title: DMSO-treated NRK-52E cells at 72h, biological rep2


title: DMSO-treated NRK-52E cells at 24h, biological rep1

status: Public on Sep 20 2020

type: RNA

city: Manchester

first: Kate

last: Bloch

address: Alderley Park, Alderley Edge

country: United Kingdom

institute: Manchester University

description: Gene expression data from cells treated with chlorothalonil

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner.

data_processing: Signal condensation and normalization was performed using GC-RMA (Robust Multiarray Analysis algorithm) using GeneSpring GX11.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

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

growth_protocol: NRK-52E cells (DeLarco and Todaro, 1978) (ATCC, CRL-1571) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with 10% fetal calf serum, penicillin 100 I.U./ml, and streptomycin solution 100 µg/ml in a humidified 5% CO2 incubator at 370C.

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

treatment_protocol: NRK-52E cells were cultured to confluence on 6-well plates. Cells were then exposed to CHL dissolved in DMSO (0.1%) at the IC10 concentration at 72h (1.1 μM CHL) or DMSO only as control. After 6h, 24h and 72h the medium was removed and RNA was extracted from the cells. Three studies were conducted at each time point.

tag: cell line

tag: cell type

value: rat kidney epithelial proximal tubule cells

tag: genotype

value: Osborne-Mendel


title: DMSO-treated NRK-52E cells at 24h, biological rep2

value: NRK-52E cells (DeLarco and Todaro, 1978) (ATCC, CRL-1571)


title: DMSO-treated NRK-52E cells at 72h, biological rep3


title: Gorilla_cA5_NPC_Gorilla

type: SRA

city: La Jolla

first: Fred

middle: H

last: Gage

state: CA

address: 10010 N Torrey Pines Rd

country: USA

institute: The Salk Institute for Biological Studies

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
Gorilla_cA5

library_source: transcriptomic

data_processing:
RNA and ChIP-Seq: trim raw FASTQ files, SolexaQA++
RNA: alignment to hg19, STAR
RNA: alignment to panTro4, STAR
RNA: alignment to gorgor3, STAR
RNA: alignment to rhemac2, STAR
RNA: join all alignments for each sample and sort by read id
RNA: select reads mapped uniquely to each genome (3mm same species, 5 mm different species)
RNA: Count reads in genes corresponding to the hg19 transcriptome reference, HT-Seq
RNA: Transform counts to TPM
ChIP-Seq: Alignment to hg19, bowtie
ChIP-Seq: Peak Calling, HOMER
Genome_build: hg19 (grch37), pantro4 (CSAC 2.1.4), gorgor3 (gorGor3.1), and rhemac2(MGSC Merged 1.0)
Supplementary_files_format_and_content: tab-delimited text file

molecule: polyA RNA

organism: Gorilla

source_name: NPC

growth_protocol: Established iPSC colonies were kept in feeder-free conditions indefinitely and passed using mechanical dissociation. To obtain NPCs from iPSCs, embryoid bodies (EBs) were formed by mechanical dissociation of iPSC clusters and plated into low-adherence dishes in DMEM/F12 plus N2 and B27 (Invitrogen) medium in the presence of Noggin (R&D) for forebrain induction for approximately 7 days. Then, floating EBs were plated onto poly-ornithine/laminin (Sigma)-coated dishes in DMEM/F12 plus N2 and B27 (Invitrogen) with the addition of Noggin. Rosettes were collected after 7 days. Rosettes were then dissociated with accutase (Chemicon) and plated again onto coated dishes in DMEM/F12 plus N2 and B27 and 10 ng/ml of FGF2 (R&D). Homogeneous populations of NPCs were obtained after 1-2 passages with accutase under the same conditions. To obtain neurons, NPCs were cultured in DMEM/F12 plus N2 and B27 with the addition of laminin (1 µg/ml), BDNF (20 ng/ml), GDNF (20 ng/ml) and cyclic AMP (500 µg/ml) for up to 8 weeks.

extract_protocol:
Total cellular RNA was extracted from ~5x106 cells using the RNeasy Protect Mini kit or RNeasy Plus kit (Qiagen, Valencia, CA), according to the manufacturer's instructions.
PolyA+ RNA was fragmented and prepared into sequencing libraries using the Illumina TruSeq RNA sample preparation kit.

treatment_protocol: No additional treatment was performed

tag: individual

tag: Sex

value: M

tag: sh


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C12_ad007

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

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

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

tag: brain region

value: DG

value: male

tag: age

tag: strain


title: Chlorothalonil-treated NRK-52E cells at 24h, biological rep2


title: Chlorothalonil-treated NRK-52E cells at 24h, biological rep3


title: DMSO-treated NRK-52E cells at 6h, biological rep2


title: DMSO-treated NRK-52E cells at 6h, biological rep1


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C12_ad006


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C12_ad004


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C11_ad012


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C12_ad001


title: DMSO-treated NRK-52E cells at 6h, biological rep3


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C2_ad008


title: 12-P3

city: University Park

first: Hardik

last: Kundariya

state: PA

address: 361 N. Frear

institute: The Pennsylvania State University

data_processing:
Illumina for basecalling
The sequences were trimmed using trim_galore 0.4.1 and cutadapt 1.15  with cutoff 20
The sequences were aligned using Bismark (version 0.19.0) with default options.The deduplicate_bismark function in Bismark with default parameters was used to remove duplicated reads, and reads with  coverage greater than 500 were removed to control PCR bias.
tab-delimited file generated with bismark2bedGraph with options -CX --ample_memory
Genome_build: ITAG3.0
Supplementary_files_format_and_content: tab-delimited file, 1-based genomic coords with <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>fields

organism: Solanum lycopersicum

growth_protocol: Plants in the greenhouse were germinated on MetroMix 200 medium (SunGro) and maintained at 26-28°C with a 15-h day length and at 20-22.8°C with 9-h dark period.

extract_protocol:
ground tissue was processed with the DNeasy Plant Kit (Qiagen, Germany) for genomic DNA with RNA removal according to manufacturer protocol for subsequent bisulfite sequencing.
Genomic DNA was sonicated to 200-300bp by Covaris and the fragmented DNAs were tested by Gel-Electrophotometric and purified with MiniElute PCR Purification Kit (Qiagen, Germany), and incubated at 20 °C after adding End Repair Mix. DNA was purified, a single “A” nucleotide was added to the 3’ ends of blunt fragments, sample was re-purified and methylated adapter was added to 5’ and 3’ ends of each fragment. Fragments of 300–400bp were purified with QIAquick Gel Extraction Kit (Qiagen, Germany) and subjected to bisulfite treatment with the Methylation-Gold Kit (ZYMO), followed by PCR and gel purification (320–420bp fragments selected). Qualified libraries were paired-end sequenced on the Xten analyzer (150 bp read length

treatment_protocol: wedge grafting was carried out with seedlings at the two- to four-leaf stage following the procedure described in Yang et al, 2015

tag: cultivar

value: Rutgers

tag: genotype/variation

tag: developmental stage

tag: tissue

value: young leaves

tag: replicate type

value: biological rep 3


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C11_ad010


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C11_ad006


title: 13-P3

source_name: Rutgers/WT

value: Rutgers/Rutgers


title: 12-P2

value: biological rep 2


title: Chlorothalonil-treated NRK-52E cells at 6h, biological rep1


title: 12-P1

value: biological rep 1


title: 13-P2


title: Chlorothalonil-treated NRK-52E cells at 6h, biological rep3


title: Chlorothalonil-treated NRK-52E cells at 6h, biological rep2


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C11_ad001


title: Gorilla_cA2_NPC_Gorilla

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
Gorilla_cA2


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C11_ad002


title: 13-P1


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C10_ad012


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C11_ad008


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C11_ad007


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C10_ad007


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C11_ad004


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C12_ad002


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C10_ad004


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C10_ad002


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C10_ad006


title: Chlorothalonil-treated NRK-52E cells at 24h, biological rep1


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C1_ad012


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C1_ad001


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C10_ad010


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C10_ad001


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C1_ad007


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C1_ad010


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C1_ad004


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C1_ad006


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C1_ad002


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C12_ad012


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B9_ad012


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B9_ad001


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C1_ad008


title: CM24_8 week neuron_Chimp

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM24_R2

organism: Pan troglodytes

source_name: 8 week neuron

value: F


title: CM21_2 week neuron_Chimp

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM21_R2

source_name: 2 week neuron


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B9_ad007


title: CM22_4 week neuron_Chimp

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM22_R2

source_name: 4 week neuron


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B9_ad010


title: 5FdUR_UGI_HCT116_rep2_ctr

city: Budapest

first: Angela

last: Bekesi

address: Műegyetem rakpart 3.

department: Department of Applied Biotechnology and Food Science

country: Hungary

institute: Budapest University of Technology and Economics, Faculty of Chemical Technology and Biotechnology

description: control

data_processing:
Alignment of fastq files with bwa mem (version 0.7.17-r1194) using default parameters
SAM to BAM conversion and read sorting based on coordinates using samtools (version 1.9-50-g18be38a, and htslib version 1.9-90-ga80f5fd)
Marking duplicated reads in BAM files using picard-tools MarkDuplicates (version 2.18.5-SNAPSHOT)
Filtering out ambiguously mapped reads was done using samtools view (version 1.9): samtools view -b -h -q 1 NAME.sorted.dedup.bam -L list_of_chr_bam.bed -o NAME.MAPQfiltered.bam
Cell-type specific blacklists were defined as described in details in the Supplementary Material of the related publication. The corresponding blacklist was applied for each bam file using samtools view: samtools view -b -h NAME.MAPQfiltered.bam -L blacklist_HCT116.bed -o NAME.blacklist.bam -U NAME.filtered_blacklisted.bam
Filtered_blacklisted bam files of the corresponding replicates were merged using samtools merge (version 1.9). The following processing steps were performed on both individual replicates and the merged data also.
Scaled and smoothened coverage tracks were generated using the bamCoverage tool of the deepTools package (version 3.2.1). Bin size was set to 100bp, smoothening was performed with 5000 bases (--smoothLength 5000), reads were normalized to 1x sequencing coverage (--normalizeUsing RPGC), --effectiveGenomeSize 2793842910 --extendReads
Log2 ratio of treatment and input samples were calculated using the bigwigCompare tool of the deepTools package(version 3.2.1) and the genome scaled coverage track files of the enriched and the corresponding input samples. Binsize was set to 100bp. The resulting log2.bw files are uploaded to the GEO.
In the case of the two control pull-down experiments, the genome scaled smoothed coverage tracks were calculated on the same way, then these were re-scaled according to the amount of the pulled-down DNA, and subtracted from the corresponding IP samples. Then log2 ratio tracks were calculated with the corrected IP and the corresponding input samples. For details, see the Supplementary file 3 of the corresponding publication.The resulting log2.bw files are uploaded to the GEO.
Interval files of the enriched regions were derived from the log2.bw files according to minor processing steps described in the Supplementary Material of the related publication.
Genome_build: GRCh38 (GRCh38.d1.vd1.fa from https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files)
Supplementary_files_format_and_content: BigWig files containing log2 ratio coverage signal of enriched vs input samples for 100bp bins, smoothened for 5000bp. Files are provided for individual replicates of each sample, as well as for merged data.
Supplementary_files_format_and_content: BED files containing regions of uracil enrichment derived from the log2.bw files. Files are provided for individual replicates of each sample, as well as for merged data.
Supplementary_files_format_and_content: BigWig files containing log2 ratio coverage signal of enriched (that was corrected with a scaled coverage of control IP) vs input samples for 100bp bins, smoothened for 5000bp. Files are provided for replicate 2 of NT_UGI and 5FdUR_UGI samples.

organism: Homo sapiens

source_name: HCT116 cells

growth_protocol: HCT116 and HCT116 chr3+ cells were maintained in McCoy’s 5A and were stably transfected using retroviral transduction of EGFP-tagged UGI. Successfully transduced cells were collected by FACS sorting using a BD FACSAria III Cell sorter.

extract_protocol:
Genomic DNA was purified by Quick-DNA Miniprep Plus Kit (Zymo Research) and sonicated with a BioRuptor (Diagenode). Immunoprecipitation was carried out by FLAG-tagged sensor protein binding to uracil residues in fragmented genomic DNA and was followed by purification with anti-FLAG beads (Sigma-Aldrich). Control IP was done using anti-FLAG beads without the sensor construct.
DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For drug-treated samples, cells were treated with 20 µM 5-fluoro-2’-deoxyuridine (5FdUR) or 100 nM raltitrexed (RTX) for 48 hours.

tag: treatment

tag: transgene

value: UGI


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B9_ad006


title: CM23_6 week neuron_Chimp

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM23_R2

source_name: 6 week neuron


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B8_ad012


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B8_ad007


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B9_ad004


title: 2 week neuron_homerTF_input_WT126

description:
processed data file:
input_WT126_S26_R1_001

source_name: 2 week neuron_homerTF_input_WT126

extract_protocol:
ChIP was performed as previously described with minor modifications (Hawkins et al., 2010).
Libraries were constructed with the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs)

value: m


title: 2 week neuron_homerTF_input_WT33

description:
processed data file:
input_WT33_S25_R1_001

source_name: 2 week neuron_homerTF_input_WT33

value: f


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B9_ad002


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B8_ad010


title: 2 week neuron_homerTF_input_ADRC40

description:
processed data file:
input_ADRC40_S27_R1_001

source_name: 2 week neuron_homerTF_input_ADRC40


title: NT_UGI_HCT116_rep2_ctr

description: control

value: non-treated


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B8_ad001


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B8_ad004


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B8_ad002


title: 2 week neuron_homerTF_GATA3_WT33

description:
processed data file:
GATA3_WT33_S28_R1_001

source_name: 2 week neuron_homerTF_GATA3_WT33

tag: chip antibody

value: GATA3, Santa Cruz, sc-22206, lot #J2815


title: CMb9_2 week neuron_Human_shGATA3

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CMb9_wt33_G_1_2_S9_R1_001


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B7_ad004


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B8_ad006


title: 2 week neuron_homerTF_GATA3_WT126

description:
processed data file:
GATA3_WT126_S29_R1_001

source_name: 2 week neuron_homerTF_GATA3_WT126


title: 2 week neuron_homerTF_GATA3_ADRC40

description:
processed data file:
GATA3_ADRC40_S30_R1_001

source_name: 2 week neuron_homerTF_GATA3_ADRC40


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B8_ad008


title: CMb7_NPC_Human_shGATA3

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CMb7_wt33_G_1_0_S7_R1_001


title: CMb8_NPC_Human_shGATA3

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CMb8_wt33_G_2_0_S8_R1_001


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B7_ad010


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B7_ad008


title: CMb23_4 week neuron_Human_shGATA3

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CMb23_wt126_G_1_4_S23_R1_001


title: CEMBA190711_8J_1_CEMBA190711_8J_2_C10_ad008


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B7_ad006


title: CMb24_4 week neuron_Human_shGATA3

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CMb24_wt126_G_2_4_S24_R1_001


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B7_ad007


title: RTX_UGI_HCT116_H3K36me3

description: enriched

data_processing:
Alignment of fastq files with bwa mem (version 0.7.17-r1194) using default parameters
SAM to BAM conversion and read sorting based on coordinates using samtools (version 1.9-50-g18be38a, and htslib version 1.9-90-ga80f5fd)
Marking duplicated reads in BAM files using picard-tools MarkDuplicates (version 2.18.5-SNAPSHOT)
Filtering out ambiguously mapped reads was done using samtools view (version 1.9): samtools view -b -h -q 1 NAME.sorted.dedup.bam -L list_of_chr_bam.bed -o NAME.MAPQfiltered.bam
Cell-type specific blacklists were defined as described in details in the Supplementary Material of the related publication. The corresponding blacklist was applied for each bam file using samtools view: samtools view -b -h NAME.MAPQfiltered.bam -L blacklist_HCT116.bed -o NAME.blacklist.bam -U NAME.filtered_blacklisted.bam
Scaled coverage tracks were generated using the bamCoverage tool of the deepTools package (version 3.2.1). Bin size was set to 100bp, reads were normalized to 1x sequencing coverage (--normalizeUsing RPGC), --effectiveGenomeSize 2793842910 –extendReads
Ratio (fold change over control) tracks were calculated using the bigwigCompare tool of the deepTools package (version 3.2.1) and the genome scaled coverage track files of the enriched and an input (ENCFF489VMD from the ENCODE; https://www.encodeproject.org/search/?searchTerm=ENCFF489VMD+) samples. Binsize was set to 100bp. The resulting ratio.bw files are uploaded to  GEO.
BroadPeak.bed files containing peaks called by the MACS2 software at broad cutoff 0.05 using ENCFF489VMD from the ENCODE as a genomic background.
Genome_build: GRCh38 (GRCh38.d1.vd1.fa from https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files)
Supplementary_files_format_and_content: BigWig files containing fold change over control ratio coverage signal for 100bp bins.
Supplementary_files_format_and_content: BED files containing broad peaks called by MACS2.

source_name: HCT116  cells

growth_protocol: HCT116 cells were maintained in McCoy’s 5A and were stably transfected using retroviral transduction of EGFP-tagged UGI. Successfully transduced cells were collected by FACS sorting using a BD FACSAria III Cell sorter.

extract_protocol:
Chromatin was isolated from HCT116 cells after cross-linking with 1% paraformaldehyde for 10 min using detergent containing lysis buffers (for details see the corresponding publication). Chromatin was fragmented by sonication in a BioRuptor instrument yielding fragments beween 100 and 500 bp. For the immunoprecipitation, Pierce Protein A/G Magnetic Beads (Thermo Fisher Scientific) and anti-H3K36me3 (CST (Danvers, MA, US), cat.no.: 4909T) antibody were used. After precleaning the chromatin fragment extract on empty beads (3h, 4°C), incubation with the antibody was done overnight at 4°C, and then with the proteinA/G beads for further 7h. Precipitates were washed extensively, then eluted by 1% SDS and 0.1 M NaHCO3. Cross-linking was reverted by heating up to 65°C overnight. After RNase and proteinase K treatment, immunoprecipitated DNA was purified using NucleoSpin Gel and PCR Clean-up Kit  (MACHEREY-NAGEL GmbH & Co. KG, Düren, Germany). The enrichment was checked by qPCR targeting the beta-actin gene.
DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For drug-treated samples, cells were treated with 100 nM raltitrexed (RTX) for 48 hours.

tag: cell line

value: RTX


title: WT_K562_rep1_son

data_processing:
alignment of fastq files with bwa mem (version 0.7.17-r1194) using default parameters
SAM to BAM conversion and read sorting based on coordinates using samtools (version 1.9-50-g18be38a, and htslib version 1.9-90-ga80f5fd)
Marking duplicate reads in BAM files using picard-tools MarkDuplicates (version 2.18.5-SNAPSHOT)
Filtering out ambiguously mapped reads was done using samtools view (version 1.9): samtools view -b -h -q 1 NAME.sorted.dedup.bam -L list_of_chr_bam.bed -o NAME.MAPQfiltered.bam
Cell-type specific blacklists were defined as described in details in the Supplementary Material of the related publication. The corresponding blacklist was applied for each bam file using samtools view: samtools view -b -h NAME.MAPQfiltered.bam -L blacklist_HCT116.bed -o NAME.blacklist.bam -U NAME.filtered_blacklisted.bam
Filtered_blacklisted bam files of the corresponding replicates were merged using samtools merge (version 1.9). The following processing steps were performed on both individual replicates and the merged data also.
Scaled and smoothened coverage tracks were generated using the bamCoverage tool of the deepTools package (version 3.2.1). Bin size was set to 100bp, smoothening was performed with 5000 bases (--smoothLength 5000), reads were normalized to 1x sequencing coverage (--normalizeUsing RPGC), --effectiveGenomeSize 2793842910 --extendReads
Log2 ratio of treatment and input samples were calculated using the bigwigCompare tool of the deepTools package(version 3.2.1) and the genome scaled coverage track files of the enriched and the corresponding input samples. Binsize was set to 100bp. The resulting log2.bw files are uploaded to the GEO.
Interval files of the enriched regions were derived from the log2.bw files according to minor processing steps described in the Supplementary Material of the related publication.
Genome_build: GRCh38 (GRCh38.d1.vd1.fa from https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files)
Supplementary_files_format_and_content: BigWig files containing log2 ratio coverage signal of enriched vs input samples for 100bp bins, smoothened for 5000bp. Files are provided for individual replicates of each sample, as well as for merged data.
Supplementary_files_format_and_content: BED files containing regions of uracil enrichment derived from the log2.bw files. Files are provided for individual replicates of each sample, as well as for merged data.

source_name: K562 cells

growth_protocol: HCT116 and K562 cells were maintained in McCoy's 5A and RPMI media (Gibco), respectively. HCT116 cells were also stably transfected using retroviral transduction of EGFP-tagged UGI. Successfully transduced HCT116 cells were collected by FACS sorting using a BD FACSAria III Cell sorter.

extract_protocol:
Genomic DNA was purified by Quick-DNA Miniprep Plus Kit (Zymo Research) and sonicated with a BioRuptor (Diagenode). Immunoprecipitation was carried out by FLAG-tagged sensor protein binding to uracil residues in fragmented genomic DNA and was followed by purification with anti-FLAG beads (Sigma-Aldrich).
DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with 20 µM 5-fluoro-2'-deoxyuridine (5FdUR) or 100 nM raltitrexed (RTX) for 48 hours.

value: no transgene

tag: sample type

value: input


title: CMb21_2 week neuron_Human_shGATA3

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CMb21_wt126_G_1_2_S21_R1_001

value: M


title: bc51234-R5

type: genomic

city: New York

first: Ze-yan

last: Zhang

state: NY

address: 522 First Ave

department: Radiation Oncology

institute: NYU Langone Health

description: Sample 17

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan System using standard recommended Illumina scanner setting

data_processing: ChAMP v3.6; Average Beta

label: Cy5 and Cy3

source_name: Melanoma

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using QIAGEN AllPrep DNA/RNA/miRNA universal kit according to standard instructions

value: melanoma

tag: group

value: PLX4032 resistance clone

tag: barcode


title: NT_UGI_HCT116_H3K36me3

description: enriched


title: WT_K562_rep1_IP

value: enriched


title: bc345-2-R3

description: Sample 8


title: CMb22_2 week neuron_Human_shGATA3

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CMb22_wt126_G_2_2_S22_R1_001

tag: individual

tag: Sex


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B7_ad012

tag: brain region

value: DG

value: male


title: bc435-1-R4b

description: Sample 11


title: CMb20_NPC_Human_shGATA3

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CMb20_wt126_G_2_0_S20_R1_001

source_name: NPC

tag: sh


title: CMb19_NPC_Human_shGATA3

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CMb19_wt126_G_1_0_S19_R1_001


title: bc534-2-R5

description: Sample 15


title: CMb12_4 week neuron_Human_shGATA3

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CMb12_wt33_G_2_4_S12_R1_001


title: bc51234-R4

description: Sample 16


title: bc45-R4

description: Sample 9


title: bc2-1-R2a

description: Sample 5


title: bc435-1-R4a

description: Sample 10


title: bc2-1-R2b

description: Sample 6


title: CMb11_4 week neuron_Human_shGATA3

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CMb11_wt33_G_1_4_S11_R1_001


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B6_ad010

source_name: C57BL/6J Male P56 Mouse Brain

tag: age

tag: strain


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B6_ad004


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B6_ad008


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B6_ad007


title: CM9_2 week neuron_Human

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM9_R2


title: CMb10_2 week neuron_Human_shGATA3

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CMb10_wt33_G_2_2_S10_R1_001


title: bc345-1-R3

description: Sample 7


title: bc5-2-R5

description: Sample 14


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B6_ad001


title: CM5_2 week neuron_Human

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM5_R2


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B5_ad001


title: CM8_8 week neuron_Human

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM8_R2


title: CM7_6 week neuron_Human

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM7_R2


title: A375

description: Sample 1

value: control

value: Parental control


title: bc12-1-R1b

description: Sample 4


title: DMSO-A375

description: Sample 2

value: Parallel control


title: CM6_4 week neuron_Human

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM6_R2


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B5_ad010


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B5_ad006


title: CM14_4 week neuron_Human

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM14_R2

value: F


title: CM35_6 week neuron_Gorilla

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM35_R2


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B6_ad012


title: bc12-1-R1a

description: Sample 3


title: CM36_8 week neuron_Gorilla

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM36_R2


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B5_ad004


title: CM13_2 week neuron_Human

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM13_R2


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B5_ad007


title: CM11_6 week neuron_Human

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM11_R2


title: CM16_8 week neuron_Human

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM16_R2


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B5_ad012


title: bc41235-R5

description: Sample 13


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B5_ad002


title: CM34_4 week neuron_Gorilla

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM34_R2


title: CM31_6 week neuron_Gorilla

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM31_R2


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B5_ad008


title: CM33_2 week neuron_Gorilla

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM33_R2


title: pre-treatment breast cancer biopsy sample 547405

type: protein

city: Manassas

first: Julia

last: Wulfkuhle

state: VA

address: 10920 George Mason Circle

institute: George Mason University

description:
HER2: the status of the HER2 gene. 1 = positive; 0 = negative.
HR: the status of hormone (estrogen and progesterone) receptors.  1 = positive; 0 = negative.
pCR: the status of a pathological complete response (pCR).  1 = complete response; 0 = failed complete response
Arm: arm of the trial per patient - MK2206 arm' or 'Control arm'.
RPPA Array:  Platform Array version.  Key to convert from raw to normalized data.

hyb_protocol: Reverse phase protein array (RPPA)

scan_protocol: Reverse phase protein array (RPPA)

data_processing:
These samples were assayed on two different RPPA arrays (RPPA.1 and RPPA.2) under GPL28470.  Each individual array (containing hundreds of samples) was standardized as follows: (1) sample w/out replacement 5000 times, maintaining a receptor subtype balance equal to that of the first ~1000 patients (HR+HER2-: 0.384, TN:0.368, HR+HER2+:0.158, HR-HER2+:0.09); (2) calculate the mean(mean) and mean(sd) for each RPPA endpoint over the samples; (3) standardize each endpoint of the array, as y=(x-mean(mean))/mean(sd).  Standardized data from the different arrays was then combined.  This procedure resulted in removal of batch effects, without 'warping' due to mismatches in subtype prevalence.
Within the normalized, combined data matrix, each value is equivalent to a z-scored expression value (unitless).  Within the raw data matrix, entries represent intensity measurements.

label: RPPA Array

molecule: protein

source_name: pre-treatment breast cancer biopsy

label_protocol: Reverse phase protein array (RPPA)

extract_protocol: not provided

value: breast cancer biopsy

tag: hr

tag: pcr

tag: arm

value: MK2206 arm

tag: rppa normalization key


title: CM10_4 week neuron_Human

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM10_R2


title: CM32_8 week neuron_Gorilla

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM32_R2

source_name: 8 week neuron


title: pre-treatment breast cancer biopsy sample 929391

tag: tissue

value: Control arm


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B7_ad002


title: CM12_8 week neuron_Human

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM12_R2


title: X8CM_2 week neuron_Human_shctl

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
8CM2woneuronWT126cl8shCTR_S18_R1_001

source_name: 2 week neuron

value: ctl


title: pre-treatment breast cancer biopsy sample 116603


title: pre-treatment breast cancer biopsy sample 218503


title: CM29_2 week neuron_Gorilla

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM29_R2


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B4_ad001


title: X7CM_2 week neuron_Human_shctl

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
7CM2woneuronWT126cl8shCTR_S17_R1_001


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B4_ad010


title: pre-treatment breast cancer biopsy sample 517870


title: pre-treatment breast cancer biopsy sample 808714


title: B cells - Input_WT

city: Bethesda

first: Michael

last: Bustin

state: MD

address: Building 37, Room 3122

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Basecalling was performed using RTA version 2.4.11
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 1.8.4) allowing 1 mismatch.
Trimming of adapters and low-quality bases was performed using CutAdapt (v.1.16).
Reads were mapped to UCSC mm9 reference genome using BWA 07.17
Peak detection of enriched binding regions was performed using MACS2 v. 2.1.1.20160309 with the default settings
Genome_build: mm9
Supplementary_files_format_and_content: peak text files

source_name: B cells

growth_protocol: ChIP-seq were performed in Hmgn1+/+n2+/+ (WT) and Hmgn1-/- n2-/- (DKO) mouse ES, MEF and splenic B cells.

extract_protocol:
DNA were blunt ended, ligated to adapters, amplified with PCR and size selected. The libraries were sequenced at 75 bp read length with Illumina NextSeq 500 or 101bp with Hiseq 2000 by the NIH CCR-sequencing facility.
Libraries were prepared according to Illumina's instructions

tag: cells

value: Mouse splenic B cells-resting

tag: genotype/variation

value: WT

tag: antibody


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B4_ad006


title: X4CM_NPC_Human_shctl

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
4CMNPCWT126cl8shCTR_S14_R1_001


title: X3CM_NPC_Human_shctl

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
3CMNPCWT126cl8shCTR_S13_R1_001


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B4_ad002


title: bc41235-R4

description: Sample 12


title: B cells - Input_DKO

value: DKO


title: CM30_4 week neuron_Gorilla

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM30_R2

source_name: 4 week neuron

value: M


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B3_ad001


title: X2CM_NPC_Human_shctl

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
2CMNPCWT33cl1shCTR_S12_R1_001


title: X9CM_2 week neuron_Human_shctl

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
9CM2woneuronWT33cl1shCTR_S19_R1_001


title: B cells - Oct2_DKO_rep1


title: B cells - Oct2_DKO_rep2


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B4_ad008


title: X1CM_NPC_Human_shctl

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
1CMNPCWT33cl1shCTR_S11_R1_001


title: pre-treatment breast cancer biopsy sample 549172


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B3_ad012


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B3_ad007


title: pre-treatment breast cancer biopsy sample 294265


title: pre-treatment breast cancer biopsy sample 343898


title: X16CM_4 week neuron_Human_shctl

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
16CM4woneuronWT33cl1shCTR_S26_R1_001


title: pre-treatment breast cancer biopsy sample 863161


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B3_ad010


title: X15CM_4 week neuron_Human_shctl

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
15CM4woneuronWT33cl1shCTR_S25_R1_001


title: pre-treatment breast cancer biopsy sample 698094


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B6_ad006


title: pre-treatment breast cancer biopsy sample 845147


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B3_ad006


title: B cells - Oct2_WT_rep1


title: B cells - Pax5_DKO_rep2


title: X14CM_4 week neuron_Human_shctl

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
14CM4woneuronWT126cl8shCTR_S24_R1_001


title: pre-treatment breast cancer biopsy sample 729732


title: X13CM_4 week neuron_Human_shctl

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
13CM4woneuronWT126cl8shCTR_S23_R1_001


title: B cells - Oct2_WT_rep2


title: B cells - Pax5_WT_rep2


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B3_ad004


title: pre-treatment breast cancer biopsy sample 266840

description:
HER2: the status of the HER2 gene. 1 = positive; 0 = negative.
HR: the status of hormone (estrogen and progesterone) receptors.  1 = positive; 0 = negative.
pCR: the status of a pathological complete response (pCR).  1 = complete response; 0 = failed complete response
Arm: arm of the trial per patient - MK2206 arm' or 'Control arm'.
RPPA Array:  Platform Array version.  Key to convert from raw to normalized data.


title: X10CM_2 week neuron_Human_shctl

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
10CM2woneuronWT33cl1shCTR_S20_R1_001


title: B cells - Pax5_WT_rep1


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B3_ad008


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B4_ad012


title: pre-treatment breast cancer biopsy sample 309830


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B3_ad002


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B2_ad012


title: SAMP-3-9

first: Shurjo

middle: Kumar

last: Sen

address: 10 Center Drive, Room 7N317

institute: NHGRI

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-Seq reads from our carotid plaque samples were aligned with the STAR aligner, using the hg19 genome assembly and Ensembl transcript database (release 74). The STAR BAM output file was converted to WIG format using the bam2wig.py script from the RSeqC suite, and these WIG files were further converted to bigwig format using the wigToBigWig tool from the UCSC Genome Browser's binary utilities directory.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: carotid endarterectomy plaque sections

extract_protocol:
Total RNA was extracted from sets of thawed plaque cryosections using the Qiagen RNeasy Mini kit (Qiagen).
RNA libraries were prepared for sequencing using Illumina TruSeq Ribo-Zero Gold chemistry

value: carotid endarterectomy plaque sections

tag: pathology

value: diffuse intimal thickening


title: SAMP-3-8

value: fibroatheroma, non-calcified


title: pre-treatment breast cancer biopsy sample 929980


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B2_ad001

value: DG


title: B cells - Irf8_DKO_rep1


title: SAMP-3-7


title: pre-treatment breast cancer biopsy sample 501303


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B2_ad007

value: male


title: pre-treatment breast cancer biopsy sample 591810


title: B cells - Irf8_WT_rep2


title: B cells - Pax5_DKO_rep1


title: pre-treatment breast cancer biopsy sample 711476


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B2_ad006


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B2_ad004


title: SAMP-3-5

value: fibroatheroma with calcification


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B2_ad002


title: B cells - Ets1_DKO_rep1


title: SAMP-3-4


title: B cells - Irf8_DKO_rep2


title: B cells - Ets1_WT_rep2


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B2_ad008


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B12_ad012


title: pre-treatment breast cancer biopsy sample 518000


title: pre-treatment breast cancer biopsy sample 342959


title: B cells - Ets1_DKO_rep2


title: SAMP-3-6


title: pre-treatment breast cancer biopsy sample 573605


title: B cells - Ikaros_DKO_rep2

value: Ikaros


title: SAMP-3-3


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B12_ad010


title: SAMP-3-1


title: pre-treatment breast cancer biopsy sample 490023


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B12_ad008


title: B cells - Ikaros_DKO_rep1


title: B cells - Irf8_WT_rep1


title: CM15_6 week neuron_Human

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM15_R2

source_name: 6 week neuron


title: SAMP-2-9


title: B cells - Ets1_WT_rep1


title: pre-treatment breast cancer biopsy sample 317641


title: B cells - Ikaros_WT_rep2


title: B cells - Ikaros_WT_rep1


title: pre-treatment breast cancer biopsy sample 361701


title: pre-treatment breast cancer biopsy sample 220471


title: SAMP-2-7


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B12_ad006


title: SAMP-3-2


title: ES cells - Input_DKO

source_name: ES cells

value: Mouse embryonic stem cells


title: pre-treatment breast cancer biopsy sample 963303


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B12_ad004


title: SAMP-2-5

value: pathologic intimal thickening (with superficial macrophages)


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B12_ad002


title: SAMP-2-8


title: SAMP-2-3


title: ES cells - Input_WT


title: ES cells - Sox2_DKO_rep1


title: pre-treatment breast cancer biopsy sample 688955

value: breast cancer biopsy


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B12_ad001


title: pre-treatment breast cancer biopsy sample 317402

value: MK2206 arm


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B12_ad007


title: SAMP-2-4


title: pre-treatment breast cancer biopsy sample 779739


title: SAMP-2-6

value: intimal xanthoma


title: pre-treatment breast cancer biopsy sample 604199


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B11_ad010


title: ES cells - Sox2_WT_rep2


title: ES cells - Sox2_DKO_rep2


title: SAMP-2-14


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B11_ad008


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B11_ad012


title: SAMP-2-13

value: pathologic intimal thickening (macrophage poor)


title: pre-treatment breast cancer biopsy sample 180663


title: pre-treatment breast cancer biopsy sample 796558

value: Control arm


title: SAMP-2-12


title: ES cells - Nanog_DKO_rep2

value: Nanog


title: pre-treatment breast cancer biopsy sample 856159


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B11_ad006


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B11_ad004


title: SAMP-2-2


title: ES cells - Nanog_DKO_rep1

value: DKO


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B11_ad002


title: pre-treatment breast cancer biopsy sample 771443


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B10_ad012


title: ES cells - Nanog_WT_rep1

value: WT


title: ES cells - CTCF_DKO_rep2

value: CTCF


title: pre-treatment breast cancer biopsy sample 609642


title: SAMP-2-11

value: carotid endarterectomy plaque sections


title: ES cells - CTCF_DKO_rep1


title: ES cells - Sox2_WT_rep1


title: SAMP-2-1


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B10_ad008


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B10_ad007


title: ES cells - Nanog_WT_rep2


title: pre-treatment breast cancer biopsy sample 363669


title: pre-treatment breast cancer biopsy sample 578975


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B10_ad010


title: SAMP-1-9


title: pre-treatment breast cancer biopsy sample 651145


title: SAMP-1-8


title: ES cells - CTCF_WT_rep1


title: ES cells - CTCF_WT_rep2


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B10_ad006


title: SAMP-1-6

value: fibroatheroma, non-calcified


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B10_ad004

value: DG


title: SAMP-1-7


title: pre-treatment breast cancer biopsy sample 159352


title: SAMP-2-10


title: pre-treatment breast cancer biopsy sample 284593


title: ES cells - Klf4_DKO_rep2


title: SAMP-1-4


title: ES cells - Klf4_DKO_rep1


title: pre-treatment breast cancer biopsy sample 422454


title: SAMP-1-3

value: diffuse intimal thickening


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B1_ad012

value: male


title: SAMP-1-2


title: ES cells - Klf4_WT_rep1


title: ES cells - Klf4_WT_rep2


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B1_ad001


title: pre-treatment breast cancer biopsy sample 689076


title: pre-treatment breast cancer biopsy sample 824234


title: pre-treatment breast cancer biopsy sample 748583


title: ES cells - Brd4_DKO_rep2


title: pre-treatment breast cancer biopsy sample 801641


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B1_ad010


title: ES cells - Brd4_DKO_rep1


title: CM40_8 week neuron_Rhesus

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM40_R2

organism: Macaca mulatta

value: MT

value: M


title: ES cells - Brd4_WT_rep2

value: Mouse embryonic stem cells


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B1_ad004


title: pre-treatment breast cancer biopsy sample 752372

value: breast cancer biopsy


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B10_ad002


title: pre-treatment breast cancer biopsy sample 287961

value: MK2206 arm


title: MEF cells - Input_DKO

source_name: MEF cells

value: Mouse Embryonic Fibroblasts


title: CM38_4 week neuron_Rhesus

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM38_R2


title: CM37_2 week neuron_Rhesus

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM37_R2


title: SAMP-1-1


title: MEF cells - CEBPB_DKO_rep2

value: CEBPB


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A9_ad010


title: hnRNPab 4

city: Providence

first: Kimberly

last: Mowry

state: RI

address: 185 Meeting Street

department: MCB

institute: Brown University

data_processing:
Aligned raw data to Xenopus 9.2 genome with STAR 2.6.1b; Genome FASTA and .GTF file were downloaded from Xenbase.org (trimming reads was not found to have significant effect)
Generated counts files using HTSeq-count 0.9.1, again using the .GTF file from Xenbase
Differential expression analysis conducted with EdgeR
Final analysis and Q-value/logFC filtering conducted in R
Genome_build: XENLA_9.2_genome.fasta.gz
Supplementary_files_format_and_content: Each processed data file generated using htseq-count 0.9.1, contains count information for one replicate indexed to gene IDs used by Xenbase

organism: Xenopus laevis

source_name: Oocyte lysate enriched for L-bodies

extract_protocol:
Oocyte lysate was passed over a size exclusion chromatography column and fractions enriched for L-bodies were pooled. RNA in the pool was then immunoprecipitated with one of three antibodies, then extracted with Trizol and precipitated.
150bp Paired-end RNA-seq conducted by Genewiz on Illumina Hi-Seq (model # not provided)

tag: rna ip antibody

value: hnRNPab

tag: oocyte stage

value: Pool stage II-III


title: Staufen 4

value: Staufen


title: MEF cells - Input_WT

value: WT


title: MEF cells - CEBPB_DKO_rep1

value: DKO


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B1_ad006


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A9_ad007


title: IgG 4

value: IgG


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A9_ad006


title: pre-treatment breast cancer biopsy sample 130892


title: pre-treatment breast cancer biopsy sample 999733


title: pre-treatment breast cancer biopsy sample 753109


title: ES cells - Brd4_WT_rep1


title: CM39_6 week neuron_Rhesus

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM39_R2

tag: individual


title: MEF cells - CEBPB_WT_rep2


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B1_ad002

tag: Sex


title: hnRNPab 3


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A9_ad004

tag: brain region


title: pre-treatment breast cancer biopsy sample 413961


title: pre-treatment breast cancer biopsy sample 879224

value: Control arm


title: MEF cells - CEBPB_WT_rep1


title: pre-treatment breast cancer biopsy sample 654064


title: pre-treatment breast cancer biopsy sample 664111


title: Staufen 3


title: MEF cells - Brd3_DKO_rep2


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A9_ad001

value: DG


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A9_ad012


title: MEF cells - Brd3_DKO_rep1


title: pre-treatment breast cancer biopsy sample 294739


title: pre-treatment breast cancer biopsy sample 345907


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A8_ad004


title: MEF cells - Brd3_WT_rep2


title: MEF cells - Brd3_WT_rep1


title: Staufen 2


title: hnRNPab 2


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A8_ad007


title: MEF cells - P300_DKO_rep2


title: pre-treatment breast cancer biopsy sample 421917


title: pre-treatment breast cancer biopsy sample 839274


title: hnRNPab 1


title: SAMP-1-10

value: carotid endarterectomy plaque sections

value: fibroatheroma with calcification


title: IgG 2


title: pre-treatment breast cancer biopsy sample 885871


title: Staufen 1


title: MEF cells - P300_WT_rep2


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A8_ad001

value: male


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A7_ad012


title: IgG 3


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A7_ad001


title: pre-treatment breast cancer biopsy sample 319324


title: pre-treatment breast cancer biopsy sample 477994


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A8_ad010


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A7_ad007


title: MEF cells - P300_WT_rep1


title: MEF cells - Histone H1_DKO_rep1

value: Histone H1


title: MEF cells - Histone H1_DKO_rep2


title: pre-treatment breast cancer biopsy sample 635632


title: pre-treatment breast cancer biopsy sample 614434


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A7_ad010


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A7_ad006


title: PLX4032 resistant clone, bc51234-R5

data_processing:
Illumina's base-calling software used for basecalling.
Reads were trimmed for adapters and quality with Trimmomatic version 0.36 and aligned to the human reference genome (hg38) with STAR version 2.5 using standard settings.
Genes-samples counts matrix was generated using featureCounts with standard settings.
Differentially expressed genes (DEGs) were analyzed with DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Comma Separated Values (CSV) file includes FPKM values for each sample

extract_protocol:
Total RNA was harvested using QIAGEN AllPrep DNA/RNA/miRNA universal kit. Illumina TruSeq Stranded mRNA Prep kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: melanoma cell line A375

tag: group

value: PLX4032 resistant clone

tag: barcode


title: MEF cells - Histone H1_WT_rep2

tag: strain


title: PLX4032 resistant clone, bc51234-R4


title: MEF cells - P300_DKO_rep1


title: pre-treatment breast cancer biopsy sample 252748

value: breast cancer biopsy

tag: hr

tag: pcr


title: pre-treatment breast cancer biopsy sample 402384

tag: arm

value: MK2206 arm

tag: rppa normalization key


title: PLX4032 resistant clone, bc534-2-R5


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A7_ad004

tag: age


title: MEF cells - Histone H1_WT_rep1

tag: cells

value: Mouse Embryonic Fibroblasts

tag: genotype/variation


title: pre-treatment breast cancer biopsy sample 834418

tag: tissue


title: PLX4032 resistant clone, bc5-2-R5


title: MEF cells - H3K27ac_DKO_rep2

tag: antibody


title: pre-treatment breast cancer biopsy sample 219545


title: pre-treatment breast cancer biopsy sample 861745


title: MEF cells - H3K27ac_DKO_rep1


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A7_ad008


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A6_ad012


title: PLX4032 resistant clone, bc41235-R5


title: IgG 1

tag: rna ip antibody

tag: oocyte stage


title: PLX4032 resistant clone, bc41235-R4


title: MEF cells - H3K27ac_WT_rep1


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A6_ad007

tag: Sex


title: MEF cells - H3K27me3_DKO_rep2


title: PLX4032 resistant clone, bc435-1-R4b


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A7_ad002

tag: brain region


title: PLX4032 resistant clone, bc435-1-R4a

tag: cell line


title: pre-treatment breast cancer biopsy sample 520986


title: pre-treatment breast cancer biopsy sample 532183


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A6_ad006


title: pre-treatment breast cancer biopsy sample 601489


title: MEF cells - H3K27me3_DKO_rep1


title: PLX4032 resistant clone, bc45-R4

tag: group


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A6_ad004


title: pre-treatment breast cancer biopsy sample 639663


title: MEF cells - H3K27me3_WT_rep2


title: PLX4032 resistant clone, bc345-2-R3

tag: barcode


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A6_ad002

tag: strain


title: MEF cells - H3K27ac_WT_rep2


title: pre-treatment breast cancer biopsy sample 263143

tag: hr


title: pre-treatment breast cancer biopsy sample 179369

tag: pcr


title: PLX4032 resistant clone, bc345-1-R3


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A6_ad001


title: MEF cells - H3K27me3_WT_rep1


title: PLX4032 resistant clone, bc2-1-R2b


title: pre-treatment breast cancer biopsy sample 778527

tag: arm


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A5_ad012


title: PLX4032 resistant clone, bc2-1-R2a


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A5_ad001


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A5_ad010


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A5_ad006


title: pre-treatment breast cancer biopsy sample 539904

tag: rppa normalization key


title: pre-treatment breast cancer biopsy sample 679787


title: pre-treatment breast cancer biopsy sample 752469


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A5_ad004

tag: age


title: PLX4032 resistant clone, bc12-1-R1b


title: PLX4032 resistant clone, bc12-1-R1a


title: pre-treatment breast cancer biopsy sample 384830


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A5_ad002


title: Control, DMSO-A375

value: Parallel control


title: pre-treatment breast cancer biopsy sample 293142


title: Control, A375

value: Parental control


title: C-dm-3

data_processing:
Illumina for basecalling
Alignments were performed using STAR (version 2.7.3a) with –twopassMode = Basic and –outFilterMultimapNmax = 1  parameters  (Grant et al., 2011)
The read count data were generated from the BAM files by using QoRTs software package (Hartley and Mullikin, 2015) --minMAPQ 25 --dropChrom Pt,Mt
edgeR (version 3.26.8) was used to calculate the differential expression.
Genome_build: Arabidopsis TAIR 10
Supplementary_files_format_and_content: Text file with GENEID and COUNTS to be used with edgeR

organism: Arabidopsis thaliana

growth_protocol: Seeds were grown on 0.5M MS growth medium at 12hrs daylenght (22 °C, 120-150 μmol/(m^2*s) light)

extract_protocol:
Total RNA from each sample was extracted by NucleoSpin RNA Plant kit (Macherey-Nagel, Germany) following manufacturer’s protocol, including genomic DNA removal.
RNA libraries were constructed as described in the TruSeq RNA Sample Preparation v2 Guide.

treatment_protocol: 3 progenies plants from each Col-0 on msh1; Col-0 on dcl2,3,4,msh1 grafts were sequenced. Roots after 12 days were flash freezed in liquid nitrogen.  Tissues were ground by motor and pestle in liquid nitrogen.

tag: ecotype background

tag: developmental stage

value: 12 days old plants

value: root

tag: replicate type

value: biological rep 3


title: pre-treatment breast cancer biopsy sample 938719

tag: tissue


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A4_ad010


title: C-dm-2

tag: genotype/variation

value: biological rep 2


title: pre-treatment breast cancer biopsy sample 506623


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A4_ad006


title: pre-treatment breast cancer biopsy sample 706169

value: Control arm


title: C-dm-1

value: biological rep 1


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A4_ad004

value: DG


title: pre-treatment breast cancer biopsy sample 783427


title: C-m-2


title: C-m-3


title: pre-treatment breast cancer biopsy sample 970839


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A4_ad008


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A5_ad008


title: pre-treatment breast cancer biopsy sample 732137


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A3_ad012


title: pre-treatment breast cancer biopsy sample 172168


title: R-18

growth_protocol: Seeds were sown on peat mix in square pots in reach-in chambers at 12hrs daylenght (22 °C, 120-150 μmol/(m^2*s) light)

treatment_protocol: 3 progenies plants from each Col-0 on msh1; Col-0 on dcl2,3,4,msh1; Col-0 on Col-0 grafts were sequenced. Leaves at bolting were flash freezed in liquid nitrogen. Tissues were ground by motor and pestle in liquid nitrogen.

value: bolting

value: rosette leaves


title: pre-treatment breast cancer biopsy sample 755914


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B1_ad007

value: male


title: C-m-1


title: pre-treatment breast cancer biopsy sample 580541


title: pre-treatment breast cancer biopsy sample 323721


title: R-16


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A3_ad010


title: R-15


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A3_ad001


title: pre-treatment breast cancer biopsy sample 414971


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A3_ad004


title: R-14


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A3_ad002


title: CEMBA190711_8J_1_CEMBA190711_8J_2_B1_ad008


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A3_ad006


title: pre-treatment breast cancer biopsy sample 887594


title: R-13


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A4_ad002


title: pre-treatment breast cancer biopsy sample 706639


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A3_ad008


title: R-17


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A2_ad004


title: pre-treatment breast cancer biopsy sample 748611


title: R-11


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A2_ad012


title: pre-treatment breast cancer biopsy sample 786753


title: R-10


title: pre-treatment breast cancer biopsy sample 332655


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A2_ad010


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A2_ad006


title: D3MGT_bcn_1

city: Chapel Hill

first: Li

last: Wang

state: NC

address: 111 Mason Farm Rd, Chapel Hill, NC 27599

department: UNC

institute: University of North Carolina at Chapel Hill

description: D3MGT_bcn_sort_deDup_merge_macs_peaks.txt

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
For RNAseq, the quality of sequencing results was first checked by FASTQC. Reads are in high-quality and no trimming was required. The processed reads were then mapped to mouse genome of mm10 by BBMap with default parameters. The generated BAM files were sorted and indexed using SAMtools. Reads were counted using featureCounts.
ATACseq reads with exact matches were used in demultiplexing with bcl2fastq (2.18.0.12). Reads were aligned to mouse reference genome (MM10_UCSC) using Bowtie2 with default parameters. Filtering  of properly paired reads with high mapping quality (MAPQ score> 10) was performed using SAMTools. PCR duplicate reads were removed using Picard tools MarkDuplicates module (http://broadinstitute.github.io/picard/).  ATACseq peak regions of merged biological duplicate samples were called using MACS2 with parameters -f BAMPE -g mm --nomodel -q 0.01. Peak raw counts were counted using bamCoverage of deepTools v. 3.1. The signal distribution around each transcription start site (TSS) (from 1kb upstream to 1kp downstream) were computed in computeMatrix and heatmaps were plotted in plotHeatmap of deeptools. Differential binding sites were identified using R package Diffbind, and those of significant difference (FDR < 0.05) between indicated samples were functionally annotated with nearby genes in GREAT v 3.0.0 with Basal plus extension mode.
Genome_build: UCSC_Mm10
Supplementary_files_format_and_content: tab-delimited text files containing CPM values for each sample

source_name: cardiac

growth_protocol: Cell were maintained in iCM medium (10% FBS in DMEM/M199 (4:1)) .

extract_protocol:
Total RNAs of cells were extracted using Trizol. Around 50,000 cells were collected from each sample and subjected to chromatin extraction, transposition, PCR amplification and purification according to standard ATACseq protocol.
Illumina libraries were prepared using TrueSeq Standard mRNA Sample Preparation Kit.

treatment_protocol: Freshly isolated cardiac fiborblasts were seeded into one well of a 6-well plate. On the following day, pMXs-LacZ or pMXs-MGT retrovirus were added to the cells. Twenty-four hours later, lentiviral shNT or shBecn1 were added to LacZ ot MGT transduced cells respectively. After another three and five days, cells were collected for either RNAseq or ATACseq.

value: heart

tag: genotype

value: wild type


title: D3MGT_bcn_2


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A2_ad002

tag: Sex


title: pre-treatment breast cancer biopsy sample 416434

value: breast cancer biopsy


title: D3MGT_NT_2

description: D3MGT_NT_sort_deDup_merge_macs_peaks.txt


title: pre-treatment breast cancer biopsy sample 727804

value: MK2206 arm


title: D3MGT_NT_1


title: pre-treatment breast cancer biopsy sample 375954


title: R-12


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A12_ad010

tag: brain region


title: D3Z_bcn_2


title: D3Z_NT_2


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A12_ad006


title: D3Z_bcn_1


title: pre-treatment breast cancer biopsy sample 132463


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A12_ad004


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A12_ad008


title: pre-treatment breast cancer biopsy sample 162562


title: D3Z_NT_1


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A12_ad002


title: pre-treatment breast cancer biopsy sample 637566


title: SR27

data_processing:
Trimmed data provided by BGI-Tech (Shenzhen, China) were used for the downstream processing
Small RNA-seq data were aligned to the Arabidopsis thaliana genome assembly (version TAIR10) using ShortStack (version 3.8.3; https://github.com/MikeAxtell/ShortStack/releases; Johnson et al., 2016) with default parameters except that the 'align-only' switch was activated
Each library was individually aligned, followed by merging the resultant bam files using samtools merge (Li et al., 2009)
Resulting clusters were used for control and treatment comparison
Genome_build: Arabidopsis thaliana genome assembly (version TAIR10)
Supplementary_files_format_and_content: tab-delimited file, <seqnames/chromosome>  <start position>  <end position> <strand> <name/cluster name>  <counts>

source_name: msh1_leaves_small RNA

extract_protocol:
sRNA extraction using NucleoSpin miRNA Plant Kit (Macherey-Nagel, Germany)
sRNA-seq libraries were constructed using the Illumina TruSeq Small RNA Sample Preparation Kit and sequenced on a BGISEQ-500 with a single-end 50-bp run length

treatment_protocol: 3 progenies plants from each Col-0 on msh1; Col-0 on dcl2,3,4,msh1 grafts were sequenced. 3 plants from msh1 mutant and dcl2,3,4,msh1 quadruple mitant rootstocks were sequenced. Leaves at bolting were flash freezed in liquid nitrogen.  Tissues were ground by motor and pestle in liquid nitrogen.

tag: molecule subtype

value: Small RNA


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A11_ad012


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A12_ad012


title: SR25


title: SR26


title: pre-treatment breast cancer biopsy sample 123660


title: pre-treatment breast cancer biopsy sample 200222


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A11_ad010


title: SR21

source_name: dcl2,3,4,msh1_leaves_small RNA


title: pre-treatment breast cancer biopsy sample 905264


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A11_ad007


title: pre-treatment breast cancer biopsy sample 535415


title: SR20


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A11_ad006


title: pre-treatment breast cancer biopsy sample 233191


title: SR19


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A11_ad004


title: pre-treatment breast cancer biopsy sample 629371


title: SR18

source_name: Col-0/dcl2,3,4,msh1_leaves_small RNA


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A11_ad002


title: SR17


title: pre-treatment breast cancer biopsy sample 797639


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A10_ad006


title: SR16


title: pre-treatment breast cancer biopsy sample 609151


title: pre-treatment breast cancer biopsy sample 700549


title: pre-treatment breast cancer biopsy sample 572793


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A10_ad010


title: SR15

source_name: Col-0/msh1_leaves_small RNA


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A10_ad012


title: pre-treatment breast cancer biopsy sample 136536


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A10_ad008


title: pre-treatment breast cancer biopsy sample 803677


title: SR14


title: pre-treatment breast cancer biopsy sample 712276


title: SR13


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A10_ad004


title: pre-treatment breast cancer biopsy sample 946927


title: pre-treatment breast cancer biopsy sample 183831


title: pre-treatment breast cancer biopsy sample 426106


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A1_ad004


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A10_ad002


title: BS-19

data_processing:
Illumina for basecalling
The sequences were trimmed using trim_galore 0.4.1 and cutadapt 1.15  with cutoff 20
The sequences were aligned using Bismark (version 0.19.0) with default options.The deduplicate_bismark function in Bismark with default parameters was used to remove duplicated reads, and reads with  coverage greater than 500 were removed to control PCR bias.
tab-delimited file generated with bismark2bedGraph with options -CX --ample_memory
Genome_build: Arabidopsis TAIR 10
Supplementary_files_format_and_content: tab-delimited file, 1-based genomic coords with <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>fields

extract_protocol:
genomic DNA extraction using DNeasy Plant kit (Qiagen, Germany).
Genomic DNA Sonicated to 100-300 bp fragments and purified with MiniElute PCR Purification Kit (Qiagen, Germany), incubated at 20 ℃ after add End Repair Mix. Then purified and added a single ‘A’ nucleotide to the 3’ ends of the blunt fragments, purified again and add Methylated Adapter to the 5’ and 3’ ends of each fragment. Then fragments with 300bp-400bp size-range were purified with QIAquick Gel Extraction kit (Qiagen, Germany) and subjected to bisulfite treatment by using Methylation-Gold kit (ZYMO). Followed with PCR and gel purification (350bp-400bp range fragments were selected). Qualified libraries sequenced pair end on the HiSeq X-ten system.

treatment_protocol: 3 progenies plants from each Col-0 on msh1; Col-0 on dcl2,3,4,msh1; Col-0 on Col-0 grafts were sequenced. 3 plants from msh1 mutant and dcl2,3,4,msh1 quadruple mitant rootstocks were sequenced. Leaves at bolting were flash freezed in liquid nitrogen.  Tissues were ground by motor and pestle in liquid nitrogen.


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A1_ad010


title: BS-20


title: BS-25


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A11_ad008


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A1_ad007


title: BS-27


title: pre-treatment breast cancer biopsy sample 255388


title: pre-treatment breast cancer biopsy sample 590220


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A1_ad008


title: BS-26


title: pre-treatment breast cancer biopsy sample 955953


title: pre-treatment breast cancer biopsy sample 771813


title: pre-treatment breast cancer biopsy sample 145513


title: BS-21


title: BS-17


title: BS-16


title: BS-18


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A1_ad001


title: pre-treatment breast cancer biopsy sample 414286


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A1_ad012


title: pre-treatment breast cancer biopsy sample 107700


title: pre-treatment breast cancer biopsy sample 960963


title: BS-15


title: pre-treatment breast cancer biopsy sample 809037


title: BS-14


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A1_ad006


title: BS-13


title: BS-12


title: pre-treatment breast cancer biopsy sample 515565


title: pre-treatment breast cancer biopsy sample 286984


title: BS-11


title: BS-10


title: pre-treatment breast cancer biopsy sample 835137


title: pre-treatment breast cancer biopsy sample 680881


title: R_DR_P3

data_processing:
Illumina for basecalling
Raw sequencing reads were quality-controlled trimmed with TrimGalore! (version 0.4.1). Trimmed reads were then aligned to the ITAG3.0 tomato reference genome using using STAR (version 2.7.3a ) with –twopassMode = Basic and –outFilterMultimapNmax = 1 parameters, retaining only uniquely mapped reads.
The read count data were generated from the BAM files by using QoRTs software package (version v1.3.0) with –minMAPQ = 25 option.
Genome_build: ITAG3.0
Supplementary_files_format_and_content: tab-delimited, <GeneID> <read count>

extract_protocol:
ground tissue was used for RNA extraction, including DNA removal, using NucleoSpin RNA Plant Kit (Macherey-Nagel, Germany).
RNA libraries were constructed as described in the TruSeq RNA Sample Preparation v2 Guide.
with the High Output, 75-bp read, paired-end option (at least 60 million reads per sample) in a NextSeq analyzer (Illumina, USA)

tag: cultivar

value: Rutgers

value: young leaves


title: CEMBA190711_8J_1_CEMBA190711_8J_2_A10_ad001

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


title: pre-treatment breast cancer biopsy sample 775346


title: Rhesus_cA3_NPC_Rhesus

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
Rhesus_cA3

data_processing:
RNA and ChIP-Seq: trim raw FASTQ files, SolexaQA++
RNA: alignment to hg19, STAR
RNA: alignment to panTro4, STAR
RNA: alignment to gorgor3, STAR
RNA: alignment to rhemac2, STAR
RNA: join all alignments for each sample and sort by read id
RNA: select reads mapped uniquely to each genome (3mm same species, 5 mm different species)
RNA: Count reads in genes corresponding to the hg19 transcriptome reference, HT-Seq
RNA: Transform counts to TPM
ChIP-Seq: Alignment to hg19, bowtie
ChIP-Seq: Peak Calling, HOMER
Genome_build: hg19 (grch37), pantro4 (CSAC 2.1.4), gorgor3 (gorGor3.1), and rhemac2(MGSC Merged 1.0)
Supplementary_files_format_and_content: tab-delimited text file

source_name: NPC

extract_protocol:
Total cellular RNA was extracted from ~5x106 cells using the RNeasy Protect Mini kit or RNeasy Plus kit (Qiagen, Valencia, CA), according to the manufacturer's instructions.
PolyA+ RNA was fragmented and prepared into sequencing libraries using the Illumina TruSeq RNA sample preparation kit.

tag: individual

value: Rhesus

value: M

tag: sh


title: R_DR_P1


title: Rhesus_cA2_NPC_Rhesus

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
Rhesus_cA2


title: R_DR_P2


title: pre-treatment breast cancer biopsy sample 520258

tag: hr


title: Rhesus_cA1_NPC_Rhesus

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
Rhesus_cA1


title: Chimp_00818_c8_NPC_Chimp

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
Chimp_00818_c8

value: F


title: R_R_P3

source_name: Rutgers/WT

value: Rutgers/Rutgers

value: biological rep 3


title: pre-treatment breast cancer biopsy sample 112606

source_name: pre-treatment breast cancer biopsy

tag: pcr

value: Control arm


title: pre-treatment breast cancer biopsy sample 357017

tag: arm


title: R_R_P2

value: biological rep 2


title: pre-treatment breast cancer biopsy sample 395076

tag: rppa normalization key


title: R_R_P1

value: biological rep 1


title: MCF7_S_1

city: Cheras

first: norlaily

last: mohd ali

state: Selangor

address: Universiti Tunku Abdul Rahman, Jln Sg Long

department: Faculty of Medicine and Health Sciences

country: Malaysia

institute: Universiti Tunku Abdul Rahman

description: Gene expression data of MCF-7 spheroid

hyb_protocol: Following ligation, 21.5ul of biotin-labeled sample were hybridized for 16 hours at 48C on GeneChip miRNA 4.0 arrays.GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The raw CEL files were processed using the Affymetrix Expression Console Software (build 1.3.1) with microRNA arrays-RNA + DABG-Human only normalization to produce CHP files for each of the 6 samples. The six CHP files were then imported into the Affymetrix Transcriptome Analysis Console (TAC) 3.0 (build 3.0.0.466) using the Gene Level Differential Analysis option. Three conditions were created using TAC. One-way between-subject ANOVA (unpaired) were used as the algorithm options, and the default filter criteria was fold change >2 and <-2. The ANOVA p-value was set at <0.05.

label: Biotin

source_name: Cultured MCF-7 spheroid cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (FlashTaq Biotin HSR RNA Labeling kit, Affymetrix, 2013).

growth_protocol: The monolayer and spheroid MCF-7 cells were cultured in tissue culture-treated flasks and as suspension spheroid respectively. Both are maintained in 5% CO2 humidified incubator.

extract_protocol: Total RNA with retention of small RNAs from the cells were extracted using miRNeasy kit according to the manufacturer's instructions

tag: cell line

tag: cell source

value: Estrogen-dependent human breast adenocarcinoma

tag: culture condition

value: Spheroid


title: pre-treatment breast cancer biopsy sample 942017


title: MCF7_S_2

description: Gene expression data of MCF-7 spheroid


title: Chimp_00818_c5_NPC_Chimp

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
Chimp_00818_c5


title: MCF7_S_3

description: Gene expression data of MCF-7 spheroid


title: MCF7_P_2

description: Gene expression data of MCF-7 monolayer

source_name: Cultured MCF-7 monolayer cells

value: Monolayer


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H9_ad002

status: Public on Sep 19 2020

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

source_name: C57BL/6J Male P56 Mouse Brain

value: CA

value: male

tag: age

tag: strain


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H8_ad008


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H8_ad007


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H8_ad001


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H8_ad002


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H9_ad008


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H7_ad008


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H6_ad007


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H6_ad001


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H7_ad007


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H5_ad008


title: MCF7_P_1

description: Gene expression data of MCF-7 monolayer


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H7_ad002


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H6_ad002


title: MCF7_P_3

description: Gene expression data of MCF-7 monolayer


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H5_ad007


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H7_ad001


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H5_ad001


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H4_ad001


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H2_ad007


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H4_ad008


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H9_ad007


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H2_ad002


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H2_ad008


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H4_ad002


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H6_ad008


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H5_ad002


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H12_ad008


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H12_ad007


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H11_ad007


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H11_ad002


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H10_ad001


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H10_ad008


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H12_ad002


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H10_ad002


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H12_ad001


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H4_ad007


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G9_ad010


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G9_ad001


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G9_ad006


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G9_ad012


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H1_ad002


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H1_ad001


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H1_ad007


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G9_ad004


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H1_ad008


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H2_ad001


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G9_ad007


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G8_ad001


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G8_ad012


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G9_ad008


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G8_ad007


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G8_ad010


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G8_ad006


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G8_ad004


title: CEMBA190716_8E_3_CEMBA190716_8E_4_H11_ad001


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G7_ad012


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G7_ad002


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G7_ad004


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G6_ad002


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G5_ad001


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G6_ad001


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G7_ad006


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G6_ad012


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G7_ad007


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G5_ad007


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G6_ad006


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G6_ad007


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G5_ad012


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G7_ad008


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G9_ad002


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G6_ad004


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G6_ad008


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G6_ad010


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G5_ad006


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G5_ad004


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G5_ad002


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G5_ad008


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G4_ad012


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G4_ad007


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G8_ad002


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G4_ad006


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G7_ad001


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G7_ad010


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G4_ad010


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G4_ad004


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G4_ad002


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G4_ad008


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G3_ad001


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G3_ad012


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G3_ad007


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G2_ad001


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G2_ad010


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G2_ad007


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G2_ad006


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G2_ad002


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G3_ad006


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G2_ad004


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G12_ad010


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G2_ad008


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G12_ad008


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G12_ad002


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G12_ad006


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G11_ad012


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G12_ad001


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G11_ad010


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G12_ad007


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G11_ad008


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G3_ad004


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G11_ad001


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G10_ad012


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G11_ad004


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G10_ad010


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G12_ad012


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G10_ad006


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G10_ad008


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G10_ad002


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G10_ad004


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G12_ad004


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G10_ad001


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G1_ad006


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G1_ad001


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G1_ad004


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G1_ad007


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G10_ad007


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G11_ad006


title: CEMBA190716_8E_3_CEMBA190716_8E_4_F9_ad012


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G1_ad008


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G11_ad002


title: CEMBA190716_8E_3_CEMBA190716_8E_4_F9_ad001


title: CEMBA190716_8E_3_CEMBA190716_8E_4_F9_ad007


title: CEMBA190716_8E_3_CEMBA190716_8E_4_F9_ad006


title: CEMBA190716_8E_3_CEMBA190716_8E_4_G3_ad010


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