title: ATAC-seq_shRNA-2_SD-3

city: Durham

first: Suzanne

middle: Bartholf

last: DeWitt

state: NC

address: 308 Research Dr.

institute: Duke University

description:
DifferentialChromatinOpenness.xlsx
SD-3

data_processing:
RNA-Seq data and ATAC-Seq data were processed using the TrimGalore toolkit which employs Cutadapt to trim low quality bases and Illumina sequencing adapters from the 3’ end of the reads.  Only reads that were 20nt or longer after trimming were kept for further analysis.
RNA-Seq Reads were mapped to the GRCh37v75 version of the human genome and transcriptome.  ATAC-Seq reads were mapped to the hg19 version of the human genome using the bowtie alignment tool.
For RNA-Seq, gene counts were compiled using the HTSeq tool. Only genes that had at least ten reads in any given library were used in subsequent analysis.
Normalization and differential expression were carried out using the DESeq2 Bioconductor package with the R statistical programming environment.  The false discovery rate was calculated to control for multiple hypothesis testing.
For ATAC-Seq, reads were kept for subsequent analysis if they mapped to a single genomic location.  Amplification artifacts were removed using the Picard toolkit
Regions of open chromatin regions were called using the MACS2 peak calling algorithm. The peaks were set to a 300nt window surrounding the mode location.  Peaks that overlapped across the two conditions being compared were merged into a single peak.
The number of reads from each individual sample that overlapped the peaks were quantified.  Normalization and differential openness of chromatin regions were calculated using the DESeq2 Bioconductor package with the R statistical programming environment. Peaks were then annotated with their nearest gene using the GRCh37v758 of the human transcriptome.
Genome_build: hg19
Supplementary_files_format_and_content: NarrowPeak files
Supplementary_files_format_and_content: Excel spreadsheet showing RNA-Seq read counts, adjusted p values, logFC comparisons of cell types
Supplementary_files_format_and_content: Excel spreadsheet showing ATAC-Seq peak locations and Log2FC comparisons across cell types.

source_name: 143B human OS cell line

growth_protocol: All cells were cultured in DMEM supplemented with 10% FBS and 1% Pen-Strep.  Cells were incubated at 37°C and 5% CO2 in a humidified incubator.

extract_protocol:
All cell types were plated in triplicate at 1 X 10^6 cells/well in 6-well culture plates.  Cells were trypsinized and counted.  16,667 cells from each cell type's 3 wells were combined to have 50,000 cells per cell type for DNA extraction for ATAC-Seq.  The remaining cells underwent RNA extraction using the ReliaPrep RNA Cell Miniprep System (Promega; catalog #Z6012).  Cells for ATAC-Seq were lysed, and the Nextera DNA Library Prep Kit was used for transposition.  DNA was purified using the Qiagen MinElute Reaction Cleanup Kit.  PCR Amplification was performed using the NEBNext High-Fidelity 2x PCR Master Mix.  AMPure XP beads were used for library purification.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 143B human osteosarcomas cells were stably transduced with either a non-silencing GFP shRNA or one of two independent shRNA constructs targeting ATRX

tag: cell line

value: human osteosarcoma cell line

value: shRNA knockdown of ATRX- construct 2


title: JGES-D7 [RNA-Seq]

status: Public on Oct 12 2022

type: SRA

city: Guangzhou

first: Li

last: Chen

state: Guangdong province

address: 190 Kai Yuan Avenue, Science Park

country: China

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
raw counts was generated by RSEM (v. 1.2.28)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: MEF cells after induction

growth_protocol: MEF cells cultured in 10%FBS, infected with WT/N12 Jdp2, Esrrb, Glis1 and WT/K5A Sall4 by retro-virus. Then change medium to iCD3 for induction

extract_protocol:
Total RNA was isolated with TRIzol (Invitrogen).
Libraries were prepared using the VAHTS mRNA-seq v2 Library Prep Kit for Illumina (Vazyme, NR601-01/02,) with 1 µg RNA per sample following the manufacturer’s instruction

treatment_protocol: knockdown Chd4 or Gatad2b by shRNA

tag: system

value: JGES

tag: time after induction


title: C_c_EPS_B5_7

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
1) RNAseq raw reads (~36.8 M/sample) were aligned to human genome (Ensembl GRCh38, release 98) using STAR v2.7.2b resulting in ~28 M/sample uniquely aligned reads.
2) Gene read coverages (~23.7 M/sample) were computed with featureCounts v1.6.2 using same human genome annotation.
3) Differential expression analysis was performed using edgeR v3.28.1 with "y ~ 0 + group" design (group represents the combinations of "Disease", "EPS treatment" and "Hormone treatment" together) while filtering low count reads using built-in function filterByExpr (n = 19,231 genes) and blocking for "Patient ID"s with voomLmFit function.
Assembly: hg38
Supplementary files format and content: counts.tsv.gz: Text file in tab separated format with gene coverages in units of read counts
Supplementary files format and content: logCPM_filtered_batchCorrected.tsv.gz: Text file in tab separated format with gene coverages in units of log2 counts per million (CPM). The logCPM values are batch corrected for "Patient IDs". See "data processing step 3" for details.

organism: Homo sapiens

source_name: myotubes obtained from vastus lateralis

growth_protocol: Myotubes were grown in α-MEM with 10% v/v fetal bovine serum, 0.5% v/v penicillin-streptomycin and 0.5% v/v amphotericin B, and later differentiated for 6 days in α-MEM with 2% v/v horse serum, 0.5% v/v penicillin-streptomycin and 0.5% v/v amphotericin B

extract_protocol:
RNA was extracted using Qiagen AllPrep DNA/RNA/miRNA universal kit (Qiagen)
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold

treatment_protocol: Treaments were applied following differentation: i) non-treated control (no treatment and no EPS); ii) TGFβ1 (5 ng/ml); iii) AMH (30 ng/ml); iv) EPS; v) EPS+TGFβ1 (5 ng/ml) and vi) EPS+AMH (30 ng/ml).  In conditions where EPS and hormone treatment were combined, the treatment (TGFB1, AMH) was applied for 16 hours then cells were washed with PBS before fresh serum free media was added and the 6 hours of EPS was applied.

tag: group

tag: participant id

tag: disease

value: CTRL

tag: eps treatment

value: EPS

tag: hormone treatment

value: tgfb

tag: cell type

value: myotubes

tag: gender

value: female

tag: age

tag: height (m)

tag: weight (kg)

tag: body mass index (kg/m2)

tag: body fat (%)

tag: lean mass (%)


title: shChd4-JGES-D0-1 [RNA-Seq]

tag: knockdown


title: ATAC-seq_shRNA-1_SD-2

country: USA

description:
DifferentialChromatinOpenness.xlsx
SD-2

library_source: genomic

molecule: genomic DNA

tag: cell line

tag: treatment

value: shRNA knockdown of ATRX- construct 1


title: C_c_EPS_B5_6


title: ATAC-seq_Non-silenced control_SD-1

description:
DifferentialChromatinOpenness.xlsx
SD-1

value: Non-silenced (GFP) control


title: YMC-084

type: RNA

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

country: Japan

institute: Toray Industries, Inc.

description: miRNA

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetected) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

source_name: serum:urothelial cancer

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: tissue

value: serum

tag: disease status

value: UC


title: YMC-083

description: miRNA


title: C_c_EPS_B5_5

tag: group

tag: participant id


title: C_c_pre_4_CTRL

tag: disease

tag: eps treatment

value: noEPS


title: JGES-D5 [RNA-Seq]

tag: system

tag: time after induction


title: JGES-D3 [RNA-Seq]


title: ATAC-seq_shRNA-2_SD12

description:
DifferentialChromatinOpenness.xlsx
SD12

tag: cell type


title: ATAC-seq_shRNA-1_SD11

description:
DifferentialChromatinOpenness.xlsx
SD11


title: JGES-D1 [RNA-Seq]


title: C_c_EPS_B5_4

tag: hormone treatment

tag: gender

tag: age

tag: height (m)


title: YMC-082

description: miRNA


title: YMC-085

description: miRNA


title: JGES-D1-2 [RNA-Seq]


title: YMC-081

description: miRNA


title: ATAC-seq_Non-silenced control_SD10

description:
DifferentialChromatinOpenness.xlsx
SD10


title: RNA-seq_shRNA-2 rep 3

description:
DifferentialExpression.xlsx
SD09


title: C_c_EPS_A30_7

value: amh

tag: weight (kg)

tag: body mass index (kg/m2)

tag: body fat (%)

tag: lean mass (%)


title: YMC-078

description: miRNA

tag: tissue


title: YMC-079

description: miRNA

tag: disease status


title: RNA-seq_shRNA-2 rep 2

description:
DifferentialExpression.xlsx
SD08

tag: cell line

tag: treatment


title: C_c_EPS_A30_6

tag: group

tag: participant id

tag: disease


title: C_c_EPS_B5_2

tag: eps treatment


title: JGES-D0 [RNA-Seq]

tag: system

tag: time after induction


title: YMC-077

description: miRNA


title: JGES(K5A)-D7-3 [RNA-Seq]


title: RNA-seq_shRNA-2 rep 1

description:
DifferentialExpression.xlsx
SD07

tag: cell type


title: JGES(K5A)-D7-1 [RNA-Seq]


title: RNA-seq_shRNA-1 rep 3

description:
DifferentialExpression.xlsx
SD06


title: C_c_EPS_A30_5

tag: hormone treatment

tag: gender

tag: age


title: C_c_EPS_A30_4

tag: height (m)

tag: weight (kg)

tag: body mass index (kg/m2)


title: RNA-seq_shRNA-1 rep 2

description:
DifferentialExpression.xlsx
SD05


title: YMC-075

description: miRNA

tag: tissue


title: C_c_EPS_A30_2

tag: body fat (%)

tag: lean mass (%)


title: RNA-seq_shRNA-1 rep 1

description:
DifferentialExpression.xlsx
SD04

tag: cell line

tag: treatment


title: YMC-076

description: miRNA

tag: disease status


title: JGES(K5A)-D3-3 [RNA-Seq]


title: JGES(K5A)-D5-2 [RNA-Seq]


title: YMC-074

description: miRNA


title: RNA-seq_Non-silenced control rep3

description:
DifferentialExpression.xlsx
SD03


title: JGES(K5A)-D3-1 [RNA-Seq]


title: RNA-seq_Non-silenced control rep2

description:
DifferentialExpression.xlsx
SD02


title: C_c_EPS_5

tag: group

tag: participant id

tag: disease


title: YMC-073

description: miRNA


title: JGES(K5A)-D1-3 [RNA-Seq]

tag: system

tag: time after induction


title: YMC-071

description: miRNA


title: YMC-072

description: miRNA


title: RNA-seq_Non-silenced control rep1

description:
DifferentialExpression.xlsx
SD01

tag: cell type


title: C_c_EPS_4

tag: eps treatment

tag: hormone treatment

tag: gender


title: YMC-070

description: miRNA


title: JGES(K5A)-D1-2 [RNA-Seq]


title: JGES(K5A)-D1-1 [RNA-Seq]


title: C_c_EPS_2

tag: age

tag: height (m)

tag: weight (kg)


title: YMC-069

description: miRNA

tag: tissue


title: C_c_EPS_6

tag: body mass index (kg/m2)

tag: body fat (%)

tag: lean mass (%)


title: JGES(K5A)-D5-1 [RNA-Seq]


title: Day 6, elongated, batch 1

city: Lausanne

first: Matthias

last: Lütolf

address: AI 1208 Station 15

department: Sciences de la vie

country: Switzerland

institute: EPFL

description:
10x Genomics
D6_barcodes.tsv.gz
D6_features.tsv.gz
D6_matrix.mtx.gz
D6_metadata.tsv.gz

library_source: transcriptomic single cell

data_processing:
alignment with cellranger v3.1
Genes expressed in fewer than three cells and in cells with less than 200 features expressed were removed. Cells with unique feature counts between 3000 and 10,000, and less than 10% mitochondrial counts were used for analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: Elongated neural tube organoid cultured in Matrigel drop for 6 days

growth_protocol: mESCs were collected by washing with PBS and dissociating with Accutase for 2 min at room temperature. The cell suspension was collected in a centrifuge tube and was centrifuged at 200 g for 5 min. After centrifugation, the cell pellet was resuspended in 1 ml of 10% serum medium and the cells were counted with a hemocytometer. After cell counting, the cells were washed twice with PBS and were resuspended in N2B27 (47.4% Neurobasal medium, 47.4% DMEM/F-12 with 2.50 mM GlutaMAX, 1 mM GlutaMAX supplement, 100 U/ml penicillin, 100 μg/ml streptomycin, 0.1 mM NEAA, 1 mM sodium pyruvate, 0.1 mM β-ME, 1% B27 supplement and 0.5% N-2 supplement) and embedded in Matrigel to a final concentration of 1125 cells/10 μl drop of Matrigel for SBr. 10 μl of the resulting Matrigel embedded cell suspension were deposited in each well of a 24-well plate (Corning). The cells in each well were cultured in 500 μl of Epi medium [N2B27 supplemented with 12 ng/ml basic fibroblast growth factor (bFGF, Thermofisher, PMG0031) and 20 ng/ml activin-A (R&D Systems, 338-AC-010)] for the first 3 days. On D3, the Epi medium of each well was substituted with 1 ml of N2B27. The medium of each well was substituted with 1 ml of N2B27 on D5 and the cells were cultured until D6. For maturation of the neural tube organoid, the organoids were harvested on D6 by washing the Matrigel drops with organoids once with PBS and then treating with 3 mg/ml collagenase IV and 1 mg/ml dispase in HBSS+/+ for 30 min on a shaker to dissolve the Matrigel. After Matrigel was dissolved, the organoids were collected with cut 1000 μl pipette tips coated with 10% serum and centrifuged at 150 g for 5 min. The supernatant was removed and the organoids were suspended in N2B27 medium. The organoids were collected and re-embedded in 10 μl of Matrigel (1 organoid/drop), plated on glass-bottomed 96-well plate and further cultured in 100 μl of N2B27 medium in 5% CO2 and 37°C incubator, and the medium was changed every day.

extract_protocol:
The sample preparation was performed according to the instructions from 10X Genomics Single Cell Protocols (10X Genomics), with some modification. The collected organoids (100 organoids per condition) were washed twice with PBS and trypsinized with TrypLE Express (Gibco, 12605-028) for 7 min in 37°C. The organoids were dissociated into single cells by pipetting up and down with a 1000 μl pipette tip, strained using 40 μm cell strainer and collected in 1.5 μl microcentrifuge tube. Those single cells were centrifuged at 300 g for 5 min and resuspended in 1 ml of PBS with 0.04% BSA after removing the supernatant. The cell concentration was then determined. After the same centrifugation step was repeated, the cells were resuspended in PBS with 0.04% BSA to achieve a final cell concentration of 1 million cells/ml. After the trypsinization, the cells were always placed on ice.
Reverse transcription and library preparation were performed using the Single Cell 3′ Reagent Kit v3 (10X Genomics), following the 10X Genomics protocol.

tag: cell line

value: Sox1::eGFP;Bra::mCherry mESCs

value: Mouse embryonic stem cell (mESCs)


title: NKR-P1B KO2 reads

city: Halifax

first: Andrew

middle: P.

last: Makrigiannis

state: ON

address: 5850 College Street, Room 7-C

department: Microbiology/Immunology

country: Canada

institute: Dalhousie University

data_processing:
OpenGalaxy software suite was used for all analysis
Trimmomatic used to trim off Illumina paired end reads
Cufflinks used to align and annotate and trimmed sequences to reference genome
cuffdiff used to assemble and normalize cufflink annotated sequences. Differential expresssion testing performemd to look for significant differences between WT and NKR-P1B KO condition
Assembly: mm10
Supplementary files format and content: single tab delimited csv spreadsheet containing FPKM values for each gene and the gene short name. every condition and replicate is labelled and included in the spreadsheet for easy browsing and sorting either by name or FPKM

source_name: lung

extract_protocol:
RNA harvested using trizol combined with Zymo Research RNA clean and concentrator kit, 1ug of RNA was used for library construction
RNA libraries were prepared in-house by Genome Quebec

value: lung

value: primary cells

value: alveolar macrophages

tag: genotype

value: NKR-P1B KO


title: JGES(K5A)-D0-1 [RNA-Seq]


title: NKR-P1B KO3 reads


title: JGES(K5A)-D0-3 [RNA-Seq]


title: C_c_B5_7

tag: group

tag: participant id

value: CTRL


title: C_c_EPS_7

tag: disease

value: EPS


title: KCC-029

description: miRNA

tag: disease status


title: C_c_B5_6

value: tgfb

tag: cell type


title: YMC-068

description: miRNA


title: YMC-067

description: miRNA


title: JGE-D7 [RNA-Seq]

tag: system

value: JEG

tag: time after induction


title: C_c_B5_4

tag: eps treatment

tag: hormone treatment

value: myotubes

tag: gender

value: female


title: WT 3 reads

value: WT


title: JGE-D5 [RNA-Seq]


title: C_c_B5_2

tag: age

tag: height (m)

tag: weight (kg)


title: JGE-D3 [RNA-Seq]


title: Day 6, non-elongated

source_name: Non-elongated neural tube organoid cultured in Matrigel drop for 6 days

tag: tissue


title: WT 2 reads


title: C_c_A30_7

tag: body mass index (kg/m2)

tag: body fat (%)

tag: lean mass (%)


title: JGE-D0 [RNA-Seq]


title: C_c_A30_5

tag: group


title: WT 1 reads

tag: cell line

tag: genotype


title: YMC-062

description: miRNA

value: serum

tag: disease status


title: YMC-065

description: miRNA

value: UC


title: JGE-D1 [RNA-Seq]


title: NKR-P1B KO1 reads

tag: cell type


title: D11-M2

city: Biberach

first: Meshal

last: Ansari

address: Birkendorfer Straße 65

country: Germany

institute: Boehringer Ingelheim

description:
Drop-seq
muc9232

data_processing:
For preprocessing of the single cell data of mouse lung tissue cells, the Dropseq computational pipeline was used (version 2.3.0) as previously described (Pubmed ID: 26000488). Briefly, STAR (version 2.5.3a) was used for mapping. Reads were aligned to the mm10 reference genome (GSE63269). For barcode filtering, we excluded barcodes with less than 200 genes detected. A high proportion (> 20%) of transcript counts derived from mitochondria-encoded genes may indicate low cell quality, and we removed these unqualified cells from the downstream analysis.   he Dropseq computational pipeline was used (version 2.0) as previously described (Pubmed ID: 26000488). Briefly, STAR (version 2.5.3a) was used for mapping. Reads were aligned to the mm10 reference genome (GSE63269). Downstream analysis was performed using the scanpy package (v1.6.0). The top 5000 cells with the highest number of transcripts were read in per sample and subjected to quality control. We excluded barcodes with less than 200 genes detected and retained those with a number of transcripts between 200 to maximal 6000 and a percentage of mitochondria-encoded genes of less than 10%.  To mitigate effects of background mRNA contamination, we employed the R library SoupX. We manually set the contamination fraction to 0.3 and corrected the count matrices with adjustCounts().
Assembly: mm10
Supplementary files format and content: Raw count matrix (MyofibroConvrsion_raw_counts.mtx) from Drop-seq experiments with 6866 genes and 68882 cells in market matrix format and corresponding column (MyofibroConversion_genes.txt) and row (MyofibroConversion_barcodes.txt) labels. Cell-level metadata (MyofibroConversion_metadata.txt).

source_name: Lung tissue

extract_protocol:
Enrichment for mesenchymal cells was carried out by negative selections using Magnetc-activated cell sorting (MACS). Cells were aliquoted in PBS supplemented with 0.04% of bovine serum albumin at a final concentration of 100 cells/µl. Using the microfluidic device, single cells (100/µl) were co-encapsulated in droplets with barcoded beads (120/µl, purchased from ChemGenes Corporation, Wilmington, MA) at rates of 4000 µl/hr. Droplet emulsions were collected for 10-20 min/each prior to droplet breakage by perfluorooctanol (Sigma-Aldrich). After breakage, beads were harvested and the hybridized mRNA transcripts reverse transcribed (Maxima RT, Thermo Fisher). Unused primers were removed by the addition of exonuclease I (New England Biolabs), following which, beads were washed, counted, and aliquoted for pre-amplification (2000 beads/reaction, equals ca. 100 cells/reaction) with 12 PCR cycles (Smart PCR primer: AAGCAGTGGTATCAACGCAGAGT (100 μM), 2x KAPA HiFi Hotstart Ready-mix (KAPA Biosystems), cycle conditions: 3 min 95°C, 4 cycles of 20s 98°C, 45s 65°C, 3 min 72°C, followed by 8 cycles of 20s 98°C, 20s 67°C, 3 min 72°C, then 5 min at 72°C).
PCR products of each sample were pooled and purified twice by 0.6x clean-up beads (CleanNA), following the manufacturer’s instructions. Prior to tagmentation, complementary DNA (cDNA) samples were loaded on a DNA High Sensitivity Chip on the 2100 Bioanalyzer (Agilent) to ensure transcript integrity, purity, and amount. For each sample, 1 ng of pre-amplified cDNA from an estimated 1000 cells was tagmented by Nextera XT (Illumina) with a custom P5-primer (Integrated DNA Technologies). Single-cell libraries were sequenced in a 100 bp paired-end run on the Illumina HiSeq4000 using 0.2 nM denatured sample and 5% PhiX spike-in. For priming of read 1, 0.5 μM Read1CustSeqB was used (primer sequence: GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC).

treatment_protocol: Mice were randomly divided into two groups: saline-only (PBS), or bleomycin (Bleo). Lung injury and pulmonary fibrosis were induced by single-dose administration of bleomycin hydrochloride (Sigma Aldrich, Germany), which was dissolved in sterile PBS and given at 2U/kg bodyweight by oropharyngeal instillation. The control group was treated with sterile PBS only. Mice were randomly sacrificed at designated time points  after instillation.

value: Lung tissue

tag: treatment

value: Bleo

tag: time point

value: day 11

tag: number of cells


title: YMC-080

description: miRNA


title: C_c_A30_4

tag: participant id

tag: disease

tag: eps treatment

value: noEPS

tag: hormone treatment

value: amh


title: YMC-059

description: miRNA


title: D21-M

description:
Drop-seq
muc9231

value: day 21


title: C_c_A30_6

tag: gender

tag: age

tag: height (m)

tag: weight (kg)


title: JEGS_Minus_Sall4_D7 [RNA-Seq]

tag: system

tag: time after induction


title: JEGS_Minus_Sall4_D6 [RNA-Seq]


title: YMC-060

description: miRNA

tag: tissue


title: D8-M2

description:
Drop-seq
muc9230

value: day 8


title: YMC-066

description: miRNA


title: YMC-058

description: miRNA


title: C_c_A30_2

tag: group

tag: body mass index (kg/m2)

tag: body fat (%)

tag: lean mass (%)


title: D6-M1

description:
Drop-seq
muc9229

tag: treatment

tag: time point

value: day 6


title: JEGS_Minus_Sall4_D5 [RNA-Seq]


title: JEGS_Minus_Sall4_D4 [RNA-Seq]


title: NB4_MZ1_2

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: NB4 sample with MZ1

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: treat


title: JEGS_Minus_Sall4_D3 [RNA-Seq]


title: D8-M1

description:
Drop-seq
muc9228

tag: number of cells


title: NB4_MZ1_1


title: JEGS_Minus_Sall4_D1 [RNA-Seq]


title: NB4_NC_2

source_name: NB4 sample with no treatment


title: NB4_NC_1


title: D10-M1

description:
Drop-seq
muc9225

value: day 10


title: D2-M1

description:
Drop-seq
muc9227

value: day 2


title: JEGS_Minus_Sall4_D2 [RNA-Seq]


title: 356258

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

data_processing:
Base calls were generated in real-time on the NovaSeq6000 instrument (RTA 3.1.5); (2) demultiplexed, unaligned BAM files produced by Picard ExtractIlluminaBarcodes and IlluminaBasecallsToSam are converted to FASTQ format using SamTools bam2fq (v1.4); (3) sequence read and base quality are checked using the FASTX-toolkit (v0.0.13); (4) sequences are aligned to GRCh38 with reference transcriptome GENCODE release 29 using STAR (v2.6.1d) and RSEM (v1.3.1).
Briefly, 100bp paired-end reads were trimmed and aligned to the GENCODE reference transcriptome using STAR and reads were quantified using HT-Seq. Gene counts were generated for each sample and collated into a singular matrix for fixed-effects regression model in DESeq2.
Genome_build: GrCh38, GENCODE release 29
Supplementary_files_format_and_content: "Pheno.csv" contains sample metadata, "counts.csv" contains raw counts, "SummaryStats.csv" contains the number and percentages of reads mapped for each sample

source_name: Colon Organoid

growth_protocol: Normal 3D colon organoids included in the study were developed from biopsies of either distal or proximal colon using a modification of the method described by Sato et al. After isolation, colon crypts were embedded in Matrigel, and cell lines were established in growth media that included: advanced DMEM/F-12, 100U/ml penicillin, 100μg/ml streptomycin, 10mM Hepes, 1x N2, 1x B27, 2mM GlutaMAX, 1mM N-acetyl-cysteine, 10mM gastrin, 50% L-WRN conditioned media, 500nM A83-01, 10uM SB202190, 10mM nicotinamide, 50ng/ml EGF, 10μM Y27632. Colon organoids were grown and passaged as needed in 48-well culture plates.

extract_protocol:
For RNA isolation, media was gently removed and 300μl RNA lysis Solution RA1 + 6μl TCEP (Machery-Nagel; Cat No: 740902.50) was added to each well. The lysate was collected in a 1.5ml Eppendorf tube. Each tube was vortexed vigorously and placed on ice. Further steps were carried out according to manufacturer’s protocol of the Machel-Nagel RNA XS kit. RNA was checked for quality using the Agilent 4200 Tapestation. Samples with RIN > =8.5 were considered for library preparation and sequencing using the Illumina NovoSeq
Total RNA is normalized to 7.5ng/ul in a total volume of 50ul on the Perkin Elmer Janus Workstation (Perkin Elmer, Janus II).  Poly-A selection and cDNA synthesis are performed using the TruSeq Stranded mRNA kit as outlined by the manufacturer (Illumina, cat#RS-122-2103).  All steps are automated on the Perkin Elmer Sciclone NGSx Workstation to reduce batch to batch variability and to increase sample throughput.  Final RNASeq libraries are quantified using the Quant-it dsDNA High Sensitivity assay, and library insert size distribution is checked using a fragment analyzer (Advanced Analytical; kit ID DNF474).  Samples where adapter dimers constitute more than 4% of the electopherogram area are failed prior to sequencing.  Technical controls (K562,Thermo Fisher Scientific, cat# AM7832), are compared to expected results to ensure that batch to batch variability is minimized.  Successful libraries are normalized to 10nM for submission to sequencing.
Libraries were multiplexed and sequenced on Illumina Novaseq6000 to generate 100bp PE reads.

treatment_protocol: One day prior to initial exposure, all organoids were passaged and grown for 24 hours in standard growth media with an ambient calcium concentration of 1.66mM. After 24 hours, one set of 3D colon organoids per subject was selected for higher calcium treatment. Standard growth media was removed from wells of the treatment group and replaced with growth media fortified with 3.34mM additional calcium chloride to bring the total calcium concentration in the media to 5mM. This concentration was based on prior studies of human colonic epithelial cells in culture in which calcium was shown to have antiproliferative effects at a concentration of 2.2mM in the absence of other additives and 10mM in the presence of butyrate and deoxycholic acid17-19. The other set of colon organoids were maintained at an ambient calcium concentration of 1.66mM. Both sets of organoids (i.e., lower and higher calcium concentrations) were grown for 72 hours under experimental conditions.

tag: cell type

value: Colon Organoid

tag: Sex

value: treated

tag: pair

value: right

tag: smoking

value: former


title: 356257

value: female

value: control

tag: age


title: YMC-054

description: miRNA

value: serum

tag: disease status

value: UC


title: YMC-056

description: miRNA


title: YMC-053

description: miRNA


title: JEGS_Minus_Sall4_D0 [RNA-Seq]

tag: system

value: JEG

tag: time after induction


title: JEGS_Minus_Jdp2_D7 [RNA-Seq]

value: EGS


title: D3-M2

description:
Drop-seq
muc9223

tag: tissue

value: Lung tissue

value: Bleo

value: day 3


title: D9-M1

description:
Drop-seq
muc9222

value: day 9


title: JEGS_Minus_Jdp2_D6 [RNA-Seq]


title: YMC-052

description: miRNA


title: YMC-055

description: miRNA


title: YMC-050

description: miRNA


title: YMC-051

description: miRNA


title: 356255

value: left

value: never


title: D7-M1

description:
Drop-seq
muc9226

value: day 7


title: JEGS_Minus_Jdp2_D5 [RNA-Seq]


title: 356254

value: Colon Organoid


title: YMC-048

description: miRNA


title: D10-M2

description:
Drop-seq
muc9221

value: day 10


title: JEGS_Minus_Jdp2_D4 [RNA-Seq]


title: 356253

value: right


title: D14-M2

description:
Drop-seq
muc9224

value: day 14


title: D3-M1

description:
Drop-seq
muc9220


title: YMC-047

description: miRNA


title: YMC-046

description: miRNA


title: JEGS_Minus_Jdp2_D3 [RNA-Seq]


title: 356256

value: female

value: treated


title: JEGS_Minus_Jdp2_D2 [RNA-Seq]


title: 356249

value: control


title: D5-M2

description:
Drop-seq
muc9219

value: day 5


title: 356250


title: D36-M2

description:
Drop-seq
muc9218

value: day 36


title: KCC-043

description: miRNA

value: serum

value: UC


title: YMC-049

description: miRNA


title: JEGS_Minus_Jdp2_D1 [RNA-Seq]

value: EGS


title: JEGS_Minus_Jdp2_D0 [RNA-Seq]


title: D5-M1

description:
Drop-seq
muc9217

value: Lung tissue

value: Bleo


title: 356248

value: male

value: left


title: D12-M1

description:
Drop-seq
muc9216

value: day 12


title: JEGS_Minus_Glis1_D7 [RNA-Seq]

value: JES


title: KCC-042

description: miRNA


title: KCC-039

description: miRNA


title: 356246

value: Colon Organoid

value: never


title: D36-M1

description:
Drop-seq
muc9215


title: JEGS_Minus_Glis1_D6 [RNA-Seq]


title: KCC-038

description: miRNA


title: D13-M1

description:
Drop-seq
muc9214

value: day 13


title: KCC-037

description: miRNA


title: JEGS_Minus_Glis1_D5 [RNA-Seq]


title: 356245

value: female

value: right


title: 356244

value: treated


title: KCC-036

description: miRNA


title: D12-M2

description:
Drop-seq
muc9213


title: JEGS_Minus_Glis1_D4 [RNA-Seq]


title: D4-M2

description:
Drop-seq
muc9212

value: day 4


title: 356243

value: control


title: JEGS_Minus_Glis1_D3 [RNA-Seq]


title: 356247


title: JEGS_Minus_Glis1_D2 [RNA-Seq]


title: 356242


title: KCC-032

description: miRNA

value: serum


title: 356241


title: JEGS_Minus_Glis1_D1 [RNA-Seq]


title: D28-M

description:
Drop-seq
muc9210

value: day 28


title: KCC-028

description: miRNA

value: UC


title: KCC-031

description: miRNA


title: 356240


title: D7-M2

description:
Drop-seq
muc9209

value: Lung tissue

value: day 7


title: JEGS_Minus_Glis1_D0 [RNA-Seq]


title: 356239

value: male


title: KCC-027

description: miRNA


title: 356238

value: former


title: JEGS_Minus_Esrrb_D6 [RNA-Seq]

value: JGS


title: KCC-033

description: miRNA


title: KCC-026

description: miRNA


title: 356237


title: D14-M1

description:
Drop-seq
muc9211

value: Bleo

value: day 14


title: JEGS_Minus_Esrrb_D4 [RNA-Seq]


title: NC-M2

description:
Drop-seq
muc9206

value: PBS

value: day 0


title: D13-M2

description:
Drop-seq
muc9207

value: day 13


title: 356236

value: Colon Organoid

value: left


title: JEGS_Minus_Esrrb_D5 [RNA-Seq]


title: D54-M2

description:
Drop-seq
muc9205

value: day 54


title: KCC-023

description: miRNA


title: JEGS_Minus_Esrrb_D3 [RNA-Seq]


title: D6-M2

description:
Drop-seq
muc9204

value: day 6


title: KCC-024

description: miRNA

value: serum


title: D4-M1

description:
Drop-seq
muc9208

value: day 4


title: KCC-025

description: miRNA

value: UC


title: JEGS_Minus_Esrrb_D7 [RNA-Seq]


title: KCC-022

description: miRNA


title: D2-M2

description:
Drop-seq
muc9203

value: Lung tissue

value: day 2


title: JEGS_Minus_Esrrb_D2 [RNA-Seq]


title: RNA-seq of adult Drosophila melanogaster epidermis [Dme_Epidermis_b]

city: Barcelona

first: Federica

last: Mantica

address: Dr. Aiguader 88

country: Spain

institute: CRG

description: Pooled epidermis from adult individuals

data_processing:
Estimated counts and TPMs were computed by Kallisto (v0.44.0)
Supplementary files format and content: Tab-delimited file with length, effective length, estimated counts and transcript per million (TPM) for all species protein coding genes in the relative GTF

organism: Drosophila melanogaster

source_name: Adult epidermis

extract_protocol:
Rneasy plus Mini Kit (Qiagen)
polyA-selected stranded RNA-seq; RNA libraries were prepared for sequencing using standard Illumina protocols

value: Epidermis

tag: genome build

tag: gtf

value: dm6 GTF (Ensembl Metazoa v26)


title: 356233

value: male

value: control

value: never


title: YMC-030

description: miRNA


title: 356234

value: treated


title: JEGS_Minus_Esrrb_D1 [RNA-Seq]

value: JGS


title: RNA-seq of adult Drosophila melanogaster epidermis [Dme_Epidermis_a]

description: Pooled epidermis from adult individuals


title: 356232

value: female


title: JEGS_Minus_Esrrb_D0 [RNA-Seq]


title: 356235

value: Colon Organoid

value: former


title: KCC-018

description: miRNA


title: JEGS_D7 [RNA-Seq]

value: JGES


title: KCC-004

description: miRNA


title: 356230

value: right


title: 356229


title: JEGS_D6 [RNA-Seq]


title: 356231

value: left


title: HESC-SI-2

city: fuzhou

first: yangfan

last: zhang

address: Fujian Normal University Qishan Campus, College Town, Fuzhou, Fujian Province

institute: FJNU

data_processing:
Quality control of raw data using fastp
Matching the raw data after QC to the reference genome
Use featureCounts to count the expression of sample genes and obtain the expression matrix
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: hESCs

growth_protocol: hESCs cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: GOLPH3 gene expression was interfered by siGOLPH3 plasmid transfection in hESCs cells, and empty vector was used as control.

value: hESCs

value: human endometrial stromal cells

tag: genotype

value: golph3 knockdown

value: decidualization


title: HESC-SI-1

tag: treatment


title: HESC-NC-3

value: wt


title: YMC-045

description: miRNA

value: serum

value: UC


title: JEGS_D4 [RNA-Seq]


title: 356228

value: male

value: current


title: HESC-SI-3


title: YMC-042

description: miRNA


title: C_c_B5_5

tag: group

tag: participant id

tag: disease

value: CTRL

tag: eps treatment

value: noEPS

tag: hormone treatment

value: tgfb

value: myotubes

tag: gender

tag: height (m)

tag: weight (kg)

tag: body mass index (kg/m2)

tag: body fat (%)

tag: lean mass (%)


title: JEGS_D5 [RNA-Seq]

tag: system

tag: time after induction


title: HESC-NC-2

tag: cell line

tag: cell type


title: YMC-041

description: miRNA

tag: tissue

tag: disease status


title: JEGS_D3 [RNA-Seq]


title: YMC-040

description: miRNA


title: HESC-NC-1

tag: genotype

tag: treatment


title: 356226

value: Colon Organoid

tag: Sex

value: female

value: treated

tag: pair

tag: age

tag: smoking


title: JEGS_D2 [RNA-Seq]

value: JGES


title: JEGS_D1 [RNA-Seq]


title: 356224

value: right

value: former


title: YMC-039

description: miRNA


title: YMC-038

description: miRNA


title: Cytotoxic T-cells baseline

city: Amsterdam

first: Alex

last: van Vliet

address: Plesmanlaan 121

department: Molecular Oncology & Immunology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
RNAseq data was aligned to hg38 with TopHat 2.1. Reads were counted with Icount, proprietary software based on HTSeq-count for uniquely mapped reads.
Differential expression analysis on baseline samples (cytotoxic T-cell-sensitive cell lines NCI-H358, EBC-1, NCI-H2122 and NCI-H441 versus resistant cell lines NCI-H460, NCI-H1975, LCLC-103H and A549) was performed with DESeq2 (version 1.32.0), using default settings. Only genes that had a minimum of 10 reads across the 8 samples used in the comparison were retained for the analysis. The deseq() function was used with default settings.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file with number of mapped reads per gene for each sample and gene annotation
Supplementary files format and content: Differential expression analysis result (Ensembl gene id, p-value, FDR, -log10(p-value), -log10(FDR), log2 fold change) with gene annotation

source_name: T-cells

growth_protocol: Cells were maintained in RPMI medium (21875034, Thermofisher) containing 1:200 of 50mg/ml hygromycin, 10% fetal bovine serum (3101120, Sigma) and 1:100 of 10000U/ml Penicillin-Streptomycin (15140-122, Invitrogen). All cell lines were checked for mycoplasma by monthly PCR analyses.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (74106, Qiagen), including an on-column DNase digestion (79254, Qiagen), according to the manufactures instructions. Quality and quantity of the total RNA was assessed by the 2100 Bioanalyzer using a Nano chip (Agilent, Santa Clara, CA). Total RNA samples having RIN>8 were subjected to library generation.
Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina Inc., San Diego, RS-122-2101/2) according to the manufacturer's instructions (Illumina, Document # 1000000040498 v00). Briefly, polyadenylated RNA from intact total RNA was purified using oligo-dT beads. Following purification the RNA was fragmented, random primed and reverse transcribed using SuperScript II Reverse Transcriptase (Invitrogen, part # 18064-014) with the addition of Actinomycin D. Second strand synthesis was performed using Polymerase I and RNaseH with replacement of dTTP for dUTP. The generated cDNA fragments were 3' end adenylated and ligated to Illumina paired-end sequencing adapters and subsequently amplified by 12 cycles of PCR. The libraries were analyzed on a 2100 Bioanalyzer using a 7500 chip (Agilent, Santa Clara, CA), diluted and pooled equimolar into a multiplex sequencing pool.

treatment_protocol: CD8+ T cells were isolated from PBMCs from buffy coats from healthy individuals, activated in a pre-coated plate with CD3 and CD28 antibodies (eBioscience, 5mg per well in 24-well plates) for 48h, and transduced with lentivirus encoding a MART-1-specific TCR (Vredevoogd et al., 2019). To determine T cell sensitivity, tumor cells were seeded into 12-well plates at 1.2x105 cells/well. T cells were added at a 1:1 ratio and incubated for 16 hours. After the co-culture, T cells were washed with PBS and cell survival was determined by fixing and Crystal violet staining.

value: T-cells

value: T-cell

tag: time

value: Baseline


title: Cytotoxic T-cells after 16 hours without cell line mixing


title: H1944 cells before T-cell exposure

source_name: Lung

value: Lung

value: NSCLC cell line (mesenchymal)


title: 356223

value: male

value: control


title: 356227

value: current


title: J(N12)GES(K5A)_D7 [RNA-Seq]


title: 356221

value: never


title: H2030 cells before T-cell exposure


title: H441 cells before T-cell exposure

value: NSCLC cell line (epithelial)


title: JEGS_D0 [RNA-Seq]


title: YMC-043

description: miRNA

value: serum

value: UC


title: 356220

value: Colon Organoid


title: 356222

value: female

value: treated


title: H2122 cells before T-cell exposure


title: J(N12)GES(K5A)_D5 [RNA-Seq]


title: YMC-035

description: miRNA


title: J(N12)GES(K5A)_D3 [RNA-Seq]


title: J(N12)GES(K5A)_D1 [RNA-Seq]


title: YMC-034

description: miRNA


title: H460 cells before T-cell exposure


title: YMC-036

description: miRNA


title: 356225

value: left


title: J(N12)GES(K5A)_D0 [RNA-Seq]


title: H4006 cells before T-cell exposure

value: NSCLC cell line (epithelial/mesenchymal)


title: 356218

value: right

value: former


title: H1975 cells before T-cell exposure

value: Baseline


title: YMC-037

description: miRNA


title: 356217


title: YMC-031

description: miRNA


title: JGES-D2-Jdp2-3Flag

data_processing:
Sequenced reads were aligned to the mouse reference genome (mm10) using Bowtie2 with the parameters: --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
sambamba was used to sort and remove duplicate reads with the following options: [XS] == null and not unmapped and not duplicate.
Alignment BAM files were transformed into read coverage files (bigWig format) using deepTools
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
Around 100,000 living cells were collected for each sample
ChIP-seq library construction was performed using Hyperactive In-Situ ChIP Library Prep Kit for Illumina（pG-Tn5）(Vazyme, TD901) and TruePrep Index Kit V2 for Illumina (Vazyme, TD202).

value: JGES

tag: chip antibody to


title: LCLC cells before T-cell exposure

value: Lung

value: NSCLC cell line (mesenchymal)


title: YMC-029

description: miRNA


title: JGES-D2-Sall4


title: 356215

value: control


title: JGES-D2-Glis1-HA


title: YMC-027

description: miRNA


title: 356216


title: EBC1 cells before T-cell exposure


title: JGES-D2-Gatad2b


title: 356219

value: male


title: 356214

value: never


title: YMC-032

description: miRNA


title: 356213


title: JGES-D1-Sall4-3Flag


title: JGES-D2-Esrrb

value: ESRRB


title: SW1573 cells before T-cell exposure


title: YMC-026

description: miRNA

value: serum


title: YMC-024

description: miRNA

value: UC


title: H520 cells before T-cell exposure

value: NSCLC cell line (epithelial)


title: H3122 cells before T-cell exposure


title: 356212

value: Colon Organoid

value: female


title: JGES-D1-H3K27ac


title: YMC-022

description: miRNA


title: 356211

value: left


title: JGES-D1-Gatad2b


title: H358 cells before T-cell exposure


title: 356210

value: treated


title: A549 cells before T-cell exposure


title: KCC-019

description: miRNA


title: 356206

value: right


title: 356209


title: KCC-020

description: miRNA


title: KCC-017

description: miRNA


title: JGES(K5A)-D1-Sall4-3Flag


title: JGES(K5A)-D1-H3K27ac


title: Cytotoxic T-cells after mixing with EBC1

source_name: T-cell

value: T-cell

value: T-cells


title: JGES(K5A)-D1-H3K27ac-2


title: 356205


title: 356204


title: H827 cells before T-cell exposure

value: Baseline


title: YMC-023

description: miRNA


title: KCC-016

description: miRNA


title: KCC-015

description: miRNA


title: JGES(K5A)-D1-Gatad2b


title: H1299 cells before T-cell exposure

value: Lung


title: Cytotoxic T-cells after mixing with H460

value: T-cell exposure


title: Cytotoxic T-cells after mixing with H3122


title: KCC-011

description: miRNA


title: 356203

value: control


title: J(N12)GES(K5A)-D1-JDP2-3F


title: 356200

value: male


title: Cytotoxic T-cells after mixing with H2030


title: JGES(K5A)-D1-JDP2-3F


title: shLuciferase-JGES-D7

description: shNuRD-RPKM.csv

data_processing:
aligned to the mouse genome assembly (mm10) using bowtie24 (v. 2.3.5.1) with the following options: -p 20 --very-sensitive -k 10
sambamba5 (v. 0.6.6) was used to sort and remove duplicate reads with the following options: [XS] == null and not unmapped and not duplicate
peaks were called using genrich (v. 0.6) with options: -j -y -r -m 30 -e MT -v -q 0.01
Then, peaks from different sample were merged to a peak set by DiffBind7 (v. 2.14.0) using RPKM
Assembly: mm10
Supplementary files format and content: Matrix table with RPKM
Supplementary files format and content: bigwig

extract_protocol:
Around 50,000 living cells were collected for each sample
ATAC-seq library construction was performed using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501-01) and TruePrep Index Kit V2 for Illumina (Vazyme, TD202).

value: JGES

tag: knockdown

value: Luciferase

value: MEF


title: Cytotoxic T-cells after mixing with H1944


title: KCC-008

description: miRNA

value: serum

value: UC


title: KCC-007

description: miRNA


title: shLuciferase-JGES-D5

description: shNuRD-RPKM.csv


title: 356199

value: Colon Organoid

value: never


title: 356198

value: female


title: KCC-013

description: miRNA


title: Cytotoxic T-cells after mixing with LCLC


title: shLuciferase-JGES-D3

description: shNuRD-RPKM.csv


title: Cytotoxic T-cells after mixing with H4006


title: 356197


title: KCC-006

description: miRNA


title: shLuciferase-JGES-D1

description: shNuRD-RPKM.csv


title: 356194

value: treated

value: left


title: Cytotoxic T-cells after mixing with H1299

value: T-cell


title: shGatad2b-JGES-D7

description: shNuRD-RPKM.csv


title: shLuciferase-JGES-D0

description: shNuRD-RPKM.csv


title: Cytotoxic T-cells after mixing with H2122

value: T-cells


title: Cytotoxic T-cells after mixing with H358


title: 356193


title: 356192

value: right


title: Cytotoxic T-cells after mixing with A549


title: KCC-010

description: miRNA


title: 356191


title: KCC-001

description: miRNA


title: KCC-002

description: miRNA


title: YMC-021

description: miRNA


title: shGatad2b-JGES-D5

description: shNuRD-RPKM.csv


title: shGatad2b-JGES-D3

description: shNuRD-RPKM.csv


title: Cytotoxic T-cells after mixing with H520


title: 356189


title: 356190


title: YMC-019

description: miRNA


title: Cytotoxic T-cells after mixing with H441


title: Cytotoxic T-cells after mixing with H1975


title: 356188

value: current


title: YMC-018

description: miRNA


title: YMC-017

description: miRNA


title: KCC-005

description: miRNA


title: Cytotoxic T-cells after mixing with H827

value: T-cell exposure


title: shChd4-JGES-D5

description: shNuRD-RPKM.csv


title: 356187

value: control


title: 356186

value: male


title: shChd4-JGES-D7

description: shNuRD-RPKM.csv

value: JGES


title: shGatad2b-JGES-D1

description: shNuRD-RPKM.csv


title: YMC-015

description: miRNA


title: 356185


title: H3122 cells after T-cell exposure

value: Lung

value: NSCLC cell line (mesenchymal)


title: shChd4-JGES-D1

description: shNuRD-RPKM.csv

value: MEF


title: YMC-013

description: miRNA

value: serum

value: UC


title: YMC-014

description: miRNA


title: YMC-012

description: miRNA


title: 356184

value: Colon Organoid

value: never


title: 356183


title: H1975 cells after T-cell exposure


title: shGatad2b-JGES-D0

description: shNuRD-RPKM.csv


title: shChd4-JGES-D0

description: shNuRD-RPKM.csv


title: Cytotoxic T-cells after mixing with SW1573


title: MEF-3

description: shNuRD-RPKM.csv

source_name: MEF


title: YMC-009

description: miRNA


title: shChd4-JGES-D3

description: shNuRD-RPKM.csv


title: MEF-2

description: shNuRD-RPKM.csv


title: MEF-1

description: shNuRD-RPKM.csv


title: H520 cells after T-cell exposure

value: NSCLC cell line (epithelial)


title: H2122 cells after T-cell exposure


title: 356182

value: treated


title: A549 cells after T-cell exposure


title: 356180


title: YMC-008

description: miRNA


title: JGES-D7


title: 356179


title: 356181


title: SW1573 cells after T-cell exposure


title: EBC1 cells after T-cell exposure


title: YMC-011

description: miRNA


title: JGES-D5


title: H1299 cells after T-cell exposure


title: YMC-010

description: miRNA


title: YMC-006

description: miRNA


title: H460 cells after T-cell exposure


title: YMC-002

description: miRNA


title: JGES-D3


title: YMC-001

description: miRNA


title: H2030 cells after T-cell exposure


title: Non-diseased2

city: Melbourne

first: Enzo

last: Porrello

state: Victoria

address: c/o Royal Children’s Hospital

department: Cell Biology

country: Australia

institute: Murdoch Children's Research Institute

data_processing:
Sequenced read were processed, aligned to human genome (GRCh38.96/hg38), counted and filtered using Cell Ranger (v3.0.2)
Genome_build: GRCh38.96/hg38
Supplementary_files_format_and_content: filtered counts of sequencing reads

source_name: human left ventricle heart muscle

extract_protocol:
Sorted cardiac nuclei were directed processed according to Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 protocol (PN-1000121).
Libraries were made according to Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 protocol (PN-1000121).
10x Chromium single nuclei RNA-seq

value: ~100mg of left ventricular heart muscle

tag: disease state

value: healthy non-cardiovascular disease

value: F

value: 4-14 years


title: JGES-D2-2

source_name: MEF cells after induction


title: Non-diseased3

value: M


title: JGES-D1


title: Non-diseased1


title: H358 cells after T-cell exposure

value: T-cell exposure


title: Fetal3

value: 19-20 weeks


title: S7_ZmCCT(+)-rep3

city: Beijing

first: Wang

last: Zi

address: NO2 Yuanmingyuan West Road, Haidian

department: ational Maize Improvement Center  of China

institute: China Agricultural University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to B73.v4 whole genome using bowtie2
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using stringtie. DGEs werw using DEseq2 in R-project.
Genome_build: B73.v4

organism: Zea mays

source_name: anther

tag: anther stage

value: ZmCCT(+)


title: S7_ZmCCT(+)-rep2


title: S7_ZmCCT(+)-rep1


title: Fetal2


title: JGES-D1-2

tag: system

value: JGES


title: JGES-D0

tag: time after induction


title: YMC-007

description: miRNA

source_name: serum:urothelial cancer


title: H827 cells after T-cell exposure

value: Lung

tag: cell line


title: Fetal1


title: S5-6_ZmCCT(+)-rep3


title: JGES(K5A)-D7

tag: cell type

value: MEF


title: DCM4

tag: tissue

value: Dilated cardiomyopathy

value: 5-10 years


title: H4006 cells after T-cell exposure

value: NSCLC cell line (epithelial/mesenchymal)


title: H1944 cells after T-cell exposure

value: NSCLC cell line (mesenchymal)


title: S5-6_ZmCCT(+)-rep1


title: JGES(K5A)-D5


title: JGES(K5A)-D3


title: DCM3


title: LCLC cells after T-cell exposure


title: DCM2


title: S3-4_ZmCCT(+)-rep3


title: JGES(K5A)-D2-2


title: Hela S3 cell line

city: beijing

first: Ying

state: chaoyang

address: No.1 West Beichen Road

institute: institute of genetics and developmental biology

data_processing:
Cell Ranger (v2.0.0) was used to process initial sequencing data. The FASTQ files were aligned to the reference genome (GRCh38-1.2.0).
Both barcode and UMI are in r1. For each of the r1 reads, the first 16bp is the barcode, and the UMI is from 17 bp to 26 bp (the read length of r1 is 27bp with a T at the last base).
Genome_build: GRCh38-1.2.0
Supplementary_files_format_and_content: comma-delimited text files include UMI values of each gene for each cell; Each column represents a cell barcode; Each row represents a gene

source_name: Hela S3

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle Medium containing 10% fetal calf serum and 2 mM L-glutamine at 37°C in a 5% CO2 incubator.

extract_protocol:
Single cell suspensions were prepared and loaded onto 10x Genomics Single Cell 3′ Chips (Single Cell A Chip Kit, #120236). Single cells ruptured in the droplets and the release mRNAs.
Single-cell libraries were constructed using ChromiumTM Single Cell 3′ Library & Gel Bead Kit v2 (#120237) and ChromiumTM i7 Multiplex Kit (#120262), following the manufacturer’s protocol (#CG00052).

value: cervical cancer cells

value: Hela S3


title: S3-4_ZmCCT(+)-rep2


title: JGES(K5A)-D1


title: mESC C646 SUZ12 Rep 2

city: Stockholm

first: Mattias

last: Mannervik

address: Arrheniuslaboratories E3

department: Molecular Biosciences, the Wenner-Gren Institute

country: Sweden

institute: Stockholm University

description: mESC C646 SUZ12 Rep 2

data_processing:
ChIP-seq reads from each sequenced library were mapped to the Mus musculus mm10 genome assembly using Bowtie2 with the default parameters. Duplicated and unmapped reads were removed using Picard. To obtain the spike-in reads, we mapped the reads to the  Drosophila virilis (dvir_caf1) genome assembly and the mouse reads were normalized based on the ratio of D. virilis reads. From the spike-in adjusted data,  RPKM normalized ChIP-seq coverage tracks were generated using the deepTools. Bigwig files of the mean RPKM were produced using the deepTools comparebigwig tool.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig for coverage

source_name: Embryonic stem (ES) cells

growth_protocol: Mouse embryonic stem cells (mESCs) (E14), (a kind gift of Johan Ericson, Karolinska Institutet, Sweden), were grown at 37°C with 5% CO2 on 0.1% gelatin-coated plates in Knockout DMEM (Gibco) supplemented with 12.5% Knockout Serum Replacement (Gibco), 2.5% ESC-qualified FBS (Gibco), 1% GlutaMAX (Gibco), 1% MEM non-essential amino acids (Gibco), 0.1 mM Beta-Mercaptoethanol (Gibco), 100 units/ml Penicillin-Streptomycin (Gibco) and 1000 units/ml of mouse recombinant leukemia inhibitory factor (LIF) (ESG1106, Millipore).

extract_protocol:
Cells were fixed in 1% formaldehyde (Sigma Aldrich, F8775) for 15 min at room temperature, quenched with 0.16 M glycine for 5 min at 4°C and washed in cold PBS. Crude nuclear extracts were obtained by sequentially washes with ChIP buffer A (10 mM HEPES pH 7.6, 10 mM EDTA pH 8.0, 0.5mM EGTA pH 8.0 and 0.25% Triton X-100) followed by ChIP buffer B (10mM HEPES pH 7.6, 100 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0 and 0.01% Triton X-100) to isolate nuclei. Nuclei were resuspended in Sonication buffer (15 mM HEPES pH 7.6, 140 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 0.1% sodium deoxycholate and 1% Triton X-100), with Complete Mini EDTA-Free protease inhibitor tablets, Roche) supplemented with 0.5% SDS and 0.2% n-lauroylsarcosine, at a final concentration of 5 – 10 x 107 cells/ml and sonicated in a Bioruptor (Diagenode) using high power settings to obtain an average fragment size distribution of 200–500 bp. The concentration of chromatin was quantified and spike-in chromatin from Drosophila virilis cells was added. Immunoprecipitations were performed by incubating 30 μg of chromatin with rabbit anti-SUZ12 (CST, 3737) overnight. Chromatin-antibody complexes were bound to Protein A and G Dynabeads (Invitrogen) and washed sequentially with Wash A (10 mM Tris pH 8.0, 1 mM EDTA pH 8.0, 140 mM NaCl, 0.1% SDS, 0.1% Sodium Deoxycholate and 1% Triton X-100), Wash B (Wash A adjusted to 500 mM NaCl), Wash C (10 mM Tris pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl, 0.5% Sodium Deoxycholate and 0.5% IGEPAL CA-630) and Tris-EDTA (TE). Beads were resuspended in 100 μl TE, treated with RNase A (20 μg/ml) at 55°C for 30 min, supplemented with SDS (0.75%) and Tris (50 mM). and crosslinks reversed at 65°C overnight. Eluted ChIP DNA was treated with Proteinase K at 55°C for 2 h and purified using the ChIP DNA Clean & Concentrator kit (ZymoResearch, D5205).
Libraries were constructed from ChIP samples (2-5 ng) with the NEBNext Ultra II DNA Library Prep Kit (NEB) and single-end (1x75 bp) sequenced on an Illumina NextSeq 550 platform at the BEA core facility, Stockholm.

treatment_protocol: Experiments were conducted on cells at 80% confluency. Cells were resuspended in FBS-free media and incubated with 30 μM of C646 or the inactive analog C37 for 1 hour.

tag: strain

tag: developmental stage

value: Early embryonic stage

tag: antibody

value: rabbit anti-SUZ12 (CST, 3737)

tag: spike-in

value: Drosophila virilis


title: mESC C646 SUZ12  Rep 1

description: mESC C646 SUZ12  Rep 1


title: JGES(K5A)-D1-3


title: H441 cells after T-cell exposure

value: NSCLC cell line (epithelial)

tag: treatment


title: DCM1

value: ~100mg of left ventricular heart muscle

tag: Sex

value: M

tag: age


title: N5

city: New York

first: Nanber

last: Zhong

address: 1050 Forest Hill Road

institute: New York State Institute for Basic Research in Developmental Disabilities

description: SAMPLES N1-5, E1-5 for study of endometriosis

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software (Illumina, San Diego, CA). Sample demultiplexing, barcode processing and single-cell 3’gene counting by using the Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-geneexpression/ software/pipelines/latest/what-is-cell-ranger, version 3.1.0) and scRNA-seq data were aligned to hg19 reference genome (http://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-hg19-3.0.0.tar.gz).
The Cell Ranger output was loaded into Seurat (version 3.3.0) be used to Dimensional reduction, clustering, and analysis of scRNA-seq data. All genes expressed in less than 3 cell were removed. Number of genes expressed per cell > 300 as low and <4000 as high cut-off, Unique Molecular Identifiers (UMI) counts less than 300, the percent of mitochondrial-DNA derived gene-expression <15%.
To visualize the data, we further reduced the dimensionality of all cells using Seurat and used uniform manifold approximation and projection (UMAP) to project the cells into 2D space, The steps include: 1. Using the LogNormalize method of the "Normalization" function of the Seurat software to calculated the expression value of genes; 2. Principal component analysis (PCA) analysis was performed using the normalized expression value, Within all the PCs, the top 10 PCs were used to do clustering and UMAP analysis；3. To find clusters, selecting weighted Shared Nearest Neighbor (SNN) graph-based clustering method[1-3]. Marker genes for each cluster were identified with the "bimod"（Likelihood-ratio test）with default parameters via the FindAllMarkers function in Seurat. This selects markers genes which are expressed in more than 25% of the cells in a cluster and average log (Fold Change) of greater than 0.25.
GO and KEGG pathway of marker genes in each cellular subgroup were retrieved using clusterProfiler (version 3. 8. 1). Seurat (version 3. 3. 0) was used to annotate cellular marker genes reported in Mihaela Pavlicev et., al (2017)[4] and Roser Vento-Tormo et., al (2018)[5]. Gene Set Variation Analysis (GSVA, version 1. 34. 0) and monocle (version 2. 10. 1) were run to analyze gene set variation and Pseudotime of cellular subgroups, respectively. Intercellular interaction analysis was performed using Scanpy (version 1. 4. 6) and weighted gene co-expression network was constructed using Weighted gene co-expression network analysis (WGCNA, version 1. 66). Futhermore, we built protein-protein interaction networks with markers within each cellular subgroup based on STRING (https://string-db.org/). Cell cycle distribution was identified using scRNAseq (version 1. 8. 0) as well.
Genome_build: hg19
Supplementary_files_format_and_content: matrix table with raw gene counts for every gene and every cell

source_name: villi

extract_protocol:
Human tissue was obtained from healthy donors and patients. Place a sterile RNase-free petri dish containing 1 ml Ca2+ and Mg2+ free Phosphate Buffer Saline (PBS) , the tissue in the protection solution  (Miltenyi, Bergisch Gladbach, Germany, 130-100-008) was transferred into the petri dish and scraped the fluff with a scalpel.
The tissue was transfered into a 2 ml centrifuge tube and digested at 37°C for 7 min in 0.25% (W/V) of trypsin. After Aspirated the trypsin solution, the cell suspension was washed twice with preheated PBS  (Ca2+, Mg2+ free) and aspirated the cleaning solution. Digestion of the cell suspension was at 37°C for 20 minutes with 1mg/ml collagenase I, 1mg/ml dispase and 0.05mg/ml DNase I and observed under microscope to obtain cells and the cell suspension was filtered by passing through a 40 μm cell sieve and centrifuged at 300g for 5 min at 4°C after digestion. The cell precipitation was resuspended in PBS (Ca2+, Mg2+ free) and lysed the red blood cells by Lysing Buffer (Gibco ACK, A1049201). The suspension was centrifuged at 300g for 5 min at 4°C to pellet cells and removed dead cells and cell debris by washing twice with PBS (Ca2+, Mg2+ free). Microscopic examination was performed to confirm the overall cell viability.

tag: individual

value: control

value: villi

tag: sample beneath

value: embryo

tag: age of pregnant women


title: S7_ZmCCT(-)-rep3

tag: genotype

value: ZmCCT(-)


title: JGES(K5A)-D0

value: MEF


title: S7_ZmCCT(-)-rep2

tag: anther stage


title: N2


title: mESC C646 Input Rep 2

description: mESC C646 Input Rep 2


title: JGES(K5A)-D1-2

tag: system


title: N3


title: N4


title: S5-6_ZmCCT(+)-rep2

value: ZmCCT(+)


title: S7_ZmCCT(-)-rep1


title: J(N12)GES(K5A)-D1-3

tag: time after induction


title: mESC DMSO SUZ12 Rep 2

description: mESC DMSO SUZ12 Rep 2


title: S5-6_ZmCCT(-)-rep3


title: N1


title: Uterus, Restf/f PR+/Cre

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

data_processing:
The data was analyzed using the 10x Genomics Chromium Single Cell software suite (cellranger-5.0.1).
The demultiplexing and conversion of Illumina base call files (BCL) to raw FASTQ files was done using "cellranger mkfastq" with default parameters.
Read 1: 26bp; Index Read 1: 8bp; Read 2: 96bp
The sequencing reads were aligned to the mouse reference (GRCm38) and analyzed using "cellranger count".
Genome_build: mm10 (mm10-2020-A)
Supplementary_files_format_and_content: cellranger generated unfiltered feature-barcode matrix file.

source_name: Uterus

extract_protocol:
Whole uteri of Restf/f PR+/Cre cKO and control mice aged 5 months were isolated immediately after euthanasia using IACUCC approved methods, washed in cold 1X PBS. Uteri were processed by mincing the tissue and digesting in DMEM (Gibco, Waltham, MA), 10% FBS (Atlanta Biologicals, Flower Branch, GA), 1.5mg/ml collagenase (Gibco, Waltham, MA), and 2400U of DNaseI (NEB, Ipswich, MA) for 5 hours in a shaking water bath at 37°C. After digestion, cells were centrifuged at 300g for 5 minutes and treated with ACK lysis buffer followed by two washes with 1X PBS  and 2% FBS. Cells were passed through a 100um cell strainer and resuspended in 1X PBS and 2% FBS. Cells were passed through a 40um cell strainer and resuspended in 1X PBS and 2% FBS. Control samples (n=2) were pooled and cKO samples (n=2) were pooled. The KUMC genomics core determined concentration and viability using the Countess II FL Automated Cell Counter (Invitrogen, Waltham, MA)
The RT reaction to generate 10X barcoded single stranded cDNA, in the single cell containing GEMs, is performed using an Eppendorf MasterCycler Pro thermal cycler. Post GEM-RT Cleanup is conducted by breaking the GEMS with 10X Recovery Agent to separate the aqueous phase from the Recovery Agent and Partitioning oil. A cleanup of the sscDNA containing aqueous phase is completed using Dynabeads MyOne Silane beads (Life Technologies 37002D). The second strand cDNA amplification is performed using the cDNA Amplification Mix on the Eppendorf MasterCycler Pro. The 3’ gene expression library construction is initiated with fragmentation, end repair and A-tailing of the dscDNA followed by adapter ligation and a sample index PCR using the Illumina compatible indexed adapters in the Chromium i7 Multiplex kit (10X Genomics 120262). Validation of the single cell library is conducted using the Agilent Tapestation 4200 ScreenTape assay (Agilent 5067-5576).
Single Cell RNA-seq (10X Genomics Chromium Single Cell 3' v3)

value: Uterus

value: Restf/f PR+/Cre


title: E5

value: endometriosis patient


title: S3-4_ZmCCT(+)-rep1


title: mESC DMSO Input Rep 2

description: mESC DMSO Input Rep 2


title: S5-6_ZmCCT(-)-rep2


title: Uterus, control


title: E4


title: mESC C646 Input  Rep 1

description: mESC C646 Input  Rep 1


title: mESC DMSO Input  Rep 1

description: mESC DMSO Input  Rep 1


title: S3-4_ZmCCT(-)-rep2


title: S3-4_ZmCCT(-)-rep3


title: E3


title: S3-4_ZmCCT(-)-rep1


title: ExC_2: ein2-5 x Col-0   Endosperm Replicate 2

city: Austin

first: Z Jeffrey

middle: Jeffrey

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

description: Collected endosperm by using LCM

data_processing:
Raw RNA-seq reads were mapped onto the Arabidopsis thaliana whole genome (TAIR10 assembly) using Tophat 2.1.1.
Uniquely mapped reads were extracted by using Samtools 1.5.
FPKM is analyzed by using Cufflinks 2.2.1.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all samples

organism: Arabidopsis thaliana

source_name: Endosperm at 6DAP from ein2-5 x Col-0 collected by using LCM

growth_protocol: All plants were grown under a long-day condition (16/8-hr light/dark cycle) at 22oC.

extract_protocol:
LCM endosperm tissues were subject to total RNA extraction by RNA Aqueous Micro Total RNA Isolation Kit (Thermo Fisher Scientific, Waltham, Massachusetts)
NEB Next Ultra RNA Library Prep Kit (New England Biolabs, Ipswich, Massachusetts)

treatment_protocol: Genetic crosses were made in one genotype (maternal parent) using the emasculated flowers 44 to 48-hr prior to pollination with the pollen from another genotype

value: Endosperm

tag: Stage

value: 6 DAP

value: ein2-5 x Col-0


title: ExE_2: ein2-5 x ein2-5  Endosperm Replicate 2

description: Collected endosperm by using LCM

source_name: Endosperm at 6DAP from ein2-5 x ein2-5 collected by using LCM

value: ein2-5 x ein2-5


title: E1


title: ExE_1: ein2-5 x ein2-5  Endosperm Replicate 1

description: Collected endosperm by using LCM


title: E2


title: AP2-ERF-6A-1_rep2

city: shanghai

first: yijing

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

data_processing:
Sequencing reads were cleaned with the fastp(version 0.20.0) and Trim Galore (version 0.4.4), which eliminated bases with low quality scores(< 25) and irregular GC contents, sequencing adapters, and short reads.
The remaining clean reads were mapped to the Chinese Spring (T. aestivum) genome with the Burrows–Wheeler Aligner(version 0.7.17-r1188).
The MACS(version 2.2.6) program was used to identify the read-enriched regions(peaks) based on the criteria: P < 1e−10. The peaks detected from samples introduced with Halo tag only were considered as non-specific bindings, and TF peaks overlapping with peaks detected from Halo samples were removed for subsequent analysis.
Assembly: IWGSC RefSeq v1.1
Supplementary files format and content: peak files and bigwig files

organism: Triticum aestivum

source_name: Triticum aestivum seedling

growth_protocol: 16h light, 8h dark, 22°C

extract_protocol:
Genomic DNA was extracted from leaves using Plant DNAzol Reagent(invitrogen). RNA was extracted using TRIzol.
Genomic DNA was fragmented. And then end repaired using the End-It kit(Lucigen) and A-tailed using Klenow(3′–5′ exo-; NEB). Truncated Illumina Y-adapter was ligated to DNA using T4 DNA Ligase(Promega). Full length TF was cloned into pIX-Halo vector. Halo-tagged TF was expressed in vitro using TNT SP6 Coupled Wheat Germ Extract System(Promega). Halo-TF was immobilized by Magne HaloTag Beads(Promega) and then incubated with the DNA library. TF specific binding DNA was eluted for 10 min at 98°C and amplified with indexed Illumina primer using Phanta Max Super-Fidelity DNA Polymerase(Vazyme). Meanwhile, to capture background DNA which captured by Halo, pIX-Halo vector without TF cloned was expressed and incubated with the DNA library as well. The PCR product was purified using VAHTS DNA Clean Beads(Vazyme).
DAP-seq

tag: dap antibody

value: Halo

tag: antibody manufacturer

value: Promega

tag: antibody catalog #

tag: cultivar

value: Chinese Spring


title: D13

description: SAMPLES A,B,C,D for the study of EPL

tag: tissue

value: gestational week 6


title: mESC DMSO SUZ12  Rep 1

description: mESC DMSO SUZ12  Rep 1

tag: strain

tag: developmental stage

value: Early embryonic stage

tag: antibody

value: rabbit anti-SUZ12 (CST, 3737)

tag: spike-in

value: Drosophila virilis


title: AP2-DREB-1B-1_rep2


title: ExC_1: ein2-5 x Col-0  Endosperm Replicate 1

description: Collected endosperm by using LCM


title: D10

description: SAMPLES A,B,C,D for the study of EPL

value: villi

value: embryo

tag: age

value: gestational week 6+


title: AP2-DREB-1D-1_rep2


title: S5-6_ZmCCT(-)-rep1

value: ZmCCT(-)


title: D9

description: SAMPLES A,B,C,D for the study of EPL

tag: sample beneath


title: CxE_2: Col-0 x ein2-5  Endosperm Replicate 2

description: Collected endosperm by using LCM

source_name: Endosperm at 6DAP from Col-0 x ein2-5 collected by using LCM

value: Col-0 x ein2-5


title: EpiCs tcf21+/+ 96 hpf [Epi-WT_2]

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

description:
Epi-WT_2
counts.matrix.norm_anno.txt

data_processing:
Trimmomatic version 0.39 was used to trim reads with a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were used in subsequent analyses.
Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 (Ensembl release 99) using STAR 2.7.3a with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package (Liao et al., 2014). Only reads mapping at least partially inside exons were admitted and aggregated per gene, while reads overlapping multiple genes or aligning to multiple regions were excluded from further analyses.
Differentially expressed genes were identified using DESeq2 version 1.26.0 (Love et al., 2014). To remove a batch effect from the comparison, the replicates were presented to DESeq2 as covariates (DMSO_1/Inhib_1 = 1, DMSO_2/Inhib_2 = 2).
The Ensembl annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers.
Genome_build: DanRer11 (GRCz11)
Supplementary_files_format_and_content: counts.matrix.norm_anno.txt: Tab-delimited text file includes library size normalized counts.

organism: Danio rerio

source_name: Sorted epicardial cells

extract_protocol:
Hearts from 96 hpf Tg(myl7:mcherry), TgBAC(tcf21:nls-EGFP) tcf21+/+ and tcf21-/- zebrafish larvae were manually dissected using forceps. Hearts were dissociated into single-cell suspensions and FACS was performed to sort cardiomyocytes and epicardial cells. Approximately 6000-1000 cells per replicate were used, and total RNA was isolated using the miRNeasy micro kit (Qiagen), combined with on-column DNase digestion.
4 ng of total RNA was used as input for SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Clontech) for cDNA pre-amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine (Covaris). Final Library Preparation was performed by Low Input Library Prep Kit v2 (Takara Clontech).

value: 96 hpf

tag: cell type

value: Epicardial cells


title: CxC_2: Col-0 x Col-0  Endosperm Replicate 2

last: Chen

description: Collected endosperm by using LCM

source_name: Endosperm at 6DAP from Col-0 x Col-0 collected by using LCM

value: Endosperm

value: 6 DAP

tag: genotype

value: Col-0 x Col-0


title: C7

description: SAMPLES A,B,C,D for the study of EPL

tag: age of pregnant women


title: CxE_1: Col-0 x ein2-5  Endosperm Replicate 1

description: Collected endosperm by using LCM


title: D8

description: SAMPLES A,B,C,D for the study of EPL


title: RNA-seq of adult Strigamia marittima ovaries [Sma_Ovary]

description: Pooled ovaries from adult individuals

organism: Strigamia maritima

source_name: Adult ovaries

extract_protocol:
Trizol
polyA-selected stranded RNA-seq; RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ovaries

tag: genome build

tag: gtf

value: Smar1 GTF (enriched from Ensembl Metazoa v26)


title: EpiCs tcf21+/+ 96 hpf [Epi-WT_1]

description:
Epi-WT_1
counts.matrix.norm_anno.txt


title: D1

description: SAMPLES A,B,C,D for the study of EPL


title: AP2-DREB-1A-1_rep2

value: Halo

value: Promega

value: Chinese Spring


title: C4

description: SAMPLES A,B,C,D for the study of EPL


title: RNA-seq of adult Blattella germanica testis [Bge_Testis_b]

description: Pooled testis from adult individuals

organism: Blattella germanica

source_name: Adult testis

value: Testis

value: GCA_000762945.2_Bger_2.0 GTF (obtained from blager_OGSv1.2.1.gff3 and enriched)


title: C2

description: SAMPLES A,B,C,D for the study of EPL

value: villi


title: EpiCs tcf21-/- 96 hpf [Epi-Mut_2]

description:
Epi-Mut_2
counts.matrix.norm_anno.txt


title: spRef20

type: genomic

city: Hamburg

first: Krystian

middle: Daniel

last: Fita

address: Martinistrasse 52

department: Department of Neurosurgery

institute: University Medical Center Hamburg-Eppendorf

description:
spinal MNG tumor DNA from FFPE sections
spinal MNG

hyb_protocol: Bisulfite treatment, whole-genome DNA amplification, hybridization and single-base extension, fluorescence staining and scanning of the chips were performed following the manufacturer´s instructions (Illumina).

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

data_processing: For methylation profiling, loading and normalization was performed using the R package chAMP (v. 2.24.0). The BMIQ method was used for normalization. 850K data sets were merged with 450K data sets. For genomic copy number variation profiling, the R packages minfi (v. 1.40.0) and conumee (v. 1.28.0, parameter undo.SD = 1.5) were used for loading and processing.

label: Cy3 and Cy5

source_name: spinal meningioma

label_protocol: Standard Illumina Protocol

extract_protocol: Sample DNA was extracted from FFPE sections according to the manufacturer´s instructions (Illumina).

tag: Sex

value: m

tag: histology

value: angiomatous

value: no

value: yes


title: spRef17

value: atypical

value: int-A


title: spRef19

value: f

value: fibroblastic


title: spRef21

value: complete

tag: recurrence


title: C1

description: SAMPLES A,B,C,D for the study of EPL

value: embryo

value: gestational week 6+


title: spRef18

value: chordoid

value: int-B


title: RNA-seq of adult Strigamia marittima guts [Sma_Gut]

description: Pooled guts from adult individuals

source_name: Adult guts

value: Guts

value: Smar1 GTF (enriched from Ensembl Metazoa v26)


title: CMs tcf21-/- 96 hpf [CM-Mut_2]

description:
CM-Mut_2
counts.matrix.norm_anno.txt

source_name: Sorted cardiomyocytes

value: 96 hpf

value: Cardiomyocytes


title: C3

description: SAMPLES A,B,C,D for the study of EPL

value: villi


title: CxC_1: Col-0 x Col-0 Endosperm Replicate 1

description: Collected endosperm by using LCM

value: Endosperm

tag: Stage

value: 6 DAP

value: Col-0 x Col-0


title: CMs tcf21+/+ 96 hpf [CM-WT_1]

description:
CM-WT_1
counts.matrix.norm_anno.txt


title: RNA-seq of adult Blattella germanica ovaries [Bge_Ovary_b]

description: Pooled ovaries from adult individuals

value: Ovaries

value: GCA_000762945.2_Bger_2.0 GTF (obtained from blager_OGSv1.2.1.gff3 and enriched)


title: CMs tcf21-/- 96 hpf [CM-Mut_1]

description:
CM-Mut_1
counts.matrix.norm_anno.txt


title: spRef12

value: f

value: meningotheliomatous

value: no


title: EpiCs tcf21-/- 96 hpf [Epi-Mut_1]

description:
Epi-Mut_1
counts.matrix.norm_anno.txt

value: Epicardial cells


title: RNA-seq of adult Strigamia marittima fat body [Sma_FatBody]

description: Pooled fat bodies from adult individuals

source_name: Adult fat body

value: Fat body


title: CMs tcf21+/+ 96 hpf [CM-WT_2]

description:
CM-WT_2
counts.matrix.norm_anno.txt


title: spRef16

value: atypical

value: int-A

value: yes


title: RNA-seq of adult Strongylocentrotus purpuratus radial nerve [Spu_RadialNerve_D]

description: Pooled radial nerves from adult individuals

organism: Strongylocentrotus purpuratus

source_name: Adult radial nerve

value: Neural

value: Spur_5.0 GTF (enriched from Ensembl metazoa v51)


title: spRef15

value: m


title: spRef09

value: psammomatous


title: spRef11

value: subtotal


title: RNA-seq of adult Blattella germanica testis [Bge_Testis_a]

description: Pooled testis from adult individuals

value: Testis


title: 16113BL PBS (bulk RNA-seq)

city: Shanghai

first: Xingguang

last: Liu

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

institute: Naval medical university

data_processing:
Sequencing read counts were calculated using Stringtie78,79 (v.1.3.0).
Then expression levels from different samples were normalized by the Trimmed Mean of M values (TMM) method79.
The normalized expression levels of different samples were converted to FPKM (Fragments Per Kilobase of transcript per Million mapped fragments).
The edgeR package of R was used to analyze the difference between intergroup gene expression, the P-values were calculated, and the multiple hypothesis test was performed.
Differentially expressed genes (DEGs) were defined as transcripts with a fold change in expression level (according to the FPKM value) greater than 2.0 and a q-value less than 0.05.
Assembly: Mmul_10
Supplementary files format and content: Tab-delimited text files include FPKM and count values for each Sample.

organism: Macaca mulatta

source_name: bronchoalveolar lavage fluid

extract_protocol:
The bronchoalveolar lavage fluid from rhesus macaue were collected 7 days post SARS-CoV-2 challenge with SW0123 vaccination or PBS administration. Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Strand-specific libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina, USA) following the manufacturer’s instructions.
The library construction and sequencing was performed at Shanghai Biotechnology Corporation.

tag: animal id

value: BALF from left lung

value: 4 years old

value: wild type

tag: treatment

value: PBS

tag: infection


title: B8

description: SAMPLES A,B,C,D for the study of EPL

tag: tissue

value: villi

value: embryo

value: gestational week 6+


title: spRef08

value: f

value: no


title: RNA-seq of adult Strongylocentrotus purpuratus lantern [Spu_Lantern_a]

description: Pooled lanterns from adult individuals

source_name: Adult lantern

value: Muscle


title: RNA-seq of adult Strongylocentrotus purpuratus epidermis [Spu_Epidermis_a]

description: Pooled epidermis from adult individuals

source_name: Adult epidermis

value: Epidermis


title: B5

description: SAMPLES A,B,C,D for the study of EPL

source_name: villi

value: gestational week 7


title: spRef03

value: transitional

value: yes


title: RNA-seq of adult Blattella germanica ovaries [Bge_Ovary_a]

description: Pooled ovaries from adult individuals

value: Ovaries

value: GCA_000762945.2_Bger_2.0 GTF (obtained from blager_OGSv1.2.1.gff3 and enriched)


title: spRef10

value: psammomatous

value: complete

value: int-A


title: spRef13

value: meningotheliomatous


title: B4

description: SAMPLES A,B,C,D for the study of EPL


title: RNA-seq of adult Blattella germanica nerve cord [Bge_NerveCord_c]

description: Pooled nerve cords from adult individuals

source_name: Adult nerve cord

value: Nerve cord


title: spRef01


title: B2

description: SAMPLES A,B,C,D for the study of EPL

value: villi


title: 16113BR PBS (bulk RNA-seq)

value: BALF from right lung

value: 4 years old

value: wild type

value: PBS


title: RNA-seq of adult Blattella germanica muscle [Bge_Muscle_b]

description: Pooled muscle from adult individuals

source_name: Adult muscle

value: Muscle


title: 16139BL PBS (bulk RNA-seq)

value: BALF from left lung


title: B1

description: SAMPLES A,B,C,D for the study of EPL

value: embryo

value: gestational week 6


title: RNA-seq of adult Strongylocentrotus purpuratus guts [Spu_Gut_D]

description: Pooled  guts from adult individuals

value: Guts

value: Spur_5.0 GTF (enriched from Ensembl metazoa v51)


title: A8

description: SAMPLES A,B,C,D for the study of EPL

value: gestational week 6+


title: RNA-seq of adult Blattella germanica muscle [Bge_Muscle_a]

description: Pooled muscle from adult individuals

value: GCA_000762945.2_Bger_2.0 GTF (obtained from blager_OGSv1.2.1.gff3 and enriched)


title: RNA-seq of adult Blattella germanica guts [Bge_Gut_a]

description: Pooled guts from adult individuals


title: 16249BR Vaccine (bulk RNA-seq)

value: mRNA vaccine SW0123


title: input_1

first: Xingying

last: Zhang

address: No. 5, Yard 1, Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

description: genomic DNA

data_processing:
RNA-seq:
The library samples were sequenced on the Illumina NovaSeq sequencer with 150 bp paired-end reads.
RNA sequencing reads of CAR-T cells and OT-1 cells were aligned to human reference sequence GRCh38 and mouse reference sequence GRCm39 separately using STAR (2.7.0f).
Read counts and FPKM (Fragments Per Kilobase of transcript per Million mapped reads) were calculated using RSEM (1.3.2).
ChIP-seq:
The obtained FASTQ files were performed quality control with FastQC (0.11.9). Sequenced reads were aligned to the human reference sequence GRCh38 with BWA (0.7.17) software to obtain the SAM files which were converted to BAM files by SAMtools (1.3.1) software.
Then BAM files were sorted with the SAMtools and were deduplicated with Picard (2.24.0).
Binding sites (peaks) are called using MACS2 (2.2.7.1) relative to a control input library and q-value threshold was set as 0.05.
The deduplicated BAM files were converted to bigwig files using bamCoverage command of deeptools (3.3.0) software and viewed using for IGV (2.7.0) visualization software.
Assembly: GRCh38 (human), GRCm39 (mouse)
Supplementary files format and content: *_readcounts_FPKM.xlsx: Excel files include read counts and FPKM values.
Supplementary files format and content: bigwig format for visualization in IGV.

source_name: blood

extract_protocol:
Ten million cells were washed twice in cold PBS buffer and cross-linked with 1% formaldehyde for 10 minutes at room temperature and then quenched by addition of glycine (125 mmol/L final concentration). Afterwards, samples were lysed and chromatins were obtained on ice. Chromatins were sonicated to get soluble sheared chromatin (average DNA length of 200-500 bp). 20 µL chromatin was saved at -20°C. For input DNA, 100 µL chromatin was used for immunoprecipitation by anti-BATF antibodies (Cat# 8638S，Cell Signaling Technology) and IgG antibodies (ab17870, Abcam) respectively. 10 μg of antibody was used in the immunoprecipitation reactions at 4°C overnight. The next day, 30 μL of protein beads was added and the samples were further incubated for 3 h. The beads were next washed once with 20 mM Tris/HCL (pH 8.1), 50 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS; twice with 10 mM Tris/HCL (pH 8.1), 250 mM LiCl, 1 mM EDTA, 1% NP-40, 1% deoxycholic acid; and twice with TE buffer 1× (10 mM Tris-Cl at pH 7.5. 1 mM EDTA). Bound material was then eluted from the beads in 300 μL of elution buffer (100 mM NaHCO3, 1% SDS), treated first with RNase A (final concentration 8 μg/mL) during 6 h at 65°C and then with proteinase K (final concentration 345 μg/mL) overnight at 45°C.
Immunoprecipitated DNA was used to construct sequencing libraries following the protocol provided by the I NEXTFLEX® ChIP-Seq Library Prep Kit for Illumina® Sequencing (NOVA-5143-02，Bioo Scientific) and sequenced on Illumina Xten with PE 150 method.

value: blood

value: Primary T cells

value: CAR-T WT

value: co-culture with NCI-H226-luciferase at E:T=2:1 for 24h

tag: chip antibody

value: IgG


title: RNA-seq of adult Blattella germanica malpighian tubes [Bge_MalpighianTubes_b]

description: Pooled malpighian tubes from adult individuals

data_processing:
Estimated counts and TPMs were computed by Kallisto (v0.44.0)
Supplementary files format and content: Tab-delimited file with length, effective length, estimated counts and transcript per million (TPM) for all species protein coding genes in the relative GTF

source_name: Adult malpighian tubes

value: Malpighian tubes


title: A7

description: SAMPLES A,B,C,D for the study of EPL

value: villi


title: input_2

description: genomic DNA


title: RNA-seq of adult Blattella germanica malpighian tubes [Bge_MalpighianTubes_a]


title: 16175BR Vaccine (bulk RNA-seq)

value: BALF from right lung

value: 4 years old

value: wild type


title: A3

description: SAMPLES A,B,C,D for the study of EPL

value: embryo


title: Control_3

city: Jinan

first: Jing

last: Li

address: No. 44-1 Wenhua Road West

institute: Shandong University

data_processing:
Illumina Casava1.7 software used for basecalling.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Homo_sapiens Ensembl release-96
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: dental pulp stem cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Dental pulp stem cells

tag: individual

value: Donor 3

value: Control lentivirus infection


title: 16139R PBS

description: 10x Genomics

data_processing:
Single cell RNA-seq data processing Reads were processed using the Cell Ranger 3.0.1 pipeline with default and recommended parameters. FASTQs generated from Illumina sequencing output were aligned to the macaca_mulata genome, version Mmul_10, using the STAR algorithm
We excluded cells with fewer than 200 or more than 6000 detected genes (where each gene had to have at least one UMI aligned in at least three cells). The expression of mitochondria genes was calculated using PercentageFeatureSet function of the seurat package.
To remove low activity cells, cells with more than 10 percent expression of mitochondria genes were excluded.
we performed principal component analysis (PCA) and reduced the data to the top 30 PCA components after scaled the data.
Identification of cell types and subtypes by nonlinear dimensional reduction (t-SNE) Cells were clustered using graph-based clustering of the PCA reduced data with the Louvain Method
Assembly: Mmul_10
Supplementary files format and content: matrix table with raw gene counts for every gene and every cell

source_name: lung

extract_protocol:
The lung tissue from rhesus macaue were harvested 7 days post SARS-CoV-2 challenge with SW0123 vaccination or PBS administration. Tissues were enzymatically digested with a mixture of trypsin and collagenase. After dissociation, cell suspensions were passed through a 40 μm Cell Strainer, followed by red blood cells lysis.
10× library preparation and sequencing Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation,so that each cell was paired with a bead in a Gel Beads-in emulsion(GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (CG000206 RevD). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific).

value: lung

tag: age

value: PBS


title: 16045BR Vaccine (bulk RNA-seq)

value: mRNA vaccine SW0123


title: RNA-seq of adult Blattella germanica guts [Bge_Gut_b]

description: Pooled guts from adult individuals

value: Guts

value: GCA_000762945.2_Bger_2.0 GTF (obtained from blager_OGSv1.2.1.gff3 and enriched)


title: BATF-IP_2

description: genomic DNA

value: blood

value: Primary T cells

value: CAR-T WT

value: anti-BATF


title: 16249R Vaccine

description: 10x Genomics

value: SARS-CoV-2 challenge


title: A2

description: SAMPLES A,B,C,D for the study of EPL

value: villi

tag: sample beneath

value: gestational week 7


title: 16045BL Vaccine (bulk RNA-seq)

value: BALF from left lung

value: 4 years old

value: wild type


title: A1

description: SAMPLES A,B,C,D for the study of EPL

value: embryo

value: gestational week 6+


title: RNA-seq of adult Blattella germanica fat body [Bge_FatBody_b]

value: Fat body


title: Hypoxia-3W-LECs-mm10-rep1

city: Milwaukee

first: Akiko

last: Mammoto

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

data_processing:
Genome alignment and expression count (STAR) were performed using Basepair.
Genome_build: mm10
Supplementary_files_format_and_content: Expression count txt files include Transcript ID, Gene Symbol, Expression Count, Fragments Per Kilobase Million (FPKM), and Transcripts Per Kilobase Million (TPM) for each sample.

source_name: Lung

extract_protocol:
Mouse lung endothelial cells were isolated from C57BL6 mouse lungs (8 week old, male) using anti-CD31 conjugated magnetic beads. RNA was extracted using QIAGEN RNeasy mini kit (Cat# 74104). 1 ug of total RNA as used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNA was collected from endothelial cells isolated from mouse lungs 3 weeks after hypoxia and normoxia treated mouse lungs

tag: strain

value: lung

tag: cell type

value: endothelial cell

value: Hypoxia 3W

value: 8 week old

value: male


title: Hypoxia-3W-LECs-mm10-rep2


title: Hypoxia-3W-LECs-mm10-rep3


title: RNA-seq of adult Blattella germanica epidermis [Bge_Epithelium_a]

first: Federica

address: Dr. Aiguader 88

institute: CRG

description: Pooled epidermis from adult individuals

value: Epidermis

value: GCA_000762945.2_Bger_2.0 GTF (obtained from blager_OGSv1.2.1.gff3 and enriched)


title: ETV2_3

value: Dental pulp stem cells

value: Donor 3


title: BATF-IP_1

description: genomic DNA

value: blood

value: Primary T cells

tag: genotype

value: CAR-T WT

value: co-culture with NCI-H226-luciferase at E:T=2:1 for 24h

value: anti-BATF


title: Normoxia-LECs-mm10-rep3

value: Normoxia


title: 16271R PBS

description: 10x Genomics

value: 4 years old

value: wild type

value: PBS


title: ETV2_1

value: Donor 1


title: RNA-seq of adult Blattella germanica brain [Bge_Brain_c]

description: Pooled brains from adult individuals

source_name: Adult brain

value: Brain

tag: genome build


title: RNA-seq of adult Blattella germanica fat body [Bge_FatBody_a]

value: Fat body

tag: gtf


title: spRef02

source_name: spinal meningioma

tag: Sex

value: f

value: transitional

value: complete

value: no

value: int-A

value: yes


title: RNA-seq of adult Blattella germanica epidermis [Bge_Epithelium_b]

description: Pooled epidermis from adult individuals

value: Epidermis

value: GCA_000762945.2_Bger_2.0 GTF (obtained from blager_OGSv1.2.1.gff3 and enriched)


title: ETV2_2

value: Dental pulp stem cells

value: Donor 2


title: 16113L PBS

description: 10x Genomics

value: lung


title: Control_2

value: Control lentivirus infection


title: Normoxia-LECs-mm10-rep2

value: endothelial cell

value: Normoxia

value: 8 week old

value: male


title: 16045R Vaccine

description: 10x Genomics

value: 4 years old

value: wild type

value: SARS-CoV-2 challenge


title: RNA-seq of adult Blattella germanica brain [Bge_Brain_a]

description: Pooled brains from adult individuals

value: Brain


title: 16045L Vaccine

description: 10x Genomics