title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A2_ad004

value: AUD


title: p1_ftb_2

status: Public on Dec 02 2020

type: SRA

city: Rehovot

first: Hassan

last: Massalha

address: Herzl St 234

country: Israel

institute: Weizmann Institute of Science

description:
tumor_LCM
processed data file: tumor_LCM_UMItab.txt.gz

library_source: transcriptomic

data_processing:
bcl2fastq/2.15.0.4. Plate demultiplexing was provided to obtain plate specific reads in two fastq files (read 1 (R1, 66bp) and read 2 (R2, UMI 10bp)), MARSseq (R1: 66bp, R2: cell barcode 7bp + UMI 8bp)
Pooled data of scRNAseq were demultiplexed using plate specific barcode. Specific sequences for each cell were demultiplexed using well specific barcode (attached - 'marsseq_cell_barcodes.txt'). Samples analyzed with laser capture microdissection were demultiplexed using sample specific barcode (attached mcSCRBseq raw files are after demultiplexing step).
Genome_build: GRCh38.91
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: patient p1 fibrotic tumor border

extract_protocol:
Samples were collected from the surgery room immediately after isolation into sterile saline solution and processed in a sterile cabinet. Each sample was divided equally into two pieces as follows: (1) scRNAseq, samples stored in cold DMEM X1, supplemented with glutamine, (2) frozed section, sample were embedded into OCT block and kept on dry ice to be sectioned using LCM and mcSCRBseq for bulk sequencing
cell extract protocol: sample collection protocol: for scRNAseq, all samples were prepared according to Liver Dissociation Kit (GentelMAX, 130-105-807). Liberase Blendzyme3 recombinant collagenase (Roche Diagnostics) were added to the enzymatic cocktail in the first step in sample preperation protocol
for scRNAseq, 3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014). For bulk analysis, mcSCRBseq protocol was used (Bagnoli et al, Nat Commun. 2018)

tag: tissue

value: Liver

tag: pateint tumor type

value: cholangiocarcinoma

tag: sequencing protocol

value: mcSCRBseq


title: TAneg2

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

country: USA

institute: University of Michigan

description:
T=total, A=Adult, neg=negative control, biological repicate=3
Sample_122434

data_processing:
FastQC version 0.11.3 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) was used to verify sample quality.
The Tuxedo Suite was used to align reads to the reference transcriptome using TopHat (version 2.0.13) and Bowtie (version 2.2.1). Default parameter settings were used for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments, as well as “--no-coverage-search” and “--no-novel-juncs” to limit the read mapping to known transcripts.
FastQC was used for a second round of quality control (post-alignment), to ensure only high quality data
Two different methods were used for expression quantitation, normalization, and differential expression analysis
Cufflinks/CuffDiff (version 2.1.1) was one method used for expression quantitation and differential expression analysis. This analysis used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile –norm” for normalization of expression values.
HTSeq (version 0.6.1)   to count non-ambiguously mapped reads only. Data were pre-filtered to remove genes with 0 counts in all samples. DESeq2 (version 1.14.1) for normalization and differential expression
Genome_build: mm10
Supplementary_files_format_and_content: text file of raw counts

organism: Mus musculus

source_name: Preoptic area of the hypothalamus

growth_protocol: For positive controls, GnRH CRE (homozygote) male mice were bred to floxed-stop-floxed  L10a-GFP (homozygote) female mice to generate offspring that express GFP tagged ribosomal protein L10a in GnRH neurons. For negative controls mice were either wild-type, Floxed-L10a-GFP only or GnRH CRE only as indicated in the table above. Each biological replicate is a pool of preoptic punches from 3-4 mice.

extract_protocol:
RNA was isolated using the RNeasy Plus Micro Kit (Qiagen; 74004) with on column DNasing and assessed for quantity and quality using the Pico or Nano Chip (Agilent).
SMARTer v4 Ultra low (poly A), fragment length 120nt.

treatment_protocol: Preoptic Area hypothalamic punches were collected from female mice at either day 21 or in adulthood (70-150days). All adult female mice are in diestrus.

tag: genotype

value: GnRH CRE only

value: Preoptic area of the hypothalamus

tag: l10a gfp-expression

value: NEG

tag: age

value: Adult

tag: rna fraction

value: Depleted Supernatant


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A2_ad006

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT 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 INTACT
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

source_name: C57BL/6J P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: strain

value: brain

tag: source

tag: target

value: MOp

tag: gender

value: male


title: p3_tc_3

source_name: patient p3 tumor core

value: colorectal metastasis


title: p1_ftb_1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A1_ad012

value: RSP

value: female


title: TAneg1

description:
T=total, A=Adult, neg=negative control, biological repicate=2
Sample_122433


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A1_ad006


title: TApos1

description:
T=total, A=Adult, pos=positive control,  biological replicate 1
Sample_122432

value: GnRH CRE x Floxed L10a-GFP

value: POS

value: GnRH Depleted Supernatant


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A1_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A3_ad006

value: AUD


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A1_ad004


title: p1_ti_3

source_name: patient p1 tumor islets

value: Liver

value: cholangiocarcinoma


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A1_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A1_ad002


title: p1_ti_1

value: mcSCRBseq


title: TYneg2

description:
T=total, Y=Young, neg=negative control, biological repicate=2
Sample_122430

value: Wild Type

value: Preoptic area of the hypothalamus

value: Young


title: p1_ti_2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A12_ad010


title: p1_fz_3

source_name: patient p1 fibrotic zone


title: TYneg1

description:
T=total, Y=Young, neg=negative control, biological repicate=1
Sample_122429

value: NEG

value: Depleted Supernatant


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A1_ad001

value: brain

value: MOp


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A12_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A12_ad004


title: p1_fz_2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A12_ad002

value: male


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A2_ad008

value: RSP


title: wildtype 17.5hpf myeloid progenitors

city: New York

first: Kelly

middle: Madigan

last: Banks

state: NY

address: 1300 York Ave, LC711

department: Surgery

institute: Weill Cornell Medicine

data_processing:
sequence data demultiplexed and converted to FASTQ files using the Illumina bcl2fastq software.
flexbar to remove adapter sequences
bismark to align reads to danio rerio 10 genome
methylKit in R for methylation calling and comparison between samples
Genome_build: danio rerio 10
Supplementary_files_format_and_content: Excel file with hyperDMRs with increased methylation in Tet23 2dpf vs WT 2dpf
Supplementary_files_format_and_content: Aligned Methylation Levels

organism: Danio rerio

source_name: zebrafish embryos, myeloid progenitors

extract_protocol:
Dneasy DNA extraction
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4354670/
Standard Next Gen Sequencing Library Prep

value: wildtype

tag: cell type

value: myeloid progenitors

value: embryos

tag: developmental stage


title: p1_fz_1


title: tet2/3DM 2dpf neutrophils

source_name: zebrafish embryos, neutrophils

value: neutrophils


title: TYneg3

description:
T=total, Y=Young, neg=negative control, biological repicate=3
Sample_122431

value: Floxed L10a-GFP only


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A11_ad002

value: AUD


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A12_ad001


title: p1_tc_3

source_name: patient p1 tumor core

value: Liver

value: cholangiocarcinoma


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A10_ad012

value: female


title: wildtype 2dpf neutrophils


title: p1_tc_2

value: mcSCRBseq


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A10_ad001


title: input_H3K9me2_ChIP-Seq_O.punctata_60d

city: Beijing

first: Lei

last: Li

state: Beijing

address: 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China

country: China

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

description: input H3K9me2 ChIP-Seq O.punctata 60d

data_processing:
Typically 16-25 million read pairs for each library were obtained after removal of adaptor and low quality reads by flexbar2.5.
Clean reads were then mapped to genomes by Bowtie with default parameters (-v 0 –m 1). For repressive marks (H3K9me2 and H3K27me), we simply let Bowtie to randomly choose multi-hit positions when reads align to repeat-rich regions (-v 0 –M1 --best).
Since a single nucleosome often occupies about 147bp DNA, we linked mapped read pairs into single end reads for all ChIP libraries.
The resulting bed file was then used to call signal enrichment peaks by MACS2 and at the same time a genome wide signal density file was generated by genomeCoverageBed. The final peaks and density results were used for downstream qualitative and quantitative analysis.
We developed a pipeline to simultaneously visualize the comparative genomic features and the chromatin state.
Genome_build: We downloaded and used the rice genome version 6.1 from the MSU official ftp.  Four IOMAP (International Oryza Map Alignment Project) genomes, Oryza glaberrima, Oryza punctata, Oryza brachyantha RS2, Leersia perrieri and the sorgJGI2.0 were applied for bowtie mapping.

organism: Oryza punctata

source_name: tillering stage plant

growth_protocol: green-house plant

extract_protocol:
Sixty-day fresh above-ground tissues were collected at the tillering stage for O. sativa vg. japonica, O. glaberrima, O. punctata, O. brachyantha, L. perrieri, and S. bicolor. Two-week fresh above-ground tissues at the seedling stage were also collected for O. sativa and O. brachyantha. ChIP experiments were performed as described in Gendrel et al. 2005 with minor modification. Briefly, 4g (for seedling stage) or 8g (for tillering stage) tissue were fine grounded in liquid nitrogen, followed by 3% formaldehyde fixation step. Nucleus were extracted and chromatin was sonicated into 300-500bp fragments in Bioruptor (Diagenode). Since each antibody has its own concentration and binding efficiency, we tested the optimal antibody volume for each antibodies. Typically we use 20ul antibody (1ug/ul) in a 350ul-400ul hybrid solution.
The final DNA precipitation was used for library construction with the NEB Next N6240 kit (New England BioLabs) and decoded by Hiseq 2000 (Ilumina) with pair end 90bp strategy.

value: aerial tissue

value: tillering stage 60d after germination

tag: antibody

value: no antibody


title: H3K9me2_ChIP-Seq_O.punctata_60d

description: H3K9me2 ChIP-Seq O.punctata 60d

value: H3K9me2 (ab1220 Abcam)


title: p1_tc_1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H9_ad002

value: brain

value: ACA

value: MOp


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A10_ad002

value: male


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A10_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H8_ad002


title: O_punctata_60d_RNASEQ

data_processing:
For data analysis, raw reads were filtered for adaptor and low quality reads by flexbar2.5.
Clean reads were mapped by Tophat2 package with default parameters.
Resulting BAM files were calculated by Cufflinks for gene expression FPKM  in each species
Genome_build: We downloaded and used the rice genome version 6.1 from the MSU official ftp.  Four IOMAP (International Oryza Map Alignment Project) genomes, Oryza glaberrima, Oryza punctata, Oryza brachyantha RS2, Leersia perrieri and the sorgJGI2.0 were applied for bowtie mapping.

molecule: total RNA

source_name: 60d after germination plant

growth_protocol: plants are grown in greenhouse

extract_protocol:
In brief, total RNA was extracted using TRIzol buffer with 4g fresh tissue from the same plant which was used for ChIP experiment. Then RNA quality was validated by Agilent Bioanalyzer and samples with good quality were purified by RNA Purification Beads and submitted to BGI (shenzhen) for RNASEQ library construction
RNASEQ library was constructed with TruSeq RNA Sample Prep Kit (Illumina) according to the standard protocol. Six RNASEQ libraries were adjusted and sequenced in the same lane with proper barcodes with pair end 90bp strategy.


title: In vitro positive control - Sequel II

city: San Francisco

first: Colin

last: McNally

address: 600 16th Street

department: Biochemistry and Biophysics

institute: University of California, San Francisco

description: Nonanucleosome DNA in a plasmid was purified by Gigaprep, isolated via restriction enzyme sites, and purified with Sephacryl S1000 super fine gel filtration. Histone octamers (Luger et al., 1999) were assembled onto purified DNA via salt gradient dialysis.

data_processing:
Library strategy: SAMOSA
Demultiplexing BAM files using Lima
Generating circular concensus sequences (CCS) using ccs
Aligning CCS to hg38 using pbmm2 (in vivo samples only)
Aligning subreads to nonanucleosomal molecule reference (in vitro samples only)
Extracting IPD measurements from subreads, summarizing them by base, and then predicting methylation status using extractIPD.py (https://github.com/RamaniLab/SAMOSA)
Supplementary_files_format_and_content: In vitro samples: A numpy matrix where each column is a base pair in the DNA molecule and each row is a sequenced molecule. The values are the probability that that base in that molecule is methylated, if the base is A/T. In vivo samples: A dictionary containing the methylation probabilities for each base in each molecule in numpy arrays, and a separate pandas dataframe containing information about each molecule, including the ZMW hole numbers used to index the dictionary.

organism: unidentified plasmid

source_name: 2.2kb DNA molecule with 9 Widom 601 repeats

growth_protocol: K562 cells were grown in RPMI 1640 (Gibco) supplemented with 10% Fetal Bovine Serum (Gemini, Lot#A98G00K) and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
Chromatin was purified with 10uL RNaseA at RT for 10 minutes (in vivo samples only), 10uL Proteinase K (20mg/mL) and 10uL 10% SDS at 65°C for a minimum of 2 hours up to overnight). DNA was extracted with Phenol-Chloroform and ethanol precipitatation.
Library preparation included DNA damage repair, end repair, blunt-end SMRTbell® ligation, Exonuclease treatment, and Ampure PB cleanup according to manufacturer’s instruction. Library quality was assessed with Agilent Bioanalyzer High Sensitivity DNA kit.
PacBio SMRTbell® library preparation

treatment_protocol:
1.5ug of chromatin was methylated with 2.5uL of the non-specific adenine methyltransferase EcoGII (New England Biolabs, HC stock 2.5e4U/mL) at 37°C for 30 minutes, supplemented with SAM to 6.25mM (NEB) after 15 minutes.
Isolated K562 nuclei were digested with Micrococcal Nuclease (Sigma) at 1U per 50e6 nuclei at varying conditions (see characteristics above). MNase-digested nuclei were treated with 300ug/mL of Lysolethicin (L-α-Lysophosphatidylcholine from bovine brain, Sigma) for nuclear lysis and liberation of chromatin fibres.

tag: mnase digestion temperature

tag: mnase digestion duration

tag: ecogii methylation

value: EcoGII Methylated


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H8_ad001

tag: tissue


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H9_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H8_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H8_ad012

value: AI


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H7_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H7_ad002


title: UWB1.289 sgALC1_1uM Tal_rep1

city: Philadelphia

first: Robert

middle: Babak

last: Faryabi

state: Pennsylvania

address: Room 553 BRB II/III, 421 Curie Boulevard

department: Pathology

institute: University of Pennsylvania

data_processing:
Reads from ATAC-seq experiments were trimmed with Trim Galore
Reads were aligned to the primary assembly including all the chromosomes and contigs using BWA
Reads mapped to contigs, ENCODE blacklist and marked as duplicates were discarded
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for genome browser viewing

source_name: ATCC

growth_protocol: DLD1 BRCA2-/- were cultured in RPMI 1640 with GlutaMAX media and supplemented with 10% FBS and 1x penicillin-streptomycin (P/S). DLD1 BRCA2-/- cells were maintained at 3% oxygen. UWB1.289 cells were cultured in 1:1 (MEGM:RPMI) media supplemented with 10% FBS and 1xP/S.  UWB1.289 were cultured at atmospheric oxygen.

extract_protocol:
50K cells were pelleted at 800 x g and washed with 50mL of ice cold 1 x PBS followed by 2min treatment with 50 uL lysis buffer. After pelleting nuclei, nuclei were re-suspended in 50uL of transposition buffer (25uL of 2x TD buffer, 22.5ul of molecular biology grade water and 2.5uL Tn5 transposase (Illumina, cat# FC-121-1030) to tag the accessible chromatin for 45min at 37C. Tagmented DNA was purified with MinElute Reaction Cleanup kit and amplified with 5 cycles. Additional number of PCR cycles was determined from the side re-action and ranged from 10-12 total cycles of PCR. Two to three replicates were performed for each condition. Libraries were purified using QiaQuick PCR purification kit and eluted in 20uL EB buffer.
Indexed libraries were assessed for nucleosome patterning on the Agilent TapeStation 2200 and paired-end sequenced (38bp+38bp) on Illumina NextSeq 550.

treatment_protocol: Cell were transduced with lentivirus vector either expressing Negative sgRNA or sgRNA for ALC1.DLD1 cells were either treated with DMSO or 1uM olaparib for 4 hours.UWB1.289 cells were either treated with DMSO or 1uM talizoparib for 4 hours.

tag: cell line

tag: cell-type

value: epithelial-like

value: BRCA1-null human ovarian cancer cell line

tag: transduction

tag: treatment

value: Tal


title: In vitro negative control - Sequel II

value: Unmethylated


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H7_ad001

tag: age


title: UWB1.289 sgNeg_1uM Tal_rep2

tag: genotype

value: sgNeg


title: In vitro chromatin - Sequel II


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H6_ad001

tag: strain


title: UWB1.289 sgNeg_1uM Tal_rep1


title: UWB1.289 sgALC1_1uM Tal_rep2


title: UWB1.289 sgALC1_rep2

value: DMSO


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H5_ad002

tag: source

value: female


title: UWB1.289 sgALC1_1uM Tal_rep3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H5_ad006

tag: target


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H5_ad012

tag: gender


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H4_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H2_ad012


title: UWB1.289 sgALC1_rep1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H2_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A11_ad001

value: AUD


title: UWB1.289 sgNeg_rep3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H2_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H1_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H1_ad006


title: BFH1R

city: Verdun

first: Nicholas

last: O'Toole

state: QC

address: 6875 Boulevard Lasalle

country: Canada

institute: Douglas Mental Health University Institute

data_processing:
Reads were aligned to the rat genome with STAR
Read counts per gene were computed with STAR
Genome_build: rn6
Supplementary_files_format_and_content: Ensembl gene Ids and read counts, tab delimited

organism: Rattus norvegicus

source_name: Basolateral Amygdala

extract_protocol:
Qiagen AllPrep RNA minikit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: brain region

value: Basolateral Amygdala

tag: Sex

value: Female


title: BFH5R


title: BFH4R


title: BFL8R


title: UWB1.289 sgNeg_rep2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H1_ad001


title: CFL9

source_name: Cingulate Gyrus

value: Cingulate Gyrus


title: UWB1.289 sgNeg_rep1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H12_ad006

value: brain


title: DLD1 BRCA2-/- sgALC1_5uM Ola_rep3

source_name: Horizon Discovery

value: This is a pseudodiploid human cell line with the modal chromosome number of 46, occurring in 86% of cells. The rate of polyploidy was high at 17.1%. The karyotype of the line was 46,XY,-2,+dir dup(2)(p13-p23). The Y chromosome was slightly longer than N22 and had a large segment of heterochromatic, fluorescent distal q arms.

value: Ola


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H12_ad001

value: ACA

value: MOp

value: male


title: BFL9R


title: CFL7


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H11_ad012

value: AI


title: DLD1 BRCA2-/- sgALC1_5uM Ola_rep2

value: epithelial-like


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H10_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H11_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H1_ad002


title: DLD1 BRCA2-/- sgALC1_5uM Ola_rep1


title: DLD1 BRCA2-/- sgNeg_5uM Ola_rep3


title: DLD1 BRCA2-/- sgNeg_5uM Ola_rep2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G9_ad006


title: NMH5

source_name: Nucleus Accumbens Shell

value: Nucleus Accumbens Shell

value: Male


title: NMH3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H10_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_H10_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G7_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G9_ad012


title: DLD1 BRCA2-/- sgALC1_rep3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G7_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G6_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G7_ad001


title: DLD1 BRCA2-/- sgALC1_rep2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G5_ad012


title: DLD1 BRCA2-/- sgNeg_5uM Ola_rep1

value: sgNeg


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G6_ad002


title: CFH12


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G5_ad006


title: DLD1 BRCA2-/- sgALC1_rep1

value: DMSO


title: BFH7R


title: BFH10R


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G5_ad001


title: DLD1 BRCA2-/- sgNeg_rep3


title: NMH9


title: NMH12


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G4_ad002

value: female


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G8_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G4_ad001


title: DLD1 BRCA2-/- sgNeg_rep2


title: BFL11


title: NML7


title: DLD1 BRCA2-/- sgNeg_rep1


title: BFL9


title: p6_Far_S9

description:
single_cell_patient_6
processed data file: single_cell_UMItab.txt.gz

data_processing:
bcl2fastq/2.15.0.4. Plate demultiplexing was provided to obtain plate specific reads in two fastq files (read 1 (R1, 66bp) and read 2 (R2, UMI 10bp)), MARSseq (R1: 66bp, R2: cell barcode 7bp + UMI 8bp)
Pooled data of scRNAseq were demultiplexed using plate specific barcode. Specific sequences for each cell were demultiplexed using well specific barcode (attached - 'marsseq_cell_barcodes.txt'). Samples analyzed with laser capture microdissection were demultiplexed using sample specific barcode (attached mcSCRBseq raw files are after demultiplexing step).
Genome_build: GRCh38.91
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each sample
Supplementary_files_format_and_content: normal_liver_zonation_UMItab.txt.gz: normal liver zonation expression matrix
Supplementary_files_format_and_content: tumor_liver_zonation_UMItab.txt.gz: tumor liver zonation expression matrix
Supplementary_files_format_and_content: single_cell_UMItab.txt.gz: single cell expression matrix
Supplementary_files_format_and_content: marsseq_cell_barcodes.txt.gz: list of barcods used for demultiplexing the cells in the single cell RNAseq experiment

source_name: patient p6 non-malignant liver

extract_protocol:
sample collection protocol: Samples were collected from the surgery room immediately after isolation into sterile saline solution and processed in a sterile cabinet. Each sample was divided equally into two pieces as follows: (1) scRNAseq, samples stored in cold DMEM X1, supplemented with glutamine, (2) frozed section, sample were embedded into OCT block and kept on dry ice to be sectioned using LCM and mcSCRBseq for bulk sequencing
cell extract protocol: for scRNAseq, all samples were prepared according to Liver Dissociation Kit (GentelMAX, 130-105-807). Liberase Blendzyme3 recombinant collagenase (Roche Diagnostics) were added to the enzymatic cocktail in the first step in sample preperation protocol
for scRNAseq, 3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014). For bulk analysis, mcSCRBseq protocol was used (Bagnoli et al, Nat Commun. 2018)

tag: subject status

value: patient who underwent liver resection

tag: subject id

value: patient p6

value: Liver

tag: patient tumor type

value: colorectal metastasis

tag: sequencing protocol

value: MARSseq


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G2_ad012

tag: tissue

value: brain


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G3_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G3_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G3_ad006


title: BFH1

value: Basolateral Amygdala

value: Female


title: p6_Far_S8


title: BFL8


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G1_ad001

value: ACA

value: MOp


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G1_ad012

value: AI


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G4_ad006


title: p6_Far_S7


title: BFH4


title: p6_Far_S6


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G11_ad001

value: male


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G10_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G10_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G10_ad001


title: BML6


title: BFH5


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F9_ad012


title: p6_Far_S5


title: BFH6


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_G2_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F8_ad001


title: p6_Far_S3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F8_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F9_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F9_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F7_ad002


title: BFH7


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F7_ad001


title: p6_Far_S1


title: NMH2

value: Nucleus Accumbens Shell


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F6_ad001


title: p5_Tumor_S4

description:
single_cell_patient_5
processed data file: single_cell_UMItab.txt.gz

source_name: patient p5 malignant liver

value: patient p5


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F5_ad012

source_name: C57BL/6J P56 Mouse Brain


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F5_ad006


title: NML9

value: Male


title: p5_Tumor_S3


title: p6_Far_S4


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F4_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F5_ad001


title: p6_Far_S2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F7_ad006


title: BFH10


title: NMH4


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F3_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F3_ad002


title: BML12


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F3_ad012


title: p5_Tumor_S2


title: p5_Tumor_S1


title: BMH1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F3_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F2_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F2_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F1_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F1_ad006


title: BML5


title: BMH5


title: p5_Far_S4

source_name: patient p5 non-malignant liver


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F1_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F12_ad001


title: p5_Far_S3


title: p5_Far_S2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F11_ad012


title: BMH9


title: p5_Far_S5


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F10_ad012


title: BMH6


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F11_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F10_ad002


title: p5_Far_S1


title: BMH10


title: BML10


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E9_ad012


title: BMH12


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E8_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E9_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E6_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E7_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E5_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E5_ad001


title: p4_Tumor_S4

description:
single_cell_patient_4
processed data file: single_cell_UMItab.txt.gz

source_name: patient p4 malignant liver

value: patient p4


title: p4_Tumor_S5


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E4_ad012

value: female


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E4_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_F10_ad001


title: BML7


title: BMH11


title: p4_Tumor_S2

value: patient who underwent liver resection


title: BFL7


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E3_ad012


title: p4_Tumor_S1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E4_ad001


title: p4_Tumor_S6


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E2_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E3_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E3_ad001


title: p4_Tumor_S7


title: BFL3


title: p4_Far_S4

source_name: patient p4 non-malignant liver


title: BM4


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E2_ad002


title: p4_Far_S3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E1_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E1_ad006


title: BML1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E1_ad001


title: p4_Far_S2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E12_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E1_ad002


title: BML11


title: BML2


title: BMH2


title: p4_Far_S1


title: p3_Tumor_S8

description:
single_cell_patient_3
processed data file: single_cell_UMItab.txt.gz

source_name: patient p3 malignant liver

value: patient p3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E11_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E11_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E11_ad001


title: p3_Tumor_S7

value: Liver


title: BML8


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E10_ad012


title: BMH3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E10_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D9_ad012


title: p3_Tumor_S6

value: colorectal metastasis


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_E10_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D9_ad001


title: NML12R


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D8_ad012


title: NML8


title: p3_Tumor_S5

value: MARSseq


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D8_ad002

value: brain


title: p3_Tumor_S3


title: p3_Tumor_S4


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D8_ad001


title: NMH10


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D7_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D7_ad001


title: NMH6


title: p3_Tumor_S2


title: NML4


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D5_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D5_ad012


title: p3_Tumor_S1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D5_ad004


title: NML12


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D4_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D4_ad006


title: BML9

value: Basolateral Amygdala


title: p3_Far_S15

source_name: patient p3 non-malignant liver


title: p3_Far_S14


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D4_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D6_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D3_ad002


title: NML5


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D3_ad001


title: NMH8


title: p3_Far_S13


title: p3_Far_S12


title: NML1


title: NML11


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D2_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D2_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D6_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D1_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D2_ad001


title: p3_Far_S16


title: BMH8


title: p3_Far_S11


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D1_ad006


title: p3_Far_S10


title: BFL2

value: Female


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D1_ad002

value: ACA


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D1_ad001

value: MOp


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D3_ad012

value: AI


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D12_ad006


title: BFL1


title: p3_Far_S9


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D12_ad001

value: male


title: BFL5


title: p3_Far_S8


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D11_ad012


title: BFL6


title: p3_Far_S7


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D11_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_D11_ad001


title: p3_Far_S6


title: BFH9


title: BFH3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C9_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C8_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C8_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C9_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C7_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C7_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C7_ad001


title: BFH2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C6_ad001


title: p3_Far_S3


title: p3_Far_S4


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C5_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C5_ad012


title: NML6

value: Nucleus Accumbens Shell


title: p3_Far_S2


title: NML3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C5_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C9_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C4_ad006


title: p3_Far_S1


title: BFH11


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C3_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C3_ad012


title: p2_Tumor_S10

description:
single_cell_patient_2
processed data file: single_cell_UMItab.txt.gz

source_name: patient p2 malignant liver

value: patient p2

value: cholangiocarcinoma


title: BFL10


title: p3_Far_S5


title: p2_Tumor_S9


title: BFH8


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C3_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C2_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C1_ad006


title: BFH12


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C2_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C1_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C12_ad002


title: BFL4


title: p2_Tumor_S8


title: p2_Tumor_S7


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C12_ad001


title: p2_Tumor_S6


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C11_ad012


title: NFH1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C11_ad002


title: NMH1

value: Male


title: NFH4


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C10_ad012

value: female


title: NFL5


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C10_ad002


title: p4_Tumor_S3

value: patient who underwent liver resection

value: patient p4


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C10_ad001


title: p2_Tumor_S4

value: Liver


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B9_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B9_ad006


title: NFH2


title: p2_Tumor_S3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B9_ad002


title: NFL1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B9_ad001


title: p2_Tumor_S2


title: p2_Far_S5

source_name: patient p2 non-malignant liver


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_C11_ad006


title: p2_Tumor_S1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B8_ad012


title: NFH11


title: NFL11


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B8_ad002


title: p2_Tumor_S5


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B7_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B7_ad001


title: NFL10


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B6_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B6_ad001


title: p2_Far_S4


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B5_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B5_ad002


title: p2_Far_S2


title: p2_Far_S3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B5_ad001


title: NFH9


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B4_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B4_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B4_ad006


title: p2_Far_S1


title: CFH11

value: Cingulate Gyrus


title: p1_Tumor_S4

description:
single_cell_patient_1
processed data file: single_cell_UMItab.txt.gz

source_name: patient p1 malignant liver

value: patient p1

value: MARSseq


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B4_ad002

value: brain


title: NFH12

value: Female


title: NFL6


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B3_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B3_ad006

value: ACA


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B1_ad012

value: MOp


title: NFH3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B2_ad001


title: p1_Tumor_S2


title: p1_Tumor_S3


title: NFH10


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B2_ad012

value: AI


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B1_ad001

value: male


title: NFL7

value: Nucleus Accumbens Shell


title: NFH8


title: p1_Far_S4

source_name: patient p1 non-malignant liver


title: NFH7


title: p1_Far_S3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B12_ad006


title: NFH5


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A9_ad006


title: p1_Far_S1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B12_ad002


title: NFL8


title: p1_Tumor_S1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A9_ad001


title: cv6_2_S12

description:
normal liver zonation
processed data file: normal_liver_zonation_UMItab.txt.gz

source_name: central vein zone 6

value: non-malignant liver

value: mcSCRBseq


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B10_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B11_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B11_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_B1_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A8_ad001


title: cv6_1_S6


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A7_ad012


title: NFL4


title: cv5_2_S11

source_name: central vein zone 5


title: NFH6


title: cv5_1_S5


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A7_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A7_ad002


title: p1_Far_S2

value: cholangiocarcinoma


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A7_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A9_ad012

value: female


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A6_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A6_ad001


title: CML12

source_name: Cingulate Gyrus

value: Male


title: cv4_2_S10

source_name: central vein zone 4


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A5_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A8_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A5_ad001


title: NFL2

source_name: Nucleus Accumbens Shell


title: CFL8R


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A4_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A4_ad006


title: CML5


title: cv3_1_S3

source_name: central vein zone 3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A4_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A3_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A2_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A3_ad001


title: CFL2


title: CFH6


title: cv3_2_S9


title: cv2_1_S2

source_name: central vein zone 2


title: cv2_2_S8


title: cv1_2_S7

source_name: central vein zone 1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A2_ad002

source_name: C57BL/6J P56 Mouse Brain


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A12_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A1_ad012


title: NFL3


title: NFL9


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A11_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H9_ad012

value: SSp


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A11_ad001


title: cv4_1_S4

value: Liver


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H9_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P1_CEMBA190826_RS2_P2_A3_ad012


title: CFH10

value: Cingulate Gyrus


title: Bisulfite-Seq_Oryza_brachyantha

description: Bisulfite-Seq DNA methylation of Oryza_brachyantha

data_processing:
Clean read pairs  were obtained after removal of adaptor and low quality reads by flexbar2.5.
We used  Bismark v0.11 to map the reads to genome and do the methylation base calling
The output files of Bismark were filtered for no-zero bases and transformed to bgzipped bedgraph files
Genome_build: O. brachyantha RS2
Supplementary_files_format_and_content: bgzipped bedgraph, four columns format. The last column shows the single base methylation ratio (0-1)

organism: Oryza brachyantha

source_name: leaf tissue of mature plant

extract_protocol:
whole genome DNA was extracted from fresh mature plant leaf.The EZ-DNA Methylation-Gold kit (ZYMO) was used for bisulfite treatment.
After that, the bisulfite transformed DNA was purified, size-selected and recovered by QIAquick Gel Extraction kit (QIAGEN). The final product was used for library construction and sequenced by Hiseq 2000 with 50bp pair end strategy.

value: leaf of mature plant

tag: developmental stage

value: mature plant


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H9_ad007

value: brain


title: input_H3K9me2_ChIP-Seq_L.perrieri_60d

description: input H3K9me2 ChIP-Seq L.perrieri 60d

organism: Leersia perrieri

source_name: tillering stage plant

value: aerial tissue

value: tillering stage 60d after germination

tag: antibody

value: no antibody


title: CMH12


title: CFH3

value: Female


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H9_ad004

value: ACA

value: VISp

value: male


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H9_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H9_ad001


title: CFH9


title: L_perrieri_60d_RNASEQ

source_name: 60d after germination plant


title: CFL5


title: CFL3


title: CFH4


title: cv1_1_S1

value: non-malignant liver

value: mcSCRBseq


title: pSer5_shPP2A-C_DLD1_rep2_ChIPSeq

city: Shanghai

first: Xuan

last: Cao

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health,  Chinese Academy of Sciences

data_processing:
CHIP-Seq reads were aligned to the human genome (UCSC hg19) by using alignment software Bowtie (1.1.1) (Langmeadet al., 2009) with the following options: -S –m 1 –k 1.
Only unique reads mapping to a single genomic location were kept. Duplicate reads were removed by using in house script.
We calculated the ChIP-seq signal as reads per million mapped reads (RPM) based on sequence depth. We counted the number of spike-in reads by aligning to the mouse genome(mm10) with bowtie. We normalized ChIP-seq signal by multiplying the RPM  by the spike-in factor a=  which  is the count of reads (in millions) mapped to mouse genome(David A. Orlando(2014)). Density genome track were generated by using bedtools genomecov program to conver bam files to bigwig files (Quinlan, 2014)
Peaks were called using macs (1.3.7.1) (Zhang, 2008)with the following parameters: --nomodel –nolambda and the peaks with 10*log10 (pvalue) > 100 were kept.
Genome_build: hg19

growth_protocol: Colorectal adenocarcinoma cell line DLD1 cells were cultured in DMEM (Dulbecco’s Modified Eagle’s medium, Hyclone) supplemented with 10% fetal bovine serum (FBS, Biowest), nonessential amino acids (Gibco) at 37 °C and 5% CO2.

extract_protocol:
Lysates were clarified from sonicated cells and INTAC-DNA complexes were isolated with antibody.
Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Universal DNA Library Prep Kit (Vazyme ND607-02). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq X Ten following the manufacturer's protocols.

treatment_protocol: One replicate was shRNA-containing lentivirus treated for 4 days.

tag: cell line

tag: cell type

value: colorectal adenocarcinoma cell line

tag: chip antibody

tag: shRNA treatment


title: pSer5_shPP2A-C_DLD1_rep3_ChIPSeq


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H8_ad010

tag: strain

tag: age

value: MOp


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H8_ad008

tag: source

value: SSp

tag: target

value: female


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H8_ad012

tag: gender


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H7_ad008


title: CFL10

tag: brain region

value: Cingulate Gyrus

tag: Sex


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H7_ad007


title: pSer5_shPP2A-C_DLD1_rep1_ChIPSeq


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H8_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H8_ad002


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H7_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H7_ad006


title: H3K9me2_ChIP-Seq_L.perrieri_60d

description: H3K9me2 ChIP-Seq L.perrieri 60d

value: H3K9me2 (ab1220 Abcam)


title: CML3

value: Male


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H7_ad002

value: brain


title: VFL9

source_name: Ventral Dentate Gyrus

value: Ventral Dentate Gyrus


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H8_ad007


title: pSer5_shINTS8_DLD1_rep3_ChIPSeq


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H7_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H6_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H6_ad006


title: pSer5_shINTS8_DLD1_rep1_ChIPSeq


title: pSer5_shINTS8_DLD1_rep2_ChIPSeq


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H6_ad004


title: CFL8


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H6_ad001


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H6_ad007


title: VFH3


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H5_ad008


title: pSer5_shINTS11_DLD1_rep3_ChIPSeq


title: pSer5_shINTS11_DLD1_rep1_ChIPSeq


title: pSer5_shINTS11_DLD1_rep2_ChIPSeq


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H5_ad007


title: CFL11


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H5_ad010


title: pSer5_NonT_DLD1_rep3_ChIPSeq

value: non target shRNA


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H5_ad006


title: pSer5_NonT_DLD1_rep2_ChIPSeq


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H5_ad004


title: CML6


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H5_ad002


title: input_H3K9me2_H3K4me3_H3K56Ac_ChIP-Seq_O.brachyantha_60d_batch2

description: input H3K9me2 H3K4me3 H3K56Ac ChIP-Seq O.brachyantha 60d batch2

value: aerial tissue

value: tillering stage 60d after germination

value: no antibody


title: pSer5_NonT_DLD1_rep1_ChIPSeq


title: CFH1

value: Female


title: H3K56Ac_ChIP-Seq_O.brachyantha_60d_batch2

description: H3K56Ac ChIP-Seq O.brachyantha 60d batch2

value: H3K56Ac (39281 Active Motif)


title: CFH8


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H6_ad002

value: ACA

value: VISp


title: CMH6


title: H3K4me3_ChIP-Seq_O.brachyantha_60d_batch2

description: H3K4me3 ChIP-Seq O.brachyantha 60d batch2

value: H3K4me3 (07-473 Millipore )


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H4_ad008

value: MOp


title: CML1


title: pSer2_shPP2A-C_DLD1_rep3_ChIPSeq

value: colorectal adenocarcinoma cell line


title: VFH12


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H4_ad010

value: SSp

value: male


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H4_ad007


title: CMH10

value: Cingulate Gyrus


title: input-H3K27me2_ChIP-Seq_O.brachyantha_60d_batch1

description: input-H3K27me2 ChIP-Seq O.brachyantha 60d batch1


title: CMH11

value: Male


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H4_ad006

value: brain

value: female


title: panicle_siRNA_O.brachyantha

description: small RNA of panicle

data_processing:
Clean read pairs  were obtained after removal of adaptor and low quality reads by flexbar2.5.
Single end reads were preprocessed and mapped to genome by Bowtie.
Signal density was calculated by genomeCoverageBed.
Genome_build: O. brachyantha RS2
Supplementary_files_format_and_content: small RNA single base density, bgizpped four columns bedgraph file

source_name: panicle tissue

extract_protocol:
18-30bp small RNA was selected from total RNA extraction by PAGE
Sequence library was constructed with TruSeq Small RNA Sample Pre Kit (Illumina) by standard protocol.

value: panicle

value: reproductive stage


title: H3K9me2_ChIP-Seq_O.brachyantha_60d_batch2

description: H3K9me2 ChIP-Seq O.brachyantha 60d batch2

value: aerial tissue

value: tillering stage 60d after germination

value: H3K9me2 (ab1220 Abcam)


title: pSer2_shPP2A-C_DLD1_rep1_ChIPSeq


title: pSer2_shINTS8_DLD1_rep3_ChIPSeq


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H4_ad004


title: CML7


title: H3K27me2_ChIP-Seq_O.brachyantha_60d_batch1

description: H3K27me2 ChIP-Seq O.brachyantha 60d batch1

value: H3K27me2 (07-452 Millipore)


title: pSer2_shINTS8_DLD1_rep2_ChIPSeq


title: input-H3K9Ac_H3K36me3_ChIP-Seq_O.brachyantha_60d_batch1

description: input-H3K9Ac H3K36me3 ChIP-Seq O.brachyantha 60d batch1

value: no antibody


title: CFH7

value: Female


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H4_ad002

value: ACA

value: VISp


title: pSer2_shINTS8_DLD1_rep1_ChIPSeq

value: colorectal adenocarcinoma cell line


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H3_ad010

value: SSp

value: MOp


title: H3K9Ac_ChIP-Seq_O.brachyantha_60d_batch1

description: H3K9Ac ChIP-Seq O.brachyantha 60d batch1

value: H3K9Ac (ab10812 Abcam)


title: VMH12

value: Ventral Dentate Gyrus

value: Male


title: pSer2_shINTS11_DLD1_rep3_ChIPSeq


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H3_ad007

value: brain

value: male


title: CMH9

value: Cingulate Gyrus


title: pSer2_shPP2A-C_DLD1_rep2_ChIPSeq


title: H3-H3K4me3_ChIP-Seq_O.brachyantha_60d_batch1

description: H3-H3K4me3 ChIP-Seq O.brachyantha 60d batch1

value: aerial tissue

value: H3 ab1791 (Abcam)


title: pSer2_shINTS11_DLD1_rep2_ChIPSeq


title: CML2


title: H3K4me3_ChIP-Seq_O.brachyantha_60d_batch1

description: H3K4me3 ChIP-Seq O.brachyantha 60d batch1

value: tillering stage 60d after germination

value: H3K4me3 (07-473 Millipore )


title: pSer2_shINTS11_DLD1_rep1_ChIPSeq


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H3_ad006

value: female


title: CMH8


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H3_ad004


title: CML9


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H3_ad002


title: pSer2_NonT_DLD1_rep3_ChIPSeq

value: non target shRNA


title: H3-H3K4me2_ChIP-Seq_O.brachyantha_60d_batch1

description: H3-H3K4me2 ChIP-Seq O.brachyantha 60d batch1


title: H3K36me3_ChIP-Seq_O.brachyantha_60d_batch1

description: H3K36me3 ChIP-Seq O.brachyantha 60d batch1

value: H3K36me3 (ab9050 Abcam)


title: H3K4me2_ChIP-Seq_O.brachyantha_60d_batch1

description: H3K4me2 ChIP-Seq O.brachyantha 60d batch1

value: H3K4me2 (ab11946 Abcam)


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H3_ad001

value: ACA

value: VISp


title: pSer2_NonT_DLD1_rep2_ChIPSeq

value: colorectal adenocarcinoma cell line


title: input-H3K9me2_ChIP-Seq_O.brachyantha_60d_batch1

description: input-H3K9me2 ChIP-Seq O.brachyantha 60d batch1

value: no antibody


title: CMH3


title: pSer2_NonT_DLD1_rep1_ChIPSeq


title: CFH5


title: H3K9me2_ChIP-Seq_O.brachyantha_60d_batch1

description: H3K9me2 ChIP-Seq O.brachyantha 60d batch1

value: H3K9me2 (ab1220 Abcam)


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H2_ad010

value: SSp

value: MOp


title: CML8

value: Male


title: input-H3K9me2_H3K4me3_H3K27me_ChIP-Seq_O.brachyantha_2weeks

description: input-H3K9me2 H3K4me3 H3K27me ChIP-Seq O.brachyantha 2weeks

source_name: seedling stage plant

value: seedling shoot

value: seedling stage 2 weeks after germination


title: PP2A-C_shPP2A-C_DLD1_rep1_ChIPSeq


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H2_ad008

value: brain


title: H3K27me_ChIP-Seq_O.brachyantha_2weeks

description: H3K27me ChIP-Seq O.brachyantha 2weeks

value: H3K27me (07448 Millipore)


title: PP2A-C_shINTS8_DLD1_rep2_ChIPSeq


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H2_ad004

value: male


title: CML11

value: Cingulate Gyrus


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H2_ad002

value: female


title: H3K4me3_ChIP-Seq_O.brachyantha_2weeks

description: H3K4me3 ChIP-Seq O.brachyantha 2weeks

value: H3K4me3 (07-473 Millipore )


title: PP2A-C_shINTS8_DLD1_rep1_ChIPSeq


title: H3K9me2_ChIP-Seq_O.brachyantha_2weeks

description: H3K9me2 ChIP-Seq O.brachyantha 2weeks


title: VFH1

value: Ventral Dentate Gyrus

value: Female


title: PP2A-C_shINTS11_DLD1_rep2_ChIPSeq


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H2_ad001

value: ACA

value: VISp


title: input_H3K9me2_ChIP-Seq_S.bicolor_60d

description: input H3K9me2 ChIP-Seq S.bicolor 60d

organism: Sorghum bicolor

value: aerial tissue

value: tillering stage 60d after germination

value: no antibody


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H2_ad012

value: SSp

value: MOp


title: O_brachyantha_60d_RNASEQ


title: VFL7


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H1_ad010


title: PP2A-C_shPP2A-C_DLD1_rep2_ChIPSeq

value: colorectal adenocarcinoma cell line


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H1_ad012


title: PP2A-C_NonT_DLD1_rep2_ChIPSeq

value: non target shRNA


title: VFH10


title: H3K9me2_ChIP-Seq_S.bicolor_60d

description: H3K9me2 ChIP-Seq S.bicolor 60d

value: H3K9me2 (ab1220 Abcam)


title: S_bicolor_60d_RNASEQ


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H1_ad008

value: brain


title: PP2A-C_NonT_DLD1_rep1_ChIPSeq


title: CMH7

value: Male


title: VFH9


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H1_ad007

value: male


title: CFL4

value: Cingulate Gyrus


title: PP2A-A_shPP2A-C_DLD1_rep2_ChIPSeq


title: VFL10


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H1_ad004


title: CFH2


title: DX53

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: kidney.dmr.results.csv.gz

data_processing:
Basic read quality was verified using summaries produced by FastQC. The raw reads were trimmed and filtered using Trimmomatic. The reads for each MeDIP sample were mapped to the Rnor 6.0 rat genome using Bowtie2 with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools.
To identify DMRs, the reference genome was broken into 1000 bp windows. Genomic windows with a mean of less than 10 mapped reads per sample were removed prior to further analysis. The MEDIPS R package was then used to calculate differential coverage between disease and non-disease sample groups. The edgeR p-value was used to determine the relative difference between the two groups for each genomic window.
Windows with an edgeR p-value less than an arbitrarily selected threshold were considered DMRs. The DMR edges were extended until no genomic window with a p-value less than 0.1 remained within 1000 bp of the DMR.
CpG density and other information was then calculated for the DMR based on the reference genome.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

source_name: Sperm

growth_protocol: Female and male rats of an outbred strain Hsd:Sprague Dawley SD (Harlan) at 70 to 100 days of age were fed ad lib with a standard rat diet and ad lib tap water. The gestating female rats treated were designated as the F0 generation. F1- F3 generation control and dioxin lineages were housed in the same room and racks with lighting, food and water. All experimental protocols for the procedures with rats were pre-approved by the Washington State University Animal Care and Use Committee (protocol IACUC # 6252).

extract_protocol:
For each sample, the epididymis was dissected free of fat and connective tissue, then, after cutting open the cauda, placed into 6 ml of phosphate buffer saline (PBS) for 20 minutes at room temperature. Further incubation at 4ºC will immobilize the sperm.  The tissue was then minced, the released sperm pelleted at 4ºC 3,000 x g for 10 min, then resuspended in NIM buffer and stored at -80ºC for further processing.   DNA protocol: While sperm are thawing, turn on the centrifuge to 4ºC.   1. Re-suspend sperm pellet with pestle (and pestle motor if available).   o If there is some liquid left with the pellet, there is no need to add any additional buffer  o If not add 100 l 1xPBS or NIM buffer  2. Take 25 to 50 l of the suspension (depending on how big the pellet is) and transfer it to a microfuge tube with 200 l 1xPBS.   o Mix  3. Sonicate suspension at 25% with probe sonicator for 5 seconds.  4. Spin at 12,000 rpm for 10 minutes at 4C.  o While waiting, turn on heat plate to 65C   5. Discard supernatant. Be careful – pellet is loose.  6. Wash with 200 l 1xPBS and spin as above.  o While waiting, retrieve DTT from freezer (make sure there is enough)    o Turn on the incubator  o Vortex DTT once it has thawed a bit  7. Resuspend pellet in 100 l 1xPBS, then continue with protocol below.  General:  1. Re-suspend tissue in 100 l PBS or NIM buffer, then   o add 820 l DNA extraction buffer   o add 50 l 0.1M DTT   o vortex briefly  o incubate at 65C for 15 minutes   o Retrieve ProteinaseK from freezer  2. Add 50 l proteinase K (20 mg/ml) and   o incubate at 55C for 2-3 hours under constant rotation  o use Eppendorf SafeLock tubes and wrap the tops with Parafilm  3. After incubation add 300 l of protein precipitation solution (Promega Genomic DNA Purification Kit, A795A)  o mix (vortex) thoroughly and make sure that the solutions are mixed   o then incubate for 20 min on ice (or longer if needed)  4. Centrifuge at 13,500 g for 30 minutes at 4C.  o Prepare 2 mL tubes  o Take glycoblue out of the freezer  5. Transfer 1 ml of the supernatant to a new 2 ml tube.   o add 2 l of glycoblue   o add 1 ml of cold 100 % isopropanol  6. Mix well by inverting tubes several times.  7. Incubate for 60 min at -20C.  8. Centrifuge for 20 min at 13,500 g at 4C.   9. Take off and discard supernatant without disturbing (blue) pellet.   10. Wash pellet 2-3 times with 70% cold ethanol.   o Add 500l of 70% ethanol to each pellet and   o return to freezer for 20 minutes  11. Centrifuge for 10 min at 4C at maximum speed (18,200 g)   o discard supernatant  12. Spin again briefly to collect residual ethanol at bottom of tube and remove as much liquid as possible with gel loading tip.  13. Air-dry at RT until pellet looks dry, but be careful not to over-dry.   o This will take about 5 minutes  14. Re-suspend in 100 l of nuclease free water or TE.  15. Measure DNA concentration using Nanodrop.   Methylated DNA immunoprecipitation protocol: Shear & Add Antibody to DNA  1. Sonicate purified genomic DNA using Covaris:  a. Dilute 6μg genomic DNA into 50 or 130 μl TE buffer in the appropriate Covaris tube.  b. Set Covaris to desired program (300 or 500 bp program works well).  c. Run program for each tube  • While waiting, turn on the dry bath to 95ºC.   2. Run 10 μl sonicated DNA & 5 μl DNA ladder on 2% agarose gel to verify fragment size.  • While waiting for gel, clean up Covaris.   3. Measure volume of sonicated DNA after gel run.  4. Dilute sonicated DNA with TE buffer to 400 μl (400 – 130 + 10 = 280 µL)  5. Heat-denature for 10min at 95˚C, and   • immediately cool on (watery) ice for 5min  6. To the denatured sonicated DNA:  a. Add 100μl of cold 5X IP buffer   b. Add 5μg (volume depending on concentration) of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006). ALWAYS check antibody concentration. Diagenode sometimes changes it.  c. Incubate the DNA-antibody mixture overnight on a rotator at 4˚C.  Rotate at a low enough speed to prevent significant foaming.  Bind Beads to DNA: Antibody Mixture  1. Pre-wash Magnetic Beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) as follows:  • Resuspend the beads in the vial (pipet up and down or rotate, do not vortex)  • Transfer desired volume (50 μl per sample) to a centrifuge tube, add the same volume of Washing Buffer (at least 1 mL), and resuspend.  • Place the tube in a magnet for 1-2 minutes and discard supernatant.   • Resuspend beads in 1 ml of washing buffer and incubate for 1 minute on bench. Put tube on magnet for 1-2 minutes and discard supernatant.  • Remove the tube from the magnet and resuspend the washed beads in the same volume of 1xIP buffer as the initial volume of beads.  2. Add 50μl of beads to the 500μl of DNA-antibody mixture from step 2  3. Incubate 2h on a rotating platform at 4˚C.  Wash DNA: Antibody: Beads Mixture & Add Proteinase K Mix  1. Wash beads three times with 1X IP buffer as follows:  • Place tube in magnet for 1-2 minutes and discard supernatant  • Remove tube from magnet  • Add 1ml cold 1X IP buffer  • Mix by inverting tube or gently vortexing (set Vortex to low).  • Incubate tube(s) for 1 minute on bench.  • Place tube in magnet for 1-2 minutes and discard supernatant  • Repeat twice for a total of 3 washes  2. Resuspend the beads in 250μl digestion buffer.  3. Add 3.5μl Proteinase K Mix (20mg/ml) to the resuspended beads.  4. Incubate 2-3 hours on a rotating platform at 55˚C (make sure to seal lids so they don’t leak). Use USA Scientific SealRite tubes or Eppendorf Safe-Lock tubes and seal top with Parafilm.  Purify DNA  • Retrieve Glycoblue from freezer.   1. Remove Parafilm and add 250μl Phenol-Chloroform-Isoamylalcohol to each tube.    • Vortex for 30 sec and centrifuge at 14,000g for 5min at RT.  • Remove the aqueous supernatant and transfer to a fresh microcentrifuge tube.  2. Add 250μl chloroform to the supernatant from step 1.    • Vortex for 30sec and centrifuge at 14,000g for 5min at RT.   • Remove the aqueous supernatant and transfer to a fresh microcentrifuge tube.  3. Add 500 μl ethanol  • Then add 20μl 5M NaCl   • Then add 2μl glyco-blue (20mg/ml)   • Vortex well   4. Precipitate in -20˚C freezer for 1 hour to overnight.  5. Centrifuge at 14,000g for 20min at 4˚C.  Carefully remove the supernatant, while not disturbing the pellet.  6. Wash the pellet with 500μl cold 75% ethanol. Leave in -20˚C freezer for 15 min.  7. Centrifuge at 14,000g for 5min at 4˚C.  Carefully remove the supernatant.  8. Completely dry samples.  9. Resuspend in 25μl H2O.    10. Measure the DNA concentration in Qubit with ssDNA kit and matching buffer.
MeDIP DNA was used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra DNA Library following the manufacturer’s protocol  and indexing each sample individually with NEBNext Multiplex Oligos for Illumina. NEBNext Ultra II Library Prep Kit for Illumina: ssDNA  • Start with 20 µl in PCR strips.   o ~40 ng of DNA  o Complete the volume to 20 µl   • Add 2.5 µL of diluted (1:10) random primer to each tube.   o for 10 samples, 27 µL 0.1x TE and 3 µL primers  o for 12 samples 36 µL 0.1x TE and 4 µL primers  o for 22 samples, 54 µL 0.1x TE and 6 µL primers  • Place strips in the thermocycler and use the Denaturation program. Immediately remove (as soon as time runs out on the program) and cool on watery ice following denaturation. Let tubes rest on watery ice for 5 minutes, then transfer to refrigerated block.   I. Second Strand cDNA Synthesis  Assemble the second strand cDNA synthesis reaction on ice by adding the following components to the 20 µl DNA.   Second Strand Synthesis Reaction  DNA          20 µL  ORANGE NEBNet 2nd Strand Synthesis Reaction Buffer  8 µL  ORANGE NEBNext 2nd Strand Synthesis Enzyme Mix 4 µL  Nuclease-free water      45.5 µL  Total Volume

treatment_protocol: Outbred Sprague Dawley gestating female rats (F0 generation) were administered an intraperitoneal dose of 100 mg/kg body weight of  dioxin (TCDD). The lowest observable adverse effects level (LOAEL) is 160 ng/kg/BW. These doses were administered at 90 days of age, during embryonic days 8-14 (E8-E14) of fetal gonadal sex determination. The F1 generation offspring was directly exposed as a fetus and F2 generation grand-offspring exposed as the germline in the F1 generation. These were each bred at 90 days of age within the lineage. The F3 generation great-grand-offspring is required to establish the transgenerational inheritance generation of ancestral exposure. A control lineage was established that used F0 gestating rats exposed to the vehicle control dimethyl sulfoxide (DMSO).

tag: measurement

value: MeDIP

tag: disease

value: kidney disease

tag: lineage

value: dioxin

value: Sperm


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H1_ad001

tag: tissue

value: ACA

value: VISp


title: PP2A-A_shINTS8_DLD1_rep2_ChIPSeq


title: PP2A-C_shINTS11_DLD1_rep1_ChIPSeq


title: DX52

description:
kidney.dmr.results.csv.gz
prostate.dmr.results.csv.gz
obesity.dmr.results.csv.gz
testis.dmr.results.csv.gz

value: no disease


title: VFH11

value: Ventral Dentate Gyrus

value: Female


title: PP2A-A_shINTS8_DLD1_rep1_ChIPSeq


title: DX51

description: This sample was not used in the analysis due to sequence quality issues.


title: CML4


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H12_ad012

value: SSp

value: MOp

value: female


title: PP2A-A_shINTS11_DLD1_rep2_ChIPSeq

value: colorectal adenocarcinoma cell line


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H12_ad010

value: brain


title: CMH5

value: Male


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H12_ad008


title: CMH4


title: PP2A-A_shINTS11_DLD1_rep1_ChIPSeq


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H12_ad007

value: male


title: DX48


title: PP2A-A_NonT_DLD1_rep2_ChIPSeq

value: non target shRNA


title: PP2A-A_shPP2A-C_DLD1_rep1_ChIPSeq


title: PP2A-A_NonT_DLD1_rep1_ChIPSeq


title: DX47

value: MeDIP


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H12_ad006


title: VFL8


title: VML10


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H12_ad004


title: VMH8


title: PolII_shPP2A-C_DLD1_rep3_ChIPSeq

value: PolII


title: DX46

value: late puberty

value: dioxin


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H11_ad006

value: ACA


title: DX50

description: testis.dmr.results.csv.gz

value: testis disease

value: Sperm


title: DX44

value: no disease


title: DX45


title: PolII_shPP2A-C_DLD1_rep2_ChIPSeq


title: PolII_shPP2A-C_DLD1_rep1_ChIPSeq


title: VFL6

value: Ventral Dentate Gyrus

value: Female


title: DX43


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H11_ad002

value: VISp


title: VFH4


title: DX49

value: prostate disease


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H10_ad010

value: SSp

value: MOp


title: VFH7


title: PolII_shINTS8_DLD1_rep3_ChIPSeq

value: colorectal adenocarcinoma cell line


title: PolII_shINTS8_DLD1_rep2_ChIPSeq


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H10_ad008

value: brain

value: female


title: DX42

description: testis.dmr.results.csv.gz

value: MeDIP


title: VFH6


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H10_ad007

value: male


title: DX41

description: testis.dmr.results.csv.gz


title: VFH2


title: PolII_shINTS8_DLD1_rep1_ChIPSeq

value: PolII


title: DX40

description: kidney.dmr.results.csv.gz

value: kidney disease

value: dioxin


title: PolII_shINTS11_DLD1_rep3_ChIPSeq


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H10_ad006

value: ACA


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H10_ad002


title: PolII_shINTS11_DLD1_rep2_ChIPSeq


title: PolII_shINTS11_DLD1_rep1_ChIPSeq


title: DX38

value: Sperm


title: VFL2


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_H10_ad001


title: DX37

value: no disease


title: PolII_NonT_DLD1_rep3_ChIPSeq

value: non target shRNA


title: PolII_NonT_DLD1_rep2_ChIPSeq


title: DX36


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G9_ad008


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G9_ad010


title: DX35


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G9_ad006


title: PolII_NonT_DLD1_rep1_ChIPSeq


title: VFL3

value: Ventral Dentate Gyrus

value: Female


title: VFH8


title: DX34

description: kidney.dmr.results.csv.gz


title: INTS5_NonT_DLD1_rep2_ChIPSeq


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G9_ad004

value: VISp


title: VFL1


title: INTS5_NonT_DLD1_rep1_ChIPSeq


title: VFL11


title: DX39


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G9_ad002


title: DX32


title: VFL4


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G9_ad001


title: VMH10

value: Male


title: VFL5


title: DX31


title: INTS3_shPP2A-C_DLD1_rep2_ChIPSeq


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G8_ad012

value: SSp

value: MOp


title: INTS3_shPP2A-C_DLD1_rep3_ChIPSeq

value: colorectal adenocarcinoma cell line


title: DX30


title: VFH5


title: VMH5


title: VMH4


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G8_ad010

value: brain


title: VML6


title: INTS3_shPP2A-C_DLD1_rep1_ChIPSeq


title: DX28

value: MeDIP


title: DX33

description: kidney.dmr.results.csv.gz


title: DX29


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G8_ad008

value: female


title: DX27


title: INTS3_shINTS8_DLD1_rep1_ChIPSeq


title: INTS3_shINTS11_DLD1_rep2_ChIPSeq


title: VML2


title: INTS3_shINTS11_DLD1_rep1_ChIPSeq


title: VML9


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G8_ad006


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G8_ad007

value: male


title: DX26


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G8_ad002


title: VMH11


title: INTS3_NonT_DLD1_rep2_ChIPSeq


title: VMH6


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G7_ad012


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G7_ad010


title: DX24

description: testis.dmr.results.csv.gz

value: testis disease


title: INTS3_NonT_DLD1_rep1_ChIPSeq


title: VMH7


title: DX23

description: prostate.dmr.results.csv.gz

value: prostate disease

value: dioxin


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G7_ad008


title: INTS11_DLD1_rep1_ChIPSeq

value: WT


title: VMH3


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G7_ad006

value: ACA


title: Input_shPP2A-C_DLD1_rep2_ChIPSeq

value: Input


title: DX22

description: testis.dmr.results.csv.gz

value: Sperm


title: VML12

value: Ventral Dentate Gyrus


title: Input_shPP2A-C_DLD1_rep1_ChIPSeq


title: VML8


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G7_ad002

value: VISp


title: DX19

description: prostate.dmr.results.csv.gz


title: DX25

description: obesity.dmr.results.csv.gz

value: obesity


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G7_ad001


title: Input_shINTS8_DLD1_rep2_ChIPSeq


title: VML3

value: Male


title: DX18

description: obesity.dmr.results.csv.gz


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G6_ad010

value: SSp

value: MOp


title: INTS11_DLD1_rep2_ChIPSeq

value: colorectal adenocarcinoma cell line


title: Input_shINTS11_DLD1_rep2_ChIPSeq


title: VMH2


title: DX17

value: MeDIP


title: VML5


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G6_ad007

value: brain


title: NMH7

value: Nucleus Accumbens Shell


title: DX16

description: testis.dmr.results.csv.gz

value: testis disease


title: Input_shINTS11_DLD1_rep1_ChIPSeq


title: DX21

description: prostate.dmr.results.csv.gz

value: prostate disease


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G6_ad006

value: female


title: INTS3_shINTS8_DLD1_rep2_ChIPSeq


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G7_ad007

value: male


title: DX20

value: no disease

value: dioxin


title: VML4


title: DX15

description: testis.dmr.results.csv.gz

value: Sperm


title: CMH2

value: Cingulate Gyrus


title: DX14

value: multiple disease


title: H3K4me1_DLD1_rep1_ChIPSeq

value: WT


title: DX13

description: kidney.dmr.results.csv.gz

value: kidney disease


title: Input_NonT_DLD1_rep1_ChIPSeq

value: Input

value: non target shRNA


title: BML4

source_name: Basolateral Amygdala

value: Basolateral Amygdala

value: Male


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G6_ad001

value: brain

value: ACA

value: VISp


title: CMH1


title: DX12

value: MeDIP


title: CML10


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G5_ad010

value: SSp

value: MOp


title: H3K27ac_DLD1_rep1_ChIPSeq

value: colorectal adenocarcinoma cell line


title: DX11

description: testis.dmr.results.csv.gz

value: testis disease

value: dioxin


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G5_ad008

value: female


title: DX10

value: no disease

value: Sperm


title: 2 weeks LPS_3

first: Jung-Seok

last: Kim

address: 234 Herzl street

department: Immunology

data_processing:
Putative open chromatin regions (peaks) were called using HOMER (Heinz et al., 2010) (using parameters compatible with IDR analysis: –L 0 –C 0 –fdr 0.9). The irreproducible discovery rate (IDR) was computed for each peak using the Homer peak score for each replicate experiment ; peaks with IDR > 0.05 were filtered away.
Genome_build: mm9
Supplementary_files_format_and_content: alignment files
Supplementary_files_format_and_content: peaks files

source_name: Mouse brain

extract_protocol:
Brain homogenization and microglia enrichment
20,000–50,000 cells were used for ATACseq (Buenrostro et al., 2013) applying described changes (Lara-Astiaso et al., 2014). Briefly, nuclei were obtained by lysing the cells and nuclei were pelleted by centrifugation for 20 min at 500 g, 4 °C using a swing rotor. Supernatant was discarded and nuclei were re-suspended in 25 μl reaction buffer. The reaction was incubated at 37 °C for 1 hr. DNA was released from chromatin by adding 5 μl of cleanup buffer, followed by an incubation for 30 min at 40 °C. Tagmentated DNA was isolated using 2× volumes of SPRI beads and eluted in 21 μl. For library amplification, two sequential PCRs (nine cycles, followed by an additional six cycles) were performed in order to enrich small tagmentated DNA fragments. We used the indexing primers as described (Buenrostro et al., 2013) and KAPA HiFi HotStart ready mix. After the first PCR, the libraries were size-selected using double SPRI bead selection. Then the second PCR was performed with the same conditions in order to obtain the final library. DNA concentration was measured with a Qubit fluorometer,  and library sizes were determined using TapeStation. Libraries where sequenced on the Illumina NextSeq 500, obtaining an average of 20 million reads per sample.

treatment_protocol: 2.5mg/kg LPS injection

value: Brain

value: Microglia

tag: treatment

value: 2 weeks post LPS i.p

tag: genotype


title: BML3

value: Ventral Dentate Gyrus


title: 2 weeks LPS_4


title: 2 weeks LPS_2


title: Input_NonT_DLD1_rep2_ChIPSeq

tag: cell line

value: Input

value: non target shRNA


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G5_ad007

value: brain

value: male


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G5_ad006

value: ACA

value: VISp


title: DX9

value: MeDIP

tag: cell type


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G6_ad004


title: 2 weeks LPS_1


title: DX8


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G5_ad004


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G5_ad012

value: SSp

value: MOp


title: 24 hrs LPS_4

value: 24hrs post LPS i.p


title: DX7

description: obesity.dmr.results.csv.gz

value: obesity

value: dioxin


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G5_ad002

value: female


title: 24 hrs LPS_3

value: Brain


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G4_ad012


title: VML7

value: Male


title: VMH9


title: NML10

value: Basolateral Amygdala


title: 24 hrs LPS_2

value: Microglia


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G4_ad010


title: NM11

value: Nucleus Accumbens Shell


title: DX5

value: no disease

value: Sperm


title: 24 hrs LPS_1


title: DX4

description: obesity.dmr.results.csv.gz


title: BMH7


title: VML1

value: Ventral Dentate Gyrus


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G4_ad008

value: brain


title: DX1

description: kidney.dmr.results.csv.gz

value: kidney disease


title: VMH1


title: 12 hrs LPS_4

value: 12hrs post LPS i.p


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G4_ad004

value: ACA

value: VISp

value: male


title: DX2

value: MeDIP

value: late puberty


title: atac_ring1ab_2

city: Seville

first: Francisco

middle: José

last: Romero-Campero

address: Americo Vespucio 49

department: Institute for Plant Biochemistry and Photosynthesis

country: Spain

institute: University of Sevilla

data_processing:
Quality control  was performed using the software packges FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Quality trimming and adapters removal were performed using Trimmomatic
PCR duplicates were discarded from the mapped reads using Picard
Reads mapped to the blacklisted genomic regions were eliminated using samtools
Read mapping to the reference genome was performed using bowtie with parameters -v 2 --best --strata -m 1 (http://bowtie-bio.sourceforge.net/index.shtml)
Peak calling was performed using MACS2 with default parameters (https://github.com/taoliu/MACS)
BigWIG files with CPM normalized signal were generated using the deepTools utility bamCoverage with a bin size of 10 (https://deeptools.readthedocs.io/en/latest/)
Subsequent data analysis and visualization was performed using the R bioconductor packages ChIPpeakAnno, ChIPSeeker, limma and ClusterProfiler.
Genome_build: tair10
Supplementary_files_format_and_content: signal in bigWIG format

organism: Arabidopsis thaliana

extract_protocol:
Nuclei was extracted from 10-day-old whole seedlings. Next, 30,000 nuclei were counted and resuspended in 50 μL transposition reaction mix using the TruePrepTM DNA Library Prep Kit V2 for Illumina® (Vazyme, TD501). Reactions were incubated for 30 min at 37°C before isolation DNA using the VAHTSTM DNA Clean Beads (Vazyme, N411)
Libraries were prepared by PCR amplification using two index (i5 and i7) Illumina barcodes (Vazyme, TD202) with 13 cycles. Libraries were purified with a VAHTSTM DNA Clean Beads.

tag: ecotype

value: seedlings


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G4_ad007

value: SSp

value: MOp


title: VML11

value: Male


title: 12 hrs LPS_2

value: Brain

value: Microglia


title: 12 hrs LPS_3


title: DX6

value: no disease

value: dioxin


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G4_ad002

value: female


title: 12 hrs LPS_1


title: atac_ring1ab_1


title: ATFS-1 (null), repeat 3

city: Worcester

first: Julie

last: Zhu

state: MA

address: 364 Plantation Street

department: Molecular Cellular and Cancer Biology

institute: UMass Medical School

description:
Sample_null_3
processed data file: featureCounts.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were aligned to the C. elegans genome (WBcel235) using STAR (version 2.5.3a) with the following parameter (--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000).
featureCounts (subread-1.5.2) was used to count the features after the alignment.
Bioconductor packages edgeR (version 3.10.0 ) was used for differential gene expression analysis.
Genome_build: WBcel235 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000002985.6/)
Supplementary_files_format_and_content: featureCounts.txt: Tab-delimited text file includes the raw count values from featureCounts for each sample.

organism: Caenorhabditis elegans

source_name: L4 Worms

growth_protocol: Grew on OP50 20c to L4 stage.

extract_protocol:
Chloroform Ethanol extraction.
Illumina Index in adapters: TruSeq.
MultiPLEX single End.

treatment_protocol: None.

tag: strain/background

tag: genotype/variation

value: atfs-1 (null)

value: Whole body

tag: developmental stage


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G4_ad001

tag: strain

tag: age

value: brain

tag: source


title: ATFS-1 (null), repeat 2

description:
Sample_null_2
processed data file: featureCounts.txt


title: atac_lhp1_2


title: NT_4 (S16)

value: Steady state


title: 190607_CEMBA_mm_P56_P63_RS2_190607_P7_190607_P8_G3_ad006

value: ACA

tag: target

value: VISp

tag: gender


title: atac_lhp1_1


title: NT_3 (S15)


title: NT_2 (S14)