title: PBMC-AIDS-rep28

description:
Gene expression of AIDS patient after ART
B11_NS

source_name: PBMCs, AIDS, replicate 28


title: D. melanogaster macrophages_WT_Rep2

status: Public on Nov 10 2021

type: SRA

city: Klosterneuburg

first: Daria

last: Siekhaus

address: Am Campus 1

department: Bertalanffy Building

country: Austria

institute: IST Austria

description: FACS-sorted labled macrophages

library_source: transcriptomic

data_processing:
Aligning the transcriptome sequence reads to the D. melanogaster reference genome (Ensembl BDGP6) with STAR version 2.5.1b using 2-pass alignment mode.
Counting the number of reads; the quality of the RNA-seq library was assessed by calculating the percentage of reads that are mapped  to exonic and intronic regions of the genome, while using polyA selection for library preparation.
the reads were associated with known genes and the number of reads aligned within each gene was counted using HTSeq tool version 0.5.4p3.
the counts were normalised using the TMM normalisation method of the edgeR R/Bioconductor package ( (R version 3.4.4, Bioconductor version 3.6)
The data were  log transformed using the voom approach in the limma package. For the visualizations and result files the TMM normalised counts are represented as TPM (Transcripts Per Kilobase Million) values.
Genome_build: the Drosophila melanogaster reference genome (Ensembl BDGP6)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for both wildtype and the mutant  samples
Supplementary_files_format_and_content: Matrix table with raw gene counts for both wildtype and the mutant  samples

molecule: total RNA

organism: Drosophila melanogaster

source_name: Embryonic macrophages

growth_protocol: Fly embryos of both genotypes were collected for stage 11 at 29°C.

extract_protocol:
Total RNA was isolated from FACS-sorted mCherry-positive macrophages using Rneasy Plus Micro Kit (QIAGEN) and stored at -80C for quality control and RNA sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina’s HiSeq2500, 50bp read length)

treatment_protocol: Dechorionated embryos were dissociated and Cherry-positive macrophages were sorted by FACS using the protocol from Attila Gyoergy et al., G3, 2018.

tag: developmental stage

value: Embryonic macrophages from stage 11

tag: cell type

value: Embryonic macrophages (hemocytes)

tag: tag

value: 3xMcherry-tagged macrophages


title: ADT_EXP20001249_Sample_03_hashed sample

city: Boston

first: Natalie

middle: Y. R.

last: Agar

state: Massachusetts

address: Harvard Medical School

department: Neurosurgery

country: USA

institute: Brigham and Women's Hospital

description: ADT

data_processing:
Base Calling TCR BCL to TCR FASTQ via Cell Ranger 3.1.0 with the flag "--delete-undetermined" in addition to the standard settings.
Base Calling GEX BCL to GEX FASTQ via Cell Ranger 3.1.0 with the flag "--delete-undetermined" in addition to the standard settings.
Base Calling ADT BCL to ADT FASTQ via Cell Ranger 3.1.0 with the flag "--delete-undetermined" in addition to the standard settings.
Base Calling tetramer BCL to tetramer FASTQ file via bcl2fastq2 version v2.20.0 with the flags "--minimum-trimmed-read-length 0 --mask-short-adapter-reads 0" in addition to the standard settings.
TCR Read Counts: FASTQ to vdj counts via Cell Ranger 3.1.0 using the standard settings.
GEX Read Counts: FASTQ to gene expression counts via Cell Ranger 3.1.0 using the standard settings.
Tetramer FASTQ to Tetramer counts via extracting tetramer barcode from uniquely observed tetramer UMI reads using python script
ADT FASTQ to ADT counts via extracting tetramer barcode from uniquely observed tetramer UMI reads using python script
TCR VDJ counts paired with tetramer and ADT counts via common hydrogel barcode using python script
VDJ and tetramer counts separated via hashtags using Seurat 4.0.3
Dehashed VDJs selected for functional assays.
Genome_build: GRCh38 (hg19)
Supplementary_files_format_and_content: The processed data files conform to the hfad AnnData format: https://anndata.readthedocs.io/en/latest/anndata.AnnData.html
Supplementary_files_format_and_content: Metadta for hashed samples including HTO oligo sequence is available in the file "GEO_upload_seq_CIPHER_2021_11_04_Supplemental_Sample_to_HTO.xlsx"

organism: Homo sapiens

source_name: CD8+ T cells

extract_protocol:
PBMCs were thawed, and CD8+ T cells were enriched by magnetic-activated cell sorting (MACS) using a CD8+ T Cell Isolation Kit (Miltenyi) following the manufacturers protocol. The CD8+ T cells were then stained with 1 nM final concentration tetramer library in the presence of 2 mg/mL salmon sperm DNA in PBS with 0.5% BSA solution for 20 minutes. Cells were then labeled with anti-TCR antibody-derived tag (ADT, IP26, Biolegend) for 15 minutes followed by washing. Tetramer bound cells were then labeled with phycoerythrin (PE) conjugated anti-DKDDDDK-Flag antibody (BioLegend) followed by dead cell discrimination using 7-amino-actinomycin D (7-AAD). The live, tetramer positive cells were sorted using a Sony MA900 Sorter (Sony). Tetramer positive cells were counted by Nexcelom Cellometer (Lawrence, MA, USA) using AOPI stain following manufacturer’s recommended conditions. Single-cell encapsulations were generated utilizing 5’ v1 Gem beads from 10x Genomics (Pleasanton, CA, USA) on a 10x Chromium controller and downstream TCR, and Surface marker libraries were made following manufacturer recommended conditions. All libraries were quantified on a BioRad CFX 384 (Hercules, CA, USA) using Kapa Biosystems (Wilmington, MA, USA) library quantified kits and pooled at an equimolar ratio. TCRs, surface markers, and tetramer generated libraries were sequenced on Illumina (San Diego, CA, USA) NextSeq550 instruments. Sequencing data were processed using the Cell Ranger Software Suite (Version 3). Samples were demultiplexed and unique molecular identifier (UMI) counts were quantified for TCRs, tetramers, and gene expression.
10X Chromium 5' single-cell

tag: tissue

value: PBMC

tag: subject

value: multiplexed sample

tag: cohort


title: ADT_EXP20001249_Sample_01_hashed sample

description: ADT


title: D. melanogaster macrophages_WT_Rep1

description: FACS-sorted labled macrophages


title: D. melanogaster macrophages_WT_Rep3

description: FACS-sorted labled macrophages


title: ADT_EXP20001249_Sample_02_hashed sample

description: ADT


title: PBMC-AIDS-rep6

type: RNA

city: Chengdu

first: Fangyuan

last: Shen

address: No.29 Wangjiang Road

country: China

institute: Sichuan University

description:
Gene expression of AIDS patient after ART
A15_NS

hyb_protocol: Each slide was hybridized with 100ng Cy3‐labeled RNA using miRNA Complete  Labeling and Hyb Kit(Cat#5190‐0456, Agilent technologies, Santa Clara, CA, US)in  hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃， 20rpm  for  20  hours  according  to  the  manufacturer’s  instructions,  hybridization  section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo  Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188‐5327,  Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides  were  scanned  by  Agilent  Microarray  Scanner(Cat#G2565BA，Agilent  technologies,  Santa  Clara,  CA,  US)and  Feature  Extraction  software  10.7  (Agilent  technologies, Santa Clara, CA, US)with default settings.

source_name: PBMCs, AIDS, replicate 6

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb  Kit(Cat#5190‐0456,  Agilent  technologies,  Santa  Clara,  CA,  US)followed  the  manufacturer’s instructions, labeling section.

tag: disease state

value: AIDS

tag: gender

value: male

value: Peripheral blood mononuclear cells


title: PBMC-AIDS-rep7

description:
Gene expression of AIDS patient after ART
A16_NS

source_name: PBMCs, AIDS, replicate 7

tag: virus load

value: HVL


title: PBMC-AIDS-rep9

description:
Gene expression of AIDS patient after ART
A18_NS

source_name: PBMCs, AIDS, replicate 9

value: LVL

value: female


title: PBMC-AIDS-rep1

description:
Gene expression of AIDS patient after ART
A1_NS

source_name: PBMCs, AIDS, replicate 1


title: PBMC-AIDS-rep3

description:
Gene expression of AIDS patient after ART
A12_NS

source_name: PBMCs, AIDS, replicate 3


title: ADT_EXP20001234_Sample_04_hashed sample

description: ADT


title: PBMC-AIDS-rep2

description:
Gene expression of AIDS patient after ART
A11_NS

source_name: PBMCs, AIDS, replicate 2


title: Organoid_S76

first: Lakshmi

last: Muthuswamy

state: MA

address: 3 Blackfan circle

department: Department of Medicine

institute: Beth Israel Deaconess Medical Center

data_processing:
Paired end reads were aligned using STAR (v2.5)
HTSeq v0.6.1 was used to count the read numbers of each gene
Genome_build: hg38
Supplementary_files_format_and_content: Excel and contains read counts

source_name: pancreatic tumor organoids

extract_protocol:
Total RNA and DNA were extracted using the Zymo-Miniprep kit
RNA libraries were prepared for sequencing using standard Illumina TrueSeq protocols

value: Patient-derived organoids

tag: disease type

value: Pancreatic Cancer


title: ADT_EXP20001234_Sample_03_hashed sample

description: ADT


title: Organoid_S68


title: ADT_EXP20001234_Sample_02_hashed sample

description: ADT


title: Organoid_S38


title: ADT_EXP20001249_Sample_04_hashed sample

description: ADT


title: ADT_EXP20001234_Sample_01_hashed sample

description: ADT


title: Organoid_S34


title: ADT_EXP20001148_Sample_04_hashed sample

description: ADT


title: Organoid_S19


title: ADT_EXP20001148_Sample_03_hashed sample

description: ADT


title: Organoid_S10


title: Organoid_S3


title: ADT_EXP20001148_Sample_01_hashed sample

description: ADT


title: ADT_EXP20001114_Sample_08

description: ADT

value: unexposed


title: Organoid_S6


title: MDA-MB-453_input

city: Salt Lake CIty

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

library_source: genomic

data_processing:
Reads were aligned to the hg19 build of the human genome using Bowtie V 1.1.2 with the following arguments: bowtie --chunkmbs 512 -m 1 -t --best -q -S -l 32 -e 80 -n 2
Peaks were called using macs2 V 2.1.0.20140616 with the following arguments: macs2 callpeak -B --SPMR --pvalue=1e-10 --mfold 15 100
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: BigWig: Pileup values for reads.
Supplementary_files_format_and_content: .*txt: Chromosome, start, stop, length, summit, pvalue, fold_enrichment, qvalue, and name values for peaks called by macs2.

molecule: genomic DNA

growth_protocol: MDA-MB-453 cells were grown in CSS media for a total of 72 hrs before treatment. 24 hrs prior to treatment, cells were trypsinized and equal cell numbers were plated on control tissue culture dishes (attached) or polyHEMA-coated dishes (suspended).

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 minutes at room temperature and then treated with 125 mM Glycine for 5 minutes to stop crosslinking. Crosslinked cells were then washed with cold PBS and scraped to harvest.
ChIP and library construction were performed as described in Reddy et al., Genome Research, 2009.

treatment_protocol: Cells were treated with DMSO (vehicle control), DHT (10 nM), or DHT+Enza (10uM) for 4hrs.

tag: cell line

tag: treatment

value: Combined input

tag: target protein

value: Input

tag: chip antibody


title: MDA-MB-453_Suspended_Vehicle_DHT_Enzalutamide

tag: culture conditions

value: Suspension

value: 10 nM Dihydrotestosterone and 10 uM enzalutamide for 4 hours

value: AR

value: anti-AR


title: ADT_EXP20001148_Sample_02_hashed sample

description: ADT

value: PBMC


title: ADT_EXP20001114_Sample_07

description: ADT


title: ADT_EXP20001114_Sample_04

description: ADT


title: ADT_EXP20001114_Sample_02

description: ADT


title: ADT_EXP20001114_Sample_03

description: ADT


title: MDA-MB-453_Suspended_Vehicle

value: DMSO (vehicle) for 4 hours


title: MDA-MB-453_Attached_DHT_Enzalutamide

value: Attached


title: MDA-MB-453_Attached_DHT

value: 10 nM Dihydrotestosterone for 4 hours


title: Organoid_S75


title: ADT_EXP20001114_Sample_01

description: ADT


title: ADT_EXP20001114_Sample_06

description: ADT


title: MDA-MB-453_Attached_Vehicle


title: TET_EXP20000768_Sample_01

description: TET

value: convalescent


title: ADT_EXP20001095_Sample_07

description: ADT


title: ADT_EXP20001095_Sample_05

description: ADT


title: THP-1-shCTRL-rep2

city: Duarte

first: Xin

last: He

address: 1500 E Duarte Rd

institute: City of Hope

data_processing:
Basecalls performed using bcl2fastq v2.18.0.12
Sequenced reads were aligned to the mouse hg38 reference genome with TopHat2 (v 2.0.14)
Gene expression level was quantified by HTSeq (v 0.6.1), and differential expression analysis by DESeq2 (v 1.14.1)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts (HTSeq counts) for each sample

source_name: AML cell line

growth_protocol: CB cells were cultured in StemSpan serum-free medium, supplemented with human growth factors including human SCF, TPO, FLT-3 ligand, IL-3 and IL-6 . MV4-11 cells were cultured with IMDM medium with 10% FBS and 1% penicillin-streptomycin. THP-1 cells were cultured in RPMI 1640 medium with 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted using Trizol Reagent (Thermo Fisher Scientific) following the manufacture's instructions. RNA quality was assessed by spectrophotometry(NanoDrop, ND1000) and gel electrophoresis. To be considered as high-quality, the RNA had to have the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).
RNA sequencing libraries were prepared with Kapa RNA HyperPrep kit with polyA kit (Kapa Biosystems, Cat KR1352) according to the manufacturer's protocol. Sequencing run was performed in the single read mode of 51cycle of read1 and 7 cycles of index read using Illumina HiSeq 2500 with HiSeq SBS V4 Kits. Real-time analysis (RTA) 2.2.38 software was used to process the image analysis.

treatment_protocol: Cells were transduced with PRMT1 shRNA or control shRNA

value: AML cell line

tag: lentiviral vector

value: shCTRL

tag: genotype

value: control


title: THP-1-shPRMT1-rep2

value: PRMT1 KO


title: MV4-11-shPRMT1-rep2


title: ADT_EXP20001114_Sample_05

description: ADT


title: MDA-MB-453_Suspended_Vehicle_DHT


title: MV4-11-shPRMT1-rep1


title: THP-1-shCTRL-rep1


title: THP-1-shPRMT1-rep1


title: ADT_EXP20001095_Sample_01

description: ADT


title: ADT_EXP20001095_Sample_04

description: ADT


title: ADT_EXP20001095_Sample_03

description: ADT


title: MV4-11-shCTRL-rep1


title: MV4-11-shCTRL-rep2


title: ADT_EXP20001003_Sample_08

description: ADT


title: CB-shPRMT1-rep2

source_name: Cord blood cells

value: FLT3-ITD transfected cord blood CD34+ cells


title: CB-shCTRL-rep2


title: ADT_EXP20001003_Sample_06

description: ADT

value: unexposed


title: ADT_EXP20001003_Sample_07

description: ADT


title: ADT_EXP20001003_Sample_04

description: ADT


title: ADT_EXP20001003_Sample_05

description: ADT


title: ADT_EXP20001095_Sample_08

description: ADT


title: CB-shCTRL-rep1


title: ADT_EXP20001003_Sample_02

description: ADT


title: second batch WT LLPS monocyte

city: Blacksburg

first: Liwu

last: Li

state: VA

address: 1015 Life Science Cir

institute: Virginia Tech

description: mRNA

data_processing:
Cellranger
Genome_build: mm10 (GRCm38)
Supplementary_archives_format_and_content: *pro.tar.gz archives with barcodes.tsv, features.tsv, and matrix that can be read by Seurat.

organism: Mus musculus

source_name: monocyte

growth_protocol: BM cells isolated from WT C57BL/6 mice and Tram-/- mice were cultured in complete RPMI 1640 medium supplemented with M-CSF (10 ng/mL).

extract_protocol:
cDNA libraries were generated from treated cells by using the 10X Genomics Chromium Single Cell 3' Reagent Kits (version 3 Chemistry).
Single-cell suspensions were loaded onto the Chromium Controller to generate 1,000 single-cell gel beads in emulsion per sample. The cDNA of each sample after amplification of 12 cycles was quantified by Qubit and quality-checked by Bioanalyzer to verify the size distribution of cDNA samples and determine indexed PCR amplification of 15 cycles to yield a sufficient and unbiased library for sequencing. After library quality control by Tapestation, indexed library samples were quantified by KAPA library quantification kit (Universal) and pooled with 15 ul of 5 nM for each sample.
Libraries were pooled together for sequencing on Illumina Hiseq4000.

treatment_protocol: Cultured monocytes were treated with PBS or 100 pg/ml LPS on day 0, 2, and 4 of the culture period.

value: Bone marrow-derived monocytes

value: low dose LPS

tag: strain

value: WT


title: second batch WT PBS monocyte

description: mRNA

tag: cell type

value: PBS


title: ADT_EXP20001095_Sample_06

description: ADT


title: Tram -/- LLPS monocyte

description: mRNA

value: Tram -/-


title: ADT_EXP20001003_Sample_01

description: ADT


title: ADT_EXP20000910_Sample_12

description: ADT


title: Tram -/- PBS monocyte

description: mRNA


title: ADT_EXP20000910_Sample_11

description: ADT


title: first batch WT LLPS monocyte 2

description: mRNA


title: ADT_EXP20001095_Sample_02

description: ADT


title: ADT_EXP20000910_Sample_10

description: ADT


title: ADT_EXP20000910_Sample_08

description: ADT


title: first batch WT LLPS monocyte 1

description: mRNA


title: CB-shPRMT1-rep1


title: first batch WT PBS monocyte 2

description: mRNA


title: ADT_EXP20000910_Sample_07

description: ADT


title: ADT_EXP20000910_Sample_09

description: ADT


title: first batch WT PBS monocyte 1

description: mRNA


title: BMDM LPS10Control R2

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm39 genome using HISAT2.
Read counts were calculated using HTSeq-count.
Differentially expressed genes were evaluated using DESeq2.
Genome_build: GRCm39
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Bone marrow-derived macrophages (BMDM)s

growth_protocol: Bone marrow-derived macrophages (BMDM)s were cultured in DMEM suplemented wth 10% (v/v) fetal bovine serum (GIBCO, Grand Island, NY, USA), 1% (w/v) sodium pyruvate, 1% (w/v) HEPES, 100 U/ml pen/strep, 20% L929 cell conditioned media and 5% horse serum.

extract_protocol:
BMDM cells were harvestd, and RNA was extracted using Trizol reagent and Direct-zol RNA isolation kit (Zymo Research, CA, USA). Illumina TruSeq RNA Sample Prep Kit  was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMDMs were stimulated by lipopolysaccharide (LPS) followed by carboplatin treatment.

value: Bone marrow-derived macrophages (BMDM)s

value: LPS 10 ng/ml


title: ADT_EXP20000910_Sample_04

description: ADT

value: PBMC


title: BMDM LPS10Control R1


title: ADT_EXP20000910_Sample_06

description: ADT


title: ADT_EXP20000910_Sample_05

description: ADT


title: BMDM Tol-Carbo25 R3

value: LPS 100 ng/ml and carboplatin followed by LPS 10 ng/ml


title: BMDM Tol-Carbo25 R2


title: ADT_EXP20000910_Sample_03

description: ADT


title: ΔaltRP ZLM1

city: Honolulu

first: Sladjana

last: Prisic

state: HI

address: 2538 McCarthy Mall

department: School of Life Sciences

institute: University of Hawaii, Manoa

data_processing:
Raw reads were initially analyzed by fastQC. Illumina adapter sequences were trimmed using trimmomatic and fastQC was done on the trimmed reads. Bowtie 2 was used to align trimmed reads and featureCounts to map reads to protein-coding and non-coding RNA from BAM files.
Reference genome files in .gtf and .fasta formats were obtained from NCBI
The tagwise abundances were normalized using trimmed means of M-values (TMM) method in edgeR to obtain logCPM values for each feature and the and Quantile-adjusted conditional maximum likelihood (qCML) linear modeling approach of normalized gene abundances was used to determine the common dispersion using limma. Differential gene expression of the linearized model was determined using an “exact-like test” that utilizes a negative binomial distribution model and Benjamini-Hochberg false discovery rate  approximation to control for the family-wise error rate
Genome_build: ASM1500v1.39
Supplementary_files_format_and_content: Mapped raw count data is provided in a comma-separated values spreadsheet that contains the mapped reads for all biological replicates of each strain and condition. Locus tags and accession numbers for each gene are provided in the first column.

organism: Mycolicibacterium smegmatis

source_name: bacterial culture

growth_protocol: Msm was grown in 7H9-ADC broth medium until mid-log phase (OD ~0.8) and centrifuged. The 7H9-ADC supernatant was removed and the cell pellets were washed three times in Sautons medium without added zinc (ZLM). Cell pellets were resuspended in ZLM and normalized to OD600=1. Polycarbonate flasks (250 mL) with 50 mL of ZLM were inoculated with 50 uL of normalized bacteria (1:1000). Zinc sulfate was added at 6 uM final concentration to the zinc-replete cultures (ZRM). Cultures were grown to late log phase (3 days) at 37oC with shaking at 120rpm. On day 3, cultures were centrifuged at 4oC and the cell pellets were resuspended in 1mL TRIzol.

extract_protocol:
Bacterial cell pellets in TRIzolTM were lysed via beating 3 times for 45 seconds at 7000 rpm in a MagNA Lyser (Roche) with cooling on ice for 3 minutes between cycles. Screw cap tubes were spun at 12,000xg for 5 minutes at 4°C and the supernatant was transferred to new 1.5 mL tubes. RNA and proteins were extracted from TRIzolTM supernatants concurrently, following the manufacturer’s protocol. Precipitated RNA from the aqueous TRIzolTM fraction was resuspended in nuclease free water and purified using High Pure RNA Isolation kit (Roche, Cat. #: 11828665001) with omission of the on-column DNase digest step. Purified RNA was quantified using the ratio of absorbance at 260 and 280 nm using a NanodropTM (Thermo ScientificTM) spectrophotometer and digested in solution twice with TURBOTM DNase (InvitrogenTM, Cat. #: AM2239) following the manufacturer’s directions. DNase-digested RNA was re-purified using the same kit as before. Ribosomal RNA was depleted from the samples using Ribo-Zero plus rRNA depletion kit (Illumina®, Cat. #:20037135) before being sequenced on an Illumina® MiSeq platform for generation of 150 base pair paired end reads. RNA sequencing (RNAseq) was performed by GENEWIZ® (South Plainfield, NJ 07080).
Ribosomal RNA was depleted from the samples using Ribo-Zero plus rRNA depletion kit (Illumina®, Cat. #:20037135) before being sequenced on an Illumina® MiSeq platform for generation of 150 base pair paired end reads. RNA sequencing (RNAseq) was performed by GENEWIZ® (South Plainfield, NJ 07080). GENEWIZ prepared the libraries using Illumina's protocols for MISeq.

value: altRP deletion

tag: zinc added to media

value: none added

value: bacterial culture


title: ΔaltRP ZLM3

tag: tissue


title: ΔaltRP/c ZLM1

value: altRP/c deletion


title: WT ZLM3

value: wild type (mc2 155)


title: BMDM LPS10Control R3


title: BMDM Tol-Carbo25 R1


title: ΔaltRP/c ZLM3


title: ΔaltRP/c ZLM2


title: BMDM Tol R3

value: LPS 100 ng/ml followed by LPS 10 ng/ml


title: WT ZLM1


title: ADT_EXP20000910_Sample_01

description: ADT

tag: subject


title: WT ZRM2

value: 6 uM


title: WT ZLM2


title: WT ZRM3


title: BMDM Tol R2


title: BMDM Tol R1


title: ΔaltRP ZLM2


title: WT ZRM1


title: BMDM LPS100-Carbo25 R3

value: LPS 100 ng/ml together with carboplatin 25 uM


title: pdgfrb-positive/um148 mutant rep3

city: Worcester

first: Nathan

middle: D.

last: Lawson

address: 364 Plantation Street

department: Molecular, Cell, and Cancer Biology

institute: University of Massachusetts Medical School

description:
mRNA
um148pdgfrb33
alldetectedWtvUm148.csv

data_processing:
Bulk RNA-seq:
Raw HiSeq2000 data files were processed with CASAVA 1.8.2 (Illumina) to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples, if index sequences were non-redundant, we allowed for 1 mismatch or N in the index.
Paired end reads were mapped to the zebrafish genome (GRCz11) using STAR.
Mapped reads were quantified using a custom annotation (V4.3.gtf) using RSEM.
Differentially expressed genes were identified using DEseq2.
Single-cell RNA-seq (scRNA-seq):
Sequencing was performed on a HiSeq4000.
Reads were mapped and quantified using cellranger, v3.1.0 (10x Genomics).
RNAseq pipelines were run in the DolphinNext environment.
Genome_build: GRz11
Supplementary_files_format_and_content: alldetectedWtvUm148.csv: Comma-separated formatted output from DEseq2 for differential gene expression.
Supplementary_files_format_and_content: MEX formatted files (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) from scRNA-seq cellranger output.

organism: Danio rerio

source_name: pdgfrb:citrine-positive cells

extract_protocol: oligo dT primed libraries were constructed using the TotalScript kit (Epicentre).

treatment_protocol: Embryos were dissociated into single cell suspensions and transgene expressing cells were isolated by fluorescence activated cell sorting.

tag: Stage

value: 5 days post fertilization

tag: source

value: FACS-isolated cells

value: pdgfrb:citrine-positive cells


title: ADT_EXP20000880_Sample_03_hashed sample

description: ADT

value: multiplexed sample

tag: cohort


title: MC-SOX9-GFPhi_rep2

city: Los Angeles

first: Denis

last: Evseenko

state: CA

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

data_processing:
Raw fastq files were analyzed in Partek flow (version 10.0.21.0801). Reads were aligned to mouse GRCm38 (mm10) genome using Gencode Release M25 reference using STAR aligner (version 2.7.3a). Transcript levels were quantified to the reference using Partek E/M with default parameters. Normalization was done using counts per million (CPM) method. Genes were considered to be differentially expressed based on fold change>2 and FDR<0.05
Genome_build: mm10-Gencode Genes- release M25
Supplementary_files_format_and_content: Normalized counts

source_name: chondrocytes

extract_protocol:
Total RNA was isolated using QIAGEN RNeasy Mini kit and quantified using Qubit fluorometer (Thermo Fisher Scientific). Quality of the isolated RNA was checked using Agilent Bioanalyzer 2100. Universal Plus mRNA-Seq Library with NuQuant (TECAN) was used to generate stranded RNA-seq libraries. Briefly, poly(A) RNA was selected followed by RNA fragmentation. Double stranded cDNA was generated thereafter using a mixture of random and oilgo(dT) priming. The library was then constructed by end repairing the cDNA to generate blunt ends, ligation of Unique Dual Index (UDI) adaptors, strand selection and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Quality of the library was checked using Agilent Bioanalyzer 2100. Sequencing was performed on Illumina Hiseq3000 with single end 50 base pair reads.
Universal Plus mRNA-Seq Library with NuQuant (TECAN)

value: SOX9-GFP (postnatal day7) chondrocytes


title: pdgfrb-positive/um148 mutant rep1

description:
mRNA
um148pdgfrb15
alldetectedWtvUm148.csv


title: BMDM LPS100-Carbo25 R2

value: Bone marrow-derived macrophages (BMDM)s


title: ADT_EXP20000880_Sample_01_hashed sample

description: ADT


title: S18_Fam6_Hom

city: Adelaide

first: Lachlan

last: Baer

address: North Terrace

country: Australia

institute: The University of Adelaide

description:
Homozygous mutant (-/-) 4-month-old zebrafish pooled brains
genes.out

data_processing:
Raw data was trimmed with AdapterRemoval v2.2.1 with parameters: --minquality 30 –minlength 50.
Trimmed data was aligned to GRCz11 sourced from Ensembl Release 98 using STAR v2.7.0a with default parameters.
Aligned data was summarised at the gene-level with featureCounts from the Subread package v1.5.2 with default parameters.
Genome_build: GRCz11
Supplementary_files_format_and_content: Estimated raw counts in tab delimited file format.

molecule: polyA RNA

source_name: Pooled whole-brains

extract_protocol:
Total RNA was extracted from pooled brains and purified for mRNA using the NEBNext® UltraTM RNA Library Prep Kit for Illumina (New England BioLabs, Massachusetts, United States) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: mfn2 genotype

tag: # of brains

tag: gender ratio

value: 2 female, 2 male

tag: family


title: BMDM LPS100-Carbo25 R1

tag: treatment


title: S17_Fam6_Het

description:
Heterozygous mutant (+/-) 4-month-old zebrafish pooled brains
genes.out


title: ADT_EXP20000854_Sample_08

description: ADT

value: PBMC

value: convalescent


title: S15_Fam5_Hom


title: ADT_EXP20000910_Sample_02

description: ADT

value: unexposed


title: S14_Fam5_Het


title: BMDM LPS100 R3

value: LPS 100 ng/ml


title: ADT_EXP20000880_Sample_04_hashed sample

description: ADT


title: MC-SOX9-GFPhi_rep1


title: S13_Fam5_WT

description:
Wild type 4-month-old zebrafish pooled brains
genes.out


title: ADT_EXP20000854_Sample_07

description: ADT


title: S10_Fam4_WT


title: S11_Fam4_Het


title: BMDM LPS100 R1


title: ADT_EXP20000854_Sample_06

description: ADT


title: S8_Fam3_Het


title: ADT_EXP20000854_Sample_04

description: ADT


title: S7_Fam3_WT


title: ADT_EXP20000880_Sample_02_hashed sample

description: ADT


title: pdgfrb-positive/um148 mutant rep2

description:
mRNA
um148pdgfrb18
alldetectedWtvUm148.csv


title: S9_Fam3_Hom


title: BMDM Unstim R3

value: Untreated control


title: BMDM Unstim R2


title: BMDM LPS100 R2


title: S6_Fam2_Hom


title: ADT_EXP20000854_Sample_03

description: ADT


title: S5_Fam2_Het


title: ADT_EXP20000854_Sample_05

description: ADT


title: S16_Fam6_WT


title: S4_Fam2_WT


title: ADT_EXP20000854_Sample_02

description: ADT


title: S3_Fam1_Hom


title: CD8TcmStim_Tcf1ko_RNA_r2

city: Nutley

first: Haihui

last: Xue

state: NJ

address: 123 Metro Boulevard, Bldg. 123, Rm. 5527

department: Center for Discovery and Innovation

institute: Hackensack University Medial Center

data_processing:
Paired end sequenced reads were trimmed for 30bp from both ends to remove the low quality base. RNA-seq reads were then mapped to mm10 genome with hisat2 and only reads with MAPQ>30 were considered in following analysis. Expression index (RPKM) is generated by Stringtie. Differential expression analysis were performed by DESeq2 with adjusted p.value < 0.1, fold change >=1.5 and RPKM in higher expression condition >=1. ATAC-seq reads were trimmed to 36bp from 3'end and then mapped to mm10 genome with bowtie2. Peaks were detected (with Q30 reads) using macs2 PE mode (with -q 0.01 and --keep-dup 1 parameters). ChIP-seq reads were trimmed to 51bp and then mapped to mm10 genome with bowtie2. Peaks were detected (with Q30 unique reads) using macs14 (with -p 1e-5, --nomodel and --shiftize 73 parameters).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files (generated by HT-seq) include raw reads count of genes in each RNA-seq Sample. Normalized signal track (in bigwig format) for each ATAC-seq and ChIP-seq sample.

source_name: CD8+ central memory T cells

growth_protocol: CD45.2+ WT or Tcf1-deficient P14 TCR transgenic CD8 T cells were adoptively transferred into CD45.1+ B6.SJL recipients, followed by i.v. infection with LCMV-Armstrong. After ≥ 30 days, CD45.2+CD8+CD62L+ Tcm cells were sort purified  for downstream analysis.

extract_protocol:
Resting or TCR-stimulated Tcm cells (WT and Tcf1-deficient) were used for total RNA extraction using standard Qiagen RNeasy columns
RNA libraries were prepared for sequencing using stardard Illumina protocol

treatment_protocol: Ex vivo sorted Tcm cells were used directly as resting cells. Another batch or portion of the sorted Tcm cells was cultured with GP33 peptide for 24 hrs and used as TCR-stimulated cells

value: splenocytes

value: TCR-stimulated Tcf1-deficient Tcm cells

tag: cell phenotype


title: S12_Fam4_Hom


title: S2_Fam1_Het


title: ADT_EXP20000854_Sample_01

description: ADT

source_name: CD8+ T cells


title: S1_Fam1_WT


title: CD8TcmStim_Tcf1ko_RNA_r1


title: CD8TcmStim_ctrl_RNA_r2

value: TCR-stimulated WT Tcm cells


title: BMDM Unstim R1


title: CD8TcmRest_Tcf1koG_RNA_r1

value: resting Tcf1-deficient Tcm cells


title: CD8TcmStim_ctrl_RNA_r1


title: CD8TcmRest_Tcf1koG_RNA_r2


title: CD8TcmRest_ctrlG_RNA_r2

value: resting WT Tcm cells


title: CD8TcmRest_ctrlG_RNA_r1


title: ADT_EXP20000780_Sample_03

description: ADT


title: ADT_EXP20000768_Sample_02

description: ADT


title: ADT_EXP20000780_Sample_02

description: ADT


title: ADT_EXP20000768_Sample_04

description: ADT


title: ADT_EXP20000768_Sample_03

description: ADT


title: ADT_EXP20000768_Sample_01

description: ADT


title: ADT_EXP20000722_Sample_07

description: ADT


title: PBMC-AIDS-rep48

description:
Gene expression of AIDS patient after ART
B7_NS

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

source_name: PBMCs, AIDS, replicate 48

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

extract_protocol: Total RNA was extracted and purified using PAXgene  Blood miRNA Kit (Cat#763134, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: disase state

value: AIDS

tag: virus load

value: LVL

tag: gender

value: male

value: Peripheral blood mononuclear cells


title: PBMC-health-rep5

description:
Gene expression of healthy control
D23_NS

source_name: PBMCs, health, replicate 3

value: healthy

value: unknown


title: PBMC-health-rep4

description:
Gene expression of healthy control
D26_NS

source_name: PBMCs, health, replicate 4


title: PBMC-health-rep2

description:
Gene expression of healthy control
D30_NS

source_name: PBMCs, health, replicate 6


title: PBMC-AIDS-rep45

description:
Gene expression of AIDS patient after ART
B4_NS

source_name: PBMCs, AIDS, replicate 45


title: CD8TcmStim_Tcf1ko_ATAC_r2

extract_protocol:
Resting or TCR-stimulated Tcm cells (WT and Tcf1-deficient) were treated with TN5 transposase to generate tagged DNA fragments.
TN5-tagged DNA fragements were purified, PCR amplified to build ATAC-seq libraries

tag: genotype


title: PBMC-AIDS-rep50

description:
Gene expression of AIDS patient after ART
B9_NS

source_name: PBMCs, AIDS, replicate 50


title: PBMC-AIDS-rep46

description:
Gene expression of AIDS patient after ART
B5_NS

source_name: PBMCs, AIDS, replicate 46

value: HVL


title: PBMC-health-rep3

description:
Gene expression of healthy control
D29_NS

source_name: PBMCs, health, replicate 5


title: PBMC-health-rep6

description:
Gene expression of healthy control
D11_NS

source_name: PBMCs, health, replicate 2


title: PBMC-health-rep7

description:
Gene expression of healthy control
D08_NS

source_name: PBMCs, health, replicate 1


title: PBMC-AIDS-rep49

description:
Gene expression of AIDS patient after ART
B8_NS

source_name: PBMCs, AIDS, replicate 49


title: PBMC-AIDS-rep47

description:
Gene expression of AIDS patient after ART
B6_NS

source_name: PBMCs, AIDS, replicate 47


title: PBMC-AIDS-rep44

description:
Gene expression of AIDS patient after ART
B3_NS

source_name: PBMCs, AIDS, replicate 44


title: CD8TcmStim_Tcf1ko_ATAC_r1


title: ADT_EXP20000722_Sample_06

description: ADT

value: PBMC

tag: cell type


title: ADT_EXP20000722_Sample_05

description: ADT

value: convalescent


title: CD8TcmStim_ctrl_ATAC_r2


title: CD8TcmStim_ctrl_ATAC_r1


title: ADT_EXP20000722_Sample_03

description: ADT


title: ADT_EXP20000722_Sample_04

description: ADT


title: ADT_EXP20000722_Sample_01

description: ADT


title: CD8TcmRest_Tcf1ko_ATAC_r2


title: CD8TcmRest_Tcf1ko_ATAC_r1


title: ADT_EXP20000683_Sample_08

description: ADT


title: CD8TcmRest_ctrl_ATAC_r2


title: ADT_EXP20000683_Sample_07

description: ADT


title: CD8TcmRest_ctrl_ATAC_r1


title: ADT_EXP20000683_Sample_01

description: ADT


title: PBMC-AIDS-rep42

description:
Gene expression of AIDS patient after ART
B28_NS

source_name: PBMCs, AIDS, replicate 42


title: PBMC-AIDS-rep43

description:
Gene expression of AIDS patient after ART
B29_NS

source_name: PBMCs, AIDS, replicate 43


title: PBMC-AIDS-rep38

description:
Gene expression of AIDS patient after ART
B22_NS

source_name: PBMCs, AIDS, replicate 38


title: PBMC-AIDS-rep34

description:
Gene expression of AIDS patient after ART
B18_NS

source_name: PBMCs, AIDS, replicate 34


title: Vismodegib_rep3

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

department: Medicine

institute: Univ of Alabama at Birmingham

description: Vismodegib- Vismodegib treated tumor sample

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software, (.bcl files) generated from Illumina HiSeq was converted into FASTQ FASTQ files were de-multiplexed using Illumina's bcl2fastq 2.17 software
Sequence reads in fastq format were trimmed at each end of reads using read quality score vendor sequencing adaptors removed, and reads aligned against mouse mm10 genome  using STAR algorithm
Adaptor sequences were removed using Cutadapt tool before alignment HISAT2 algorithm.  Reads Per Kilobase of transcript per million mapped reads (RPKM) methods were  applied for normalization after PCR replicates were removed using SAMtools.  Gene level quantification and statistics were performed using Partek Genomic Suite (PGS, St Louis, MO).
Genome_build: mm10

source_name: RNA extracted from mammary tumors (Balb/c 4T1 model)

growth_protocol: 4T1 Cells were maintained in culture in DMEM F12 supplemented with 10% FBS

extract_protocol:
Tumors were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNA was then sent to GENEWIZ for sample anaylsis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 500,000 4T1 cells were injected into the inguinal mammary fat pat of Balb/c mice. After tumor establishment, mice were treated with either DMSO (Vehicle control) or Vismodegib (2mg per mouse) 3 times weekly for 3 weeks

tag: strain

value: Balb/c

value: Mammary Tumor Tissue

tag: age

value: 10 week old mice


title: PBMC-AIDS-rep39

description:
Gene expression of AIDS patient after ART
B24_NS

source_name: PBMCs, AIDS, replicate 39

tag: tissue


title: PBMC-AIDS-rep36

description:
Gene expression of AIDS patient after ART
B2_NS

source_name: PBMCs, AIDS, replicate 36


title: PBMC-AIDS-rep33

description:
Gene expression of AIDS patient after ART
B17_NS

source_name: PBMCs, AIDS, replicate 33

value: female


title: PBMC-AIDS-rep41

description:
Gene expression of AIDS patient after ART
B26_NS

source_name: PBMCs, AIDS, replicate 41


title: PBMC-AIDS-rep28

description:
Gene expression of AIDS patient after ART
B11_NS

source_name: PBMCs, AIDS, replicate 28


title: PBMC-AIDS-rep40

description:
Gene expression of AIDS patient after ART
B25_NS

source_name: PBMCs, AIDS, replicate 40


title: PBMC-AIDS-rep29

description:
Gene expression of AIDS patient after ART
B12_NS

source_name: PBMCs, AIDS, replicate 29


title: PBMC-AIDS-rep32

description:
Gene expression of AIDS patient after ART
B16_NS

source_name: PBMCs, AIDS, replicate 32


title: PBMC-health-rep1

description:
Gene expression of healthy control
D31_NS

source_name: PBMCs, health, replicate 7


title: PBMC-AIDS-rep31

description:
Gene expression of AIDS patient after ART
B15_NS

source_name: PBMCs, AIDS, replicate 31


title: Vismodegib_rep2


title: PBMC-AIDS-rep30

description:
Gene expression of AIDS patient after ART
B13_NS

source_name: PBMCs, AIDS, replicate 30


title: ADT_EXP20000654_Sample_06

description: ADT

source_name: CD8+ T cells

tag: subject


title: ADT_EXP20000654_Sample_04

description: ADT


title: PBMC-AIDS-rep37

description:
Gene expression of AIDS patient after ART
B21_NS

source_name: PBMCs, AIDS, replicate 37


title: ADT_EXP20000654_Sample_05

description: ADT


title: DMSO_rep3

description: DMSO- DMSO treated tumor sample


title: ADT_EXP20000654_Sample_03

description: ADT


title: PBMC-AIDS-rep27

description:
Gene expression of AIDS patient after ART
B10_NS

source_name: PBMCs, AIDS, replicate 27


title: PBMC-AIDS-rep25

description:
Gene expression of AIDS patient after ART
A7_NS

source_name: PBMCs, AIDS, replicate 25


title: PBMC-AIDS-rep23

description:
Gene expression of AIDS patient after ART
A5_NS

source_name: PBMCs, AIDS, replicate 23


title: PBMC-AIDS-rep24

description:
Gene expression of AIDS patient after ART
A6_NS

source_name: PBMCs, AIDS, replicate 24


title: DMSO_rep2

description: DMSO- DMSO treated tumor sample

source_name: RNA extracted from mammary tumors (Balb/c 4T1 model)


title: Vismodegib_rep1

description: Vismodegib- Vismodegib treated tumor sample


title: DMSO_rep1

description: DMSO- DMSO treated tumor sample


title: PBMC-AIDS-rep22

description:
Gene expression of AIDS patient after ART
A4_NS

source_name: PBMCs, AIDS, replicate 22


title: VDJ-seq_EXP20001394_Sample_06_hashed sample

description: VDJ-seq

value: multiplexed sample


title: PBMC-AIDS-rep26

description:
Gene expression of AIDS patient after ART
B1_NS

source_name: PBMCs, AIDS, replicate 26


title: VDJ-seq_EXP20001394_Sample_04_hashed sample

description: VDJ-seq


title: SK_SGN_AD009

city: London

first: Mohi

last: Ahmed

address: Great Maze Pond

country: United Kingdom

institute: King's College London

data_processing:
Galaxy version 2.1.0
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HiSAT2 version 2.1.0 with the default parameters in Galaxy version 2.1.0
DESeq2 (2.11.40.6) with parametric fit was used for normalisation
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 normalised counts

source_name: Neurons - HOM

extract_protocol:
Spiral ganglia neurons and cochlear hair cells were isolated from the inner ears, FACS-sorted and processed using the NEB Monarch kit (T2010S/L) for polyA+ RNA isolation.
NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina [E6420S] and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) [E7335S] was used for library preparation (as per kit instructions).
RNA and cDNA quality were analysed using Agilent Total RNA 6000 Pico or High Sensitivity DNA Assay on a Bioanalyser (Agilent, 2100) and RNA-sequencing performed using Illumina HiSeq 4000 75bp paired-end reads.

value: Spiral Ganglion

value: Postnatal day 4


title: VDJ-seq_EXP20001394_Sample_05_hashed sample

description: VDJ-seq


title: ADT_EXP20000654_Sample_02

description: ADT


title: SK_SGN_AD010


title: SK_SGN_AD008


title: SH_SGN_AD007

source_name: Neurons - HET


title: VDJ-seq_EXP20001394_Sample_02_hashed sample

description: VDJ-seq


title: PBMC-AIDS-rep21

description:
Gene expression of AIDS patient after ART
A30_NS

source_name: PBMCs, AIDS, replicate 21


title: PBMC-AIDS-rep16

description:
Gene expression of AIDS patient after ART
A25_NS

source_name: PBMCs, AIDS, replicate 16


title: PBMC-AIDS-rep17

description:
Gene expression of AIDS patient after ART
A26_NS

source_name: PBMCs, AIDS, replicate 17


title: PBMC-AIDS-rep35

description:
Gene expression of AIDS patient after ART
B19_NS

source_name: PBMCs, AIDS, replicate 35


title: PBMC-AIDS-rep18

description:
Gene expression of AIDS patient after ART
A27_NS

source_name: PBMCs, AIDS, replicate 18


title: PBMC-AIDS-rep20

description:
Gene expression of AIDS patient after ART
A3_NS

source_name: PBMCs, AIDS, replicate 20


title: PBMC-AIDS-rep12

description:
Gene expression of AIDS patient after ART
A21_NS

source_name: PBMCs, AIDS, replicate 12


title: PBMC-AIDS-rep14

description:
Gene expression of AIDS patient after ART
A23_NS

source_name: PBMCs, AIDS, replicate 14


title: PBMC-AIDS-rep11

description:
Gene expression of AIDS patient after ART
A20_NS

source_name: PBMCs, AIDS, replicate 11


title: VDJ-seq_EXP20001394_Sample_01_hashed sample

description: VDJ-seq

source_name: CD8+ T cells


title: SH_SGN_AD006


title: PBMC-AIDS-rep10

description:
Gene expression of AIDS patient after ART
A2_NS

source_name: PBMCs, AIDS, replicate 10


title: VDJ-seq_EXP20001265_Sample_02_hashed sample

description: VDJ-seq


title: VDJ-seq_EXP20001265_Sample_03_hashed sample

description: VDJ-seq


title: SH_SGN_AD005


title: SC_SGN_AD002

source_name: Neurons - CTRL


title: PBMC-AIDS-rep19

description:
Gene expression of AIDS patient after ART
A28_NS

source_name: PBMCs, AIDS, replicate 19


title: VDJ-seq_EXP20001394_Sample_03_hashed sample

description: VDJ-seq


title: SC_SGN_AD001


title: VDJ-seq_EXP20001265_Sample_01_hashed sample

description: VDJ-seq


title: CH_HC_AD011

source_name: Hair Cells - CTRL

value: Cochlea

value: Embryonic day 16.5


title: PBMC-AIDS-rep15

description:
Gene expression of AIDS patient after ART
A24_NS

source_name: PBMCs, AIDS, replicate 15

value: AIDS


title: VDJ-seq_EXP20001260_Sample_05_hashed sample

description: VDJ-seq


title: VDJ-seq_EXP20001260_Sample_04_hashed sample

description: VDJ-seq


title: PBMC-AIDS-rep6

description:
Gene expression of AIDS patient after ART
A15_NS

source_name: PBMCs, AIDS, replicate 6

value: male


title: PBMC-AIDS-rep5

description:
Gene expression of AIDS patient after ART
A14_NS

source_name: PBMCs, AIDS, replicate 5

value: Peripheral blood mononuclear cells


title: PBMC-AIDS-rep2

description:
Gene expression of AIDS patient after ART
A11_NS

source_name: PBMCs, AIDS, replicate 2

value: LVL


title: PBMC-AIDS-rep7

description:
Gene expression of AIDS patient after ART
A16_NS

source_name: PBMCs, AIDS, replicate 7


title: PBMC-AIDS-rep1

description:
Gene expression of AIDS patient after ART
A1_NS

source_name: PBMCs, AIDS, replicate 1


title: CH_HC_AD010


title: PBMC-AIDS-rep3

description:
Gene expression of AIDS patient after ART
A12_NS

source_name: PBMCs, AIDS, replicate 3


title: CD8TcmRest_ctrl_HiC_r1

data_processing:
HiC data was processed by distiller-nf pipeline (v0.3.3) in 10kb resolution for Resting Tcm cells (WT and Tcf1-deficient), with 2 replicates for each condition.Resulting HiC raw count cool files were then processed into sparse interaction matrices by cooler(v0.8.11).
Genome_build: mm10
Supplementary_files_format_and_content: raw count interaction matrices in cool format for HiC sample.

source_name: CD8+ central memory T cells

extract_protocol:
WT resting Tcm cells were sort-purified from the spleen, crosslinked, digested with three restriction enzymes and underwent proximity ligation.
The biotinylated DNA segments were captured, and ligated to the Illumina Paired End Adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-2000 platform.

treatment_protocol: Ex vivo sorted Tcm cells were used directly as resting cells.

value: splenocytes

value: resting WT Tcm cells


title: PBMC-AIDS-rep8

description:
Gene expression of AIDS patient after ART
A17_NS

source_name: PBMCs, AIDS, replicate 8


title: PBMC-AIDS-rep9

description:
Gene expression of AIDS patient after ART
A18_NS

source_name: PBMCs, AIDS, replicate 9


title: PBMC-AIDS-rep4

description:
Gene expression of AIDS patient after ART
A13_NS

source_name: PBMCs, AIDS, replicate 4


title: CD8_Tcf1ko_TCF1_r1

data_processing:
ChIP-seq reads were mapped to mm10 genome with bowtie2. Peaks were detected (with Q30 unique reads) using macs14 (with -p 1e-5, --nomodel and --shiftize 73 parameters).
Genome_build: mm10
Supplementary_files_format_and_content: Normalized signal track (in bigwig format) for each ChIP-seq sample.

extract_protocol:
Naive CD8+ T cells from the spleen were sort-purified, crosslinked and immunoprecipitated with anti-Tcf1 antiserum
The DNA segments from ChIP were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-2000 platform.

value: Tcf1-deficient CD8+ T cells

value: TCRbeta high, CD62L+, CD44 low-med, CD8+


title: CD8_Tcf1ko_TCF1_r2


title: VDJ-seq_EXP20001260_Sample_03_hashed sample

description: VDJ-seq

extract_protocol:
PBMCs were thawed, and CD8+ T cells were enriched by magnetic-activated cell sorting (MACS) using a CD8+ T Cell Isolation Kit (Miltenyi) following the manufacturers protocol. The CD8+ T cells were then stained with 1 nM final concentration tetramer library in the presence of 2 mg/mL salmon sperm DNA in PBS with 0.5% BSA solution for 20 minutes. Cells were then labeled with anti-TCR antibody-derived tag (ADT, IP26, Biolegend) for 15 minutes followed by washing. Tetramer bound cells were then labeled with phycoerythrin (PE) conjugated anti-DKDDDDK-Flag antibody (BioLegend) followed by dead cell discrimination using 7-amino-actinomycin D (7-AAD). The live, tetramer positive cells were sorted using a Sony MA900 Sorter (Sony). Tetramer positive cells were counted by Nexcelom Cellometer (Lawrence, MA, USA) using AOPI stain following manufacturer’s recommended conditions. Single-cell encapsulations were generated utilizing 5’ v1 Gem beads from 10x Genomics (Pleasanton, CA, USA) on a 10x Chromium controller and downstream TCR, and Surface marker libraries were made following manufacturer recommended conditions. All libraries were quantified on a BioRad CFX 384 (Hercules, CA, USA) using Kapa Biosystems (Wilmington, MA, USA) library quantified kits and pooled at an equimolar ratio. TCRs, surface markers, and tetramer generated libraries were sequenced on Illumina (San Diego, CA, USA) NextSeq550 instruments. Sequencing data were processed using the Cell Ranger Software Suite (Version 3). Samples were demultiplexed and unique molecular identifier (UMI) counts were quantified for TCRs, tetramers, and gene expression.
10X Chromium 5' single-cell

value: PBMC


title: VDJ-seq_EXP20001260_Sample_02_hashed sample

description: VDJ-seq


title: HH_HC_AD007

source_name: Hair Cells - HET


title: HH_HC_AD005


title: VFAT Western Diet + NaKtide Replicate 3

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

data_processing:
Reads were trimmed using Trimmomatic v0.38 to remove the first 12 bases, any adapter content, and low-confidence base calls. Resulting reads were filtered for a minimum length of 25bp
Reads were aligned to the grcm38 mouse reference genome using HISAT2 v2.1.0
Read counts per transcript per sample were computed using the GenomicAlignments R/Bioconductor package v1.16.0
By-sample normalization and FPKM values were computed using DESeq2 v 1.20.0
Genome_build: GRCm38 and Enesembl genes v93.
Supplementary_files_format_and_content: raw_counts.csv contains raw read counts per gene per sample, as calculated by the GenomicAlignments R/Bioconductor package, in comma-separated value format
Supplementary_files_format_and_content: normalized_counts.csv contains read counts per gene per sample, normalized by sample using DESeq2 v 1.20.0 with default settings, in comma-separated value format
Supplementary_files_format_and_content: fpkm.csv  contains FPKM values as computed by DESeq2 v 1.20.0, in comma-separated value format

source_name: Visceral Adipose Tissue

growth_protocol: Mice were placed on their respective diets for 12 weeks and given free access to water. At the time of euthenization, all brain parts and other tissues were flash-frozen in liquid nitrogen and maintained at -80οC, preserved in optimal cutting temperature (OCT) compound for sectioning or placed in paraformaldehyde for paraffin embedding.

extract_protocol:
Total RNA was extracted from visceral adipose tissue, subcutaneous adipose tissue, liver, hippocampus, and cerebellum using RNeasy Protect Mini Kit (Qiagen, Germantown, MD)
Libraries were prepared from 1 ug total RNA per sample using the Truseq strand mRNA kit (Illumina , San Diego, CA) according to the manufacturers’ instructions.

treatment_protocol: Mice were placed on a normal chow diet containing 11% fat, 62% carbohydrate, and 27.0% protein with total calories of 12.6 KJ/g and had free access to water or the mice were placed on WD containing 42% fat, 42.7 % carbohydrate, and 15.2% protein yielding 4.5 KJ/g and had free access to water (Pratt et al., 2019). To induce NaKtide expression in Tg mice, custom normal chow or WD (Envigo RMS, Inc.-Teklad Diets) with doxycycline, at a concentration of 300 mg/kg (Cawthorne et al., 2007; Redelsperger et al., 2016), was used (Normal chow with doxycycline: TD.180829; WD with Doxycycline: TD.180830).

value: Visceral Adipose Tissue

tag: diet

value: Western Diet

value: NaKtide


title: VFAT Western Diet + NaKtide Replicate 5


title: CD8TcmRest_Tcf1ko_HiC_r2

value: resting Tcf1-deficient Tcm cells


title: VFAT Western Diet + NaKtide Replicate 4


title: VDJ-seq_EXP20001260_Sample_01_hashed sample

description: VDJ-seq

source_name: CD8+ T cells

value: multiplexed sample

tag: cohort


title: CD8TcmRest_Tcf1ko_HiC_r1


title: CD8TcmRest_ctrl_HiC_r2


title: KH_HC_AD004

source_name: Hair Cells - HOM


title: VFAT Western Diet + NaKtide Replicate 1


title: VDJ-seq_EXP20001249_Sample_06_hashed sample

description: VDJ-seq


title: KH_HC_AD003


title: VDJ-seq_EXP20001249_Sample_05_hashed sample

description: VDJ-seq


title: VFAT Western Diet Replicate 2

value: Control


title: VDJ-seq_EXP20001249_Sample_04_hashed sample

description: VDJ-seq


title: VFAT Western Diet Replicate 4


title: VFAT Western Diet Replicate 5


title: VFAT Western Diet Replicate 1


title: VFAT Western Diet Replicate 3


title: VDJ-seq_EXP20001249_Sample_03_hashed sample

description: VDJ-seq


title: VFAT Western Diet + NaKtide Replicate 2


title: VDJ-seq_EXP20001249_Sample_02_hashed sample

description: VDJ-seq


title: dICSI-AOA (D4)

city: 黄浦区

first: yin

last: mingru

state: 上海市

address: 上海市黄浦区制造局路639号

institute: 上海交通大学医学院附属第九人民医院

data_processing:
Paired-end reads were acquired from the Illumina HiSeq 4000 sequencer. After 3′ adaptor-trimming and removing low quality reads by cutadapt software (v1.9.3), the high quality trimmed reads were used to analyse mRNAs.
The high quality reads were aligned to the mouse reference genome (UCSC mm10) with hisat2 software. Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified.
GO and Pathway enrichment analysis were also performed based on the differentially expressed mRNAs. Alternative splicing was performed by SplAdder software. Differentially expressed mRNAs with statistical significance between groups were identified using fold change cut-off or volcano plot filtering, respectively.
Genome_build: mm10
Supplementary_files_format_and_content: Number of raw junction read

extract_protocol:
Blastocysts were collected, flash frozen on dry ice,and RNA preprocessing for constructing the sequencing library was implemented with the TruSeq Stranded Total RNA Library Prep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: day 3.5 after fertilization

value: dICSI-AOA

value: blastocysts


title: VFAT Control + NaKtide Replicate 2


title: VFAT Control + NaKtide Replicate 4


title: VFAT Control + NaKtide Replicate 3


title: dICSI-AOA (D5)

address: 上海市黄浦区制造局路639号

institute: 上海交通大学医学院附属第九人民医院


title: VFAT Control + NaKtide Replicate 5


title: HH_HC_AD008

value: Cochlea

value: Embryonic day 16.5


title: VDJ-seq_EXP20001249_Sample_01_hashed sample

description: VDJ-seq

data_processing:
Base Calling TCR BCL to TCR FASTQ via Cell Ranger 3.1.0 with the flag "--delete-undetermined" in addition to the standard settings.
Base Calling GEX BCL to GEX FASTQ via Cell Ranger 3.1.0 with the flag "--delete-undetermined" in addition to the standard settings.
Base Calling ADT BCL to ADT FASTQ via Cell Ranger 3.1.0 with the flag "--delete-undetermined" in addition to the standard settings.
Base Calling tetramer BCL to tetramer FASTQ file via bcl2fastq2 version v2.20.0 with the flags "--minimum-trimmed-read-length 0 --mask-short-adapter-reads 0" in addition to the standard settings.
TCR Read Counts: FASTQ to vdj counts via Cell Ranger 3.1.0 using the standard settings.
GEX Read Counts: FASTQ to gene expression counts via Cell Ranger 3.1.0 using the standard settings.
Tetramer FASTQ to Tetramer counts via extracting tetramer barcode from uniquely observed tetramer UMI reads using python script
ADT FASTQ to ADT counts via extracting tetramer barcode from uniquely observed tetramer UMI reads using python script
TCR VDJ counts paired with tetramer and ADT counts via common hydrogel barcode using python script
VDJ and tetramer counts separated via hashtags using Seurat 4.0.3
Dehashed VDJs selected for functional assays.
Genome_build: GRCh38 (hg19)
Supplementary_files_format_and_content: The processed data files conform to the hfad AnnData format: https://anndata.readthedocs.io/en/latest/anndata.AnnData.html
Supplementary_files_format_and_content: Metadta for hashed samples including HTO oligo sequence is available in the file "GEO_upload_seq_CIPHER_2021_11_04_Supplemental_Sample_to_HTO.xlsx"


title: PBMC-AIDS-rep13

description:
Gene expression of AIDS patient after ART
A22_NS

source_name: PBMCs, AIDS, replicate 13

value: AIDS

value: HVL

value: female

value: Peripheral blood mononuclear cells


title: ICSI-AOA (B5)

address: 上海市黄浦区制造局路639号

institute: 上海交通大学医学院附属第九人民医院

value: ICSI-AOA


title: dICSI-AOA (D1)

address: 上海市黄浦区制造局路639号

institute: 上海交通大学医学院附属第九人民医院


title: VFAT Control Replicate 5


title: VFAT Control Replicate 4


title: VFAT Control + NaKtide Replicate 1


title: VDJ-seq_EXP20001234_Sample_04_hashed sample

description: VDJ-seq

value: PBMC


title: VFAT Control Replicate 3

value: Visceral Adipose Tissue


title: KH_HC_AD001


title: ICSI-AOA (B4)

address: 上海市黄浦区制造局路639号

institute: 上海交通大学医学院附属第九人民医院


title: VFAT Control Replicate 2


title: VDJ-seq_EXP20001234_Sample_03_hashed sample

description: VDJ-seq


title: VFAT Control Replicate 1


title: ICSI-AOA (B1)

address: 上海市黄浦区制造局路639号

institute: 上海交通大学医学院附属第九人民医院


title: VDJ-seq_EXP20001234_Sample_02_hashed sample

description: VDJ-seq


title: ICSI (A6)

address: 上海市黄浦区制造局路639号

institute: 上海交通大学医学院附属第九人民医院

value: ICSI


title: SFAT Western Diet + NaKtide Replicate 5

source_name: Subcutaneous Adipose Tissue

value: Subcutaneous Adipose Tissue

value: Western Diet

value: NaKtide


title: SFAT Western Diet + NaKtide Replicate 3


title: VDJ-seq_EXP20001234_Sample_01_hashed sample

description: VDJ-seq

value: multiplexed sample


title: SFAT Western Diet + NaKtide Replicate 4


title: SFAT Western Diet + NaKtide Replicate 1


title: VDJ-seq_EXP20001148_Sample_04_hashed sample

description: VDJ-seq


title: SFAT Western Diet Replicate 4

value: Control


title: ICSI (A5)

address: 上海市黄浦区制造局路639号

institute: 上海交通大学医学院附属第九人民医院

value: day 3.5 after fertilization


title: VDJ-seq_EXP20001148_Sample_03_hashed sample

description: VDJ-seq


title: SFAT Western Diet Replicate 3


title: SFAT Western Diet Replicate 5


title: ICSI (A2)

address: 上海市黄浦区制造局路639号

institute: 上海交通大学医学院附属第九人民医院

value: blastocysts


title: SFAT Western Diet Replicate 2


title: VDJ-seq_EXP20001148_Sample_02_hashed sample

description: VDJ-seq


title: SFAT Control + NaKtide Replicate 5


title: VDJ-seq_EXP20001148_Sample_01_hashed sample

description: VDJ-seq


title: Organoid (biopsy)-derived CoEpiCs on Day 5 of Colon Intestine-Chip culture stimulated for 6h with 1nM IL-22, rep2

first: Lorna

last: Ewart

address: 27 Drydock Avenue

institute: Emulate Inc.

description:
IL22_RNAseq_count.csv
1nM_IL22_17_L7.D711
Organoid (biopsy)-derived colonic epithelial cells on Day 5 of the Colon Intestine-Chip culture stimulated basolaterally for 6h with 1nM IL-22

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. trimmed reads were mapped to Homo sapiens GRCh38 reference genome available on ENSEMBL using STAR aligner v.2.5.2b. STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from Subread package v.1.5.2. Only unique reads that fell within exon regions were counted
Supplementary_files_format_and_content: counts

source_name: organoid (biopsy)-derived colonic epithelial cells from epithelial channel of Colon Intestine-Chip

growth_protocol:
Colon Intestine-Chips (Emulate Inc., Boston, MA, Catalog No: 10231- 2), consist of two parallel channels separated by a porous PDMS membrane (diameter: 7μm, spacing: 40μm, thickness: 50μm), and two lateral channels where vacuum is applied. dimensions of top channel, where colonic epithelial cells reside, are 1000μm x 1000μm (width x height), its volume is 28.041μL and its cell culture surface is 28mm2. endothelial cells were introduced in bottom channel dimensions of which are 1000μm x 200μm (width x height), its volume equal to 5.584μL, and its cell culture surface equal to 24.5mm2. interface of two cell types extended in an area of 17.1mm2. timeline of establishment of Colon Intestine-Chips was following (Figure 1):
Day -1: PDMS membrane was activated using ER1 and ER2 reagents (Emulate, Catalog No: 10465). A solution of 0.5mg/mL ER1 in ER2 was prepared and 50μL was introduced in each channel. Chips were incubated under UV light for 10min, followed by 3min of incubation at room temperature and another 10min of UV treatment. Subsequently, both channels were washed with ER2, then PBS 1X, and coated overnight at 37oC, with 200μg/mL Collagen IV (Sigma Aldrich, Catalog No: C5533) and 100μg/mL Matrigel (Corning), and 200μg/mL Collagen IV (Sigma Aldrich) and 30μg/mL Fibronectin (Corning, Catalog No: 356008), in top and bottom channel respectively.
Day 0: In order to be seeded on Chips, colonoids were recovered from Matrigel using Cell Recovery Solution (Corning), and fragmented by incubation at 37oC for 2min, in a digestion solution containing TrypLE (Thermo Fischer Scientific), diluted with PBS1X 1:1 (vol/vol) and supplemented with 10μM Y-27632. They were resuspended in IntestiCult™ medium, supplemented with 10μm Y-27632 (Sigma- Aldrich) and 5μm CHIR99021 (Stemgent), and introduced in apical channel of Colon Intestine-Chip, in a seeding density of 7 X 106 cells/mL. In order to assess cell density, part of seeding cell suspension was incubated in ACCUTASETM (STEMCELL Technologies, Catalog No: 07920) for 30min and fragmented to a single-cell level. 10μM Y-27632 and 5μM CHIR99021 were maintained in culture medium for 72h thereafter.
When investigating interaction between epithelial and endothelial cells, cHIMECs were seeded on basal side of PDMS membrane 1h prior to seeding of epithelial cells in top channel. Briefly, 20μL of suspension of endothelial cells, in a seeding density of 8 X 10^6 cells/mL were introduced in bottom channel, and Colon Intestine-Chips were incubated inverted at 37oC, in a humidified environment. bottom channel was washed and thereafter immersed in EGM-MV2 medium.
Day 1: Both channels were washed with corresponding media in order to remove non-adherent cells. Colon Intestine-Chips were attached to devices called Pod™ Portable Modules (Emulate Inc., Catalog No: 10153) and connected in automated cell culture system Zoë™ Culture Module (Emulate Inc.). Each Zoë is connected to an OrbTM Hub Module that supplies gas, vacuum, and power. flow rate was set at 60μL/h in both channels.
Day 2: Medium without Y-27632 and CHIR99021, was replenished in both channels.
Day 3: Colon Intestine- Chips were acclimated to mechanical forces, using 2% strain, 0.15Hz frequency.
Day 4: Stretching was increased to 10% strain, 0.15Hz frequency, and culture medium was replenished. Both channels were perfused at 1000μL/h for 5min to flush out any detached cells.
Day 5-8: Culture media was refreshed, and detached cells were removed by flushing (1000µL/h, 5min) every other day of culture.
conventional suspension culture was performed in Matrigel (Corning, Corning, NY, Catalog No: 356231) and in presence of commercially available medium IntestiCult™ Organoid Growth Medium (Human) (STEMCELL Technologies, Vancouver, Canada, Catalog No: 06010), supplemented with antibiotic primocin (Invivogen, San Diego, CA, Catalog No: ant-pm-2) in a concentration of 1:500 (vol/vol).

extract_protocol:
RNA was extracted using TRIzol (Life Technologies) according to manufacturer’s guidelines
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Addition of exogenous Interleukin 22 (IL-22) to vascular channel: Human recombinant IL-22 was purchased from R&D (R&D, Minneapolis, MN, Catalog No: 782-IL-010), and was diluted in Endothelial Cell Growth Medium MV 2 to a final concentration of 10pM 100pM or 1nM. cytokine supplemented medium was refreshed every 24h and appropriate vehicle controls were used in each stimulation experiment. On Day 5, bottom channel of Colon Intestine-Chip was exposed to IL-22, and 6h later epithelial cells were harvested for transcriptomic analysis.

tag: applied mechanostimulation

value: flow (60 μL/h), stretch (10%, 0.15Hz)

tag: air liquid interface


title: Organoid (biopsy)-derived CoEpiCs on Day 5 of Colon Intestine-Chip culture stimulated for 6h with 1nM IL-22, rep3

description:
IL22_RNAseq_count.csv
1nM_IL22_18_L7.D712
Organoid (biopsy)-derived colonic epithelial cells on Day 5 of the Colon Intestine-Chip culture stimulated basolaterally for 6h with 1nM IL-22

value: organoid (biopsy)-derived colonic epithelial cells


title: SFAT Control + NaKtide Replicate 4


title: SFAT Western Diet Replicate 1


title: Organoid (biopsy)-derived CoEpiCs on Day 5 of Colon Intestine-Chip culture stimulated for 6h with 1nM IL-22, rep1

description:
IL22_RNAseq_count.csv
1nM_IL22_16_L7.D710
Organoid (biopsy)-derived colonic epithelial cells on Day 5 of the Colon Intestine-Chip culture stimulated basolaterally for 6h with 1nM IL-22


title: VDJ-seq_EXP20001114_Sample_08

first: Natalie

last: Agar

description: VDJ-seq

value: unexposed


title: SFAT Control + NaKtide Replicate 2


title: SFAT Control + NaKtide Replicate 3


title: SFAT Control + NaKtide Replicate 1


title: VDJ-seq_EXP20001114_Sample_07

description: VDJ-seq


title: SFAT Control Replicate 4


title: Organoid (biopsy)-derived CoEpiCs on Day 5 of Colon Intestine-Chip culture stimulated for 6h with 100pM IL-22, rep3

description:
IL22_RNAseq_count.csv
100pM_IL22_15_L7.D709
Organoid (biopsy)-derived colonic epithelial cells on Day 5 of the Colon Intestine-Chip culture stimulated basolaterally for 6h with 100pM IL-22


title: SFAT Western Diet + NaKtide Replicate 2


title: Organoid (biopsy)-derived CoEpiCs on Day 5 of Colon Intestine-Chip culture stimulated for 6h with 100pM IL-22, rep2

description:
IL22_RNAseq_count.csv
100pM_IL22_14_L6.D708
Organoid (biopsy)-derived colonic epithelial cells on Day 5 of the Colon Intestine-Chip culture stimulated basolaterally for 6h with 100pM IL-22


title: SFAT Control Replicate 3


title: SFAT Control Replicate 2


title: Organoid (biopsy)-derived CoEpiCs on Day 5 of Colon Intestine-Chip culture stimulated for 6h with 10pM IL-22, rep3

description:
IL22_RNAseq_count.csv
10pM_IL22_12_L6.D706
Organoid (biopsy)-derived colonic epithelial cells on Day 5 of the Colon Intestine-Chip culture stimulated basolaterally for 6h with 10pM IL-22


title: SFAT Control Replicate 1


title: Organoid (biopsy)-derived CoEpiCs on Day 5 of Colon Intestine-Chip culture stimulated for 6h with 100pM IL-22, rep1

description:
IL22_RNAseq_count.csv
100pM_IL22_13_L6.D707
Organoid (biopsy)-derived colonic epithelial cells on Day 5 of the Colon Intestine-Chip culture stimulated basolaterally for 6h with 100pM IL-22


title: Organoid (biopsy)-derived CoEpiCs on Day 5 of Colon Intestine-Chip culture stimulated for 6h with 10pM IL-22, rep2

description:
IL22_RNAseq_count.csv
10pM_IL22_11_L6.D705
Organoid (biopsy)-derived colonic epithelial cells on Day 5 of the Colon Intestine-Chip culture stimulated basolaterally for 6h with 10pM IL-22


title: VDJ-seq_EXP20001114_Sample_05

description: VDJ-seq


title: Liver Western Diet + NaKtide Replicate 3

source_name: Liver

value: Liver


title: VDJ-seq_EXP20001114_Sample_03

description: VDJ-seq


title: Liver Western Diet + NaKtide Replicate 2


title: Liver Western Diet + NaKtide Replicate 4


title: VDJ-seq_EXP20001114_Sample_02

description: VDJ-seq


title: Liver Western Diet + NaKtide Replicate 1


title: Unstimulated organoid (biopsy)-derived CoEpiCs on Day 5 of Colon Intestine-Chip culture, rep3

description:
IL22_RNAseq_count.csv
Vehicle_9_L5.D703
Unstimulated organoid (biopsy)-derived colonic epithelial cells on Day 5 of the Colon Intestine-Chip culture


title: Liver Western Diet Replicate 4


title: Liver Western Diet Replicate 5


title: VDJ-seq_EXP20001114_Sample_06

description: VDJ-seq


title: Liver Western Diet Replicate 3


title: VDJ-seq_EXP20001114_Sample_01

description: VDJ-seq


title: SFAT Control Replicate 5


title: Unstimulated organoid (biopsy)-derived CoEpiCs on Day 5 of Colon Intestine-Chip culture, rep2

description:
IL22_RNAseq_count.csv
Vehicle_8_L5.D702
Unstimulated organoid (biopsy)-derived colonic epithelial cells on Day 5 of the Colon Intestine-Chip culture


title: VDJ-seq_EXP20001095_Sample_08

description: VDJ-seq

value: convalescent


title: Liver Western Diet Replicate 1


title: Liver Western Diet Replicate 2


title: Liver Control + NaKtide Replicate 5


title: Liver Control + NaKtide Replicate 4


title: VDJ-seq_EXP20001095_Sample_07

description: VDJ-seq


title: Unstimulated organoid (biopsy)-derived CoEpiCs on Day 5 of Colon Intestine-Chip culture, rep1

description:
IL22_RNAseq_count.csv
Vehicle_7_L5.D701
Unstimulated organoid (biopsy)-derived colonic epithelial cells on Day 5 of the Colon Intestine-Chip culture


title: Liver Western Diet + NaKtide Replicate 5


title: VDJ-seq_EXP20001114_Sample_04

description: VDJ-seq


title: VDJ-seq_EXP20001095_Sample_06

description: VDJ-seq


title: Liver Control + NaKtide Replicate 3


title: Organoid (biopsy)-derived CoEpiCs on Day 5 of Colon Intestine-Chip culture stimulated for 6h with 10pM IL-22, rep1

description:
IL22_RNAseq_count.csv
10pM_IL22_10_L5.D704
Organoid (biopsy)-derived colonic epithelial cells on Day 5 of the Colon Intestine-Chip culture stimulated basolaterally for 6h with 10pM IL-22


title: VDJ-seq_EXP20001095_Sample_05

description: VDJ-seq


title: Liver Control + NaKtide Replicate 1


title: Liver Control Replicate 4


title: Liver Control Replicate 5


title: VDJ-seq_EXP20001095_Sample_04

description: VDJ-seq


title: Organoid (biopsy)-derived CoEpiCs, presence of endothelium and stretch in Colon Intestine-Chip, 8 days, rep1

description:
colon_int.csvestine_chip_count.csv
Chip_Day8_peps_col63
Organoid (biopsy)-derived colonic epithelial cells cultured in the presence of endothelium and stretch in the Colon Intestine-Chip for 8 days


title: VDJ-seq_EXP20001095_Sample_03

description: VDJ-seq


title: Liver Control Replicate 2


title: Liver Control Replicate 1


title: VDJ-seq_EXP20001095_Sample_02

description: VDJ-seq


title: VDJ-seq_EXP20001095_Sample_01

description: VDJ-seq


title: Hippocampus Western Diet + NaKtide Replicate 5

source_name: Hippocampus

value: Hippocampus


title: Organoid (biopsy)-derived CoEpiCs, presence of endothelium and stretch in Colon Intestine-Chip, 8 days, rep3

description:
colon_int.csvestine_chip_count.csv
Chip_Day8_peps_col65
Organoid (biopsy)-derived colonic epithelial cells cultured in the presence of endothelium and stretch in the Colon Intestine-Chip for 8 days


title: Organoid (biopsy)-derived CoEpiCs, presence of endothelium and absence of stretch in Colon Intestine-Chip, 8 days, rep2

description:
colon_int.csvestine_chip_count.csv
Chip_Day8_pems_col135
Organoid (biopsy)-derived colonic epithelial cells cultured in the presence of endothelium and absence of stretch in the Colon Intestine-Chip for 8 days

value: flow (60 μL/h)


title: Hippocampus Western Diet + NaKtide Replicate 3


title: Liver Control + NaKtide Replicate 2


title: Hippocampus Western Diet + NaKtide Replicate 2


title: Organoid (biopsy)-derived CoEpiCs, presence of endothelium and absence of stretch in Colon Intestine-Chip, 8 days, rep1

description:
colon_int.csvestine_chip_count.csv
Chip_Day8_pems_col134
Organoid (biopsy)-derived colonic epithelial cells cultured in the presence of endothelium and absence of stretch in the Colon Intestine-Chip for 8 days


title: Organoid (biopsy)-derived CoEpiCs, absence of endothelium and presence of stretch in Colon Intestine-Chip, 8 days, rep4

description:
colon_int.csvestine_chip_count.csv
Chip_Day8_meps_col62
Organoid (biopsy)-derived colonic epithelial cells cultured in the absence of endothelium and presence of stretch in the Colon Intestine-Chip for 8 days


title: Hippocampus Western Diet Replicate 5


title: Hippocampus Western Diet + NaKtide Replicate 1


title: Hippocampus Western Diet Replicate 4


title: Hippocampus Western Diet + NaKtide Replicate 4


title: Hippocampus Western Diet Replicate 3


title: Organoid (biopsy)-derived CoEpiCs, absence of endothelium and presence of stretch in Colon Intestine-Chip, 8 days, rep3

description:
colon_int.csvestine_chip_count.csv
Chip_Day8_meps_col61
Organoid (biopsy)-derived colonic epithelial cells cultured in the absence of endothelium and presence of stretch in the Colon Intestine-Chip for 8 days


title: Hippocampus Western Diet Replicate 2


title: Liver Control Replicate 3


title: Organoid (biopsy)-derived CoEpiCs, absence of endothelium and presence of stretch in Colon Intestine-Chip, 8 days, rep2

description:
colon_int.csvestine_chip_count.csv
Chip_Day8_meps_col60
Organoid (biopsy)-derived colonic epithelial cells cultured in the absence of endothelium and presence of stretch in the Colon Intestine-Chip for 8 days


title: Organoid (biopsy)-derived CoEpiCs, presence of endothelium and absence of stretch in Colon Intestine-Chip, 8 days, rep4

description:
colon_int.csvestine_chip_count.csv
Chip_Day8_pems_col137
Organoid (biopsy)-derived colonic epithelial cells cultured in the presence of endothelium and absence of stretch in the Colon Intestine-Chip for 8 days


title: Hippocampus Western Diet Replicate 1


title: Organoid (biopsy)-derived CoEpiCs, presence of endothelium and absence of stretch in Colon Intestine-Chip, 8 days, rep3

description:
colon_int.csvestine_chip_count.csv
Chip_Day8_pems_col136
Organoid (biopsy)-derived colonic epithelial cells cultured in the presence of endothelium and absence of stretch in the Colon Intestine-Chip for 8 days


title: VDJ-seq_EXP20001003_Sample_05

description: VDJ-seq

value: PBMC


title: Hippocampus Control + NaKtide Replicate 5


title: Organoid (biopsy)-derived CoEpiCs, absence of endothelium and presence of stretch in Colon Intestine-Chip, 8 days, rep1

description:
colon_int.csvestine_chip_count.csv
Chip_Day8_meps_col59
Organoid (biopsy)-derived colonic epithelial cells cultured in the absence of endothelium and presence of stretch in the Colon Intestine-Chip for 8 days


title: Hippocampus Western Diet + NaKtide Replicate 6


title: Hippocampus Control + NaKtide Replicate 4


title: VDJ-seq_EXP20001003_Sample_08

description: VDJ-seq


title: VDJ-seq_EXP20001003_Sample_04

description: VDJ-seq


title: Organoid (biopsy)-derived CoEpiCs, presence of endothelium and stretch in Colon Intestine-Chip, 8 days, rep2

description:
colon_int.csvestine_chip_count.csv
Chip_Day8_peps_col64
Organoid (biopsy)-derived colonic epithelial cells cultured in the presence of endothelium and stretch in the Colon Intestine-Chip for 8 days


title: Organoid (biopsy)-derived CoEpiCs, absence of endothelium and stretch in Colon Intestine-Chip, 8 days, rep4

description:
colon_int.csvestine_chip_count.csv
Chip_Day8_mems_col133
Organoid (biopsy)-derived colonic epithelial cells cultured in the absence of endothelium and stretch in the Colon Intestine-Chip for 8 days


title: VDJ-seq_EXP20001003_Sample_02

description: VDJ-seq


title: Hippocampus Control + NaKtide Replicate 3


title: Hippocampus Control + NaKtide Replicate 2


title: VDJ-seq_EXP20001003_Sample_07

description: VDJ-seq


title: Organoid (biopsy)-derived CoEpiCs, absence of endothelium and stretch in Colon Intestine-Chip, 8 days, rep2

description:
colon_int.csvestine_chip_count.csv
Chip_Day8_mems_col131
Organoid (biopsy)-derived colonic epithelial cells cultured in the absence of endothelium and stretch in the Colon Intestine-Chip for 8 days


title: Organoid (biopsy)-derived CoEpiCs, absence of endothelium and stretch in Colon Intestine-Chip, 8 days, rep3

description:
colon_int.csvestine_chip_count.csv
Chip_Day8_mems_col132
Organoid (biopsy)-derived colonic epithelial cells cultured in the absence of endothelium and stretch in the Colon Intestine-Chip for 8 days


title: VDJ-seq_EXP20001003_Sample_01

description: VDJ-seq


title: VDJ-seq_EXP20001003_Sample_06

description: VDJ-seq


title: Hippocampus Control Replicate 4


title: Hippocampus Control + NaKtide Replicate 1


title: Hippocampus Control Replicate 5


title: VDJ-seq_EXP20000910_Sample_12

description: VDJ-seq


title: Hippocampus Control Replicate 2


title: Hippocampus Control Replicate 1


title: VDJ-seq_EXP20000910_Sample_11

description: VDJ-seq


title: Organoid (biopsy)-derived CoEpiCs, presence of endothelium and stretch in Colon Intestine-Chip, 5 days, rep6

description:
colon_int.csvestine_chip_count.csv
Chip_Day5_peps_col127
Organoid (biopsy)-derived colonic epithelial cells cultured in the presence of endothelium and stretch in the Colon Intestine-Chip for 5 days


title: Hippocampus Control Replicate 3


title: Cerebellum Western Diet + NaKtide Replicate 5

source_name: Cerebellum

value: Cerebellum


title: Organoid (biopsy)-derived CoEpiCs, absence of endothelium and stretch in Colon Intestine-Chip, 8 days, rep1

description:
colon_int.csvestine_chip_count.csv
Chip_Day8_mems_col130
Organoid (biopsy)-derived colonic epithelial cells cultured in the absence of endothelium and stretch in the Colon Intestine-Chip for 8 days


title: VDJ-seq_EXP20000910_Sample_10

description: VDJ-seq


title: Cerebellum Western Diet + NaKtide Replicate 3


title: VDJ-seq_EXP20000910_Sample_09

description: VDJ-seq


title: Cerebellum Western Diet + NaKtide Replicate 4


title: Organoid (biopsy)-derived CoEpiCs, presence of endothelium and stretch in Colon Intestine-Chip, 5 days, rep5

description:
colon_int.csvestine_chip_count.csv
Chip_Day5_peps_col126
Organoid (biopsy)-derived colonic epithelial cells cultured in the presence of endothelium and stretch in the Colon Intestine-Chip for 5 days


title: Cerebellum Western Diet + NaKtide Replicate 2


title: Hippocampus Control Replicate 6


title: Cerebellum Western Diet + NaKtide Replicate 1


title: Cerebellum Western Diet Replicate 5


title: Organoid (biopsy)-derived CoEpiCs, presence of endothelium and stretch in Colon Intestine-Chip, 5 days, rep4

description:
colon_int.csvestine_chip_count.csv
Chip_Day5_peps_col125
Organoid (biopsy)-derived colonic epithelial cells cultured in the presence of endothelium and stretch in the Colon Intestine-Chip for 5 days


title: Organoid (biopsy)-derived CoEpiCs, presence of endothelium and stretch in Colon Intestine-Chip, 5 days, rep3

description:
colon_int.csvestine_chip_count.csv
Chip_Day5_peps_col58
Organoid (biopsy)-derived colonic epithelial cells cultured in the presence of endothelium and stretch in the Colon Intestine-Chip for 5 days


title: VDJ-seq_EXP20000910_Sample_08

description: VDJ-seq


title: VDJ-seq_EXP20000910_Sample_07

description: VDJ-seq


title: Cerebellum Western Diet Replicate 4


title: Organoid (biopsy)-derived CoEpiCs, presence of endothelium and stretch in Colon Intestine-Chip, 5 days, rep2

description:
colon_int.csvestine_chip_count.csv
Chip_Day5_peps_col57
Organoid (biopsy)-derived colonic epithelial cells cultured in the presence of endothelium and stretch in the Colon Intestine-Chip for 5 days


title: Cerebellum Western Diet Replicate 1


title: Cerebellum Control + NaKtide Replicate 5


title: Cerebellum Western Diet Replicate 3


title: Cerebellum Control + NaKtide Replicate 3


title: Organoid (biopsy)-derived CoEpiCs, presence of endothelium and absence of stretch in Colon Intestine-Chip, 5 days, rep3

description:
colon_int.csvestine_chip_count.csv
Chip_Day5_pems_col123
Organoid (biopsy)-derived colonic epithelial cells cultured in the presence of endothelium and absence of stretch in the Colon Intestine-Chip for 5 days


title: VDJ-seq_EXP20000910_Sample_06

description: VDJ-seq


title: Cerebellum Control + NaKtide Replicate 2


title: VDJ-seq_EXP20000910_Sample_04

description: VDJ-seq


title: Organoid (biopsy)-derived CoEpiCs, presence of endothelium and stretch in Colon Intestine-Chip, 5 days, rep1

description:
colon_int.csvestine_chip_count.csv
Chip_Day5_peps_col56
Organoid (biopsy)-derived colonic epithelial cells cultured in the presence of endothelium and stretch in the Colon Intestine-Chip for 5 days


title: VDJ-seq_EXP20000910_Sample_03

description: VDJ-seq


title: VDJ-seq_EXP20000910_Sample_05

description: VDJ-seq


title: Cerebellum Control + NaKtide Replicate 1


title: Cerebellum Control Replicate 5


title: Cerebellum Control Replicate 4


title: Organoid (biopsy)-derived CoEpiCs, presence of endothelium and absence of stretch in Colon Intestine-Chip, 5 days, rep2

description:
colon_int.csvestine_chip_count.csv
Chip_Day5_pems_col122
Organoid (biopsy)-derived colonic epithelial cells cultured in the presence of endothelium and absence of stretch in the Colon Intestine-Chip for 5 days


title: Cerebellum Control Replicate 3


title: Organoid (biopsy)-derived CoEpiCs, presence of endothelium and absence of stretch in Colon Intestine-Chip, 5 days, rep1

description:
colon_int.csvestine_chip_count.csv
Chip_Day5_pems_col121
Organoid (biopsy)-derived colonic epithelial cells cultured in the presence of endothelium and absence of stretch in the Colon Intestine-Chip for 5 days


title: Cerebellum Control Replicate 2


title: Organoid (biopsy)-derived CoEpiCs, absence of endothelium and presence of stretch in Colon Intestine-Chip, 5 days, rep4

description:
colon_int.csvestine_chip_count.csv
Chip_Day5_meps_col55
Organoid (biopsy)-derived colonic epithelial cells cultured in the absence of endothelium and presence of stretch in the Colon Intestine-Chip for 5 days


title: Cerebellum Control Replicate 1


title: Cerebellum Western Diet Replicate 2


title: VDJ-seq_EXP20000910_Sample_02

description: VDJ-seq


title: VDJ-seq_EXP20000880_Sample_04_hashed sample

description: VDJ-seq


title: VDJ-seq_EXP20000910_Sample_01

description: VDJ-seq


title: d10 2 16.7 TST G9a KO Input

first: Attila

last: Szanto

address: 185 Cambridge St.

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
Sequenced reads were trimmed for adaptor sequence, and aligned Mus musculus musculus (mus) and Mus musculus casteneus (cas) genomes using Novoalign with parameters: -i1000 350 -F ILM1.8 -t180 -rRandom  -h180 180 -v180 -oSAM
After alignment, coordinates were lifted over to mm9 genome using in-house pipeline to assign reads to alleles and allele-specific coverages were calculated along with composite (comp) total coverage.
macs2 was uesd to call peaks in case of H3K9Ac by comparing to input samples using parameters: -f BAMPE -p 0.01 --broad -g mm --broad-cutoff 0.01
Normalized coverages were calculated after normalizing to total coverage.
Genome_build: mm9
Supplementary_files_format_and_content: bw files of comp, cas and mus coverages contain normalized coverage according to total coverage of the sample. Broadpeak files were generated by macs2 as above for H3K9Ac samples.

source_name: 16.7 Tsix +/TST

growth_protocol: Mouse embryonic stem cells from 16.7 Tsix +/TST female cell lines were used as parental line for deleting G9a. Cells were grown without differentiation, day 0 (d0) or differentiated with LIF withdrawal for 4 days in suspension and the placed on gelatinized plates for another 6 days and harvested on day 10 (d10).

extract_protocol:
After reversal of crosslinks,genomic DNA was phenol-extracted and ethanol precipitated. Chromatin was saved as input DNA and extracted similarly.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cell were not treated. Day 0 indicated undifferentiated, while day 10 the differentiated states. Chromatin immunoprecipitation was performed with H3K9me2 (Abcam ab1220) and H3K9Ac (Abcam ab4441) antibodies.

tag: cell line

value: 16.7 Tsix +/TST

value: embryonic stem cells

tag: donor

tag: time of differentiation

value: day 10

tag: antibody

value: ChIP input

tag: genotype/variation

value: G9a KO

value: female


title: Cerebellum Control + NaKtide Replicate 4

value: Control

tag: treatment

value: NaKtide


title: d10 1 16.7 TST WT Input

value: day 0

value: WT

tag: gender


title: Organoid (biopsy)-derived CoEpiCs, presence of endothelium and absence of stretch in Colon Intestine-Chip, 5 days, rep4

description:
colon_int.csvestine_chip_count.csv
Chip_Day5_pems_col124
Organoid (biopsy)-derived colonic epithelial cells cultured in the presence of endothelium and absence of stretch in the Colon Intestine-Chip for 5 days

value: organoid (biopsy)-derived colonic epithelial cells


title: VDJ-seq_EXP20000880_Sample_03_hashed sample

address: Harvard Medical School

institute: Brigham and Women's Hospital

description: VDJ-seq

value: multiplexed sample


title: Organoid (biopsy)-derived CoEpiCs, absence of endothelium and presence of stretch in Colon Intestine-Chip, 5 days, rep3

description:
colon_int.csvestine_chip_count.csv
Chip_Day5_meps_col54
Organoid (biopsy)-derived colonic epithelial cells cultured in the absence of endothelium and presence of stretch in the Colon Intestine-Chip for 5 days

value: flow (60 μL/h), stretch (10%, 0.15Hz)


title: d0 1 16.7 TST WT Input


title: Organoid (biopsy)-derived CoEpiCs, absence of endothelium and presence of stretch in Colon Intestine-Chip, 5 days, rep2

description:
colon_int.csvestine_chip_count.csv
Chip_Day5_meps_col53
Organoid (biopsy)-derived colonic epithelial cells cultured in the absence of endothelium and presence of stretch in the Colon Intestine-Chip for 5 days


title: d10 2 16.7 TST G9a KO H3K9Ac

value: ChIP H3K9Ac


title: VDJ-seq_EXP20000880_Sample_01_hashed sample

description: VDJ-seq


title: VDJ-seq_EXP20000880_Sample_02_hashed sample

description: VDJ-seq


title: Organoid (biopsy)-derived CoEpiCs, absence of endothelium and presence of stretch in Colon Intestine-Chip, 5 days, rep1

description:
colon_int.csvestine_chip_count.csv
Chip_Day5_meps_col52
Organoid (biopsy)-derived colonic epithelial cells cultured in the absence of endothelium and presence of stretch in the Colon Intestine-Chip for 5 days


title: d10 2 16.7 TST G9a KO H3K9me2

value: ChIP H3K9me2


title: d0 2 16.7 TST G9a KO H3K9Ac


title: d10 1 16.7 TST WT H3K9Ac


title: d10 1 16.7 TST WT H3K9me2


title: d0 2 16.7 TST G9a KO H3K9me2


title: Organoid (biopsy)-derived CoEpiCs, absence of endothelium and stretch in Colon Intestine-Chip, 5 days, rep4

description:
colon_int.csvestine_chip_count.csv
Chip_Day5_mems_col120
Organoid (biopsy)-derived colonic epithelial cells cultured in the absence of endothelium and stretch in the Colon Intestine-Chip for 5 days

value: flow (60 μL/h)


title: d0 1 16.7 TST WT H3K9Ac


title: VDJ-seq_EXP20000854_Sample_08

description: VDJ-seq

value: PBMC

value: convalescent


title: VDJ-seq_EXP20000854_Sample_07

description: VDJ-seq


title: Organoid (biopsy)-derived CoEpiCs, absence of endothelium and stretch in Colon Intestine-Chip, 5 days, rep3

description:
colon_int.csvestine_chip_count.csv
Chip_Day5_mems_col119
Organoid (biopsy)-derived colonic epithelial cells cultured in the absence of endothelium and stretch in the Colon Intestine-Chip for 5 days


title: Organoid (biopsy)-derived CoEpiCs, absence of endothelium and stretch in Colon Intestine-Chip, 5 days, rep2

description:
colon_int.csvestine_chip_count.csv
Chip_Day5_mems_col118
Organoid (biopsy)-derived colonic epithelial cells cultured in the absence of endothelium and stretch in the Colon Intestine-Chip for 5 days


title: d0 1 16.7 TST WT H3K9me2

value: 16.7 Tsix +/TST

value: embryonic stem cells


title: VDJ-seq_EXP20000854_Sample_06

description: VDJ-seq


title: d10 3 16.7 TST G9a KO

description:
processed data file: d0_d10_tst_ko_cond_as_analyze.txt
processed data file: d0_d10_tst_ko_comp_diff_expr.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and aligned Mus musculus musculus (mus) and Mus musculus casteneus (cas) or mm9 genomes using Tophat with parameters -p 2 --no-coverage-search --read-edit-dist 3 --read-mismatches 2 --read-gap-length 2 --b2-very-sensitive --mate-inner-dist 20 --mate-std-dev 20 --library-type fr-firststrand
After alignment coverages from mm9 mapping were calculated to get composite (comp) tracks. Allele-specific analysis was performed using in-house scripts for liftover to mm9 genome.
For differential gene expression analysis HOMER was used with parameters: rna mm9 -noadj -count genes -strand + -condenseGenes
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Allelic read counts are summarized in d0_d10_tst_ko_cond_as_analyze.txt.
Supplementary_files_format_and_content: Normalized composite read counts are summarized in d0_d10_tst_ko_comp_diff_expr.txt, and d0-d10, parental-ko comparisons are shown.
Supplementary_files_format_and_content: bw files of comp, cas and mus coverages are separated by strands and normalized by sequencing depth.

source_name: embryonic stem cells

extract_protocol:
Total RNA was extracted using Qiagen RNeasy kit and rRNA was removed using Epicentre Ribo-Zero kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were not treated. Day 0 indicated undifferentiated, while day 10 the differentiated states.

value: Embryonic stem cells

value: Female

value: day 10


title: Organoid (biopsy)-derived CoEpiCs, absence of endothelium and stretch in Colon Intestine-Chip, 5 days, rep1

description:
colon_int.csvestine_chip_count.csv
Chip_Day5_mems_col117
Organoid (biopsy)-derived colonic epithelial cells cultured in the absence of endothelium and stretch in the Colon Intestine-Chip for 5 days


title: d0 2 16.7 TST G9a KO Input

value: ChIP input

value: G9a KO

value: female


title: VDJ-seq_EXP20000854_Sample_05

description: VDJ-seq

value: unexposed


title: d10 2 16.7 TST G9a KO


title: Biopsy- derived colonoids at Day 0 in conventional suspension organoids culture, rep3

description:
colon_int.csvestine_chip_count.csv
Colonoid_Day0_col47

source_name: organoid (biopsy)-derived colonic epithelial cells from conventional suspension organoids culture

value: Biopsy-derived colonoids


title: d10 2 16.7 TST WT

value: WT


title: d10 1 16.7 TST G9a KO


title: VDJ-seq_EXP20000854_Sample_04

description: VDJ-seq


title: d10 1 16.7 TST WT


title: d10 3 16.7 TST WT


title: Biopsy- derived colonoids at Day 0 in conventional suspension organoids culture, rep2

description:
colon_int.csvestine_chip_count.csv
Colonoid_Day0_col48


title: d0 2 16.7 TST G9a KO

value: day 0


title: follicular granulosa cell layers-POF Hi-C replicate_2

city: chengdu

first: hua

last: kui

address: No 211 Huimin Road

institute: Sichuan Agricultural University

data_processing:
Reads were mapped to the chicken reference genome (GRCg6a) by BWA (v 0.7.15).
Juicer were used HiC data processing to filter duplication, low-quality alignment read pairs (MAPQ < 30) as well as intra-fragment read pairs.
High-quality reads  normalized with Knight-Ruiz [KR] algorithm and quantile  algorithm to structure contact matrixes at 20 or 100 kb resolution.
Compartments A/B were identified with principal component analysis (PCA) as described by Lieberman-Aiden E, et al. science 2009 (PMID: 19815776).
Locations of topologically associated domains (TADs) were computed by combining  directionality index (Dixon et al. Nature. 2012 [PMID: 22495300]) and insulation index (Emily Crane et al. Nature. 2017)
Genome_build: GRCg6a
Supplementary_files_format_and_content: 20 and 100 kb matrixes, hic file
location of paired reads, gz file
A-B index, xls file
locations of TAD for each sample, bed file

organism: Gallus gallus

source_name: follicular granulosa cell layers

extract_protocol:
Hi-C experiment were conducted using DpnII, according to the protocol published by Suhas S P Rao. et al. Cell 2014 (PMID: 25497547) .
DNA libraries were prepared during Hi-C protocol according to experimental procedures described in Suhas S P Rao. et al. Cell 2014 (PMID: 25497547).

tag: breed

value: Luhua hens

tag: developmental stage

value: postovulatory follicles

value: 31 weeks

value: follicular granulosa cell layers


title: d0 3 16.7 TST G9a KO

tag: cell type


title: T24

city: Bethesda

first: Sunita

middle: K

last: Agarwal

state: MD

address: Bldg. 10, Room 8C101

department: NIDDK

institute: National Institutes of Health

description:
RNA (ribosomal RNA depleted)
Adaptor sequence:
CTCAGAAT

data_processing:
Data processing was outsourced to QUICK BIOLOGY INC., Pasadena, CA.
Supplementary_files_format_and_content: File format: comma separated value (csv). Content: Normalized reads count per million for every gene/transcript in each sample. This file can be viewed in Microsoct Excel.

source_name: normal thymus (US Biomax)

extract_protocol:
RNA from FFPE tissue samples was isolated with the RNAstorm FFPE RNA extraction kit (Cell Data Sciences). From this total RNA, the Ribosomal RNA was depleted by QUICK BIOLOGY INC., Pasadena, CA.
Library construction, sequencing and data processing was outsourced to QUICK BIOLOGY INC., Pasadena, CA

value: thymus

tag: sample preparation

value: FFPE tissue section


title: Biopsy- derived colonoids at Day 0 in conventional suspension organoids culture, rep1

city: Boston

description:
colon_int.csvestine_chip_count.csv
Colonoid_Day0_col49


title: follicular granulosa cell layers-POF Hi-C replicate_1

tag: age

tag: tissue


title: d0 1 16.7 TST G9a KO

value: 16.7 Tsix +/TST


title: VDJ-seq_EXP20000854_Sample_03

description: VDJ-seq

value: PBMC

tag: subject

value: convalescent


title: T23

description:
RNA (ribosomal RNA depleted)
Adaptor sequence:
CTATACTT

source_name: normal thymus (Zyagen)

value: unknown


title: VDJ-seq_EXP20000854_Sample_02

description: VDJ-seq

tag: cohort


title: VDJ-seq_EXP20000780_Sample_03

description: VDJ-seq


title: T17B

description:
RNA (ribosomal RNA depleted)
Adaptor sequence:
ATCTATTT

source_name: normal thymus (MEN1) of TC17

value: Male


title: VDJ-seq_EXP20000854_Sample_01

description: VDJ-seq


title: d0 3 16.7 TST WT

value: Embryonic stem cells

value: Female


title: VDJ-seq_EXP20000780_Sample_02

description: VDJ-seq


title: follicular granulosa cell layers-F1 Hi-C replicate_1

value: preovulatory follicles


title: T12

description:
RNA (ribosomal RNA depleted)
Adaptor sequence:
AGCATCAT

source_name: normal thymus (MEN1)


title: d0 1 16.7 TST WT


title: follicular granulosa cell layers-SWF Hi-C replicate_2

value: prehierarchical follicles


title: VDJ-seq_EXP20000768_Sample_04

description: VDJ-seq