title: Arab-4G-R2-3

description: processed data file: otu_table_tax.txt


title: Arab-4G-R1-1

status: Public on Sep 20 2021

type: SRA

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description: processed data file: otu_table_tax.txt

library_source: genomic

data_processing:
RNA-seq reads were mapped to the Pseudomonas sringae 1448A (NC_005773.3) using TopHat (version 2.1.1). Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using Cufflinks（version 2.2.0）.
Raw data were processed using the QIIME (v1.7.0) to get the OUT table.USEARCH software (v8.0.1) were used to generated the OUT table file by aligning the original reads back to the OTUs.
Genome_build: Pseudomonas sringae 1448A NC_005773.3
Supplementary_files_format_and_content: txt files were generated from RNA-seq/root metagenome

molecule: genomic DNA

organism: root metagenome

source_name: 16S amplicon sequencing of  Arabidopsis plants root microbiome sample UGT84A3 mutant

growth_protocol: MM

extract_protocol:
Psph strains were grown, harvested and washed as above, then the bacteria were transferred to MM at 28 ℃ for 6 hours. Total RNA was extracted by using RNeasy Mini Kit (QIAGEN, USA). Genomic DNA was removed by using DNaseI (NEB, USA) for 30 min.
After removing rRNA by using the MICROBExpress kit (Ambion), mRNA was used to generate the cDNA library according to the NEBNext UltraTM II RNA Library Prep Kit protocol (NEB, USA), which was then sequenced using the HiSeq 2000 system (Illumina, USA). All RNA-seq samples have two biological replications.
NEBNext UltraTM II RNA Library Prep Kit protocol (NEB, USA)

treatment_protocol: Grow until mid-log phase in KB and transfer to  minimal medium with the presence of indicated drugs

tag: genotype/variation

value: UGT84A3 mutant

tag: growth condition

value: grown in natural soil


title: Arab-4G-R2-1

description: processed data file: otu_table_tax.txt


title: Acesulfame potassium_3

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

library_source: transcriptomic

data_processing:
Base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp.
The clean reads of each sample were aligned to the E. coli reference genome (NC_005966) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/).
Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM), a normalized value generated from the frequency of detection and the length of a given gene.
Genome_build: NC_005966
Supplementary_files_format_and_content: Excel files include log2(Fold Change) values for each sample

molecule: total RNA

organism: Acinetobacter baylyi ADP1

growth_protocol: Liquid LB culture at 30℃

extract_protocol:
Bacterial cells were then harvested by centrifugation at 8000 × g for 10 min. Total RNA was extracted from the mutants using the QIAGEN miRNeasy Mini Kit (QIAGEN, Germany) manufacturer’s protocol with one extra bead-beating step to completely lyse the bacterial cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Acinetobacter baylyi ADP1 and pWH1266 plasmid were mixed and cultured in triplicate in 10 mL 0 and 3 mg/L artificial sweeteners (SAC, SUC, ASP, and ACE-K), at 25 °C, without shaking

tag: treatment

value: 3 mg/L Acesulfame potassium


title: Arab-4G-R2-2

description: processed data file: otu_table_tax.txt


title: Acesulfame potassium_1

source_name: Acinetobacter baylyi ADP1 and pWH1266 plasmid


title: Arab-4G-R5-3

description: processed data file: otu_table_tax.txt


title: Aspartame_2

value: 3 mg/L Aspartame


title: Arab-4G-R5-2

description: processed data file: otu_table_tax.txt


title: Tendon, Piezo1 GOF rep1

city: Bunkyo-ku

first: Hiroshi

last: Asahara

state: Tokyo

address: 1-5-45 Yushima

department: Department of Systems BioMedicine

country: Japan

institute: Institute of Science Tokyo

data_processing:
Basecalls performed using bcl2fastq
Sequenced reads were aligned to mouse genome (mm10) with STAR
RSEM was used for read counting and generating count matrix.
Differentially expressed genes were analyzed by edgeR
Genome_build: mm10
Supplementary_files_format_and_content: count_matrix.txt (Text file of matrix table with raw gene counts for every gene and every sample)

organism: Mus musculus

source_name: Tendon

extract_protocol:
Total RNA from the Achilles tendon was isolated using Zymo Direct-zol RNA MicroPrep kit (R2061, Zymo Research)
RNA libraries were prepared by using GenNext RamDA-seq Single Cell Kit with NSR primer for mouse (Toyobo, Osaka, Japan)

tag: strain

tag: tissue

value: Tendon

tag: genotype

value: Scx-Cre/Piezo1 GOF


title: Tendon, Piezo1 GOF rep2


title: Tendon, Piezo1 GOF rep3


title: Arab-4G-R4-3

description: processed data file: otu_table_tax.txt


title: Sucralose_3

value: 3 mg/L Sucralose


title: Tendon, WT rep3

value: WT


title: Sucralose_2


title: Aspartame_1


title: Tfh replicate 3

city: Toronto

first: Ramanandan

last: Prabhakaran

state: Ontario

address: 610 University Avenue

country: Canada

institute: University Health Network-Princess Margaret Cancer Center

data_processing:
Read alignment:  HiSAT2 aligner version 2.1.0c was used to map reads against the reference genome GRCm38_92 (mouse).
Read counting: Htseq-count (0.9.1) was used to generate read count for annotated genes from GRCm38_92 (mouse).
CPM countimg: EdgeR was used to generate CPM count for genes for all samples.
Genome_build: GRCm38_92
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Spleen

extract_protocol:
Splenocytes were harvested from mice and Th1 and Tfh SMARTA cells FACS-sorted directly into RLT buffer. RNA was isolated using a single-cell RNA purification kit. SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing was used per manufacturer’s instructions for amplification of RNA and subsequent cDNA synthesis.
All samples proceeded through NexteraXT DNA Library Preparation (Illumina) using NexteraXT Index Kit V1 or V2 Set A following manufacturer’s instructions.

treatment_protocol: Virus-specific SMARTA CD4 T cells were injected into mice that were subsequently LCMV-Arm infected a day later. Mice were sacrificed at Day 7 post-infection.

value: spleen

tag: cell type

value: Tfh SMARTA cells


title: Saccharin_3

value: 3 mg/L Saccharin


title: Saccharin_1


title: Tendon, WT rep2


title: Saccharin_2


title: Control_1

value: control


title: Control_2


title: Th1 replicate 2

value: Th1 SMARTA cells


title: Sucralose_1


title: Ebf1 Repeat 2

city: MInneapolis

first: Michael

last: Farrar

state: MN

address: 2101 6th Street SE

department: Lab Medicine and Pathology

country: USA

institute: University of Minnesota

data_processing:
Reads were aligned to the mouse genome (mm10) using Tophat2
FPKM values were estimated using Cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: txt file of FPKM values for all RNA-Seq samples

source_name: Bone Marrow

growth_protocol: Mice were maintained according to IACUC protocols at the University of Minnesota.

extract_protocol:
RNA was isolated using a Qiagen Miniprep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Single cell suspensions were created from the lymph nodes of leukemic mice, flash frozen and stored at -80 degrees.  Progenitor B cells were purified from the bone marrow using column purification.

value: Progenitor B Cells

tag: number of mice


title: Ebf1 Repeat 1


title: Tfh replicate 1


title: mouse34 scTCR-seq

city: Boston

first: Elliot

last: Akama-Garren

state: MA

address: 200 Longwood Ave

institute: Harvard Medical School

description:
VDJ_T34_M34
mouse34 scTCR-seq
scTCR-seq_barcodes.csv
scTCR-seq_barcodes.csv

data_processing:
Library strategy: TCR-seq
Cellranger (v4.0.0) was used to generate count and vdj matrices by aligning to the GRCm38 (mm10) reference genome
Gene expression matrices were read using Seurat (v3.1.4) and filtered for cells with at least 200 genes detected and genes in at least 3 cells
Cells were further filtered for 1000-3500 genes detected, more than 2000 reads detected, less than 7% mitochondrial RNA content, less than 20% ribosomal R content, S phase score less than 0.15, and G2/M phase score less than 0.15
Samples were merged, normalized, and integrated by condition in Seurat (v3.1.4)
TCRs were filtered for cell barcodes with productive alpha and beta chain sequences
Genome_build: mm10
Supplementary_files_format_and_content: Matrix with normalized gene counts for every gene (columns) for each cell barcode (rows)
Supplementary_files_format_and_content: Matrix with feature and sample-level metadata (columns) for each cell barcode (rows)
Supplementary_files_format_and_content: Matrix with TCR and sample-level metadata (columns) for each cell barcode (rows)

extract_protocol:
CD4 T cells were enriched using MACS, then stained for FACS and CD4+CXCR5+PD1+ cells were sorted and captured in droplets according to 10X Genomics protocols.
Gene expression or VDJ libraries were prepared following reverse transcription according to 10X Genomics protocols.

treatment_protocol: Bone marrow chimeras were generated by irradiating recipient mice and reconstituting with congenic bone marrow (WT) or congenic bone marrow mixed with an autoreactive B cell clone (564Igi).  After six weeks WT chimeras were immunized with NP-OVA in alum, and all chimeras were sacrificed 10 weeks after irradiation.

value: Spleen

tag: chimera condition

tag: Sex

value: F

tag: sequenced molecule

value: VDJ enriched


title: Th1 replicate 1


title: mouse21 scTCR-seq

description:
VDJ_T12_M21
mouse21 scTCR-seq
scTCR-seq_barcodes.csv
scTCR-seq_barcodes.csv


title: ApcMin Strap KO rep2

city: Birmingham

first: Pran

middle: K

last: Datta

state: AL

address: 1824 6th Ave S

department: Medicine

institute: University of Alabama at Birmingham

data_processing:
Reads were filtered by SOAPnuke  v1.5.2 with parameters -l 15 -q 0.5 -n 0.1.
Clean reads were mapped to mm10 whole genome using  Bowtie v2.2.5 with parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --nomixed --no-discordant -p 1 -k 200.
Gene expression was calculated by RSEM v1.2.12 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: Colon adenoma

extract_protocol:
Intestinal adenomas were removed and RNA was harvested using Trizol reagent. RNA samples were sent to BGI.
The poly-A containing mRNA molecules were purified using poly-T oligoattached  magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent  cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using  reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA  Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and  subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification.  We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle  (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle  by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs  were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the  BGISEQ-500 platform for the following data analysis study. For this step, the BGISEQ-500 platform  combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-  Anchor Synthesis Sequencing Method.

value: Colon adenoma

tag: age

value: 110 days

value: ApcMin Strap KO


title: ApcMin Strap WT rep2

value: ApcMin Strap WT


title: Ebf1 Repeat 3


title: mouse12 scTCR-seq

description:
VDJ_T4_M12
mouse12 scTCR-seq
scTCR-seq_barcodes.csv
scTCR-seq_barcodes.csv


title: mouse36 scTCR-seq

description:
VDJ_T36_M36
mouse36 scTCR-seq
scTCR-seq_barcodes.csv
scTCR-seq_barcodes.csv

value: M


title: Pax5 x Ebf1 Leukemia Repeat 4

data_processing:
Reads were aligned to the mouse genome (mm10) using BWA (0.7.12).
Variant calling was done using freebayes (0.9.21), ignoring multi-nucleotide polymorphisms and complex events.
For wild type variant filtering: variants were kept with a minimum total depth of 20 reads and a quality score of 20. Next all variants found in dbSNP (v142) were removed. Finally the wild type replicates were filtered to a minimum depth of 1000 reads, which was determined to be the noise threshold, i.e. the minimum read depth at which the variation between wild type replicates was minimized.
For PE variant filtering: unique PE variants were identified by removing any calls with a read depth less than 1000 and a quality score below 20. Finally any calls that were found in either dbSNP (v142) or the filtered wild type samples were removed from the call set.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: vcf files for each RNA-Seq sample.

source_name: Lymph Node

extract_protocol:
RNA was isolated using a Qiagen Miniprep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Single cell suspensions were created from the lymph nodes of leukemic mice, flash frozen and stored at -80 degrees. Progenitor B cells were purified from the bone marrow using column purification.

value: Leukemic B Cells


title: Tendon, WT rep1

value: Tendon


title: mouse11 scTCR-seq

description:
VDJ_T3_M11
mouse11 scTCR-seq
scTCR-seq_barcodes.csv
scTCR-seq_barcodes.csv

value: WT


title: Tfh replicate 2

value: spleen


title: mouse17 scTCR-seq

description:
VDJ_T2_M17
mouse17 scTCR-seq
scTCR-seq_barcodes.csv
scTCR-seq_barcodes.csv


title: mouse24 scTCR-seq

description:
VDJ_T7_M24
mouse24 scTCR-seq
scTCR-seq_barcodes.csv
scTCR-seq_barcodes.csv


title: Control_3


title: mouse23 scTCR-seq

description:
VDJ_T11_M23
mouse23 scTCR-seq
scTCR-seq_barcodes.csv
scTCR-seq_barcodes.csv


title: mouse13 scTCR-seq

description:
VDJ_T8_M13
mouse13 scTCR-seq
scTCR-seq_barcodes.csv
scTCR-seq_barcodes.csv


title: mouse34 scRNA-seq

description:
GEX_T34_M34
mouse34 scRNA-seq
scRNA-seq_features.csv
scRNA-seq_features.csv

data_processing:
Cellranger (v4.0.0) was used to generate count and vdj matrices by aligning to the GRCm38 (mm10) reference genome
Gene expression matrices were read using Seurat (v3.1.4) and filtered for cells with at least 200 genes detected and genes in at least 3 cells
Cells were further filtered for 1000-3500 genes detected, more than 2000 reads detected, less than 7% mitochondrial RNA content, less than 20% ribosomal R content, S phase score less than 0.15, and G2/M phase score less than 0.15
Samples were merged, normalized, and integrated by condition in Seurat (v3.1.4)
TCRs were filtered for cell barcodes with productive alpha and beta chain sequences
Genome_build: mm10
Supplementary_files_format_and_content: Matrix with normalized gene counts for every gene (columns) for each cell barcode (rows)
Supplementary_files_format_and_content: Matrix with feature and sample-level metadata (columns) for each cell barcode (rows)
Supplementary_files_format_and_content: Matrix with TCR and sample-level metadata (columns) for each cell barcode (rows)

value: total RNA


title: WT Repeat 3

value: Wild Type


title: Pax5 x Ebf1 Leukemia Repeat 5


title: ApcMin Strap WT rep1


title: Th1 replicate 3


title: Pax5 x Ebf1 Leukemia Repeat 2


title: mouse23 scRNA-seq

description:
GEX_T11_M23
mouse23 scRNA-seq
scRNA-seq_features.csv
scRNA-seq_features.csv


title: mouse14 scTCR-seq

description:
VDJ_T1_M14
mouse14 scTCR-seq
scTCR-seq_barcodes.csv
scTCR-seq_barcodes.csv


title: Pax5 x Ebf1 Leukemia Repeat 3


title: Pax5 x Ebf1 Leukemia Repeat 1


title: mouse36 scRNA-seq

description:
GEX_T36_M36
mouse36 scRNA-seq
scRNA-seq_features.csv
scRNA-seq_features.csv


title: WT Repeat 2


title: ApcMin Strap KO rep1


title: WT Repeat 1


title: mouse21 scRNA-seq

description:
GEX_T12_M21
mouse21 scRNA-seq
scRNA-seq_features.csv
scRNA-seq_features.csv


title: ND8

type: RNA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: A total of 600 ng Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE3 Mouse 8x60k v2 gene expression microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were rinsed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and dried by slowly removing from Wash buffer 2.

scan_protocol: Following posthybridization rinses, arrays were scanned using an Agilent SureScan microarray Scanner at 3 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw microarray data were log transformed to yield z-scores. The z-ratio was calculated as the difference between the observed gene z-scores for the experimental and the control comparisons, and dividing by the standard deviation associated with the distribution of these differences. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a 5% false discovery rate (FDR) threshold. The complete set was tested for gene set enrichment using parametric analysis of gene set enrichment. For each pathway z-score, a p-value was computed using JMP 6.0 software to test for the statistical significance.

organism: Homo sapiens

source_name: B cell_non-diseased

label_protocol: Cy3-labeled cRNA was prepared from 200 ng of total RNA using the Agilent Low-Input Quick Amp Labeling Kit and was purified and quantitated according to the manufacturer’s instructions.

growth_protocol: All primary human samples were collected with written informed consent, including human bone marrow aspirates, by the Health Apheresis Unit and the Clinical Core Laboratory, NIA, under Human Subject Protocol # 2003054 and Tissue Procurement Protocol # 2003-071. Cancer patient PBMC were collected before the clinical trial (protocol # NCT02203513) from people with metastatic/recurrent triple-negative breast cancer The trial was approved by the Institutional Review Board of the Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.  Blood was collected in tubes with 2 mg/ml of Na-heparin (Sigma). All experiments were performed on PBMC which were cryopreserved after collection.

extract_protocol: Total  RNA was isolated using RNeasy Plus Micro (Qiagen, Germantown, MD, USA).Total RNA quantity and quality were evaluated using the Bioanalyzer RNA 6000 Chip (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Cryopreserved PBMCs were placed in a 37℃ water bath for 60 seconds, and thawed PBMCs poured into 5ml complete RPMI in a 15 ml conical tube and centrifuged at 1000 rpm for 5 mins at room temperature. The supernatant was discarded and  1mL of pre-warmed complete RPMI added, cells were pipette mixed before resting at room temperature for 1h. Cell concentration and viability was assesed using ViaStain AO/PI viability stains, before staining with anti-CD19-PE antibody after incubation in human Fc block for 15mins in 4℃. Cells were rinsed twice with MACs buffer,  incubated with anti-PE beads for 15 mins in 4℃. The cells were rinsed twice in MACs buffer and  loaded onto the autoMACs cell separator to isolate CD19+ B cells.

value: PBMC-derived B  cell

tag: patient diagnosis

value: non-diseased


title: ND2


title: ND1


title: mouse12 scRNA-seq

description:
GEX_T4_M12
mouse12 scRNA-seq
scRNA-seq_features.csv
scRNA-seq_features.csv


title: mouse13 scRNA-seq

description:
GEX_T8_M13
mouse13 scRNA-seq
scRNA-seq_features.csv
scRNA-seq_features.csv


title: mouse17 scRNA-seq

description:
GEX_T2_M17
mouse17 scRNA-seq
scRNA-seq_features.csv
scRNA-seq_features.csv


title: ND7


title: mouse24 scRNA-seq

description:
GEX_T7_M24
mouse24 scRNA-seq
scRNA-seq_features.csv
scRNA-seq_features.csv


title: ND5


title: BC9


title: ND3


title: ND6


title: mouse14 scRNA-seq

description:
GEX_T1_M14
mouse14 scRNA-seq
scRNA-seq_features.csv
scRNA-seq_features.csv


title: BC8

source_name: B cell_breast cancer

value: breast cancer


title: BC7


title: mouse11 scRNA-seq

description:
GEX_T3_M11
mouse11 scRNA-seq
scRNA-seq_features.csv
scRNA-seq_features.csv

value: Spleen


title: GMR>Rh-1G69D rep 2

city: New York

first: Brian

middle: Scott

last: Brown

state: NY

address: 540 1st Avenue, SKI 5-2

department: Department of Cell Biology

institute: NYU School of Medicine

data_processing:
RNA librares were run on one lane of an SP100 paired-end 50 Illumina NovaSeq 6000
Basecalling was performed with RTA v3.4.4 software, and per-read per-sample FASTQ files were generated using the bcl2fastq2 Conversion software (v2.20) to convert per-cycle BCL base call files into the FASTQ format
The alignment program STAR (v2.6.1d) was used for mapping reads of 6 samples to the Drosophila melanogaster reference genome dm6 and the application Fastq Screen (v0.13.0) was utilized to check for contaminants.
The featureCounts software (Subread package v1.6.3) was used to generate matrices of read counts for annotated genomic features.
The DESeq2 package (R v3.6.1) in the R statistical programming environment was utilized for differential gene statistical comparisons between groups of samples contrasted by "WT" and "GMR-G69D" with 3 replicates each
Genome_build: dm6
Supplementary_files_format_and_content: comma-separated value spreadsheets include raw, normalized and FPKM-normalized count values for all samples

organism: Drosophila melanogaster

source_name: eye imaginal disc nuclei

extract_protocol:
Eye imaginal disc nuclei were extracted from dissected tissues by mechanical lysis, then GMR>EGFP::Msp300-KASH expressing nuclei were isolated by immunoprecipitating with anti-EGFP antibodies. Isolated nuclei were then washed and total RNA was extracted with Trizol reagent before purification on Qiagen RNeasy MinElute columns.
Libraries were prepared using Nugen Ovation Trio low-input RNA seq library preparation kit

value: eye imaginal disc nuclei

tag: developmental stage

value: late third instar


title: BC4

value: F


title: GMR>Rh-1G69D rep 3


title: BC6


title: WT rep 3

value: GMR-GAL4, uas-EGFP::Msp300-KASH


title: BC2


title: GMR>Rh-1G69D rep 1


title: BC3


title: placental DNA 93

type: genomic

city: Beaverton

first: Lyndsey

middle: Elizabeth

last: Shorey-Kendrick

state: Oregon

address: 505 NW 185th Ave

institute: Oregon Health and Science University

hyb_protocol: standard Illumina protocol

scan_protocol: Placental DNAM was assessed on the MethylationEPIC BeadChips, measuring over 850,000 CpGs at a nucleotide resolution, at the Fred Hutchinson Cancer Research Center Genomics Resource. In brief, 500ng of DNA was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research) following the Illumina-specified instructions.  Converted DNAs were applied to Illumina Infinium Methylation EPIC 8-Sample Beadchips following the Infinium HD Methylation 15019521v01 protocol.  Processed BeadChips were scanned using the Illumina iScan+ with ICS v3.3.28 and intensity data was extracted with Illumina GenomeStudio software (GenomeStudio v2011.1 with Methylation Analysis Module v1.9.0).

data_processing: Data normalization and QC were performed using ChAMP: non-CpG probes, probes with a beadcount <3 in at least 5% of samples, probes annotated to SNPs, probes with a detection p-value > 0.01 in one or more samples, cross-hybridizing probes, and probes on X/Y chromosomes were removed and remaining probes (n=714,666) were normalized using via functional normalization.

label: Cy3 and Cy5

source_name: placenta

label_protocol: standard Illumina protocol

extract_protocol: DNA, RNA, and miRNA were simultaneously extracted from placenta, powdered under liquid N2, using the AllPrep miRNA kit (Qiagen) and the QIAcube for automated nucleic acid extraction (Qiagen, USA).

tag: gestational age weeks

tag: smoking

value: smoker


title: WT rep 2


title: can4-/- (homo) rep5 (16281X15)

city: Salt Lake City

first: Yijie

last: Geng

state: UT

institute: University of Utah

description: 16281X15_190809_A00421_0099_AHKTNNDMXX_S47

data_processing:
Sequencing reads were aligned using STAR version 2.7.0f
Quality control was performed using MultiQC
Differential expression analysis was conducted using DESeq2 version 1.24.0  and the hciR package on Github
Data were normalized using the regularized log (rlog) counts method in DESeq2. The can4-/- mutant data was compared to WT data to identify genes with significantly altered expressions.
Genome_build: GRCz11
Supplementary_files_format_and_content: raw and normalized counts; differential gene expression

organism: Danio rerio

source_name: 3 dpf can4-/- zebrafish

extract_protocol:
We first incrossed heterozygous can4 mutants to produce a mixture of can4+/- (heterozygous), can4-/- (homozygous), and can4+/+ (wild type; WT) embryos. We then lysed 3 dpf larvae individually by rigorously pipetting in 55 µl DNA/RNA Shield (Zymo Research) at RT followed by overnight incubation at 4°C. We extracted genomic DNA from 5 µl lysate of each larvae using Zymo 96 genomic DNA purification kit and genotyped each sample by PCR and Sanger sequencing. The remaining lysates were stored at -80°C while awaiting genotyping results. Once genotyped, larvae with the same genetic background were pooled for mRNA extraction using Direct-zol RNA Miniprep Kit with TRI Reagent from Zymo Research. We prepared 5 biological replicates for each genetic background – can4-/- and WT – with each sample containing mRNA extracted from 9 larvae.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Ribo-Zero Gold Kit.

tag: strain background

value: AB

value: can4-/- (homozygous Top2a mutant)

value: 3 dpf whole zebrafish larvae


title: placental DNA 95

value: nonsmoker


title: placental DNA 84


title: placental DNA 94


title: placental DNA 90


title: WT rep 1


title: can4-/- (homo) rep4 (16281X14)

description: 16281X14_190809_A00421_0099_AHKTNNDMXX_S49


title: placental DNA 88


title: placental DNA 85


title: placental DNA 86


title: BC1


title: placental DNA 91


title: can4-/- (homo) rep3 (16281X13)

description: 16281X13_190809_A00421_0099_AHKTNNDMXX_S38


title: placental DNA 81

value: M


title: can4-/- (homo) rep2 (16281X12)

description: 16281X12_190809_A00421_0099_AHKTNNDMXX_S40


title: NHEkd 3

city: Tucson

first: Pawel

middle: R.

last: Kiela

state: AZ

address: 1501 N. Campbell Ave.

department: Pediatrics

institute: University of Arizona

description: Gene expression data from NHE3 knockdown SK-CO15 cells

hyb_protocol: Following fragmentation, 100 ng of cRNA were hybridized for 16 h at 45°C. Arrays were processed with FS450 fluidics station with FS450_00002 protocol

scan_protocol: Follwing washing, microarrays were scanned using Affymetrix GeneArray Scanner 3000.

data_processing:
CEL files were imported into GeneSpring software (Agilent) and summarized using  ExonRMA  Summarization Algorithm. After quantile normalization,  Normalization: Quantile   baseline transformation was performed to the mean of Control samples for visualization   Baseline Transformation: mean of Control Samples
probe group file: Affymetrix.ExonExprChip.HuGene-2_0-st_na36_hg19_2016-07-06 (from Agilent)

label: biotin

source_name: SK-CO15 colon adenocarcinoma cells

label_protocol: The Ambion Whole-Transcript (WT) Expression kit was used in conjunction with the Affymetrix HuGene-2_0-st chips  WT Terminal Labeling and Controls Reagent kit

growth_protocol: SK-CO15 cells stably transfected with a lentivirus carring scrambled shRNA or shRNA pool targeting SCL9A3 (NHE3) expression were grown to confluence in DMEM supplemented with 10% FBS, penicillin (50 mU/ml), streptomycin (50 μg/ml), 1 mM sodium pyruvate, 15 mM HEPES, and 1× nonessential amino acids.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions follwed by Qiagen column purification

tag: cell line

value: colon adenocarcinoma cells

tag: nhe3 expression

value: Knock-down


title: placental DNA 89


title: can4-/- (homo) rep1 (16281X11)

description: 16281X11_190809_A00421_0099_AHKTNNDMXX_S42


title: NHEkd 10


title: NHEkd 2


title: placental DNA 73


title: placental DNA 92


title: placental DNA 80


title: placental DNA 78


title: placental DNA 77


title: placental DNA 82


title: WT rep5 (16281X5)

description: 16281X5_190809_A00421_0099_AHKTNNDMXX_S45

source_name: 3 dpf WT zebrafish

value: wild type


title: placental DNA 79


title: placental DNA 70


title: WT rep4 (16281X4)

description: 16281X4_190809_A00421_0099_AHKTNNDMXX_S46


title: placental DNA 75


title: placental DNA 83


title: placental DNA 96


title: placental DNA 76


title: placental DNA 71


title: placental DNA 87


title: WT rep1 (16281X1)

description: 16281X1_190809_A00421_0099_AHKTNNDMXX_S51


title: WT rep3 (16281X3)

description: 16281X3_190809_A00421_0099_AHKTNNDMXX_S48


title: WT rep2 (16281X2)

description: 16281X2_190809_A00421_0099_AHKTNNDMXX_S50


title: placental DNA 66


title: Ctrl 1

description: Gene expression data from control SK-CO15 cells

value: Control


title: Ctrl 4


title: placental DNA 72


title: sAML_Control_2

city: Houston

first: Kapil

last: Bhalla

state: TX

address: 1515 Holcombe Blvd

department: Leukemia

institute: MD Anderson Cancer Center

data_processing:
Reads were mapped with TopHat 2.0. Only uniquely mapping reads were allowed.
The mapped reads were then assembled into transcripts with Cufflinks 2.0 and the UCSC RefSeq gene model.
Gene expression (FPKM) was quantile normalized using the R statistical system.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include quantile normalized FPKM values for each Sample

source_name: CD34+ sAML blast progenitor cells

growth_protocol: Fresh PD CD34+ cells were cultured in 20% FBS containing RPMI1640 media.

extract_protocol: Total RNA was isolated with a kit from Ambion, Inc. The RNA was DNAse I treated to eliminate genomic DNA, then the purified RNA was utilized to make libraries for next generation sequencing.

treatment_protocol: PD CD34+ sAML cells were plated in 20% FBS containing RPMI media. Cells were treated with 200 nM of BC2059 and incubated at 37°C for 8 hours. Total RNA was isolated with a kit from Ambion, Inc

value: leukemia blast cells

tag: treatment

value: untreated


title: sAML_Control_1


title: SECs_day 56, replicate 3 [SEC_d56_4]

city: Zurich

first: Cesar

last: Nombela-Arrieta

address: Häldeliweg, 4

department: Medical Oncology and Hematology

country: Switzerland

institute: University of Zurich

description: infected - day 56 post infection

data_processing:
Samples were sequenced Bioinformatic analysis was performed using the R package ezRun (https://github.com/uzh/ezRun) within the data analysis framework SUSHI (Hatakeyama et al., 2016).
Quality of raw reads was checked using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
Quality controlled reads (adaptor trimmed, minimum average quality Q20, minimum tail quality Q20, minimum read length 20nt) were aligned to the reference genome (Ensembl GRCm38.p5) using the STAR aligner.
Expression counts were computed using featureCounts in the Bioconductor package Subread.
Quality checkpoints, such as quality control of the alignment and count results, were implemented in ezRun (https://github.com/uzh/ezRun) and applied throughout the analysis workflow to ensure correct data interpretation.
Genome_build: Ensembl GRCm38.p5
Supplementary_files_format_and_content: the file X contains FPKM or all genes detected in all samples

source_name: bone marrow stromal SEC

growth_protocol: Bone marrow was harvested from 12-20 week old mice untreated or infected with LCMV-cl13 (56 dpi)

extract_protocol:
RNA extraction using RNeasy Plus Micro Kit (Qiagen) was employed to extract RNA
Clontech SMRTer Stranded total RNA-Seq Kit-Pico Input Mammalian Total RNA

treatment_protocol: Enzymatic digestion of bone marrow tissues, fluorescent activated cell sorting (FACS) directly into RLT lysis buffer (Qiagen)

tag: strain

value: bone marrow

value: SECs mice infected with LCMV 56 dpi


title: SECs_day 56, replicate 2 [SEC_d56_3 ]

description: infected - day 56 post infection

tag: tissue


title: placental DNA 68


title: placental DNA 69


title: placental DNA 65


title: RNA-seq_CUTLL1_shCTCF_rep3

city: Charlottesville

first: Zhenjia

last: Wang

state: VIRGINIA

address: 1300 Jefferson Park Avenue

department: Center for Public Health Genomics

institute: University of Virginia

data_processing:
ChIP-seq sequence reads were aligned to the hg38 genome using bwa, MACS2 was used to call peaks.
ATAC-seq sequence reads were aligned to the hg38 genome using bowtie.
RNA-seq datasets were processed using Salmon.
Hi-C data were processed using HiC-Pro.
Methylation calls were performed with Bismark.
Genome_build: GRCH38/hg38
Supplementary_files_format_and_content: sf

extract_protocol:
Cells were spun down and lysed with RLT buffer; RNA extraction was conducted using the Aurum BioRad RNA isolation kit
rRNA depletion with TruSeq® Stranded Total RNA Library Prep kit

value: shCTCF


title: RNA-seq_CUTLL1_shCTCF_rep2


title: sAML_200 nM BC2059_2

value: Beta Catenin antagonist BC2059 at a concentrations of 200 nM for 8 hours


title: SECs_day 0, replicate 3 [SEC_d0_2]

description: untreated- day 0

value: SECs untreated mice


title: Ctrl 9


title: placental DNA 74

value: smoker


title: placental DNA 62


title: RNA-seq_CUTLL1_shCTCF_rep1


title: sAML_200 nM BC2059_1


title: placental DNA 63

value: F


title: RNA-seq_CUTLL1_shControl_rep3

value: shControl


title: SECs_day 0, replicate 1 [SEC_d0_1]

description: untreated- day 0


title: placental DNA 67


title: placental DNA 52


title: placental DNA 57


title: placental DNA 55


title: placental DNA 60


title: CARc_day 56, replicate 3 [CARc_d56_4]

description: infected - day 56 post infection

source_name: bone marrow stromal CARc

value: CARc mice infected with LCMV 56 dpi


title: RNA-seq_CUTLL1_shControl_rep2


title: placental DNA 56


title: SECs_day 56, replicate 1 [SEC_d56_2]

description: infected - day 56 post infection


title: RNA-seq_CUTLL1_shControl_rep1


title: CARc_day 56, replicate 2 [CARc_d56_3]

description: infected - day 56 post infection


title: placental DNA 61

value: nonsmoker


title: placental DNA 53


title: placental DNA 58

value: M


title: placental DNA 54


title: placental DNA 49


title: Skin_biopsy_Pemphigus_case4

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

hyb_protocol: Hybridizations were performed per Nanostring manufacturer's protocol overnight for 18h in a BioRad C1000 touch thermocycler

scan_protocol: Cartridges were run on a Nanostring Sprint machine

data_processing: Data were analyzed with nSolver software version 4.0

label: fluorescent probe

organism: Canis lupus familiaris

source_name: archival skin biopsy

label_protocol: Probe labeling was performed per Nanostring manufacturer's protocol

extract_protocol: RNA was isolated from 30 micron curls from archival skin biopsies using Qiagen FFPE RNEasy kit with Deparaffinization solution per the manufacturer's instructions.

tag: disease status

value: Pemphigus foliaceous


title: Skin_biopsy_Pemphigus_case3

tag: breed

value: German Shepherd Cross

value: Female

value: Pemphigus erythematosus

value: archival skin biopsy


title: SECs_day 0, replicate 2 [SEC_d0_3]

description: untreated- day 0


title: placental DNA 59


title: IBD [VEOIBDXLP2_030]

city: Munich

first: Monica

last: Yabal

address: Ismaninger straße 22

country: Germany

institute: Technical University of Munich

data_processing:
Dropseq tools v1.12 was used for mapping the raw sequence reads to the reference genome and to generate transcript counts
Differential expression analysis with DESeq2 v1.18.1 was utilized to identify differentially expressed genes
Genome_build: GRCh38
Supplementary_files_format_and_content: normalized_data.txt

source_name: IBD

extract_protocol:
RNA extraction was performed using an automated nucleic acid extraction system (Promega Maxwell RSC16) and the LEV RNA FFPE Purification Kit (Promega).
Library preparation for bulk 3’-sequencing of poly(A)-RNA was done as described previously in Drop-Seq pipeline. Briefly, barcoded cDNA of each sample was generated with a Maxima RT polymerase (Thermo Fisher) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adapter. 5’ ends of the cDNAs were extended by a template switch oligo (TSO) and after pooling of all samples full-length cDNA was amplified with primers binding to the TSO-site and the adapter. cDNA was tagmented with the Nextera XT kit (Illumina) and 3’-end-fragments finally amplified using primers with Illumina P5 and P7 overhangs. The P5 and P7 sites were exchanged to allow sequencing of the cDNA in read1 and barcodes and UMIs in read2 to achieve a better cluster recognition. The library was sequenced on a NextSeq 500 (Illumina) with 75 cycles for the cDNA in read1 and 16 cycles for the barcodes and UMIs in read2.

tag: subject status

value: IBD patient

value: transverse colon


title: IBD [VEOIBDXLP2_029]

value: ascending colon


title: placental DNA 50


title: CARc_day 0, replicate 3 [CARc_d0_1]

description: untreated- day 0

value: bone marrow

value: CARc untreated mice


title: IBD [VEOIBDXLP2_028]


title: placental DNA 46


title: Skin_biopsy_Pemphigus_case2

value: Labrador Cross


title: CARc_day 0, replicate 2 [CARc_0_2 ]

description: untreated- day 0


title: CARc_day 56, replicate 1 [CARc_d56_2]

description: infected - day 56 post infection


title: IBD [VEOIBDXLP2_027]


title: placental DNA 64

value: smoker


title: Skin_biopsy_Pemphigus_case1

value: Miniature Schnauzer

value: Pemphigus vulgaris


title: CARc_day 0, replicate 1 [CARc_d0_3]

description: untreated- day 0


title: IBD [VEOIBDXLP2_026]

value: sigmoid colon


title: JDS548

city: Hamilton

first: Katherine

last: Morrison

address: 1280 Main street west

institute: McMaster

data_processing:
Library strategy: 16S rRNA-seq
BaseCalling on the MiSeq uses software called "RTA" v1.18.54.
For demultiplexing and FastQ generation: "bcl2fastq2" v2.20; allow 0 index mismatches for 16S data. After the bcl2 program from the sequencing facility we 1) trim the primers using Cutadapt, 2) error correct using dada2, 3) classify ASVs using SILVA version 132
Genome_build: The data were trimmed of adapters and denoised using dada2
Supplementary_files_format_and_content: .CSV files contain ASV counts.

organism: feces metagenome

source_name: Stool from mouse with microbrial transfer from L-BAT/NAFLD+D4 human

extract_protocol:
Purified DNA was used for amplification of the 16S rRNA gene using paired end reads of the V3 region.  Amplification of the bacterial 16S rRNA gene for the germ-free mice microbiota was done for the V3-V4 region. 50 ng of DNA was used as template with 1U of Taq, 1x buffer, 1.5 mM MgCl2, 0.4 mg/mL BSA, 0.2 mM dNTPs, and 5 pmoles each of 341F (CCTACGGGAGGCAGCAG) and 518R (ATTACCGCGGCTGCTGG) Illumina adapted primers, as previously described (doi: 10.1128/AEM.02772-10. Epub 2011 Apr 1).  The reaction was carried out at 94◦C for 5 minutes, 25 cycles of 94◦C for 30 seconds, 50◦C for 30 seconds and 72◦C for 30 seconds, with a final extension of 72◦C for 10 minutes. PCR products were then visualized on a 1.5% agarose gel.  Positive amplicons were normalized using the SequalPrep Normalization Plate kit (Thermo Fisher, Wlatham, Massachusetts, USA).
custom amplicon

treatment_protocol: DNA extraction was carried out as described previously (doi: 10.1038/ismej.2014.250. Epub 2015 Jan 9), with few modifications,  from 0.2g of stool sample that was mechanically lysed with 2.8mm ceramic beads (Mo Bio Laboratories Carlsbad, CA) and 0.1mm glass beads (Mo Bio Laboratories, Carlsbad, CA) for 2 cycles of 3 minutes at 3000rpm with a 45 seconds  delay between cycles in 800μl of 200mM of monobasic NaPO4 (pH=8) and 100μl of guanidinium thiocyanate buffer. Samples were further centrifuged at 13,500g for 5 minutes and processed using the MagMAX-96 DNA Multi-sample kit (Life Technologies, Carlsbad, CA) via the MagMAX Express 96-Deep Well Magnetic Particle Processor (Applied Biosystems, Foster City, CA).

tag: source

value: Mouse

tag: rna population

value: 16s rRNA


title: placental DNA 47

tag: Sex

value: F


title: placental DNA 45


title: JDS547

source_name: Stool from mouse with microbrial transfer from L-BAT/NAFLD+D3 human


title: placental DNA 51

value: M

value: nonsmoker


title: IBD [VEOIBDXLP2_025]


title: Btn1a1-KO rep7

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

description:
Sample 12 Mouse #328
328_KO

data_processing:
12 mRNA-Seq samples were pooled and sequenced on HiSeq4000 using Illumina TruSeq Stranded Total RNA Library Prep and paired-end sequencing.
Basecalling was performed by RTA (version 1.18.64).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Reads were filtered with a base call quality >94% of bases with Q30 and and above.
Trimming of adapters and low-quality bases was performed using Trimmomatic (version 0.33).
First pass alignment of reads to the hg19 reference genome was performed using STAR (version 2.5.2b) with parameters: STAR --genomeDir /path/to/genomeDir --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1  --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --clip3pAdapterSeq - --readFilesIn /path/to/read1.fastq.gz /path/to/read2.fastq.gz --readFilesCommand zcat --runThreadN 32 --outFileNamePrefix <prefix> --outSAMtype BAM Unsorted
Second pass alignment of reads to the hg19 reference genome was performed using STAR (version 2.5.2b) with parameters: STAR --genomeDir /path/to/genomeDir --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1  --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --clip3pAdapterSeq - --readFilesIn /path/to/read1.fastq.gz /path/to/read2.fastq.gz --readFilesCommand zcat --runThreadN 32 --outFileNamePrefix <prefix> --outSAMunmapped Within --outWigType None --outWigStrand Stranded --sjdbFileChrStartEnd /path/to/sjdbFile.txt --sjdbGTFfile /path/to/annotations.gtf --limitSjdbInsertNsj 4000000 --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate
Gene-level expression quantificiation and library size normalization in counts-per-million was performed using RSEM (version 1.3.0).
Quantile-normalization and differential expression was performed using limma-voom (version 3.34.5).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files are limma-voom normalized differential expression output.

source_name: Mammary gland

growth_protocol: Mice were either fed Formulab Diet 5008 (PMI Nutrition, Richmond, IN), or NIH 31 Open Formula Diet 7017 (Envigo, Madison, WI) and supplied with water ad libitum.

extract_protocol:
Lactating mammary glands were removed, homogenised and flash frozen on dry ice in Trizol reagent (Zymo Research Corp).
mRNA was fractionated from total RNA (2 mg/sample) using an Illumina TruSeq mRNA library preparation kit.  The mRNA was then fragmented and coverted to double-stranded cDNA and amplified by PCR to generate libraries for pair-end sequencing..

treatment_protocol: The wild-type mouse strains were harem bred one male to two females per cage and both mutant mouse strains were separately maintained by mating single-pair heterozygotes.

value: Lactating mammary gland

tag: age

value: Lactation 1, day 10

tag: genotype


title: Btn1a1-KO rep6

description:
Sample 11 Mouse #327
327_KO


title: JDS546

source_name: Stool from mouse with microbrial transfer from L-BAT/NAFLD+D2 human

tag: patient diagnosis


title: placental DNA 41

tag: gestational age weeks


title: Btn1a1-KO rep5

description:
Sample 10 Mouse #309
309_KO


title: JDS545

source_name: Stool from mouse with microbrial transfer from L-BAT/NAFLD+D1 human


title: IBD [VEOIBDXLP2_024]

value: IBD patient


title: IBD [VEOIBDXLP2_023]


title: placental DNA 42

tag: smoking


title: HEALTHY [VEOIBDXLP2_022]

source_name: HEALTHY

value: healthy control

value: proximal colon


title: Btn1a1-KO rep3

description:
Sample 8 Mouse #277
277_KO

value: Lactation 1, day 8


title: HEALTHY [VEOIBDXLP2_021]


title: JDS544

source_name: Stool from mouse with microbrial transfer from L-BAT/NAFLD+C3 human


title: Btn1a1-KO rep4

description:
Sample 9 Mouse #306
306_KO

value: Lactation 1, day 11


title: Btn1a1-KO rep2

description:
Sample 7 Mouse #238
238_KO


title: placental DNA 44


title: JDS542

source_name: Stool from mouse with microbrial transfer from L-BAT/NAFLD+C1 human


title: JDS543

source_name: Stool from mouse with microbrial transfer from L-BAT/NAFLD+C2 human


title: HEALTHY [VEOIBDXLP2_020]


title: JDS541

source_name: Stool from mouse with microbrial transfer from H-BAT/NAFLD-C3 human


title: Btn1a1-KO rep1

description:
Sample 6 Mouse #204
204_KO


title: Btn1a1 WT rep5

description:
Sample 5 Mouse #278
278_WT

value: wild type


title: HEALTHY [VEOIBDXLP2_019]


title: placental DNA 38

source_name: placenta

value: smoker


title: placental DNA 43


title: HEALTHY [VEOIBDXLP2_018]


title: JDS539

source_name: Stool from mouse with microbrial transfer from H-BAT/NAFLD-C1 human


title: HEALTHY [VEOIBDXLP2_017]


title: JDS540

source_name: Stool from mouse with microbrial transfer from H-BAT/NAFLD-C2 human


title: placental DNA 39


title: Btn1a1 WT rep4

description:
Sample 4 Mouse #263
263_WT


title: JDS133

source_name: Stool from mouse with microbrial transfer from L-BAT/NAFLD+B3 human


title: Btn1a1 WT rep3

description:
Sample 3 Mouse # 233
233_WT


title: placental DNA 37


title: placental DNA 48


title: HEALTHY [VEOIBDXLP2_016]


title: JDS132

source_name: Stool from mouse with microbrial transfer from L-BAT/NAFLD+B2 human


title: Btn1a1 WT rep2

description:
Sample 2 Mouse #181
181_WT

value: Lactation 1, day 9


title: HEALTHY [VEOIBDXLP2_015]


title: placental DNA 35


title: placental DNA 32


title: placental DNA 36


title: JDS131

source_name: Stool from mouse with microbrial transfer from L-BAT/NAFLD+B1 human


title: HEALTHY [VEOIBDXLP2_014]


title: Btn1a1 WT rep1

description:
Sample 1 Mouse #179
179_WT


title: JDS130

source_name: Stool from mouse with microbrial transfer from H-BAT/NAFLD-B3 human


title: FACS-isolated GFP+ cells from Hlxb9-GFP spinal cord Clp1R140H-_2_3READS_plus

city: Farmington

first: Scott

last: Adamson

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

description:
Clp1R140H-_2_3READS_plus
3'READS+ library

data_processing:
Spinal cord RNA-seq adaptors were trimmed with cutadapt (v1.18) with parameters -u 1 -U 1 --minimum-length 50 -a AGATCGGAAGAG -A AGATCGGAAGAG
Spinal cord RNA-seq was quantified using kallisto version 0.42.4 and psuedo-aligned to the Gencode vM24 transcript reference.
UMIs for 3'READS+ libraries were marked with UMItools (v1.0.1) and parameters --bc-pattern = NNN and --bc-pattern2 = NNN
3'READS+ adaptors were trimmed from reads using cutadapt (v1.18) with parameters -a NNNNTGGAATTCTCGGGTGCCAAGG -A NNNNGATCGTCGGACTGTAGAACTCTGAAC, then polyA tails were removed with cutadapt using parameters "A{100}"X --overlap 1 -m 20 -G X"T{100}" --overlap 2 -m 20.
Trimmed 3'READS+ reads were then mapped to mm10 using hisat2 (v2.1.0) with a gencode vM24 annotation.
PCR duplicated 3'READS + reads were then removed using UMItools dedup.
3'READS + reads with polyA tails trimmed were compared to the same reads without trimming and custom python scripts were used to identify reads with untemplated A's at the 3' end and considered poly adenylation sites.
Polyadenylation sites were clustered using bedtools (v2.29.2) cluster with paramters -d 25 and -s to establish PACs, and PACs with five or more total reads associated with them were retained.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include kallisto estimated counts and TPM values for each forebrain RNA-seq sample at the transcript level.
Supplementary_files_format_and_content: tab-delimited text files include read counts and genomic coordinates for poly-adenylation clusters (PACs) as well as overlapping gene features annotated.

extract_protocol:
For 3’READS+ libraries, spinal cords were dissociated and lightly fixed in preparation for cell sorting using protocol adapted from previous publications (M-J Beaudet et al., 2015 and ER Thomsen et al., 2015). These RNA samples were pooled so that the input for each library consisted of 175 ng of RNA derived from six spinal cords. For RNA-seq libraries, RNA was extracted from individual spinal cords using Trizol and miRNeasy Mini kit columns (Qiagen) with on-column DNase digestion.
3’READS+ libraries were prepared as described (D Zheng, X Liu, and B Tian 2016 and D Zheng and B Tian 2017), with some modifications: RNase III fragmentation was reduced to 5 min. and adapter and primer sequences came from the NEXTFLEX Small RNA-Seq Kit v3 (Bioo Scientific). 100-nt paired-end reads were generated on a HiSeq 4000. RNA-Seq libraries were made with the Kapa Stranded mRNA-Seq Kit in accordance with the manufacturer’s instructions. 100-nt paired-end reads were generated on a NovaSeq 6000.

value: Cerebellum


title: FACS-isolated GFP+ cells from Hlxb9-GFP spinal cord Clp1R140H-_1_3READS_plus

description:
Clp1R140H-_1_3READS_plus
3'READS+ library


title: JDS129

source_name: Stool from mouse with microbrial transfer from H-BAT/NAFLD-B2 human


title: placental DNA 40


title: HEALTHY [VEOIBDXLP2_012]


title: JDS128

source_name: Stool from mouse with microbrial transfer from H-BAT/NAFLD-B1 human


title: JDS127

source_name: Stool from mouse with microbrial transfer from L-BAT/NAFLD+A3 human


title: placental DNA 34


title: FACS-isolated GFP+ cells from Hlxb9-GFP spinal cord WT_1_3READS_plus

description:
WT_1_3READS_plus
3'READS+ library


title: placental DNA 31


title: HEALTHY [VEOIBDXLP2_010]


title: placental DNA 33


title: HEALTHY [VEOIBDXLP2_011]


title: placental DNA 29


title: placental DNA 28


title: FACS-isolated GFP+ cells from Hlxb9-GFP spinal cord WT_2_3READS_plus

description:
WT_2_3READS_plus
3'READS+ library


title: placental DNA 27


title: HEALTHY [VEOIBDXLP2_013]


title: HEALTHY [VEOIBDXLP2_009]


title: JDS125

source_name: Stool from mouse with microbrial transfer from L-BAT/NAFLD+A1 human


title: JDS126

source_name: Stool from mouse with microbrial transfer from L-BAT/NAFLD+A2 human


title: HEALTHY [VEOIBDXLP2_008]

source_name: HEALTHY


title: placental DNA 26


title: XLP2 [VEOIBDXLP2_007]

value: pediatric XLP2 patients with IBD

value: transverse colon


title: JDS124

source_name: Stool from mouse with microbrial transfer from H-BAT/NAFLD-A3 human

value: Mouse

value: 16s rRNA


title: JDS123

source_name: Stool from mouse with microbrial transfer from H-BAT/NAFLD-A2 human


title: XLP2 [VEOIBDXLP2_006]

value: sigmoid colon


title: placental DNA 30

value: F


title: placental DNA 25

value: M


title: Donor E MDSC

city: Nijmegen

first: Glenn

middle: van

last: Wigcheren

address: Geert Grooteplein Zuid 28

department: Tumor Immunology

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences

description:
Single cell suspension
Gene expression data from in vitro generated M-MDSC.

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in Affymetrix Hyb., wash and stain kit, Ref 900720-C.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan platform.

data_processing: Packages and libraries developed for hgu133plus2.0 affymetrix data analysis were obtained from the Bioconductor Project (www.bioconductor.org) and assessed in Rstudio (Version 1.2.1335, RStudio Team 2018).

source_name: Healthy Donor E in vitro generated M-MDSC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.

growth_protocol: Monocytes were isolated from healthy donor PBMCs using CD14 microbeads and plated in 6 well culture plates at 37C at 5% CO2 for seven days in X-Vivo-15 + 2% human AB male serum.

extract_protocol: Cells were washed twice with PBS before snap freezing dry pellets using liquid nitrogen and storage at -80°C. Total RNA was extracted from cell pellets using Quick-RNA MiniPrep Plus Kit (Zymo Research) according to manufacturer’s instructions.

treatment_protocol: M-MDSC, MoDCs and TolDCs were generated according generation protocols using specific recombinant human cytokines and/or dexamethasone (see reference).

tag: cell type

value: in vitro generated M-MDSC

tag: donor

value: E

tag: diagnosis

value: Healthy


title: Donor E MoDC

description:
Single cell suspension
Gene expression data from in vitro generated MoDC.

source_name: Healthy Donor E in vitro generated MoDC

value: in vitro generated MoDC


title: Donor D MDSC

source_name: Healthy Donor D in vitro generated M-MDSC

value: D


title: XLP2 [VEOIBDXLP2_004]

value: Del of exon 1

value: descending colon


title: MC3T3_3D_shLacZ_Rep1

city: Dallas

first: Jialiang

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Sequenced libraries were evaluated with FastQC.
Sequencing reads were mapped to the mouse reference genome (mm10) using STAR v.2.7.2b.
Gene expression counts were calculated using HTSeq v.0.9.1.
Differential expression analysis was performed using EgdeR package based on the criteria of more than two-fold change in expression value versus control and false discovery rates (FDR) <0.05.
Genome_build: mm10
Supplementary_files_format_and_content: txt files include read counts for each sample

extract_protocol:
Cells were collected and total RNA was isolated using QIAshredder (QIAGEN) and PureLink RNA Mini Kit (Invitrogen).
mRNAs were isolated by PAGE, followed by adaptor ligation and RT with PCR amplification. PCR products were again purified by PAGE and dissolved in EB solution. Double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The ssCir DNA was formatted as the final sequencing library. The library was amplified with phi29 to general DNA nanoballs (DNBs) which were loaded into the patterned nanoarray. Libraries were sequenced on the BGISEQ500 platform.

tag: cell line

value: Osteocyte-like cell line


title: XLP2 [VEOIBDXLP2_005]

value: ascending colon


title: placental DNA 23

source_name: placenta

value: smoker


title: Donor D TolDC

description:
Single cell suspension
Gene expression data from in vitro generated dexTolDC.

source_name: Healthy Donor D in vitro generated dexTolDC

value: in vitro generated dexTolDC


title: Donor E TolDC

source_name: Healthy Donor E in vitro generated dexTolDC


title: MC3T3_2D_shLacZ_Rep2


title: XLP2 [VEOIBDXLP2_002]

value: pediatric XLP2 patients with IBD

value: intestine


title: MC3T3_3D_shLacZ_Rep2


title: placental DNA 24


title: placental DNA 21

value: nonsmoker


title: Donor D MoDC

source_name: Healthy Donor D in vitro generated MoDC


title: MC3T3_2D_shLacZ_Rep1


title: XLP2 [VEOIBDXLP2_001]


title: Donor C MDSC

source_name: Healthy Donor C in vitro generated M-MDSC

value: C


title: Donor C TolDC

source_name: Healthy Donor C in vitro generated dexTolDC


title: XLP2 [VEOIBDXLP2_003]

value: sigmoid colon


title: placental DNA 19

value: F


title: Chip-seq H3K4me1 K562

city: Marseille

first: Salvatore

last: Spicuglia

state: France

address: Luminy

country: France

institute: Aix-Marseille University, INSERM, TAGC, UMR 1090

data_processing:
Reads were aligned using STAR aligner (v2.4.2a) with arguments “outFilterMismatchNoverLmax” and “outFilterMultimapNmax” set to 0.08 and 1, respectively.
To create bigwig files, reads from Watson and Crick strands were selected using SAMtools (v0.1.9) and provided to the bam2wig.py script from the RseQC program suite (v2.6.4).
Peaks were called using Macs v2.1.1 with –broad argument
Genome_build: hg19
Supplementary_files_format_and_content: bw

source_name: K562 Cell line

growth_protocol: Exponentially growing K562 cells in RPMI medium complemented with 10% FBS for 18 hours at 37°C with 5% CO2

extract_protocol:
Phenol-chroloform
Phenol-chroloform
Library preparation was carried out as per manufacturer’s instructions (Illumina) using 10ng material. Samples were subsequently size-selected via gel migration and extraction, with average cut sizes at about 230 bp, including adapters. Sequencing was carried out on an Illumina NextSeq 500. The quality of libraries was checked with the Bioanalyser DNA High sensitivity and by Q-PCR.

treatment_protocol: Non treated

tag: cells used

tag: treatment

value: Untreated

tag: antibody

value: Diagenode (C15410194)

tag: antibody quantity

value: 1 µg

tag: magnetic beads

value: Protein G dynabeads

tag: estimated fragment size


title: MC3T3_Ostn_OE_in_Sp7_KD_Rep2

value: Sp7 knockdown and ostn overexpression


title: JDS122

source_name: Stool from mouse with microbrial transfer from H-BAT/NAFLD-A1 human

tag: source

value: Mouse

tag: rna population

value: 16s rRNA


title: placental DNA 22

tag: Sex

value: M


title: Donor C MoDC

source_name: Healthy Donor C in vitro generated MoDC

value: in vitro generated MoDC

value: Healthy


title: placental DNA 16

value: smoker


title: Chip-seq H3K4me1 K562 + IFNa 6h

treatment_protocol: K562 cells were cultured at 5E+5 cells/mL and stimulated with 50 ng/mL interferon alpha 2a (Sigma-Aldrich) in RPMI medium for 6 hours at 37°C

value: IFNa stimulation for 6 hours


title: placental DNA 17


title: placental DNA 18


title: placental DNA 20


title: MC3T3_Sp7_KD_Rep2

value: Osteocyte-like cell line

tag: genotype

value: Sp7 knockdown


title: MC3T3_Ostn_OE_in_Sp7_KD_Rep1


title: Chip-seq K562-input

data_processing:
Reads were aligned using STAR aligner (v2.4.2a) with arguments “outFilterMismatchNoverLmax” and “outFilterMultimapNmax” set to 0.08 and 1, respectively.
Differential gene expression was performed using DESeq2 (v1.6.3) Bioconductor package implemented in the R statistical environment and transcripts associated with promoters analysed by CapSTARR-seq were retrieved.
To create bigwig files, reads from Watson and Crick strands were selected using SAMtools (v0.1.9) and provided to the bam2wig.py script from the RseQC program suite (v2.6.4).
Genome_build: hg19
Supplementary_files_format_and_content: bw

source_name: Chip-seq K562-input

extract_protocol:
Phenol-chroloform
Library preparation was carried out as per manufacturer’s instructions (Illumina) using 10ng material. Samples were subsequently size-selected via gel migration and extraction, with average cut sizes at about 230 bp, including adapters. Sequencing was carried out on an Illumina NextSeq 500. The quality of libraries was checked with the Bioanalyser DNA High sensitivity and by Q-PCR.


title: Donor C Monocytes

description:
Single cell suspension
Gene expression data from purified monocytes.

source_name: Healthy Donor C purified Monocytes

value: Purified monocytes

value: C


title: Chip-seq H3K4me3 K562 + IFNa 6h

source_name: Chip-seq H3K4me3 K562 + IFNa 6h

value: Diagenode (C15410003)

tag: bead volume

value: 20 µl


title: Chip-seq H3K4me3 K562

source_name: Chip-seq H3K4me3 K562

value: Untreated


title: MC3T3_Sp7_KD_Rep1


title: placental DNA 15

value: F

tag: gestational age weeks

value: nonsmoker


title: MC3T3_WT_(LacZ)_Rep1

value: wild type


title: placental DNA 13

tag: smoking


title: Donor B MDSC

source_name: Healthy Donor B in vitro generated M-MDSC

tag: cell type

value: in vitro generated M-MDSC

value: B


title: Chip-seq H3K27ac K562 + IFNa 6h

source_name: Chip-seq H3K27ac K562 + IFNa 6h

value: Diagenode (C15410016)

value: 1 µg

value: Protein G dynabeads


title: Donor B MoDC

source_name: Healthy Donor B in vitro generated MoDC

value: in vitro generated MoDC

tag: donor

value: Healthy


title: Chip-seq H3K27ac K562

source_name: Chip-seq H3K27ac K562


title: Donor A MDSC

source_name: Healthy Donor A in vitro generated M-MDSC

value: A

tag: diagnosis


title: Ocy454_FLAG_Sp7_Rep2

tag: cell line

value: Osteocyte-like cell line

value: Sp7 overexpression


title: Ocy454_FLAG_Sp7_Rep1


title: H-SB2Naive_3

first: James

middle: Teak

last: Lim

address: 1515 N Campbell Ave Room 4951

data_processing:
The final sequences were demultiplexed using bcl2fastq and trimmed using trimmomatic (version 0.32)
RNA-seq alignment was performed using TopHat (v2.0.13) and Bowtie2 (v2.2.4)
The following parameters were used for TopHat: --microexon-search, --prefilter-multihits, --mate-inner-dist 30, and --mate-std-dev 50.
The expression counts were generated using HTseq-count
Differential expression was carried out using DEseq2 (R package v1.22.2) with default parameters
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file includes raw gene HTseq-count values for each Sample

growth_protocol: HSB-2 cells were cultured in RPMI-1640 supplemented with 2 mM Glutamax (Life Technologies), 10% fetal bovine serum, 1% penicillin and streptomycin at 37°C under 5% CO2

extract_protocol:
Total RNA was isolated using the RNeasy kit (QIAGEN)
RNA samples were processed using paired end sequencing on the Illumina HiSeq2500.

treatment_protocol: PIM inhibitor resistance in HSB-2 cells was induced by growing the cells in the presence of increasing concentrations of AZD1208 over a 4-month period until resulting cell populations were able to maintain their growth in 1 µM AZD1208.

value: T cell leukemia

tag: azd1208 status

value: Naïve


title: Ocy454_WT_(GFP)_Rep2


title: CapStarr_K562_IFN_rep2_Seq2

tag: cells used

tag: treatment

value: IFNa stimulation for 6 hours


title: Donor B TolDC

source_name: Healthy Donor B in vitro generated dexTolDC

value: in vitro generated dexTolDC


title: Donor A TolDC

source_name: Healthy Donor A in vitro generated dexTolDC


title: H-SB2Naive_2


title: Donor A MoDC

source_name: Healthy Donor A in vitro generated MoDC


title: Chip-seq IRF9 K562 + IFNa 6h

source_name: Chip-seq IRF9 K562 + IFNa 6h

tag: antibody

value: Cell signaling (D2T8M)

tag: antibody quantity

value: 5 µg


title: Donor A Monocytes

source_name: Healthy Donor A purified Monocytes

value: Purified monocytes


title: placental DNA 8

source_name: placenta

value: M

value: smoker


title: Ocy454_WT_(GFP)_Rep1

value: wild type


title: H-SB2Naive_1


title: Ocy454_Sp7_KD_Rep1

value: Sp7 knockdown


title: CapStarr_K562_IFN_rep1_Seq2


title: placental DNA 9


title: Ocy454_Sp7_KD_Rep2


title: placental DNA 7

value: F


title: Ocy454_WT_(LacZ)_Rep2


title: H-SB2-AZDR1_2

value: Resistant


title: K562_IFN_R3


title: Ocy454_WT_(LacZ)_Rep1


title: H-SB2-AZDR1_1


title: CapStarr_K562_IFN_rep1


title: placental DNA 14


title: placental DNA 11


title: UDC613

city: Southampton

first: Tilman

last: Sanchez-Elsner

state: Hampshire

address: Southampton General Hospital, Tremona Road

country: United Kingdom

institute: University of Southampton

description:
sample name:
SL147068

data_processing:
Real time image analysis and base calling were performed on the HiSeq 2500 using the HiSeq Sequencing Control Software version 2.2.58
Sequences that failed Illumina's chastity filter were removed
Sequence alignment to the hg38 human reference genome was performed using TopHat v2.1.0 with fr-unstranded as the library type. The mate-inner-distance and mate-std-dev settings were determined for each sample by non-gapped alignment of a portion of the reads to the human mRNA reference using Bowtie2.  All other TopHat settings were left as default.
The Bioconductor easyRNASeq v2.4.72 package running on the R version 3.2.2 platform was used for exon and gene level counting. A binary annotation file (gAnnot_GRCh38.83.rda) was created using the built in annotation file generation function of EasyRNASeq (annotation method=”BiomaRt”), using the Ensembl release 83 gtf file as input (ensembl_Homo_sapiens.GRCh38.83.chr.gtf). The following easyRNASeq settings were used: organism = Hsapiens, read length = 100, annotation method = rda, annotation file = gAnnot_GRCh38.83.rda. For exon counting the count method was "exons" and the summarization was NULL while for gene counting the count method was "genes" and the summarization was "geneModels".
Gene-level counts were filtered to retain only genes with at least one read in any of the samples.
DESeq2 was used for analysis of differential expression between Normal Control, Ulcerative Colitis, and Crohn's Disease
Genome_build: hg38
Supplementary_files_format_and_content: tab separated value file containing normalized and replaced counts from DESeq2 for each of the 36,497 detectable genes in each of the 28 samples

source_name: intestinal macrophages

extract_protocol:
Gut biopsies from patients with Ulcerative Colitis, Crohn’s Disease and Healthy donors were harvested. Using Fluorescence-activated cell sorting a purified CD14+/CD163+ intestinal macrophage population was isolated and total RNA was extracted.
DNA libraries were prepared by WTA amplification followed by TruSeq Nano DNA library preparation

tag: patient diagnosis

value: Ulcerative Colitis

tag: tissue

value: intestine

tag: disease

value: macrophages

tag: smoking status

value: Never smoked

tag: mayo score

tag: immunosuppression

value: Not treated with immunosupression

tag: hbi score


title: MC3T3_WT_(LacZ)_Rep2

value: Osteocyte-like cell line

tag: genotype


title: K562_IFN_R1

value: IFNa stimulation for 6 hours


title: H-SB2-AZDR1_3

tag: cell type

value: T cell leukemia


title: K562_WT

value: Untreated


title: K562_IFN_R2


title: UDC546

description:
sample name:
SL147060

value: Previous smoker

tag: Sex

value: systemic immunosupression


title: UDC608

description:
sample name:
SL147066


title: K562_WT_rep2


title: UCC604

description:
sample name:
SL147065

value: M


title: placental DNA 4

data_processing: Data normalization and QC were performed using ChAMP: non-CpG probes, probes with a beadcount <3 in at least 5% of samples, probes annotated to SNPs, probes with a detection p-value > 0.01 in one or more samples, cross-hybridizing probes, and probes on X/Y chromosomes were removed and remaining probes (n=714,666) were normalized using via functional normalization.

extract_protocol: DNA, RNA, and miRNA were simultaneously extracted from placenta, powdered under liquid N2, using the AllPrep miRNA kit (Qiagen) and the QIAcube for automated nucleic acid extraction (Qiagen, USA).

tag: gestational age weeks

tag: smoking

value: smoker


title: UDC612

description:
sample name:
SL147067


title: K562_WT_rep1

tag: cell line


title: placental DNA 5


title: atg5 submerged for 48h, biological rep1

city: guangzhou

first: mk

last: yang

address: wushan

country: China

institute: scau

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: Affymetrix ATH1 Arabidopsis chips (Affymetrix) were used for labeling, hybridization, scanning, and detection. Affymetrix Gene Chip software MAS 5.0 and GeneSpring 12.6 (Agilent) were applied for raw data collection. Raw data were processed by R packages affy, and normalized with gcRMA method.

organism: Arabidopsis thaliana

source_name: atg5 submerged for 48h

label_protocol: standard protocol

growth_protocol: plants were grown under 12 h L/ 12 h D for 28 days

extract_protocol: Total RNA was extracted using the RNeasy Plant Mini kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Whole Arabidopsis plants (4-week-old) were gently submerged at depths of 10 cm beneath the water surface under normal light/dark cycle condition. Plant samples for microarray were collected after 0 h or 48 h submergence treatment.

tag: genotype/variation

value: submerged for 48h

value: leaf


title: placental DNA 6

first: Lyndsey


title: placental DNA 10

value: nonsmoker


title: PBRM1_C1233W

first: Cheryl

middle: L

last: Walker

address: 1 Baylor Plaza

department: Center for Precision Environmental Health

institute: Baylor College of Medicine

data_processing:
Samples were trimmed using TrimGalore!
After trimming samples were aligned to hg38 using HISAT2
Features were quantified using featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited , feature counts

source_name: Human embryonic kidney 293 cell line

growth_protocol: The PBRM1 CRISPR KO HEK293T cells were grown in DMEM media having 10% FBS. The cells were passage every 3-4 days once they reach to 80-90% confluency level.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Ambion, Life Technologies) and cleaned up using RNeasy Mini Kit (Qiagen Inc., Valencia, CA) according to the manufacturer’s instructions. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Qiagen's Qiaseq Stranded Protocol

treatment_protocol: PBRM1 CRISPR KO HEK293T cells were transfected with GFP-PBRM1-WT, GFP-PBRM1 P1048R, GFP-PBRM1 T1202K and GFP-PBRM1 C1233W plasmid for 48 hour.

value: PBRM1 C1233W


title: UCC595

description:
sample name:
SL147063

value: Ulcerative Colitis


title: placental DNA 12

last: Shorey-Kendrick

address: 505 NW 185th Ave

institute: Oregon Health and Science University

value: F


title: atg5 submerged for 48h, biological rep2

tag: treatment


title: PBRM1_T1202K

value: PBRM1 T1202K


title: placental DNA 2


title: PBRM1_P1048R

value: PBRM1 P1048R


title: col submerged for 48h, biological rep3

source_name: col submerged for 48h

value: col


title: atg5 submerged for 48h, biological rep3


title: UCC602

description:
sample name:
SL147064

value: intestine

value: macrophages

value: Never smoked

value: Not treated with immunosupression


title: SN_Z103

city: Shanghai

first: Yun

last: Tan

state: Shanghai

address: Room 1109, Building 11, 197 Ruijin Er Rd

department: Shanghai Institute of Hematology

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
All reads were mapped to the Homo sapiens (human) genome assembly GRCh38 (hg38) by the STAR software. The read counts were extracted by HTseq algorithm. Differential expressed genes were analyzed by DESeq2 and genes with two-fold change and adjusted P-value < 0.01  were kept.
Genome_build: hg38
Supplementary_files_format_and_content: Read_counts

source_name: PMBC

growth_protocol: About 4 mL of fresh collected peripheral blood samples in anticoagulant tubes were resuspended with equal volume phosphate buffer saline (PBS), the diluted samples were then gently transferred into a 15 mL tube contains 4mL of Ficoll-paque PLUS (GE Healthcare Life Sciences). The tubes were then centrifugated for 30 min at 400 g, and the PBMCs in the middle layer of the tubes were collected and transferred to a new 15 mL tube (BD Falcon, USA). Then PBMCs were washed twice with PBS and lysed in 1 mL Trizol reagent.

extract_protocol:
RNAs were extracted by the Trizol reagent according to the manufacturer’s instructions.
The mRNA-seq library wasconstructed according to the manufacturer’s instructions of the VAHTSTM mRNA-seq V3 Library Prep Kit for Illumina®. The libraries were sequenced in the Illumina’s Nova-seq 6000 platform.

value: PMBC

value: SARS-CoV-2 Infection

tag: disease state

value: Severe without secondary infection


title: SN_Z102


title: placental DNA 3

city: Beaverton


title: SN_Z106


title: col submerged for 48h, biological rep2


title: UCC588

description:
sample name:
SL147062

value: Previous smoker


title: UCC583

description:
sample name:
SL147061

value: M

value: systemic immunosupression


title: SN_Z101


title: atg5 control, biological rep3

source_name: atg5 control

value: control

value: leaf


title: col submerged for 48h, biological rep1

value: submerged for 48h


title: CapStarr_K562_IFN_rep2

tag: cells used

value: IFNa stimulation for 6 hours


title: SN_Z37

tag: patient diagnosis


title: UCC535

description:
sample name:
SL147059

value: Ulcerative Colitis

tag: tissue

value: F


title: atg5 control, biological rep2


title: PBRM1_WT

value: PBRM1 WT


title: SN_Z23


title: placental DNA 1

value: nonsmoker


title: NAC605

description:
sample name:
SL147087

value: Normal Control

value: intestine

tag: disease

value: macrophages


title: SN_Z17

value: PMBC


title: CSF1R-minus-Spleen-rep3

city: Baltimore

first: Bongsoo

last: Park

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

description: Open Chromatin Regions

data_processing:
cutadapt
BWA-mem alignment
macs2 peak-calling
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak

source_name: Macrophage

extract_protocol:
The engineered hyperactive Tn5 transposase that is preloaded with DNA adapters thus removing the need for a separate annealing step.
ATAC-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Csf1r +/- macrophages from Born Marrow, and Spleen were treated with tn5 enzyme

value: Macrophage


title: NAC603

description:
sample name:
SL147086

tag: smoking status


title: CSF1R-plus-Spleen-rep3

description: Open Chromatin Regions


title: NAC601

description:
sample name:
SL147085

value: Current smoker

tag: mayo score


title: atg5 control, biological rep1


title: CSF1R-minus-Spleen-rep1

description: Open Chromatin Regions


title: SN_Z15

value: SARS-CoV-2 Infection

value: Severe without secondary infection


title: CSF1R-plus-Spleen-rep2

description: Open Chromatin Regions


title: Lung_Untreated_4_CD45_2

city: CAMBRIDGE

first: Duncan

middle: Matthew

last: Morgan

address: 500 Main St

department: Koch Institute

institute: MIT

data_processing:
Raw read processing of single-cell RNA sequencing reads was performed as previously described in Macosko et al. Briefly, reads were aligned to the mm10 reference genome and collapsed by cell barcode and unique molecular identifier (UMI).
Correction for ambient RNA contamination was performed using SoupX v1.2.1.
Data was further analyzed in Seurat v2.3.4.
Genome_build: mm10
Supplementary_files_format_and_content: DGE: single-cell genes/cell count matricies

source_name: Tumor

growth_protocol: Tumor cell lines were cultured at 37°C and 5% CO2 in DMEM (Gibco) supplemented with 10% 782 FBS (Atlanta Biologicals), 1% penicillin/streptomycin (Gibco), and 1X HEPES (Gibco). Tumor cells were harvested by trypsinization (Gibco) and washed 2 times with 1X PBS (Gibco). Cells were resuspended in PBS, and 2.5x105 tumor cells were injected subcutaneously into the flanks of mice, or intravenously via the tail vein.

extract_protocol:
Tumor-bearing mice were injected retro-orbitally with fluorescently-labeled anti-CD45 antibodies (CD45-IV) 3 minutes prior to euthanasia to differentiate tumor- and lung-infiltrating immune cells from circulating immune cells. Spleens and lymph nodes were dissected from mice and physically dissociated through a 70 µm filter to generate single cell suspensions. Splenocyte suspensions were lysed with ACK lysis buffer (Gibco) for 3 minutes to deplete red blood cells. Subcutaneous tumors and tumor-bearing lungs were dissected from mice, weighed, and collected in 5 mL DMEM (Gibco) containing the human tumor dissociation kit (Miltenyi) enzymes. Tumors were dissociated using the gentleMACS Octo Dissociator (Miltenyi). Following the digestion, tumor or lung pieces were mashed through a 70 µm filter with a 1 mL syringe plunger to generate a single cell suspension. The dissociated cells were washed 2 times with PBS and were layered over Ficoll (GE). Cells were spun over Ficoll at 450 g for 30 minutes with the lowest settings of acceleration and brakes. The layer at the interface of Ficoll and PBS, which contained the majority of the live immune cells, was collected and washed with PBS.
Cell suspensions were washed twice with cold PBS + 0.5% BSA + 2mM EDTA and then enriched for tumor-resident immune cells by performing negative selection with anti-PE microbeads (Miltenyi Biotec) followed by positive or negative selection with anti-CD45 microbeads (Miltenyi Biotec).
Seq-Well

treatment_protocol: Mice were injected intraperitoneally with anti-CTLA-4 (clone UC10-4F10-11, Bio X Cell) and anti-PD-L1 (clone 10F.9G2, Bio X Cell) antibodies on days 7, 10, 13, and 16 post-tumor inoculation. Each mouse received 100 µg of each antibody per treatment.

value: Untreated

tag: enrichment protocol

tag: mouse


title: CSF1R-plus-Spleen-rep1

description: Open Chromatin Regions


title: NAC597

description:
sample name:
SL147089

value: Never smoked

value: M

tag: immunosuppression

tag: hbi score


title: NAC599

description:
sample name:
SL147084

tag: Sex


title: SN_Z11


title: col control, biological rep3

source_name: col control

value: col

value: control

value: leaf


title: Lung_Untreated_4


title: CSF1R-minus-Spleen-rep2

description: Open Chromatin Regions

tag: cell type


title: SN_Z10


title: SN_Z8


title: col control, biological rep2


title: col control, biological rep1


title: NAC573

description:
sample name:
SL147082


title: CSF1R-minus-BM-rep2

description: Open Chromatin Regions


title: Lung_Untreated_3_CD45_2


title: CSF1R-minus-BM-rep3

description: Open Chromatin Regions


title: SN_Z7


title: NAC580

description:
sample name:
SL147083


title: CSF1R-plus-BM-rep3

description: Open Chromatin Regions


title: Lung_Untreated_4_CD45_1


title: SN_Z3


title: NAC564

description:
sample name:
SL147081


title: SN_Z14


title: Lung_Untreated_3_CD45_1


title: CSF1R-minus-BM-rep1

description: Open Chromatin Regions


title: CDC610

description:
sample name:
SL147079

value: Crohn's Disease

value: Not treated with immunosupression


title: SN_Z4


title: NAC572

description:
sample name:
SL147088

value: Previous smoker

value: F


title: CSF1R-plus-BM-rep1

description: Open Chromatin Regions


title: CSF1R-plus-BM-rep2

description: Open Chromatin Regions


title: Lung_Untreated_3


title: Lung_Untreated_1_CD45


title: Lung_Untreated_1


title: CDC565

description:
sample name:
SL147072

value: intestine


title: SN_L11


title: SS_Z13

value: Severe with secondary infection


title: Lung_CBT_4_CD45_2

value: Checkpoint blockade


title: Lung_CBT_4_CD45_1


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 30

city: MInneapolis

first: Michael

last: Farrar

address: 2101 6th Street SE

institute: University of Minnesota

description:
SB-PE-30
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt

data_processing:
Reads were aligned with HiSat2 to the mouse genome (mm10) with the SB transposon sequence appended.
Counts were estimated using the Subread featureCounts tool.
FPKM data were generated using the detailed protocol described here: Sarver A. (2019) Identification of Cancer Genes Based on De Novo Transposon Insertion Site Analysis Using RNA and DNA Sequencing. In: Starr T. (eds) Cancer Driver Genes. Methods in Molecular Biology, vol 1907. Humana Press, New York, NY.
Genome_build: mm10 (GRCm38) + SB transposon sequence
Supplementary_files_format_and_content: Two processed data files (tab-delimited text) are provided: (1) counts_gsea_analysis.txt: subread counts txt file with gene counts for all samples, (2) fpkm_fusion_analysis.txt: Cufflinks FPKM values for all samples.

source_name: Lymph Node

extract_protocol:
RNA was isolated using a Qiagen Miniprep Kit.
TruSeq RNA v2 libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Single cell suspensions were created from the lymph nodes of leukemic mice, flash frozen and stored at -80 degrees Celsius. Progenitor B cells were purified from the bone marrow using column purification.

tag: strain

tag: genotype

value: Pax5+/- x Ebf1+/- x CD79a-Cre+ x SB15

value: Leukemic B Cells

tag: number of mice


title: CDC609

description:
sample name:
SL147078

value: macrophages

value: systemic immunosupression


title: CDC541

description:
sample name:
SL147071


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 31

description:
SB-PE-31
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: CDC527

description:
sample name:
SL147069


title: SS_Z16

value: PMBC

value: SARS-CoV-2 Infection


title: Isotype treated virus-specific CD4 T cells (pooled from 5 independent mice)

city: Toronto

first: Ramanandan

last: Prabhakaran

address: 610 University Avenue

institute: University Health Network-Princess Margaret Cancer Center

data_processing:
Cell Ranger mkfastq to generate FASTQ files and Cell Ranger count to generate count matrix and BAM file.
Raw sequencing data was processed using Cell Ranger (v1.3.1, 10x Genomics) to generate expression matrix of RNAs (gene-level counts) for each cell in each sample.
All subsequent downstream analysis was performed in the R statistical programming language using Seurat (v3.1.0) package. For various quality control steps involving cell filtering, normalization, and removal of technical variation, we merged both ISO and aPDL cells into single Seurat object.
Genome_build: mm10
Supplementary_files_format_and_content: matrix file with cell and gene names

source_name: Spleen

extract_protocol:
Splenocytes were harvested from mice that were treated with anti-PDL1 or isotype treated antibodies and FACS sorted to obtain virus-specific SMARTA CD4 T cells. Sorted anti-PDL1 treated and isotype treated SMARTA cells were then washed 2x with PBS + 0.04% BSA and mixed with 10X Genomics Chromium single cell RNA master mix and loaded onto a 10x chromium chip according to the manufacturer’s protocol to obtain single cell cDNA.
Library generation was performed following the Chromium Single Cell 3ʹ Reagents Kits v2 User Guide: CG00052 Rev B.

treatment_protocol: Virus-specific CD4 T cells were injected into mice that were then LCMV-Cl13 infected. Anti-PDL1 blocking antibody or isotype control antibody was administered intraperitoneally beginning 25 days after infection and subsequently on day 28 and day 31 for a total of 3 treatments. Mice were sacrificed following the 3rd treatment (day 33 post-infection)

value: spleen

tag: treatments

value: 3 Isotype Treatments


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 29

description:
SB-PE-29
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: SN_L7

tag: disease state

value: Severe without secondary infection


title: SS_Z5


title: SS_Z9


title: PDL1 treated virus-specific CD4 T cells (pooled from 5 independent mice)

value: 3 anti-PDL1 treatments


title: CCC607

description:
sample name:
SL147077

value: Crohn's Disease

value: Current smoker


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 27

description:
SB-PE-27
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: Lung_CBT_4

tag: treatment


title: Lung_CBT_3_CD45_2


title: Lung_CBT_3_CD45_1


title: CCC579

description:
sample name:
SL147073

tag: patient diagnosis

value: Previous smoker

value: Not treated with immunosupression


title: Lung_Untreated_2

value: Untreated


title: Lung_Untreated_2_CD45


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 26

description:
SB-PE-26
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: CDC606

description:
sample name:
SL147076

tag: tissue

value: intestine

value: F


title: CCC536

description:
sample name:
SL147070

tag: disease

value: Never smoked

value: M


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 23

description:
SB-PE-23
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt

value: Pax5+/- x Ebf1+/- x CD79a-Cre+ x SB15

value: Leukemic B Cells


title: Lung_CBT_3

value: Checkpoint blockade


title: MM_R42

value: PMBC

value: SARS-CoV-2 Infection

value: Mild


title: MM_R51


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 25

description:
SB-PE-25
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: Lung_CBT_2_CD45


title: SS_Z2

value: Severe with secondary infection


title: combination 3

city: Beijing

first: Xiaojuan

last: He

address: Dongzhimennei Nanxiaojie 16#

institute: China Academy of Chinese Medical Sciences

data_processing:
bcl2fastq software used for basecalling.
The sequenced reads were removed reads containing adapters,N>10% and low quality base.
The software Hisat2 was used to establish index file of the Rattus norvegicus genome (rn6), RNA-Seq data was mapped to the generated index file to obtain SAM format sequence alignment results.
Genome_build: rn6
Supplementary_files_format_and_content: FPMK

organism: Rattus norvegicus

source_name: CD4+T cells

extract_protocol:
After treatment, CD4+T lymphocytes from peripheral blood of rats were collected. Total RNA was isolated by the Trizol extraction method.  Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: SD rats

tag: age

value: 8-10 week


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 28

description:
SB-PE-28
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: MM_R49


title: Lung_CBT_1_CD45


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 21

description:
SB-PE-21
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: Flank_Untreated_4_CD45_1


title: Lung_CBT_2


title: model 3


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 22

description:
SB-PE-22
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 24

description:
SB-PE-24
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: combination 2


title: model 1


title: model 2


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 20

description:
SB-PE-20
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: combination 1


title: MM_R46


title: MM_R21


title: MM_R44


title: Lung_CBT_1


title: normal 3


title: Flank_Untreated_4


title: Flank_Untreated_4_CD45_2


title: MM_R30


title: normal 2


title: MM_R23


title: MM_R20


title: MM_R19


title: normal 1


title: Flank_Untreated_3_CD45_1


title: MM_R18


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 17

description:
SB-PE-17
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: Flank_Untreated_3_CD45_2


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 18

description:
SB-PE-18
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: Flank_Untreated_3


title: K562-Nanopore

first: Sheng

last: Li

address: 10 Discovery Dr

institute: The Jackson Laboratory For Genomic Medicine

data_processing:
Nanopore reads (.FAST5 files) were base-called by Guppy (v4.2.2) with default high-accuracy model (dna_r9.4.1_450bps_hac.cfg). The base-called reads were then aligned to human reference genome (GRCh38/hg38) with minimap2
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: bed file or tsv file contains methylated cytosines positions and methylation frequencies

source_name: K562 (Human Chronic Myelogenous Leukemia)

growth_protocol: K562 were cultivated in Roswell Park Memorial Institute (RPMI) 1640 Medium (Gibco, A10491-01) with 10% fetal bovine serum (FBS) (Gibco, 26140079) and 1% Antibiotic-Antimycotic (Gibco, 15240062). Incubator conditions were 37°C and 5% CO2.

extract_protocol:
HMW genomic DNA were extracted from 5m cells using phenol chloroform approach (PMID30933081)
Libraries were prepared using the Rapid Sequencing Kit (SQK-RAD004, ONT) according to manufacturer’s recommendation. Briefly 1200ng DNA was incubated with 2.5ul of FRA at 30°C for 1 min and 80°C 1 min. This is followed by an addition of 3ul of adaptor (RAP) to the reaction mix and incubated at 5 min  at room temperature. The libraries were sequenced on the flowcell R9.4.1 (FLO-MIN106, ONT) on a GridION (ONT) using the MinKNOW software for 48hr

tag: cell line

value: lymphoblast


title: Flank_Untreated_2_CD45

tag: enrichment protocol


title: MM_R12


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 15

description:
SB-PE-15
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 19

description:
SB-PE-19
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 14

description:
SB-PE-14
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: MM_R10


title: Flank_Untreated_2

tag: mouse


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 13

description:
SB-PE-13
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: Flank_Untreated_1_CD45


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 12

description:
SB-PE-12
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt

value: Pax5+/- x Ebf1+/- x CD79a-Cre+ x SB1


title: MM_R9


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 16

description:
SB-PE-16
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: Flank_Untreated_1


title: MM_R8


title: MM_R6


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 11

description:
SB-PE-11
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: Flank_CBT_4_CD45_2


title: Flank_CBT_4


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 10

description:
SB-PE-10
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: Flank_CBT_4_CD45_1


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 9

description:
SB-PE-9
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: MM_R4


title: Flank_CBT_3_CD45_2


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 8

description:
SB-PE-8
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: MM_R15


title: MM_R3


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 7

description:
SB-PE-7
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: Flank_CBT_3_CD45_1


title: Flank_CBT_3


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 6

description:
SB-PE-6
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: MM_R1


title: MM_R5


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 5

description:
SB-PE-5
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: 45-yo Gastric ORGs MOCK [CoV_122020_12_S12]

city: Santander

first: Lucio

last: Di Filippo

state: Cantabria

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

data_processing:
Illumina novaSeq base call (BCL) files are converted in fastq file through bcl2fastq (version v2.20.0.422)
Alignment was performed with STAR 2.6.0a on hg38 reference assembly obtained from cellRanger website (Ensembl 93)
The expression levels of genes were determined with RSEM 1.3.0 by using gencode pre-build genes annotations (hg38 primary assembly)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include expected counts for each sample as output from RSEM

source_name: 45-yo Gastric ORGs MOCK

growth_protocol: Fully grown gastric organoids at day 7 after single cell disaggregation were removed from surrounding extracellular matrix using a modified published protocol. Matrigel was dissolved with 60 min treatment of the droplets with Cell Recovery Solution (Corning) at 4°C. Organoids were retrieved from the plates using 1% BSA-coated cut-end tips and transferred to 1% BSA-coated 15 mL tubes. Cells were extensively washed with ice-cold PBS and centrifuged at 200 g for 5 min at 4°C. Supernatant was discarded, the pellet was resuspended in complete medium and transferred to non-tissue culture treated low-adhesive multiwell plates (pre-coated in 1% BSA). Organoids were cultured in suspension for 3 days to allow reversion of polarity, before use in infection experiments.

extract_protocol:
Pelletted organoids were extracted in RLT buffer
cDNA was synthesized using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, following manufacturer suggested protocol. cDNA generated with SMART-Seq v4 Kit were used for preparation of library with NEXTERA XT DNA Library Preparation kit, following the suggested protocol().

treatment_protocol: Reversed-polarity organoids were infected at a MOI of 1 by incubation with 250 µl of an expansion medium viral suspension for 2 hours. After infection, organoids were washed twice in DMEM to remove unbound virus. RP-GOs were dispersed in a 400 µl expansion medium at 37 °C with 5% CO2. For all organoid cultures 50 µl of supernatant were harvested at 0, 24, 48, and 72 hours post infection. An equal volume of expansion medium replaced the sampled supernatant at each collection time. An extra sample at 96 hours post infection was collected for the RP-GOs. Samples were stored at -80°C before titration through the FFA.

value: Cultured organoid (RP-Gos) from adult stomach tissue (age 45 year)

tag: passage

tag: sars-cov-2 infection

value: negative paired control


title: Flank_CBT_2_CD45_2


title: 45-yo Gastric ORGs MOCK [CoV_122020_11_S11]


title: Flank_CBT_2_CD45_1