converted


title: GFP knockdown control day1 #4

description: bisulfitute converted


title: S_b06_4mo_b2_2


title: S_b06_4mo_b2_3


title: GFP knockdown control day2 #2

description: bisulfitute converted


title: GFP knockdown control day0 #5

description: bisulfitute converted


title: 1204_Crohn's inflamed terminal ileum


title: 1810_Crohn's uninflamed ascending/descending colon


title: 1356_Crohn's uninflamed terminal ileum


title: 1356_Crohn's inflamed terminal ileum


title: S_b06_4mo_b1_3


title: 1681_Crohn's uninflamed ascending/descending colon


title: 2203_Crohn's inflamed terminal ileum


title: GFP knockdown control day0 #4

description: bisulfitute converted


title: 2006_Crohn's uninflamed ascending/descending colon


title: 1824_Crohn's uninflamed ascending/descending colon


title: S_b06_2mo_b3_4


title: S_b06_4mo_b1_1


title: 1810_Crohn's inflamed ascending/descending colon


title: 1717_Crohn's uninflamed ascending/descending colon


title: GFP knockdown control day0 #3

description: bisulfitute converted


title: 1356_Crohn's uninflamed ascending/descending colon


title: 2203_Crohn's uninflamed terminal ileum


title: 2006_Crohn's uninflamed terminal ileum


title: 2203_Crohn's uninflamed ascending/descending colon


title: 1824_Crohn's inflamed terminal ileum


title: 1824_Crohn's uninflamed terminal ileum


title: GFP knockdown control day0 #2

description: bisulfitute converted


title: 1342_Crohn's inflamed terminal ileum


title: 1343_Crohn's uninflamed ascending/descending colon


title: GFP knockdown control day0 #1

description: bisulfitute converted


title: S_b06_4mo_b1_2


title: Apobec2 knockdown  day2 #3

description: bisulfitute converted


title: S_b06_2mo_b3_3


title: Apobec2 knockdown  day2 #5

description: bisulfitute converted


title: S_b06_2mo_b3_1


title: 1343_Crohn's uninflamed terminal ileum


title: 1332_Crohn's uninflamed ascending/descending colon


title: Apobec2 knockdown  day2 #4

description: bisulfitute converted


title: 1342_Crohn's uninflamed ascending/descending colon


title: S_b06_2mo_b2_3


title: 1342_Crohn's uninflamed terminal ileum


title: S_b06_2mo_b2_2


title: S_b06_2mo_b2_4


title: S_b06_2mo_b3_2


title: Apobec2 knockdown  day2 #2

description: bisulfitute converted


title: S_b06_2mo_b2_1


title: 2004_Crohn's uninflamed ascending/descending colon


title: 1332_Crohn's inflamed ascending/descending colon


title: S_b06_2mo_b1_4


title: Apobec2 knockdown  day1 #4

description: bisulfitute converted


title: S_b06_2mo_b1_2


title: 1927_Crohn's inflamed terminal ileum


title: 2506_Crohn's uninflamed terminal ileum


title: Apobec2 knockdown  day1 #5

description: bisulfitute converted


title: 2004_Crohn's uninflamed terminal ileum


title: 1927_Crohn's uninflamed ascending/descending colon


title: S_b06_2mo_b1_1


title: 1507_Crohn's inflamed ascending/descending colon_rep1


title: 2502_Crohn's inflamed terminal ileum


title: 2206_Crohn's uninflamed ascending/descending colon


title: 1507_Crohn's inflamed ascending/descending colon_rep3


title: 2506_Crohn's uninflamed ascending/descending colon


title: 1507_Crohn's inflamed ascending/descending colon_rep4


title: Apobec2 knockdown  day1 #3

description: bisulfitute converted


title: Apobec2 knockdown  day1 #2

description: bisulfitute converted


title: 1507_Crohn's inflamed ascending/descending colon_rep2


title: 1355_Crohn's uninflamed terminal ileum


title: Apobec2 knockdown  day1 #1

description: bisulfitute converted


title: 2005_Crohn's uninflamed ascending/descending colon


title: 1338_Crohn's uninflamed ascending/descending colon


title: 1338_Crohn's inflamed terminal ileum


title: Apobec2 knockdown  day0 #5

description: bisulfitute converted


title: S_b06_2mo_b1_3


title: 1338_Crohn's uninflamed terminal ileum


title: Apobec2 knockdown  day0 #4

description: bisulfitute converted


title: 2005_Crohn's uninflamed terminal ileum


title: 1357_Crohn's uninflamed terminal ileum


title: Apobec2 knockdown  day2 #1

description: bisulfitute converted


title: S_72f02_6mo_b3_3


title: 1357_Crohn's uninflamed ascending/descending colon


title: Apobec2 knockdown  day0 #3

description: bisulfitute converted


title: S_72f02_6mo_b3_2


title: 1352_Crohn's inflamed terminal ileum


title: S_72f02_6mo_b2_4


title: 1352_Crohn's uninflamed ascending/descending colon


title: Apobec2 knockdown  day0 #2

description: bisulfitute converted


title: Apobec2 knockdown  day0 #1

description: bisulfitute converted


title: 1357_Crohn's inflamed terminal ileum


title: S_72f02_6mo_b3_4


title: RNA-seq_Apobec2 knockdown  day2 #3

data_processing:
Paired-end reads were aligned to mm10 genome using the subjunc function in the Bioconductor Rsubread (Liao et al., 2013) package.
Reads to genomic features (gene) were counted using the featureCounts function in the Bioconductor Rsubread (Liao et al., 2013) package
bigWig files for visualization were generated from aligned reads using the Bioconductor rtracklayer (Lawrence et al., 2009) and GenomicAlignments packages (Lawrence et al., 2013).
Transcript quantifications were performed using Salmon (Patro et al., 2017) in quasi-mapping mode. Gene expression values were calculated from transcript quantifications using tximport (Soneson et al., 2016).
Gene expression changes were identified using the Wald test implemented in DESeq2 (Love et al., 2014).
Annotation files used: BSgenome.Mmusculus.UCSC.mm10 (v1.4.0); org.Mm.db(v3.5.0); TxDb.Mmusculus.UCSC.mm10.knownGene.gtf.gz (v3.4.0)
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 results are the output from the results function of DESeq2 (Love et al., 2014). It contains log2 fold change, the effect size estimate, or the  gene expression changes  between  two groups (comparison are indicated in the file name eg G_d0 = control sample at day0 and A2_d0 is Apobec2 knockdown sample at day0). Here gene ID and name included is based on annotation using TxDb.Mmusculus.UCSC.mm10.knownGene.gtf.gz (v3.4.0) and org.Mm.db(v3.5.0).
Transcript per million (TMP) results  contains TPM results for each of the biological replicates for each group (on series record).
bigWig file contains normalised RNA-seq signal across the genome. Useful for display of the normalized RNA-Seq signal at their location in the genome in a track format for uploading into a genome browser such as the UCSC genome browser or Broad Institute's IGV.
Gene read counts is the output of the featureCounts of  Rsubread (Liao et al., 2013) package, showing the number of reads to each genomic feature (gene)

molecule: polyA RNA

growth_protocol: C2C12 cells (CRL-1772, ATCC) were maintained in DMEM (30-2002, ATCC) with 10% fetal bovine serum (FBS) and feed every two days. To differentiate equal number of cells (0.25 x 10^6) were seeded in 6-well plates followed by media change to DMEM with 2% horse serum after 12 hours. For generating single cell clones for RNA- seq experiment C2C12s were sorted using fluorescence-activated cell sorting (FACS) and seeded into a 96 well plate. Each clone was expanded and tested for successful knockdown through immunoblotting. RNA was extracted at these timepoints following differentiation: Day0 (no differentiation), Day1 (one day after inducing differentiation, Day2 (two days after inducing differentiation).

extract_protocol:
Total RNA was extracted using TRIzol LS Reagent (ambion, 10296-010) per manufacter's instruction
Library preparation and sequencing were done using TruSeq Stranded mRNA Sample Prep kit as per manufacturer’s instruction. The procedure includes purification of poly-adenylated RNAs.


title: 1329_Crohn's uninflamed ascending/descending colon


title: 1352_Crohn's uninflamed terminal ileum


title: 1350_Crohn's uninflamed ascending/descending colon


title: S_72f02_6mo_b2_3


title: S_72f02_6mo_b2_2


title: S_72f02_6mo_b2_1


title: RNA-seq_Apobec2 knockdown  day2 #2


title: RNA-seq_Apobec2 knockdown  day2 #1


title: S_72f02_6mo_b1_4


title: S_72f02_6mo_b3_1


title: RNA-seq_Apobec2 knockdown  day1 #3


title: 1700_Crohn's uninflamed ascending/descending colon


title: 1504_Crohn's inflamed ascending/descending colon


title: 1341_Crohn's uninflamed ascending/descending colon


title: 1341_Crohn's uninflamed terminal ileum


title: 1203_Crohn's uninflamed terminal ileum


title: RNA-seq_Apobec2 knockdown  day1 #1


title: S_72f02_6mo_b1_3


title: RNA-seq_Apobec2 knockdown  day0 #3


title: 1700_Crohn's inflamed terminal ileum


title: S_72f02_6mo_b1_2


title: S_72f02_6mo_b1_1


title: 1504_Crohn's uninflamed ascending/descending colon


title: 1926_Crohn's uninflamed terminal ileum


title: 1823_Crohn's inflamed terminal ileum


title: RNA-seq_Apobec2 knockdown  day0 #2


title: RNA-seq_Apobec2 knockdown  day1 #2


title: 1418_Crohn's uninflamed terminal ileum


title: 1814_Crohn's uninflamed ascending/descending colon


title: 1413_Crohn's inflamed terminal ileum


title: 1926_Crohn's uninflamed ascending/descending colon


title: 1418_Crohn's uninflamed ascending/descending colon


title: 1413_Crohn's inflamed ascending/descending colon


title: S_72f02_4mo_b3_4


title: S_72f02_4mo_b3_3


title: RNA-seq_Apobec2 knockdown  day0 #1


title: S_72f02_4mo_b3_2


title: RNA-seq_GFP knockdown control day2 #3


title: 1923_Crohn's uninflamed terminal ileum


title: 1335_Crohn's uninflamed ascending/descending colon


title: RNA-seq_GFP knockdown control day2 #2


title: 1205_Crohn's uninflamed ascending/descending colon


title: 1813_Crohn's inflamed ascending/descending colon


title: 1813_Crohn's uninflamed ascending/descending colon


title: RNA-seq_GFP knockdown control day2 #1


title: S_72f02_4mo_b3_1


title: 1823_Crohn's uninflamed ascending/descending colon


title: 1205_Crohn's uninflamed terminal ileum


title: 1336_Crohn's inflamed ascending/descending colon


title: 1421_Crohn's inflamed ascending/descending colon


title: RNA-seq_GFP knockdown control day1 #1


title: RNA-seq_GFP knockdown control day1 #3


title: S_72f02_4mo_b2_2


title: 1336_Crohn's uninflamed terminal ileum


title: S_72f02_4mo_b2_4


title: S_72f02_4mo_b2_3


title: 1696_Crohn's uninflamed terminal ileum


title: S_72f02_4mo_b2_1


title: RNA-seq_GFP knockdown control day0 #3


title: 1336_Crohn's uninflamed ascending/descending colon


title: RNA-seq_GFP knockdown control day0 #2


title: 1696_Crohn's uninflamed ascending/descending colon


title: RNA-seq_GFP knockdown control day1 #2


title: 1696_Crohn's inflamed terminal ileum


title: S_72f02_4mo_b1_1


title: RNA-seq_GFP knockdown control day0 #1


title: 1680_Crohn's inflamed terminal ileum


title: S_72f02_2mo_b3_4


title: S_72f02_4mo_b1_4


title: 1331_Crohn's uninflamed ascending/descending colon


title: 1346_Crohn's uninflamed ascending/descending colon


title: 1680_Crohn's uninflamed ascending/descending colon


title: 2002_Crohn's uninflamed terminal ileum


title: 1331_Crohn's inflamed terminal ileum


title: S_72f02_4mo_b1_2


title: 1419_Crohn's uninflamed terminal ileum


title: S_72f02_4mo_b1_3


title: 1808_Crohn's uninflamed ascending/descending colon


title: 1353_Crohn's uninflamed ascending/descending colon


title: 1928_Crohn's uninflamed ascending/descending colon


title: 2002_Crohn's inflamed terminal ileum


title: S_72f02_2mo_b3_2


title: 1694_Crohn's uninflamed ascending/descending colon


type: genomic

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

description:
Biological replicate 1 of 2. Chd1ΔN occupancy by ChIP-chip in 3HA-tagged chd1ΔN cells.  Chd1ΔN ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against a similar ChIP sample performed from an isogenic strain where the CHD1 gene is not tagged (Cy3-labeled).
SmthBED_yFR3369vs3370_3HA-chd1deltaNvsNoTag_20210315_rep1-2__S.cerevisiaeApr11_994869.bed

hyb_protocol: ChIP and control samples were combined and dried by SpeedVac. Combined samples were resuspended in 110 µL of fresh hybridization mix (5 µL 10 mg/mL Salmon Sperm DNA (Thermo Fisher Scientific, 15632011), 5 µL 8 mg/mL Yeast tRNA (Thermo Fisher Scientific, 15401011) and 100 µL DIG Easy Hyb (Roche, 11603558001)) and incubated 5 min at 95˚C followed by 5 min at 45˚C. Samples were hybridized to Agilent microarrays in SureHyb enabled chambers (Agilent, G2534A) with rotation at 42˚C for at least 18 hr. Microarrays were washed on an orbital shaker for 5 min at room temperature with Wash I buffer (6X SSPE, 0.005% N-Lauroylsarcosine), followed by a second wash with pre-warmed (31˚C) Wash II buffer (0.06X SSPE) for 5 min at room temperature. The microarrays used were described before (Jeronimo and Robert, 2014) and were custom designed by Agilent Technologies and contain a total of about 180,000 Tm-adjusted 60-mer probes covering the entire yeast genome with virtually no gaps between probes.

scan_protocol: Microarrays were scanned using an InnoScan900 (Innopsys) at 2 µm resolution.

data_processing:
BED description: A genome browser-ready file for Chd1ΔN occupancy by ChIP-chip (IP tag/IP No tag) in 3HA-tagged chd1ΔN cells.
BED method: The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = limma loess (subgrid)

organism: Saccharomyces cerevisiae

label_protocol: The ChIP and Input samples were blunted as follow. 40 µL of ChIP DNA or about 400 ng of Input DNA were added to 70 µL of blunting¬¬ mix (11 µL 10X NEBuffer 2 (NEB, B7002S), 0.5 µL 10 mg/mL BSA, 0.5 µL 20 mM dNTPs and 0.2 µL (0.6 units) of T4 DNA polymerase (NEB, M0203L)) and incubated at 12˚C for 20 min. Then, the blunted DNA was extracted with phenol/chloroform/isoamyl alcohol (25:24:1) in the presence of 280 mM of NaOAc pH 5.2 and 10 μg of glycogen, precipitated with ethanol and resuspended in 25 µL ddH2O. Blunted DNA was ligated to 100 pmol of annealed linkers (see Table S2) with 2.5 units of T4 DNA ligase (Thermo Fisher Scientific, 15224041) in the supplied buffer, in a final volume of 50 µL, overnight at 16˚C. Samples were precipitated with 6 µL of 3 M NaOAc pH 5.2 and 130 µL ethanol, and resuspended in 25 µL ddH2O. 15 µL of labeling mix (4 µL 10X ThermoPol Reaction buffer (NEB, B9004S), 2 µL of 5 mM aa-dUTP/dNTP mix (5 mM each dATP, dGTP and dCTP, 3 mM dTTP and 2 mM 5-(3-aminoallyl)-dUTP (Thermo Fisher Scientific, AM8439)) and 1.25 µL of 40 µM oligo 1) were added to each sample. Samples were placed in a thermocycler and when temperature reached 55˚C, 10 µL of enzyme mix (1 µL 10X ThermoPol Reaction buffer, 1 µL (5 units) Taq DNA polymerase (Thermo Fisher Scientific, 18038240) and 0.01 µL (0.025 units) Pfu DNA polymerase (Thermo Fisher Scientific, EP0502)) were added and the following program was run. 1) 72˚C, 5 min; 2) 95˚C, 2 min; 3) 32 cycles: 95˚C, 30sec; 55˚C, 30sec; 72˚C, 1 min; 4) 72˚C, 4 min; 5) 4˚C, forever. PCR products were purified using QIAquick PCR Purification kit (QIAGEN, 28106) with few modifications: PE buffer was replaced by Phosphate wash buffer (5 mM KPO4 pH 8.5 and 80% ethanol) and EB buffer was replace by Phosphate elution buffer (4 mM KPO4 pH 8.5). Eluates were dried by SpeedVac and pellets were resuspended in 4.5 µL of freshly prepared 0.1 M Na2CO3 pH 9.0 buffer. 4.5 µL of Cy5 Mono-Reactive NHS Ester Fluorescent Dye (ChIP samples) or Cy3 Mono-Reactive NHS Ester Fluorescent Dye (control samples Input DNA or no-tag ChIP) (GE Healthcare, PA25001 and PA23001) were added. Samples were incubated 1 hr in the dark at room temperature. 35 µL of 0.1 M NaOAc pH 5.2 were added and samples were purified using QIAquick PCR Purification kit according to the manufacturers’ instructions.

growth_protocol: 50 mL of YPD (yeast extract-peptone-2% glucose, supplemented with 44 µM adenine) medium was inoculated at OD600 0.1 from an overnight preculture in the same medium and allowed to grow to an OD600 of 0.7-0.9 before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 30 min and quenched with 125 mM glycine. Crosslinked cells were collected by centrifugation and washed twice with 1X TBS (20 mM Tris-HCl pH 7.5, 150 mM NaCl). Cell pellets were snap-freezed in liquid nitrogen and stored at -80°C.

extract_protocol: IP protocol: Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation. 600 μL of the chromatin sample was taken per immunoprecipitation (IP) and, when necessary, 6 μL (1%) were saved as Input sample. The following amount of antibody per IP was used: anti-HA (Santa Cruz Biotechnology sc-7392, 15 μL). 50 μL of Dynabeads coated with Pan Mouse IgG antibodies (Thermo Fisher Scientific, 11042) pre-coupled with the indicated antibody were added to the chromatin sample and incubated overnight at 4°C. Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 100 % EtOH. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.

tag: strain

tag: antibody

value: anti-HA (Santa Cruz Biotechnology sc-7392, 15 uL)


title: yFR3075vs3084_3HA-chd1K407RvsNoTag_20210315_rep2

description:
Biological replicate 2 of 2. Chd1 K407R occupancy by ChIP-chip in 3HA-tagged chd1K407R cells. Chd1 K407R ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against a similar ChIP sample performed from an isogenic strain where the CHD1 gene is not tagged (Cy3-labeled).
SmthBED_yFR3075vs3084_3HA-chd1K407RvsNoTag_20210315_rep1-2__S.cerevisiaeApr11_610103.bed

data_processing:
BED description: A genome browser-ready file for Chd1K407R occupancy by ChIP-chip (IP tag/IP No tag) in 3HA-tagged chd1K407R cells.
BED method: The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = limma loess (subgrid)


title: yFR3369vs3370_3HA-chd1deltaNvsNoTag_20210315_rep2

description:
Biological replicate 2 of 2. Chd1ΔN occupancy by ChIP-chip in 3HA-tagged chd1ΔN cells.  Chd1ΔN ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against a similar ChIP sample performed from an isogenic strain where the CHD1 gene is not tagged (Cy3-labeled).
SmthBED_yFR3369vs3370_3HA-chd1deltaNvsNoTag_20210315_rep1-2__S.cerevisiaeApr11_994869.bed


title: S_72f02_2mo_b3_1


title: S_72f02_2mo_b3_3


title: 1358_Crohn's uninflamed ascending/descending colon

tag: Sex


title: S_72f02_2mo_b2_4


title: 1806_Crohn's uninflamed ascending/descending colon

tag: diagnosis


title: S_72f02_2mo_b2_3


title: 1806_Crohn's inflamed terminal ileum

tag: inflammation


title: 1419_Crohn's uninflamed ascending/descending colon

tag: batch


title: S_72f02_2mo_b2_2


title: 1694_Crohn's uninflamed terminal ileum

tag: sample type


title: 1822_Crohn's uninflamed ascending/descending colon


title: yFR3061vs116_WT_3HA-Chd1vsNoTag_20210315_rep3

description:
Biological replicate 2 of 2. Chd1 occupancy by ChIP-chip in WT (3HA-tagged Chd1) cells. Chd1 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against a similar ChIP sample performed from an isogenic strain where the CHD1 gene is not tagged (Cy3-labeled).
SmthBED_yFR3061vs116_WT_3HA-Chd1vsNoTag_20210315_rep1-3__S.cerevisiaeApr11_269498.bed

data_processing:
BED description: A genome browser-ready file for Chd1 occupancy by ChIP-chip (IP tag/IP No tag) in WT (3HA-tagged Chd1) cells.
BED method: The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = limma loess (subgrid)


title: 1806_Crohn's uninflamed terminal ileum


title: 1345_Crohn's inflamed ascending/descending colon


description:
Biological replicate 1 of 2. Chd1 K407R occupancy by ChIP-chip in 3HA-tagged chd1K407R cells. Chd1 K407R ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against a similar ChIP sample performed from an isogenic strain where the CHD1 gene is not tagged (Cy3-labeled).
SmthBED_yFR3075vs3084_3HA-chd1K407RvsNoTag_20210315_rep1-2__S.cerevisiaeApr11_610103.bed


title: 1344_Crohn's uninflamed terminal ileum


title: 1822_Crohn's inflamed terminal ileum


title: 1345_Crohn's inflamed terminal ileum


title: yFR930_chd1D_Spt16vsInput_20210128_rep1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in chd1Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR930_chd1D_Spt16vsInput_20210128_rep1-2__S.cerevisiaeApr11_790173.bed

data_processing:
BED description: A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in chd1Δ cells.
BED method: The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = limma loess (subgrid)

extract_protocol: IP protocol: Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation. 600 μL of the chromatin sample was taken per immunoprecipitation (IP) and, when necessary, 6 μL (1%) were saved as Input sample. The following amount of antibody per IP was used: anti-Spt16 (a gift from T. Formosa, 1 μL). 50 μL of Dynabeads coated with Protein G (Thermo Fisher Scientific, 10004D) pre-coupled with the indicated antibody were added to the chromatin sample and incubated overnight at 4°C. Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 100 % EtOH. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.

value: anti-Spt16 (a gift from T. Formosa, 1 uL)

extract_protocol: IP protocol: none


description:
Biological replicate 1 of 2. Chd1 occupancy by ChIP-chip in WT (3HA-tagged Chd1) cells. Chd1 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against a similar ChIP sample performed from an isogenic strain where the CHD1 gene is not tagged (Cy3-labeled).
SmthBED_yFR3061vs116_WT_3HA-Chd1vsNoTag_20210315_rep1-3__S.cerevisiaeApr11_269498.bed


title: yFR930_chd1D_Spt16vsInput_20210128_rep2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in chd1Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR930_chd1D_Spt16vsInput_20210128_rep1-2__S.cerevisiaeApr11_790173.bed


title: S_72f02_2mo_b2_1


title: S_72f02_2mo_b1_4


title: 1420_Crohn's uninflamed ascending/descending colon


title: S_72f02_2mo_b1_3


title: S_72f02_2mo_b1_2


title: 1345_Crohn's uninflamed ascending/descending colon


title: 1420_Crohn's uninflamed terminal ileum


title: S_72b12_6mo_b3_4


title: yFR930_chd1D_Rpb3vsInput_20210128_rep2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in chd1Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR930_chd1D_Rpb3vsInput_20210128_rep1-2__S.cerevisiaeApr11_341126.bed

data_processing:
BED description: A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in chd1Δ cells.
BED method: The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = limma loess (subgrid)

extract_protocol: IP protocol: Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation. 600 μL of the chromatin sample was taken per immunoprecipitation (IP) and, when necessary, 6 μL (1%) were saved as Input sample. The following amount of antibody per IP was used: anti-Rpb3 (BioLegend 665004, 1.5 μL). 50 μL of Dynabeads coated with Pan Mouse IgG antibodies (Thermo Fisher Scientific, 11042) pre-coupled with the indicated antibody were added to the chromatin sample and incubated overnight at 4°C. Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 100 % EtOH. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.

value: anti-Rpb3 (BioLegend 665004, 1.5 uL)


title: yFR930_chd1D_Rpb3vsInput_20210128_rep1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in chd1Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR930_chd1D_Rpb3vsInput_20210128_rep1-2__S.cerevisiaeApr11_341126.bed


title: 1697_Crohn's uninflamed terminal ileum


title: 1340_Crohn's uninflamed ascending/descending colon


title: 1698_Crohn's inflamed terminal ileum


title: 1697_Crohn's uninflamed ascending/descending colon


title: 1340_Crohn's inflamed terminal ileum


title: S_72b12_6mo_b3_3


title: yFR3369_chd1deltaN_Spt16vsInput_20210128_rep2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in chd1deltaN cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3369_chd1deltaN_Spt16vsInput_20210128_rep1-2__S.cerevisiaeApr11_58934.bed

data_processing:
BED description: A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in chd1ΔN cells.
BED method: The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = limma loess (subgrid)


title: S_72f02_2mo_b1_1


title: 1698_Crohn's uninflamed ascending/descending colon


title: 1344_Crohn's uninflamed ascending/descending colon


title: 1354_Crohn's uninflamed ascending/descending colon


title: S_72b12_6mo_b3_2


title: S_72b12_6mo_b3_1


title: yFR3369_chd1deltaN_Rpb3vsInput_20210128_rep2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in chd1deltaN cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3369_chd1deltaN_Rpb3vsInput_20210128_rep1-2__S.cerevisiaeApr11_181947.bed

data_processing:
BED description: A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in chd1ΔN cells.
BED method: The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = limma loess (subgrid)


description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in chd1deltaN cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3369_chd1deltaN_Rpb3vsInput_20210128_rep1-2__S.cerevisiaeApr11_181947.bed


title: 1417_Crohn's uninflamed terminal ileum


title: 1340_Crohn's uninflamed terminal ileum


title: 2205_Crohn's uninflamed ascending/descending colon


description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in chd1deltaN cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3369_chd1deltaN_Spt16vsInput_20210128_rep1-2__S.cerevisiaeApr11_58934.bed


title: 2007_Crohn's inflamed terminal ileum


title: 2007_Crohn's uninflamed terminal ileum


title: 1815_Crohn's inflamed terminal ileum


title: 2601_Crohn's uninflamed terminal ileum


title: 1351_Crohn's uninflamed terminal ileum


title: 1417_Crohn's uninflamed ascending/descending colon


title: yFR3075_chd1K407R_Spt16vsInput_20210128_rep2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in chd1K407R cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3075_chd1K407R_Spt16vsInput_20210128_rep1-2__S.cerevisiaeApr11_589333.bed

data_processing:
BED description: A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in chd1K407R cells.
BED method: The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = limma loess (subgrid)


description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in chd1K407R cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3075_chd1K407R_Spt16vsInput_20210128_rep1-2__S.cerevisiaeApr11_589333.bed


description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in chd1K407R cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3075_chd1K407R_Rpb3vsInput_20210128_rep1-2__S.cerevisiaeApr11_205113.bed

data_processing:
BED description: A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in chd1K407R cells.
BED method: The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = limma loess (subgrid)


title: 1815_Crohn's uninflamed ascending/descending colon


title: yFR3061_WT_Spt16vsInput_20210128_rep2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3061_WT_Spt16vsInput_20210128_rep1-2__S.cerevisiaeApr11_326391.bed

data_processing:
BED description: A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in WT cells.
BED method: The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = limma loess (subgrid)


title: 2205_Crohn's inflamed terminal ileum


title: yFR3075_chd1K407R_Rpb3vsInput_20210128_rep2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in chd1K407R cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3075_chd1K407R_Rpb3vsInput_20210128_rep1-2__S.cerevisiaeApr11_205113.bed


title: 1817_Crohn's uninflamed terminal ileum


title: S_72b12_6mo_b2_4


title: S_72b12_6mo_b1_4


title: S_72b12_6mo_b2_3


title: yFR3061_WT_Spt16vsInput_20210128_rep1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3061_WT_Spt16vsInput_20210128_rep1-2__S.cerevisiaeApr11_326391.bed


title: S_72b12_6mo_b2_2


title: S_72b12_6mo_b2_1


title: 1351_Crohn's inflamed terminal ileum


title: 2507_Crohn's uninflamed ascending/descending colon


title: 1351_Crohn's uninflamed ascending/descending colon


title: 1818_Crohn's inflamed terminal ileum


title: S_72b12_6mo_b1_2


title: S_72b12_6mo_b1_1


title: 1817_Crohn's uninflamed ascending/descending colon


title: 2207_Crohn's uninflamed terminal ileum


title: 1695_Crohn's inflamed terminal ileum


title: S_72b12_4mo_b3_4


title: 2207_Crohn's inflamed terminal ileum


title: yFR3061_WT_Rpb3vsInput_20210128_rep2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3061_WT_Rpb3vsInput_20210128_rep1-2__S.cerevisiaeApr11_413731.bed

data_processing:
BED description: A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in WT cells.
BED method: The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = limma loess (subgrid)


title: 2010_Crohn's uninflamed terminal ileum


title: yFR3061_WT_Rpb3vsInput_20210128_rep1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3061_WT_Rpb3vsInput_20210128_rep1-2__S.cerevisiaeApr11_413731.bed


title: 1695_Crohn's uninflamed terminal ileum


description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells treated with rapamycin for 90 min to anchor-away the endogenous FRB-tagged Chd1 protein. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3401_FRB-GFP-Chd1_90minRapa_Spt16vsInput_20210212_rep1-2__S.cerevisiaeApr11_924756.bed

data_processing:
BED description: A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in WT cells treated with rapamycin for 90 min to anchor-away the endogenous FRB-tagged Chd1 protein.
BED method: The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = limma loess (subgrid)

growth_protocol: 50 mL of YPD (yeast extract-peptone-2% glucose, supplemented with 44 µM adenine) medium was inoculated at OD600 0.1 from an overnight preculture in the same medium and allowed to grow to an OD600 of 0.5. Cell cultures were treated with 1 μg/mL of rapamycin for 90 min before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 30 min and quenched with 125 mM glycine. Crosslinked cells were collected by centrifugation and washed twice with 1X TBS (20 mM Tris-HCl pH 7.5, 150 mM NaCl). Cell pellets were snap-freezed in liquid nitrogen and stored at -80°C.

treatment_protocol: 1 μg/mL rapamycin for 90 min

value: MATa, tor1-1, fpr1::loxP-LEU2-loxP, RPL13A-2xFKBP12::loxP, pdr5∆::loxP, FRB-GFP-CHD1


title: 1811_UC uninflamed sigmoid colon

data_processing: Raw intensity data were background subtracted using the normal + exponential method from the limma Bioconductor package. The test/reference ratio was log2 transformed and normalized using loess normalization for each array. Loess normalized log2 ratios were then subjected to quantiles normalization across all arrays in the dataset.

source_name: UC uninflamed sigmoid colon

value: not determined

value: Ulcerative colitis


title: 1347_Crohn's uninflamed ascending/descending colon

value: Uninflamed


title: 1695_Crohn's uninflamed ascending/descending colon


title: 2010_Crohn's uninflamed ascending/descending colon


title: S_72b12_4mo_b3_3


title: yFR3401_FRB-GFP-Chd1_90minRapa_Spt16vsInput_20210212_rep2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells treated with rapamycin for 90 min to anchor-away the endogenous FRB-tagged Chd1 protein. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3401_FRB-GFP-Chd1_90minRapa_Spt16vsInput_20210212_rep1-2__S.cerevisiaeApr11_924756.bed


title: 1691_UC uninflamed sigmoid colon


title: S_72b12_4mo_b3_2


title: 2101_UC uninflamed sigmoid colon


title: 1906_UC uninflamed sigmoid colon


title: 1907_UC uninflamed sigmoid colon


description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT cells treated with rapamycin for 90 min to anchor-away the endogenous FRB-tagged Chd1 protein. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3401_FRB-GFP-Chd1_90minRapa_Rpb3vsInput_20210212_rep1-2__S.cerevisiaeApr11_701813.bed

data_processing:
BED description: A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in WT cells treated with rapamycin for 90 min to anchor-away the endogenous FRB-tagged Chd1 protein.
BED method: The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = limma loess (subgrid)


title: yFR3401_FRB-GFP-Chd1_90minRapa_Rpb3vsInput_20210212_rep2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT cells treated with rapamycin for 90 min to anchor-away the endogenous FRB-tagged Chd1 protein. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3401_FRB-GFP-Chd1_90minRapa_Rpb3vsInput_20210212_rep1-2__S.cerevisiaeApr11_701813.bed


title: yFR3401_FRB-GFP-Chd1_90minDMSO_Spt16vsInput_20210212_rep2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells treated with DMSO for 90 min. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3401_FRB-GFP-Chd1_90minDMSO_Spt16vsInput_20210212_rep1-2__S.cerevisiaeApr11_303077.bed

data_processing:
BED description: A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in WT cells treated with DMSO for 90 min.
BED method: The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = limma loess (subgrid)

growth_protocol: 50 mL of YPD (yeast extract-peptone-2% glucose, supplemented with 44 µM adenine) medium was inoculated at OD600 0.1 from an overnight preculture in the same medium and allowed to grow to an OD600 of 0.5. Cell cultures were treated with DMSO for 90 min before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 30 min and quenched with 125 mM glycine. Crosslinked cells were collected by centrifugation and washed twice with 1X TBS (20 mM Tris-HCl pH 7.5, 150 mM NaCl). Cell pellets were snap-freezed in liquid nitrogen and stored at -80°C.

treatment_protocol: DMSO for 90 min


title: 1687_UC inflamed ascending/descending colon

source_name: UC inflamed ascending/descending colon


title: 2001_UC uninflamed sigmoid colon


title: yFR3401_FRB-GFP-Chd1_90minDMSO_Rpb3vsInput_20210212_rep2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT cells treated with DMSO for 90 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3401_FRB-GFP-Chd1_90minDMSO_Rpb3vsInput_20210212_rep1-2__S.cerevisiaeApr11_800141.bed

data_processing:
BED description: A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in WT cells treated with DMSO for 90 min.
BED method: The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = limma loess (subgrid)


title: 1918_UC uninflamed sigmoid colon


title: 2001_UC uninflamed ascending/descending colon


description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells treated with DMSO for 90 min. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3401_FRB-GFP-Chd1_90minDMSO_Spt16vsInput_20210212_rep1-2__S.cerevisiaeApr11_303077.bed


title: S_72b12_4mo_b3_1

data_processing:
Paired end reads were trimmed for Illumina TruSeq adapters
Reads were aligned to the hg38 genome, and samples were counted for reads, both using the STAR aligner (v2.5.2b).
Genes were filtered by expression abundance (Counts per million (CPM) >0.1 in 5 or more samples)
Library sizes were estimated by the trimmed mean of M-values normalization (TMM) using edgeR (v3.26.8)
Differential gene expression was predicted by linear mixed model analysis using the variancePartition package (v1.14.1)
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files of raw read counts


title: S_72b12_4mo_b2_2


title: 1692_UC uninflamed sigmoid colon


title: S_72b12_4mo_b2_4


title: S_72b12_4mo_b2_3


title: 1921_UC uninflamed sigmoid colon


title: 1921_UC inflamed sigmoid colon

source_name: UC inflamed sigmoid colon


title: S_72b12_4mo_b2_1


title: S_72b12_4mo_b1_4


title: S_72b12_6mo_b1_3


title: 1912_UC uninflamed sigmoid colon


title: 1690_UC uninflamed sigmoid colon


title: 1686_UC inflamed sigmoid colon


description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT cells treated with DMSO for 90 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3401_FRB-GFP-Chd1_90minDMSO_Rpb3vsInput_20210212_rep1-2__S.cerevisiaeApr11_800141.bed


title: 1686_UC uninflamed sigmoid colon


title: S_72b12_4mo_b1_3


title: yFR999_srb10D_Spt16vsInput_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in srb10Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR999_srb10D_Spt16vsInput_rep1-2_S.cerevisiaeApr11_999171.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in srb10Δcells.
BED method:  The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalization = limma loess (subgrid)

extract_protocol:
IP protocol:  Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation. 600 μL of the chromatin sample was taken per immunoprecipitation (IP) and, when necessary, 6 μL (1%) were saved as Input sample. The following amount of antibody per IP was used: anti-Spt16 (a gift from T. Formosa, 1 μL). 50 μL of Dynabeads coated with Protein G (Thermo Fisher Scientific, 10004D) pre-coupled with the indicated antibody were added to the chromatin sample and incubated overnight at 4°C. Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 100 % EtOH. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.
Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation.
Cleanup protocol:  Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 70% ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.

tag: chip antibody

extract_protocol:
IP protocol:  none
Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation.
Cleanup protocol:  Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 70% ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.


title: 1688_UC uninflamed sigmoid colon


title: 2009_UC uninflamed sigmoid colon


title: S_72b12_2mo_b3_4


title: 2302_UC inflamed sigmoid colon


title: yFR999-srb10D_Rpb3vsInput_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in srb10Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR999-srb10D_Rpb3vsInput_rep1-2_S.cerevisiaeApr11_34421.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in srb10Δ cells.
BED method:  The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalization = limma loess (subgrid)

extract_protocol:
IP protocol:  Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation. 600 μL of the chromatin sample was taken per immunoprecipitation (IP) and, when necessary, 6 μL (1%) were saved as Input sample. The following amount of antibody per IP was used: anti-Rpb3 (Neoclone W0012, 3 μL). 50 μL of Dynabeads coated with Pan Mouse IgG antibodies (Thermo Fisher Scientific, 11042) pre-coupled with the indicated antibody were added to the chromatin sample and incubated overnight at 4°C. Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 100 % EtOH. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.
Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation.
Cleanup protocol:  Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 70% ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.

value: anti-Rpb3 (Neoclone W0012, 3 uL)


title: yFR999-srb10D_Rpb3vsInput_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in srb10Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR999-srb10D_Rpb3vsInput_rep1-2_S.cerevisiaeApr11_34421.bed


title: yFR999_srb10D_Spt16vsInput_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in srb10Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR999_srb10D_Spt16vsInput_rep1-2_S.cerevisiaeApr11_999171.bed


title: S_72b12_2mo_b3_3


title: 1714_UC uninflamed sigmoid colon


title: S_72b12_4mo_b1_1


title: 2302_UC uninflamed sigmoid colon


title: S_72b12_4mo_b1_2


title: yFR999_srb10D_Pob3vsInput_repl2

description:
Biological replicate 2 of 2. FACT (Pob3) occupancy by ChIP-chip in srb10Δ cells. Pob3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Pob3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR999_srb10D_Pob3vsInput_rep1-2_S.cerevisiaeApr11_374842.bed

data_processing:
BED description:  A genome browser-ready file for Pob3 occupancy by ChIP-chip (IP/Input) in srb10Δ cells.
BED method:  The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalization = limma loess (subgrid)

extract_protocol:
IP protocol:  Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation. 600 μL of the chromatin sample was taken per immunoprecipitation (IP) and, when necessary, 6 μL (1%) were saved as Input sample. The following amount of antibody per IP was used: anti-Pob3 (a gift from T. Formosa, 1 μL). 50 μL of Dynabeads coated with Protein G (Thermo Fisher Scientific, 10004D) pre-coupled with the indicated antibody were added to the chromatin sample and incubated overnight at 4°C. Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 100 % EtOH. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.
Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation.
Cleanup protocol:  Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 70% ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.

value: anti-Pob3 (a gift from T. Formosa, 1 uL)


title: 2503_UC inflamed sigmoid colon


title: 1714_UC inflamed sigmoid colon

value: Male


title: S_72b12_2mo_b3_1


title: 1821_UC inflamed sigmoid colon

value: pooled human reference RNA


title: yFR974_spt6-1004_Spt16vsInput_20180718_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in spt6-1004 temperature-sensitive cells switched to 37°C for 80 min. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_Spt16vsInput_20180718_rep1-2_S.cerevisiaeApr11_796888.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in spt6-1004 cells switched to 37°C for 80 min.
BED method:  The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalization = limma loess (subgrid)

growth_protocol: 50 mL of YPD (yeast extract-peptone-2% glucose, supplemented with 44 µM adenine) medium was inoculated at OD600 0.1 from an overnight preculture in the same medium and allowed to grow to an OD600 of 0.5. Cells were then transferred to 37°C for 80 min before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 30 min and quenched with 125 mM glycine. Crosslinked cells were collected by centrifugation and washed twice with 1X TBS (20 mM Tris-HCl pH 7.5, 150 mM NaCl). Cell pellets were snap-freezed in liquid nitrogen and stored at -80°C.

treatment_protocol: switch to 37°C for 80 min

value: MAT{alpha}, his3{delta}200, leu2{delta}1, lys2-128{delta}, ura3-52, spt6-1004-FLAG


title: yFR974_spt6-1004_Rpb3vsInput_20180718_repl2

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in spt6-1004 temperature-sensitive cells switched to 37°C for 80 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_Rpb3vsInput_20180718_rep1-2_S.cerevisiaeApr11_22712.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in spt6-1004 cells switched to 37°C for 80 min.
BED method:  The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalization = limma loess (subgrid)

extract_protocol:
IP protocol:  Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation. 600 μL of the chromatin sample was taken per immunoprecipitation (IP) and, when necessary, 6 μL (1%) were saved as Input sample. The following amount of antibody per IP was used: anti-Rpb3 (BioLegend 665004, 1.5 μL). 50 μL of Dynabeads coated with Pan Mouse IgG antibodies (Thermo Fisher Scientific, 11042) pre-coupled with the indicated antibody were added to the chromatin sample and incubated overnight at 4°C. Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 100 % EtOH. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.
Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation.
Cleanup protocol:  Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 70% ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.


title: 1508_UC inflamed sigmoid colon

value: Inflamed

value: Colon


title: 1359_UC inflamed sigmoid colon


title: S_72b12_2mo_b3_2

value: iPSC-derived cerebral organoid


title: yFR974_spt6-1004_Spt16vsInput_20180718_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in spt6-1004 temperature-sensitive cells switched to 37°C for 80 min. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_Spt16vsInput_20180718_rep1-2_S.cerevisiaeApr11_796888.bed


title: yFR999_srb10D_Pob3vsInput_repl1

description:
Biological replicate 1 of 2. FACT (Pob3) occupancy by ChIP-chip in srb10Δ cells. Pob3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Pob3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR999_srb10D_Pob3vsInput_rep1-2_S.cerevisiaeApr11_374842.bed


title: 1816_UC uninflamed sigmoid colon


title: S_72b12_2mo_b2_3


title: 1821_UC uninflamed sigmoid colon


title: 1816_UC inflamed sigmoid colon


title: 1819_UC uninflamed sigmoid colon


title: S_72b12_2mo_b2_4


title: 1929_UC inflamed sigmoid colon


title: S_72b12_2mo_b2_1


title: S_72b12_2mo_b2_2


title: S_72b12_2mo_b1_4


title: S_72b12_2mo_b1_3


title: 1415_UC uninflamed sigmoid colon


title: yFR974_spt6-1004_Rpb3vsInput_20180718_repl1


title: S_72b12_2mo_b1_2


title: 1348_UC uninflamed sigmoid colon


title: 2104_UC uninflamed sigmoid colon


title: yFR974_spt6-1004_Pob3vsInput_20180718_repl1

description:
Biological replicate 1 of 2. FACT (Pob3) occupancy by ChIP-chip in spt6-1004 temperature-sensitive cells switched to 37°C for 80 min. Pob3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Pob3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_Pob3vsInput_20180718_rep1-2_S.cerevisiaeApr11_604966.bed

data_processing:
BED description:  A genome browser-ready file for Pob3 occupancy by ChIP-chip (IP/Input) in spt6-1004 cells switched to 37°C for 80 min.
BED method:  The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalization = limma loess (subgrid)


title: 1415_UC inflamed sigmoid colon


title: 1505_UC inflamed sigmoid colon


title: 1414_UC uninflamed sigmoid colon


title: S_72b12_2mo_b1_1


title: yFR974_spt6-1004_Pob3vsInput_20180718_repl2

description:
Biological replicate 2 of 2. FACT (Pob3) occupancy by ChIP-chip in spt6-1004 temperature-sensitive cells switched to 37°C for 80 min. Pob3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Pob3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_Pob3vsInput_20180718_rep1-2_S.cerevisiaeApr11_604966.bed


title: 1328_UC uninflamed sigmoid colon

value: Female


title: yFR972_WT_Spt16vsInput_20180718_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells switched to 37°C for 80 min. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR972_WT_Spt16vsInput_20180718_rep1-2_S.cerevisiaeApr11_219494.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in WT cells switched to 37°C for 80 min.
BED method:  The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalization = limma loess (subgrid)

value: MATa, leu2{delta}1, lys2-128{delta}, trp1{delta} 63, ura3-52


title: 2104_UC inflamed sigmoid colon


title: yFR972_WT_Pob3vsInput_20180718_repl2

description:
Biological replicate 2 of 2. FACT (Pob3) occupancy by ChIP-chip in WT cells switched to 37°C for 80 min. Pob3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Pob3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR972_WT_Pob3vsInput_20180718_rep1-2_S.cerevisiaeApr11_476371.bed

data_processing:
BED description:  A genome browser-ready file for Pob3 occupancy by ChIP-chip (IP/Input) in WT cells switched to 37°C for 80 min.
BED method:  The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalization = limma loess (subgrid)


title: 1904_UC inflamed sigmoid colon


title: yFR972_WT_Rpb3vsInput_20180718_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT cells switched to 37°C for 80 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR972_WT_Rpb3vsInput_20180718_rep1-2_S.cerevisiaeApr11_837027.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in WT cells switched to 37°C for 80 min.
BED method:  The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalization = limma loess (subgrid)


title: S_72a01_6mo_b3_4


title: 1349_UC inflamed sigmoid colon


title: 1718_UC uninflamed sigmoid colon


title: yFR972_WT_Rpb3vsInput_20180718_repl2


title: yFR930-chd1D_Spt16vsInput_20190519_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in chd1Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR930-chd1D_Spt16vsInput_20190519_rep1-2_S.cerevisiaeApr11_469822.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in chd1Δcells.
BED method:  The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalization = limma loess (subgrid)


title: 1328_UC inflamed sigmoid colon


title: 1904_UC uninflamed sigmoid colon


title: 1820_UC inflamed sigmoid colon


title: yFR972_WT_Spt16vsInput_20180718_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells switched to 37°C for 80 min. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR972_WT_Spt16vsInput_20180718_rep1-2_S.cerevisiaeApr11_219494.bed


title: 1908_UC inflamed sigmoid colon


title: 2501_UC inflamed sigmoid colon


title: 2008_UC uninflamed sigmoid colon


title: 2003_UC uninflamed sigmoid colon


title: yFR972_WT_Pob3vsInput_20180718_repl1

description:
Biological replicate 1 of 2. FACT (Pob3) occupancy by ChIP-chip in WT cells switched to 37°C for 80 min. Pob3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Pob3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR972_WT_Pob3vsInput_20180718_rep1-2_S.cerevisiaeApr11_476371.bed


title: S_72a01_6mo_b3_3


title: S_72a01_6mo_b3_2


title: S_72a01_6mo_b3_1


title: S_72a01_6mo_b2_4


title: S_72a01_6mo_b2_2


title: X1-800K_K4m3

city: Lexington

first: Elizabeth

last: Duncan

state: KY

address: 675 Rose St

department: Biology

institute: University of Kentucky

data_processing:
FASTQ files were aligned to dd_Smes_g4 using bowtie2 under default parameters.
Peaks were called with MACS2 under default parameters.
Genome_build: dd_Smes_g4
Supplementary_files_format_and_content: BED files representing reproducible peak locations

organism:
Drosophila melanogaster
Schmidtea mediterranea

source_name: X1 cells, S2 cells

growth_protocol: X1 planarian stem cells were isolated using a well-established protocol in the field in which animals were dissociated into a single cel suspension, stained with Hoechst 33342, then sorted by FACS; the X1 gate is set in comparison to the profile of Hoechst stained cells from lethally iradiated worms, in which no dividing stem cells remain.

extract_protocol:
chromatin was solubilized to mononucleosomes with Micrococcal nuclease and histone-DNA particles were precipitated with antibody.
DNAseq libraries were   made using an optimized protocol with reagents from the Illumina TruSeq RNA kit

tag: cell type

value: S. mediterannea stem cells (X1 cells)

value: Drosophila S2 cells

value: H3K4me3 (Millipore, #07-473)


title: S_72a01_6mo_b2_1


title: S_72a01_6mo_b2_3


title: S_72a01_6mo_b1_4


title: yFR930-chd1D_Spt16vsInput_20190519_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in chd1Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR930-chd1D_Spt16vsInput_20190519_rep1-2_S.cerevisiaeApr11_469822.bed

value: anti-Spt16 (a gift from T. Formosa, 1 uL)


title: 1339_UC inflamed sigmoid colon

value: not determined


title: S_72a01_6mo_b1_3


title: 1679_UC inflamed sigmoid colon

value: Ulcerative colitis


title: 1416_UC uninflamed sigmoid colon

value: Uninflamed


title: 1339_UC uninflamed sigmoid colon


title: 1506_UC inflamed sigmoid colon


title: X1-800K_input


title: yFR930_chd1D_Rpb3vsInput_20150711_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in chd1Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR930_chd1D_Rpb3vsInput_20150711_rep1-2_S.cerevisiaeApr11_732197.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in chd1Δ cells.
BED method:  The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalization = limma loess (subgrid)

value: anti-Rpb3 (Neoclone W0012, 3 uL)