title: CEMBA181015_5H_3_CEMBA181015_5H_4_H2_ad004


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H3_ad001

status: Public on Sep 21 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

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

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

tag: brain region

value: PAL

tag: Sex

value: male

tag: age

tag: strain


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H12_ad012


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H12_ad010


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title: CEMBA181015_5H_1_CEMBA181015_5H_2_B3_ad007


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B3_ad008


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B3_ad006


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B2_ad008


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B3_ad002


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B2_ad006


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B3_ad001


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B2_ad004


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B2_ad012


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B2_ad010


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B12_ad004


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B12_ad010


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B12_ad012


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B12_ad002


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B12_ad001


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B2_ad002


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B11_ad007


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B11_ad001


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B11_ad012


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B11_ad008


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B12_ad006


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B11_ad002


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B11_ad006


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B11_ad010


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B10_ad006


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B10_ad010


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B10_ad004


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B10_ad012


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B10_ad007


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B10_ad002


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B1_ad010


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B12_ad007


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B10_ad001


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B1_ad012


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B2_ad007


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B1_ad004


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B1_ad007


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B1_ad006


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B12_ad008


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A9_ad007


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A9_ad008


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B1_ad008


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A9_ad010


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A9_ad002


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A9_ad001


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A8_ad001


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A8_ad004


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A8_ad007


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A8_ad010


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A8_ad012


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A8_ad002


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A8_ad006


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A7_ad002


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A7_ad012


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A7_ad008


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A8_ad008


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A6_ad008


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A7_ad001


title: CEMBA181015_5H_1_CEMBA181015_5H_2_B1_ad002


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A7_ad004


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A7_ad006


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A7_ad007


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A7_ad010


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A6_ad007


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A9_ad004


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A6_ad012


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A6_ad006


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A6_ad001


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A5_ad008


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A6_ad002


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A5_ad010


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A6_ad010


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A5_ad004


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A9_ad012


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A4_ad008


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A4_ad007


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A4_ad006


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A6_ad004


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A4_ad001


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A4_ad010


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A4_ad012


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A3_ad012


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A4_ad004


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A3_ad006


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A4_ad002


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A3_ad008


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A3_ad002


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A3_ad007


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A5_ad001


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A5_ad012


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A2_ad007


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A3_ad010


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A2_ad002


title: iPSC Mock Infection 2

city: San Francisco

first: Todd

last: McDevitt

address: 1650 Owens St

department: GICD

institute: Gladstone Institutes

library_source: transcriptomic

data_processing:
Demultiplex with bcl2fastq v2.20.0
Align to GRCh38 and NC_045512 with hisat2 v2.1.0
Generate counts matrices with featureCounts v1.6.2
Merge counts across technical replicates of samples
Genome_build: GRCh38,NC_045512
Supplementary_files_format_and_content: tab separated value file of counts

molecule: total RNA

organism: Homo sapiens

source_name: iPSCs

growth_protocol: hiPSCs were maintained in mTeSR or mTeSR+ (STEMCELL Technologies). Cardiomyocytes were differentiated using the GiWi protocol (Lian et al, Nat Prot. 2013). Cardiac fibroblasts were differentiated following the GiFGF protocol (Zhang et al. Nat Comms. 2019). Cardiac endothelial cells were differentiated following a modified E7BVi protocol (Schwartz et al. PNAS, 2015). The WA-1 strain (BEI resources) of SARS-CoV-2 was passaged in Vero cells (ATCC), viral titer was determined by plaque assay.

extract_protocol:
Extraction using Qiagen Rneasy Mini Kit or ThermoFisher Quick-RNA MicroPrep
Library prep using Takara Biosciences SMARTer Stranded Total RNA Sample Prep Kit

treatment_protocol: Cells were treated with either vehicle or virus for 48 hours at a multiplicity of infection of either 0.0006 (low), 0.01 (mid), or 0.1 (high).

tag: infection status

value: mock infection

tag: cell type

value: iPSCs


title: iPSC Low MOI 2

value: low MOI


title: iPSC Mock Infection 1


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A5_ad006


title: iPSC Low MOI 1


title: Endothelial Cell Low MOI 3

source_name: iPSC-derived endothelial cell

value: iPSC-derived endothelial cell


title: Endothelial Cell Low MOI 2


title: Endothelial Cell Low MOI 1


title: Endothelial Cell Mock Infection 3


title: Endothelial Cell Mock Infection 4


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A2_ad012


title: Endothelial Cell Mock Infection 2


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A2_ad006


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A2_ad001


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A12_ad006


title: Endothelial Cell Mock Infection 1


title: Cardiac Fibroblast Low MOI 5

source_name: iPSC-derived cardiac fibroblast

value: iPSC-derived cardiac fibroblast


title: LEC_6

type: RNA

city: Sapporo

first: Daigo

last: Hashimoto

state: Hokkaido

address: N15W7 Kita-ku

department: Department of Hematology

country: Japan

institute: Hokkaido University

description: Gene expression of VECs isolated from small intestines

hyb_protocol: cRNA (600 ng) was hybridized to the microarray chip (SurePrint G3 Mouse Gene Expression v2 8x60K, Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan resolution 3um, Dye channel is set to Green PMT sensitivity is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: LECs of small intestines

label_protocol: Cyanine3-labeled cRNA from each sample was prepared subsequent to mRNA amplification by using Low Input Quick Amp Labeling Kit (one-color) (Agilent Technologies, Tokyo, Japan) according to the manufacture's instruction.

extract_protocol: Up to 10,000 cells of target populations were sorted directly to Trizol reagent (Life Technologies). Total RNA was extracted in accordance with the manufacture's instruction.

tag: tissue

value: Small intestine

tag: gender

value: female


title: VEC_4

source_name: VECs of small intestines


title: LEC_8


title: LEC_7


title: VEC_3


title: VEC_2


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A2_ad008


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A12_ad001


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A2_ad010


title: Cardiac Fibroblast Low MOI 2


title: Cardiac Fibroblast Mock Infection 1


title: Cardiac Fibroblast Low MOI 4


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A12_ad012


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A12_ad008


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A12_ad010


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A11_ad006


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A10_ad001


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A12_ad007


title: Cardiac Fibroblast Low MOI 1


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A10_ad007


title: Cardiomyocyte High MOI 3

source_name: iPSC-derived cardiomyocyte

value: high MOI

value: iPSC-derived cardiomyocyte


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A12_ad004


title: Cardiac Fibroblast Low MOI 3


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A12_ad002


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A10_ad006


title: Cardiac Fibroblast Mock Infection 2


title: Cardiomyocyte High MOI 2


title: Cardiomyocyte Mid MOI 3

value: mid MOI


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A10_ad002


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A10_ad010


title: Cardiomyocyte Md MOI 2


title: Cardiomyocyte Low MOI 3


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A10_ad012


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A10_ad004


title: Cardiomyocyte Low MOI 2


title: Cardiomyocyte Low MOI 1


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A1_ad008


title: Cardiomyocyte High MOI 1


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A1_ad004


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A1_ad001


title: Cardiomyocyte Mock Infection 3


title: Cardiomyocyte Mock Infection 1


title: Cardiomyocyte Mock Infection 2


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A1_ad002


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A1_ad010


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A1_ad006


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A1_ad012


title: iAT2 SARS-CoV-2 4dpi replicate 2

city: Boston

first: Carlos

last: Villacorta-Martin

state: MA

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

data_processing:
The quality of the raw sequencing data was assessed using FastQC v.0.11.7. Sequence reads were aligned to a combination of the human and SARS-CoV-2 genome reference (GRCh38 and Wuhan Hu-1 isolate) and the TdTomato reporter sequence, using STAR v.2.5.2b (Dobin et al. 2013).
Counts per gene were summarized using the featureCounts function from the subread package v.1.6.2.
The edgeR package v.3.25.10 was used to import, organize, filter and normalize the data. Genes that were not expressed in at least one of the experimental groups were filtered out (keeping only genes that had at least 10 reads in at least 3 libraries, that is, a worthwhile number of samples as determined by the replicate number in the design matrix). The TMM method was used for normalization.
Genome_build: GRCh38 + SARS-CoV-2 Wuhan Hu-1 isolate
Supplementary_files_format_and_content: Counts per million, normalized using TMM (edgeR)

molecule: polyA RNA

source_name: iPSC-derived alveolar epithelial type II-like cells at ALI

growth_protocol: The human induced pluripotent stem cell (iPSC) line, SPC2-ST-B2, engineered to carry a tdTomato reporter targeted to one allele of the endogenous SFTPC locus (Hurley et al., 2020), underwent directed differentiation to generate iPSC-derived alveolar epithelial type II like cells (iAT2s) in 3D Matrigel cultures using methods we have previously published (Jacob et al., 2017; Jacob et al., 2019). As previously described (Jacob et al., 2017) we performed PSC directed differentiation via definitive endoderm into NKX2-1 lung progenitors as follows. In short, cells maintained on mTESR1 media were differentiated into definitive endoderm using the STEMdiff Definitive Endoderm Kit (StemCell Technologies) and after the endoderm-induction stage, cells were dissociated with gentle cell dissociation reagent (GCDR) and passaged into 6 well plates pre-coated with growth factor reduced Matrigel in ‘‘DS/SB’’ anteriorization media, consisting of complete serum-free differentiation medium (cSFDM) base as previously described (Jacob et al., 2017) supplemented with 10 µm SB431542 (‘‘SB’’; Tocris) and 2 µm Dorsomorphin (‘‘DS’’; Stemgent). For the first 24 hr after passaging, 10 µm Y-27632 was added to the media. After anteriorization in DS/SB media for 3 days (72 hr), cells were cultured in ‘‘CBRa’’ lung progenitor-induction media for 9-11 days. ‘‘CBRa’’ media consists of cSFDM containing 3 µm CHIR99021 (Tocris), 10 ng/mL recombinant human BMP4 (rhBMP4, R&D Systems), and 100nM retinoic acid (RA, Sigma), as previously described (Jacob et al., 2017). On day 15 of differentiation, live cells were sorted on a high-speed cell sorted (MoFlo Legacy or MoFlo Astrios EQ) to isolate NKX2-1+ lung progenitors based on CD47hi/CD26neg gating (Hawkins et al., 2017). Sorted day 15 progenitors were then resuspended in undiluted growth factor-reduced Matrigel (Corning) and distal/alveolar differentiation of cells was performed in ‘‘CK+DCI’’ medium, consisting of cSFDM base, with 3 µm CHIR99021, 10 ng/mL rhKGF, and 50 nM dexamethasone (Sigma), 0.1mM8-Bromoadenosine 30,50-cyclic monophosphate sodium salt (Sigma) and 0.1mM3-Isobutyl-1-methylxanthine (IBMX; Sigma) (DCI) with a brief period of CHIR99021 withdrawal on days 31-35 to achieve iAT2 maturation. To establish pure cultures of iAT2s, cells were sorted by flow cytometry to isolate SFTPC-tdTomato+ cells on day 41 and again on day 69 of differentiation. iAT2s were then maintained through serial passaging as self-renewing monolayered epithelial spheres (“alveolospheres”) by plating in Matrigel (Corning) droplets at a density of 400 cells/μl with refeeding every other day in CK+DCI medium as previously published (Jacob et al., 2019). iAT2 culture quality and purity was monitored at each passage by flow cytometry, with >80% of cells expressing SFTPC-tdTomato over time, as we have previously detailed (Hurley et al., 2020; Jacob et al., 2019).

extract_protocol:
Triplicate (n=3) samples of iAT2 cells were collected in Trizol (ThermoFisher), then RNA was extracted using the RNAeasy mini kit (Qiagen)
Total mRNA was isolated using magnetic beads-based poly(A) selection, fragmented, and randomly fragmented for reverse transcription, followed by synthesis of cDNA fragments. cDNA fragments were then end-paired, and ligated to Illumina Paired-End sequencing adapters. The products were end-paired and PCR-amplified to create the final cDNA library.

treatment_protocol: iAT2 cells plated in ALI culture were infected with purified SARS-CoV-2 stock at MOI=140 as a 100 μl inoculum prepared in CK+DCI media (or mock-infected with medium-only). Inoculum was added to the apical chamber of each Transwell and incubated for 1 hour at 37 deg C and 5% CO2.  After the adsorption period, the inoculum was removed and cells were incubated at 37oC for 1 or 4 days post-infection (dpi).

value: infected with SARS-CoV-2 MOI 140

tag: days post infection

tag: developmental stage

value: day 222 distal lung directed differentiation

tag: culture media

value: CK+DCI

tag: isolation method

value: unsorted on day of isolation


title: iAT2 SARS-CoV-2 1dpi replicate 3

value: day 219 distal lung directed differentiation


title: iAT2 SARS-CoV-2 1dpi replicate 2


title: iAT2 SARS-CoV-2 1dpi replicate 1


title: iAT2 SARS-CoV-2 4dpi replicate 3


title: Cardiomyocyte Mid MOI 1


title: CEMBA181015_5H_1_CEMBA181015_5H_2_A1_ad007

value: PAL


title: GSK-J4 rep1

city: Shenzhen

first: Xing-sheng

last: Shu

state: Guangdong

address: No 3688, Nanhai Avenue

department: Medical School

country: China

institute: Shenzhen University

data_processing:
After QC of library by Agilent 2100 Bioanalyzer, sequencing was performed on MGISEQ-2000 platform. Primary sequencing data, called as raw reads, is subjected to quality control (QC) to determine if a resequencing step is needed. After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences. Briefly, the pair-end 150bp sequence tags from MGISEQ-2000 sequencer were subjected to data cleaning by SOAPnuke first, which includes getting rid of the low quality tags and several kinds of contaminants. We then used Hisat and Bowtie2 to align the clean data after filtering to reference genome (hg19) and gene respectively.
The bowtie2 was used to get the bam file of each sample from fastq  using -3 5 --local -x hg19 -1 PE1_clean.fq -2 PE2_clean.fq
htseq-count was used to get the count of each gene from bam using -r name -f bam bamfile gencode.v19.annotation.gtf
edgeR was used to find the differential gene in the two groups
Genome_build: hg19

source_name: colon cancer cells

growth_protocol: HCT116 cells were maintained in RPMI1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted from  cells using Trizol reagent from Thermofisher according to manufacturer's instructions
Oligo (dT) magnetic beads are used to select mRNA with polyA tail. Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate adaptor with stickiness 'T' at 3' end to the dscDNA. Two specific primers are used to amplify the ligation product. Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol: HCT116 cells were treated with 15 μm GSK-J4 or veichle for 48 hours before havestation for RNA extraction.

tag: treatment

value: 15 um GSK-J4


title: iAT2 mock replicate 3

value: uninfected


title: iAT2 mock replicate 2


title: iAT2 mock replicate 1


title: WT rep3

value: control


title: RNASeq Pom Dose Titration - Pomlow HRI Donor2

city: Philadelphia

first: Gerd

last: Blobel

state: Pennsylvania

address: 3615 Civic Center Blvd., Abramson Research Center 316H

department: Hematology

institute: Children's Hospital of Philadelphia

data_processing:
The sequence reads were processed using the ENCODE3 long RNA-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL002LPE/).
Gene set Gencode v29 was used for mapping the reads to the human genome (hg38 assembly) using STAR, followed by RSEM for gene quantifications.
Genome_build: hg38 assembly
Supplementary_files_format_and_content: TSV Files

source_name: Primary CD34+ cell culture

growth_protocol: For in vitro cell culture, peripheral blood mononuclear cells were obtained from the University of Pennsylvania Human Immunology Core (Philadelphia, PA). CD34+ cells were purified using MACS MicroBead kit (Miltenyi) and cultured in three-phase in vitro culture. For Phase I medium, IMDM was supplemented with 100 ng/mL human SCF, 1 ng/mL IL-3, 3 units/mL erythropoietin, 2% penicillin/streptomycin, 200 μg/mL holo-transferrin, 10 μg/ml insulin, 5% human A/B plasma and 10 μg/mL heparin. For Phase II medium, the IL-3 was withdrawn after 9 days of culture. For Phase III medium, the cells were cultured with IMDM supplemented with 3 units/mL erythropoietin, 2% penicillin/streptomycin, 1 mg/mL holo-transferrin, 10 μg/ml insulin, 5% human A/B plasma and 10 μg/mL heparin. Cells were maintained in Phase I from the day of collection until day 8, at which time cells were spin-infected and transitioned to Phase II media. On day 13 of culture, cells were transitioned to Phase III media

extract_protocol:
RNA samples were harvested in TRIzol (ThermoFisher Scientific) and purified with the RNeasy Mini kit (Qiagen). For RNA-Seq, approximately 200 ng of RNA was then depleted for rRNA and globins using the Ribo-Zero removal reagents and protocol from the ScriptSeq Complete kit (Illumina Cat # BHMR1224), followed by purification using the RNeasy MinElute Clean Up kit (Qiagen Cat # 74202).
Sequencing libraries were then constructed from depleted RNA using the TruSeq Stranded Total RNA kit (Illumina Cat # 20020598) and PCR-amplified for 13 cycles. The size and quality of each library were then evaluated by Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), and quantified using qPCR. Libraries were sequenced in paired-end mode on the NextSeq 500 to generate 2 x 76 bp reads using Illumina-supplied kits as appropriate.

treatment_protocol: For pharmacologic treatments, cells were treated starting on day 6 of culture with DMSO (vehicle control) 1 uM or 0.1 uM of pomalidomide (Sigma-Aldrich), or 0.125 μM of UNC0638 (Tocris Biosciences) Drugs were replenished every 2-3 days. RNA samples for RT-qPCR were harvested on day 13 of culture for optimal RNA yield. For shRNA treatments, two independent shRNAs targeting HRI were utilized for each sample, while scrambled non-targeting shRNA was used as control. Lentivirus for the above shRNA were produced in HEK293T and concentrated using Lenti-X Concentrator (Takara Bio) as per manufacturer’s specifications. Spin-infection were performed on day 8 of culture at 2250 RPM for 90 minutes.

value: Three-phase in vitro culture of CD34+ primay human cells

tag: day of isolation

value: Day 13 of culture

tag: data file subset

value: RNASeq Pom Dose Titration

tag: shRNA depletion type

value: HRI

tag: pharmacologic treatment type

value: Pomalidomide 0.1 uM (low dose)


title: GSK-J4 rep3


title: RNASeq Pom Dose Titration - Pomlow HRI Donor1


title: iAT2 SARS-CoV-2 4dpi replicate 1


title: RNASeq Pom Dose Titration - Pomlow Control Donor2

value: Control


title: WT rep2


title: GSK-J4 rep2


title: RNASeq Pom Dose Titration - Pomhigh HRI Donor2

value: Pomalidomide 1 uM (high dose)


title: RNASeq Pom Dose Titration - Pomlow Control Donor1


title: RNASeq Pom Dose Titration - Pomhigh Control Donor2


title: RNASeq Pom Dose Titration - Pomhigh HRI Donor1


title: WT rep1


title: KTC1-SLC6A15 rep1

city: Guangzhou

first: Yu

middle: xin

last: Chen

address: 58 Zhongshan Road II

department: Department of Endocrinology and Diabetes Center

institute: The First Affiliated Hospital of Sun Yat-sen University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2).
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set.
The expression level of gene was calculated by RSEM  (v1.2.12).
Differential expression analysis was performed using the DESeq2(v1.4.5) with Q value £0.05
Genome_build: GCF_000001405.38_GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: thyroid cancer cells

growth_protocol: KTC1 cells were incubated in DMEM supplemented with 10% FBS.

extract_protocol:
Total RNA was extracted using Trizol.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented  into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was  generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA  synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end  repair. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library.

treatment_protocol: Cells were transfected with vector control or vector expressing SLC6A15. Stable cell lines were selected by treatment with 200μg/ml G418 for 14 days.

value: papillary thyroid cancer cells

tag: genotype/variation

value: SLC6A15 overexpression


title: KTC1-SLC6A15 rep2


title: KTC1-Vector rep2

value: vector control


title: KTC1-Vector rep1


title: GlobeFB-3

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
After sequencing, the reads were demultiplexted using bcl2fastq.
The fastq reads were aligned to the virus genome using bwa mem command.
bigWig files were generated using the bamCoverage command.
Genome_build: Lenti/βAS3-FB is an 8.9-kb LV carrying a complex anti-sickling β-globin gene cassette, as previously described by Romero et al. The β-globin gene is driven by FASTA files on series record. the endogenous β-globin promoter and enhancers in the anti-sense (reverse) orientation, with the expression regulated by a “mini” locus control region (LCR) comprised of portions of the β-globin locus DNAse hypersensitive sites (HS) HS2, HS3 and HS4. In addition, Lenti/βAS3-FB contains the Woodchuck Hepatitis Virus post-transcriptional regulatory element (wPRE) and a 77-bp insulator in the U3 region of the 3’ LTR, termed as FB (FII-BEAD). GlobeFB is a 6.5-kb LV carrying an anti-sickling β-globin gene cassette. The expression is regulated by a shortened LCR comprised of HS2 and HS3 and a shortened 3'UTR of the β-globin locus. EFS-ADA is a 4-kb LV for treating adenosine deaminase severe combined immunodeficiency (ADA-SCID) that is capable of high-level and consistent ADA gene transfer and expression.  The EFS-ADA vector consists of the human elongation factor-α gene “short” promoter (EFS) driving the expression of a codon-optimized human ADA gene cassette followed by the wPRE, all in the sense (forward) orientation. All vectors consist of a pCCL backbone and differ only by the internal promoters and transgene cassettes.
Supplementary_files_format_and_content: bigWig file

organism: synthetic construct

source_name: GlobeFB is an 6.5-kb LV carrying a complex anti-sickling β-globin gene cassette

growth_protocol: 293T cells were cultured in Dulbecco's modified Eagle's mediun, 10% Fetal Bovine Serum, and 1% Penicillin, Streptomycin, and Glutamine

extract_protocol:
Total RNA was extracted from raw viral supernatant using the QIAmp Viral RNA Mini Kit (Qiagen). Viral RNA was treated with TurboDNAse (Invitrogen) and sent to the UCLA Technology Center for Genomics and Bioinformatics Core for downstream library preparation.
cDNA library was prepared using the KAPA RNA HyperPrep Kit with RiboErase (Roche Sequencing, Pleasanton, CA) following the manufacturer’s manual without rRNA depletion to avoid bias. Briefly, RNA was fragmented into ~400 bp fragments; 1st strand cDNA was synthesized with random priming followed by 2nd strand synthesis.

treatment_protocol: LVs were packaged by transient transfection of 293T cells with fixed amounts of HIV Gag/Pol, Rev and VSV-G expression plasmids and equimolar amounts of each of the different vector transfer plasmids using TransIT-293 (Mirus Bio, Madison, WI) as described in the supplemental method and Cooper et al. Virus was collected 3 days post transfection.

tag: lentiviral vector

value: GlobeFB

tag: vector length


title: J4-H3K27me3

data_processing:
Raw reads were aligned to hg19 using bowtie2. The sam files were converted to bam with samtools. MACS2 was used to call peaks on the bam files with signals from input DNA as reference.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
Cells were cross-linked in 1% formaldehyde for 10 min at room temperature (RT) with gentle swirling, and crosslinking was stopped by adding glycine to a final concentration of 0.125 M and incubating at RT for 5 min. Cells were harvested and an aliquot of 1 × 107 cells were used per ChIP reaction. Each cell aliquot was resuspended in 0.5 mL of RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS in PBS, pH 7.4), and chromatin was fragmented on ice to 200 to 500 bp in size with 5 pulses of 30 sec at 50% power with a Sonics VibraCell sonicator. 2 μg primary antibodies as listed in Supplementary Table S4 or control IgG were pre-conjugated with Protein G magnetic beads (Pierce) at 4°C overnight. 1% of sheared chromatin was saved as input, and the rest was incubated with pre-conjugated antibody on a rotator at 4°C overnight. The beads were washed 5 times with LiCl wash buffer (0.1 M Tris, 0.5 M LiCl, 1% NP-40, 1% sodium deoxycholate, pH 7.5) followed by a single wash with TE buffer (10 mM Tris-HCl, 0.1 mM Na2EDTA, pH 7.5). The beads were then resuspended in 200 μL IP elution buffer (1% SDS, 0.1 M NaHCO3) and incubated at 65°C for 1 hour in a heat block with vortexing. The supernant was collected and together with input was incubated at 65°C for 16 hours to reverse cross-links. DNA was purified with QIAquick PCR Purification Kit (Qiagen) and eluted in 50 μL EB.
ChIP’s DNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated fragments. Fragments were amplified by PCR and PCR products were purified and selected with the Agencourt AMPure XP-Medium kit. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library. Library was qualified by Qubit ssDNA kit.

tag: chip antibody


title: GlobeFB-1


title: DMSO-H3K27me3


title: GlobeFB-2


title: EFSADA-3

source_name: EFS-ADA is a 4.2-kb LV for treating adenosine deaminase severe combined immunodeficiency

value: EFS-ADA


title: DMSO-H3K27ac


title: RNASeq Pom Dose Titration - DMSO HRI Donor2

value: DMSO


title: RNASeq Pom Dose Titration - Pomhigh Control Donor1


title: RNASeq Pom Dose Titration - DMSO Control Donor2


title: RNASeq Pom Dose Titration - DMSO HRI Donor1


title: RNASeq Pom Dose Titration - DMSO Control Donor1


title: J4-H3K27ac


title: RNASeq - UNC0638 HRI Rep2

value: RNASeq


title: HFD3

city: Ann Arbor

first: Jun Hee

last: Lee

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

description: Sample_124712/124712_TCCTGAGC_S4_L004_R1_001

data_processing:
Sequencing by Illumina HiSeq-4000 High-Output system.
Raw reads were processed following Drop-seq Laboratory Protocol v3 using DropSeqTools (v1.13) and aligned to mm10 mouse genome using STAR (v.2.6.0a).
The aligned reads were further processed using popscle dsc-pileup to produce the digital expression matrix.
Through a series of multi-dimensional clustering and subtraction of irrelevant droplets with soup-like profiles (clusters overlapping with random shuffled droplets), higher mitochondrial contents (cutoff: 30%) and lower UMI counts (cutoff: 1000), we isolated a total of 454 droplets that represent 216 cells from two LFD liver samples and 238 cells from three HFD liver samples.
For HFD.LFD.magic.txt, we performed the imputation of the data using magic R package with the default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts of the transcript for each barcode

source_name: Mouse hepatocytes

growth_protocol: 8-week-old C57BL/6J male littermate mice were separated into two groups and were fed on a regular chow diet or high fat diet

extract_protocol:
single cell RNA libraries were prepared by Drop-seq method for sequencing using Hiseq4000 Illumina protocols
single cell RNA-Seq

treatment_protocol: Either a regular diet (LFD) or high fat diet (HFD) were provided for 12 weeks

value: Hepatocytes

tag: condition

value: HFD


title: EFSADA-2


title: HFD2

tag: cell type


title: SEM_resistant_SAHA

city: Charlestown

first: Maolin

last: Ge

state: Massachusetts

address: 149 13th Street

department: MGH Cancer Center

institute: Harvard Medical School

data_processing:
Basecalls performed using BGISEQ-500.
SOAPnuke was used to get the "clean reads".
Mapping clean reads to hg19 whole genome using HISAT2.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample.

source_name: pro-B MLL leukemia cell line SEM

growth_protocol: Cells were cultured in Gibco RPMI 1640 containing 10% FBS at 37°C with 5% CO2 and were maintained between a density of 5 × 10^5 cells/ml and 2 × 10^6 cells/ml.

extract_protocol:
Tissue blocks were lysed in TRIzol reagent (Sigma-Aldrich). The lysate was well mixed with chloroform and spun for 15 min at 13000 g at 4 °C. RNA in top aqueous phase was collected and mixed with propan-2-ol to precipitate total RNA.
RNA libraries were prepared for sequencing using MGIEasymRNA Library Prep Kit V2.

treatment_protocol: Induced drug-resistant cells were generated by treating parental MLL leukemia cell lines SEM and RS4;11 with gradually increasing concentration of bortezomib for at least 4 weeks. Bortezomib treatment was started with a concentration of 1 nM and the concentration of bortezomib was increased by 1 nM every 3 days. The remaining cells after the treatment were considered as bortezomib-resistant cells and were collected for analysis. SEM resistant cells were treated with DMSO, LBH589 (5 nM), or SAHA (2 uM) for 20 hours. RS4;11 resistant cells were treated with DMSO, LBH589 (50 nM), or SAHA (2 uM) for 20 hours.

tag: tissue

value: pro-B mix linage leukemia (MLL) cell line

tag: cell line

value: bortezomib-derived pro-B MLL leukemia cell line SEM

tag: drug treatment

value: SAHA


title: HFD1


title: EFSADA-1


title: RNASeq - UNC0638 HRI Rep1

value: Three-phase in vitro culture of CD34+ primay human cells

value: Day 13 of culture


title: RNASeq - UNC0638 Control Rep2


title: SEM_resistant_LBH589


title: LFD2

value: LFD


title: LFD1


title: SEM_parental

value: parental SEM


title: RNASeq - Pom HRI Rep2

value: HRI

value: Pomalidomide