title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_F10_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_D2_AD012_indexed

status: Public on Aug 24 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: Sex

value: male

tag: brain region

value: MOs

tag: age

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_D2_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_D2_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_D1_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_D1_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_D1_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_D8_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_D8_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_D8_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_D12_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_E10_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_D11_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_D12_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_D10_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_D11_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_D10_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_D10_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_D11_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_D12_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_C9_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_C9_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_C9_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_D2_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_C7_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_C8_AD012_indexed


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title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_C8_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_D11_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_C4_AD012_indexed


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title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_C3_AD012_indexed


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title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_B8_AD012_indexed


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title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_B1_AD008_indexed


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title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_B11_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_B11_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_B11_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_B10_AD010_indexed


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title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_B10_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A9_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_B4_AD008_indexed


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title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A8_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A8_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A8_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A6_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A5_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A6_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A7_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A7_AD007_indexed


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title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A5_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A3_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_B10_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A12_AD012_indexed


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title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A12_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A11_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A2_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A7_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A2_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A11_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A1_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A11_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A11_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A1_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A10_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A1_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A10_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A3_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A2_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A4_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C6_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_H9_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F3_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_H9_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_H9_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_H9_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_H8_AD006_indexed


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title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_H7_AD006_indexed


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title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A7_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A4_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A3_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A2_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A4_AD001_indexed


title: Patient_7197

type: RNA

city: Buenos Aires

first: Juan

middle: Martín

last: Sendoya

state: Buenos Aires

address: Avenida Patricias Argentinas 435

department: Laboratory of Molecular and Cellular Therapy

country: Argentina

institute: Fundación Instituto Leloir

hyb_protocol: Tumor RNA and a Universal Human Reference RNA (Stratagene) were amplified, differentially labeled (Tumor:Cy5, Reference:Cy3) and subsequently hybridized with Human Gene Expression v2 4x44K Microarrays using the Human Gene Expression v2 4x44K Microarray kit (Agilent), according to manufacturer instructions.

scan_protocol: The output was analyzed with Feature Extraction 11.5.1.1 software (Agilent Technologies)

data_processing: Additional quality control and scale normalization between arrays were performed using the R package Agi4x44.2c

molecule: total RNA

organism: Homo sapiens

source_name: Rectal tumor pre-treatment biopsy

extract_protocol: Baseline tumor biopsies were collected as part of the rectoscopy diagnostic procedure and were divided into two blocks: one block underwent snap-freezing with liquid nitrogen and the other was prepared as FFPE. The latter was analyzed for the presence of at least 60% adenocarcinoma with hematoxylin/eosin staining. The snap-frozen mirror biospecimen was processed for these molecular profilings. Cold ischemia times were strictly monitored and registered in order not to exceed 30 minutes from extraction to fixation (formalin or freezing). Total tumor RNA was extracted from each snap-frozen biopsy with Allprep DNA/RNA/miRNA Universal Kit (QIAGEN) according to the manufacturer’s instructions.  RNA was quality assessed and quantified using NanoDrop 2000 and Qubit Fluorometer’s High Sensitivity RNA Kit (Thermofisher Scientific). RNA integrity was also evaluated for RIN > 6 on a 2100 Bioanalyzer (Agilent).

value: M

tag: tissue

value: rectal cancer

tag: ptrg

tag: response

value: Poor

source_name: Stratagene Universal Human Reference RNA (740000)

tag: sample type

value: Reference RNA


title: Patient_7038

label_protocol: Tumor RNA and a Universal Human Reference RNA (Stratagene) were amplified, differentially labeled (Tumor:Cy5, Reference:Cy3) and subsequently hybridized with Human Gene Expression v2 4x44K Microarrays using the Human Gene Expression v2 4x44K Microarray kit (Agilent), according to manufacturer instructions.


title: Patient_9084

value: Good


title: Patient_8707

value: F


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A3_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A2_AD001_indexed


title: Patient_9184


title: Patient_9972


title: Patient_9111


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A12_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_D10_AD002_indexed


title: Patient_6918


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A5_AD002_indexed


title: Patient_3682


title: Patient_5269

value: Unresectable


title: Patient_3251


title: Patient_2726


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A1_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_D10_AD006_indexed


title: Patient_2541


title: Patient_7366


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A11_AD004_indexed


title: Patient_6599


title: Patient_5889


title: Patient_3660


title: Patient_3056


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A1_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A1_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_B10_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A12_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A2_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A11_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A1_AD006_indexed


title: Patient_1821


title: Patient_2314


title: Patient_65


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A11_AD006_indexed


title: Patient_426


title: Patient_1028


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A10_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A11_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H9_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H9_AD012_indexed


title: Patient_8659


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A10_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H9_AD007_indexed


title: Patient_8571


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H9_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H9_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H9_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H9_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H8_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_C4_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H9_AD002_indexed


title: Patient_6800


title: Patient_8777


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H8_AD006_indexed


title: Patient_4738


title: Patient_5019


title: Patient_2028


title: Patient_3095


title: Patient_1564


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H8_AD012_indexed


title: U266_1_IRF4

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: The University of York

data_processing:
Before aligning, reads were trimmed to remove adapters and low confidence regions using a python script. A 4 base sliding window was run along each read, if the average Q Phred score for a window was < 20 the read was trimmed at the window start, finally any match to adapter sequences were trimmed
Trimmed reads were aligned using Bowtie2 with the --very-senstive parameter.  The resultant SAM files were converted to BAM using Samtools with the quality filter set to 20 (i.e. -q 20)
Trimmed reads were aligned to GRCh38 (UCSC analysis set) using Bowtie2 (v2.3.5.1) with the --very-sensitive parameter. The resultant SAM files were converted to BAM using samtools (v1.9) with the quality filter set to 20 (-q 20). The BAM files were analysed for peaks using GEM (v3.4), with quality filter set to 1 (-q 1) and MACS2 (v2.1.2) with quality filter set to 0.05 (-q 0.05).
ChIP-seq quality was assessed by cross-correlation using the MaSC and Phantompeakqual programs.   Reads were extended to the length reported by MaSC, scaled to reads per million and converted to BigWig files, these were used for visualisation of the data
Genome_build: GRCh38
Supplementary_files_format_and_content: BED files (converted from GEM events)
Supplementary_files_format_and_content: BED files (converted from MACS2 peaks)
Supplementary_files_format_and_content: BigWig coverage files (extended to MaSC predicted frament length)

extract_protocol:
OCI-Ly3 and OCI-Ly10 were grown in IMDM with Glutamax™ (Life Technologies™), 10% HIFBS, 50µM betamercaptoethanol. Each batch of chromatin from each cell line were harvested from 2*10^7 cells. Batches were pooled together and distributed in aliquots. Individual CHIP were obtained from 4*10^6 cells.  H929 and U266 were grown in RPMI 1640, 10% HIFBS, 1% L-Glutamine. Each batch of chromatin were harvested from 2*10^7 cells. Batches were pooled together and distributed in aliquots. Individual CHIP were obtained from 4*10^6 cells.
Peripheral blood was obtained from healthy donors after informed consent. Mononuclear cells were isolated by Lymphoprep (Axis Shield) density gradient centrifugation. Total B-cells were isolated by negative selection with the Memory B-cell Isolation Kit (Miltenyi Biotec). Memory-enriched B cells fractions were isolated by negative selection following incubation of total, negatively selected B cell fractions with CD23 Biotin and anti-Biotin Microbeads (Miltenyi Biotec)
Cells were grown in 24 well plates in Iscove Modified Dulbecco Medium (IMDM) supplemented with Glutamax and 10% heat-inactivated fetal bovine serum (HIFBS, Invitrogen). This was supplementetd from Day 3 onwards with Hybridomax hybridoma growth supplement (11 µl/ml), Lipid Mixture 1, chemically defined and MEM Amino Acids solution (both at 1x).
B cells were cultured at 2.5 X 10^5/ml with IL-2 (20 U/ml), IL-21 (50 ng/ml), F(ab’)2 goat anti-human IgM & IgG (10 µg/ml) on γ-irradiated CD40L expressing L cells (6.25 X 10^4/well).
At day-3 cells were detached from the CD40L L-cell layer and reseeded at 1 X 10^5/ml in media supplemented with IL-2 (20 U/ml) and IL-21 (50 ng/ml).
For the G9Ai (small molecule inhibitor UNC0638) experiments, ABCs were treated at day-3 with UNC0638 inhibitor (2 µM). Cells were sampled at the indicated time points without further addition of inhibitor
ChIP-seq libraries were prepared using the MicroPlex Library Preparation™ kit (Diagenode) for ChIP, size selected using AMPure XP beads (Beckman Coulter) and run on an Illumina Hiseq 2500

tag: cell line

tag: cell type

value: Multiple myeloma cell line

tag: chip antibody


title: OCILY10_2_Input

value: Diffuse large B-cell lymphoma (DLBCL) - ABC cell-of-origin


title: OCILY10_1_Input


title: Patient_1790


title: Patient_1885


title: Patient_1803


title: OCILY10_2_IRF4


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H8_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H8_AD010_indexed


title: U266_1_Input


title: OCILY10_1_IRF4


title: Patient_434


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H7_AD008_indexed


title: Patient_1722


title: Patient_1870


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H7_AD001_indexed


title: OCILY3_2_Input


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H7_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H7_AD004_indexed


title: OCILY3_1_Input


title: H929_1_Input


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H6_AD010_indexed


title: Day3BC_2_Input_Std

source_name: Peripheral blood

extract_protocol:
OCI-Ly3 and OCI-Ly10 were grown in IMDM with Glutamax™ (Life Technologies™), 10% HIFBS, 50µM betamercaptoethanol. Each batch of chromatin from each cell line were harvested from 2*10^7 cells. Batches were pooled together and distributed in aliquots. Individual CHIP were obtained from 4*10^6 cells.  H929 and U266 were grown in RPMI 1640, 10% HIFBS, 1% L-Glutamine. Each batch of chromatin were harvested from 2*10^7 cells. Batches were pooled together and distributed in aliquots. Individual CHIP were obtained from 4*10^6 cells.
b-cell isolation: Peripheral blood was obtained from healthy donors after informed consent. Mononuclear cells were isolated by Lymphoprep (Axis Shield) density gradient centrifugation. Total B-cells were isolated by negative selection with the Memory B-cell Isolation Kit (Miltenyi Biotec). Memory-enriched B cells fractions were isolated by negative selection following incubation of total, negatively selected B cell fractions with CD23 Biotin and anti-Biotin Microbeads (Miltenyi Biotec)
culture conditions general: Cells were grown in 24 well plates in Iscove Modified Dulbecco Medium (IMDM) supplemented with Glutamax and 10% heat-inactivated fetal bovine serum (HIFBS, Invitrogen). This was supplementetd from Day 3 onwards with Hybridomax hybridoma growth supplement (11 µl/ml), Lipid Mixture 1, chemically defined and MEM Amino Acids solution (both at 1x).
culture conditions (day 0--3): B cells were cultured at 2.5 X 10^5/ml with IL-2 (20 U/ml), IL-21 (50 ng/ml), F(ab’)2 goat anti-human IgM & IgG (10 µg/ml) on γ-irradiated CD40L expressing L cells (6.25 X 10^4/well).
culture conditions (day 3--6): At day-3 cells were detached from the CD40L L-cell layer and reseeded at 1 X 10^5/ml in media supplemented with IL-2 (20 U/ml) and IL-21 (50 ng/ml).
culture conditions G9Ai: For the G9Ai (small molecule inhibitor UNC0638) experiments, ABCs were treated at day-3 with UNC0638 inhibitor (2 µM). Cells were sampled at the indicated time points without further addition of inhibitor
ChIP-seq libraries were prepared using the MicroPlex Library Preparation™ kit (Diagenode) for ChIP, size selected using AMPure XP beads (Beckman Coulter) and run on an Illumina Hiseq 2500

value: Day3 B-cell


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H7_AD006_indexed


title: OCILY3_1_IRF4


title: H929_1_IRF4


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H7_AD010_indexed


title: Day3BC_2_IRF4_Std


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H6_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H6_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H7_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H6_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H6_AD004_indexed


title: Day3BC_1_Input_Std


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H5_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H5_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H6_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H6_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H6_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H5_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H5_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H4_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H5_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H5_AD001_indexed


title: Group2_RRBS_30

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then processed using the bowtie2 sequence analysis programs. Reads were mapped to the ensembl reference human genome.
To analyze the sequence data, a reference genome is created that contains only the 36 base pairs adjacent to every MspI site and every C in those sequences is changed to T. A converted sequence read file is then created by changing each C in the original sequence reads to a T. The converted sequence reads are aligned to the converted reference genome, and only reads that map uniquely to the reference genome are kept. Once reads are aligned the percent methylation is calculated for each CpG using the original sequence reads. The percent methylation and number of reads is reported for each CpG.
Methylation percentage for each CpG sites were calcualted by methylKit
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include rlogTransformed values for each sample.

source_name: sural nerve

extract_protocol:
Tissues [sural nerve (flash frozen on dry ice, and DNA/RNA was harvested using Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA and RNA quantity was assessed using a Qubit fluorometer, and the quality was evaluated using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #s RS‐122‐2001, RS‐122‐2002; Illumina, San Diego, CA, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
Briefly, DNA was digested with the MspI restriction enzyme and purified using phenol:chloroform extraction and ethanol precipitation, blunt-end digested, phosphorylated, and ligated into an adapter duplex with methylated cytosines. The ligated fragments were cleaned and size selected by an agarose gel. Bisulfite conversion was performed for selected fragments followed by PCR amplification and cleanup using AMPure XP beads. The Qubit assay and Agilent’s High Sensitivity D1000 assay were used to quantify the libraries.

value: sural nerve

value: Intermediate


title: Group2_RRBS_28

value: Regenerator


title: Group2_RRBS_29


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H4_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H4_AD008_indexed


title: Group2_RRBS_31

value: Degenerator


title: Group2_RRBS_27


title: Group2_RRBS_32


title: Day3BC_1_IRF4_Std


title: Group2_RRBS_26


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H5_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H4_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H3_AD007_indexed


title: Patient_7326


title: Group2_RRBS_24


title: Group2_RRBS_23


title: Group2_RRBS_25


title: Group2_RRBS_22


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H4_AD002_indexed


title: Group2_RRBS_20


title: Group2_RRBS_21


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H3_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H3_AD010_indexed


title: Group2_RRBS_19


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H3_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H5_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H3_AD004_indexed


title: Group2_RRBS_18


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H2_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H4_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H3_AD006_indexed


title: Group2_RRBS_14


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H4_AD006_indexed


title: Group2_RRBS_15


title: Group2_RRBS_17


title: Group2_RRBS_16


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H3_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H2_AD006_indexed


title: Group2_RRBS_12


title: Group2_RRBS_13


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H2_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H2_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H2_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H3_AD002_indexed


title: Group2_RRBS_9


title: Group2_RRBS_10


title: Group2_RRBS_11


title: Group2_RRBS_8


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H2_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H2_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H2_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H1_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H11_AD004_indexed


title: Group2_RRBS_5


title: Group2_RRBS_7


title: Group2_RRBS_2


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H1_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H11_AD006_indexed


title: Group2_RRBS_3


title: Group2_RRBS_1


title: OCILY3_2_IRF4


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H1_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H1_AD002_indexed


title: Group1_RRBS_20


title: Group1_RRBS_21


title: Group1_RRBS_19


title: Group2_RRBS_6


title: Group1_RRBS_16


title: Group1_RRBS_17


title: Group1_RRBS_15


title: Group1_RRBS_18


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H12_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H12_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H12_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H1_AD012_indexed


title: Group2_RRBS_4


title: Group1_RRBS_13


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H11_AD008_indexed


title: Group1_RRBS_12


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H1_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H11_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H11_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H11_AD001_indexed


title: Group1_RRBS_9


title: Group1_RRBS_10


title: Group1_RRBS_11


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H12_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H1_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H11_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H10_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H11_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H10_AD012_indexed


title: Group1_RRBS_7


title: Group1_RRBS_14


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_3_CEMBA180306_2B_5_A10_AD002_indexed


title: Group1_RRBS_5


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H10_AD008_indexed


title: Group1_RRBS_6


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G9_AD010_indexed


title: Group1_RRBS_4


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H10_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G9_AD004_indexed


title: Group1_RRBS_2


title: Group1_RRBS_1


title: Group1_RRBS_3


title: Group3_24

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then processed using the Hisat2 sequence alignment programs. Reads were mapped to the hg19 genome reference to identify transcripts.
Count value were calculated by featureCount
Normalized by DESeq2 with rlogTransformed
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include rlogTransformed values for each Sample ...

extract_protocol:
Tissues [sural nerve (flash frozen on dry ice, and DNA/RNA was harvested using Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA and RNA quantity was assessed using a Qubit fluorometer, and the quality was evaluated using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #s RS‐122‐2001, RS‐122‐2002; Illumina, San Diego, CA, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Group3_23


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H10_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G9_AD007_indexed


title: Group3_22


title: Group3_20


title: Group3_21


title: Group1_RRBS_8


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G9_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G9_AD001_indexed


title: Group3_19


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G9_AD008_indexed


title: Group3_18


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G9_AD002_indexed


title: Group3_17


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G8_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H10_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G8_AD007_indexed


title: Group3_13


title: Group3_12


title: Group3_11


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G9_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G8_AD001_indexed


title: Group3_14


title: Group3_10


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G8_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G7_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H10_AD001_indexed


title: Group3_16


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G7_AD012_indexed


title: Group3_9


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G7_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G7_AD008_indexed


title: Group3_7


title: Group3_8


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G7_AD007_indexed


title: Group3_6


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G8_AD004_indexed


title: Group3_5


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G7_AD002_indexed


title: Group3_4


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G8_AD010_indexed


title: Group3_15


title: Group3_3


title: Group3_2


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G7_AD001_indexed


title: Group3_1


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G6_AD008_indexed


title: Group2_32


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G6_AD002_indexed


title: Group2_30


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G6_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G6_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G6_AD001_indexed


title: Group2_28


title: Group2_29


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G6_AD007_indexed


title: Group2_26


title: Group2_27


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G4_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G4_AD004_indexed


title: Group2_25


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G6_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G7_AD006_indexed


title: Group2_24


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G4_AD010_indexed


title: Group2_23


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G5_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G5_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G4_AD001_indexed


title: Group2_20


title: Group2_21


title: Group2_22


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G6_AD004_indexed


title: Group2_31


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G5_AD012_indexed


title: Group2_18


title: Group2_16


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G4_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G5_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G4_AD002_indexed


title: Group2_15


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G5_AD004_indexed


title: Group2_14


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G4_AD008_indexed


title: Group2_13


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G5_AD002_indexed


title: Group2_11


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G5_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G4_AD007_indexed


title: Group2_10


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G3_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G3_AD010_indexed


title: Group2_8


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G2_AD004_indexed


title: Group2_9


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G3_AD007_indexed


title: Group2_19


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G2_AD006_indexed


title: Group2_6


title: Group2_7


title: Group2_5


title: Group2_17


title: Group2_4


title: Group2_2


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G2_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G5_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G2_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G12_AD004_indexed


title: Group2_3


title: Group2_12


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G3_AD002_indexed


title: Group2_1


title: Group1_21


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G2_AD012_indexed


title: Group1_19


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G2_AD007_indexed


title: Group1_20


title: Group1_18


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G3_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G3_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G2_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G1_AD012_indexed


title: Group1_14


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G1_AD010_indexed


title: Group1_17


title: Group1_16


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G3_AD006_indexed


title: Group1_15


title: Group1_13


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G1_AD007_indexed


title: Group1_12


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G3_AD008_indexed


title: Group1_11


title: Group1_10


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G12_AD007_indexed


title: Group1_7


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G12_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G1_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G2_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G1_AD002_indexed


title: Group1_8


title: Group1_6


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G1_AD004_indexed


title: Group1_4


title: Group1_5


title: Group1_9


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G1_AD006_indexed


title: Group1_3


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G1_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G12_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G12_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G11_AD004_indexed


title: Group1_2


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G11_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G11_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G11_AD008_indexed


title: Day6PB-memB_Input_G9Ai

value: Day6 Plasmablast (memory B cell, CD23 negatively selected)

tag: treatment


title: Day6PB-memB_H3K27Ac_G9Ai


title: Day6PB-memB_H3K4me3_G9Ai


title: Day6PB-memB_BLIMP1_G9Ai


title: Day6PB-memB_Input_Std


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G11_AD006_indexed

value: male


title: Day6PB-memB_IRF4_Std


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G11_AD001_indexed

value: MOs


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G11_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_H10_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G11_AD002_indexed


title: Day6PB-memB_H3K4me3_Std


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G10_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G10_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G10_AD007_indexed


title: Day6PB-memB_BLIMP1_Std


title: Group1_1


title: Day6PB-B_Input_Std

value: Day6 Plasmablast


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G10_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G10_AD004_indexed


title: Day6PB-B_XBP1_Std

value: Biolegend, 619502


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F9_AD008_indexed


title: case3

city: Potsdam

first: Alexander

last: Bartholomaeus

address: Telegrafenberg C

department: Department 3 Geochemie

country: Germany

institute: Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences

data_processing:
Quality trimming and adapter cutting using Cutadapt, version 2.5, parameters: -m 50 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Genome read mapping using bowtie2, version 2.3.4.1, parameters: -I 50 -X 1000 -q
Read counting using bedtools, version 2.26.0, parameter: -s
Genome_build: Homo sapiens Ensemble build GRCh38.p12
Supplementary_files_format_and_content: Read counts per gene (Ensemble  GRCh38.97)

source_name: Primary human dermal fibroblast

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle medium (DMEM; ThermoFisher) supplemented with 10% fetal bovine serum (FBS; GE Healthcare) and penicillin-streptomycin (100 U/mL and 100 mg/mL, respectively; ThermoFisher) under 5% CO2 and at 37°C.

extract_protocol:
Total RNA was extracted with the RNAeasy mini kit (Qiagen) from primary fibroblasts that were in all in the same passage, passage 8
Library preparation and transcriptome sequencing was performed at Novogene. Briefly, a total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Primary human dermal fibroblast

tag: passages

value: passage 8

tag: genotype/variation

value: AGO mutation


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G10_AD008_indexed


title: Day6PB-memB_CTCF_Std


title: case14


title: case2


title: control4

value: control


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F9_AD007_indexed


title: Day6PB-memB_H3K27Ac_Std


title: control3


title: control2


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G10_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F9_AD006_indexed


title: control1


title: control5


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F8_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F9_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F9_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F9_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F8_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F9_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F9_AD002_indexed


title: SW480_capture_bisulphite_sequencing

city: Basel

first: Alejandro

last: Reyes

address: Fabrikstrasse 22

department: Data Sciences

country: Switzerland

institute: Novartis Institutes For BioMedical Research

data_processing:
BSMAP version 2.74 (Xi et al., 2009) was used both to map the sequenced reads to the reference genome (hg19) and to calculate the fraction of methylated CpGs for each CpG across the genome. Data was further analyzed within the framework of the bsseq Bioconductor package (Hansen et al, 2012).
processed data files format and content: Methylation data format (.cpg). As described by the bsmap manual. Output format: tab delimited txt file with the following columns: (1) chromorome, (2) coordinate (1-based), (3) strand, (4) sequence context (2nt upstream to 2nt downstream in Watson strand direction), (5) methylation ratio, (6) number of converted and unconverted Cs covering this locus (7) number of unconverted Cs covering this locus, (8) lower bound of 95% confidence interval of methylation ratio (9) upper bound of 95% confidence interval of methylation ratio.
Genome_build: hg19

source_name: Cell line

extract_protocol: Total genomic DNA was isolated using the DNAeasy Blood & Tissue Kit (Qiagen) and sheared using the Covaris LE220. Ampure XP beads (Agencourt) were then used to size select gDNA fragments within 150-320bp, and sheared distribution was verified via BioAnalyzer (Agilient) prior to continuation. Sheared genomic DNA (1 ug) was then generated into a sequencing library via end repair, 3‚Äô A base tailing (KAPA Hyper Prep Kit #KK8502) and sequencing adapter ligation (Roche SeqCap Epi Enrichment System). Post-ligation clean-up was performed using Ampure XP beads. Following bead clean-up, DNA library was then bisulfite converted using the EZ DNA Methylation-Lightning Kit (Zymo Research) and amplified via PCR using KAPA HiFi U+ HotStart ReadyMix (KAPA #KK2800). Equal concentration of each bisulfite-converted library was then combined in sets of either three or four libraries/per pool along with SeqCap Epi universal & indexing oligos and bisulfite capture enhancer (SeqCap Epi Accessory Kit). Each pool was subsequently lyophilized using TOMY Micro-Vac (MV100) and resuspended in hybridization buffer (SeqCap Epi Hybridization and Wash Kit) prior to being hybridized to SeqCap Epi Probe Pool (Roche) for 72 hours at 47C in a thermocycler with a heated lid at 57C. Following the 72-hour incubation, captured bisulfite-converted libraries were recovered (SeqCap Pure Capture Bead Kit) at 47C in a thermocycler for 45 minutes, with intermediate vortexing every 15 minutes.  Capture beads were then washed (SeqCap Hybridization and Wash Kit) in a 47C water bath at room temperature, respectively. Captured bisulfite-converted libraries were amplified via PCR (SeqCap Epi Accessory Kit).  Libraries were sequenced with 10% PhiX spike-in as 100-base paired end reads on the HiSeq2500 in rapid run mode.

value: SW480 Cell line

tag: biological sample


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F8_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F8_AD006_indexed


title: MGH8416_capture_bisulphite_sequencing

source_name: Colon tumor

value: Colon tumor


title: RKO_capture_bisulphite_sequencing

value: RKO Cell line

value: RKO


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F8_AD004_indexed


title: MGH7476_capture_bisulphite_sequencing


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F8_AD010_indexed


title: MGH5328_capture_bisulphite_sequencing


title: MGH4963_capture_bisulphite_sequencing


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F7_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F8_AD001_indexed


title: MGH3535_capture_bisulphite_sequencing


title: MGH29208_capture_bisulphite_sequencing


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F7_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F7_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F7_AD012_indexed


title: MGH29328_capture_bisulphite_sequencing


title: MGH28891_capture_bisulphite_sequencing


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F6_AD007_indexed


title: MGH12299_capture_bisulphite_sequencing


title: MGH1904_capture_bisulphite_sequencing


title: MGH2231_capture_bisulphite_sequencing


title: LS174T_capture_bisulphite_sequencing

value: LS174T Cell line


title: HCT116-DMSO-7d-1_capture_bisulphite_sequencing

value: HCT116 Cell line

value: 5-azacytidine was obtained from SelleckChem (S1782) and HCT116 cells were cultured in the presence of 5 uM or 1:2000 DMSO control.  Cells were plated in media containing 5-aza or DMSO and harvested at 24 h and 7 days.  Media was refreshed with fresh 5-aza every 2nd day for the 7 day culture.


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F6_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F6_AD012_indexed


title: HCT116-DMSO-24h-4_capture_bisulphite_sequencing


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F5_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F6_AD004_indexed


title: HCT116-DMSO-0h-2_capture_bisulphite_sequencing


title: HCT116-DMSO-24h-3_capture_bisulphite_sequencing


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F5_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F6_AD002_indexed


title: HCT116-5AZA-7d-1_capture_bisulphite_sequencing


title: HCT116_capture_bisulphite_sequencing


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F5_AD010_indexed


title: MGH2834_capture_bisulphite_sequencing


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F5_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F6_AD006_indexed


title: HCT116-5AZA-24h-4_capture_bisulphite_sequencing


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F4_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F5_AD007_indexed


title: HCT116-5AZA-24h-3_capture_bisulphite_sequencing


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F7_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F4_AD012_indexed


title: FHC_capture_bisulphite_sequencing

value: FHC Cell line

value: FHC


title: HCT116-5AZA-0h-2_capture_bisulphite_sequencing


title: BRD3514_capture_bisulphite_sequencing


title: BRD3462_capture_bisulphite_sequencing


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F4_AD008_indexed

value: male


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F7_AD002_indexed

value: MOs


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F4_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F5_AD006_indexed


title: BRD3412_capture_bisulphite_sequencing


title: BRD3202_capture_bisulphite_sequencing


title: BRD3378_capture_bisulphite_sequencing


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F7_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F5_AD001_indexed


title: BRD3195_capture_bisulphite_sequencing


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F3_AD010_indexed


title: BRD3187N_capture_bisulphite_sequencing

source_name: Normal colon

value: Normal colon


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F5_AD002_indexed


title: BRD3187_capture_bisulphite_sequencing


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F4_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F4_AD006_indexed


title: BRD3179_capture_bisulphite_sequencing


title: BRD3179N_capture_bisulphite_sequencing


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F4_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F3_AD012_indexed


title: BRD3174_capture_bisulphite_sequencing


title: BRD3170N_capture_bisulphite_sequencing


title: BRD3170_capture_bisulphite_sequencing


title: BRD3162_capture_bisulphite_sequencing


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F3_AD007_indexed


title: BRD3149_capture_bisulphite_sequencing


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F2_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F3_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F4_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F2_AD012_indexed


title: BRD3120_capture_bisulphite_sequencing


title: BRD3129_capture_bisulphite_sequencing


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F2_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F2_AD004_indexed


title: SW480-2_HiC

data_processing:
Data were controlled for quality, mapped to the reference genome (hg19) and converted into interaction matrices using HiC-Pro (Servant et al., 2015). Within sample normalization was performed using the Iterative Correction and Eigenvector decomposition (ICE) method (Imakaev et al., 2012).
processed data files format and content: HiC Interaction matrix files (.matrix). As provided by the HiCPro pipeline. A matrix, stored as standard triplet sparse format (i.e. list format). Based on the observation that a contact map is symmetric and usually sparse, only non-zero values are stored for half of the matrix.
processed data files format and content: HiC all valid interaction read pairs (allValidPairs). As provided by the HiCPro pipeline. Columns are: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size.
Genome_build: hg19

extract_protocol: In situ HiC was performed as described previously (Rao et al., 2014).  In brief, crosslinked cells or tumor were thawed on ice in HiC lysis buffer. Tissue samples were mechanically disrupted with the Biomasher tissue grinder (Kimble Chase).  Tissue and cell line samples were permeabilized in 0.5% SDS at 37 degrees, quenched with Triton X100 and chromatin was digested with 100-200U MboI at 37 degrees overnight.  Nuclei were then pelleted, ends were marked with biotin-14-dATP (ThermoFisher 19524016) and chromatin was ligated for 5 hours by T4 DNA ligase (M0202).  Samples were treated with proteinase K at 55 degrees for 30 minutes and cross-links were reversed at 68 degrees overnight.  DNA was ethanol precipitated and sheared on a Covaris LE220 as per Rao et al., 2014.  DNA was cleaned up via AMPure XP beads (Beckman Coulter, A63881) and quantified by Qubit dsDNA High Sensitivity Assay (Life Technologies, Q32854).  Samples were bound to Dynabeads MyOne Streptavidin T1 beads (Life technologies, 65602) and washed.  End repair, dATP attachment and adapter ligation was performed.  Final PCR amplification was performed using barcoded sequencing primers and PCR.  Libraries were purified using AMPure XP beads and sequenced on either a NextSeq500 (150 cycle kit) or the HiSeq2500 (high output; 200 cycle kit).


title: RKO-2_HiC


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F1_AD004_indexed


title: MGH8416_HiC


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F2_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F3_AD002_indexed


title: MGH5328_HiC


title: MGH2834_HiC


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F2_AD006_indexed


title: MGH2231-sb_HiC


title: MGH1904-sb_HiC


title: MGH1904_HiC


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F1_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F1_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F1_AD007_indexed


title: LS174T-2_HiC


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_G10_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F1_AD012_indexed


title: MGH8416_HiChIP

data_processing:
Library strategy: HiChIP
Data were controlled for quality, mapped to the reference genome (hg19) and converted into interaction matrices using the HiC-Pro pipeline (Servant et al., 2015). Chromatin loops were called using the hichipper pipeline (Lareau et al. 2018) and diffloop (Lareau et al. 2017) was used for quality control, statistical inference of between-group differences and annotation of chromatin loops.
processed data files format and content: HiChIP loop contacts (.bedpe). As provided by hichipper. Intrachromosomal looping between anchor loci where loops meet min/max distance requirements.
processed data files format and content: HiC all valid interaction read pairs (allValidPairs). As provided by the HiCPro pipeline. Columns are: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size.
Genome_build: hg19

extract_protocol: HiChip was performed as described previously (Mumbach et al., 2016).  Briefly, crosslinked samples were lysed in HiC lysis buffer and chromatin was permeabilized in 0.5% SDS at 63C for 10 minutes.  Chromatin was digested with MboI for 2 hours at 37C.  Overhangs were filled in and marked with Biotin-dATP (ThermoFisher 19524016), and ends were ligated with T4 DNA Ligase (NEB M0202) for 4 hours at room temperature.   Nuclei were pelleted and lysed and chromatin was sheared on the Covaris E220 with the following conditions: Fill level 5, Duty Cycle 5, PIP 140, Cycles/burst 200, Time 4 minutes.  Samples were clarified, diluted in ChIP dilution buffer and precleared with Protein G beads (Invitrogen 11205D) for 1 hour at 4C.  Samples were cleared on magnet and supernatant was added to antibody.  Chromatin was ChIP‚Äôd overnight at 4C with rotation.  Protein G beads were added and incubated for 2 hours at 4C with rotation.  Beads were washed with low salt, high salt and LiCl buffer.  Sample was eluted in ChIP elution buffer, treated with Proteinase K and crosslinks were reversed.  DNA was purified using the Zymo clean & concentrate kit (DCC-100).  Streptavidin M280 beads (Invitrogen 11205D) were washed and resuspended in 2x biotin binding buffer and DNA was bound for 15 minutes at room temperature.  Beads were washe and Tn5 fragmentation was carried out as per Mumbach et al.,2016, with dilutions of Tn5 to process low input samples.  Libraries were amplified using the Nextera DNA Library Prep kit (Illumina).  Material was cleaned up using Ampure XP beads.  Libraries were sequenced on NextSeq500 (150 cycle kit) or the HiSeq2500 (high output; 200 cycle kit).


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F1_AD010_indexed


title: MGH5328_HiChIP


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F3_AD001_indexed


title: SW480-1_HiC


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F1_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F2_AD010_indexed


title: RKO-1_HiC


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F12_AD006_indexed


title: MGH1904_HiChIP


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F1_AD002_indexed


title: BRD3187_HiChIP


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F2_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F12_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F12_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F12_AD004_indexed


title: LS174T-1_HiC


title: BRD3179_HiChIP


title: BRD3174_HiChIP


title: HCT116-DMSO-24h-2_HiC


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F12_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F3_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F12_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F12_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F11_AD004_indexed


title: HCT116-5AZA-24h-2_HiC


title: HCT116-5AZA-24h-1_HiC


title: HCT116-DMSO-24h-1_HiC


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F11_AD012_indexed


title: BRD3187N_HiChIP


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F11_AD007_indexed


title: FHC-2_HiC


title: HCT116-0h-2_HiC


title: HCT116-0h-1_HiC


title: BRD3179N_HiChIP


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F11_AD006_indexed


title: FHC-1_HiC


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F11_AD010_indexed


title: BRD3462N-sb_HiC


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F12_AD002_indexed


title: BRD3462N_HiC


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F11_AD001_indexed


title: BRD3162_HiChIP


title: BRD3409N-sb_HiC


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F10_AD010_indexed


title: BRD3328N_HiC


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F10_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F11_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F11_AD008_indexed


title: BRD3187_HiC


title: BRD3179_HiC


title: BRD3170N-sb_HiC


title: BRD3187N_HiC


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F10_AD008_indexed


title: BRD3179N_HiC


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F10_AD007_indexed


title: Calu-3, TS_NS_rep2

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

institute: University of Geneva Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads
Genome_build: GRCh38.80
Supplementary_files_format_and_content: Raw counts measurements

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Kit (Qiagen, Hombrechtikon, Switzerland)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: flagellin (1mg/ml) was added for 6h

value: airway epithelial cells

tag: cell origin

value: Lung adenocarcinoma

value: Submucosal glands

value: Non-stimulated

tag: genotype

value: CFTR knockdown culture


title: BRD3162N-sb_HiC


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E9_AD012_indexed

tag: Sex


title: Calu-3, TS_NS_rep1


title: BRD3162_HiC


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F10_AD002_indexed

tag: brain region


title: Calu-3, TS_Flag_rep1

value: flagellin-stimulated


title: Calu-3, TS_Flag_rep2


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E9_AD001_indexed

tag: age


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E9_AD010_indexed

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E9_AD007_indexed


title: Calu-3, Ctrl_NS_rep2

tag: tissue

value: control culture


title: Calu-3, Ctrl_NS_rep1


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E9_AD004_indexed


title: Calu-3, Ctrl_Flag_rep2


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F10_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E9_AD002_indexed


title: Calu-3, Ctrl_Flag_rep1


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F10_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E8_AD012_indexed