title: CEMBA181023_6B_1_CEMBA181023_6B_2_G1_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_G1_ad010

status: Public on Sep 23 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: SSp

tag: Sex

value: male

tag: age

tag: strain


title: CEMBA181023_6B_1_CEMBA181023_6B_2_G1_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_G1_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_G1_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F9_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_G1_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_G11_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F9_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_G11_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F9_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F8_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F8_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F9_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F9_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F8_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F8_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F8_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F8_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F8_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F7_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F7_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F7_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F7_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F7_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F7_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F7_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F6_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F6_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F6_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F6_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F5_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F6_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F6_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F9_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F5_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F8_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F5_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F5_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F5_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F5_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F5_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F4_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F5_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F4_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F6_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F4_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F4_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F4_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F4_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F3_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F3_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F3_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F3_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F3_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F3_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F2_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F2_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F2_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F4_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F2_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F2_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F2_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F12_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F2_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F12_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F12_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F12_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F12_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F12_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F12_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F12_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F11_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F11_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F11_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F11_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F11_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F11_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F11_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F10_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F10_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F10_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F10_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F10_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F10_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F10_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F1_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F1_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F1_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F1_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E9_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E9_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F1_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F1_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F1_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E9_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E9_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E9_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E8_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E8_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E8_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E8_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F10_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E7_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E7_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E7_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_F1_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E6_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E7_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E9_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E6_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E9_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E6_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E8_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E5_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E5_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E5_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E4_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E8_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E5_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E4_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E7_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E4_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E6_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E6_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E4_ad006


title: miRNC_inflammation

type: RNA

city: Chapel Hill

first: Hossein

last: Sendi

state: NC

address: 125 Mason Farm Rd

department: Radiation Oncology

institute: University of North Carolina at Chapel Hill

description:
Control
This sample represents the average of 5 replicates.

data_processing:
Thermal cycling was performed using QuantStudio 6 Pro RT PCT System (Applied Biosystems, USA) with an initial denaturation at 95⁰C for 10 minutes, 40 cycles at 95⁰C for 15 seconds, and 60⁰C for 1 minute. Values of cycle threshold (Ct) obtained in quantification were used for calculations of fold changes in mRNA abundance using 2-ΔΔCt method. Data was analyzed using RT2 profiler PCR array data analysis at GeneGlobe Data Analysis Center online (GeneGlobe, Qiagen, MD).
For normalization, 3 housekeeping genes (Gapdh, Gusb,Hsp90ab1) were used

label: CYBR Green

molecule: total RNA

source_name: miRNC treated liver

label_protocol: Then, mixed with RT2 SYBR Green/ROX qPCR Master Mix added into a 384-well RT2 PCR Arrays of cancer inflammation and immunity cross talk (Qiagen, PMAM-181Z)

growth_protocol: Liver tissue from balb/c mice with CT26 hemi-splenectomy induction of liver metastasis

extract_protocol: Total RNA was extracted with miRNAeasy kit and cDNA was made using RT2, First Strand kit (Qiagen, MD)

treatment_protocol: Mice were treated with LCP nanoparticle containing miR-122 or miRNC 3 times a week for 3 weeks

tag: tissue

value: liver

value: balb/c


title: miR122_inflammation

description:
Test
This sample represents the average of 5 replicates.

source_name: miR-122 treated liver


title: E838-LoM-Naive

first: Paul

middle: O

last: Grant

address: 3105 Neuoscience Research Building

department: BARC

institute: UNC SOM

library_source: transcriptomic

data_processing:
Sequence quality was assessed using FASTQC (v).
No issues were detected with the data and quality was typical for RNA extracted from fresh frozen material.
A small amount of index hopping was detected (0.09%) due to the single indices used in the library preparation.
Raw reads were mapped to the human, mouse, and SARS-CoV-2 reference genomes simultaneously (GRCh38.p13, GRCm38.p6 M25, NC_045512, respectively) using the BBsplit function in BBmap (version 38.86). This step minimized cross mapping of reads among genomes.
We then mapped and quantified on a transcript and gene model basis using STAR (version 2.7.5a) and Salmon (version 1.2.1)
Reads mapping to multiple locations were dropped from analysis.
Genome_build: GRCh38.p13, GRCm38.p6 M25, NC_045512
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: Lung organoid

growth_protocol: Viruses were directly injected into the human lung tissue of LoMs and lung tissue collected either 2, 6, or 14 days post-exposure for virus titer determination and/or analysis by histology, electron microscopy, or RNA-seq

extract_protocol:
Trizol Plus RNA extraction kit (Thermo Fisher)
NEBNext Ultra II library prep kit with polyA RNA selection

treatment_protocol: SARS-CoV-2 infected LoM

tag: mouse model

value: LoM

tag: time point (days post infection)

value: Naive

tag: disease state

value: Lung organoid

tag: cell lining

value: Epithelial


title: E832-LoM-14

value: Infected with SARS-CoV-2


title: E128-LoM-Naive


title: E844-LoM-Naive


title: E840-LoM- Naive

description: E840-LoM- Naive


title: E739-LoM-14


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E6_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E3_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E5_ad006


title: E127-LoM-14


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E3_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E3_ad010


title: E434-LoM-6


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E3_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E4_ad007


title: E732-LoM-2


title: E827-LoM-2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E4_ad012


title: E126-LoM-2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E3_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E3_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E2_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E3_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E2_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E2_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E2_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E2_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E2_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E2_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E12_ad010


title: E829-LoM-6


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E12_ad007


title: E130-LoM-6


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E12_ad006


title: R19028452LR01-22, Paracancerous benign tissue

city: Beijijng

first: Xingbo

last: Long

address: No 1, Dongdan Dahua Road, Dongcheng District

department: Urology

country: China

institute: Beijing Hospital

data_processing:
The quality of raw reads was first assessed using the FastQC. After filtering out low quality bases and adaptors by using Trimmomatic-0.36 reads were mapped to human genome assembly GRCh38  (ftp://ftp.ensembl.org/pub/release-90/fasta/homo_sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz) using HISAT2.
Differentially expressed genes were identified by counting the number of reads mapping to each gene from Ensembl 90 (ftp://ftp.ensembl.org/pub/release-90/gtf/homo_sapiens/Homo_sapiens.GRCh38.90.gtf.gz) using Htseq-count.
Transcripts Per Million (TPM) was analyzed using the Stringtie software.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include count and TPM values for each Sample.

organism: Homo sapiens

source_name: Paracancerous benign tissue

extract_protocol:
RNA was extracted from formalin-fixed, paraffin-embedded tissue. After hematoxylin and eosin (H&E)-stained slide review, tumor and paracancerous benign tissues were selected. We then manually microdissected the corresponding tissue from unstained, 5-μm-thick tissue sections (10 sections for RNA). For RNA sequencing, we purified RNA using the RNeasy FFPE Kit from FFPE slides. RNA quality was determined with the DV200 value (DV200 > 30%) by a Caliper BioAnalyzer 2100 Instrument.
RNA samples were submitted to WuXi NextCode for next-generation sequencing with TruSeq RNA Exome. Paired-end sequencing (2 × 150 bp reads) was performed on successful RNA libraries using the Illumina HiSeq X-Ten platform.

treatment_protocol: Six paired pre- and post-ADT PCa lesions and 5 paired paracancerous benign tissues were obtained from six patients receiving neoadjuvant ADT (bicalutamide 50 mg per day and goserelin and 3.6 mg every four weeks with 2 cycles) with locally advanced PCa.

tag: treatment

value: Pre-ADT

tag: individual

value: Paracancerous benign tissue


title: R19028449LR01-19, Pca tissue

source_name: Pca tissue

value: Post-ADT

value: Pca tissue


title: R19028451LR01-21, Pca tissue


title: R19028448LR01-18, Paracancerous benign tissue


title: R19028450LR01-20, Pca tissue


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E12_ad002


title: R19028447LR01-17, Pca tissue


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E11_ad004


title: R19028446LR01-16, Pca tissue


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E12_ad001


title: R19028445LR01-15, Paracancerous benign tissue


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E2_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E11_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E11_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E11_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E11_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E11_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E10_ad004


title: R19023187LR01-11, Pca tissue


title: R19023188LR01-12, Paracancerous benign tissue


title: R19023185LR01-9, Pca tissue


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E10_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E10_ad007


title: R19023183LR01-8, Paracancerous benign tissue


title: R19023181LR01-7, Pca tissue


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E10_ad001


title: R19023179LR01-6, Paracancerous benign tissue


title: R19023175LR01-4, Paracancerous benign tissue


title: R19023177LR01-5, Pca tissue


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E1_ad001


title: R19023190LR01-14, Paracancerous benign tissue


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E1_ad010


title: R19023171LR01-2, Paracancerous benign tissue


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E1_ad008


title: R19023186LR01-10, Paracancerous benign tissue


title: HCT116 cells, input DNA

city: Hanghou

first: Chunxiao

last: Li

state: Zhejiang

address: 79 Qingchun Road

department: Department of Gastroenterology

institute: The First Affiliated Hospital, College of Medicine, Zhejiang University

data_processing:
Basecalls performed using CASAVA version 1.4
Version hg19 of the human genome was used as a reference. The sequencing quality was evaluated with FastQC, (Version 0.11.5) and low-quality data were filtered using NGSQC (v0.4)
MACS1.4.2 was used to perform the peak-calling analyses, and the cutoff P value was set to 10e-5. To assess the confidence level of the peaks, FDR values were provided
All peaks were recorded in detail and then annotated based on the annotation of the reference genome and public databases using ChIPseeker. MEME-ChIP was used to perform the motif analyses. The functional enrichment analyses were performed using KOBAS software
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were generated using python (version 2.7) scripts. Scores represent normalized mapped fragments.

source_name: Human colon cancer cells

growth_protocol: HCT116 cells (Institute of Biochemistry and Cell Biology, China Academy of Sciences, Shanghai, China) were cultured in DMEM (Invitrogen, Carlsbad, CA, USA) and supplemented with 10% fetal calf serum (Invitrogen, USA) and 100 U/ml penicillin-streptomycin (Sigma-Aldrich, St. Louis, MO, USA) at 37 ℃ in a humidified 5% CO2 atmosphere.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HCT116 cells were treated with TNFα and MS-275

tag: cell line

tag: cell type

value: colon cancer cells

tag: passages

tag: chip antibody

value: none (input)


title: R19023189LR01-13, Pca tissue


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E1_ad007


title: HCT116 cells, H3k9acetylation4_TNFaMS275, ChIPSeq

value: TNFa, MS275

value: Acetyl-Histone H3 (Lys9) (CST 9649)


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E10_ad012

value: SSp


title: HCT116 cells, H3k9acetylation3_TNFa, ChIPSeq

value: TNFa


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E1_ad004

value: male


title: HCT116 cells, H3k9acetylation2_MS275, ChIPSeq


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E1_ad002


title: HCT116 cells, H3k9acetylation1_NC, ChIPSeq

value: NC


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E1_ad012


title: Force H3K27me3 rep2

city: Beijing

first: Yu

last: Zhang

address: Xueyuan Road

institute: Peking University Health Science Center

description: Force H3K27me3

data_processing:
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. Low-quality reads include two types, and the reads meeting any one of the two conditions will be removed: 1) Unknown bases are more than 10%; 2) The ratio of bases whose quality was less than 20 was over 10%. After filtering, the remaining reads are called "clean reads" and stored as FASTQ format.
The clean data was mapped to the reference genome by BOWTIE, and the duplication reads were further removed.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files record reads coverage of ChIP-seq data.

source_name: Periodontal ligament

growth_protocol: Briefly, the PDL tissues were separated from the mid-third of the root surface and then minced into small tissue cubes. Subsequently, the tissue cubes were digested with a solution of 3 mg/mL type I collagenase with 4 mg/mL dispase in α-minimum essential medium (α-MEM) for 15 min at 37°C with vigorous shaking. The tissue explants were then plated into culture dishes containing α-MEM supplemented with 10% fetal bovine serum (FBS), 0.292 mg/mL glutamine, 100 units/mL penicillin streptomycin, and 100 μM ascorbic acid and incubated at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
For ChIP-seq, the histone-DNA complexes were extracted from the sonicated nuclei and isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Static compressive force was applied to PDLSCs in vitro using the method previously described. Briefly, a glass cylinder was placed over a confluent cell layer in the well of a 6-well plate. The compressive force was adjusted by adding lead granules to the cylinder. Cells were subjected to different continuous compressive forces ranging from 0 to 2 g/cm2 for 24 hours or at 1.5 g/cm2 for different durations ranging from 0 to 24 hours.

value: Periodontal ligament

value: mesenchymal stem cell


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D9_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E8_ad002


title: Force H3K27me3 rep1

description: Force H3K27me3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D9_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D9_ad010


title: R19023169LR01-1, Pca tissue


title: Input rep2

description: Input


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D9_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D9_ad007


title: Input rep1

description: Input


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E1_ad006


title: Force H3K27ac rep2

description: Force H3K27ac


title: Force H3K27ac rep1

description: Force H3K27ac


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D8_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D9_ad002


title: Force+EZH2 H3K27ac rep2

description: Force+EZH2 H3K27ac


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D9_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D8_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D8_ad008


title: peCArG mutant 4 female

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

description:
experiment2_deSeq2_counts.txt
experiment2_deSeq2_NormCounts.txt

data_processing:
FastP version 0.20.0 with the following parameters: "--length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y -r"
STAR_2.7.0f with the following parameters: "—twopass Mode Basic --runMode alignReads --outSAMtype BAM SortedByCoordinate – outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical –outReads UnmappedFastx"
subread-1.6.4 package (featureCounts) with the following parameters: "-s 2 -t exon -g gene_name"
Differential expression analysis was performed using DESeq2-1.22.1
Genome_build: GRCm38 + M22 Annotation
Supplementary_files_format_and_content: Raw and normalized counts

source_name: aortas

extract_protocol:
Aortas were isolated and smap frozen in liquid nitrogen, total RNA was extrated by miRNeasy kit.
The total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 100ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 8pM per lane. Single end reads of 100nt are generated for each sample and aligned to the organism specific reference genome.

tag: genotype

value: peCArG mutant

value: 8 weeks

value: aortas

tag: gender

value: female


title: Force+EZH2 H3K27ac rep1

description: Force+EZH2 H3K27ac


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D8_ad007

tag: brain region


title: peCArG mutant 2 female


title: peCArG mutant 3 female


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D8_ad006

tag: Sex


title: Control H3K27me3 rep1

description: Control H3K27me3


title: Control H3K27ac rep2

description: Control H3K27ac


title: Control H3K27me3 rep2

description: Control H3K27me3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D8_ad004

tag: age


title: peCArG mutant 1 female

tag: strain


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D8_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D8_ad012


title: peWT 4 male

value: peWT

tag: tissue


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D7_ad001


title: Control H3K27ac rep1

description: Control H3K27ac


title: Force rep2

data_processing:
The clean reads from RNA-seq were aligned to the human genome with TopHat.
We used Cufflinks to call mechanical stress induced differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include gene expression levels

extract_protocol:
Total cellular RNAs were extracted using Trizol reagent according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Static compressive force


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D7_ad010


title: peWT 3 female


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D7_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D7_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D7_ad007


title: peWT 2 female


title: Force rep1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E10_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D7_ad006


title: peWT 1 female


title: Control rep1

value: control


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D7_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D7_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D6_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D6_ad001


title: sgCArG mutant 5 male

description:
experiment1_deSeq2_counts.txt
experiment1_deSeq2_NormCounts.txt

value: sgCArG mutant

value: 12 weeks


title: sgCArG mutant 4 male


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D6_ad006


title: sgWT 5 male

value: sgWT


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D6_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D6_ad004


title: sgWT 4 male


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D5_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D9_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D5_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D6_ad002


title: sgCArG mutant 3 female


title: sgCArG mutant 2 female


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D5_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D5_ad007


title: Control rep2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D5_ad006


title: sgCArG mutant 1 female


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D5_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D5_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D5_ad002


title: sg WT 3 female

value: sg WT


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D4_ad001

value: SSp


title: sg WT 2 female


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D4_ad008


title: sg WT 1 female


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D4_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D4_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D4_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D4_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D3_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D3_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D3_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D3_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D3_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D3_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D3_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D3_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D2_ad001


title: CortexmiR324KO2

city: NEWCASTLE UPON TYNE

first: David

last: Young

address: Centre For Life

country: United Kingdom

institute: Newcastle University

data_processing:
Kallisto was used for pseudo-alignment and quantification, against the mouse GRCh38 (release 92) transcriptome.
Mapped transcripts were converted to a gene level using Tximport.
DESeq2 was used to calculate P-values and log2 fold-changes (logFC), using the Benjamini-Hochberg method to adjust for multiple testing.
Genome_build: Mouse GRCh38 (release 92)
Supplementary_files_format_and_content: abundance measurements

source_name: Cerebral cortex

extract_protocol:
RNA was extracted from murine tissue using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific), following the manufacturer’s protocol to isolate total RNA.
The sequencing library was prepared using the Illumina TruSeq Stranded mRNA sample preparation kit following the manufacturer’s protocol.

value: Cerebral cortex

value: 13.5 month old


title: CortexmiR324KO4


title: CortexmiR324KO5


title: CortexmiR324KO1


title: CortexmiR324KO3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D2_ad008

value: male


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D2_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D2_ad007


title: CortexWT5

value: wild-type control


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D2_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D2_ad012


title: CortexWT3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D12_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D12_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D12_ad007


title: CortexWT2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D12_ad006


title: CortexWT1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D12_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D12_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D12_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D11_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D11_ad012


title: HippocampusmiR324KO4

source_name: Hippocampus

value: Hippocampus


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D11_ad004


title: CortexWT4


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D11_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D11_ad007


title: HippocampusmiR324KO2


title: HippocampusmiR324KO3


title: HippocampusmiR324KO1


title: HEK 293T VbP rep4

city: New York

first: Daniel

middle: A.

last: Bachovchin

address: 408 E 69th St

department: Chemical Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
An average of 41 x 10^6 paired reads was generated per sample.
At most, the ribosomal reads represented 3.5% of the total reads generated and the percent of mRNA bases averaged 70%.
FASTQ output files were aligned to the human genome using rnaStar aligner software.
2-pass mapping method was performed as described in Engstrom et al. Expression count matrix R/Bioconductor package DESeq.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: HEK 293T cells

growth_protocol: HEK 293T cells were grown and maintained in Dulbecco's Modified Eagle's Medium (DMEM) with L-glutamine and 10% fetal bovine serum (FBS). Cell line was regularly tested for mycoplasma.

extract_protocol:
Cellular RNA was harvested using the Rneasy Mini Kit (Qiagen). 500 ng of total RNA underwent polyA selection and Illumina TruSeq library preparation with 8 cycles of PCR.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Four replicates were Val-boroPro treated while four additional replicates were treated with DMSO, each for 48 hours.

value: Embryonic kidney

value: Val-boroPro


title: HEK 293T VbP rep2


title: HEK 293T VbP rep3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D11_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D10_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D11_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D10_ad010


title: HippocampusWT5


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D10_ad008


title: HEK 293T DMSO rep4

value: DMSO


title: HippocampusWT4


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D10_ad006


title: HEK 293T DMSO rep3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D10_ad002


title: HippocampusmiR324KO5


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D11_ad008


title: HippocampusWT3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D10_ad001


title: HEK 293T DMSO rep2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D1_ad001


title: HippocampusWT2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D1_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D10_ad004


title: HEK 293T VbP rep1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D1_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D1_ad012


title: HippocampusWT1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D1_ad007


title: HEK 293T DMSO rep1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D1_ad006


title: KC_SAAD_3

city: Bethesda

first: Ian

middle: A

last: Myles

state: MD

address: 9000 Rockville Pike, BLD 29B, Rm 5NN24

department: NIAID

institute: NIH

data_processing:
Reads were trimmed using cutadapt to remove adaptor sequences and low quality bases.
After trimming, reads were aligned to the human hg38 reference genome and Gencode release28 using STAR v2.5.2b.
RSEM v1.3.0  was used for gene-level expression quantification.
Genome_build: hg38
Supplementary_files_format_and_content: raw counts and FPKM

source_name: Primary keratinocyte

extract_protocol:
After 24 hours, RNA was extracted using RNAeasy kit from QIAGEN per manufacturers recommendations.
RNA-seq libraries were created in triplicate for all cell types using Illumina TruSeq Stranded TotalRNA Library Prep, pooled, and sequenced on a HiSeq4000 producing paired-end 150 base-pair reads.

treatment_protocol: Primary human fibroblasts and  primary human keratinocytes were collected and cultured as previously described (Anderson ED, et al. PLoS One, e01988652; 2018).  Dendritic cells were purchased and cultured (Myles IA, et al. JLB, 302-320; 2017).  All cells were stimulated with bacterial isolates at an MOI=1 in 6-well plates.

tag: bacterial isolate

value: Staphylococcus aureus

tag: bacteria source

value: Atopic dermatitis


title: P7 incisor

city: Sendai

first: Yuta

last: Chiba

state: Miyagi

address: 4-1 Seiryo-cho, Aoba-ku

country: Japan

institute: Tohoku University

description: Single cell RNA-seq

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the 10X Genomics CellRanger v2.0.0 pipeline using default settings.
Secondary analysis was performed using the Seurat2 and Monocle2 R packages.
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger v2.0.0 gene counts matrices.

source_name: P7 incisor

extract_protocol:
Incisors were dissected with sharp tweezers from seven littermates of P7 Krt14-RFP mice. Single cell dissociation was essentially performed as previously described (Li et al. 2015). Briefly, dissected incisors were incubated in 4 mg/ml Dispase II (Roche) for 14 min at 37°C. Then incisors were placed in cold DMEM/F12 and dental epithelium and mesenchyme were separated under microscope. The tissues are then placed in Accutase (Sigma) for 30min at 37°C. After pipetting up and down using 1000 μm tips, single cell suspension was further produced through a 70 μm sterile cell strainer. The cells were resuspended with 0.04% BSA containing cold PBS.
Library preparation was performed according to the manufacturer’s instructions for the 10× Chromium single-cell kit (10x Genomics). The libraries were then pooled and sequenced on four lanes on a NextSeq500 sequencer (Illumina).


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D1_ad004


title: KC_SAAD_2


title: KC_SAAD_1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C9_ad012


title: KC_RmHV_3

value: Roseomonas mucosa

value: Healthy volunteers


title: SMG-WT

city: Buffalo

first: Jonathan

middle: E

last: Bard

state: New York

address: 701 Ellicott Street

department: Genomics and Bioinformatics Core

institute: University at Buffalo

description: scRNA-Sequencing

data_processing:
Illumina RTA 2.2.68 Basecaller
Cellranger 2.1.0 mkoutput with Bcl2Fastq 2.19.1
Cellranger 2.1.0 Count against mm10 genome to produce count matrix
Seurat 3.1.2 used for marker gene analysis and visualization
Genome_build: mm10
Supplementary_files_format_and_content: CSV File containing UMI corrected read counts

source_name: Primary Mouse Epithelial Progenitor Cells

extract_protocol:
Whole mouse Salivary gland was dissociated into single cells and sujected to single-cell sequencing
Chromimum Single Cell 3' v2 (10x Genomics)
TruSeq Stranded RNA (illumina)

value: Adult (12wk)

value: Salivary Gland

tag: genotype/variation

value: p63 WildType mouse


title: SMG-KO

description: scRNA-Sequencing

value: p63 KO mouse


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C9_ad010

value: SSp


title: CEMBA181023_6B_1_CEMBA181023_6B_2_D1_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_E10_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C9_ad008


title: R19023173LR01-3, Pca tissue

value: Pre-ADT

value: Pca tissue


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C9_ad006

value: male


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C9_ad002


title: KC_RmHV_1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C9_ad001


title: SARS-CoV-2 72 hpi rep2

city: Philadelphia

first: Sarshan

middle: R.

last: Pather

state: PA

address: 415 Curie Boulevard

department: Department of Neuroscience

institute: University of Pennsylvania

data_processing:
Basecalling was performed with bcl2fastq2 v2.17.1.14 (Illumina).
Sequence reads were trimmed using Trimmomatic v0.32 software (Bolger et al., 2014). Alignment was performed using STAR v2.5.2a (Dobin et al., 2013). A combined reference genome consisting of GENCODE human genome release 28 (GRCh38.p12) and Ensembl SARS-CoV-2 Wuhan-Hu-1 isolate genome (genome assembly: ASM985889v3, GCA_009858895.3; sequence: MN908947.3) was used for alignment. Multimapping and chimeric alignments were discarded, and uniquely mapped reads were quantified at the exon level and summarized to gene counts using STAR --quantMode GeneCounts.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Raw counts for unstranded RNA-seq output from STAR using --quantMode GeneCounts. SARS-CoV-2 (genome assembly: ASM985889v3, GCA_009858895.3; sequence: MN908947.3) genes are located at bottom of matrix.

source_name: Choroid plexus organoids (CPOs)

extract_protocol:
To minimize variability due to sampling and processing, each biological replicate consisted of 3 organoids and the replicates for all experimental conditions were processed in parallel for RNA-extraction, library preparation and sequencing. At the desired experimental endpoints, organoids were homogenized in TRIzol (Thermo Fisher Scientific) using a disposable pestle and handheld mortar and stored at -80 ⁰C until processing. RNA clean-up was performed using the RNA Clean & Concentrator kit (Zymo Research) after TRIzol phase separation according to the manufacturer’s protocol. RNA concentration and quality were assessed using a Nanodrop 2000 (Thermo Fisher Scientific).
Library preparation was performed as previously described with some minor modifications (Weng et al., 2017). About 300 ng of RNA in 3.2 µL was combined with 0.25 µL RNase inhibitor (NEB) and 1 µL CDS primer (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’) in an 8-well PCR tube strip, heated to 70 ºC for 2 min, and immediately placed on ice. 5.55 µL RT mix, containing 2 µL of 5X SMARTScribe RT buffer (Takara), 0.5 µL of 100 mM DTT (Millipore Sigma), 0.3 µL of 200 mM MgCl2 (Thermo Fisher Scientific), 1 µL of 10 mM dNTPs (Takara), 1 µL of 10 µM TSO primer (5’-AAGCAGTGGTATCAACGCAGAGTACATrGrGrG-3’), 0.25 µL of RNase inhibitor (NEB), and 0.5 µL SMARTScribe reverse transcriptase (Takara) was added to the reaction. RT was performed under the following conditions: 42 ºC for 90 minutes, 10 cycles of 50 ºC for 2 minutes and 42 ºC for 2 minutes, 70 ºC for 15 minutes, and 4 ºC indefinitely. For cDNA amplification, 2 µL of the RT reaction was combined with 2.5 µL of 10X Advantage 2 buffer (Takara), 2.5 µL of 2.5 mM dNTPs (Takara), 0.25 µL of 10 µM IS PCR primer (5’-AAGCAGTGGTATCAACGCAGAGT-3’), 17.25 µL nuclease free water (ThermoFisher), and 0.5 µL Advantage 2 DNA Polymerase (Takara). Thermocycling conditions were as follows: 94 ºC for 3 minutes, 8 cycles of 94 ºC for 15 s, 65 ºC for 30 s, and 68 ºC for 6 minutes, 72 ºC for 10 minutes, and 4 ºC indefinitely. Amplified cDNA was purified using 0.8X AMPure XP beads (Beckman Coulter), eluted in 15 µL nuclease-free water, and quantified using Qubit dsDNA HS assay kit (Thermo Fisher Scientific). cDNA was fragmented by combining 100 pg cDNA in 1 µL nuclease free water, 2X TD buffer (20 mM Tris, pH 8.0; Thermo Fisher Scientific), 10 mM MgCl2, and 16% PEG 8000 (MilliporeSigma), and 0.5 µL Tn5 (Lucigen). The mixture was heated to 55 ºC for 12 minutes, and the reaction was terminated upon the addition of 1.25 µL of 0.2% SDS (Fisher) and incubated at room temperature for 10 minutes. Fragments were amplified by adding 16.75 µL nuclease free water (Thermo Fisher Scientific), 1 µL of 10 mM Nextera i7 primer, 1 µL of 10 mM Nextera i5 primer, and 25 µL KAPA HiFi hotstart readymix (EMSCO/FISHER). Thermocycling conditions were as follows: 72 ºC for 5 minutes, 95 ºC for 1 minute, 14 cycles of 95 ºC for 30 s, 55 ºC for 30 s, and 72 ºC for 30 s, 72 ºC for 1 minute, and 4 ºC indefinitely. DNA was purified twice with 0.8X AMPure XP beads (Beckman Coulter) and eluted in 10 µL of 10 mM Tris, pH 8 (Thermo Fisher Scientific). Samples were quantified by qPCR (KAPA) and pooled at equal molar amounts. Final sequencing library fragment sizes were quantified by bioanalyzer (Agilent) with an average size of ~420 bp, and concentrations were determined by qPCR (KAPA). Samples were loaded at concentrations of 2.7 pM and sequenced on a NextSeq 550 (Illumina) using 1x72 bp reads to an average depth of 40 million reads per sample.

value: hiPSC-derived choroid plexus organoids (CPOs)

value: SARS-CoV-2 72 hpi


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C8_ad001


title: SARS-CoV-2 72 hpi rep3


title: KC_RmHV_2


title: KC_RmAD_3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C8_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C8_ad007


title: KC_RmAD_2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C8_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C8_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C8_ad004


title: SARS-CoV-2 72 hpi rep1


title: SARS-CoV-2 24 hpi rep3

value: SARS-CoV-2 24 hpi


title: KC_RmAD_1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C7_ad001


title: SARS-CoV-2 24 hpi rep1


title: KC_Dil_3

value: Diluent control


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C7_ad010


title: KC_Dil_2


title: Mock 72 hpi rep3

value: Mock 72 hpi


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C7_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C7_ad008


title: SARS-CoV-2 24 hpi rep2


title: Mock 72 hpi rep2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C7_ad007


title: KC_Dil_1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C7_ad006


title: Mock 72 hpi rep1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C7_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C6_ad001


title: KC_CoNS_HV_3

value: Coagulase negative Staphylococci


title: KC_CoNS_HV_2


title: human_hct116_chip_input-dmso-mock-60min-r1_LT

first: Nathaniel

last: Delos Santos

address: 9500 Gilman Drive MC 0640

institute: University of California San Diego

description:
Input Background on HCT116 Cells.
processed data file: ifnb.deseq2.dba_report.tsv

data_processing:
Binary base calls retrieved from NextSeq 500.
Conversion to fastq performed with bcl2fastq 2.17.
Reads preprocessed for quality and adapter removal with fastp 0.19.3.
Preprocessed reads aligned using bowtie2 2.25.
Duplicates marked with samtools markdup 1.7.
Peaks called against Input Background with MACS2.
Differential peak statistics called with DiffBind using DESeq2 backend.
Genome_build: GRCh38
Supplementary_files_format_and_content: ifnb.deseq2.dba_report.tsv: Tab-delimited text file; DIffBind whole differential peaks report.

source_name: colorectal carcinoma

growth_protocol: HCT116 CMV-osTIR1 RAD21-mAC cells were obtained from Masato T. Kanemaki and cultured in McCoy’s 5A medium supplemented with 10% FBS. Cells were grown in a 37˚C incubator with 5% CO2.

extract_protocol:
Crosslinking and ChIP-seq were performed as described in Heinz et al., 2018 with few adjustments. Briefly, cells were fixed directly by adding formaldehyde into media to a final concentration of 1% formaldehyde for 10min at room temperature and quenched with 125mM Glycine. Cells were then pelleted at 300g for 5min at 4˚C, washed twice with cold PBS (with 0.5% BSA), snap frozen in liquid nitrogen and stored at -80˚C. ChIP-seq was performed on 500,000 cells as described in Heinz et al., 2018. H3K27ac antibodies were obtained from Active Motif (cat#:39133).
Libraries were single-end sequenced for 75bp to a depth of 5.5 - 8.6 reads on an Illumina NextSeq500 instrument.

treatment_protocol: Cells were treated with 0.1% final DMSO for 6 hours and then treated with either IFN-β (1000 unit/ml) for one hour or not further treated.

value: Colon colorectal carcinoma cells

value: Not further treated


title: human_hct116_chip_h3k27ac-dmso-mock-0min-r2_LT

description:
H3K27ac ChIP-seq on HCT116 Cells After Unstimulated Control, replicate 2.
processed data file: ifnb.deseq2.dba_report.tsv

value: H3K27ac (Active Motif cat#:39133)


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C8_ad002

source_name: C57BL/6J Male P56 Mouse Brain


title: KC_CoNS_HV_1

value: Healthy volunteers


title: human_hct116_chip_h3k27ac-dmso-mock-0min-r1_LT

description:
H3K27ac ChIP-seq on HCT116 Cells After Unstimulated Control, replicate 1.
processed data file: ifnb.deseq2.dba_report.tsv


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C6_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C6_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C6_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C5_ad010


title: FB_SAAD_2

source_name: Primary fibroblast

value: Staphylococcus aureus

value: Atopic dermatitis


title: human_hct116_chip_h3k27ac-dmso-ifnb-60min-r1_LT

description:
H3K27ac ChIP-seq on HCT116 Cells After Interferon Beta stimulation, 1 hour, replicate 1.
processed data file: ifnb.deseq2.dba_report.tsv

value: IFN-beta (1000 unit/ml) for one hour


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C5_ad006

value: SSp


title: FB_SAAD_1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C4_ad001


title: FB_RmHV_3

value: Roseomonas mucosa


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C5_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C4_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C6_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C4_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C6_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C4_ad012


title: FB_RmHV_1


title: c30_1(1383D6)

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

description: processed data file: rnaseq_Murase2020_counts.txt

data_processing:
All reads were processed with cutadapt v1.9.1 to remove low-quality (quality value < 30) or adapter sequences.
Reads (≥ 30 mer) were mapped on Human genome, GRCh38.p2 using Tophat (v2.1.0)/Bowtie2 (v2.2.7) (Kim et al., 2013) with the “-no-coverage-search” option (Kim et al., 2013), followed by HTSeq (v0.9.1) (Anders et al., 2015) to estimate forward read counts per gene.
Read counts were converted to reads per million mapped reads (RPM) using sum of all forward read counts for all genes.
Genome_build: GRCh38.p2
Supplementary_files_format_and_content: rnaseq_Murase2020_counts.txt: Tab-delimited text file includes read counts for each Sample.

source_name: expanded hPGCLC derived from 1383D6 iPSC, EpCAM-high/INTEGRINA6-high cells were collected at expansion culture day 30, rep1

growth_protocol: The defined hPGCLC expansion culture medium is: DMEM (1.0 g/L glucose; GIBCO, 11054-020) with 15% of KSR, 2.5% of FBS, 1% of NEAA, 2mM of GlutaMAX (GIBCO, 35050-061), 1% penicillin & streptomycin, and 0.1 mM of 2-Mercaptoethanol (GIBCO, 21985-023) supplemented with 10 µM of forskolin, 100 ng/mL of SCF and 20 ng/mL of bFGF.

extract_protocol:
For the RNA extraction, cells collected in Cellotion were pelleted and lysed and stored at −80°C until use. RNA extraction was performed with RNeasy Micro Kit (QIAGEN, 74004) or NucleoSpin RNA XS (MACHEREY-NAGEL, U0902A) according to the manufacturer’s instruction. When using NucleoSpin RNA XS, we added an additional centrifugation just before the elution step. The concentration of RNA was measured with Qubit RNA HS Assay Kit (Invitrogen, Q32855). 1 ng of total RNA from each sample was used for the reverse transcription and the cDNA amplification was performed as described previously. When the RNA concentration was too low to be measured (in the present study, RNA extraction was performed with 1,606 to 6,516 cells), we centrifuged the RNA solution to reduced its volume and used the whole concentrated RNA solution for the reverse transcription and the cDNA amplification.
For RNA-seq analysis, sequence libraries were constructed with amplified cDNAs as described previously (Nakamura et al., 2015; Ishikura et al., 2016) with some modifications. When purifying cDNA libraries, we used Axyprep MAG PCR Clean-up Kit (Axygen, MAG-PCR-CL-250), instead of Agencourt AMPure XP (Beckman Coulter, A63881). Sequences were performed on Illumina NextSeq 500/550 platform with NextSeq 500/550 High output kit v2.5 (75 cycles) (Illumina).

tag: transgene


title: c10_ITGA6low_2

source_name: expanded hPGCLC derived from 1383D6 iPSC, EpCAM-high/INTEGRINA6-low cells were collected at expansion culture day 10, rep2


title: c10_ITGA6low_1

source_name: expanded hPGCLC derived from 1383D6 iPSC, EpCAM-high/INTEGRINA6-low cells were collected at expansion culture day 10, rep1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C4_ad006


title: FB_SAAD_3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C6_ad002


title: FB_RmAD_3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C4_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C3_ad001


title: human_hct116_chip_h3k27ac-dmso-ifnb-60min-r2_LT

description:
H3K27ac ChIP-seq on HCT116 Cells After Interferon Beta stimulation, 1 hour, replicate 2.
processed data file: ifnb.deseq2.dba_report.tsv

tag: treatment


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C5_ad004


title: c10_2(1383D6)

source_name: expanded hPGCLC derived from 1383D6 iPSC, EpCAM-high/INTEGRINA6-high cells were collected at expansion culture day 10, rep2


title: c30_2(1383D6)

source_name: expanded hPGCLC derived from 1383D6 iPSC, EpCAM-high/INTEGRINA6-high cells were collected at expansion culture day 30, rep2


title: c10_1(1383D6)

source_name: expanded hPGCLC derived from 1383D6 iPSC, EpCAM-high/INTEGRINA6-high cells were collected at expansion culture day 10, rep1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C3_ad010


title: FB_RmAD_1


title: FB_Dil_3


title: FB_RmHV_2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C3_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C4_ad007


title: d6hPGCLC_1(1383D6)

source_name: day6 human PGCLC, from 1383D6 iPSC, rep1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C3_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C3_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C4_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C3_ad002


title: FB_Dil_1


title: iMeLC_1(1383D6)

source_name: iMeLC, from 1383D6 iPSC, rep1


title: iMeLC_2(1383D6)

source_name: iMeLC, from 1383D6 iPSC, rep2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C2_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C2_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C2_ad008


title: FB_CoNS_HV_3


title: iPSC_2(1383D6)

source_name: iPSC, from 1383D6 iPSC, rep2


title: FB_RmAD_2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C2_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C3_ad008


title: d6hPGCLC_2(1383D6)

source_name: day6 human PGCLC, from 1383D6 iPSC, rep2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C2_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C2_ad012


title: FB_CoNS_HV_2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C3_ad007


title: iPSC_1(1383D6)

source_name: iPSC, from 1383D6 iPSC, rep1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C2_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C2_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C12_ad004


title: DC_SAAD_3

source_name: Dendritic cell


title: c120_3

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 120, rep3

value: BLIMP1-tdTomato, TFAP2C-EGFP


title: FB_Dil_2


title: c90_3

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 90, rep3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C12_ad012

source_name: C57BL/6J Male P56 Mouse Brain

value: male


title: DC_SAAD_2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C12_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C12_ad008


title: c70_3

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 70, rep3


title: DC_SAAD_1


title: FB_CoNS_HV_1

source_name: Primary fibroblast


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C12_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C12_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C11_ad012


title: DC_RmHV_2


title: DC_RmHV_3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C11_ad004


title: DC_RmHV_1


title: c10_3

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 10, rep3


title: c120_2

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 120, rep2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C12_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C11_ad010


title: c30_3

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 30, rep3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C11_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C12_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C11_ad002


title: c90_2

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 90, rep2


title: DC_RmAD_2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C11_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C11_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C10_ad012


title: DC_RmAD_3


title: DC_RmAD_1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C10_ad007


title: c70_2

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 70, rep2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C10_ad010


title: c50_3

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 50, rep3


title: c50_2

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 50, rep2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C10_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C10_ad006


title: DC_Dil_3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C10_ad004


title: c10_2(585B1-BTAG)

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 10, rep2


title: DC_Dil_2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C1_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C1_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C1_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C1_ad007


title: DC_CoNS_HV_3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C1_ad006


title: c90_1

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 90, rep1


title: c120_1

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 120, rep1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C1_ad002


title: c70_1

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 70, rep1


title: DC_CoNS_HV_1

source_name: Dendritic cell


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B9_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B9_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B9_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B9_ad006


title: c30_1(585B1-BTAG)

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 30, rep1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B9_ad004


title: c30_2(585B1-BTAG)

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 30, rep2


title: combo-3

city: Ann Arbor

first: Weiping

last: Zou

state: MI

address: 109 Zina Pitcher PI

institute: University of Michigan

data_processing:
Data was analyzed by the University of Michigan Bioinformatics Core. The quality of the raw reads data for each sample was first evaluated using FastQC (version 0.11.3).
The Tuxedo Suite software package was used for alignment, differential expression analysis, and post-analysis diagnostics. Briefly, reads were aligned to the reference transcriptome (hg19) using TopHat (version 2.0.13) and a second round of quality control was performed after alignment. Cufflinks/CuffDiff (version 2.2.1) was used for expression quantitation, normalization, and differential expression analysis. Locally developed scripts were used to format and annotate the differential expression data output from CuffDiff. Diagnostic plots were generated using the CummeRbund R package.
Different conditions were compared using ballgown R package.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: HT1080_RT_IFNg_CountsGeneNames.csv RPKM data in CSV file

growth_protocol: Cells are cultured in Eagle's Minimum Essential Medium from ATCC. For subculture, 0.25% Trypsin was used to disperse cells.Subcultivation ratio is 1:4 to 1:8.

extract_protocol:
Total RNA was isolated from cells by column purification (Direct-zol RNA Miniprep Kit, Zymo Research) with DNase treatment.
The Ribo-Zero Gold rRNA Removal Kit (Illumina) and TruSeq® Stranded Total RNA Library Prep Globin kit (Illumina) were used to prepare the library for RNA-sequencing. Sequencing was performed by the University of Michigan DNA Sequencing Core, using the Illumina Hi-Seq 4000 platform, paired end, 50 cycles.

treatment_protocol: IFNγ (10ng/ml) or/and irradiation (20Gy) treatment, and harvest after 24h

value: human derived fibrosarcoma cells

tag: passage

value: IFNγ-10ng/ml and irradiation (20Gy)


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B9_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

source_name: C57BL/6J Male P56 Mouse Brain

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: combo-2

tag: cell line


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B9_ad012


title: c10_1(585B1-BTAG)

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 10, rep1


title: DC_Dil_1


title: c30ag77_2

source_name: BT+AG+ cells from ag77 xrOvary derived from c30 expanded PGCLC, rep2


title: combo-1

tag: cell type


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B8_ad010


title: RT-3

value: irradiation (20Gy)


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B8_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B8_ad008


title: DC_CoNS_HV_2


title: RT-2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B8_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B8_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_C1_ad004


title: c50_1

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 50, rep1


title: RT-1


title: ag77_2 (Murase)

source_name: BT+AG+ cells from ag77 xrOvary derived from d6hPGCLC, rep2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B8_ad002


title: c30ag35_2

source_name: BT+AG+ cells from ag35 xrOvary derived from c30 expanded PGCLC, rep2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B7_ad001


title: ag35_2 (Murase)

source_name: BT+AG+ cells from ag35 xrOvary derived from d6hPGCLC, rep2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B7_ad010


title: IFNG-3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B7_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B7_ad012


title: IFNG-2


title: c30ag77_1

source_name: BT+AG+ cells from ag77 xrOvary derived from c30 expanded PGCLC, rep1


title: IFNG-1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B7_ad006


title: Untreated-3

value: non-treated


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B7_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B7_ad002


title: ag77_1 (Murase)

source_name: BT+AG+ cells from ag77 xrOvary derived from d6hPGCLC, rep1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B6_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B7_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B6_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B6_ad008


title: Untreated-2


title: Untreated-1


title: ag35_1 (Murase)

source_name: BT+AG+ cells from ag35 xrOvary derived from d6hPGCLC , rep1


title: d6hPGCLC_3(585B1-BTAG)

source_name: day6 human PGCLC, from 585B1-BTAG iPSC, rep3


title: c30ag35_1

source_name: BT+AG+ cells from ag35 xrOvary derived from c30 expanded PGCLC, rep1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B6_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B6_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B6_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B6_ad007


title: Clone 27b - mitotic

first: Ofer

last: Shoshani

state: California

address: 9500 Gilman Drive

institute: Ludwig Institute for Cancer Research

data_processing:
Paired-end HiC sequencing reads were mapped using BWA-MEM to the reference genome (hg19) in single-end mode with default parameter setting for each of the two ends separately. The independently mapped ends were then paired-up and the read pairs were kept if both ends uniquely mapped to the genome (MQAL>10).
Read pairs were further removed if either end was mapped more than 500bp apart away from the closest MboI cutter site
Read pairs were next sorted based on genomic coordinates followed by PCR duplicate removal using samtools rmdup
Processed Hi-C data is converted to .hic file and is visualized using juicebox
Genome_build: hg19
Supplementary_files_format_and_content: bedpe files include valid read pairs for each sample; hic files were generated by juicebox using valid read pairs;

source_name: HeLa clone

growth_protocol: Cells were grown in DMEM (Gibco) containing 10% fetal bovine serum (Omega), supplemented with 100U/ml penicillin, 100U/ml streptomycin, and 2mM l-glutamine, at 37°C in a 5% CO2 incubator

extract_protocol:
In-situ Hi-C experiments were performed as previously described (Rao et al., 2014). Cells were fixed with 1% of formaldehyde at room temperature for 10 minutes. After inactivating with glycine, crosslinked cell pellets were washed with cold PBS once before snap freezing with liquid nitrogen. 1-3 million crosslinked cells were used per Hi-C experiment as follows: Briefly, the crosslinked cell pellets were thawed on ice, lysed on ice for 15 minutes (lysis buffer: 10 mM Tris, pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630 with proteinase inhibitor) followed by a washing with lysis buffer. The pellets were then resuspended in 50 µl 0.5% of SDS and incubated at 62°C for 10 minutes. Permeabilization was quenched by adding 25 µl 10% Triton X-100 and 145 µl water, and incubation at 37°C for 15 minutes. Digestion was performed overnight at 37°C, shaking at 1,000 rpm with 1xNEBuffer 2 and 100 units of MboI, followed by inactivation of MboI at 62°C for 20 minutes. Biotin fill-in reaction was performed for 1.5 hours at 37°C with 15 nmol of dCTP, dGTP, dTTP, biotin-14-dATP each and 40 unit of Klenow. In-situ ligation was then performed at room temperature with slow rotation in a total volume of 1.2 ml containing 1xT4 ligase buffer, 0.1mg/ml BSA, 1% Triton X-100 and 4000 unit of T4 ligase. After ligation, the DNA was reverse crosslinked at 55°C for 30 minutes followed by 68°C overnight in the presence of SDS, NaCl and proteinase K. Afterwards, DNA was extracted by ethanol precipitation and then sheared to an average of 400bp with Covaris M220. Ampure beads were used to further purify the sheared DNA and select the fragments between 300 to 700bp.
The biotin pull-down enrichment and library construction were performed as previously described (Rao et al., 2014).

treatment_protocol: Methotrexate was used at indicated concentrations to generate resistant clones. To obtain mitotic samples, cells were arrested at mitosis with nocodazole for 6 hours and mitotic cells were collected by shake-off

tag: resistance

value: Naïve cells

tag: amplification type

tag: cell cycle stage

value: mitotic


title: d6hPGCLC_2(585B1-BTAG)

source_name: day6 human PGCLC, from 585B1-BTAG iPSC, rep2


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B5_ad010

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute


title: Clone 26a - mitotic

value: Resistant to 40nM methotrexate

value: HSR


title: Clone 27k - mitotic

value: Resistant to 80nM methotrexate

value: Double minutes


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B5_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B5_ad008


title: SB1172-T

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

data_processing:
BaseCall performed with CASAVA v1.8.2
Reads were aligned to the hg19 ersion of the human genome as reference using STAR v2.5.3a after removal of contaminants  (rDNA, tRNA, mtrDNA) were removed using Bowtie2 (version 2.2.5)
Reads aligned to STAR were quantified to the hg19-Ensembl Transcript release 75 and normalized by log2 (x+1) transformation
Normalized counts were used to determine differential gene expression between tumor and non-tumor (control) with gene specific analysis (GSA)
All analyses were corrected for multiple comparisons at false discovery rate (FDR) 0.05 (at least)
Genome_build: hg19
Supplementary_files_format_and_content: txt files contain raw counts and normalized counts

source_name: Tumor tissue (Colon)

extract_protocol:
RNA was isolated from tumor and adjacent non-tumor (control) tissues using the Universal RNA/DNA Isolation kit (Qiagen, Germantown, MD) following the manufacturer's protocol
Paired-end libraries (2 x 75) were prepared (600ng per sample) using the TruSeq Stranded mRNA Library Prep kit

tag: individual

value: Tumor tissue (Colon)

tag: isolate


title: SB1172-N

source_name: Adjacent non-tumor tissue Colon

value: Adjacent non-tumor tissue Colon

tag: Sex


title: Clone 27b - async

value: asynchronized


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B5_ad006

tag: brain region

value: SSp

tag: age


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B5_ad007

tag: strain


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B5_ad004


title: SB1140-T

tag: tissue

value: missing


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B5_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B4_ad002


title: Clone 26a - async


title: Clone 27k - async


title: SB1140-N


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B5_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B4_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B4_ad012


title: d6hPGCLC_1(585B1-BTAG)

source_name: day6 human PGCLC, from 585B1-BTAG iPSC, rep1

value: BLIMP1-tdTomato, TFAP2C-EGFP


title: SB1092-T

value: female


title: SB1092-N


title: SB1043-T


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B4_ad007

source_name: C57BL/6J Male P56 Mouse Brain

value: male


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B4_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B4_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B3_ad010


title: SB1043-N


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B3_ad001


title: SB979-T


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B3_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B3_ad008


title: SB979-N


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B3_ad006


title: SB967-T


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B3_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B3_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B2_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B2_ad010


title: SB967-N


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B2_ad007


title: whole blood, zHD stage2 19, year 3

city: Leicester

first: Christopher

last: Mitchell

address: University Road

department: Neuroscience, Psychology & Behaviour

institute: University of Leicester

description: Gene expression data from peripheral whole blood of patient diagnosed with Huntington’s disease

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (Affymetrix GeneChip® Expression Analysis Technical Manual).

scan_protocol: Affymetrix® GeneChip® Scanner 3000 (Affymetrix GeneChip® Expression Analysis Technical Manual).

data_processing: Probe sets were normalised using robust multi-array averaging (RMA) with the R/Bioconductor package affy.

label: biotin

source_name: Peripheral whole blood

label_protocol: Year 1 Samples: The Ovation Whole Blood Kit and Encore Biotin Module (Nugen, Inc.) was used according to the manufacturer’s protocol.    Year 3 Samples: The Ovation RNA Amplification System V2 (Nugen, Inc.) was used according to the manufacturer’s protocol.

extract_protocol: Blood was stored in PAX Gene tubes from which RNA was extracted using the PAX RNA isolation kit according to manufacturer’s protocol.

tag: year

value: Male

tag: age at year 1

tag: location

value: vancouver

tag: disease stage

value: zHD stage2

tag: expanded allele cag repeat count

tag: uhdrs tms

tag: uhdrs tfc


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B4_ad008


title: SB950-T


title: whole blood, zHD stage2 19, year 1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B2_ad012


title: whole blood, zHD stage2 18, year 1


title: SB950-N


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B2_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B2_ad002


title: whole blood, zHD stage2 17, year 1

value: london


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B2_ad004


title: whole blood, zHD stage1 03, year 1

value: zHD stage1


title: whole blood, zHD stage2 17, year 3


title: SB920-T


title: whole blood, zHD stage2 16, year 3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B12_ad004


title: SB920-N


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B12_ad010


title: whole blood, zHD stage2 16, year 1


title: whole blood, zHD stage2 18, year 3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B12_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B12_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B12_ad008


title: whole blood, zHD stage2 15, year 3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B12_ad001


title: SB693-T


title: whole blood, zHD stage2 15, year 1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B11_ad004


title: SB670-T

value: Uknown


title: whole blood, zHD stage2 14, year 3

value: Female


title: SB670-N


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B11_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B11_ad008


title: SB647-T


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B11_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B11_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B11_ad006


title: whole blood, zHD stage2 13, year 1


title: whole blood, zHD stage2 13, year 3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B10_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B11_ad001


title: SB693-N


title: SB647-N


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B10_ad012


title: SB597-T


title: whole blood, zHD stage2 12, year 3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B11_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B10_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B10_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B10_ad007


title: whole blood, zHD stage2 12, year 1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B10_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B10_ad002


title: whole blood, zHD stage2 11, year 3


title: whole blood, zHD stage2 11, year 1


title: SB526-N


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B10_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B1_ad001


title: SB526-T


title: SB396-T


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B1_ad010


title: SB396-N


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B1_ad012


title: SB394-T


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B1_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B1_ad008


title: SB597-N


title: whole blood, zHD stage2 10, year 1


title: SB298-T


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B1_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B1_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B1_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A9_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A9_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A9_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A9_ad010


title: SB178-T

value: Unkown


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B12_ad006


title: whole blood, zHD stage2 10, year 3


title: SB178-N


title: whole blood, zHD stage2 09, year 1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_B3_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A9_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A8_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A9_ad004


title: whole blood, zHD stage2 14, year 1


title: SB141-T


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A8_ad010


title: whole blood, zHD stage2 08, year 1


title: whole blood, zHD stage2 09, year 3


title: whole blood, zHD stage2 07, year 3


title: SB141-N


title: whole blood, zHD stage2 08, year 3


title: whole blood, zHD stage2 07, year 1


title: whole blood, zHD stage2 06, year 3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A8_ad008


title: SB298-N


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A8_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A8_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A9_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A8_ad004


title: whole blood, zHD stage2 06, year 1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A8_ad002


title: whole blood, zHD stage2 05, year 3


title: DS19-T

description: AfricanAmericanSamples_DS_Gene_counts.txt


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A7_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A7_ad012


title: whole blood, zHD stage2 05, year 1


title: whole blood, zHD stage2 03, year 3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A7_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A7_ad008


title: DS19-N


title: DS18-T


title: DS21-T


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A7_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A7_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A7_ad002


title: DS17-T


title: DS16-T


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A6_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A6_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A6_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A6_ad008


title: whole blood, zHD stage2 01, year 1


title: DS21-N


title: DS17-N


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A6_ad007


title: whole blood, zHD stage2 04, year 1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A6_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A7_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A6_ad004


title: whole blood, zHD stage1 17, year 3


title: whole blood, zHD stage1 18, year 3


title: whole blood, zHD stage2 03, year 1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A5_ad001


title: whole blood, zHD stage2 02, year 1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A6_ad002


title: DS15-T


title: whole blood, zHD stage1 17, year 1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A5_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A5_ad006


title: DS15-N


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A5_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A5_ad012


title: DS14-T


title: whole blood, zHD stage1 18, year 1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A5_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A4_ad001


title: DS14-N


title: DS16-N


title: whole blood, zHD stage1 16, year 3


title: whole blood, zHD stage1 16, year 1


title: DS10-T


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A4_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A4_ad008


title: whole blood, zHD stage1 15, year 3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A4_ad006


title: whole blood, zHD stage1 15, year 1


title: DS8-T


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A4_ad004


title: whole blood, zHD stage1 14, year 3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A3_ad001


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A4_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A4_ad010


title: DS8-N


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A3_ad010


title: whole blood, zHD stage1 14, year 1


title: DS7-N


title: DS7-T


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A3_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A3_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A3_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A3_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A4_ad012


title: whole blood, zHD stage1 13, year 3


title: DS10-N


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A3_ad004


title: whole blood, zHD stage1 13, year 1


title: whole blood, zHD stage1 12, year 3


title: DS6-T


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A3_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A12_ad004


title: DS6-N


title: whole blood, zHD stage1 11, year 3


title: DS5-T


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A12_ad008


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A12_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A12_ad007


title: DS5-N


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A12_ad006


title: whole blood, zHD stage1 11, year 1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A12_ad002


title: DS4-N


title: whole blood, zHD stage1 10, year 3


title: whole blood, zHD stage1 10, year 1


title: whole blood, zHD stage1 12, year 1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A11_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A12_ad010


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A11_ad008


title: DS2-N


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A11_ad006


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A11_ad002


title: DS2-T


title: DS4-T


title: DS1-N


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A10_ad004


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A11_ad004


title: DS1-T


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A10_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A10_ad008


title: whole blood, zHD stage1 09, year 1


title: whole blood, zHD stage1 07, year 1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A11_ad007


title: whole blood, zHD stage1 06, year 3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A10_ad007


title: HeLa_mixTrail

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
Hela cells in culture were treated with TRAIL vehicle
Hashtag barcode:
Hela cells in culture (control) = A0251.txt
Hela cells in culture were treated with TRAIL vehicle (25ng/ml for 50mn) = A0252.txt
Hela cells in culture were treated with TRAIL vehicle (10ng/ml for 120mn) = A0253.txt
Hela cells in culture were treated with TRAIL vehicle (25ng/ml for 120mn) = A0254.txt
He5.la cells in culture were treated with TRAIL vehicle (40ng/ml for 120mn) = A0255.txt

data_processing:
The Cell Ranger Single Cell Software Suite 2.0 was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting.
Sample demultiplexing and analyses were performed using Seurat toolkit V3.
Cellranger v2.0 possorted_genome.bam BAM files are provided as raw data.
Genome_build: hg19
Supplementary_files_format_and_content: Filtered gene barcodes matrices. Tab-delimited text files of cell barcodes per sample (hashing experiment) generated using CITE-seq-count (bam file cell barcode tag: CB)

source_name: Mixed samples of HeLa cells, treated with TRAIL (10, 25 or 40ng/ml) or with the drug vehicle ("Control"), for 50 minutes or 2 hours.

growth_protocol: DMEM Glutamax supplemented with 10% fetal bovine serum and penicillin / streptomycin (Thermo Fisher Scientific, France).

extract_protocol:
Cell Hashing protocol with Hashtag oligonucleotide (HTO) was then conduct with 10x Genomics single-cell 3' V2 chemistry to generate single-cell emulsion.
Single-cell RNA-seq was performed following manufacturer’s protocol (Chromium™ Single Cell 3' Reagent Kit, V2 Chemistry) to obtain single cell 3’ libraries for Illumina sequencing. PCR of 12 cycles was performed for cDNA amplification with HTO primer {Stoeckius:2018fd}. For HTO library preparation, 10 cycles of PCR amplification (REF Stoeckius M, 2018) followed by a size selection with Blue Pippin 3% agarose gel cassette (BDQ3010) Marker Q3 were necessary to select 180bp specific amplicon. Final cDNA library was then pooled with 10% of HTO library in final pool for sequencing.

treatment_protocol: Cells from each treatment conditions were detached with trypsin (filtered, counted) and incubated with Hashtag antibodies (Biolegend TotalSeq™, San Diego, CA) for 20min at 4dC. Live cells from each treatment conditions were then counted and merged into one sample according to the manufacturer’s recommendations

tag: cell line

value: HeLa


title: whole blood, zHD stage1 09, year 3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A1_ad001

city: La Jolla


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A11_ad001


title: high response profile cell 17

description:
Hela cells in culture were treated with TRAIL for 50min, then isolated using laser capture microdissection.
High.17

data_processing:
Mapping of cDNA reads was performed using STAR against human hg19 build following encode RNA-seq recommendations. Drop-seq tools (http://mccarrolllab.com, Macosko et al, 2015) was then used to tag SAM records with cell barcode (XC) and molecule identifier (XM) and produce the digital expression count matrix.
ERCC were removed from the count table, then size factors were calculated for each cell using the TMM method, and librairies were normalized and converted to log2(CPMs+1). All processing was performed using the R package edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files includes a raw count table and  a filtered and normalized count table. Normalized counts are provided as log2(CPM + 1).

source_name: HeLa cells, modified with stable retroviral transformation of plasmid IC-RP: Addgene Plasmid #24553

growth_protocol: DMEM Glutamax supplemented with 10% fetal bovine serum and penicillin / streptomycin (Thermo Fisher Scientific, France)

extract_protocol:
Laser-captured single-cells were catapulted into 0.2ml domed caps tube (strips) containing 4.3 µl of lysis buffer (0,2% w/v Tween 20, 1.5U/µl Promega RNAseIN Plus). Tubes where kept on ice and frozen in dry ice directly after collection. Samples were thawed on ice and 2.43μl of a mix containing 10,000 molecules Life Technologies ERCC spike-In Mix 1, 2.5mM dNTPs, and 3.7µM single barcoded reverse transcription primer was added to each tube, incubated for 10 min at room temperature, 3 min at 70°C and kept at 10°C. Immediately after lysis, 8.27 µl 1.8X reverse transcription buffer (Invitrogen), 4.53mM DTT, 1.8M Betaïne, 10.8 mM MgCl2, 3.62 µM template switching oligonucleotide, 0.6U/µl Promega RNAse IN Plus, 7.5 U/µl Invitrogen SuperScript II reverse transcriptase were added and samples were reverse transcribed 10 min at 25°C, 90 min at 42°C, 15 min at 70°C and kept at 10°C until PCR amplification. Samples were PCR amplified (KAPA HiFi Hotstart) 20 cycles in 31 μl with 0.8µM forward PCR primer, 0.8µM biotinylated reverse PCR primer. Samples were incubated 3 min at 98°C followed by 20 cycles at 98°C for 20 sec, 64°C for 15 sec, 72°C for 6 min followed by a final extension for 5 min at 72°C. After PCR amplification, samples were pooled and purified with 0.8X Beckman Coulter SPRIselect beads, washed once with 85% EtOH and eluted in 30 μl.
Batches of barcoded cDNAs were pooled, purified with SPRIselect beads (0.8x) and eluted in 12µl. Nine µl (typically 10 – 20 ng of cDNA) were used for tagmentation and Illumina library preparation as described in Arguel MJ et al. NAR 2017

treatment_protocol: Recombinant human (rh) TRAIL (R&D Systems Europe - Lille, France) was added to culture media for 50 minutes at a final concentration of 25 nanograms per millilitre.

tag: cell response

value: High

tag: treatment

value: TRAIL 25ng/ml for 50min


title: high response profile cell 19

description:
Hela cells in culture were treated with TRAIL for 50min, then isolated using laser capture microdissection.
High.19

source_name: HeLa cells, modified with stable retroviral transformation of plasmid IC-RP: Addgene Plasmid #24554


title: whole blood, zHD stage1 07, year 3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A10_ad002


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A10_ad010


title: whole blood, zHD stage1 06, year 1


title: high response profile cell 15

description:
Hela cells in culture were treated with TRAIL for 50min, then isolated using laser capture microdissection.
High.15

source_name: HeLa cells, modified with stable retroviral transformation of plasmid IC-RP: Addgene Plasmid #24552


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A1_ad008


title: whole blood, zHD stage1 05, year 1


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A1_ad012


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A1_ad007


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A1_ad006


title: high response profile cell 14

description:
Hela cells in culture were treated with TRAIL for 50min, then isolated using laser capture microdissection.
High.14

source_name: HeLa cells, modified with stable retroviral transformation of plasmid IC-RP: Addgene Plasmid #24551


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A1_ad004


title: whole blood, zHD stage1 05, year 3


title: whole blood, zHD stage1 08, year 1


title: whole blood, zHD stage1 04, year 3


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A1_ad002


title: high response profile cell 12

description:
Hela cells in culture were treated with TRAIL for 50min, then isolated using laser capture microdissection.
High.12

source_name: HeLa cells, modified with stable retroviral transformation of plasmid IC-RP: Addgene Plasmid #24549


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A1_ad010


title: high response profile cell 13

description:
Hela cells in culture were treated with TRAIL for 50min, then isolated using laser capture microdissection.
High.13

source_name: HeLa cells, modified with stable retroviral transformation of plasmid IC-RP: Addgene Plasmid #24550


title: DS18-N

tag: individual

value: Adjacent non-tumor tissue Colon


title: high response profile cell 11

description:
Hela cells in culture were treated with TRAIL for 50min, then isolated using laser capture microdissection.
High.11

source_name: HeLa cells, modified with stable retroviral transformation of plasmid IC-RP: Addgene Plasmid #24548


title: high response profile cell 10

description:
Hela cells in culture were treated with TRAIL for 50min, then isolated using laser capture microdissection.
High.10

source_name: HeLa cells, modified with stable retroviral transformation of plasmid IC-RP: Addgene Plasmid #24547


title: high response profile cell 8

description:
Hela cells in culture were treated with TRAIL for 50min, then isolated using laser capture microdissection.
High.8

source_name: HeLa cells, modified with stable retroviral transformation of plasmid IC-RP: Addgene Plasmid #24546


title: high response profile cell 6

description:
Hela cells in culture were treated with TRAIL for 50min, then isolated using laser capture microdissection.
High.6

source_name: HeLa cells, modified with stable retroviral transformation of plasmid IC-RP: Addgene Plasmid #24545


title: high response profile cell 5

description:
Hela cells in culture were treated with TRAIL for 50min, then isolated using laser capture microdissection.
High.5

source_name: HeLa cells, modified with stable retroviral transformation of plasmid IC-RP: Addgene Plasmid #24544


title: CEMBA181023_6B_1_CEMBA181023_6B_2_A10_ad006

value: SSp


title: whole blood, zHD stage1 04, year 1


title: whole blood, zHD stage1 02, year 3


title: whole blood, zHD stage1 01, year 1


title: whole blood, zHD stage1 02, year 1


title: high response profile cell 2

description:
Hela cells in culture were treated with TRAIL for 50min, then isolated using laser capture microdissection.
High.2

source_name: HeLa cells, modified with stable retroviral transformation of plasmid IC-RP: Addgene Plasmid #24543


title: whole blood, zHD stage1 01, year 3


title: whole blood, preHD B 18, year 1

description: Gene expression data from peripheral whole blood of pre-symptomatic Huntingtin gene change carrier

value: preHD B


title: NHP16.D005.fresh.a1

city: Cambridge

first: Dylan

last: Kotliar

state: MA

address: 4 Garnder Rd, Apt 2

department: Viral genomics

institute: Broad Institute

description:
Animal: NHP16; Day post infection: D005; Fresh or freeze-thawed: fresh; MDCK Spike in: False; Array number: a1
Data for a given Seq-Well array for a specific biological sample
Combined data from Illumina NovaSeq 6000 and NextSeq 550 High Output
PBMC purification: We centrifuged whole blood in K3EDTA tubes at 1800 x g for 10 min at room temperature, removed EDTA plasma, and added phosphate buffered saline (PBS, Thermo Fisher Scientific, Waltham, MA, USA) to the pelleted cells to double the original whole blood volume. We gently poured the PBS-blood cell mixture into an Accuspin tube containing Histopaque (Sigma-Aldrich, St. Louis, MO, USA) and centrifuged at 1000 x g for 10 min at room temperature with the brake set to 1. Following centrifugation, we removed the top, clear supernatant layer to within 0.5 cm of the cloudy white layer containing PBMCs. We transferred the cloudy PBMC layer to a clean 15 mL conical tube and increased the volume to 10 mL using PBS supplemented with 2% heat-inactivated fetal bovine serum (PBS/2%HI-FBS) and mixed by inversion. We then centrifuged at 300 x g for 10 min at 4 °C with the brake set to 1. Following centrifugation, we removed the supernatant, resuspended the cell pellet with PBS/2%HI-FBS to a final volume of 10 mL, and mixed using gentle raking to wash the cells. We repeated the wash step 2 more times with the centrifuge set to 200 x g for 10 min at 4 °C with the brake set to 1. We then resuspended the cell pellet in 9.5mL PBS/2%HI-FBS for counting using the Countess Cell Counting system (Thermo Fisher Scientific). We aliquoted 0.5 mL for Seq-Well, and used the remaining 9 mL volume for CyTOF.
Seq-Well: We performed Seq-Well as described previously (Gierahn et al., 2017), with the S3 protocol (Hughes et al., 2019) and some controls and modifications to adhere to the BSL-4 environment. After loading and sealing beads and cells in Seq-Well arrays, we placed them in a -80 °C freezer until further processing – this step was required due to time constraints in the BSL-4. Later, we removed sealed Seq-Well arrays from the -80 °C freezer, placed them in 4-well dishes, and allowed them to equilibrate to room temperature for at least 30 min. We then covered arrays in 5 mL Seq-Well Lysis Buffer per protocol. We performed RNA hybridization and RT as specified in the protocol (Hughes et al., 2019). After RT, we collected beads by centrifugation at 1000 x g for 1 min at room temperature. We resuspended beads with GeneXpert Lysis Buffer (Cepheid, Sunnyvale, CA, USA) for inactivation, which was required prior to removal from the BSL-4 laboratory according to standard operating procedures. After removal, we washed beads thrice with TE buffer containing 0.01% Tween 20 and shipped at 4 °C for further library construction and sequencing.

data_processing:
Library strategy: scRNA-Seq
Raw sequencing files were demultiplexed and converted to fastq using bcl2fastq version 2.20.
Reads were then trimmed, aligned to a reference transcriptome, and parsed into a digital gene expression matrix using the previously published Dropseq-tools pipeline (Macosko et al., 2015)
The scRNA-Seq data was preprocessed, clustered, and visualized using Scanpy (Wolf et al., 2018). We removed cells with <300 genes detected, >10% of their UMIs derived from mitochondrial genes, or >95% of UMIs mapped to non-genic regions. We excluded ribosomal genes, genes correlated with the percentage of UMIs assigned to mitochondrial genes (Pearson R > 0.1), and HBB as these were largely driven by the technical covariate of whether cells had loaded into Seq-Well arrays fresh or had undergone a freeze-thaw cycle with cryoprotectant. We also excluded EBOV genes and cell-cycle genes (defined by correlation with TOP2A, Pearson R > 0.1) prior to clustering so that these signals would not influence identification of cell types.
See https://www.biorxiv.org/content/10.1101/2020.06.12.148957v2 for details
Genome_build: hybrid of Mmul_8.01 and KU182905.1
Supplementary_files_format_and_content: digital gene expression matrix were generated using the previously published Dropseq-tools pipeline

organism: Macaca mulatta

source_name: Peripheral blood mononuclear cells (PBMC)

extract_protocol: Library construction and sequencing was performed with the S3 protocol (Hughes et al., 2019). We sequenced all libraries on either NextSeq 550 High Output or NovaSeq 6000 S2 flowcells (Illumina, San Diego, CA, USA), with 20 cycles for Read 1 (cell barcode and unique molecular index [UMI]) and 88 cycles for Read 2 (cDNA of interest). In some cases, we merged fastq files from multiple sequencing runs for increased coverage.

tag: fresh_vs_freezethawed (frz)

value: fresh

value: FALSE

tag: library_treatment (standard, dash, dashx2 if dash was applied sequentially, or mixed if dash-treated and standard libraries were combined)

value: mixed