title: FAIRE_C2C12_NFIA_day0

city: Tokyo

first: Hironori

last: Waki

address: Hongo 7-3-1, Bunkyo-ku

institute: The University of Tokyo

data_processing:
Sequence reads were aligned to the mm9 genome assembly using Bowtie2 version 2.3.4 with default parameters.
Peak calling were performed using MACS2 version 2.1.1.20160309 with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files showing the peaks of each samples.

source_name: C2C12 myoblasts

growth_protocol: C2C12 myoblasts were mainteined in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
Samples were treated by nuclear extraction buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) for 10 minutes and immediately cross-linked with 1% formaldehyde for 7.5 minutes at room temperature. Cross-linking was quenched using 125 mM glycine for 5 minutes. The chromatin was sheared by probe sonicator (Branson) and was spun at 15,000rpm for 5 minutes. Antibodies were added for overnight incubation at 4C. Mix of Protein A and Protein G magnetic beads (Thermo Scientific) were added to samples for 4h at 4C. Subsequent procedures were performed as described previously (Hiraike Y., Waki H. et.al. 2017).
ChIP-seq libraries were prepared using KAPA hyper prep kit (KAPA Biosystems) according to the manufacturer's instructions.

treatment_protocol: At the confluence, cells were treated for 48 hours in medium containing 10% FBS, 0.5mM isobuylmethylxanthine, 125nM indomethacin, 1 μM dexamethosone, 850nM insulin, 1nM T3 and 1 μM rosiglitazone. After 48 hours, cells were switched to medium containing 10% FBS, 850nM insulin, 1nM T3 and 1 μM rosiglitazone.

tag: time course

value: day 0

tag: antibody

tag: cell line

value: myoblasts


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E3_ad008

status: Public on Sep 22 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

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

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

tag: brain region

value: PAL

tag: Sex

value: male

tag: age

tag: strain


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E3_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E3_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E4_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E2_ad002


title: BC6017: primary breast cancer patient 214

type: RNA

city: Mainz

first: Marcus

last: Schmidt

address: Langenbeckstr. 1

department: Universitäres Centrum für Tumorerkrankungen

country: Germany

institute: Universitätsmedizin Mainz

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133a Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Raw expression data (CEL files) were normalized using frozen robust multiarray analysis (fRMA)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: primary breast cancer tissue

label_protocol: Starting from 5 µg total RNA, labeled cRNA was prepared using the Roche Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit, according to the manufacturerâ€™s instructions

extract_protocol: Approximately 50 mg of frozen breast tumor tissue was crushed in liquid nitrogen. RLT-Buffer was added and the homogenate was centrifuged through a QIAshredder column (QIAGEN, Hilden, Germany). RNeasy extraction (QIAGEN) of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: For all tumors, samples were snap frozen and stored at -80°C. Tumor cell content exceeded 40% in all samples.

tag: tissue

value: primary breast cancer

tag: node

tag: grade

tag: t-size (mm)

tag: adjuvant treatment

tag: intrinsic subtype


title: PBMC CR replicate 04

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent Gene Expression Hybridization Kit. Samples were applied to 4*44K microarrays enclosed in Agilent SureHyb hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations and finally covered with an ozone-barrier slide.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (10.7.3.1) to obtain raw median signal and background values for both Cy5 and Cy3. QC checks were done on raw data and all arrays passed. Spots with a mean signal higher than twice the background value over all arrays and both channels were considered to be expressed. Data was normalized according to Pellis et al. (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.

organism: Rattus norvegicus

label_protocol: 200 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously by van Schothorst et al. (Anal Biochem 2007;363:315-7). We selected 5 random samples per genotype for Cy3 labelling as basis for the reference pool.

extract_protocol: Total RNA was isolated from peripheral blood mononuclear cells (PBMC) using RNeasy Mini columns (Qiagen) according to the manufacturer’s instruction, quantified using Nanodrop (IsoGen Life Science) and qualified using Experion Automated Electrophoresis System (BioRad).

treatment_protocol: Sixteen rats were mated and the dams continued pregnancy (controls) or were subsequently caloric restricted (CR) for 20% during days 1-12. Control female/male offspring continued normal lactation, while offspring of CR-treated dams received either normal lactation (CR group) or received during lactation until PN21 leptin supplementation at an average level of five times the amount in mother's milk (CR-L group). After four months ad libitum feeding with chow, a blood sample was drawn and PBMC were isolated and snap frozen in liquid nitrogen.

tag: cell type

value: Rat PBMC

source_name: PBMC, reference pool of all samples


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E2_ad001


title: PBMC WT replicate 05

source_name: peripheral blood mononuclear cells (PBMC)


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E2_ad008


title: BC6012: primary breast cancer patient 209


title: PBMC WT replicate 04


title: BC6015: primary breast cancer patient 212


title: BC6014_E: primary breast cancer patient 211


title: FAIRE_C2C12_ctrl_day0

country: Japan


title: PBMC WT replicate 02


title: PBMC WT replicate 03


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E2_ad010


title: BC6009: primary breast cancer patient 207


title: BC6013: primary breast cancer patient 210


title: PBMC WT replicate 01


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E3_ad002


title: BC6011: primary breast cancer patient 208


title: BC6008: primary breast cancer patient 206


title: BC6006: primary breast cancer patient 204


title: BC6007: primary breast cancer patient 205


title: BC6005wdh: primary breast cancer patient 203


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E2_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E2_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E12_ad002


title: BC6003wdh: primary breast cancer patient 201


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E12_ad004


title: BC6002wdh: primary breast cancer patient 200


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E12_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E12_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E2_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E12_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E12_ad008


title: BC6001wdh: primary breast cancer patient 199


title: BC6004wdh: primary breast cancer patient 202


title: BC5602: primary breast cancer patient 198

value: tamoxifen


title: BC5496_2: primary breast cancer patient 195


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E12_ad010


title: BC5601: primary breast cancer patient 197

data_processing:
CEL file not available for this patient
Raw expression data (CEL files) were normalized using frozen robust multiarray analysis (fRMA)

value: adj chemo


title: BC5600: primary breast cancer patient 196


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E11_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E11_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E11_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E11_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E11_ad012


title: BC5491: primary breast cancer patient 193


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E11_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E11_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E11_ad006


title: BC5488: primary breast cancer patient 190


title: BC5490: primary breast cancer patient 192


title: BC5489: primary breast cancer patient 191


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E10_ad012


title: BC5486: primary breast cancer patient 189


title: BC5478: primary breast cancer patient 186


title: BC5482: primary breast cancer patient 188


title: BC5480: primary breast cancer patient 187


title: BC5475: primary breast cancer patient 184


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E10_ad002


title: BC5493_3: primary breast cancer patient 194


title: BC5476: primary breast cancer patient 185


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E10_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E1_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E1_ad008


title: BC5471_2: primary breast cancer patient 180


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E1_ad012


title: BC5473: primary breast cancer patient 182


title: BC5474: primary breast cancer patient 183


title: BC5472_2: primary breast cancer patient 181


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E10_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E1_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E1_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E1_ad001


title: BC5464: primary breast cancer patient 176


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D9_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E1_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D9_ad012


title: BC5470_2: primary breast cancer patient 179


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D9_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E10_ad008


title: BC5462: primary breast cancer patient 174


title: BC5468: primary breast cancer patient 178


title: BC5466: primary breast cancer patient 177


title: BC5463: primary breast cancer patient 175


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E1_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D9_ad006


title: BC5460: primary breast cancer patient 172


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D9_ad002


title: BC5461: primary breast cancer patient 173


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D8_ad012


title: BC5459: primary breast cancer patient 171


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D9_ad004


title: BC5455: primary breast cancer patient 167


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D9_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D9_ad008


title: BC5456: primary breast cancer patient 168


title: BC5458: primary breast cancer patient 170


title: BC5451: primary breast cancer patient 164


title: BC5457: primary breast cancer patient 169


title: BC5452: primary breast cancer patient 165


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D8_ad001


title: BC5449: primary breast cancer patient 163


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D8_ad002


title: BC5453_2: primary breast cancer patient 166


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D8_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D8_ad008


title: BC5448: primary breast cancer patient 162


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D7_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D7_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D7_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D7_ad010


title: BC5445: primary breast cancer patient 159


title: BC5447: primary breast cancer patient 161


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D7_ad008


title: BC5443: primary breast cancer patient 157


title: BC5444: primary breast cancer patient 158


title: BC5442: primary breast cancer patient 156


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D7_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D7_ad004


title: BC5441: primary breast cancer patient 155


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D8_ad010


title: BC5440: primary breast cancer patient 154


title: BC5438: primary breast cancer patient 153


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D8_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D7_ad001


title: BC5434: primary breast cancer patient 150


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D6_ad012


title: BC5436: primary breast cancer patient 151


title: BC5446: primary breast cancer patient 160


title: BC5431: primary breast cancer patient 148


title: BC5430: primary breast cancer patient 147


title: BC5427: primary breast cancer patient 145


title: BC5429: primary breast cancer patient 146


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D6_ad010


title: BC5437: primary breast cancer patient 152


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D6_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D6_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D6_ad008


title: BC5426: primary breast cancer patient 144


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D4_ad007


title: BC5432_3: primary breast cancer patient 149


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D4_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D4_ad010


title: BC5424_2: primary breast cancer patient 142


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D4_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D6_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D4_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D3_ad012


title: BC5421: primary breast cancer patient 140


title: MDA-MB-231_Silencer-KO_Clone1

city: Macau

first: Gang

last: Li

address: Avenida da Universidade, Taipa

department: Faculty of Health Sciences

country: Macau

institute: University of Macau

description: MDA-MB-231_WT_vs_Silencer-KO_Gene_RawCount_RefSeq.txt

library_source: transcriptomic

data_processing:
Illumina RTA software was used for basecalling and Illumina bcl2fastq 2.17 software was used for demultiplexing.
Sequencing reads were trimmed using TrimGalore v0.4.5 and mapped to GRCh38 human reference genome using STAR v2.6.1d with default parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene expression was quantified using featureCount v1.6.3 with RefSeq gene annotation.

source_name: Breast cancer cell line

growth_protocol: MDA-MB-231 and MCF-7 cells were cultured at 37 °C in DMEM supplemented with 10% fetal bovine serum (Invitrogen) in an incubator with 5% CO2.

extract_protocol:
Cells were harvested at desired time points for total RNA isolation using RNeasy Mini kit (Qiagen).
RNA-seq library was prepared using the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina.

treatment_protocol: We used CRISPR-Cas9 system to delete 1780 bp fragment of the silencer region and transfected the PX459-sgRNAs to MDA-MB-231 and MCF-7 cells. After 48h, the cells were selected with 1ug/ml puromacin to get positive clones.

tag: genotype

value: Silencer KO


title: BC5416_3: primary breast cancer patient 136


title: BC5420: primary breast cancer patient 139


title: BC5422: primary breast cancer patient 141


title: BC5418: primary breast cancer patient 138


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D6_ad002


title: BC5415: primary breast cancer patient 135


title: BC5425: primary breast cancer patient 143


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D3_ad008


title: BC5413: primary breast cancer patient 133


title: MDA-MB-231_WT_Rep1

value: WT


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D4_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D3_ad004


title: BC5414: primary breast cancer patient 134


title: MCF-7_Silencer-KO_Clone1

description: MCF-7_WT_vs_Silencer-KO_Gene_RawCount_RefSeq.txt


title: MDA-MB-231_WT_Rep2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D8_ad004


title: MCF-7_Silencer-KO_Clone2


title: MDA-MB-231_Silencer-KO_Clone2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D3_ad006


title: MCF-7_WT_Rep2


title: MCF-7_WT_Rep1


title: AC_2019_01_15_55 [DS4]

city: Genova

first: Laura

last: Cancedda

state: Genova

address: Via Morego, 30

department: Brain Development and Disease

country: Italy

institute: Italian Institute of Technology

data_processing:
Single end reads underwent quality check using FastQC
Sequence reads were trimmed using Trim Galore software (0.5.0) to remove adapter sequences and low-quality end bases.
Alignment was performed with STAR (v2.7) on the indication provided by the UCSC Genome Browser for human (hg38) genome build.
Aligned reads were counted using htseq-count in HTSeq package (v0.10.0) with -mode=intersection-nonempty.
Only uniquely mapped reads were used for gene expression analysis and all genes multiple mapping (>20%) were removed.
Genes with <1 cpm (counts per million) in less than n-1 samples were also removed. Outlier samples after performing PCA were filtered out.
Differential expression analysis was performed using edgeR (v3.26.8)
Genome_build: hg38
Supplementary_files_format_and_content: processed files contain normalized counts for all samples and differential expression values from edgeR, in tab delimited format

molecule: polyA RNA

source_name: Down syndrome_brain

extract_protocol:
QIAzol, Qiagen miRNeasy kit
Lexogen Quantseq 3’mRNA-Seq Library Prep Kit FWD

tag: diagnosis

value: Down syndrome

value: hippocampus

tag: rin


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D3_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D3_ad002


title: AC_2019_01_15_52 [DS1]


title: BC5417_2: primary breast cancer patient 137


title: AC_2019_01_15_56 [DS5]


title: AC_2019_01_15_51 [C5]

source_name: Neurologically normal_brain

value: Neurologically normal


title: AC_2019_01_15_50 [C4]


title: AC_2019_01_15_54 [DS3]


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D3_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D3_ad007


title: AC_2019_01_15_48 [C2]


title: BC5408: primary breast cancer patient 129


title: AC_2019_01_15_47 [C1]


title: BC5411: primary breast cancer patient 131


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D2_ad001


title: AC_2019_01_15_49 [C3]


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D2_ad006


title: ChIP_C2C12_deltapro#3_day0

tag: time course

value: FLAG M2


title: BC5405: primary breast cancer patient 126


title: ChIP_C2C12_ctrl_day0

tag: antibody


title: BC5412: primary breast cancer patient 132


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D2_ad008


title: BC5406: primary breast cancer patient 127


title: BC5410: primary breast cancer patient 130


title: BC5407: primary breast cancer patient 128


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D2_ad012


title: BC5404: primary breast cancer patient 125


title: BC5403: primary breast cancer patient 124


title: H_vestibular_vascular_endothelium

city: Baltimore

first: Seth

last: Ament

state: MD

address: 670 W Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

data_processing:
Sequenced reads were mapped to Mouse GRCm38 reference using the TopHat v 1.0.0 aligner
Read counts were calculated for each sample
Genome_build: M. musculus (GRCm38)
Supplementary_files_format_and_content: Matrix table with TPM for each sample.

source_name: vestibular vascular endothelium

extract_protocol:
Inner ears from newborn ICR mice were dissociated, stained antibodies for CD326, CD49f and CD34, and soted to the different cell types.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental time point

value: Postnatal Day 0

value: vestibule

value: vascular endothelium


title: F_vestibular_mesenchyme

source_name: vestibular mesenchyme

value: mesenchyme


title: G_vestibular_neurons

source_name: vestibular neurons

value: neurons


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D12_ad006

tag: brain region

value: PAL


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D12_ad004

tag: Sex

value: male


title: B_cochlea_mesenchyme

source_name: cochlea mesenchyme

value: cochlea


title: E_vestibular_sensory

source_name: vestibular sensory

value: epithelial


title: C_cochlea_neurons

source_name: cochlea neurons


title: D_cochlea_vascular_endothelium

source_name: cochlea vascular endothelium


title: A_cochlea_sensory

source_name: cochlea sensory


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D12_ad007

tag: age


title: FAIRE_C2C12_deltapro#3_day0

value: day 0

tag: cell line

value: myoblasts


title: BC5399: primary breast cancer patient 120

tag: tissue

value: primary breast cancer

value: tamoxifen


title: Lacrimal gland, PI3K-aa_Rep2

city: New york

first: Xin

last: Zhang

state: New york

department: Ophthalmology

institute: Columbia University

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming.
We map the reads to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm9) using Tophat [1] (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.
We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks [2] (version 2.0.2) with default settings.
We test for differentially expressed genes under various conditions using DEseq [3]. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Genome_build: Mouse: UCSC/mm9
Supplementary_files_format_and_content: counts, Excel file with normalized values using DE-seq

source_name: Lacrimal gland

extract_protocol: After tissue harvest, RNA was extracted using Qiagen kit. Conversion to cDNA as well as amplification was performed by Clontech SMART-seq v4 Ultra low input RNA kit, as well as cDNA library construction was performed using Nextera XT DNA library preparation kit by core facility at Columbia university prior to RNA sequencing. After preparation of cDNA library, each sample was sequenced using Illumina platform.

treatment_protocol: Embryos were flash frozen in OCT

value: Le-Cre; PI3K alpha flox/flox, PI3K beta flox/flox

tag: strain

value: mixed background

value: Lacrimal gland


title: Lacrimal gland, PI3K-aR_Rep3

value: Le-Cre; PI3K alpha RBD/flox,  PI3K beta flox/flox


title: Lacrimal gland, PI3K-aR_Rep2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D12_ad012


title: Lacrimal gland, PI3K-aR_Rep1


title: BC5400: primary breast cancer patient 121

tag: node

tag: grade


title: Lacrimal gland, PI3K-aa_Rep3


title: Lacrimal gland, PI3K-aa_Rep1


title: ChIP_C2C12_NFIA_day0

source_name: C2C12 myoblasts

value: FLAG M2


title: BC5398: primary breast cancer patient 119

tag: t-size (mm)

tag: adjuvant treatment


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D12_ad002

source_name: C57BL/6J Male P56 Mouse Brain


title: Lacrimal gland, WT_Rep2

value: Le-Cre


title: BC5397: primary breast cancer patient 118

source_name: primary breast cancer tissue

tag: intrinsic subtype


title: Lacrimal gland, WT_Rep3

tag: genotype


title: BC5396_2: primary breast cancer patient 117


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D12_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D12_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D11_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D11_ad007


title: BC5402: primary breast cancer patient 123


title: BC5401: primary breast cancer patient 122


title: Lacrimal gland, WT_Rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D11_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D11_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D11_ad006


title: BC5395: primary breast cancer patient 116


title: WT MO VACV rep3

city: New York

middle: M

last: Luna

state: NY

address: 1230 York Ave #64

institute: The Rockefeller University

data_processing:
Alignment: Fastq files were processed with kallisto on a transcript index built from Ensembl release 95 mm10 trancripts with VACV transcripts derived from accession no. NC_006998.1
Expression testing: kallisto transcript output was processed with tximport to convert to gene level count, transformed with limma-voom, and expression testing was performed for for indicated contrasts after fitting a linear model.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes gene symbol, count matrix per sample, and DGE testing for key contrasts

source_name: Monocytes

extract_protocol:
Lung AECII or monocyte RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kits or NEBNext Ultra II Directional RNA Library Prep Kits were used with 100ng - 1ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina of NEB protocols for poly A mRNA selection and library construction

tag: treatment

value: VACV

value: Wildtype


title: WT MO C7 rep1


title: WT MO VACV rep1


title: WT MO VACV rep2


title: WT MO C7 rep4


title: WT MO C7 rep3


title: WT MO VACV rep4


title: WT MO C7 rep2


title: WT MO mock rep3

value: mock


title: WT MO mock rep1


title: WT MO mock rep2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D11_ad010

value: PAL


title: BC5394: primary breast cancer patient 115


title: BC5393: primary breast cancer patient 114


title: BC5391: primary breast cancer patient 112


title: WT AECII IFNB rep2

source_name: AECII

value: IFNB


title: WT AECII IFNB rep1


title: WT AECII C7 rep2


title: BC5390: primary breast cancer patient 111


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D11_ad004

value: male


title: BC5389: primary breast cancer patient 110


title: BC5388: primary breast cancer patient 109


title: WT AECII C7 rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D10_ad001


title: WT AECII mock rep2


title: MDA5/STING KO AECII C7 rep2

value: MDA5/STING KO


title: WT AECII mock rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D10_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D10_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D10_ad006


title: MDA5/STING KO AECII C7 rep1


title: BC5387: primary breast cancer patient 108


title: MDA5/STING KO AECII mock rep2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D10_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D10_ad004


title: RNA_ingSVF_Cre_NFIA_day7_rep3

data_processing:
Sequence reads were aligned to the mm9 genome assembly using STAR version 2.5.3a with the following parameters --runThreadN 10 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --limitBAMsortRAM 16000000000 --genomeDir MMUC --readFilesIn Read1.fastq Read2.fastq  --outFilterMultimapNmax 1
Read counts for each gene were derived from the STAR output file named "ReadsPerGene.out.tab" and the matched strand count was used for further processes.
Genome_build: mm9
Supplementary_files_format_and_content: txt files showing FPKM value of each samples .

source_name: ingSVF

growth_protocol: SVF cells were mainteined in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using Trizol reagent (Life Techologies) and RNeasy Mini Kit (Qiagen).
Libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.

value: ingSVF cells


title: RNA_ingSVF_Cre_deltapro#3_day7_rep1


title: RNA_ingSVF_Cre_deltapro#3_day7_rep2


title: RNA_ingSVF_Cre_deltapro#3_day7_rep3


title: RNA_ingSVF_Cre_NFIA_day7_rep2


title: BC5386: primary breast cancer patient 107


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D1_ad007


title: BC5385: primary breast cancer patient 106


title: BC5383: primary breast cancer patient 104


title: BC5384: primary breast cancer patient 105


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D1_ad010


title: BC5382_2: primary breast cancer patient 103

value: adj chemo


title: BC5392: primary breast cancer patient 113

value: primary breast cancer


title: MDA5/STING KO AECII mock rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D1_ad001


title: Patient3' plasma cells exosome

city: Chengdu

first: Shentao

last: Zhou

address: Chengdu

country: China

institute: West China Second University Hospital

data_processing:
For RNA-seq data, reads were aligned to the human genome (hg38) using STAR (v2.5). Gene expression counts were calculated by STAR with parameter: --quantMode GeneCounts. RNA-Seq expression file contains raw counts for all genes
For small RNA-Seq, adpters were removed by Cutadapt. Clean reads were mapped to miRBase version 21 (www.mirbase.org) by BWA software.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each Sample.

source_name: Primary plasma cells

growth_protocol: cells were cultured in RPMI-1640 containing 10% FBS and 100 U/ml penicillin-streptomycin mixture(both from Gibco-BRL, Grand Island, NY, USA).

extract_protocol:
Total RNA was extracted using the High Pure RNA paraffin kit (Roche Applied Science, Indianapolis, IN). And for small RNA sequencing, small RNA was isolated from total RNA by gel electrophoresis.
The libraries were sequenced on the Illumina HiSeq platform (Novogen, China).
Small RNA-Seq and RNA-Seq

treatment_protocol: miR-330-3p mimic and respective contronls were obtained from RiboBio(Guangzhou, China). They were separately transfected into cells using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer's instructions.

value: Primary plasma cells

tag: cell type

value: protocell

value: harvest the cell cultured medium


title: Patient2' plasma cells exosome


title: BC5379: primary breast cancer patient 101

value: tamoxifen


title: RNA_ingSVF_Cre_NFIA_day7_rep1

tag: time course


title: RNA_ingSVF_Cre_day7_rep3


title: Patient1' plasma cells exosome


title: OVCAR3 transfected with miR-330-3p mimic

source_name: ovarian cancer cell line,transfected with miR-330-3p mimic

value: ovarian cancer cell line

value: miR-330-3p mimic


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D1_ad004


title: COV318 transfected with miR-330-3p mimic rep2


title: BC5380: primary breast cancer patient 102


title: BC5377: primary breast cancer patient 99


title: RNA_ingSVF_Cre_day7_rep1


title: BC5378: primary breast cancer patient 100


title: RNA_ingSVF_Cre_day7_rep2


title: RNA_ingSVF_ctrl_day7_rep3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D1_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D1_ad002


title: BC5376: primary breast cancer patient 98


title: COV318 transfected with miR-330-3p mimic rep1


title: RNA_ingSVF_ctrl_day7_rep1


title: RNA_ingSVF_ctrl_day7_rep2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D1_ad012


title: RNA_ingSVF_Cre_deltapro#3_day0_rep3


title: COV318 transfected with miR-330-3p mimic rep3


title: COV318 control rep3

source_name: ovarian cancer cell line,treatment-naïve

value: Treatment-naive


title: RNA_ingSVF_Cre_deltapro#3_day0_rep2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C9_ad004


title: BC5374: primary breast cancer patient 96


title: CEMBA181016_5H_1_CEMBA181016_5H_2_D1_ad008


title: COV318 control rep2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C9_ad008


title: BC5375: primary breast cancer patient 97


title: COV318 control rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C9_ad012


title: BC5373: primary breast cancer patient 95


title: RNA_ingSVF_Cre_deltapro#3_day0_rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C9_ad006


title: EHC16 (0186_030_CE_NOR_1TR1)

city: CDMX

first: Luis Manuel

last: Teran Juarez

state: Ciudad de México

address: Calz. de Tlalpan 4502, Belisario Domínguez Secc 16, Tlalpan,

department: immunogenetics and allergy

country: Mexico

institute: Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas

data_processing:
basecalling and demultiplexing with Illumina bcl2fastq v2
alignment to reference genome with hisat2-2.0.1-beta (default parameters)
read counting and RPKM calculation with in-house software
R package DESQ 2 was used
Genome_build: GRCh38

source_name: Nasal turbinate

growth_protocol: Nasal airway epithelial cells were isolated from nasal polyps and N-ERD non-affected nasal mucosal epithelial cells, which were obtained from N-ERD patients undergoing polypectomy for therapeutic reasons. Cells were grown in Bronchial Epithelial Cell Growth Medium BulletKit (BEGM), Clonetics, USA under standard conditions. When cells reached 80% confluence, they were harvested and the pellet was dissolved in 0.01 M PBS, and 3 to 4 volumes of RNAlater (Invitrogen, USA) was added for future RNA extraction and was stored in -70ºC.

extract_protocol:
Epithelial cells are pelleted and RNAlater is removed and resuspended with RLT and beta mercaptoethanol and was extracted with RNeasy microkit using QIAcube standard protocol. QC, Agilent bioanalyzer pico RNA and HS DNA kits, and invitrogen qubit for quantifications (both RNA and DNA)
Library was prepared using Illumina Truseq RNA V2, TruSeq PE Cluster Kit v3-cBot-HS and TruSeq SBS Kit v3 - HS (50-cycles) (twice) sequencing on Illumina hiseq 2500 using standard Illumina protocols

value: Primary epithelial cells

value: N-ERD non polyp nasal mucosa


title: BC5372: primary breast cancer patient 94


title: RNA_ingSVF_Cre_NFIA_day0_rep2


title: EP16 (0186_029_CE_DIS_1TR1)

value: N-ERD nasal polyps


title: BC5371: primary breast cancer patient 93


title: OVCAR3 control


title: EHc13 (0186_024_CE_NOR_1TR1)


title: EHc9 (0186_021_CE_NOR_1TR1)


title: RNA_ingSVF_Cre_day0_rep3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C9_ad007

value: PAL


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C8_ad008


title: BC5368: primary breast cancer patient 90


title: BC5370: primary breast cancer patient 92


title: RNA_ingSVF_Cre_day0_rep1


title: RNA_ingSVF_Cre_day0_rep2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C8_ad010


title: BC5369: primary breast cancer patient 91


title: EHc5 (0186_018_CE_NOR_1TR1)


title: RNA_ingSVF_Cre_NFIA_day0_rep3


title: BC5367: primary breast cancer patient 89


title: EHc6 (0186_019_CE_NOR_1TR1)


title: BC5366: primary breast cancer patient 88


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C9_ad010


title: RNA_ingSVF_ctrl_day0_rep3


title: BC5365: primary breast cancer patient 87


title: BC5364: primary breast cancer patient 86


title: RNA_ingSVF_ctrl_day0_rep2


title: EHc3 (0186_016_CE_NOR_1TR1)


title: EHc8 (0186_020_CE_NOR_1TR1)


title: BC5361: primary breast cancer patient 84


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C8_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C8_ad007


title: RNA_ingSVF_ctrl_day0_rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C8_ad012


title: RNA_ingSVF_Cre_NFIA_day0_rep1


title: EP11 (0186_011_CE_DIS_1TR1)


title: EP10 (0186_010_CE_DIS_1TR1)


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C8_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C7_ad007


title: EHc4 (0186_017_CE_NOR_1TR1)


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C7_ad008


title: leukemic iMLL-AF9+ Lin- ckitlow cells from mice with nestin+ cell depletion (I)

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
The quality, quantity and the size distribution of the Illumina libraries were determined using the DNA-1000 Kit (Agilent Bioanalyzer).
Libraries were sequenced on the Illumina HiSeq 2500 system following the standard RNA sequencing protocol with the TruSeq SBS Kit v5.
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline.
Sequencing adaptor contaminations were removed from reads using cutadapt (Marcel Martin) and the resulting reads were mapped on the transcriptome (GRCm38 Ensembl gene-build 76) and quantified using RSEM v1.17 (Li and Dewey, 2011).
Genome_build: GRCm38 assembly, Ensembl genebuild 76
Supplementary_files_format_and_content: TMM normalized counts per million table with genes as rows and samples as columns

source_name: Bone marrow

growth_protocol: Fresh mouse primary cells; leukemia was induced with doxycicline and mice were sacrificed once leukemia was evident due to high WBC in peripheric blood.

extract_protocol:
Total RNA was isolated using the Arcturus Picopure RNA Isolation Kit (Thermo Fisher Scientific).
The RNA sequencing library was prepared with the TruSeq RNA Sample Preparation v2 Kit (Illumina, San Diego, CA) to construct index-tagged cDNA.
RNA was amplified and prepared for RNA-Seq using the Ovation RNA-Seq System v2 (NuGEN).

treatment_protocol: Bones were crushed to get a cell suspension. After RBC lysis, cells were sortered as MLL-AF9+ Lin- ckitlow cells. Pellets were frozen at -80C to following obtain mRNA.

value: leukemic iMLL-AF9+ Lin- ckitlow cells

tag: genotype/variation

value: nestin+ cell depletion


title: leukemic iMLL-AF9+ Lin- ckitlow cells from mice with nestin+ cell depletion (III)


title: BC5359: primary breast cancer patient 82


title: BC5360: primary breast cancer patient 83


title: leukemic iMLL-AF9+ Lin- ckitlow cells from mice with nestin+ cell depletion (II)


title: BC5358: primary breast cancer patient 81


title: EP8 (0186_008_CE_DIS_1TR1)


title: leukemic iMLL-AF9+ Lin- ckitlow cells from control mice  (III)

value: control


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C7_ad006

value: male


title: BC5356_2: primary breast cancer patient 79


title: BC5362_3: primary breast cancer patient 85


title: BC5357: primary breast cancer patient 80


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C7_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C8_ad006


title: EP7 (0186_007_CE_DIS_1TR1)


title: EP6 (0186_006_CE_DIS_1TR1)


title: leukemic iMLL-AF9+ Lin- ckitlow cells from control mice (I)


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C7_ad001


title: BC5355: primary breast cancer patient 78


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C7_ad012


title: RNA_C2C12_deltapro#3_day7fsk_rep3

value: 10 uM forskoline for 4 hours

value: myoblasts


title: EP5 (0186_005_CE_DIS_1TR1)


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C7_ad010


title: BC5353: primary breast cancer patient 76

value: primary breast cancer


title: BC5354: primary breast cancer patient 77


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C7_ad002


title: EP3 (0186_003_CE_DIS_1TR1)


title: RNA_C2C12_deltapro#3_day7fsk_rep2


title: RNA_C2C12_deltapro#3_day7fsk_rep1


title: EP2 (0186_002_CE_DIS_1TR1)


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C6_ad001


title: RNA_C2C12_NFIA_day7fsk_rep3


title: BC5352: primary breast cancer patient 75


title: EP1 (0186_001_CE_DIS_1TR1)


title: BC5350: primary breast cancer patient 73


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C6_ad010


title: BC5351: primary breast cancer patient 74


title: RNA_C2C12_NFIA_day7fsk_rep2


title: RNA_C2C12_NFIA_day7fsk_rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C6_ad008


title: leukemic iMLL-AF9+ Lin- ckitlow cells from control mice  (II)


title: EP4 (0186_004_CE_DIS_1TR1)


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C6_ad012


title: RNA_C2C12_ctrl_day7fsk_rep3


title: U87 treated CM cells - H3K9ac

city: GuangZhou

first: liu

last: xincheng

address: zhongshan Road 74

institute: sysu

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
Raw reads were filtered first to remove low-quality or adaptor sequences by SOAPnuke with parameters:filter-15-q0.5-n0.1-Q2-51-c50.Cleaned reads were mapped to the reference genome of NCBI hg38 genome using SOAPaligner/SOAP2(version:2.2.5),whose parameters is-v2-s 35.We used SICER for histone modification which use 1 as the redundancy threshold, 200bp as the window size, 200 as the fragment size, 0.8 as the effective genome fraction, 600bp as the gap size and 0.01 as the FDR threshold respectively). The different enrichment peaks from different samples was plotted by MAnorm(v1.1)14), the significant regions were picked up if [M|≥1 and p-value ≤10-5. Also the gene element annotation of peak or different enrichment peak from different samples was carry out by bedtools intersect mode with overlap 50% . To identify the characteristic of peak , motif discovery was analyzed using HOMER (v4.10.3) or MEME (v4.10.1) Finally, the GO(http://www.geneontology.org)andKEGG(https://www.kegg.jp/) enrichment of peak-related genes was performed using phyper (https://en.wikipedia.org/wiki/Hypergeometric distribution)to calculate p-value, cooperate with the false discovery rate (FDR) by Bonferronil7
Genome_build: hg38

growth_protocol: The cells were cultured according to the guideline of ATCC

extract_protocol:
Formaldehyde is used to cross-link the proteins to the DNA. The 4ug antibody combine with 400uL PBS and BSA will used to incubation. Washing was carried out with 1mL cold PBS combine to 10uLPIC followed by centrifugation for 5 m at 2800xg in 4 ° after 4-6h incubation. This followed by cell lysis with 100xPIC added to 200 ul lysis buffer. those cell who has been lysis and the DNA has been break into proper length (100-500) by bioruptor (Lysate sonication). With which about 180ml supernatant was added into magnetic bead to do IP while others were regarded as Input . Elute DNA by adding elution buffer (respectively with RIPA buffer, NaCI, LiCI, TE buffer in turns ). The crucial step by this is to added primary antibody and beads to suspend supernatant of IP samples. Finally, phenol-chloroform method was used to obtain the extract after the reversal of cross-links. the Qubit Fluorometer was applied to detected concentration of supernatant. After the qPCR applying for quality Control, thesample is ready for ChIP-seq library construction.
The DNA is combined with End Repair Mix, and incubate at 20° for 30 min. Purify the end-repaired DNA with QIAquick PCR Purification Kit(Qiagen), then add A-Tailing Mix, incubate at 37° for 30 min. Combine the purified Adenylate 3'Ends DNA, Adapter and Ligation Mix, incubate the ligation reaction at 20° for 15 min. Purify the Adapter-ligated DNA with the QIAquick PCR Purification Kit. Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix are performed to enrich the Adapter-ligated DNA fragments. Then the PCR products are selected(about 100 300bp, including adaptor sequence) by running a 2% agarose gel to recover the target fragments. Purify the gel with QIAquick Gel Extraction kit (QIAGEN). The final library is quantitated in two ways: Determine the average molecule length and sample integrity well as purity using the Agilent 2100 bioanalyzer instrument (Agilent DNA 1000 Reagents) and quantify the library by real-time quantitative PCR (QPCR). The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the finary was qualified by Qubit ssDNA kit. The sequencing will be performed with the BGISEQ-500 sequencing system featuring combinatorial probe-anchor synthesis (cPAS) and DNA Nanoballs (DNB) technology for superior data quality (BGI-Shenzhen, China).

treatment_protocol: U87 cells were treated with bulk control or a combination of 0.5mM 8-cpt-cAMP and 1nM MS275  for 48 hours.

tag: chip antibody

value: treated with differentiation agents(0.5mM 8-cpt-cAMP combined with 1nM MS275) for 48h


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C6_ad006

tag: brain region


title: U87 treated CM cells - H3K14ac


title: BC5349: primary breast cancer patient 72


title: U87 treated CM cells - Input


title: U87 vehicle cells - H3K14ac

value: untreated


title: RNA_C2C12_ctrl_day7fsk_rep2


title: BC5348: primary breast cancer patient 71

value: tamoxifen


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C6_ad004

tag: Sex


title: EP9 (0186_009_CE_DIS_1TR1)


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C6_ad007

tag: age


title: RNA_C2C12_deltapro#3_day7_rep3

tag: cell line


title: BC5345: primary breast cancer patient 68

tag: tissue


title: BC5346: primary breast cancer patient 69


title: BC5344: primary breast cancer patient 67

value: adj chemo


title: RNA_C2C12_deltapro#3_day7_rep2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C5_ad002

tag: strain


title: RNA_C2C12_deltapro#3_day7_rep1


title: CENP-A  IAA WO Cut&Run-seq

city: Paris

first: Riccardo

last: Gamba

address: 12 rue Lhomond

country: France

institute: Insitut Curie

source_name: Retina, eye; pigmented epithelium

growth_protocol: 37 ° 5%CO2 DMEM/F12 medium with 10% FBS 0.123% Sodium Bicarbonate 100U/mL penicillin 100U/mL streptomycin 2mM L-glutamine

extract_protocol:
according to the CUT&RUN protocol reported by Skene and Henikoff, eLife, 2017
Illumina TruSeq ChIP Library Preparation Kit

treatment_protocol: Indol-3-Acetic Acid (IAA) 500 μM 4-8 hours and washout for 24-48 hours

tag: sample type

value: hTERT immortalized


title: BC5343: primary breast cancer patient 66

tag: node

tag: grade


title: U87 vehicle cells - Input


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C5_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C5_ad007


title: BC5342: primary breast cancer patient 65

tag: t-size (mm)

tag: adjuvant treatment


title: BC5347: primary breast cancer patient 70

tag: intrinsic subtype


title: RNA_C2C12_NFIA_day7_rep3

tag: treatment


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C5_ad010


title: CASP8AP2 Mutant_rep2

city: Bethesda

first: Ashish

middle: K

last: Sharma

address: 14 Service Rd West Building 14A Room 176 MS-5522

department: National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)

institute: National Institute of Health

data_processing:
Bcl2fastq2 software was used for base-calling.
The sequenced reads were trimmed to remove the low quality bases with the following parameters Trim based on : Quality score; Min read length : 25; Max N : FALSE ; End min quality level (Phred) : 20 ; Trim from end : 3-prime (right end).
STAR method was used to align the RNA-seq reads with the reference Human genome hg38 ( - Ensembl Transcripts release 92).
The quantification of transcriptome abundance was performed using Partek E/M algorithm in PartekFlow software.
Data was normalized using TPM method and differential gene expression were predicted across comparisions using ANOVA.
Genome_build: hg38 (Ensembl Transcripts release 92)
Supplementary_files_format_and_content: tab-delimited text files contains results from ANOVA and includes fold change calculations among CASP8AP2 Mutant vs Parental along with p-value, FDR stepup etc.

source_name: HEK293 cell line

growth_protocol: Cells were cultured in Dulbecco’s modified eagle media, supplemented with 10% FBS and incubated at 37ᵒC, 5% CO2 in a humidity-controlled incubator.

extract_protocol:
Total RNA was isolated using the RNeasy Mini kit (Qiagen cat# 74104)
The NEBNext® Ultra™ RNA Library Prep Kit for Illumina was used to prepare the complete RNA-seq library preparation. First strand cDNA synthesis was performed using NEBNext first strand synthesis reaction buffer, random primers, Protoscript II reverse. To the same reaction mix, second strand synthesis enzyme mix was added, and second strand synthesis was. The synthesized cDNA strands were purified using a 1:1 ratio of Agencourt AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). Later steps involved end repair of extracted cDNA, adapter ligation using blunt/TA ligase and cleavage by USER enzyme, purification with AMPure XP beads and PCR enrichment of cDNA library using different sets of Multilex oligos for Illumina. The enriched library was again purified with Agencourt AMPure XP beads, and its quality was checked on a Bioanalyzer using Agilent DNA high sensitivity chips according to the manufacturer’s instructions.

treatment_protocol: Cells were dislodged with trypsin and pellets were frozen at -20ᵒC until RNA extraction

tag: genotype

value: CASP8AP2 Mutant


title: RNA_C2C12_ctrl_day7fsk_rep1

tag: time course

tag: cell type


title: CASP8AP2 Mutant_rep3


title: CASP8AP2 Mutant_rep1


title: U87 vehicle cells - H3K9ac

tag: chip antibody


title: RNA_C2C12_NFIA_day7_rep1


title: BC5340: primary breast cancer patient 64


title: Parental_rep3

value: Parent


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C5_ad006

tag: brain region


title: BC5339: primary breast cancer patient 63


title: RNA_C2C12_ctrl_day7_rep3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C5_ad004

tag: Sex


title: Parental_rep2


title: RNA_C2C12_ctrl_day7_rep2


title: BC5338: primary breast cancer patient 62

tag: age


title: RNA_C2C12_ctrl_day7_rep1

tag: cell line


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C4_ad006


title: Parental_rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C4_ad012


title: RNA_C2C12_NFIA_day7_rep2


title: BC5337: primary breast cancer patient 61

tag: tissue


title: RNA_C2C12_deltapro#3_day0_rep3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C4_ad004

tag: strain


title: BC5336_2: primary breast cancer patient 60


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C4_ad010


title: RNA_C2C12_deltapro#3_day0_rep1


title: RNA_C2C12_NFIA_day0_rep3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C5_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C4_ad001


title: BC5335: primary breast cancer patient 59


title: RNA_C2C12_NFIA_day0_rep2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C4_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C4_ad008


title: BC5334: primary breast cancer patient 58


title: RNA_C2C12_NFIA_day0_rep1


title: BC5333: primary breast cancer patient 57


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C3_ad004


title: BC5330: primary breast cancer patient 56


title: RNA_C2C12_ctrl_day0_rep3


title: BC5328: primary breast cancer patient 54


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C3_ad012


title: RNA_C2C12_ctrl_day0_rep2


title: BC5329: primary breast cancer patient 55


title: RNA_C2C12_deltapro#3_day0_rep2


title: BC5327: primary breast cancer patient 53


title: BC5325: primary breast cancer patient 52


title: RNA_C2C12_ctrl_day0_rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C3_ad008


title: BC5323: primary breast cancer patient 51


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C3_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C3_ad002


title: siGFP_rep2

city: Guangzhou

first: zhiwei

last: Guo

state: Guangdong

address: NO.1838 Guangzhou Road

institute: Southern medical university

description: si GFP control replicate 2

data_processing:
Ion Proton software was used for basecalling
Sequencing reads were mapped to hg19 and bioinformatics analysis was conducted using TAMP and life default RNA-Seq analysis plugin of Life technology for expression analyses
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen, GE) as recommended by the manufacturer. Polyadenylated RNA was isolated from total RNA using standard protocols (Dynabeads mRNA Direct Micro Kit, Ambion/Life Technologies, USA) starting with 5 μg total RNA.
Library preparation for NGS using Ion Torrent technology (Life Technologies, USA) was carried out according to the manufacturers recommendations (Ion Total RNA-Seq Kit v2, Ion torrent/Life Technologies, USA), and sequenced using an Ion Proton system (Life Technologies, USA). Quality control, quantification of RNA and libraries was carried out using using Agilent RNA 6000 Nano Kit or Agilent High Sensitivity DNA kit and Agilent Bioanalyzer (Agilent Technologies, USA). In brief, approximately 50 ng polyA RNA was fragmented down to 100-300 base fragments using RNaseIII for 1-3 min followed by adapter ligation, amplification for 9-14 cycles and barcoding using Ion Express RNA-Seq Barcode kit (Ion Torrent/Life Technologies, USA). The final library fragment size and concentration was determined by Agilent Bioanalyzer analysis followed by template preparation using Ion PI Template OT2 200 Kit v3 (Life Technologies, USA) and Ion One Touch System followed by NGS on an Ion Proton system using Ion PI™ Chip Kit v2. In general two transcriptome libraries were barcoded and analyzed on one Ion PI v2 chip.

tag: cell lines

tag: treament

value: siGFP


title: siZFAS1_rep1

description: si ZFAS1 replicate 1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C3_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C3_ad001


title: siZFAS1_rep2

description: si ZFAS1 replicate 2


title: siGFP_rep1

description: si GFP control replicate 1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C2_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C3_ad010


title: ZFAS1_ORF_rep1

description: ZFAS1_ORF overexpression replicate 1

value: ZFAS1 ORF


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C2_ad001

value: PAL


title: BC5318: primary breast cancer patient 48

tag: node

tag: grade


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C2_ad012


title: PCDH_mRNA_rep2

description: PCDH control replicate 2

value: PCDH


title: PCDH_mRNA_rep1

description: PCDH control replicate 1


title: BC5319_2: primary breast cancer patient 49

tag: t-size (mm)

tag: adjuvant treatment


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C2_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C2_ad006


title: BC5317: primary breast cancer patient 47

tag: intrinsic subtype


title: BC5315: primary breast cancer patient 45


title: BC5320: primary breast cancer patient 50


title: BC5316_2: primary breast cancer patient 46


title: ZFAS1_ORF_rep2

description: ZFAS1_ORF overexpression replicate 2


title: K562_CST-9733_H3K27me3

city: Chicago

first: Rohan

middle: Nishant

last: Shah

state: IL

address: CLSC 856, 920 E. 58th Street

institute: University of Chicago

description: ICeChIP-seq conducted on K562 cells against H3K27me3 using the antibody CST 9733 anti-H3K27me3.

data_processing:
To align reads, a reference genome was first created, consisting of the human genome (GRCh38/hg38) appended by the sequences of each of the nucleosome standard barcodes. Reads were then mapped to this reference genome using Bowtie2 using the sensitive preset and end-to-end alignment options.
Using SAMTools, any reads which were not paired, not mapped in a proper pair, or mapped with a map quality below 20 were then discarded to prevent low-quality mapping or sequencing reads from impacting downstream analyses. Reads were then flattened to create a single mapping from each matched pair of reads, and any mappings with lengths greater than 200bp were also discarded to ensure only mononucleosomes were being analyzed.
Bedgraphs of genome coverage were then generated using BEDTools, and IP and input genome coverage bedgraphs were merged using BEDTools7. The sum of reads across ladder members for each nucleosomal standard was computed for each sample and HMD bedgraphs were then generated from the merged bedgraphs using awk to apply the following formula: HMD (%) = 100% * (IPlocus/INlocus) / (IPbarcode/INbarcode). Error and 95% confidence intervals were computed with Poisson statistics and error propagation from the merged bedgraphs using awk to apply the following formula: 95CI Error (%) = 1.96 * HMD (%) * sqrt(1/IPlocus + 1/INlocus). Bigwig files were generated for visualization using the bedGraphToBigWig tool.
To compute average HMD across a series of intervals, a “double mapping” procedure was used. First, the HMD bedgraph was mapped onto 1bp windows made for each interval using BEDTools. Then, the mapped windows were mapped onto the original intervals using BEDTools. This procedure ensured that the degree of overlap of the interval with each value of the HMD bedgraph was accounted for in the mapping procedure.
Peak calling was conducted using Macs2 using the bdgpeakcall, with the input being the HMD bedgraphs computed for each sample. Peaks within 200bp of each other were then merged using BEDTools. The average HMD and average 95% CI Error of each called peak was computed. At this point, those peaks with greater average HMD than average 95% CI Error were selected as “high-confidence” peaks. All subsequent peak analyses were conducted with these “high-confidence” peaks.
Genome_build: hg38_bar_Ca1-17 (GRCh38/hg38 appended by synthetic DNA barcodes used with semisynthetic nucleosome standards)
Supplementary_files_format_and_content: Bedgraph files all have the form <chromosome> <start> <end> <value>, where the fourth field represents the value of the measurement. Bigwig files are bedgraph files in binary format, appropriate for viewing on a genome browser. Bed files all have the form <chromosome> <start> <end> and represent a list of intervals. Fasta file (with extension .fa) represents the reference genome used in this study, with the human genome (GRCh38/hg38) appended by the DNA barcode sequences used for the semisynthetic nucleosome standards.

source_name: Cell culture

growth_protocol: K562 cells were grown in DMEM (Invitrogen) containing 10% (v/v) HyClone FBS Characterized U.S. and 1x Penicillin/Streptomycin. Cells were grown in supplemented medium in suspension in 25 cm-squared vented flasks. The cells were seeded at 100,000 to 200,000 cells per mL and were grown until they reached a density of 1 million cells per mL, at which point they were passaged 1:10. Cells used in ChIP experiments were harvested at a concentration of approximately 1 million cells per mL.

extract_protocol:
K562 cell pellets were washed twice with 5 mL of PBS, then washed twice with 5 mL of Buffer N (15 mM Tris-HCl pH 7.5, 15 mM NaCl, 60 mM KCl, 8.5% w/v Sucrose, 5 mM MgCl2, 1 mM CaCl2, 1 mM DTT, 200 uM PMSF, 50 ug/mL BSA, 1x Roche Protease Inhibitor Cocktail, Filter Sterilized), with each wash consisting of complete resuspension of the pellet, centrifugation at 500 g for 5 minutes at 4°C, and removal of supernatant. The washed pellet was then resuspended in at least 2 packed cell volumes (PCV) of Buffer N and mixed with 1 volume of Lysis Buffer (Buffer N supplemented with 0.6% NP-40 Substitute) and incubated on ice for 10 minutes to lyse cells. The crude nuclei were spun down at 500 g for 5 minutes at 4°C before being resuspended in at least 6 packed nuclear volumes (PNV) of Buffer N and applied to the top of 7.5 mL of Sucrose Cushion N (15 mM Tris-HCl pH 7.5, 15 mM NaCl, 60 mM KCl, 30% w/v Sucrose, 5 mM MgCl2, 1 mM CaCl2, 1 mM DTT, 200 uM PMSF, 50 ug/mL BSA, 1x Roche Protease Inhibitor Cocktail, Filter Sterilized) in a 15 mL centrifuge tube, then spun down at 500 g for 12 minutes at 4°C in a swinging-bucket rotor. The supernatant was discarded after centrifugation, and the pellet was resuspended in approximately 2 PNV of Buffer N. The nuclei were then quantified by diluting 2 uL of nuclei suspension into 48 uL of 2 M NaCl, water-bath sonicating to solubilize DNA, and spectroscopically measuring DNA concentration by Nanodrop measurement, where 1 A280nm¬ = 50 ng/uL chromatin in the measurement sample. After accounting for the 25-fold dilution of the measurement sample, the concentration of the nuclei was adjusted down to 1ug/uL of chromatin. Nuclei were aliquoted into 100 uL aliquots, flash frozen, and stored at -80°C until use. When nuclei aliquots were used, they were first thawed and spiked approximately 1 uL of each barcoded nucleosome standard per 50 ug of chromatin to be used. The nuclei suspension with spiked calibrants was then mixed with a pipette and transferred to a new tube, then warmed to 37°C for 2 minutes. After warming, 1 unit of micrococcal nuclease (MNase) per 4.375 ug of chromatin was added to the nuclei suspension and incubated at 37°C while shaking at 900 rpm for 12 minutes. After incubation, the digestion was stopped by adding 1/9 volume of 10x MNase Stop Buffer (100 mM EDTA, 100 mM EGTA, Filter Sterilized) while slowly vortexing, and nuclei were lysed by adding 5 M NaCl to a final concentration of 600 mM NaCl while slowly vortexing. 66 mg of HAP resin (BioRad, CHTTM Ceramic Hydroxyapatite, Type I, 20 um) per 100 ug of chromatin digested was rehydrated with 200 uL of HAP Buffer 1 (5 mM Sodium Phosphate pH 7.2, 600 mM NaCl, 1 mM EDTA, 200 uM PMSF, Filter Sterilized) per 100 ug of chromatin digested. The lysed nuclei were then spun down at 18,000 g for 1 minute to pellet insoluble nuclear debris, and the soluble fraction was added to the rehydrated HAP resin and incubated for 10 minutes on a rotator at 4°C. After incubation, the HAP resin slurry was added to a centrifugal filter unit (Millipore Ultrafree MC–HV Centrifugal Filter 0.45 um) and spun at 1000 g for 30 seconds at 4°C. The HAP resin left on the filter unit was then washed 4 times with 200 uL HAP Buffer 1 and 4 times with 200 uL HAP Buffer 2 (5 mM Sodium Phosphate pH 7.2, 100 mM NaCl, 1 mM EDTA, 200 uM PMSF, Filter Sterilized) by spinning at 1000 g for 30 seconds at 4°C. Into a clean tube, the HAP resin was eluted with three elutions of 100 uL HAP Elution Buffer (500 mM Sodium Phosphate pH 7.2, 100 mM NaCl, 1 mM EDTA, 200 uM PMSF, Filter Sterilized). The DNA content of the elution was then quantified spectroscopically with a Nanodrop, and the chromatin concentration was adjusted to 20 ng/uL with ChIP Buffer 1 (25 mM Tris pH 7.5, 5 mM MgCl2, 100 mM KCl, 10% v/v glycerol, 0.1% v/v NP-40 Substitute, Filter Sterilized) with 100 ug/mL of BSA. With the exception of the Koide Lab 304M3B antibody, every ICeChIP was conducted with 12.5 uL of Protein A Dynabeads (Invitrogen) and 3 ug of antibody. The Protein A Dynabeads for each ICeChIP were washed with 50 uL of ChIP Buffer 1 by use of a magnetic rack, then resuspended in 50 uL of ChIP Buffer 1. In a separate set of tubes, 3 ug of each antibody was diluted to 100 uL with ChIP Buffer 1. The antibody suspension and the Protein A Dynabeads suspension were combined and incubated on a rotator at 4°C for at least 1 hour, then washed with 200 uL of ChIP Buffer 1 by use of a magnetic rack and resuspended in 50 uL of ChIP Buffer 1. After antibody washing, 150 uL of the diluted chromatin elution was added to each antibody-bead conjugate and incubated for 15 minutes on a rotator at 4°C. After this incubation, the beads were washed twice with ChIP Buffer 2 (25 mM Tris pH 7.5, 5 mM MgCl2, 300 mM KCl, 10% v/v glycerol, 0.1% v/v NP-40 Substitute, Filter Sterilized) and once with ChIP Buffer 3 (10 mM Tris pH 7.5, 250 mM LiCl, 1 mM EDTA, 0.5% Sodium Deoxycholate, 0.5% v/v NP-40 Substitute, Filter Sterilized), with a wash consisting of removal of the existing supernatant by use of a magnetic rack, resuspension into 150 uL of buffer, transfer to a new siliconized tube, and incubation on the rotator for 10 minutes at 4°C. After these washes, the supernatant was removed, and the beads were resuspended in ChIP Buffer 1, transferred to a new siliconized tube, then rinsed once with 200 uL of TE before being resuspended in 50 uL of ChIP Elution Buffer and incubated at 55°C for 5 minutes. After incubation, the supernatant was transferred to a new set of siliconized tubes, and the beads were discarded. To each supernatant was then added 2 uL of 5 M NaCl, 1 uL of 500 mM EDTA, and 1 uL of 10 mg/mL Proteinase K. 15 uL of Input DNA was also diluted to 50 uL with 35 uL of ChIP Elution Buffer (50 mM Tris pH 7.5, 1 mM EDTA, 1% w/v SDS, Filter Sterilized) and was supplemented with 2 uL of 5 M NaCl, 1 uL of 500 mM EDTA, and 1 uL of 10 mg/mL Proteinase K. The IP elutions and diluted input were then incubated at 55°C for 2 hours for a Proteinase K digestion. After digestion, the DNA was purified by adding 1.5 volumes of Serapure HD (1:50 dilution of Sera-Mag SpeedBeads [Fisher], 20% PEG-8000, 2.5 M NaCl, 10 mM Tris pH 7.5, 1 mM EDTA, 0.05% Tween-20, Filter Sterilized prior to addition of SpeedBeads), incubating at room temperature for 15 minutes, then collecting the beads on a magnetic rack, washing twice with 150 uL of 70% ethanol, and eluting into 50 uL of water, which was then recovered and stored at -20°C.
DNA purified with Serapure was quantified using Quant-iT TM PicoGreen (Thermo Fisher) per manufacturer instructions. Up to 10 ng of each DNA sample for which libraries were to be prepared were then carried forward. Libraries were then generated from the NEBNext Ultra II DNA Library Prep kit (New England Biolabs) per manufacturer instructions. The DNA content of the library was then quantified and pooled for Illumina sequencing.

value: Cell Signaling Technology 9733, monoclonal anti-H3K27me3

tag: amplification cycles


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C2_ad002

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

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: BC5313: primary breast cancer patient 43

data_processing: Raw expression data (CEL files) were normalized using frozen robust multiarray analysis (fRMA)

extract_protocol: Approximately 50 mg of frozen breast tumor tissue was crushed in liquid nitrogen. RLT-Buffer was added and the homogenate was centrifuged through a QIAshredder column (QIAGEN, Hilden, Germany). RNeasy extraction (QIAGEN) of total RNA was performed according to the manufacturer's instructions.


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C2_ad008


title: NCF_3_SC

city: Jouy-en-Josas Cedex

first: Vinciane

last: Saint-Criq

address: Centre de recherche Ile-de-France-Jouy-en-Josas, Domaine de Vilvert

institute: INRAE

data_processing:
Reads were quantified against transcripts using Salmon, a program for quantifying expression of transcripts from RNA-Seq data
The Salmon workflow can be summarised as follows: • (1) Build index file using the ‘salmon index’ command. The index was built from Gencode  and • (2) Run the quantification algorithm ‘salmon quant’ for each FASTQ file against the indexRelease 29
Salmon quantifies reads against transcripts. To obtain gene-level counts, the R package ‘tximport’ was used
Gene annotation was obtained from Ensembl gene ids using the R package ‘biomaRt’
Differential expression analysis was carried out using the R package DESeq2. DESeq2 estimates fold change between experimental conditions using a Negative Binomial GLM with a logarithmic link function.
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

source_name: airway epithelial cells from explant

growth_protocol: Cells, preserved in liquid nitrogen, were thawed and seeded at the same density (10^5/cm2) in either UNC or BEGM with media in both apical and basolateral compartments. After 2 days, BEGM was replaced by SC medium bilaterally and 5 days after seeding, apical medium was removed in order to generate an air-liquid interface (ALI). Differentiation was allowed to occur for 23 to 30 days after which the cells were then washed and lysed.

extract_protocol:
RNA isolation from fully differentiated cells was performed using the PureLink® RNA Mini Kit (12183018A, Ambion, Life Technologies), following the manufacturer’s instructions. Briefly, lysates were mixed with 70% ethanol and loaded onto a silica-membrane column. Columns were washed and total RNA was eluted in nuclease-free water and stored at -80 °C until use.
TruSeq Stranded mRNA Sample Preparation Kit (Illumina)

tag: genotype

value: WT-CFTR

tag: growth medium

value: SC

value: airway epithelial cells from explant


title: BC5308: primary breast cancer patient 39


title: NCF_3_UNC

value: UNC


title: NCF_2_SC


title: BC5311: primary breast cancer patient 41

value: primary breast cancer


title: BC5312: primary breast cancer patient 42


title: BC5309: primary breast cancer patient 40


title: NCF_2_UNC


title: BC5314: primary breast cancer patient 44


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C12_ad002

city: La Jolla

last: Ecker

institute: HHMI-Salk-Institute

value: male


title: NCF_1_SC


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C12_ad007


title: NCF_1_UNC


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C12_ad008


title: CF_3_SC


title: CF_3_UNC


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C12_ad004


title: BC5306: primary breast cancer patient 37

city: Mainz

last: Schmidt

institute: Universitätsmedizin Mainz


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C12_ad006


title: BC2426NS: primary breast cancer patient 33

data_processing:
CEL file not available for this patient
Raw expression data (CEL files) were normalized using frozen robust multiarray analysis (fRMA)


title: BC2421NS: primary breast cancer patient 32


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C12_ad010


title: BC5302: primary breast cancer patient 34


title: CF_2_UNC


title: CUT&RUN: H3K4me2 rep1

city: Pasadena

first: Akiko

last: Kumagai

state: California

address: 1200 E. California Blvd

department: Division of Biology and Biological Engineering

institute: California Institute of Technology

description:
CUT&RUN with H3K4me2 antibody
CAR23_1_CKDL200151331-1a_H7N3JBBXX_L7_1_195905
CAR23_1_CKDL200151331-1a_H7N3JBBXX_L7_2_195903

data_processing:
Sequence reads were processed using Trim Galore to remove adapter and low-quality reads (q < 20).
Reads were mapped to the human hg38 genome assembly using Bowtie2 with options:  --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10.
MACS2 was used to call peaks on the reads for CUT&RUN experiments using options:  --keep-dup 1 -f BAMPE --nolambda -q 0.01.  Summits were also called in MACS2 and the highest summit for each peak was identified.
Peaks of EdU-seq were called using HOMER findPeaks (region -size 6000 -minDist 12000 -F 2).
Genome_build: hg38
Supplementary_files_format_and_content:
MTBP_WT.bw, MTBP_deltaC.bw, and MTBP_cont.bw files are the averages of three replicates.  The scores for MTBP_WT.bw represent RPGC (reads per genomic content).  The scores for MTBP_deltaC.bw and MTBP_cont.bw were normalized to MTBP_WT.bw using spike-in DNA.
MTBP_peaks.txt contains the locations of MTBP_peaks called using MACS2 in a tab-separated file.  The locations of summits of the peaks were also included.
H3K4me2.bw and Control_IgG.bw files are the averages of two replicates.   The scores for H3K4me2.bw represent RPGC (reads per genomic content).  The scores for Control_IgG.bw were normalized to H3K4me2.bw using spike-in DNA.
H3K4me2.bed file contains the locations of H3K4me2 peaks identified using MACS2.
EdU_seq_WT.bw and EdU_seq_deltaC.bw are the average of three replicates.  The scores represent  log2 ratio of EdU_seq reads over control reads.
Initiation_zones.txt contains the initiation zones (peaks of EdU-seq-WT) called by HOMER findPeaks (region -size 6000 -minDist 12000 -F 2).

source_name: colorectal adenocarcinoma

extract_protocol: Sequencing libraries were prepared using NEBNext Ultra DNA library preparation kit.  In brief, the DNA was end-repaired, adaptor-ligated, and PCR-amplified.

tag: genotype/variation

value: MTBP-mAID/MTBP-WT-FLAG

tag: molecule subtype

value: CUT&RUN released DNA


title: BC5305: primary breast cancer patient 36

value: tamoxifen


title: CUT&RUN: control IgG rep2

description:
CUT&RUN with control IgG
CAR24_3_CKDL200151337-1a_H7N3JBBXX_L7_1_195929
CAR24_3_CKDL200151337-1a_H7N3JBBXX_L7_2_195928


title: CF_2_SC


title: CF_1_SC


title: BC5307: primary breast cancer patient 38


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C11_ad002

first: Joseph

address: 10010 North Torrey Pines Road

tag: brain region

tag: Sex


title: CUT&RUN: H3K4me2 rep2

description:
CUT&RUN with H3K4me2 antibody
CAR24_4_CKDL200151338-1a_H7N3JBBXX_L7_1_195933
CAR24_4_CKDL200151338-1a_H7N3JBBXX_L7_2_195932

tag: cell line


title: BC5304: primary breast cancer patient 35

first: Marcus

address: Langenbeckstr. 1

tag: tissue

tag: age


title: CUT&RUN: control IgG rep1

description:
CUT&RUN with control IgG
CAR23_5_CKDL200151334-1a_H7N3JBBXX_L7_1_195917
CAR23_5_CKDL200151334-1a_H7N3JBBXX_L7_2_195909


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C11_ad010

tag: strain


title: BC2418NS: primary breast cancer patient 31

value: adj chemo


title: BC2415: primary breast cancer patient 30


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C11_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C11_ad012


title: T-cell_ATAC_seq_rep2

city: Memphis

first: Shengdar

last: Tsai

state: TN

address: 262 Danny Thomas Pl, Memphis, TN

department: Department of Hematology

institute: St. Jude Children’s Research Hospital

description:
ATAC-seq
ATAC_FE.bdg.bw

data_processing:
Adapter sequences were trimmed by skewer. BWA mem mapping to hg38
generate MACS2 signal tracks: macs2 callpeak --nomodel --shift -100 --extsize 200 -g hs -B
Generate normalized signals (fold enrichment): macs2 bdgcmp -t treat_pileup.bdg -c control_lambda.bdg -m FE -o FE.bdg
Genome_build: hg38
Supplementary_files_format_and_content: bw

source_name: Human primary CD4/CD8 T cells

growth_protocol: Human primary CD4+/CD8+ T-cells were cultured in X-Vivo 15 media (Lonza) supplemented with 5% human heat-inactivated serum (Fisher), 10 ng/ml IL-7 (Miltenyi), and 10 ng/ml IL-15 (Miltenyi). T-cells were stimulated with MACS GMP T-cell TransAct polymeric nanomatrix (Miltenyi) for 3 days according to the manufacturer’s instructions prior to transfection.

extract_protocol: ATAC-seq libraries were constructed on 50,000 CD4+/CD8+ T-cells per sample. Libraries were sequenced with 100 bp paired-end reads using an Illumina HiSeq 4000.

tag: cell type

value: Human primary CD4/CD8 T cells


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C11_ad006


title: T-cell_ATAC_seq_rep1

description:
ATAC-seq
ATAC_FE.bdg.bw


title: IMIQpDC_omni_D8_rep1

city: Stanford

first: Juliana

last: Idoyaga

address: 299 Campus Dr, Fairchild Science Building

department: Microbiology & Immunology

institute: Stanford University

data_processing:
Library strategy: Omni-ATAC
Processing of raw sequencing data was performed with the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline). Briefly, adapters were trimmed with cutadapt.
Trimmed reads were aligned to the hg19 reference genome with Bowtie2.
Aligned reads were filtered with Picard tools.
Peaks were called on each sample with MACS2 (p<0.01).
A 500 bp fixed-width union peak set was created for each dataset by merging peak sets from each sample and removing overlapping peaks as described (Corces et al., Science 2018).
Read counts were calculated with bedtools multicov.
Genome_build: hg19
Supplementary_files_format_and_content: Raw read counts per peak in tab-delimited text format for each sample

source_name: peripheral blood mononuclear cells

extract_protocol:
Samples were prepared according to Buenrostro et al., Nature Methods 2015 for ATAC-seq or Corces et al., Nature Methods 2017 for Omni-ATAC-seq. Briefly, 5,000-50,000 sorted cells were centrifuged, washed, and resuspended in lysis buffer to extract nuclei. Nuclei were centrifuged and resuspended in Tn5 transposition reaction mix for 30 min at 37ºC. Reactions were scaled according to number of cells. Transposed DNA was column purified and stored at -20ºC.
Samples were PCR amplified. In accordance with published protocols (Buenrostro et al., Nature Methods 2015; Corces et al., Nature Methods 2017) qPCR was used to determine the optimal number of PCR cycles to reduce GC and size bias. Samples were barcoded using custom primers as described (Buenrostro et al., Nature Methods 2013). Libraries were quantified with an Agilent Bioanalyzer and pooled for sequencing.

treatment_protocol: For non-stimulated samples, sorted cells were processed for ATAC-seq immediately. For stimulated pDCs, sorted cells were cultured for 2 days with 100 ng/mL CD40L or 5 µg/mL Imiquimod, then re-sorted to isolate live cells and immediately processed for ATAC-seq.

value: IMIQpDC

tag: donor id

tag: donor sex

value: M

tag: treatment

value: 5 µg/mL IMIQ 48hours

tag: sequencing batch

tag: dataset


title: BC2412NS: primary breast cancer patient 28

tag: node

tag: grade

tag: t-size (mm)

tag: adjuvant treatment

tag: intrinsic subtype


title: IMIQpDC_omni_D6_rep1


title: IMIQpDC_omni_D4_rep1

value: F


title: EdU-seq-deltaC rep3

description:
EdU-seq: released into S-phase
processed data file: EdU_seq_deltaC.bw
RO091912_CKDL190139553-1a_H3NTKBBXX_L5

data_processing:
Sequence reads were processed using Trim Galore to remove adapter and low-quality reads (q < 20).
Reads were mapped to the human hg38 genome assembly using Bowtie2 with options:  --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10.
MACS2 was used to call peaks on the reads for CUT&RUN experiments using options:  --keep-dup 1 -f BAMPE --nolambda -q 0.01.  Summits were also called in MACS2 and the highest summit for each peak was identified.
Peaks of EdU-seq were called using HOMER findPeaks (region -size 6000 -minDist 12000 -F 2).
Genome_build: hg38
Supplementary_files_format_and_content:
MTBP_WT.bw, MTBP_deltaC.bw, and MTBP_cont.bw files are averages of three replicates.  The scores for MTBP_WT.bw represent RPGC (reads per genome coverage).  The scores for MTBP_deltaC.bw and MTBP_cont.bw were normalized to MTBP_WT.bw using spike-in DNA.
MTBP_peaks.txt contains the locations of MTBP_peaks called using MACS2 in a tab-separated file.  The locations of summits of the peaks were also included.
H3K4me2.bw and Control_IgG.bw files are the averages of two replicates.   The scores for H3K4me2.bw represent RPGC (reads per genomic content).  The scores for Control_IgG.bw were normalized to H3K4me2.bw using spike-in DNA.
H3K4me2.bed file contains the locations of H3K4me2 peaks identified using MACS2.
EdU_seq_WT.bw and EdU_seq_deltaC.bw are the average of three replicates.  The scores represent  log2 ratio of EdU_seq reads over control reads.
Initiation_zones.txt contains the initiation zones (peaks of EdU-seq-WT) called by HOMER findPeaks (region -size 6000 -minDist 12000 -F 2).

extract_protocol:
EdU-seq: Cells were labeled with 10 µM EdU for 3 hr. Cells were fixed with 70% ice-cold ethanol, washed, and incubated in click-reaction buffer containing 100 µM biotin-dPEG11-azide (Quanta Biodesign), 2 mM CuSO4, and 10 mM sodium ascorbate in TBS for 15 min. Genomic DNA was isolated and sonicated to 300-500 bp with a Branson 450 sonifier. Biotinylated DNA was collected on 20 µl of Dynabeads MyOne Streptavidin T1 magnetic beads.
Sequencing libraries were prepared using NEBNext Ultra DNA library preparation kit.  In brief, the DNA was end-repaired, adaptor-ligated, and PCR-amplified.

value: colorectal adenocarcinoma

tag: genotype/variation

value: MTBP-mAID/MTBP-deltaC-FLAG

tag: molecule subtype

value: EdU-labeled DNA


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C11_ad001

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region

value: PAL

tag: Sex


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C11_ad007

tag: age


title: EdU-seq-WT rep2

description: EdU-seq: released into S-phase

data_processing:
Library strategy: EdU-seq
Sequence reads were processed using Trim Galore to remove adapter and low-quality reads (q < 20).
Reads were mapped to the human hg38 genome assembly using Bowtie2 with options:  --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10.
MACS2 was used to call peaks on the reads for CUT&RUN experiments using options:  --keep-dup 1 -f BAMPE --nolambda -q 0.01.  Summits were also called in MACS2 and the highest summit for each peak was identified.
Peaks of EdU-seq were called using HOMER findPeaks (region -size 6000 -minDist 12000 -F 2).
Genome_build: hg38
Supplementary_files_format_and_content:
MTBP_WT.bw, MTBP_deltaC.bw, and MTBP_cont.bw files are averages of three replicates.  The scores for MTBP_WT.bw represent RPGC (reads per genome coverage).  The scores for MTBP_deltaC.bw and MTBP_cont.bw were normalized to MTBP_WT.bw using spike-in DNA.
MTBP_peaks.txt contains the locations of MTBP_peaks called using MACS2 in a tab-separated file.  The locations of summits of the peaks were also included.
H3K4me2.bw and Control_IgG.bw files are the averages of two replicates.   The scores for H3K4me2.bw represent RPGC (reads per genomic content).  The scores for Control_IgG.bw were normalized to H3K4me2.bw using spike-in DNA.
H3K4me2.bed file contains the locations of H3K4me2 peaks identified using MACS2.
EdU_seq_WT.bw and EdU_seq_deltaC.bw are the average of three replicates.  The scores represent  log2 ratio of EdU_seq reads over control reads.
Initiation_zones.txt contains the initiation zones (peaks of EdU-seq-WT) called by HOMER findPeaks (region -size 6000 -minDist 12000 -F 2).

extract_protocol:
Sequencing libraries were prepared using NEBNext Ultra DNA library preparation kit.  In brief, the DNA was end-repaired, adaptor-ligated, and PCR-amplified.
EdU-seq:  Cells were labeled with 10 µM EdU for 3 hr.  Cells were fixed with 70% ice-cold ethanol, washed, and incubated in click-reaction buffer containing 100 µM biotin-dPEG11-azide (Quanta Biodesign), 2 mM CuSO4, and 10 mM sodium ascorbate in TBS for 15 min.  Genomic DNA was isolated and sonicated to 300-500 bp with a Branson 450 sonifier.  Biotinylated DNA was collected on 20 µl of Dynabeads MyOne Streptavidin T1 magnetic beads.

tag: cell line

tag: tissue


title: CF_1_UNC

tag: genotype

tag: growth medium

value: airway epithelial cells from explant


title: CD40LpDC_omni_D8_rep1

tag: cell type

tag: donor id

tag: donor sex

tag: treatment

value: 100 ng/mL CD40L 48hours


title: EdU-seq-deltaC rep2

description:
EdU-seq: released into S-phase
processed data file: EdU_seq_deltaC.bw
RO0919_2_CKDL190139543-1a_H3NTKBBXX_L5


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C10_ad001

tag: strain


title: IMIQpDC_omni_D3_rep1

tag: sequencing batch

tag: dataset


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C11_ad008


title: BC2410: primary breast cancer patient 27

source_name: primary breast cancer tissue

value: primary breast cancer

tag: node

tag: grade

tag: t-size (mm)

tag: adjuvant treatment

tag: intrinsic subtype


title: CD40LpDC_omni_D6_rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C10_ad007

tag: brain region

tag: Sex

value: male

tag: age


title: EdU-seq-WT rep3

description: EdU-seq: released into S-phase

tag: cell line

tag: tissue

tag: genotype/variation

value: MTBP-mAID/MTBP-WT-FLAG

tag: molecule subtype


title: BC2393: primary breast cancer patient 24


title: BC2409: primary breast cancer patient 26


title: CD40LpDC_omni_D4_rep1

tag: cell type

tag: donor id

tag: donor sex


title: BC2413NS: primary breast cancer patient 29


title: EdU-cont rep3

description: EdU-seq: G1-arrested


title: BC2395: primary breast cancer patient 25


title: BC2389NS: primary breast cancer patient 22


title: EdU-cont rep2

description: EdU-seq: G1-arrested


title: CUT&RUN: MTBP-deltaC-FLAG rep3

description: CUT&RUN with FLAG antibody

data_processing:
Library strategy: CUT&RUN
Sequence reads were processed using Trim Galore to remove adapter and low-quality reads (q < 20).
Reads were mapped to the human hg38 genome assembly using Bowtie2 with options:  --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10.
MACS2 was used to call peaks on the reads for CUT&RUN experiments using options:  --keep-dup 1 -f BAMPE --nolambda -q 0.01.  Summits were also called in MACS2 and the highest summit for each peak was identified.
Peaks of EdU-seq were called using HOMER findPeaks (region -size 6000 -minDist 12000 -F 2).
Genome_build: hg38
Supplementary_files_format_and_content:
MTBP_WT.bw, MTBP_deltaC.bw, and MTBP_cont.bw files are averages of three replicates.  The scores for MTBP_WT.bw represent RPGC (reads per genome coverage).  The scores for MTBP_deltaC.bw and MTBP_cont.bw were normalized to MTBP_WT.bw using spike-in DNA.
MTBP_peaks.txt contains the locations of MTBP_peaks called using MACS2 in a tab-separated file.  The locations of summits of the peaks were also included.
H3K4me2.bw and Control_IgG.bw files are the averages of two replicates.   The scores for H3K4me2.bw represent RPGC (reads per genomic content).  The scores for Control_IgG.bw were normalized to H3K4me2.bw using spike-in DNA.
H3K4me2.bed file contains the locations of H3K4me2 peaks identified using MACS2.
EdU_seq_WT.bw and EdU_seq_deltaC.bw are the average of three replicates.  The scores represent  log2 ratio of EdU_seq reads over control reads.
Initiation_zones.txt contains the initiation zones (peaks of EdU-seq-WT) called by HOMER findPeaks (region -size 6000 -minDist 12000 -F 2).

extract_protocol:
Sequencing libraries were prepared using NEBNext Ultra DNA library preparation kit.  In brief, the DNA was end-repaired, adaptor-ligated, and PCR-amplified.
CUT&RUN: After the CUT&RUN procedure, MNase-digested DNA was purified using the Monarch PCR & DNA Cleanup Kit (NEB).

value: CUT&RUN released DNA


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C10_ad012

tag: strain


title: CD40LpDC_omni_D3_rep1

tag: treatment

tag: sequencing batch

tag: dataset


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C10_ad004


title: BC2392: primary breast cancer patient 23

tag: node

tag: grade

tag: t-size (mm)


title: BC2383: primary breast cancer patient 21

tag: adjuvant treatment

tag: intrinsic subtype


title: BC2382: primary breast cancer patient 20

tag: age


title: CD11chitDC_omni_D8_rep1


title: CUT&RUN: MTBP-deltaC-FLAG rep2

description: CUT&RUN with FLAG antibody

tag: cell line


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C10_ad002

tag: brain region

tag: Sex


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C10_ad008


title: CUT&RUN: MTBP-WT-FLAG rep3

description: CUT&RUN with FLAG antibody

tag: tissue

tag: genotype/variation

tag: molecule subtype


title: CUT&RUN: control rep3

description: CUT&RUN with FLAG antibody

value: MTBP-mAID/MTBP-mAID


title: CD11chitDC_omni_D3_rep1

tag: cell type

tag: donor id

tag: donor sex


title: CD11chitDC_omni_D4_rep1

tag: treatment

tag: sequencing batch


title: CD11clotDC_omni_D8_rep1

tag: dataset


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C10_ad010

tag: strain


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C1_ad004


title: CUT&RUN: control rep2

description: CUT&RUN with FLAG antibody


title: CD11chitDC_omni_D6_rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C10_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C1_ad008


title: BC2381: primary breast cancer patient 19

tag: node

tag: grade

tag: t-size (mm)

value: adj chemo


title: CD11clotDC_omni_D6_rep1


title: BC2380: primary breast cancer patient 18

tag: age

tag: adjuvant treatment

tag: intrinsic subtype


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C1_ad007

tag: brain region

tag: Sex


title: BC2290: primary breast cancer patient 15

tag: tissue


title: CUT&RUN: MTBP-WT-FLAG rep2

description: CUT&RUN with FLAG antibody

tag: cell line

tag: genotype/variation

tag: molecule subtype


title: CD11clotDC_omni_D3_rep1

tag: cell type

tag: donor id

tag: donor sex


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C1_ad006


title: pDC_omni_D6_rep1

value: pDC

tag: treatment

tag: sequencing batch

tag: dataset


title: BC2349: primary breast cancer patient 17

tag: node

tag: grade


title: BC2348: primary breast cancer patient 16

tag: age

tag: t-size (mm)


title: BC2288: primary breast cancer patient 14

tag: adjuvant treatment

tag: intrinsic subtype


title: BC2285: primary breast cancer patient 12


title: pDC_omni_D4_rep1


title: HAEC_oxLDL_Rep3 (mRNA)

city: Shanghai

first: Zhen

last: Sheng

address: F13, Building 2, 4560 Jinke Road

institute: Amgen Biopharmaceutical Research & Development (Shanghai) Co., Ltd

description: gene expression of HAEC cells with treatment of oxLDL (mRNA)

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: human aorta endothelial cells, treated with oxLDL, replicate 3

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Human aortic endothelial cells (HAECs) were purchased from the American Type Culture Collection (ATCC, PCS-100-011) and cultured in Vascular Cell Basal Medium (ATCC, PCS-100-030) supplemented with Endothelial Cell growth kit (ATCC, PCS-100-041) and 0.1% penicillin/streptomycin (ATCC, PCS-999-002) at 37°C in an incubator with 5% CO2.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1561, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: HAECs were treated with oxLDL 100 μg/ml for 48 h.

tag: cell

value: human aorta endothelial cells

value: oxLDL


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C1_ad001

tag: brain region

tag: Sex

tag: strain


title: BC2286: primary breast cancer patient 13

tag: tissue


title: HAEC_oxLDL_Rep1 (mRNA)

source_name: human aorta endothelial cells, treated with oxLDL, replicate 1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C1_ad012


title: HAEC_oxLDL_Rep2 (mRNA)

source_name: human aorta endothelial cells, treated with oxLDL, replicate 2


title: pDC_omni_D3_rep1

tag: cell type


title: Large Wound Pheripheral Hic1:tdTomato-ve 14DPI aligned to tdTomato custom reference

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

data_processing:
All raw FASTQs reads were aligned to either the mouse GRCm38.p5 or to our custom tdTomato genome (primary assembly) reference genome using the STAR algorithm and quantified through the 10X Genomics cellranger v2.0.1 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat (v2.1.0 ) R toolkit for quality control and all downstream analysis. All functions were run with default or recommended parameters, unless specified otherwise. Low quality cells (<400 genes/cell and <20 cells/gene) were excluded from the overall experiment. Gene expression was log normalized to a scale factor of 10,000. To begin unsupervised clustering of cells, a selection of highly variable genes (1195 genes) was obtained and used to calculate up to 75 principle components. Significance of principle components was determined using JackStraw analysis and by creating a PCElbowPlot. PCs 1 to 20 were used to run and plot a tSNE plot for all cells. Expression of selected marker genes across cell clusters identified by graph based clustering (run in Seurat at: res = 0.2) was used to select only fibroblasts for all subsequent analysis. Differential and marker gene analysis of cells defined by FACS sorting sample or graph-clustering was also run in Seurat using the negative binomial test for genes expressed by at least 25% of cells in the defined cell group being compared.
Genome_build: Modified mm10 (GRCm38.p5) reference genome with several transgenes added (custom reference genome is attached with submission)
Supplementary_files_format_and_content: Filtered gene - barcode matrix output from CellRanger

source_name: 14 days post injury skin wound

extract_protocol:
Large and small wounds from adult mice (n = 2 per sample) were dissected and enzymatically dissociated with dispase (StemCell Technologies) for 20 mins at 37 oC to remove the epidermis. Remaining dermis was dissociated using 0.2% collagenase for 2 hours at 37 oC. Cell suspensions were diluted with cold Hank’s Buffered Salt Solution (HBSS; Life Technologies), strained through 40 µm cell filters (Falcon) and centrifuged at 280 X g. Liberated single cells were re-suspended in 0.5% bovine serum album in HBSS before FACS purification. For FACS purification, a stringent initial forward and side scatter gates were used to exclude debris, and cell doublets. Wildtype cells were used as negative control to determine gates for detection of tdTomato-fluorescence, then cells from Hic1CreERT2:tdTomato mice were purified.
Libraries were prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v2 Chemistry as per the manufacturer’s protocol. In brief, single cells were sorted into 0.1% BSA–PBS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed first using Illumina MiSeq SR50 to approximate the number of recovered cells in each sample. We recovered 4061, 3776, 2604, and 3293 cells for Samples 1-4, respectively, with an estimated doublet rate of ≈3%. Based on this, we determined lane distributions for sequencing using Illumina HiSeq 4000 PE (75 bp paired-end reads) with a targeted sequencing depth of ~115,000 reads/cell.

treatment_protocol: Cre-recombination was initiated with two intraperitoneal injections of 4-hydroxy-tamoxifen (4-OHT; 1mg/20g in sterile sunflower oil, Sigma-Aldrich) at postnatal day (P) 3 and 4.

tag: transgenic strain

tag: background

tag: facs strategy

value: tdTomato-neg


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B9_ad006