title: Time after treatment 20.5 h, rep1

data_processing:
Raw reads were checked quality and trimmed using FastQC (Andrews, 2010)
the trimmed reads were mapped to the Arabidopsis thaliana genome (TAIR10) using STAR (Dobin et al., 2013)
 After alignment, the gene-level raw count data files were generated using HTSeq (Anders et al., 2015)
Genome_build: Arabidopsis thaliana genome (TAIR10)
Supplementary_files_format_and_content: HTSeq count file (TXT)

source_name: Excised leaf

extract_protocol:
Total mRNA was extracted from leaves using WelPrep.
Library construction and sequencing were performed using Illumina Hiseq 2500 platform.

value: Excised leaf

value: 21-day-old plant

value: dark and cold


title: LCL161 (single cell)

status: Public on Apr 30 2021

type: SRA

city: Boston

first: Stephanie

last: Dougan

state: MA

address: 1 Jimmy Fund Way

department: Cancer Immunology & Virology

country: USA

institute: Dana-Farber Cancer Institute

description: CD45+ cells from pancreatic tumors treated with LCL161

library_source: transcriptomic

data_processing:
FASTQs were aligned against the mm10 genome and gene-level counts were generated using the 10x CellRanger (v3.0.0) pipeline.
Cells were called from barcodes using the R package "Seurat" (v3.1.4)
Count normalization, clustering, and differential expression analysis was done in Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: Hierarchical Data Format (HDF5) containing raw gene-level counts for all sequenced barcodes

molecule: total RNA

organism: Mus musculus

source_name: Orthotopic 6694c2 pancreatic tumor

extract_protocol:
Pancreatic tumors were excised, minced, digested in RPMI containing collagenase and anti-trypsin, filtered through a 40 um cell strainer, washed with PBS, and sorted by FACS for CD45+ cells.
RNA libraries were prepared using the Chromium Single Cell 5’ Kit (10x Genomics PN-1000006).

tag: tissue

value: Orthotopic 6694c2 pancreatic tumor

tag: treatment


title: Vehicle (single cell)

description: CD45+ cells from pancreatic tumors treated with Vehicle

value: Vehicle


title: LNCaP_siControl_Veh

status: Public on May 01 2021

type: RNA

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

description:
Control_veh_LN
Gene expression data from LNCaP cells treated with vehicle (ethanol) after transfected with siControl

hyb_protocol: The samples were hybridized to Human Clariom S-arrays or D-arrays according to standardized protocols from Affymetrix.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
The microarray data were preprocessed with Affymetrix Expression Console software using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.
affymetrix-algorithm-name = gc-correction,scale-intensities,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0

label: biotin

organism: Homo sapiens

source_name: prostate cancer

label_protocol: Total RNA was labeled employing the Affymetrix GeneChip Whole Transcript (WT) Terminal Labeling kit according to the manufacturer’s instructions

growth_protocol: DU145, LNCaP, DU145-CR, PC3-CR, and 22Rv1 cells were cultured in RPMI 1640 containing 10% FBS.  Before hormone treatment, cells were incubated in Phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days.

extract_protocol: Total RNAs were extracted using ISOGEN (Nippon gene) according to the manufacturer's instructions.

treatment_protocol: LNCaP and 22Rv1 cells were transfected with each siRNA 48 h before hormone treatment. Cells were treated with vehicle or dihydrotestosterone (DHT) (10 nM) for 24 h. DU145, DU145-CR, and PC3-CR cells were treated with siRNA for 72 h before RNA extraction. DU145 and DU145-CR cells were treated with vehicle or riba 10 μM for 48 h.

tag: cell line

value: LNCaP

tag: cell type

value: AR-negative Castration-resistant prostate cancer (CRPC) cell line

tag: sirna

value: siControl

tag: ligand/treatment


title: HEK293_pEWSFLI1_rep3

city: Tucson

first: Jacob

middle: C.

last: Schwartz

state: AZ

address: 1501 N Campbell Ave, LSN649

department: Pharmacology

institute: University of Arizona

data_processing:
alignments made to GRCh38 reference genome downloaded from UCSC genome browser
data was aligned and reads per gene quantified by STAR 2.7.8a
Reads per gene quantified by STAR 2.7.8a
Genome_build: GRCh38
Supplementary_files_format_and_content: Reads per gene quantified by STAR 2.7.8a

molecule: polyA RNA

extract_protocol:
HEK293T/17 cells were transfected as described above. Cells were collected 72 hours post-transfection and total RNA was extracted using TRIzol reagent (ThermoFisher, cat. no. 15596026).
Stranded RNA-seq libraries were prepared by Novogene Co., Ltd following mRNA enrichment by oligo(dT) beads using the company in-house procedure.

treatment_protocol: HEK293T/17 cells were reverse transfected with siRNA or plasmid at 4.0 × 10^5 in 6-well dishes 24 hours before to transfection using the TransIT-X2 reagent (Mirus Bio cat. no. MIR6000). A final concentration of 50 nM of siRNA and 2 ug of plasmid was transfected and cells were harvested 72 hours post-transfection. Knockdown of EWSR1 or expression of V5-EWS-FLI1 was confirmed by western blot analysis.

tag: cell origin

value: human kidney (fetal)

value: 72 hours post-siRNA transfection

value: plasmid expression of V5-EWS-FLI1


title: LNCaP_siControl_DHT

description:
Control_DHT_LN
Gene expression data from LNCaP cells treated with DHT 10 nM after transfected with siControl

value: DHT 10 nM


title: HEK293_siEWSR1treated_rep2

value: siRNA "siEWSR1", 5' CUACUAGAUGCAGAGACCCUU 3'


title: HEK293_pEWSFLI1_rep2


title: HEK293_pEWSFLI1_rep1


title: HEK293_siEWSR1treated_rep3


title: HEK293_SCRtreated_rep2

value: siRNA "SCR", 5' GAUGCAGACAUUCAGGAUGUU 3'


title: CKO_1

city: Nanjing

first: You-Qiang

last: Su

state: Jiangsu

address: 140 Hanzhong Road

department: State Key Laboratory of Reproductive Medicine

country: China

institute: Nanjing Medical University

data_processing:
All RNA-seq reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads then were aligned to the mm10 reference genome using tophat2 (v2.0.8b)
Reads aligned to genes are counted by cufflinks (v2.1.1). The FPKMs are normalized usingcuffnorm. Differentially expressed genes are calculated using cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Oocyte

extract_protocol:
Reverse transcription was carried out directly on the whole oocyte lysate using the SMARTer Ultra Low Input RNA for Illumina Sequencing - HV kits (Takara Bio Inc., Kusatsu, Japan) according to the manufacturer’s instructions. The resulting first strand cDNA was purified and then amplified for 17 cycles by PCR. After amplification, the cDNA was purified and subjected to library construction for deep sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 22-day old mice were primed with PMSG at the dose of 5 IU/mouse, and 48 hours later, they were injected with hCG at the dose of 5 IU/mouse. The mice were euthanized 14 hour later and the ovulated oocytes were collected from the oviduct. 3 sets of samples were collected for each genotype with each sample containing 5 ovulated oocytes in less than 3 μl of lysis buffer.

tag: strain

tag: cell

value: Oocyte

tag: age

value: post natal day 24

tag: genotype/variation

value: CKO


title: HEK293_SCRtreated_rep1


title: fxr +/+ zebrafish intestinal epithelial cells

city: Durham

first: Gilberto

last: Padilla Mercado

state: NC

address: 213 Research Drive 327 CARL Building

department: Molecular Genetics & Microbiology

institute: Duke University

data_processing:
UMIs were demultiplexed and reads were aligned to the reference genome, danRer11, following the CellRanger pipeline
In Seurat 3.1.0 (https://satijalab.org/seurat/) cell barcodes with <3000 detected genes, >30,000 UMIs, >25%  mitochondrial transcripts were removed.
Log-normalized and integrated datasets based on WT library
Scaled data and performed PCA with 100 priciple components
Ran UMAP dimensionality reduction with 54 principle components
Used FindNeighbors and FindClusters function at resolution of 0.82
Ran UMAP dimensionality reduction with 54 principle components
Genome_build: danRer11
Supplementary_files_format_and_content: count matrix

organism: Danio rerio

source_name: Intestine

growth_protocol: Approximately 600-700 6 dpf TgBAC(cldn15la-GFP) zebrafish larvae of the fxr+/+ and the fxr-/- genotypes were collected for the FACS experiment, respectively.

extract_protocol:
Larvae zebrafish were dissociated using standard protocol, after which the fxr+/+; TgBAC(cldn15la-GFP) and fxr-/-; TgBAC(cldn15la-GFP) cells were subjected to FACS at the Duke Cancer Institute Flow Cytometry Shared Resource and were sorted side by side with two identical Beckman Coulter Astrios instruments. Non-transgenic and single transgenic controls (pools of 50 fish/genotype) were prepared as above and used for gating and compensation. Approximately 120 k GFP positive 7-AAD negative cells per genotype were collected in 1.5 mL of DMEM/F12 supplemented with 10% heat-inactivated FBS and 10 μM Y-27632 ROCK1 inhibitor and were immediately subjected to the library construction.
Each single-cell RNA sequencing library was generated from 10,000 FACS sorted TgBAC(cldn15la-GFP) IECs of the indicated genotype following the 10x Genomics Single Cell 3’ protocol by the Duke Molecular Genomics Core.
The sequencing ready libraries were cleaned with both Silane Dynabeads and SPRI beads, and quality controlled for size distribution and yield with the Agilent D5000 screenTape assays using the Agilent 4200 TapeStation system. Illumina P5 and P7 sequences, a sample index, and TruSeq read 2 primer sequence were ligated for Illumina bridge amplification. Sequence was generated using paired-end sequencing on the Novaseq SP flow cell sequencing platform at a minimum of 40 k reads/cell.

tag: transgenic background

value: 6 dpf

tag: genotype

value: fxr +/+

value: Intestine

value: intestinal epithelial cells

tag: sorting fluorescence

value: GFP+ 7AAD-


title: mouse - Epwhg2_3

city: Kaifeng

first: Haigang

last: wu

state: Henan province

address: dongjing Road

department: School of Life Sciences

institute: Henan University

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimed for adaptor sequence, and masked for low-complexity or low quality sequence, then mapped to the mm8 hole genome using bowtie v0.12.2 with parameters set as defaults.
Reads for kilobased of exon per megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: mm8
Supplementary_files_format_and_content: fpkm

source_name: BALB/c mouse brain tissue

growth_protocol: The mouse was cultured in the SPF level environment

extract_protocol:
Brain tissue samples were lyzed and harvested using Trizol reagent. THe purification of RNA was performed using protocol provided by extracting kits (Total RNA Extraction Kit, Cat. R1200, Solarbio life science, China).
RNA library were prepared for sequencnig using standard illumina protocols

treatment_protocol: The mouse was received the 5-ALA injection (dosage 20 mg/kg) and further circulating in blood for 30 min. Then, the mouse received the 635 nm laser radiation (doage 10 J/cm2 and 20 J/cm, respectively) and continued to culture for 90 min. The brain tissues of mouse brain was obtained after downern injection and prefusion using 0.9% NaCl solution.

value: BALB/c mouse brain tissue

value: treated with PDT with 20 J/cm2


title: mouse - Epwhg1_3

value: treated with PDT with 10 J/cm2


title: mouse - Epwhg2_2


title: LNCaP_siOCT4_DHT

description:
siOCT4_DHT_LN
Gene expression data from LNCaP cells  treated with DHT 10 nM after trasfected with siOCT4

value: LNCaP

value: AR-negative Castration-resistant prostate cancer (CRPC) cell line


title: mouse - Epwhg1_1


title: mouse - Cwhg_3

value: untreated


title: mouse - Cwhg_2


title: fxr -/- zebrafish intestinal epithelial cells

value: fxr -/-


title: BRI-752 scRNA-seq

first: Tanya

last: Mayadas

address: 77 Avenue Louis Pasteur

department: Department of Pathology

institute: Brigham and Women's Hospital

data_processing:
BCLs processed into FASTQS with cellranger v3.1.0
FASTQS aligned to GRCh38 with cellranger v3.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: genes x cells UMI matrix for all samples

source_name: Spleen and in vitro culture of neutrophils

extract_protocol: Libraries were prepared using standard 10X Genomics V3 3' kit and protocol

tag: multiplexing

value: multiplexed cells from i) Ly6G+CD11c+MHCII+ 1, ii) Ly6G+CD11c+MHCII+ 2, iii) Ly6G+CD11c+MHCII+ 3, iv) Ly6G+CD11c-MHCII- 1, v) Ly6G+CD11c-MHCII- 2, vi) Ly6G+CD11c-MHCII- 3, vii) in vitro Day 0, viii) in vitro Day 1, ix) in vitro Day 2, x) in vitro Day 3, xi) WT untreated splenic, xii) humanized untreated splenic

value: i-vi) injected with 30 ug of 3G8-conjugate at day -3, vii) untreated, viii-x) treated with FcgRIIIB (3G8)-FITC-Ova, xi-xii) untreated


title: diploid-3

city: Shanghai

first: Jian

last: Bing

address: Songhu Road, Yangpu District

institute: Fudan University

description:
83-2-3
C.glabrata_haploid_and_diploid.txt

data_processing:
Illumina OLB_1.9.4 were used for basecalling.
Filter dirty raw reads by removing reads with adaptors and low quality, the obtained clean reads were mapped to reference sequences using SOAPaligner/soap2 according to Li et al., Bioinformatics, 2009. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads) according to Mortazavi et al., Nature Methods, 2008, and the formula is shown as follows: RPKM=106C/(NL/103). C is the number of reads that uniquely aligned to a gene, N is total number of reads that uniquely aligned to all genes, and L is the number of bases on a gene.
Genome_build: Candida glabrata CBS138 (GCA_000002545.2).
Supplementary_files_format_and_content: C.glabrata_haploid_and_diploid.txt: Tab-delimited text file containing FPKM values for each Sample.

organism: Nakaseomyces glabratus

source_name: diploid

growth_protocol: C. glabrata cells were inoculated into YPD and cultured at 35 oC for 24h.

extract_protocol:
Cells were lysed by Mini-beadbeater and total RNA was harvested using GeneJET RNA Purification Kit (Thermo Scientific #K0731, #K0732).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: wild type

tag: chromosome set

value: diploid


title: haploid-3

description:
83-1-3
C.glabrata_haploid_and_diploid.txt

source_name: haploid

value: haploid


title: diploid-2

description:
83-2-2
C.glabrata_haploid_and_diploid.txt


title: BRI-754 scRNA-seq

value: multiplexed hashing from i) Ly6G+CD11c+MHCII+ 1, ii) Ly6G+CD11c+MHCII+ 2, iii) Ly6G+CD11c+MHCII+ 3, iv) Ly6G+CD11c-MHCII- 1, v) Ly6G+CD11c-MHCII- 2, vi) Ly6G+CD11c-MHCII- 3, vii) in vitro Day 0, viii) in vitro Day 1, ix) in vitro Day 2, x) in vitro Day 3, xi) WT untreated splenic, xii) humanized untreated splenic

value: Spleen and in vitro culture of neutrophils


title: diploid-1

description:
83-2-1
C.glabrata_haploid_and_diploid.txt


title: HEK293_siEWSR1treated_rep1

value: human kidney (fetal)

value: 72 hours post-siRNA transfection

value: siRNA "siEWSR1", 5' CUACUAGAUGCAGAGACCCUU 3'


title: HEK293_SCRtreated_rep3

value: siRNA "SCR", 5' GAUGCAGACAUUCAGGAUGUU 3'


title: haploid-2

description:
83-1-2
C.glabrata_haploid_and_diploid.txt


title: 231D_3

city: Pittsburgh

first: Shivendra

middle: V

last: Singh

state: PA

address: 5117 Centre Avenue UPMC HCC Research Pavilion Suite 2.32A

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh

data_processing:
STAR v2.6.1d was used to count the read numbers mapped of each gene. The fragments per kilobase per million mapped (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: Homo Sapiens(GRCh38/hg38)
Supplementary_files_format_and_content: FPKM represents summary of gene expression level analysis by FPKM; DEG represents differential gene expression analysis

source_name: breast cancer cells

growth_protocol: MCF-7 and MDA-MB-231 cells were plated in 10-cm dish at a density of 1×106 cells/dish and incubated overnight for attachment.

extract_protocol:
The cells were harvested by trypsin treatment and total RNA was extracted using the RNeasy mini kit (Qiagen, Germantown, MD).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with DMSO (final concentration- 0.07%) or 20 µM of DATS for 16 hours prior to RNA isolation and RNA-Seq analysis. Samples were prepared three times independently.

value: Cells were treated with 20 µM of DATS for 16 hours.


title: 231D_1


title: 231C_3

value: Cells were treated with vehicle (DMSO) for 16 hours.


title: mouse - Epwhg2_1

value: BALB/c mouse brain tissue

value: treated with PDT with 20 J/cm2


title: 231D_2


title: Huh7, shNC

city: Changsha

first: yuan

middle: yu

last: zi

address: Changsha Xiangya Road

institute: Xiangya hospital

data_processing:
using Illumina Novaseq platform
Index of the reference genome was built using Hisat2 v2.0.5
Genome_build: hg18
Supplementary_files_format_and_content: FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.

source_name: cell line

extract_protocol:
RNA was harvested using Trizol reagent. Sequencing was completed by Novogene.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver cancer

value: control


title: Huh7, shPANK1

value: PANK1 knockdown


title: mouse - Epwhg1_2

value: treated with PDT with 10 J/cm2


title: 231C_2


title: 7D_1


title: 7D_2


title: mouse - Cwhg_1

value: untreated


title: 7C_2


title: 7C_3


title: 7C_1


title: 7D_3


title: HT8-cas1-2

value: Colon cancer

value: PPDPF knockdown


title: HT8-1


title: HT8-cas1-1


title: HT8-2


title: haploid-1

description:
83-1-1
C.glabrata_haploid_and_diploid.txt

value: wild type

value: haploid


title: 231C_1


title: spinal cord neurospheres in dedifferentiation condition with  EGF and FGF2, mouse   1

status: Public on Apr 28 2021

city: MOntpellier

first: jean-philippe

last: hugnot

state: languedoc

address: IGF INSERM UM 141 rue de la cardonille

country: France

institute: inserm inm u1191

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on MoGene-2_1-st and HT_MG-430_PM mouse microarrays for cultures and microdissected ependymal region respectively

scan_protocol: The microarrays were scanned using the Affymetrix Gene Atlas scanner.

data_processing: The data files were generated with Affymetrix Expression Console v1.2.1 and gene expression data were normalized with RMA algorithm. Gene expression profiles were analyzed using the Affymetrix TAC 4.0 software

source_name: neurosphere culture derived from spinal cord, dedifferentiation condition

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

growth_protocol: neurospheres derived from the adult spinal cord and differentiated on P-D-Lysin/Laminin coated coverslip for 3 days without growth factors and  in the presence of fetal bovine serum 2%., then  treated for 3 days with EGF,  FGF2 and Heparin after fetal bovine serum removal

extract_protocol: total RNA extraction was performed with  ReliaPrep RNA cell Miniprep System (Promega)  according to the manufacturer's instructions.

value: neurosphere culture

tag: passage

value: passage 1


title: spinal cord neurospheres in dedifferentiation condition with  EGF and FGF2, mouse   2

tag: tissue


title: spinal cord neurospheres in differentiation condition without  EGF and FGF2, mouse  2

source_name: neurosphere culture derived from spinal cord, differentiation condition

growth_protocol: neurospheres derived from the adult spinal cord  and differentiated on P-D-Lysin/Laminin coated coverslip for 3 days without growth factors and  in the presence of fetal bovine serum 2%.


title: spinal cord neurospheres in growing condition with EGF and FGF2, mouse  4

source_name: neurosphere culture derived from spinal cord, growth condition

growth_protocol: neurospheres derived from adult spinal cord  and grow in the presence of EGF, FGF2 and heparin


title: spinal cord neurospheres in differentiation condition without  EGF and FGF2, mouse   4


title: spinal cord neurospheres in dedifferentiation condition with  EGF and FGF2, mouse   4


title: spinal cord neurospheres in differentiation condition without  EGF and FGF2, mouse   3


title: spinal cord neurospheres in growing condition with EGF and FGF2, mouse  1


title: spinal cord ependymal region, 3 days post injury mouse  4

source_name: micro-dissected ependymal region, 3 days after injury

growth_protocol: injuried spinal cord with needle insertion. Ependymal region was microdissected with a laser 3 days after injury

value: micro-dissected ependymal region

value: adult mice, 3 months


title: spinal cord neurospheres in growing condition with EGF and FGF2, mouse  3


title: spinal cord ependymal region, 3 days post injury mouse  3


title: spinal cord ependymal region, control, mouse  6

source_name: micro-dissected ependymal region, non injured

growth_protocol: non injuried but sham operated spinal cord. Ependymal region was microdissected with a laser


title: spinal cord ependymal region, 3 days post injury mouse  1


title: spinal cord ependymal region, control, mouse  3


title: spinal cord ependymal region, control, mouse  1


title: spinal cord ependymal region, control, mouse  4


title: spinal cord neurospheres in dedifferentiation condition with  EGF and FGF2, mouse   3


title: STBD1 WT 1

city: Chengdu

first: Han

last: Zhu

state: China, Sichuan

address: No.17 People's South Road

institute: Sichuan University

data_processing:
Clean data are obtained by removing reads containing adapter, poly-N and low-quality reads from raw data.
Clean reads are aligned to the reference genome (Hg38) using STAR 2.7.1a. The reads counts mapped to each gene are counted using R package GenomicAlignments v1.18.1.
Gene expression abundance are calculated by RSEM v1.3.1, and transcripts per kilobase of exon model per million mapped reads (TPM) of each gene is calculated based on the length of the gene and reads count, and used to represent gene expression abundance.
Genome_build: Hg38
Supplementary_files_format_and_content: abundance measurements

source_name: HCT116_STBD1 WT

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Gibco), supplemented with 10% fetal bovine serum (FBS, Excellbio) and penicillin-streptomycin (Hyclone) at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted according to the manufacture’s protocol. RNA was then analyzed for purity by measuring the ratio of absorbance at 260 nm and 280 nm using the NanoPhotometer Spectrometer (IMPLEN CA, USA).
cDNA libraries were synthesized using NEBNext UltraTM RNA library Prep Kit for Illumina (NEB, USA) according to the manufacture’s protocol. The size of the library insert fragments was measured by Agilent 2100 bioanalyzer. The suitable library fragments were sequenced on an Illumina platform using 125 bp/150 bp paired-end technology.

tag: tissue source

value: colon

value: STBD1 WT


title: plvx neo 3

source_name: HCT116_plvx neo

tag: cell line

value: plvx neo


title: STBD1 WT 2


title: STBD1 W203C 3

source_name: HCT116_STBD1 W203C

value: STBD1 W203C


title: STBD1 W203C 1


title: STBD1 WT 3


title: STBD1 W203C 2


title: spinal cord neurospheres in growing condition with EGF and FGF2, mouse  2


title: spinal cord ependymal region, control, mouse  2


title: spinal cord ependymal region, 3 days post injury mouse  6


title: spinal cord ependymal region, 3 days post injury mouse  2


title: spinal cord ependymal region, control, mouse  5


title: spinal cord ependymal region, 3 days post injury mouse  5


title: plvx neo 1


title: plvx neo 2


title: shSTBD1 3


title: NeuroD_rep2_overexpression

city: Princeton

first: Chen

last: Cao

state: New Jersey

address: Icahn lab

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

data_processing:
Raw sequencing reads were filtered by Illumina NovaSeq Control Software and only pass-filtered reads were used for further analysis.
Reads that aligned to phix (using Bowtie version 1.1.1) were removed, as were reads that failed Illumina’s default chastity filter.
We then combined the FASTQ files from each lane and separated the samples using the barcode sequences allowing one mismatch (using barcode_splitter version 0.18.2).
In the read 2 of each sample, the rightmost bases after to position 100 were trimmed to keep only high-quality reads.
Using 10x CellRanger version 3.0.2, the count pipeline was run with default settings on the trimmed FASTQ files to generate gene–barcode matrices for each sample. The integration of scRNA-Seq data of NeuroD overexpressed embryos and the control embryos were performed with Seurat v3.0
Genome_build: KH gene models (ver.2013, http://ghost.zool.kyoto-u.ac.jp/download_kh.html)
Supplementary_files_format_and_content: gene–barcode matrices; Hierarchical Data Format

organism: Ciona intestinalis

growth_protocol: Adult Ciona intestinalis (Pacific species also named Ciona robusta) collected in the Pacific Ocean were purchased from M-Rep San Diego, CA and MarinUS, Long Beach, CA. The gametes were collected as previously described in Christiaen et al, 2009.

extract_protocol:
At the late tailbud stage I, morphologically normal embryos were selected, and at late tailbud II, GFP+ embryos were dissociated as previously described in Cao et al, 2019. The dissociation was performed in duplicate. The cell concentration of each sample was checked by TC20 Automated Cell Counter to ensure it was within 1,000–2,000 cells per microlitre. Single-cell suspensions were loaded onto The Chromium Controller (10x Genomics). For all of the samples, cells were lysed, cDNAs were barcoded and amplified with Chromium Single Cell 3′ Library and Gel Bead Kit v3 (10x Genomics) following the instructions of the manufacturer.
Illumina sequencing libraries were prepared from the cDNA samples using the Nextera DNA library prep kit (Illumina). All of the libraries were sequenced on Illumina NovaSeq 6000 with S1 reagent kit (300 cycles, paired-end) following standard Illumina protocols.

treatment_protocol: After fertilization using gametes from the same individual, one-cell stage embryos were electroporated with Dmrt1>H2B:GFP and Dmrt1>LacZ (control condition) or Dmrt1>H2B:GFP and Dmrt1>NeuroD (NeuroD overexpression condition).

tag: developmental stage

value: late tailbud II

tag: treatment

value: electroporated with Dmrt1>H2B:GFP and Dmrt1>NeuroD

tag: tissue/cell type

value: whole embryos


title: shControl 2

value: shControl


title: shControl 1


title: shControl 3


title: shSTBD1 2


title: shSTBD1 1


title: NeuroD_rep1_lacz

value: electroporated with Dmrt1>H2B:GFP and Dmrt1>Lacz


title: SN2_30_D9

status: Public on Apr 27 2021

city: Seoul

first: Sung Noh

last: Hong

address: 81 Irwon-Ro, Gangnam-gu

department: Gastroenterolgy

country: South Korea

institute: Samsung Medical Center

data_processing:
For cluster generation, the library is loaded into a flow cell where fragments are captured on a lawn of surface-bound oligos complementary to the library adapters. Each fragment is then amplified into distinct, clonal clusters through bridge amplification. When cluster generation is complete, the templates are ready for sequencing.
Illumina SBS technology utilizes a proprietary reversible terminator-based method that detects single bases as they are incorporated into DNA template strands. As all 4 reversible, terminator-bound dNTPs are persent during each sequencing cycle, natural competition minimizes incorporation bias and greatly reduces raw error rates compared to other technologies. The result is highly accurate base-by-base sequencing that virtually eliminates sequence-context-specific errors, even within repetitive sequence regions and homopolymers.
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file include raw read counts for samples

source_name: intestinal organoid

growth_protocol: The epithelium was isolated by endoscopic biopsy samples with 10 mM ethylenediaminetetraacetic acid (EDTA) and 1 mM dithiothreitol (DTT) in PBS for 30 min at 4 °C on a rocker at 50 rpm. The supernatant containing villi and debris was decanted and discarded. To release the large amounts of intestinal crypts, the mucosal surface of biopsy samples were gently scraped using glass coverslips under a dissecting microscope. The detached crypts were suspended in PBS and were broken down using pipetting with bended pipette tip. The fraction was centrifuged at 200× g for 2 min at 4 °C, and the pellet was suspended in basic medium. Isolated crypts were pelleted with three quick spins, resuspended in Matrigel, and plated in 48-well culture plates. After incubating at 37 °C for 15 min, 250 μl maintenance media (50% Wnt3a conditioned medium + 50% 2× basic medium supplemented with 50 ng/ml recombinant human epidermal growth factor (EGF), 100 ng/ml recombinant human noggin, 500 ng/ml recombinant human R-spondin 1, 10 mM nicotinamide, 10 μM p160ROCK inhibitor (Y27632), 10 μM p38 MAP kinase inhibitor (SB202190), and 10 nM PGE2) was added. GSK3 inhibitor (CHIR99021; 2.5 μM) was included in the medium for the first 2 days. The medium was changed every 2 days and organoids were passaged 1:2 at day 7 after crypt plating. For passaging, the organoids and Matrigel were mechanically disrupted using a P1000 pipette and further mechanical dissociation was achieved using a P200 pipette. The dissociated organoids were washed with 10 ml basal culture medium and centrifuged at 200× g for 30 s at 4 °C. The supernatant was discarded, the pellet was resuspended in 2 ml of cell dissociation enzyme, and then incubated for 5 min at 37 °C in a water bath. The solution was gently mixed using a P200 pipette and centrifuged at 500× g for 5 min at 4 °C. The supernatant was discarded and the cell pellet was resuspended in Matrigel using pre-chilled pipet tips. The crypt suspension (50 μl) was plated in Matrigel in each well of the pre-warmed 48-well culture plate. The plate was incubated at 37 °C in a 5% CO2 atmosphere for 20 min to allow complete polymerization of Matrigel prior to the addition of 250 μl maintenance media. The entire medium was changed every 2 days and organoids were passaged 1:2 every week. After 4–6 passages, most organoids in the maintenance medium were uniform spheroids and able to passage stably for a long time. To recapitulate the organ physiological parameters, spheroids were cultured in differentiation medium, which was the maintenance medium without Wnt3A conditional medium, SB202190, nicotinamide, and PGE2. The entire medium was changed every 2 days and enteroids were cultured for 8 days after passage. And then, total RNA was extracted from intestinal organoids using the RNeasy Mini Kit according to the manufacturer’s instructions.

extract_protocol:
For library construction, RNA is extracted from a sample. After performing quality control (QC), qualified samples
The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified.

treatment_protocol: Organoids were cultured in the maintenance medium for 2 days to obtain a stable number of organoids before inducing organoid differentiation. On day 2, the maintenance medium for organoids was replaced with the TNFɑ(30 ng/ml)-containing enteroid medium. Control and Crohn’s organoids—cultured for the long-term (passage ≥ 6)—were treated with 30 ng/ml TNFɑ every 24 hours until harvest.

value: small intestine (ileum)

tag: disease

value: Crohn's disease

tag: status

value: add 30 ng/ml of TNFɑ into the organic culture medium.


title: SN2_0_D9

value: conventional organoid culture condition


title: SN2_30_D6


title: spinal cord neurospheres in differentiation condition without  EGF and FGF2, mouse  1

value: neurosphere culture


title: SN2_0_D6


title: SN2

source_name: endoscopic biopsy

value: endoscoic biopsy of small intestine


title: S95_30_D9

value: control


title: NeuroD_rep2_lacz


title: S93_30_D3

value: small intestine (jejunum)


title: S95_0_D6


title: S95_0_D9


title: S95


title: S93_0_D9


title: S95_30_D6


title: S93_30_D6


title: S93_30_D9


title: S93_0_D6


title: S93_0_D3


title: S93


title: S170_30_D6


title: NeuroD_rep1_overexpression


title: S170_30_D9


title: S170_30_D3


title: S170_0_D6


title: S170_0_D9


title: S170


title: plasma-pregnancy-ZT20084

city: Los Angeles

first: Helen

middle: Bermudez

last: Foley

email: hfoley@usc.edu, helenbfoley@gmail.com

state: CA

address: 1441 Eastlake

department: Preventive Medicine

institute: University of Southern California

hyb_protocol: Hybridization was perfomed according to the manufacturer's directions. In the following step, instead of 1:10 dilution, 1:2 dilution was performed using 5uL hybridized sample and 5uL.

scan_protocol: Scans were completed with Nanostring Ncounter.

data_processing: Nanostring count data from RCC files were normalized with R Package NanoStringNorm. miRNA expressed above sample-specific backgrounds in 50% of samples in early or late pregnancy were retained.

source_name: Maternal plasma

label_protocol: Nanostring miRNA master kits were used per manufacturer's instructions, except for the dilution step after hybridization. Instead of 1:10 dilution, 1:2 dilution was performed using 5uL hybridized sample and 5uL DEPC water.

growth_protocol: Maternal blood was collected in lavender-top EDTA tubes early and late during pregnancy. Tubes were transported on ice to the laboratory.

extract_protocol: 500uL of plasma was extracted with the Qiagen ExoRNeasy kit according to the instructions. A second phase-separation step used an additional 90uL chloroform and combined with the supernatant from the first phase-separation.

treatment_protocol: Within one hour of collection, plasma was isolated by centrifugation at 1300g for 15 minutes.

tag: weeks gestation

tag: race/ethnicity

value: Maternal plasma

tag: geographical location

value: Los Angeles


title: plasma-pregnancy-ZU71364


title: plasma-pregnancy-ZW54665


title: plasma-pregnancy-ZS32145


title: plasma-pregnancy-ZV98191


title: plasma-pregnancy-ZV77850


title: plasma-pregnancy-ZP44664


title: plasma-pregnancy-ZM93894


title: plasma-pregnancy-ZM33249


title: S170_0_D3


title: plasma-pregnancy-ZJ62807


title: plasma-pregnancy-ZL70475


title: plasma-pregnancy-YX27822


title: plasma-pregnancy-ZJ14692


title: plasma-pregnancy-ZD17061


title: plasma-pregnancy-YX96839


title: plasma-pregnancy-YV19480


title: plasma-pregnancy-ZA73515


title: plasma-pregnancy-YX38363


title: plasma-pregnancy-ZB06262


title: plasma-pregnancy-YV68569


title: plasma-pregnancy-YW73369


title: plasma-pregnancy-YV08162


title: plasma-pregnancy-YU07228


title: plasma-pregnancy-YT37005


title: plasma-pregnancy-YT80031


title: plasma-pregnancy-YO40880


title: plasma-pregnancy-YO00560


title: plasma-pregnancy-YO62453


title: plasma-pregnancy-YL16572


title: plasma-pregnancy-YN28823


title: plasma-pregnancy-YN85561


title: plasma-pregnancy-YN85148


title: plasma-pregnancy-YH64545


title: plasma-pregnancy-YG54167


title: plasma-pregnancy-YO63997


title: plasma-pregnancy-YG40227


title: plasma-pregnancy-YD05615


title: plasma-pregnancy-YC73335


title: plasma-pregnancy-YC94785


title: plasma-pregnancy-XW70906


title: plasma-pregnancy-YA48843


title: plasma-pregnancy-YA28799


title: plasma-pregnancy-XQ24349


title: plasma-pregnancy-XV88651


title: plasma-pregnancy-YA55079


title: plasma-pregnancy-XQ53476


title: plasma-pregnancy-XP46888


title: plasma-pregnancy-XM14268


title: plasma-pregnancy-XK12348


title: plasma-pregnancy-XQ01383


title: plasma-pregnancy-XV89233


title: plasma-pregnancy-XV10990


title: plasma-pregnancy-XH72602


title: plasma-pregnancy-YJ62548


title: plasma-pregnancy-XH13255


title: plasma-pregnancy-XH45499


title: plasma-pregnancy-YL57694


title: plasma-pregnancy-XI52232


title: plasma-pregnancy-XD31208


title: plasma-pregnancy-XD07922


title: plasma-pregnancy-XD08400


title: plasma-pregnancy-WT16402


title: plasma-pregnancy-XC30155


title: plasma-pregnancy-WT00208


title: plasma-pregnancy-WR34884


title: plasma-pregnancy-WQ05510


title: plasma-pregnancy-WK75521


title: plasma-pregnancy-WL58233


title: plasma-pregnancy-WG78460


title: plasma-pregnancy-WE87293


title: plasma-pregnancy-WC65729


title: plasma-pregnancy-VZ52428


title: plasma-pregnancy-WD72164


title: plasma-pregnancy-WJ97585


title: plasma-pregnancy-WB48484


title: plasma-pregnancy-VW06610


title: plasma-pregnancy-WC64188


title: plasma-pregnancy-VW54223


title: plasma-pregnancy-VV76892


title: plasma-pregnancy-VW80858


title: plasma-pregnancy-VV71072


title: plasma-pregnancy-VX80217


title: plasma-pregnancy-VS08154


title: plasma-pregnancy-XA13401


title: plasma-pregnancy-VO00636


title: plasma-pregnancy-VT78415


title: plasma-pregnancy-VN94526


title: plasma-pregnancy-WM41737


title: plasma-pregnancy-VJ38442


title: plasma-pregnancy-VI31477


title: plasma-pregnancy-VJ41667


title: plasma-pregnancy-VC32028


title: plasma-pregnancy-WG12430


title: plasma-pregnancy-WK17355


title: plasma-pregnancy-VB86362


title: plasma-pregnancy-VI31036


title: plasma-pregnancy-VA54135


title: plasma-pregnancy-UY88188


title: plasma-pregnancy-UR54270


title: plasma-pregnancy-UV86108


title: plasma-pregnancy-UO02617


title: plasma-pregnancy-UT13365


title: plasma-pregnancy-UR51784


title: plasma-pregnancy-UO00704


title: plasma-pregnancy-UJ79269


title: plasma-pregnancy-UM79738


title: plasma-pregnancy-UP08036


title: plasma-pregnancy-UJ61366


title: plasma-pregnancy-UG50984


title: plasma-pregnancy-UE53236


title: plasma-pregnancy-UJ34771


title: plasma-pregnancy-UH22481


title: plasma-pregnancy-UL34271


title: plasma-pregnancy-UE27022


title: plasma-pregnancy-UB07180


title: plasma-pregnancy-UB51056


title: plasma-pregnancy-UD09251


title: plasma-pregnancy-TV04638


title: plasma-pregnancy-TX13155


title: plasma-pregnancy-UJ09392


title: plasma-pregnancy-TU84485


title: plasma-pregnancy-TU45045


title: plasma-pregnancy-TP75854


title: plasma-pregnancy-TS65576


title: plasma-pregnancy-TS67289


title: plasma-pregnancy-TM47805


title: plasma-pregnancy-TL24815


title: plasma-pregnancy-TL93651


title: plasma-pregnancy-TK73513


title: plasma-pregnancy-TM23424


title: plasma-pregnancy-TF65705


title: plasma-pregnancy-TF32944


title: plasma-pregnancy-TY07604


title: plasma-pregnancy-TD43914


title: plasma-pregnancy-TD77115


title: plasma-pregnancy-SS57526


title: plasma-pregnancy-SY19694


title: plasma-pregnancy-SY17276


title: plasma-pregnancy-SP25737


title: plasma-pregnancy-SQ38620


title: plasma-pregnancy-SR32251


title: plasma-pregnancy-ST18231


title: plasma-pregnancy-SO76804


title: plasma-pregnancy-SU17760


title: plasma-pregnancy-SW84358


title: plasma-pregnancy-SQ46121


title: plasma-pregnancy-SM00471


title: plasma-pregnancy-SM20319


title: plasma-pregnancy-SN55779


title: plasma-pregnancy-SR68533


title: plasma-pregnancy-SL17870


title: plasma-pregnancy-SG50430


title: plasma-pregnancy-SE05211


title: plasma-pregnancy-SE77858


title: plasma-pregnancy-SB76415


title: plasma-pregnancy-SD63273


title: plasma-pregnancy-SA67418


title: plasma-pregnancy-RZ60718


title: plasma-pregnancy-SM67105


title: plasma-pregnancy-SB36546


title: plasma-pregnancy-RX14080


title: plasma-pregnancy-RX25613


title: plasma-pregnancy-RY75327


title: plasma-pregnancy-RW86010


title: plasma-pregnancy-RW32868


title: plasma-pregnancy-RR65675


title: plasma-pregnancy-RK51652


title: plasma-pregnancy-RI77655


title: plasma-pregnancy-RG42622


title: plasma-pregnancy-RV42804


title: plasma-pregnancy-RS83160


title: plasma-pregnancy-RO70160


title: plasma-pregnancy-RF73133


title: plasma-pregnancy-RK34780


title: plasma-pregnancy-RL16053


title: plasma-pregnancy-RF60772


title: plasma-pregnancy-QV18000


title: plasma-pregnancy-QP79884


title: plasma-pregnancy-QQ63750


title: plasma-pregnancy-QY44546


title: plasma-pregnancy-QQ16640


title: plasma-pregnancy-QO92856


title: plasma-pregnancy-QP17308


title: plasma-pregnancy-QO77045


title: plasma-pregnancy-RR70478


title: plasma-pregnancy-QL56451


title: plasma-pregnancy-RL60415


title: plasma-pregnancy-QL05127


title: plasma-pregnancy-QG80408


title: plasma-pregnancy-QY70368


title: plasma-pregnancy-QF63733


title: plasma-pregnancy-QF61134


title: plasma-pregnancy-QB12268


title: plasma-pregnancy-QC34500


title: plasma-pregnancy-QD77674


title: plasma-pregnancy-PW53862


title: plasma-pregnancy-PW27380


title: plasma-pregnancy-PZ75546


title: plasma-pregnancy-PT85284


title: plasma-pregnancy-PT92024


title: plasma-pregnancy-PV68119


title: plasma-pregnancy-PS55478


title: plasma-pregnancy-PT09239


title: plasma-pregnancy-PS04852


title: plasma-pregnancy-PR47140


title: plasma-pregnancy-QO53865


title: plasma-pregnancy-PQ68590


title: plasma-pregnancy-PP60159


title: plasma-pregnancy-PQ58741


title: plasma-pregnancy-PO60458


title: plasma-pregnancy-PI50456


title: plasma-pregnancy-PW73614


title: plasma-pregnancy-PM28401


title: plasma-pregnancy-PK22112


title: plasma-pregnancy-QB41182


title: plasma-pregnancy-PE13814


title: plasma-pregnancy-PF21921


title: plasma-pregnancy-PE34242


title: plasma-pregnancy-PD61050


title: plasma-pregnancy-OY88961


title: plasma-pregnancy-PM28074


title: plasma-pregnancy-OW50312


title: plasma-pregnancy-ON48741


title: plasma-pregnancy-OP09508


title: plasma-pregnancy-OT72563


title: plasma-pregnancy-OM51482


title: plasma-pregnancy-OC23020


title: plasma-pregnancy-OA20563


title: plasma-pregnancy-OA41861


title: plasma-pregnancy-OB80171


title: plasma-pregnancy-NW83082


title: plasma-pregnancy-OI11755


title: plasma-pregnancy-PM32020


title: plasma-pregnancy-OA00414


title: plasma-pregnancy-NP09428


title: plasma-pregnancy-OU34532


title: plasma-pregnancy-OO07336


title: plasma-pregnancy-OL63898


title: plasma-pregnancy-NT52711


title: plasma-pregnancy-NU20420


title: plasma-pregnancy-NU65949


title: plasma-pregnancy-OU85445


title: plasma-pregnancy-NR01600


title: plasma-pregnancy-NN08178


title: plasma-pregnancy-NF42841


title: plasma-pregnancy-NL63351


title: plasma-pregnancy-NK16318


title: plasma-pregnancy-NK53466


title: plasma-pregnancy-ON24396


title: plasma-pregnancy-NI58350


title: plasma-pregnancy-NF12804


title: plasma-pregnancy-NE14245


title: plasma-pregnancy-ND48036


title: plasma-pregnancy-ND25308


title: plasma-pregnancy-NC42671


title: plasma-pregnancy-NB02754


title: plasma-pregnancy-MT74873


title: plasma-pregnancy-MY51622


title: plasma-pregnancy-MU14774


title: plasma-pregnancy-MO28881


title: plasma-pregnancy-MI25056


title: plasma-pregnancy-MM32851


title: plasma-pregnancy-ND17488


title: plasma-pregnancy-MH30313


title: plasma-pregnancy-MD88723


title: plasma-pregnancy-MH21330


title: plasma-pregnancy-MD82478


title: plasma-pregnancy-MF84926


title: plasma-pregnancy-MB12824


title: plasma-pregnancy-LW97176


title: plasma-pregnancy-LQ14275


title: plasma-pregnancy-LS17555


title: plasma-pregnancy-MO54830


title: plasma-pregnancy-LP85812


title: plasma-pregnancy-LN64682


title: plasma-pregnancy-LL50178


title: plasma-pregnancy-KZ16461


title: plasma-pregnancy-LK43475


title: plasma-pregnancy-LF00547


title: plasma-pregnancy-KY83645


title: plasma-pregnancy-LF51383


title: plasma-pregnancy-KU13564


title: plasma-pregnancy-KS25949


title: plasma-pregnancy-KW06468


title: plasma-pregnancy-KR07603


title: plasma-pregnancy-LQ30854


title: plasma-pregnancy-LX38584


title: plasma-pregnancy-LV46281


title: plasma-pregnancy-LN70886


title: plasma-pregnancy-KQ52211


title: plasma-pregnancy-LN63678


title: plasma-pregnancy-KP47177


title: plasma-pregnancy-KN48724


title: plasma-pregnancy-KK42330


title: plasma-pregnancy-KK16310


title: plasma-pregnancy-KF50784


title: plasma-pregnancy-JU50149


title: plasma-pregnancy-KD41132


title: plasma-pregnancy-KC02868


title: plasma-pregnancy-KD00545


title: plasma-pregnancy-KJ38280


title: plasma-pregnancy-JQ28863


title: plasma-pregnancy-JP22317


title: plasma-pregnancy-JP47370


title: plasma-pregnancy-JL56219


title: plasma-pregnancy-JM52974


title: plasma-pregnancy-JK50183


title: plasma-pregnancy-JM49487


title: plasma-pregnancy-JC25234


title: plasma-pregnancy-JA30360


title: plasma-pregnancy-JH60122


title: plasma-pregnancy-JI23618


title: plasma-pregnancy-IV33154


title: plasma-pregnancy-IP20899


title: plasma-pregnancy-IN62086


title: plasma-pregnancy-IL55635


title: plasma-pregnancy-IP35877


title: plasma-pregnancy-IQ37545


title: plasma-pregnancy-IV06027


title: plasma-pregnancy-IQ26517


title: plasma-pregnancy-II46040


title: plasma-pregnancy-II19110


title: plasma-pregnancy-IE72477


title: plasma-pregnancy-II30910


title: plasma-pregnancy-HW36784


title: plasma-pregnancy-ID78013


title: plasma-pregnancy-IB32880


title: plasma-pregnancy-ID41231


title: plasma-pregnancy-HV08232


title: plasma-pregnancy-IZ35612


title: plasma-pregnancy-HW75882


title: plasma-pregnancy-JD66420


title: plasma-pregnancy-HU79611


title: plasma-pregnancy-HU50197


title: plasma-pregnancy-HU32300


title: plasma-pregnancy-HR20165


title: plasma-pregnancy-HQ88401


title: plasma-pregnancy-HQ84626


title: plasma-pregnancy-HL67490


title: plasma-pregnancy-HM43070


title: plasma-pregnancy-HK51821


title: plasma-pregnancy-HL03522


title: plasma-pregnancy-HI65011


title: plasma-pregnancy-HH93022


title: plasma-pregnancy-HJ55837


title: plasma-pregnancy-HG08847


title: plasma-pregnancy-HF64739


title: plasma-pregnancy-HH53251


title: plasma-pregnancy-HF14404


title: plasma-pregnancy-HC83354


title: plasma-pregnancy-HC71404


title: plasma-pregnancy-GR53722


title: plasma-pregnancy-HQ60841


title: plasma-pregnancy-GP12241


title: plasma-pregnancy-GY01666


title: plasma-pregnancy-HA48862


title: plasma-pregnancy-GO82534


title: plasma-pregnancy-GW03032


title: plasma-pregnancy-GE52393


title: plasma-pregnancy-GJ12923


title: plasma-pregnancy-GE13707


title: plasma-pregnancy-GK14849


title: plasma-pregnancy-GA71894


title: plasma-pregnancy-GA87417


title: plasma-pregnancy-GJ27958


title: plasma-pregnancy-FW08415


title: plasma-pregnancy-FU25011


title: plasma-pregnancy-GB37031


title: plasma-pregnancy-FU72054


title: plasma-pregnancy-FU22670


title: plasma-pregnancy-FT41217


title: plasma-pregnancy-FP83171


title: plasma-pregnancy-FR82658


title: plasma-pregnancy-FQ06345


title: plasma-pregnancy-FP85843


title: plasma-pregnancy-FR25483


title: plasma-pregnancy-FO94760


title: plasma-pregnancy-FM93972


title: plasma-pregnancy-FX12166


title: plasma-pregnancy-FO13262


title: plasma-pregnancy-FI42688


title: plasma-pregnancy-FF37661


title: plasma-pregnancy-FG42676


title: plasma-pregnancy-FK61412


title: plasma-pregnancy-FK07578


title: plasma-pregnancy-FH40404


title: plasma-pregnancy-FE14238


title: plasma-pregnancy-FD87644


title: plasma-pregnancy-FA78506


title: plasma-pregnancy-FC85479


title: plasma-pregnancy-FD20218


title: plasma-pregnancy-FA83320


title: plasma-pregnancy-EW62546


title: plasma-pregnancy-EV48848


title: plasma-pregnancy-ET55837


title: plasma-pregnancy-EU90126


title: plasma-pregnancy-EK66712


title: plasma-pregnancy-EK43505


title: plasma-pregnancy-EQ50972


title: plasma-pregnancy-EJ04400


title: plasma-pregnancy-EK26463


title: plasma-pregnancy-FT62182


title: plasma-pregnancy-EF42321


title: plasma-pregnancy-EY74647


title: plasma-pregnancy-EE77263


title: plasma-pregnancy-EE30882


title: plasma-pregnancy-EC42440


title: plasma-pregnancy-DY76239


title: plasma-pregnancy-EC94482


title: plasma-pregnancy-EC85086


title: plasma-pregnancy-ED72676


title: plasma-pregnancy-DV42653


title: plasma-pregnancy-DY73080


title: plasma-pregnancy-DX88045


title: plasma-pregnancy-DP35341


title: plasma-pregnancy-DX80585


title: plasma-pregnancy-DQ63320


title: plasma-pregnancy-DP12578


title: plasma-pregnancy-DQ47858


title: plasma-pregnancy-ES48023


title: plasma-pregnancy-DM63727


title: plasma-pregnancy-DN80339


title: plasma-pregnancy-ER64862


title: plasma-pregnancy-DK20659


title: plasma-pregnancy-EH45840


title: plasma-pregnancy-DJ76075


title: plasma-pregnancy-DG66665


title: plasma-pregnancy-DI34681


title: plasma-pregnancy-DC83582


title: plasma-pregnancy-DG23433


title: plasma-pregnancy-DH77785


title: plasma-pregnancy-DH14061


title: plasma-pregnancy-DC18707


title: plasma-pregnancy-DC14585


title: plasma-pregnancy-DC11137


title: plasma-pregnancy-DA13356


title: plasma-pregnancy-DA63277


title: plasma-pregnancy-CZ06869


title: plasma-pregnancy-DB02844


title: plasma-pregnancy-CZ11574


title: plasma-pregnancy-CZ38393


title: plasma-pregnancy-CP05460


title: plasma-pregnancy-CV91217


title: plasma-pregnancy-BX65106


title: plasma-pregnancy-CD69397


title: plasma-pregnancy-CO32770


title: plasma-pregnancy-CO72532


title: plasma-pregnancy-CD61261


title: plasma-pregnancy-BV53215


title: plasma-pregnancy-CR16036


title: plasma-pregnancy-CO56413


title: plasma-pregnancy-CK05050


title: plasma-pregnancy-CF83266


title: plasma-pregnancy-CO73326


title: plasma-pregnancy-BU55044


title: plasma-pregnancy-BS80866


title: plasma-pregnancy-BU14783


title: plasma-pregnancy-BI37729


title: plasma-pregnancy-BN40463


title: plasma-pregnancy-BJ17347


title: plasma-pregnancy-BR63266


title: plasma-pregnancy-CL96495


title: plasma-pregnancy-BO77173


title: plasma-pregnancy-BM39723


title: plasma-pregnancy-BH32682


title: plasma-pregnancy-BH62082


title: plasma-pregnancy-BG51731


title: plasma-pregnancy-BF11205


title: plasma-pregnancy-BD64103


title: plasma-pregnancy-BE41222


title: plasma-pregnancy-AW60347


title: plasma-pregnancy-BB11681


title: plasma-pregnancy-AW37681


title: plasma-pregnancy-AQ76864


title: plasma-pregnancy-AZ83240


title: plasma-pregnancy-AO00882


title: plasma-pregnancy-AZ30215


title: plasma-pregnancy-AQ28860


title: plasma-pregnancy-AO54308


title: plasma-pregnancy-BD32566


title: plasma-pregnancy-AW01775


title: plasma-pregnancy-AR51268


title: plasma-pregnancy-AP67189


title: plasma-pregnancy-AN86000


title: Input  3 day differentiated cells

city: London

first: Andrea

last: Cerase

address: Newark st

country: United Kingdom

institute: QMUL

description: HYFJCBGX5_9U-_input__18s001707-1-1_Cerase_lane118s001707_noDups_q2_RPKM_50.bw

library_source: genomic

data_processing:
Reads were trimmed with cutadapt (http://cutadapt.readthedocs.io/en/stable/index.html) and aligned to the genome with bowtie2 using the ‘very sensitive’ alignment option
Picard tools were used to remove duplicate reads and samTools to filter out reads with mapping quality below two (https://broadinstitute.github.io/picard/)
Subsequently, coverage plots were generated with deepTools using a bin size of 50 (or 100b) and RPKM (reads per kilobase per million) normalization
The software MACS2 called peaks with 0.05 as FDR cut-off and consensus peak sets were derived for the duplicated experiments using Bioconductor`s package DiffBind (http://liulab.dfci.harvard.edu/MACS/; https://www.bioconductor.org)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

source_name: 3day differntiated cells

growth_protocol: Cells were grown in 2i conditions as previously published. For differentiation experiments, the wells of a 6-well plate or a 10cm TC dish were pre-coated with gelatin (0.1%) containing laminin (1:1000) solution and incubated at 37°C for 15 min.  About 150,000 cells per well in 6 well plate were plated in each well in Neuronal Differentiation Medium (NDM) as previously published. The cells were differentiated for 3 days and harvested for RNA-seq, qRT-PCR or IF analysis.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: In order to obtain Chd8 KD, we used Dharmacon Smart pool-of-four siRNAs (#67772) or single siRNA (YY1, from Thermo Fisher, Cat # AM16708) at a 50nM final concentration, in accordance with the manufacturers protocol. Chd8 KD was initiated at day 1 of differentiation using lipofectamine transfection (RNAi-MAX Invitrogen).   In order to generate stable Chd8 KD lines, we used lentiviral mediated KD using pre-packaged lentiviral particles (SIGMA). In brief, Fa2L-S4 cell line was infected either with a scrambled shRNA control (SHC002) or 2 independent Chd8 targeting constructs (SIGMA shRNA clones - CloneIDs : NM_201637.2-847s1c1 (Chd8.1); NM_201637.2-3342s21c1 (Chd8.2)). Two days after transfection, puromycin selection was applied for 7-9 days (2µg/ml). Colonies were picked and expanded using standard protocols. Chd8 KD was assessed by conventional qRT-PCR analysis.

tag: strain

value: KO

value: Fa2L (subclone)

tag: antibody

value: ChIP-seq Ab:no Ab


title: plasma-pregnancy-AM24834


title: plasma-pregnancy-AF65082


title: INO80  3-day differentiated cells replica 2

description: HYFJCBGX5_13_18s001702-1-1_Cerase_lane118s001702_noDups_q2_RPKM_50.bw

tag: genotype

value: ChIP-seq Ab:Abcam ab105451


title: plasma-pregnancy-AD03083


title: plasma-pregnancy-AA58724


title: plasma-pregnancy-AB80632


title: INO80  3-day differentiated cells replica 1

description: HYFJCBGX5_12_18s001701-1-1_Cerase_lane118s001701_noDups_q2_RPKM_50.bw


title: plasma-pregnancy-AE42240


title: Input undifferentiated cells

description: HYFJCBGX5_1U-_input__18s001706-1-1_Cerase_lane118s001706_noDups_q2_RPKM_50.bw

source_name: ES cells


title: plasma-pregnancy-BC13346


title: IgG Undifferentiated cells

description: HYFJCBGX5_1_18s001690-1-1_Cerase_lane118s001690_noDups_q2_RPKM_50.bw

value: ChIP-seq Ab:Santa Cruz SC-2025


title: INO80 undifferentiated cells replica 1

description: HYFJCBGX5_4_18s001693-1-1_Cerase_lane118s001693_noDups_q2_RPKM_50.bw


title: Chd8 KO.2 ATAC-seq differentiated cells biological replica 1


title: Chd8 KO.2 ATAC-seq differentiated cells biological replica 2


title: Chd8 KO.1 ATAC-seq differentiated cells biological replica 2


title: Chd8 KO.1 ATAC-seq Undifferentiated cells


title: Chd8 KO.1 ATAC-seq differentiated cells biological replica 1


title: Chd8 KO.2 ATAC-seq Undifferentiated cells


title: WT ATAC-seq Undifferentiated cells

value: WT


title: WT ATAC-seq differentiated cells biological replica 1


title: IgG 3-day differentiated cells EXp2

description: HYFJCBGX5_9_18s001698-1-1_Cerase_lane118s001698_noDups_q2_RPKM_50.bw

value: ChIP-seq Ab:Santa Cruz SC-2026


title: IgG  3-day differentiated cells Exp1

description: HGHGFBGXX _sample17_noDups_q2_RPKM_50.bw

value: ChIP-seq Ab:Santa Cruz SC-2027


title: Input Exp2 Differentiated cells

value: ChIP-seq Ab:No ab


title: IgG Undifferentiated cells Exp2


title: IgG 3-day differentiated cells


title: Input Exp1 Undifferentiated cells

description: HMNG7BGXX_sample11_115s013509_noDups_q2_RPKM_50.bw


title: Input Exp1 Differentiated cells

description: HMNG7BGXX_sample12_115s013512_noDups_q2_RPKM_50.bw


title: H3k4me3 3-day differentiated cells Exp2

value: ChIP-seq Ab:Active Motif 39162


title: H3k4me3 3-day differentiated cells Exp1

description: HMNG7BGXX_sample16_115s0135016_noDups_q2_RPKM_50.bw

value: ChIP-seq Ab:Active Motif 39161


title: H3K4me3 Undifferentiated cells Exp1

description: HMNG7BGXX_sample08_115s013508_noDups_q2_RPKM_50.bw

value: ChIP-seq Ab:Active Motif 39159


title: H3K4me3 Undifferentiated cells  Exp2

value: ChIP-seq Ab:Active Motif 39160


title: Chd8 3-day differentiated cells Exp2

value: ChIP-seq Ab:Bethyl A301-224A


title: Chd8 Undifferentiated cells Exp2


title: Chd8 3-day differentiated cells Exp1

description: HYFJCBGX5_15_18s001704-1-1_Cerase_lane118s001704_noDups_q2_RPKM_50.bw


title: Chd8 Undifferentiated cells Exp1

description: HYFJCBGX5_7_18s001696-1-1_Cerase_lane118s001696_noDups_q2_RPKM_50.bw


title: WT ATAC-seq differentiated cells biological replica 2


title: IgG Undifferentiated cells Exp1

description: HGHGFBGXX  _sample1_noDups_q2_RPKM_50.bw

value: ChIP-seq Ab:Santa Cruz SC-2028


title: Sample 39 WT

description: Sample 39

data_processing:
Data QC and pre-processing : Quality control on the raw reads was performed using FastQC whereas quality trimming and adapter removal was carried out using cutadapt
Read Mapping: Trimmed reads were aligned to the reference genome using STAR v2.6.1a. FeatureCounts was used to count the reads on a gene basis
Genome_build: ENSEMBL Mus Musculus GRCm38.88
Supplementary_files_format_and_content: gene counts, csv format

source_name: Undifferentiated ES cells

extract_protocol:
RNA was extracted using the RNAesy mini kit according to the producer’s manual (Qiagen). RNA was DNAse treated for 30 minutes at 37 degrees and DNAse was then inactivated using a cDNA kit (Turbo DNase, Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Sample 37 WT

description: Sample 37

source_name: 3-day differentiated cells


title: Sample 38 WT

description: Sample 38


title: Input Exp2 Undifferentiated cells


title: Sample 34 Chd8.KO

description: Sample 34


title: Sample 35 WT

description: Sample 35


title: Sample 33 Chd8.KO

description: Sample 33


title: Sample 32 WT

description: Sample 32


title: Sample 30 Chd8.KO

description: Sample 30


title: Sample 29 Chd8.KO

description: Sample 29


title: Sample 31 WT

description: Sample 31


title: Sample 26 Chd8 shRNa clone 8.2

description: Sample 26

tag: sirna

value: Chd8 shRNa clone 8.2


title: Sample 28 Chd8 shRNa clone 8.1

description: Sample 28

value: Chd8 shRNa clone 8.1


title: Sample 27 Scrambled sfRNA (control)

description: Sample 27

value: Scrambled sfRNA (control)


title: Sample 25 Chd8 shRNa clone 8.1

description: Sample 25

value: Fa2L (subclone)


title: Sample 24 Scrambled sfRNA (control)

description: Sample 24


title: Sample 22 Chd8 shRNa clone 8.1

description: Sample 22


title: Sample 21 Scrambled sfRNA (control)

description: Sample 21


title: Sample 19 Chd8 shRNa clone 8.1

description: Sample 19


title: Sample 23 Chd8 shRNa clone 8.2

description: Sample 23


title: Sample 20 Chd8 shRNa clone 8.2

description: Sample 20


title: Sample 17 Chd8 shRNa clone 8.2

description: Sample 17


title: Sample 15 Chd8 shRNa clone 8.1

description: Sample 15


title: Sample 16 Chd8 shRNa clone 8.2

description: Sample 16


title: Sample 12 Scrambled sfRNA (control)

description: Sample 12


title: Sample 10 Chd8 siRNA

description: Sample 10

value: Chd8 siRNA


title: Sample 36 WT

description: Sample 36


title: Sample 11 Scrambled siRNA (control)

description: Sample 11

value: Scrambled siRNA (control)


title: Sample 13 Scrambled sfRNA (control)

description: Sample 13


title: Sample 8 none (untreated)

description: Sample 8

value: none (untreated)


title: Sample 6 Chd8 siRNA

description: Sample 6


title: Sample 5 none (untreated)

description: Sample 5


title: Sample 1 none

description: Sample 1


title: Sample 7 Chd8 siRNA

description: Sample 7


title: Sample 2 Chd8 siRNA

description: Sample 2


title: Sample 18 Scrambled sfRNA (control)

description: Sample 18


title: Bb+_mouse_3

city: San Francisco

first: Seemay

last: Chou

address: 499 Illinois St, 4th Floor

institute: Chan Zuckerberg Biohub

description: rRNA-depleted RNA

data_processing:
RNA-seq reads were trimmed of adapters and bases with quality score lower than 20 using Cutadapt via Trim Galore! v0.6.5 and then mapped to the Ixodes scapularis ISE6 genome (assembly GCF_002892825.2_ISE6_asm2.2_deduplicated) accessed from NCBI RefSeq, using STAR v2.7.3a
Reads mapping to predicted genes (GCF_002892825.2_ISE6_asm2.2_deduplicated_genomic.gtf) were tabulated using Subread FeatureCounts v2.0.0, counting primary hits only
DESeq2 v1.26.0, was used to determine differential expression between groups
Genome_build: GCF_002892825.2_ISE6_asm2.2_deduplicated_genomic.gtf
Supplementary_files_format_and_content: raw gene counts

organism: Ixodes pacificus

source_name: whole-bodied tick

extract_protocol:
Prior to extraction, ticks were thoroughly surface sterilized with successive 1 mL washes of 3% hydrogen peroxide, 70% ethanol, and de-ionized H2O to remove surface contaminants. The tick was then lysed and homogenized using the Qiagen TissueLyser II (QIAGEN, Valencia, CA, USA). Tick samples were extracted simultaneously for total DNA and RNA using the Qiagen AllPrep DNA/RNA Micro Kit (QIAGEN, Valencia, CA, USA). We pooled three individual ticks for each experimental replicate.  RNA-seq libraries were prepared from total RNA extracted from ticks followed by rRNA depletion using Depletion of Abundant Sequences by Hybridization (DASH). The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7760S) was used to make RNA-seq libraries following the standard manual protocol.
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7760S) was used to make RNA-seq libraries following the standard manual protocol.

treatment_protocol: Larval I. pacificus larval ticks were fed on either western fence lizards (Sceloporous occidentalis) or deer mice (Peromyscus maniculatus). Replete ticks from lizard and mouse feeding procedures were collected and stored under standard rearing conditions of 23°C and 90% relative humidity until they molted eight weeks later. A subset of six molted nymphs from both the lizard and mouse feeding were set aside, acting as our unfed experimental condition, flash frozen using liquid nitrogen, and stored at -80 degrees until nucleic acid extraction. The remaining nymphs that fed as larvae on either lizards or mice were then placed on either Bb infected or uninfected C3H/HeJ mice for their nymphal feeding. After completing their bloodmeal, nymphs were placed under standard rearing conditions for 24 hours, flash frozen, and stored at -80°C until nucleic acid extraction.

value: whole-bodied

tag: life stage

value: nymph

tag: replicate

tag: bloodmeal sources

value: larval bloodmeal:Peromyscus maniculatis, nymphal bloodmeal:Borrelia burgdorferi infected C3H/HeJ mouse


title: Bb+_mouse_2

description: rRNA-depleted RNA

tag: tissue


title: Bb+_lizard_1

description: rRNA-depleted RNA

value: larval bloodmeal:Sceloporous occidentalis, nymphal bloodmeal:Borrelia burgdorferi infected C3H/HeJ mouse


title: Sample 14 Chd8 shRNa clone 8.1

description: Sample 14

tag: cell line


title: Bb+_lizard_2

description: rRNA-depleted RNA


title: Bb-_mouse_3

description: rRNA-depleted RNA

value: larval bloodmeal:Peromyscus maniculatis, nymphal bloodmeal:uninfected C3H/HeJ mouse


title: Bb+_lizard_3

description: rRNA-depleted RNA


title: Bb-_mouse_2

description: rRNA-depleted RNA


title: Bb-_lizard_3

description: rRNA-depleted RNA

value: larval bloodmeal:Sceloporous occidentalis, nymphal bloodmeal:uninfected C3H/HeJ mouse


title: Bb-_mouse_1

description: rRNA-depleted RNA


title: Bb-_lizard_1

description: rRNA-depleted RNA


title: Sample 9 Chd8 siRNA

description: Sample 9


title: Bb-_lizard_2

description: rRNA-depleted RNA


title: UF_mouse_3

description: rRNA-depleted RNA

value: larval bloodmeal:Peromyscus maniculatis, nymphal bloodmeal:unfed


title: UF_mouse_2

description: rRNA-depleted RNA


title: UF_lizard_1

description: rRNA-depleted RNA

value: larval bloodmeal:Sceloporous occidentalis, nymphal bloodmeal:unfed


title: UF_lizard_2

description: rRNA-depleted RNA


title: UF_lizard_3

description: rRNA-depleted RNA


title: Sample 4 Scrambled siRNA (control)

description: Sample 4


title: Sample 3 Chd8 siRNA

description: Sample 3


title: blood_Transwomen_pretreatment_rep1 [TV533]

type: genomic

city: A Coruña

first: Rosa

last: Fernandez

state: None / N/A

address: Campus Elviña

department: Psychology

country: Spain

institute: University of A Coruña

description:
204088100012_R07C01
TV533
Trans women

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation850 BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
DNA quality checks, data normalization, and statistical filters were performed with the Partek® Genomics Suite® v7.19.1018 Methylation Module.
Average Beta

source_name: blood, trans, pre treatment

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNAs were extracted from peripheral blood samples using the DNeasy Blood & Tissue Kit from Qiagen.

value: blood

tag: gender

value: female

tag: birth sex

value: male

tag: age

value: 47 years

tag: population

value: Caucasian


title: blood_Transwomen_pretreatment_rep1 [TV517]

description:
204088100012_R05C01
TV517
Trans women

value: 50 years

tag: treatment


title: Bb+_mouse_1

description: rRNA-depleted RNA


title: blood_Transwomen_pretreatment_rep1 [TV502]

description:
204088100012_R02C01
TV502
Trans women

value: 28 years


title: blood_Transwomen_pretreatment_rep1 [TV493]

description:
203717910113_R02C01
TV493
Trans women

value: 36 years


title: blood_Transwomen_pretreatment_rep1 [TV513]

description:
204088100012_R03C01
TV513
Trans women

value: 27 years


title: blood_Transwomen_pretreatment_rep1 [TV486]

description:
204088100012_R01C01
TV486
Trans women

value: 59 years


title: blood_Transmen_pretreatment_rep1 [TM534]

description:
204088090160_R05C01
TM534
Trans men

value: 19 years


title: blood_Transmen_pretreatment_rep1 [TM535]

description:
204088090160_R06C01
TM535
Trans men

value: 21 years


title: blood_Transmen_pretreatment_rep1 [TM501]

description:
203717910075_R08C01
TM501
Trans men

value: 65 years


title: blood_Transmen_pretreatment_rep1 [TM499]

description:
203717910075_R07C01
TM499
Trans men

value: 42 years


title: blood_Transmen_pretreatment_rep1 [TM491]

description:
203717910075_R04C01
TM491
Trans men

value: 24 years


title: UF_mouse_1

description: rRNA-depleted RNA

value: whole-bodied

value: nymph

value: larval bloodmeal:Peromyscus maniculatis, nymphal bloodmeal:unfed


title: blood_Transmen_pretreatment_rep1 [TM490]

description:
203717910075_R03C01
TM490
Trans men

value: blood

value: female

value: 30 years


title: blood_Transmen_pretreatment_rep1 [TM531]

description:
204088090160_R04C01
TM531
Trans men

value: male

value: Caucasian


title: blood_Ciswomen_pretreatment_rep1 [CV23]

description:
203717910049_R04C01
CV23
Cis women

source_name: blood, cis, pre treatment

value: 20 years


title: blood_Ciswomen_pretreatment_rep1 [CV51]

description:
203717910049_R07C01
CV51
Cis women

value: 43 years


title: blood_Cismen_pretreatment_rep1 [CM45]

description:
203717910051_R07C01
CM45
Cis men

value: 32 years


title: blood_Cismen_pretreatment_rep1 [CM27]

description:
203717910051_R06C01
CM27
Cis men

value: 28 years


title: blood_Cismen_pretreatment_rep1 [CM35]

description:
203717910051_R08C01
CM35
Cis men

value: 27 years


title: blood_Cismen_pretreatment_rep1 [CM21]

description:
203717910051_R03C01
CM21
Cis men


title: blood_Cismen_pretreatment_rep1 [CM25]

description:
203717910051_R04C01
CM25
Cis men

value: 21 years


title: blood_Cismen_pretreatment_rep1 [CM2]

description:
203717910051_R02C01
CM2
Cis men


title: blood_Transwomen_pretreatment_rep1 [TV514]

description:
204088100012_R04C01
TV514
Trans women

value: 31 years


title: blood_Ciswomen_pretreatment_rep1 [CV16]

description:
203717910049_R06C01
CV16
Cis women


title: blood_Cismen_pretreatment_rep1 [CM11]

description:
203717910051_R01C01
CM11
Cis men


title: blood_Ciswomen_pretreatment_rep1 [CV14]

description:
203717910049_R08C01
CV14
Cis women

value: 47 years


title: blood_Cismen_pretreatment_rep1 [CM17]

description:
203717910051_R05C01
CM17
Cis men

value: 29 years


title: blood_Transmen_pretreatment_rep1 [TM484]

description:
204088090160_R01C01
TM484
Trans men

value: 18 years


title: blood_Transmen_pretreatment_rep1 [TM497]

description:
203717910075_R05C01
TM497
Trans men

value: 24 years


title: blood_Ciswomen_pretreatment_rep1 [CV6]

description:
203717910049_R02C01
CV6
Cis women

value: 22 years


title: blood_Ciswomen_pretreatment_rep1 [CV7]

description:
203717910049_R01C01
CV7
Cis women

value: blood


title: blood_Ciswomen_pretreatment_rep1 [CV28]

description:
203717910049_R03C01
CV28
Cis women

value: female


title: non-COVID_6_SARS-CoV-2_ISIRB

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
The sequencing data were primarily analyzed by the 10X cellranger pipeline (v3.0.2)
cellranger mkfastq was used for sample demultiplexing and fastq generation.
cellranger count was used to align reads to the 10X pre-built human reference genome (GRCh38 v3.0.0) plus SARS-CoV-2 viral genome (NC_045512.2) and to extract gene expression UMI counts matrix.
Genome_build: GRCh38
Supplementary_files_format_and_content: UMI counts matrix generated by 10X cellranger count; matrix.mtx.gz stores UMI counts per gene per cell; features.tsv.gz stores gene annotations; barcodes.tsv.gz stores cell barcodes.

source_name: Pancreatic Islets

growth_protocol: The pancreatic organs were obtained from the local organ procurement organization under the United Network for Organ Sharing (UNOS). The islets were isolated in the Human Islet Core at University of Pennsylvania following the guidelines of Clinical Islet Transplantation consortium protocol (Ricordi et al., 2016). Briefly, the pancreas was digested following intraductal injection of Collagenase & Neutral Protease in Hanks’ balanced salt solution. Liberated islets were then purified on continuous density gradients (Cellgro/Mediatech) using the COBE 2991 centrifuge and cultured in CIT culture media and kept in a humidified 5% CO2 incubator.

extract_protocol:
Cells were then washed twice in 1x PBS and filtered using a 40 m Flowmi cell strainer (Bel-Art Scienceware). Cell count and cell viability were then determined using trypan blue staining and a Countess II automatic cell counter (ThermoFisher Scientific).
Target cell inputs of 10,000 cells for each condition were then loaded into a Chromium Controller using Chromium Next GEM (Gel Bead-In Emulsion) single Cell 5’ Library & Gel Bead Kit v1.1 (10x Genomics) according to manufacturer’s instructions. After generation of GEMs, cDNA synthesis and subsequent library preparation of all samples was completed using the Chromium Single Cell 5’ Library Kit v1.1 (10x Genomics) according to manufacturer’s instructions.
The 10X Libraries (Single Cell 5’ R2-only library) were sequenced on the Illumina NovaSeq6000 sequencer with pair-end reads (28 bp for read 1 and 91 bp for read 2).

treatment_protocol: Approximately 1 × 10^6 untreated, control or integrated stress response inhibitor treated (ISRIB) treated, and Sal003 treated  primary human pancreatic islet cells were infected with passage-3 SARS-CoV-2 at an MOI of 1 for 24 h in CIT culture media. After 24 hours, infected and mock infected pancreatic islets were dissociated into a single cell suspension using Accutase cell detachment solution (Innovative Cell Technologies) and incubation at 37C for ~20 minutes followed by gentle pipetting to break apart groups of cells.

tag: tissue/cell type

value: primary human pancreatic islet cells

value: infected with SARS-CoV-2


title: non-COVID_6_SARS-CoV-2


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB905UCK)

status: Public on Apr 22 2021

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR135XMY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR135XMY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB905UCK

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens female adult (33 years) activated CD8-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 4 h, 100 ng/mL Interleukin-12 subunit alpha for 4 h, 100 ng/mL Interleukin-12 subunit beta for 4 h

value: primary cell

tag: biosample encode accession

tag: Sex

tag: dev stage

value: adult

value: 33 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:4; duration_units:hour; treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; duration:4; duration_units:hour; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; duration:4; duration_units:hour;

tag: link

value: ENCBS270NGZ at ENCODE; https://www.encodeproject.org/ENCBS270NGZ/

value: Derived from ENCODE donor ENCDO299FMV; https://www.encodeproject.org/ENCDO299FMV/


title: Primary_control_cell_line_1

city: Oulu

first: Mervi

last: Kreus

address: Aapistie 5A

country: Finland

institute: University of Oulu

description: Gene expression data from stromal cells cultured from histologically normal lung tissue

hyb_protocol: GeneChips were washed and stained in the Affymetrix GeneChip® Fluidics Station 450; fluidics script: FS450_0001.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 7G.

data_processing: Analysis of the microarray expression data was done using the R/Bioconductor through a graphical user interface, Chipster 3.12.5. Normalization was performed using custom chip description file for hgu133Aplus2. Intensity data were log2-transformed, and quantile normalized using robust multi-array average (RMA).

source_name: Primary pulmonary fibroblasts from normal control lung 1

label_protocol: Biotinylated cRNA were prepared with 3'IVT Express Kit and Affymetrix GeneChip® Hybridization, Wash and Stain Kit.

growth_protocol: Cells were plated at a density of 2000 cells/cm2 and grown for 72 hours.

extract_protocol: Total RNA was extracted using Qiagen Rneasy mini kit.

treatment_protocol: No additional treatments were applied to the cultured cell lines.

value: Primary pulmonary fibroblasts

value: Female

tag: smoking status

value: Non-smoker


title: non-COVID_5_SARS-CoV-2


title: non-COVID_6_Mock

value: mock


title: Primary_control_cell_line_4

source_name: Primary pulmonary fibroblasts from normal control lung 4


title: non-COVID_5_Mock


title: Primary_ADC_cell_line_4

description: Gene expression data from stromal cells cultured from lung adenocarcinoma tumor tissue

source_name: Primary pulmonary fibroblasts from Lung adenocarcinoma patient 4


title: Primary_ADC_cell_line_2

source_name: Primary pulmonary fibroblasts from Lung adenocarcinoma patient 2

value: Male


title: Primary_IPF_cell_line_4

description: Gene expression data from stromal cells cultured from IPF lung tissue

source_name: Primary pulmonary fibroblasts from Idiopathic pulmonary fibrosis patient 4

value: Ex-smoker


title: Primary_control_cell_line_3

source_name: Primary pulmonary fibroblasts from normal control lung 3


title: Primary_IPF_cell_line_3

source_name: Primary pulmonary fibroblasts from Idiopathic pulmonary fibrosis patient 3

value: Smoker


title: Primary_control_cell_line_2

source_name: Primary pulmonary fibroblasts from normal control lung 2


title: Primary_IPF_cell_line_1

source_name: Primary pulmonary fibroblasts from Idiopathic pulmonary fibrosis patient 1


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB943FBQ)

description:
https://www.encodeproject.org/experiments/ENCSR998IXQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR998IXQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB943FBQ

source_name: Homo sapiens male adult (38 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 1 hour, 100 ng/mL Interleukin-15 for 1 hour

value: male

value: 38 year

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:1; duration_units:hour; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS930EJX at ENCODE; https://www.encodeproject.org/ENCBS930EJX/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: Primary_IPF_cell_line_2

source_name: Primary pulmonary fibroblasts from Idiopathic pulmonary fibrosis patient 2


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCLB589TWJ)

description:
https://www.encodeproject.org/experiments/ENCSR250GDW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR250GDW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB589TWJ

source_name: Homo sapiens female adult (39 years) CD4-positive, alpha-beta T primary cell treated with Interleukin-4 for 1 hour

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: description

value: female

value: adult

value: 39 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS718CKJ at ENCODE; https://www.encodeproject.org/ENCBS718CKJ/

value: Derived from ENCODE donor ENCDO222BBW; https://www.encodeproject.org/ENCDO222BBW/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB227BZP)

description:
https://www.encodeproject.org/experiments/ENCSR987GUS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR987GUS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB227BZP

source_name: Homo sapiens male adult (38 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 100 ng/mL Interleukin-15 for 24 hours

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS486HQE at ENCODE; https://www.encodeproject.org/ENCBS486HQE/


title: DNase-seq from coronary artery (ENCLB740GJK)

description:
https://www.encodeproject.org/experiments/ENCSR999TSD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR999TSD
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2017-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB740GJK

source_name: Homo sapiens female adult (51 years) coronary artery tissue

value: coronary artery

value: tissue

value: 51 year

value: Kristin Ardlie

value: ENCBS533FWX at ENCODE; https://www.encodeproject.org/ENCBS533FWX/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: INO80 undifferentiated cells replica 2

description: HYFJCBGX5_5_18s001694-1-1_Cerase_lane118s001694_noDups_q2_RPKM_50.bw

source_name: ES cells

tag: strain

tag: genotype

value: KO

value: Fa2L (subclone)

tag: antibody

value: ChIP-seq Ab:Abcam ab105451


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB565ABM)

description:
https://www.encodeproject.org/experiments/ENCSR536VAY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR536VAY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB565ABM

source_name: Homo sapiens male adult (38 years) activated CD8-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 h, 100 ng/mL Interleukin-12 subunit alpha for 24 h, 100 ng/mL Interleukin-12 subunit beta for 24 h

value: primary cell

value: male

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS976KKD at ENCODE; https://www.encodeproject.org/ENCBS976KKD/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: DNase-seq from sigmoid colon (ENCLB016MKC)

description:
https://www.encodeproject.org/experiments/ENCSR462XTM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR462XTM
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2017-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB016MKC

source_name: Homo sapiens female adult (51 years) sigmoid colon tissue

value: sigmoid colon

value: female

value: ENCBS776XVO at ENCODE; https://www.encodeproject.org/ENCBS776XVO/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB906JLA)

description:
https://www.encodeproject.org/experiments/ENCSR252NVI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR252NVI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB906JLA

source_name: Homo sapiens female adult (37 years) activated CD4-positive, alpha-beta T primary cell treated with Interleukin-10 for 8 hours

value: 37 year

value: Shelly Heimfeld

value: treatment_term_id:UniProtKB:P22301; treatment_term_name:Interleukin-10; treatment_type:protein; duration:8; duration_units:hour;

value: ENCBS731CKT at ENCODE; https://www.encodeproject.org/ENCBS731CKT/

value: Derived from ENCODE donor ENCDO514TDF; https://www.encodeproject.org/ENCDO514TDF/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB299ICN)

description:
https://www.encodeproject.org/experiments/ENCSR457JOG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR457JOG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB299ICN

source_name: Homo sapiens male adult (42 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 50 U/mL Interleukin-2 for 48 hours

value: 42 year

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS043VTG at ENCODE; https://www.encodeproject.org/ENCBS043VTG/

value: Derived from ENCODE donor ENCDO833KUM; https://www.encodeproject.org/ENCDO833KUM/


title: DNase-seq from testis (ENCLB131TNO)

description:
https://www.encodeproject.org/experiments/ENCSR978QUT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR978QUT
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2017-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB131TNO

source_name: Homo sapiens male adult (54 years) testis tissue

value: testis

value: tissue

value: male

value: adult

value: 54 year

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS141OYJ at ENCODE; https://www.encodeproject.org/ENCBS141OYJ/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB798WPN)

description:
https://www.encodeproject.org/experiments/ENCSR731DJH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR731DJH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB798WPN

source_name: Homo sapiens male adult (38 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 100 ng/mL TNF-alpha for 24 hours

value: primary cell

value: 38 year

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P01375; treatment_term_name:TNF-alpha; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS462DWB at ENCODE; https://www.encodeproject.org/ENCBS462DWB/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: DNase-seq from effector memory CD4-positive, alpha-beta T cell (ENCLB197AHQ)

description:
https://www.encodeproject.org/experiments/ENCSR732IFV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR732IFV
assay title: DNase-seq
assembly: GRCh38
possible controls: ENCSR692PKU
encode release date: 2020-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB197AHQ

source_name: Homo sapiens male adult (38 years) effector memory CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 16 hours, 50 U/mL Interleukin-2 for 16 hours

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:16; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:16; duration_units:hour;

value: ENCBS450AUA at ENCODE; https://www.encodeproject.org/ENCBS450AUA/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB411BZJ)

description:
https://www.encodeproject.org/experiments/ENCSR724QTW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR724QTW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB411BZJ

source_name: Homo sapiens male adult (42 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 4 hours, 100 ng/mL Interleukin-12 subunit alpha for 4 hours, 100 ng/mL Interleukin-12 subunit beta for 4 hours

value: 42 year

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:4; duration_units:hour; treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; duration:4; duration_units:hour; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; duration:4; duration_units:hour;

value: ENCBS505QSC at ENCODE; https://www.encodeproject.org/ENCBS505QSC/

value: Derived from ENCODE donor ENCDO833KUM; https://www.encodeproject.org/ENCDO833KUM/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB412MDA)

description:
https://www.encodeproject.org/experiments/ENCSR245AXW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR245AXW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB412MDA

source_name: Homo sapiens male adult (42 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 100 ng/mL Interleukin-2 for 24 hours

value: male

value: adult

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS738ZRW at ENCODE; https://www.encodeproject.org/ENCBS738ZRW/


title: DNase-seq from activated CD4-positive, alpha-beta memory T cell (ENCLB150TSP)

description:
https://www.encodeproject.org/experiments/ENCSR720TCN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR720TCN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB150TSP

source_name: Homo sapiens male adult (43 years) activated CD4-positive, alpha-beta memory T primary cell treated with 10 ng/mL Interleukin-2 , anti-CD3 and anti-CD28 coated beads

value: 43 year

value: Yijun Ruan, JAX

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS027VFH at ENCODE; https://www.encodeproject.org/ENCBS027VFH/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB517HZF)

description:
https://www.encodeproject.org/experiments/ENCSR971MMF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR971MMF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB517HZF

source_name: Homo sapiens male adult (38 years) activated CD8-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours

value: primary cell

value: 38 year

value: John Stamatoyannopoulos, UW

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour;

value: ENCBS473HLX at ENCODE; https://www.encodeproject.org/ENCBS473HLX/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCLB688ATC)

description:
https://www.encodeproject.org/experiments/ENCSR250GDW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR250GDW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB688ATC

source_name: Homo sapiens female adult (26 years) CD4-positive, alpha-beta T primary cell treated with Interleukin-4 for 1 hour

value: CD4-positive, alpha-beta T cell

value: female

value: 26 year

value: Shelly Heimfeld

value: treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS830YCO at ENCODE; https://www.encodeproject.org/ENCBS830YCO/

value: Derived from ENCODE donor ENCDO134JGU; https://www.encodeproject.org/ENCDO134JGU/


title: IP-93T449-BG4_rep1

status: Public on Apr 26 2021

city: Planegg-Martinsried

first: Filippo M.

last: Cernilogar

address: Grosshaderner Strasse 9

department: Biomedical Center

country: Germany

institute: LMU Munich

description: 93T449 cell line was established from a well-differentiated liposarcoma from the retroperitoneum of a 68 year old female.

data_processing:
reads were mapped to the human genome (hg38) using bowtie (Langmead et al., 2009).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files were generated from Homer tag directories using makeBigWig.pl

growth_protocol:
93T449 cells were seeded in T75 flasks in the presence of RPMI 1640 Medium supplemented with 10 % FBS and grown to 80 % confluence.
93T449 cells were routinely subcultured with a 1:2 to 1:4 ratio using Trypsin-EDTA solution and typically kept into a T75 flask of uncoated plastic in RPMI 1640 medium (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% heat inactivated FBS.

extract_protocol:
2 million cells were fixed in RPMI containing 1 % (v/v) formaldehyde (Thermo Scientific™ Pierce™  #28906) and 10 % (v/v) FBS for 10 min at RT. After 5 min quenching with 125 mM glycine, cells were pelleted and washed twice with PBS containing 10 % FBS. The flash frozen pellets were lysed for 5 min on ice in 100 μl of 50 mM tris-HCl pH 8.0, 10 mM EDTA, 0.5 % SDS and protease inhibitor cocktail. Samples were sonicated using the Covaris E220 to shear chromatin to an average size of 100-500 bp (2 % duty cycle, 105 W peak incident power, 200 cycles per burst, 25 min). Sheared chromatin was diluted 1:5 in IP-buffer (10 mM Tris-HCl pH 7.5, 1mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1 % SDS, 0.1 % Na-deoxycholate and 140 mM NaCl) supplemented with protease inhibitor cocktail. After centrifuging 10 min at 13,000g at 4 °C, the supernatant containing soluble chromatin fraction was recovered and incubated with 0.7 mg/ml RNase A (Thermo Scientific™ #EN0531) for 30 min at 37 °C. For chromatin immunoprecipitation 10 μl protein-G magnetic beads (Thermo Scientific™  Pierce™  #88848) were washed in IP-buffer and incubated with 1 μg Anti-FLAG Ab (Sigma-Aldrich #F3165) for 1 h at 4 °C on a rotating wheel. 50 μl of RNA digested chromatin were incubated with 250 ng BG4 Ab (or without for the mock negative control) for 1h at 16 °C. The anti-FLAG coated beads were washed with IP-buffer and incubated with chromatin-BG4 complex for 3 h at 4 °C on a rotating wheel. Beads were washed 4 times with IP-buffer and once in wash buffer (10 mM Tris-HCl pH 8.0, 10 mM EDTA). Elution of immonoprecipitates and chromatin crosslink reversal were performed incubating beads with 70 μl elution buffer (10 mM Tris-HCl pH 8.0, 5 mM EDTA, 300 mM NaCl and 0.5 % SDS) containing 0.3 mg/ml RNase A (Thermo Scientific™ Pierce™ #EN0531) for 30 min at 37 °C followed by the addition of 0.5 mg/ml proteinase K for 1h at 55 °C and 8 h at 65 °C shaking. Supernatant was then recovered and incubated for 1 additional h at 55 °C in the presence of 0.25 mg/ml proteinase K (Thermo Scientific™ #EO0491). The eluate was finally purified with SPRI AMPure XP beads (Beckman Coulter #A63881).
NEBNext Ultra II DNA library Prep Kit for Illumina, NEB

tag: cell line

value: BG4 (in house purified from BG4 encoding plasmid pSANG10-3F-BG4 transformed into BL21(DE3)).


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB735XVC)

description:
https://www.encodeproject.org/experiments/ENCSR226LVB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR226LVB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-23
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB735XVC

source_name: Homo sapiens male adult (42 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 100 ng/mL Interleukin-4 for 48 hours

value: male

value: adult

tag: age

value: 42 year

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS671KXW at ENCODE; https://www.encodeproject.org/ENCBS671KXW/

value: Derived from ENCODE donor ENCDO833KUM; https://www.encodeproject.org/ENCDO833KUM/