title: Cecum, WT [zr4936_19V3V4]

description: Zymo Quick-16STM Primer Set V3-V4


title: Cecum, WT [zr4936_20V3V4]

status: Public on Apr 10 2022

type: SRA

city: Charlottesville

first: Alban

last: Gaultier

state: VA

address: 409 Lane Rd

country: USA

institute: University of Virginia

description: Zymo Quick-16STM Primer Set V3-V4

library_source: transcriptomic

data_processing:
Demultiplexed reads were preprocessed using DADA2, and the first 20 base pairs were trimmed from forward and reverse reads prior to merging.
Chimeric reads were filtered out, and taxonomic identification was performed with the standard DADA2 classifier using the 13_8 Greengenes 16S database.
Supplementary files format and content: tab separated values absolute counts of OTUs by sample with taxonomic annotations attached

molecule: total RNA

organism: Mus musculus

source_name: Cecum Contents

growth_protocol: Cecum Contents

extract_protocol:
ZymoBIOMICS -96 MagBead DNA kit (Zymo Research, Irvine, CA)
V3-V4 region Quick-16S NGS Library Prep Kit (Zymo Reseach, Irvine, CA)

treatment_protocol: Separately Housed Cd4creAhrfl/fl or Ahrfl/fl

tag: tissue

value: Cecum Contents

tag: genotype

value: Ahrfl/fl

tag: treatment

value: Separately Housed

tag: Sex

value: Female


title: F338K-F0

city: Ottawa

first: Lauren

middle: E

last: Carter

state: ON

address: 251 SIR FREDERICK BANTING

country: Canada

institute: Health Canada

data_processing:
Quality filtering and trimming; Bbduk (38.84); maq=12 qtrim=rl trimq=12 minlength=20 tpe tbo
Alignment; STAR (2.7.1a); OutFilterScoreMinOverLread=0.25 outFilterMatchNminOverLread=0.25
Gene reads counting; FeatureCounts (2.0.0); -p -Q=12 -C -t exon -g gene_id
Differential Expression calling; DESeq2 (1.26.0); alpha=0.05 min_reads_gene=5 min_reads_library=1000000 shrinkage=apeglm
Assembly: Rnor_6.0
Supplementary files format and content: gene counts assigned by featureCounts and differentially expressed genes assigned by DESeq2

organism: Rattus norvegicus

source_name: Kidney

extract_protocol:
Kidneys were removed and flash frozen in liquid N2, RNA was harvested using QIAzol reagent. Libraries were prepared using Illumina TruSeq Stranded mRNA Sample Preparation guide (Illumina, San Diego, CA) with 250ng total RNA.
cDNA libraries were prepared for sequencing using standard Illumina protocols

value: Kidney

tag: diet

value: Diet 6 - 1.000mg/kg OTA Diet

tag: strain

value: Fischer

tag: generation

tag: dose timeline


title: Cecum, WT [zr4936_18V3V4]

description: Zymo Quick-16STM Primer Set V3-V4

value: Male


title: F337K-F0


title: Cecum, WT [zr4936_17V3V4]

description: Zymo Quick-16STM Primer Set V3-V4


title: Microwell-seq datasets of FetalMaleGonad_2

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

country: China

institute: Center for Stem Cell and Regenerative Medicine

data_processing:
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. Cellbarcode:In read1, the bases 1-6,22-27,43-48 merge (18bp)； UMI:In read1, the　bases　49-54 (6bp)
ScRNA-seq reads were aligned to the Mus_musculus.GRCm38.88 genome assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.The cell barcode is tagged with XC, the UMI is tagged with XM, the gene is tagged with GE.
Genome_build: Mus_musculus.GRCm38.88 genome
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

molecule: polyA RNA

extract_protocol:
Tissue dissociation and  single-cell lysate
Library preparations were performed with the Microwell-seq protocol

tag: age

value: Testis


title: C10T2_CD45

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
RNA-Seq: Illumina Casava1.7 software used for basecalling.
RNA-Seq: Quality check of the called bases of the reads were performed using the FastQC tool (Babraham Bioinformatics).
RNA-Seq: Datasets were aligned to the rattus norvegius reference rn6 genome using the STAR RNA-Seq aligner (2.7.0f), and HTS. Two-pass mapping was performed using the following modified parameters: --outSAMstrandField intronMotif, --outFilterMultimapNmax 20, -- alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, -- outFilterMismatchNoverLmax 0.1, --alignIntronMin 20, --alignIntronMax 1000000, -- alignMatesGapMax 1000000, --outFilterType BySJout, --outFilterScoreMinOverLread 0.33, -- outFilterMatchNminOverLread 0.33, --limitSjdbInsertNsj 1200000, --chimSegmentMin 15, -- chimJunctionOverhangMin 15, --twopassMode Basic.
RNA-Seq: Raw read counts for individual genes were extracted using --quantMode GeneCounts in STAR using the UCSC rn6 refGene annotation file
Genome_build: rn6
Supplementary_files_format_and_content: RNA-Seq: Tab-separated file of the raw read counts of each samples for each gene.

source_name: CD45 cells from Tumor in NMU treated Sprague Dawley rats

growth_protocol: To induce tumors, virgin Sprague Dawley rats were injected 1-3 times with 50mg/kg N-nitroso N-methylurea (NMU) intraperitoneally at ages 35-53 days

extract_protocol:
Tumor tissue was dissociated to a single-cell suspension in a collagenase solution (2mg/ml collagenase in DMEM/F12 (Life Technologies) with constant stirring at 37'C for 1-2 hours. Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
RNA-seq libraries were prepared using Clontech Low Input mRNA Library (Clontech SMARTer) v4 kit from less than 10ng of purified total RNA according to the manufacturer’s protocol. The concentrations of finished dsDNA library were measured by Qubit Fluorometer, the size of library fragment was measured by Agilent TapeStation 2200, and RT-qPCR for adapted library molar concentration measurement according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on Illumina Illumina NextSeq 500 or NovaGene ...

treatment_protocol: In the immunotherapy cohort, animals were followed by weekly inspections and treatment with LY2157299, anti-PD-L1 mAb, the combination or vehicle initiated when palpable tumors were detected

tag: fraction

tag: cohort

value: Characterization

tag: ratid

tag: tumorid

tag: tissuetype

value: Tumor


title: F336K-F0


title: Cecum, WT [zr4936_16V3V4]

description: Zymo Quick-16STM Primer Set V3-V4


title: Microwell-seq datasets of FetalMaleGonad_1


title: F334K-F0


title: F335K-F0


title: Cecum, WT [zr4936_15V3V4]

description: Zymo Quick-16STM Primer Set V3-V4


title: Microwell-seq datasets of AdultStomach_2

value: Stomach


title: 247-M1_L

value: Diet 1 - 0mg/kg OTA Diet (Control)

value: In Utero to PND90


title: F333K-F0


title: Microwell-seq datasets of AdultStomach_1


title: Microwell-seq datasets of NeonatalTestis_1

value: neonatal


title: F332K-F0


title: Cecum, KO [zr4936_12V3V4]

description: Zymo Quick-16STM Primer Set V3-V4


title: Cecum, WT [zr4936_13V3V4]

description: Zymo Quick-16STM Primer Set V3-V4


title: Cecum, WT [zr4936_14V3V4]

description: Zymo Quick-16STM Primer Set V3-V4


title: Microwell-seq datasets of ThreeWeeksStomach_1


title: Microwell-seq datasets of TenDaysStomach_2


title: F329K-F0


title: Microwell-seq datasets of TenDaysStomach_3


title: Microwell-seq datasets of TenDaysStomach_1


title: Cecum, KO [zr4936_10V3V4]

description: Zymo Quick-16STM Primer Set V3-V4


title: Microwell-seq datasets of NeonatalStomach_1


title: F322K-F0

value: Diet 5 - 0.400mg/kg OTA Diet


title: F320K-F0


title: Cecum, KO [zr4936_9V3V4]

description: Zymo Quick-16STM Primer Set V3-V4


title: THP-1 derived macrophages infected with BCG Mexico (M.BCG). Biological replicate 3

type: RNA

city: Ciudad de México

first: Antonia

middle: Isabel

last: Castillo-Rodal

state: Ciudad de México

address: Av. Universidad 3000, Circuito Exterior S/N, Facultad de Medicina, Alcaldía Coyoacán,

department: Microbiología y Parasitología

country: Mexico

institute: Universidad Nacional Autónoma de México

hyb_protocol: Fragmented and labeled cDNA was hybridized onto Affymetrix

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G

data_processing:
Raw data were background-corrected using Robust Multiarray Average (RMA) and normalized using Quantile Normalization.
probe group file: HuGene-1_0-st-v1.r4.pgf

label: Biotin

organism: Homo sapiens

source_name: THP-1 derived macrophages infected with BCG Mexico (M.BCG) at 1:10 ratio. 24 h

label_protocol: Target cDNA was prepared according to the WT Expression Sense Target Kit (Ambion, USA). Purified sense-strand cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling Kit (Affymetrix, USA).

growth_protocol: The THP-1 cell line (ATCC TIB-202) of human monocyte origin was maintained in the RPMI-1640 medium (Gibco) supplemented with 10% fetal bovine serum (Gibco) at 37 °°C and 5% CO2. After reaching confluence of 1 x106 × 106 THP-1 cells/well in 12-well plates, monocytes were stimulated using 50 ng/mL of Phorbol 12-myristate 13-acetate (PMA) (Sigma) for 48 h.

extract_protocol: Total RNA was recovered using the TRIzol reagent (Sigma-Aldrich, St. Louis, USA), following the manufacturer’s instructions.

treatment_protocol: THP-1-derived macrophages were infected with either M.BCG Mexico or Phippsor P.BCG at a 1:10 ratio, with using non-infected macrophages as a negative control. After 24 h, macrophages were homogenized

tag: cell line

value: ATCC TIB-202

value: BCG Mexico


title: THP-1 derived macrophages infected with BCG Mexico (M.BCG). Biological replicate 2


title: Cecum, KO [zr4936_8V3V4]

description: Zymo Quick-16STM Primer Set V3-V4

value: Cecum Contents


title: Microwell-seq datasets of FetalStomach_2


title: THP-1 derived macrophages infected with BCG Phipps (P.BCG). Biological replicate 2

source_name: THP-1 derived macrophages infected with BCG Phipps (P.BCG) at a 1:10 ratio. 24 h

value: BCG Phipps


title: THP-1 derived macrophages infected with BCG Phipps (P.BCG). Biological replicate 1


title: THP-1 derived macrophages non infected. Biological replicate 3

source_name: THP-1 derived macrophages non infected. 24 h


title: THP-1 derived macrophages infected with BCG Phipps (P.BCG). Biological replicate 3


title: Cecum, KO [zr4936_7V3V4]

description: Zymo Quick-16STM Primer Set V3-V4

value: Separately Housed

value: Female


title: Cecum, KO [zr4936_11V3V4]

description: Zymo Quick-16STM Primer Set V3-V4


title: Cecum, KO [zr4936_6V3V4]

description: Zymo Quick-16STM Primer Set V3-V4


title: F319K-F0

value: Kidney


title: THP-1 derived macrophages non infected. Biological replicate 2


title: Test 2

city: Turku

first: Anssi

last: Malinen

address: Tykistökatu 6

department: Life technologies

country: Finland

institute: University of Turku

data_processing:
fastp removed reads containing adapter and poly-N, to get clean reads.
Paired-end clean reads were mapped to A. flavus NRRL 3357 genome using HISAT2 software
Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) values were calculated using a protocol from Trapnell et al., nature biotechnology, 2010.
The differentially expressed genes (DGEs) between the control and test samples were analyzed using the DESeq2 R package
Genome_build: refernce sequence used for read alignment
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample
Supplementary_files_format_and_content: Excel file with readcounts for every gene and every sample

organism: Aspergillus flavus

source_name: Fungi

extract_protocol:
Fungal mycelia were removed from 4 days old cultures and grinded to fine powder in liquid nitrogen. The cell mass was supplemented with 1 µl RiboLock RNase inhibitor and immediately used to extract RNA with Trizol Reagent according to the manufacturer´s instructions.
cDNA libraries were prepared and sequenced at Novogene company (Cambridge, UK) using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (New England Biolabs, USA) and index codes were added to attribute sequences to each sample.

value: Fungi

value: 4 days


title: Test 3


title: Microwell-seq datasets of AdultPancreas_1

value: Pancreas


title: THP-1 derived macrophages non infected. Biological replicate 1


title: Microwell-seq datasets of FetalStomach_1


title: THP-1 derived macrophages infected with BCG Mexico (M.BCG). Biological replicate 1


title: F318K-F0

value: Fischer


title: Cecum, KO [zr4936_5V3V4]

description: Zymo Quick-16STM Primer Set V3-V4

value: Male


title: Test 1


title: F315K-F0


title: F323K-F0


title: Microwell-seq datasets of ThreeWeeksPancreas_1


title: Control 3


title: Cecum, KO [zr4936_4V3V4]

description: Zymo Quick-16STM Primer Set V3-V4


title: Microwell-seq datasets of TenDaysPancreas_2


title: F309K-F0


title: Microwell-seq datasets of TenDaysPancreas_1


title: F312K-F0


title: Control 2


title: Microwell-seq datasets of NeonatalPancreas_2


title: F307K-F0

value: Diet 4 - 0.160mg/kg OTA Diet


title: Cecum, KO [zr4936_3V3V4]

description: Zymo Quick-16STM Primer Set V3-V4


title: Vero_GC_WT_0

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

data_processing:
The reads of the ribo-seq libraries were trimmed to remove the linker CTGTAGGCACCATCAAT by using cutadapt. For the Shishkin protocol libraries the linker was AGATCGGAAGAGCACACGT.
Reads aligned to hg19 based rRNA and tRNA reference were removed. Then reads were aligned to combined reference of the host and the virus.
Reads that failed to align to genome, were aligned to the host transcriptome and to the viral breaking points according to strong break point at Kim et al., plus few breakpoints from our STAR runs.
The alignments above were made with Bowtie1. In the ribo-seq libraries the p-site was calculated as an offset (adjusted to the read length) from the read start site.
The STAR alignment was made with the flags recommended by Kim et al. to get all the breakpoints.
Assembly: Host: Human hg19 (GRCh37); Chlorocebus sabaeus genome and annotation ENSEMBL release 99; Mesocricetus auratus genome and annotation ENSEMBL release 104; Virus Genbank NC_045512.2.
Supplementary files format and content: *.csv: Comma-separated files of the cytosolic to nuclear ratio of transcripts, half-life of transcripts, and the read counts of all transcripts in each experiment (either for coding RNAs or for all transcripts).

organism:
Chlorocebus sabaeus
Severe acute respiratory syndrome coronavirus 2

source_name: Monkey + Virus

extract_protocol:
For RNA-seq, cells were harvested with Tri-Reagent (Sigma-Aldrich), total RNA was extracted, and poly-A selection was performed using Dynabeads mRNA DIRECT Purification Kit (Invitrogen). For ribosome profiling, medium was aspirated from dishes, which were immediately placed on ice and rinsed with 10 ml ice-cold PBS supplemented with drugs used in pretreatment of the cells. PBS was aspirated and 800 μl ice-cold lysis buffer (20 mM Tris, pH 7.4, 250 mM NaCl, 15 mM MgCl2, 1 mM dithiothreito, 0.5% Triton X-100 and 24 U / ml Turbo DNase (Ambion, AM2239), along with any drugs used for sample treatment) was dripped onto dishes. Cells were scraped and the lysate was removed and incubated 10 min on ice. The lysate was then clarified by centrifugation for 10 min at 20,000 × g, 4°C and ∼1.1 ml supernatant was recovered.
RNA-seq: mRNA sample was subjected to DNaseI treatment and 3’ dephosphorylation using FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific) and T4 PNK (NEB) followed by 3’ adaptor ligation using T4 ligase (NEB). The ligated products used for reverse transcription with SSIII (Invitrogen) for first strand cDNA synthesis. The cDNA products were 3’ ligated with a second adaptor using T4 ligase and amplified for 8 cycles in a PCR for final library products of 200-300bp.

treatment_protocol: For Ribo-seq libraries, all samples were treated with 100μg/mL CHX for 1 minute. Cells were placed on ice immediately after treatment, washed twice with PBS containing 100μg/mL CHX.

tag: infection

tag: hours post infection


title: Cecum, KO [zr4936_2V3V4]

description: Zymo Quick-16STM Primer Set V3-V4

tag: tissue


title: F305K-F0


title: Vero_GC_Del_48_B


title: Microwell-seq datasets of NeonatalPancreas_1


title: Cecum, KO [zr4936_1V3V4]

description: Zymo Quick-16STM Primer Set V3-V4

tag: genotype


title: F306K-F0


title: Vero_GC_WT_48_B


title: Microwell-seq datasets of FetalPancreas_2


title: Feces, co-housed, WT [S00B3-0012_S72]

description: Zymo Quick-16STM Primer Set V3-V4

source_name: Feces

growth_protocol: Feces

extract_protocol:
Qiagen MagAttract PowerSoil DNA KF Kit (Thermofisher)
Dual-barcoded primers targeting the 16S V4 region

treatment_protocol: Cohoused Cd4creAhrfl/fl or Ahrfl/fl

value: Feces

value: Ahrfl/fl

tag: treatment

value: Cohoused


title: Vero_GC_Del_48_A


title: Feces, co-housed, WT [S00B3-0011_S71]

description: Zymo Quick-16STM Primer Set V3-V4

tag: Sex


title: F301K-F0

tag: diet


title: Feces, co-housed, WT [S00B3-0010_S70]

description: Zymo Quick-16STM Primer Set V3-V4


title: F302K-F0

tag: strain


title: Microwell-seq datasets of AdultLung_3

value: Lung


title: F300K-F0

tag: generation


title: Vero_GC_WT_48_A


title: Microwell-seq datasets of FetalPancreas_1


title: Control 1


title: Microwell-seq datasets of AdultLung_2


title: F296K-F0

tag: dose timeline


title: Feces, co-housed, WT [S00B3-0008_S68]

description: Zymo Quick-16STM Primer Set V3-V4


title: Vero_GC_WT_24_B


title: F289K-F0

value: Diet 3 - 0.064mg/kg OTA Diet


title: Microwell-seq datasets of AdultLung_1

tag: age


title: Microwell-seq datasets of ThreeWeeksLung_1


title: Feces, co-housed, WT [S00B3-0007_S67]

description: Zymo Quick-16STM Primer Set V3-V4


title: Vero_GC_Del_24_B


title: Vero_GC_Del_24_A


title: F285K-F0


title: Microwell-seq datasets of TenDaysLung_3


title: Vero_GC_WT_24_A


title: Feces, co-housed, KO [S00B3-0006_S66]

description: Zymo Quick-16STM Primer Set V3-V4


title: F284K-F0


title: Feces, co-housed, KO [S00B3-0005_S65]

description: Zymo Quick-16STM Primer Set V3-V4


title: F282K-F0


title: F281K-F0


title: Feces, co-housed, KO [S00B3-0003_S63]

description: Zymo Quick-16STM Primer Set V3-V4


title: Feces, co-housed, KO [S00B3-0004_S64]

description: Zymo Quick-16STM Primer Set V3-V4


title: Vero_GC_Del_11_B


title: Microwell-seq datasets of TenDaysLung_1


title: Vero_GC_WT_11_B


title: Microwell-seq datasets of NeonatalLung_2

value: neonatal


title: Feces, co-housed, WT [S00B3-0009_S69]

description: Zymo Quick-16STM Primer Set V3-V4


title: Vero_GC_Del_11_A


title: Feces, co-housed, KO [S00B3-0002_S62]

description: Zymo Quick-16STM Primer Set V3-V4


title: F279K-F0


title: Feces, co-housed, KO [S00B3-0001_S61]

description: Zymo Quick-16STM Primer Set V3-V4


title: Vero_GC_WT_11_A


title: F278K-F0


title: Vero_GC_Del_0


title: F274K-F0

value: Diet 2 - 0.026mg/kg OTA Diet


title: Microwell-seq datasets of AdultLiver_2

value: Liver


title: F275K-F0


title: Microwell-seq datasets of FetalLung_1


title: Day 6 differentiated cells

city: Palo Alto

first: Ziming

last: Luo

state: CA

address: 1651 Pagemill Rd.

department: Ophthalmology

institute: Stanford University

library_source: transcriptomic single cell

data_processing:
We applied fastp with the default parameters filtering the adaptor sequence, and removed the low-quality reads to achieve clean data.
Then the feature-barcode matrices were obtained by aligning reads to the human genome using CellRanger v3.0.0.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: stem cell-derived neurons

growth_protocol: hiPSCs were treated with 0.5% EDTA and plated on Matrigel (BD Biosciences)-coated plates at 70% confluence in StemFlex (Thermo) on day -2. On day -1, lentivirus prepared as previously described was added in fresh StemFlex medium. On day 0, the culture medium was replaced with NBF (1% B27 supplement, 0.5% N2 supplement, 20 ng/ml fibroblast growth factor and 1% penicillin/streptomycin in DMEM-F12 medium). Doxycycline (2 µg/ml, Clontech) was added on day 0 to induce TetO expression. On day 1, 2ug/ml puromycin was added in fresh NBF medium for a 24 hr selection. On day 2, the culture medium was replaced with RGC culture medium (Full Sato, prepared as previously described), including insulin (5 μg/ml, Sigma), sodium pyruvate (1 mM, Sigma), penicillin/streptomycin (1%, Thermo Fisher Scientific), Sato supplement (1:100), L-glutamine (1 mM, Sigma), triiodothyronine (T3, 40 ng/ml, Sigma), N-acetyl cysteine (5 μg/ml, Sigma), brain-derived neurotrophic factor (50 ng ml-1, Peprotech), ciliary neurotrophic factor (10 ng ml-1, Peprotech), forskolin (5 mM, Sigma) plus Notch inhibitor DAPT (10 μM, EMD Millipore) and glial derived neurotrophic factor (50ug/ml, Peprotech) for another 4 days, changing half of the medium every other day.

extract_protocol:
Differentiated cells were dissociated using Accutase (Innovative Cell Technologies) for 15-20 minutes on day 6. Cell pellets were resuspended in PBS containing 0.04% bovine serum albumin and filtered through a 40 μm cell strainer (Falcon, Cat#352340) to remove cell clumps before counting with a hemocytometer.
Barcoded 3’ single-cell libraries were prepared from single cell suspensions using the Chromium Single Cell 3’ Library and Gel Bead kit (10X Genomics, Pleasanton, California) for sequencing according to the recommendations of the manufacturer. The cDNA and library fragment size distribution were verified via micro-capillary gel electrophoresis on a Bioanalyzer 2100 (Agilent, Santa Clara, CA). The libraries were quantified by fluorometry on a Qubit instrument (LifeTechnologies, Carlsbad, CA) and by qPCR with a Kapa Library Quant kit (Kapa Biosystems-Roche) prior to sequencing. Eight libraries were sequenced per lane on a NovaSeq 6000 sequencer (Illumina, San Diego, CA) with paired-end 150 bp reads.
scRNA-seq on a NovaSeq 6000 sequencer (Illumina, San Diego, CA)

tag: cell type

value: human induced pluripotent stem cells


title: Microwell-seq datasets of TenDaysLung_2

value: Female


title: F270K-F0

value: Kidney


title: Microwell-seq datasets of AdultLiver_1


title: Microwell-seq datasets of NeonatalLung_3


title: F268K-F0


title: GGO_95.2

city: New York

first: Olivier

last: Elemento

state: NY

address: 1305 York Ave

department: Biochemistry

institute: Weill Cornell Medicine

data_processing:
The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
All reads were independently aligned with STAR_2.4.0f1 for sequence alignment against the human genome build hg19, downloaded via the UCSC genome browser, and SAMTOOLS v0.1.19 for sorting and indexing reads.
Cufflinks (2.0.2) was used to get the expression values (FPKMs), and Gencode v19 GTF file for annotation.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files includes matrix of sample by gene geen expression values quantified as FPKMs

source_name: Lung Tissue, Archival FFPE

growth_protocol: Archival FFPE human lung tissue

extract_protocol:
RNA was extracted from FFPE samples with RNeasy FFPE kit from Qiagen, Part# 73504.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760, New England BioLabs, Ipswich, MA) was used for sample library preparation according to the manufacturer’s instruction.  PCR enrichment of adaptor ligated cDNA were pooled and hybridized with probes from Twist Exome Kit #2 (Twist Bioscience, San Francisco, CA). After post capture PCR amplification and purification, the quality of final libraries was checked and loaded to Illumina NovaSeq6000 for sequencing at PE2x100 cycles

treatment_protocol: Not applicable

tag: tissue type

value: Solid CT density Tumor


title: Microwell-seq datasets of ThreeWeeksLiver_2


title: MM1S_IT848_1

city: Nutley

first: Johannes

last: Zakrzewski

state: New Jersey

address: 111 Ideation Way

institute: Hackensack Meridian Health

data_processing:
Illumina bcl2fastq was used for basecalling.
The sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner uses a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Extracting gene hit counts; Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Hit Counts converted to TPM with R script. The TPM was normalized and log transformed.
Assembly: hg19
Supplementary files format and content: Expression count

source_name: MM.1S treated

growth_protocol: Cell were cultured in RPMI + 20% FBS

extract_protocol:
Cell were lysed and total RNA was extracted using an AllPrep DNA/RNA extraction kit (Qiagen, Hilden, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols.
RNAseq; Illumina HiSeq 2x150 bp sequencing, single index

treatment_protocol: Cells were treated with either DMSO or IT848 6uM for 6 hrs

value: treated with IT848 6 uM for 6 hours

value: Multiple myeloma cell line


title: GGO_98


title: MM1S_IT848_2


title: Microwell-seq datasets of NeonatalLung_1


title: MM1S_IT848_3


title: F267K-F0

value: Fischer


title: MM1S_DMSO_2

source_name: MM.1S control

value: treated with DMSO for 6 hours


title: MM1S_DMSO_3


title: GGO_91


title: GGO_95.1


title: F266K-F0


title: Microwell-seq datasets of TenDaysLiver_2


title: MM1S_DMSO_1


title: Microwell-seq datasets of TenDaysLiver_1


title: GGO_89


title: U266_IT848_3

source_name: U266 treated


title: F263K-F0


title: U266_IT848_2


title: GGO_87


title: GGO_88


title: Microwell-seq datasets of NeonatalLiver_1


title: F258K-F0

value: Diet 1 - 0mg/kg OTA Diet (Control)


title: Microwell-seq datasets of FetalLiver_1


title: Microwell-seq datasets of ThreeWeeksLiver_1


title: Microwell-seq datasets of AdultKidney_2


title: GGO_86


title: U266_IT848_1


title: F257K-F0


title: U266_DMSO_3

source_name: U266 control


title: U266_DMSO_2


title: F256K-F0


title: F254K-F0


title: GGO_82


title: Microwell-seq datasets of AdultKidney_1


title: U266_DMSO_1


title: F249K-F0


title: Microwell-seq datasets of TenDaysKidney_2


title: Microwell-seq datasets of ThreeWeeksKidney_1


title: Untreated biological replicate 2 library 6

city: London

first: Caroline

middle: S

last: Hill

address: 1 Midland Road

department: Developmental Signalling

country: United Kingdom

institute: Francis Crick Institute

description:
UNT_R2_L6
processed data file: UNT.broadPeak.gz

library_source: genomic

data_processing:
Raw reads from each sample were adapter-trimmed using cutadapt 1.9.1 with parameters “-a CTGTCTCTTATA -A CTGTCTCTTATA, minimum-length = 25 – quality-cutoff = 20”.
BWA 0.6.2 (Li and Durbin, 2009) with default parameters was then used to perform genome-wide mapping of the adapter-trimmed reads to the mouse mm10 genome downloaded from the UCSC (Karolchik et al., 2004).
Read group addition, duplicate marking and insert size assessment was performed using, respectively, the picard tools AddOrReplaceReadGroups, MarkDuplicates and CollectMultipleMetrics 2.1.1.
Reads mapped to mitochondrial DNA were removed using the pairToBed command from BEDTools 2.26.0-foss-2016b (Quinlan and Hall, 2010).
Additional filtering was performed to remove read pairs that were discordant, mapped to different chromosomes, ambiguously mapped, had an insert size > 2kb, and mismatch > 2 in any reads.
When individual samples were combined to increase the read depth, the filtered alignments from each library were merged using the picard MergeSamFiles command. Duplicate marking was re-performed on the merged alignments, and they were subsequently filtered for duplicate reads, leading to 500 – 600 million reads for merged sample.
Genome-wide ATAC-seq peaks for the merged samples were obtained using MACS2 callpeak 2.1.1.20160309 (Zhang et al., 2008) with the parameters “gsize = mm, keep-dup all, nomodel, shift – 100, extsize 200 - B, SPMR, cutoff-analysis – broad”.
Genome_build: mm10
Supplementary_files_format_and_content: Unfiltered MACS2 broadPeak files obtained from BAM files created after merging samples from the same condition.

molecule: genomic DNA

source_name: P19 mouse embryonic teratoma cells

growth_protocol: P19 cells were cultured in Dulbecco’s Modified Eagle Medium containing 10% FCS.

extract_protocol:
DNA was isolated as previously described (Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213–1218, 2013).
100000 cells were used for the transposition reaction, that was carried out for 30 min at 37°C. Library fragments were amplified using 1× NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min - this was done for 12 cycles.

treatment_protocol: Treatment with Nodal/Activin signalling inhibitor (SB-431542, 10 µM) or Activin (20ng/ml) was administered with the culture medium.

value: P19 mouse embryonic teratoma cells

tag: timepoint

value: 0 hours

value: untreated


title: GGO_81


title: Microwell-seq datasets of TenDaysKidney_1


title: F247K-F0


title: F265K-F0


title: GGO_79


title: Untreated biological replicate 2 library 5

description:
UNT_R2_L5
processed data file: UNT.broadPeak.gz


title: F245K-F0


title: M238K-F0

value: Diet 6 - 1.000mg/kg OTA Diet

value: Male


title: GGO_80


title: GGO_78


title: Microwell-seq datasets of NeonatalKidney_2

value: neonatal


title: Untreated biological replicate 2 library 4

description:
UNT_R2_L4
processed data file: UNT.broadPeak.gz


title: GGO_83


title: Microwell-seq datasets of NeonatalKidney_1


title: M237K-F0


title: Untreated biological replicate 2 library 1

description:
UNT_R2_L1
processed data file: UNT.broadPeak.gz


title: GGO_76


title: Untreated biological replicate 2 library 3

description:
UNT_R2_L3
processed data file: UNT.broadPeak.gz


title: Microwell-seq datasets of FetalKidney_2


title: M236K-F0


title: GGO_75


title: Microwell-seq datasets of FetalKidney_1


title: GGO_72


title: M234K-F0


title: Microwell-seq datasets of AdultIntestine_3

value: Intestine


title: Untreated biological replicate 1 library 5

description:
UNT_R1_L5
processed data file: UNT.broadPeak.gz


title: M233K-F0


title: Untreated biological replicate 1 library 4

description:
UNT_R1_L4
processed data file: UNT.broadPeak.gz


title: Microwell-seq datasets of AdultIntestine_1


title: GGO_71


title: Untreated biological replicate 1 library 6

description:
UNT_R1_L6
processed data file: UNT.broadPeak.gz


title: Microwell-seq datasets of AdultIntestine_2


title: GGO_67


title: Microwell-seq datasets of ThreeWeeksIntestine_1


title: Microwell-seq datasets of TenDaysIntestine_2


title: M232K-F0


title: Untreated biological replicate 1 library 2

description:
UNT_R1_L2
processed data file: UNT.broadPeak.gz


title: Untreated biological replicate 1 library 3

description:
UNT_R1_L3
processed data file: UNT.broadPeak.gz


title: Untreated biological replicate 2 library 2

description:
UNT_R2_L2
processed data file: UNT.broadPeak.gz


title: M230K-F0


title: Microwell-seq datasets of TenDaysIntestine_1


title: M222K-F0

value: Diet 5 - 0.400mg/kg OTA Diet


title: M220K-F0


title: GGO_69


title: GGO_64

value: Pure non-solid CT density Tumor


title: M221K-F0


title: SB-431542 biological replicate 2 library 5

description:
SB_R2_L5
processed data file: SB.broadPeak.gz


title: M235K-F0


title: Untreated biological replicate 1 library 1

description:
UNT_R1_L1
processed data file: UNT.broadPeak.gz


title: GGO_60


title: SB-431542 biological replicate 2 library 6

description:
SB_R2_L6
processed data file: SB.broadPeak.gz


title: Microwell-seq datasets of NeonatalIntestine_1

value: Female


title: GGO_66


title: Microwell-seq datasets of FetalIntestine_1


title: M218K-F0

value: Kidney


title: GGO_51


title: SB-431542 biological replicate 2 library 4

description:
SB_R2_L4
processed data file: SB.broadPeak.gz


title: M216K-F0


title: GGO_65


title: Microwell-seq datasets of AdultHeart_3

value: Heart


title: SB-431542 biological replicate 2 library 3

description:
SB_R2_L3
processed data file: SB.broadPeak.gz


title: GGO_44


title: GGO_43


title: M215K-F0


title: Microwell-seq datasets of AdultHeart_2


title: Microwell-seq datasets of AdultHeart_1


title: GGO_42


title: SB-431542 biological replicate 2 library 2

description:
SB_R2_L2
processed data file: SB.broadPeak.gz


title: Microwell-seq datasets of ThreeWeeksHeart_1


title: SB-431542 biological replicate 2 library 1

description:
SB_R2_L1
processed data file: SB.broadPeak.gz


title: SB-431542 biological replicate 1 library 6

description:
SB_R1_L6
processed data file: SB.broadPeak.gz


title: M206K-F0

value: Diet 4 - 0.160mg/kg OTA Diet


title: Microwell-seq datasets of AdultHeart_4


title: GGO_46


title: GGO_41


title: M213K-F0


title: Microwell-seq datasets of TenDaysHeart_2


title: SB-431542 biological replicate 1 library 5

description:
SB_R1_L5
processed data file: SB.broadPeak.gz


title: GGO_40


title: M217K-F0


title: Microwell-seq datasets of TenDaysHeart_1


title: M205K-F0


title: SB-431542 biological replicate 1 library 4

description:
SB_R1_L4
processed data file: SB.broadPeak.gz


title: GGO_38


title: Microwell-seq datasets of NeonatalHeart_1


title: SB-431542 biological replicate 1 library 2

description:
SB_R1_L2
processed data file: SB.broadPeak.gz


title: M204K-F0


title: SB-431542 biological replicate 1 library 3

description:
SB_R1_L3
processed data file: SB.broadPeak.gz


title: M202K-F0


title: Microwell-seq datasets of FetalHeart_1


title: SB-431542 biological replicate 1 library 1

description:
SB_R1_L1
processed data file: SB.broadPeak.gz


title: Microwell-seq datasets of FetalHeart_2


title: GGO_28


title: GGO_26


title: GGO_25


title: M201K-F0


title: Microwell-seq datasets of AdultBrain_2

value: Brain


title: M199K-F0

value: Fischer


title: Microwell-seq datasets of AdultBrain_1


title: Microwell-seq datasets of ThreeWeeksBrain_1


title: M197K-F0


title: GGO_24


title: M198K-F0


title: GGO_23


title: Microwell-seq datasets of TenDaysBrain_2


title: M190K-F0

value: Diet 3 - 0.064mg/kg OTA Diet


title: Activin 8 hour biological replicate 2 library 6

description:
ACT_8H_R2_L6
processed data file: ACT_8H.broadPeak.gz

value: 8 hours

value: activin


title: Activin 8 hour biological replicate 2 library 5

description:
ACT_8H_R2_L5
processed data file: ACT_8H.broadPeak.gz

value: P19 mouse embryonic teratoma cells


title: Activin 8 hour biological replicate 2 library 4

description:
ACT_8H_R2_L4
processed data file: ACT_8H.broadPeak.gz


title: Activin 8 hour biological replicate 2 library 3

description:
ACT_8H_R2_L3
processed data file: ACT_8H.broadPeak.gz


title: Microwell-seq datasets of TenDaysBrain_1


title: M189K-F0


title: Activin 8 hour biological replicate 2 library 2

description:
ACT_8H_R2_L2
processed data file: ACT_8H.broadPeak.gz


title: GGO_19


title: M188K-F0


title: Microwell-seq datasets of NeonatalBrain_3


title: GGO_18


title: Activin 8 hour biological replicate 2 library 1

description:
ACT_8H_R2_L1
processed data file: ACT_8H.broadPeak.gz


title: Microwell-seq datasets of NeonatalBrain_2


title: GGO_16


title: Activin 8 hour biological replicate 1 library 6

description:
ACT_8H_R1_L6
processed data file: ACT_8H.broadPeak.gz


title: GGO_21


title: Microwell-seq datasets of NeonatalBrain_1


title: Activin 8 hour biological replicate 1 library 5

description:
ACT_8H_R1_L5
processed data file: ACT_8H.broadPeak.gz


title: M183K-F0


title: GGO_12


title: Microwell-seq datasets of FetalBrain_1


title: Activin 8 hour biological replicate 1 library 3

description:
ACT_8H_R1_L3
processed data file: ACT_8H.broadPeak.gz


title: GGO_20


title: Bulk_RNAseq_Humanized_lung_uninfected_matched_to_14dpi#2

city: New Haven

first: Rihao

last: Qu

state: CT

address: 300 George Street

institute: BBS Program, Yale University

description: Uninfected MSITRG6-hACE2 mice matched to 14dpi samples- Low input RNA seq approach

data_processing:
For RNA-seq raw data processing, trimming was performed using cutadapt.
Alignment was performed using STAR (version 2.5.3) and raw read counts were generated using HTSeq.
Differential analysis was performed using DESeq2 R package.
Assembly: hg19-mm10-covid
Supplementary files format and content: Txt file including gene count for each sample separately

source_name: homogenized lung tissue from humanized MISTRG6 mice

growth_protocol: Newborn MISTRG6 mice were reconstitued with human CD34+ fetal liver cells. Mice were administered with AAV encoding human ACE2 at approximately 8 weeks post-engrafted. Mice were then infected with SARS-CoV-2.

extract_protocol:
Whole lungs were homogenized and RNA was extracted with the RNeasy mini kit (Qiagen) per the manufacturer’s protocol.
Libraries were prepared with an Illumina rRNA depletion kit and sequenced on a NovaSeq.

treatment_protocol: SARS-CoV-2 infected MISTRG6-hACE2 were treated with dexamethasone at 10mg/kg for 3 days starting at 7dpi. Mice were treated subcutaneously with Remdesivir at 25mg/kg dosing  for 3 consecutive days starting at 7dpi. Mice were treated with anti-IFNAR2 antibody at 1.5mg/kg dosing on days 7 and 11 post infection.

value: MISTRG6 in Balb/c

value: Lung

value: MCSF(h/h),IL/GMCSF(h/h),THPO(h/h), SIRP(h/m), Rag2-/-IL2rg-/- IL6(h/h) (h=human; m=mouse)


title: M182K-F0

value: Male


title: GGO.N_71

value: Tumor adjacent normal lung


title: GGO.N_72


title: M181K-F0


title: Activin 8 hour biological replicate 1 library 2

description:
ACT_8H_R1_L2
processed data file: ACT_8H.broadPeak.gz


title: M174K-F0

value: Diet 2 - 0.026mg/kg OTA Diet


title: Activin 8 hour biological replicate 1 library 1

description:
ACT_8H_R1_L1
processed data file: ACT_8H.broadPeak.gz


title: Bulk_RNAseq_Humanized_lung_uninfected #2

description: Uninfected MSITRG6-hACE2 mice matched to 28dpi samples


title: Bulk_RNAseq_Humanized_lung_uninfected_matched_to_14dpi#1


title: M187K-F0


title: Activin 1 hour biological replicate 2 library 6

description:
ACT_1H_R2_L6
processed data file: ACT_1H.broadPeak.gz

value: 1 hour


title: Bulk_RNAseq_Humanized_lung_uninfected #1


title: M171K-F0


title: M186K-F0


title: GGO.N_51


title: Bulk_RNAseq_Humanized_lung_14dpi #2

description: SARS-Cov-2 infected MISTRG6-hACE2 mice


title: Activin 1 hour biological replicate 2 library 5

description:
ACT_1H_R2_L5
processed data file: ACT_1H.broadPeak.gz


title: Activin 8 hour biological replicate 1 library 4

description:
ACT_8H_R1_L4
processed data file: ACT_8H.broadPeak.gz


title: GGO_10

value: Pure non-solid CT density Tumor


title: GGO.N_43


title: M169K-F0

value: Kidney


title: Bulk_RNAseq_Humanized_lung_14dpi #1

description: SARS-Cov-2 infected MISTRG6-hACE2 mice


title: Activin 1 hour biological replicate 2 library 4

description:
ACT_1H_R2_L4
processed data file: ACT_1H.broadPeak.gz


title: GGO.N_28


title: M167K-F0


title: GGO.N_23


title: Activin 1 hour biological replicate 2 library 3

description:
ACT_1H_R2_L3
processed data file: ACT_1H.broadPeak.gz


title: Bulk_RNAseq_Humanized_lung_14dpi_IFNAR_RDV#2

description: SARS-Cov-2 infected MISTRG6-hACE2 mice were treated with Remdesivir 7-9dpi and anti-IFNAR2 antibody on days 7 and 9 post infection


title: Bulk_RNAseq_Humanized_lung_14dpi_IFNAR_RDV#1


title: GGO.N_21


title: Activin 1 hour biological replicate 2 library 2

description:
ACT_1H_R2_L2
processed data file: ACT_1H.broadPeak.gz


title: GGO.N_64


title: M173K-F0


title: Activin 1 hour biological replicate 2 library 1

description:
ACT_1H_R2_L1
processed data file: ACT_1H.broadPeak.gz


title: GGO.N_17


title: M165K-F0


title: Bulk_RNAseq_Humanized_lung_28dpi_IFNAR_RDV#2


title: GGO.N_12


title: Activin 1 hour biological replicate 1 library 6

description:
ACT_1H_R1_L6
processed data file: ACT_1H.broadPeak.gz


title: M158K-F0

value: Diet 1 - 0mg/kg OTA Diet (Control)


title: Bulk_RNAseq_Humanized_lung_28dpi_IFNAR_RDV#1


title: Activin 1 hour biological replicate 1 library 5

description:
ACT_1H_R1_L5
processed data file: ACT_1H.broadPeak.gz


title: M166K-F0


title: Bulk_RNAseq_Humanized_lung_28dpi#2

description: SARS-Cov-2 infected MISTRG6-hACE2 mice


title: Activin 1 hour biological replicate 1 library 4

description:
ACT_1H_R1_L4
processed data file: ACT_1H.broadPeak.gz


title: Bulk_RNAseq_Humanized_lung_28dpi_dex#1

description: SARS-Cov-2 infected MISTRG6-hACE2 mice were treated with dexamethasone 7-9dpi


title: 24h rep1

city: shanghai

first: sen

last: li

state: Shanghai

address: shanghai

institute: B

data_processing:
Raw data (Fastq files) was processed by FASTQC
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence  by Trimmo  matic, then mapped to hg19 whole genome using bwa
The bam file generated by the unique mapped reads as an input file, using MACS2 software for callpeak with cutoff qvalue < 0.05
ATAC-seq signal tracks were visualized through Integrative Genomics Viewer
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files include signal values

source_name: adipose

growth_protocol: The hASCs were proliferated in Mesenchymal Stem Cell Growth Media (Cyagen).

extract_protocol:
The cells were harvested and lysed in lysis buffer, The pellet was continued on to Transposition Reaction and Purification section.
The Nextera DNA Library Preparation Kit (Illumina) was used to execute the transposition. The library were prepared for sequencing using standard Illumina protocols was purified by the MinElute PCR Purification Kit (Qiagen) and subjected to sequencing on Illumina Novaseq 6000.

treatment_protocol: The hASCs were  induced differentiation to adipocytes by Adipogenesis Basal Medium (Cyagen). Cells were respectively collected at 0h, 2h, 8h, 24h after in-duced adipogenesis.

value: Adipose-Derived Stem Cells

tag: time point


title: 24h rep2


title: M156K-F0

source_name: Kidney


title: 8h rep2


title: M168K-F0


title: Activin 1 hour biological replicate 1 library 2

description:
ACT_1H_R1_L2
processed data file: ACT_1H.broadPeak.gz


title: 8h rep1


title: M155K-F0


title: M154K-F0


title: Bulk_RNAseq_Humanized_lung_28dpi#1


title: Bulk_RNAseq_Humanized_lung_14dpi_dex #2


title: Bulk_RNAseq_Humanized_lung_28dpi_dex#2


title: 2h rep2


title: M153K-F0


title: Bulk_RNAseq_Humanized_lung_14dpi_dex #1

description: SARS-Cov-2 infected MISTRG6-hACE2 mice were treated with dexamethasone on 7-9 days post-infection (dpi)


title: 2h rep1


title: M152K-F0


title: M157K-F0


title: M149K-F0


title: 0h rep2

value: ohour


title: Activin 1 hour biological replicate 1 library 3

description:
ACT_1H_R1_L3
processed data file: ACT_1H.broadPeak.gz


title: 0h rep1


title: Mitotic_WT129_H3.3S31Ph_Input

city: Clayton

first: Hsiao Phin

middle: Joanna

last: Voon

state: Victoria

address: Monash University, Wellington Road

department: Biochemistry and Molecular Biology

country: Australia

institute: Monash University

data_processing:
ChIP-seq of H3.3 S31Ph and input sequencing were aligned to the mouse genome (mm9) with Bowtie (v1.0.0) with default settings except (m -5) to allow restricted multi-mapping to short repeats.
SAM files from 2 lanes of sequencing were merged and converted into a single bigWig file.
Fastq files of H3.3 S31Ph ChIP-seq and matched input samples were aligned to a repeat database with Repeat Enrichment Estimator v1.0 (Day et al., 2010).
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated with Wig/BedGraph-to-bigWig (v1.1.0) in Galaxy with default parameters.
Supplementary_files_format_and_content: CSV files are contain reads counts at genome repeats mapped with Repeat Enrichment Estimator v1.0 (Day et al., 2010).

source_name: ES Cells

growth_protocol: Mouse ESCs were cultured in Dulbecco's modified Eagle's medium supplemented with 15% heat-inactivated foetal calf serum, 10e3 units/ml leukemia inhibitory factor and 0.1 mM β-mercaptoethanol.

extract_protocol:
5 million cells were fixed in growth media with 0.4% formaldehyde for 10 min and quenched with 125 mM glycine. Chromatin was released by sequential lysis with cells lysis buffer (10 mM Tris pH 8, 10 mM NaCl, 0.2% Igepal) and nuclear lysis buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS). Chromatin was sheared to ≈300 bp with 12 rounds of sonication (30 s on, 30 s off) on a Bioruptor (Diagenode) and incubated overnight at 4 ᵒC with either 10 μg H3.3S31ph antibody (Active Motif, 39637). Samples were immunoprecipitated with Protein A Agarose beads (Sigma-Aldrich, 05015979001) and washed sequentially with low salt (20 mM Tris pH 8, 2 mM EDTA, 50 mM NaCl, 1% Triton X-100, 0.1% SDS), high salt (20 mM Tris pH 8, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.01% SDS), and LiCl buffers (10 mM Tris pH 8, 1 mM EDTA, 0.25 M LiCl, 1% Igepal, 1% sodium deoxycholate). Chromatin was eluted with elution buffer (1% SDS, 100 mM NaHCO3), decrosslinked overnight at 65ᵒC, incubated with Proteinase K, phenol chloroform extracted and ethanol precipitated.
Sample concentrations were determined by Qubit (ThermoFisher Scientific) and 20 ng of DNA was used as starting material. ChIP libraries were prepared with Nugen Ovation Ultralow System V2 (Nugen protocol M01379v1, 2014) with 10 cycles of amplification. Libraries quality was assessed by Qubit, Bioanalyzer (Agilent) and qPCR, and a single equimolar pool was made based on size adjusted qPCR quantitation. Following denaturation, 12 pM of library pools were used for cBot hybridisation and cluster generation (Illumina Protocol 15006165 v02 Feb 2016), and samples were sequenced on an Illumina HiSeq 1500 rapid mode (50 bp SR sequencing, Illumina Protocol 15035788 Rev D, Apr 2014).

treatment_protocol: Cells were arrested with 9 μM of RO-3306 (Sigma-Aldrich) for 12 hours and released with 3 x PBS washes. Mitotic synchronised cells were harvested 11 hours after release.

value: WT ES cells

tag: passages

tag: chip antibody

value: No antibody, input


title: Mitotic_WT129_H3.3S31Ph_ChIPSeq

value: Histone H3.3S31ph (Active Motif, 39637)


title: Activin 1 hour biological replicate 1 library 1

description:
ACT_1H_R1_L1
processed data file: ACT_1H.broadPeak.gz

value: activin


title: 28dpi_scRNA_lung_human_immune

description: sorted human immune cells from digested lungs of SARS-CoV-2 infected MISTRG6-hACE2 mice

data_processing:
Raw sequencing data was aligned using Cellranger
Seurat v3 was used to perform data preprocessing and downstream analysis
Assembly: hg19_mm10_scv2
Supplementary files format and content: TSV file which includes cell barcodes or gene names; MTX file which includes gene-by-cell count matrix

organism:
Homo sapiens
Mus musculus

source_name: lung immune cells

growth_protocol: Newborn MISTRG6 mice were reconstitued with human CD34+ fetal liver cells.

extract_protocol:
For whole tissue transcriptional analysis, homogenized lung RNA was extracted with the RNeasy mini kit (Qiagen) per the manufacturer’s protocol. For single cell transcriptome analysis,  lungs from infected mice were collected and digested at 37°C for 20 min using digestion cocktail containing 1 mg/ml collagenase D (Sigma) and 30 µg/ml DNase I (Sigma-Aldrich) in RPMI. Human immune cells were then sorted using BD-Aria based on expression of human CD45 and lack of expression of mouse CD45. Cell viability was assessed by DAPI.
10x single cell RNA-seq protocol

treatment_protocol: Immune-reconstituted MISTRG6 mice were injected with AAV9 encoding hACE2  (purchased from Vector Biolabs) intratracheally at 8 weeks post engraftment.  These mice were then infected with  SARS-CoV-2. SARS-CoV-2 infected MISTRG6-hACE2 mice were treated with dexamethasone and Remdesivir on days 7,8,9 post-infection and with anti-IFNAR2 at 7dpi and 11 dpi. Mice were analyzed either at 14dpi or 28dpi.

value: 10wk old

tag: infection


title: 14dpi_scRNA_lung_human_immune

value: MISTRG6 in Balb/c


title: Uninfected_scRNA_lung_human_immune


title: PD mtRunx1#11 Single Cell 100 nM HHT

status: Public on Apr 09 2022

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

data_processing:
cellranger V4.0.0 mkfastq
cellranger V4.0.0 count
reads are mapped to hg38
UMI counts are summarized are gene expression levels
Genome_build: hg38
Supplementary_files_format_and_content: filtered feature matrix, barcodes, features

source_name: Patient Derived AML Cells

growth_protocol: Primary, patient-derived (PD) human AML cells were cultured in 20% FBS containing RPMI.

extract_protocol:
GEMs were processed according to the manufactures protocol.
Libraries were constructed following standard Illumina protocols for scRNA sequencing in a sequencing and microarray core facility.

treatment_protocol: 1 x 10^6 Primary human AML cells were treated for 8 hours with DMSO or 100 nM of HHT. Cells were harvested and prepared for 10x Genomics Chromium Controller single cell seperation.

value: 100 nM HHT, 8hr


title: PD mtRunx1#11 Single Cell Mock

value: Control, 8hr


title: MPA_ControlSi_AEW

city: Durham

first: Sarah

middle: Jean

last: Cunningham

state: NC

address: 101 Science Dr, IGSP Box 3382

institute: Duke University

data_processing:
Illumina adapters were removed using Trimmomatric v0.32
Reads less than 20 nucleatides were filtered out from further analysis
Seqeunces were aligned to the GRCh38 human referende genome using the alignment too STARv2.4.2a with the default parameter except for "--outFilterMultimapNmax1' to remove multimapping reads.
Reads per Killobase Mapped and Transcripts per Million were computed for each mapped gene using RSEM v1.2.25
Assembly: human NCBI genome build 38
Supplementary files format and content: Gene counts for each library

source_name: Patient 3 amnion Control siRNA MPA

growth_protocol: Amnion epithelial cells from healthy cesearean section patients were harvested and isolated.

extract_protocol:
Cells were lyzed with Trizol reagent and the RNA was isolated with Qiagen Rneasy kit with optional on column Dnase
Libraries were seqeunced using Illumina's TruSeq stranded mRNA-seq kit. They were then sequenced on an Illumina Illumina NextSeq using 50 base pair dual end sequencing

treatment_protocol: Cells were treated with 10-6M medroxyprogesterone acetate. A portion of cells were treated with 10 ng/mL TNFa.

value: Amnion epithelial cells

tag: patient

value: Patient 3

tag: sirna

value: control siRNA

tag: tnfa challenge

value: No


title: MPA_ControlSi_AEN

source_name: Patient 1 amnion Control siRNA MPA

value: Patient 1


title: MPA.TNF_ControlSi_AEU

source_name: Patient 2 amnion Control siRNA MPA+TNF

value: Patient 2

value: Yes


title: MPA.TNF_GRkd_AEW

source_name: Patient 3 amnion GR siRNA MPA+TNF

value: glucocorticoid receptor knockdown


title: MPA_ControlSi_AEU

source_name: Patient 2 amnion Control siRNA MPA


title: OCIAML2 Runx1R174*/wt 100nM HHT replicate 4

data_processing:
alignment and gene count by STAR (version 2.6.0b)
gene annotation used GENCODE v29
differential expression analysis carried out in R (4.0.0) using Bioconductor package DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-deliminated data matrix of raw gene counts

source_name: Cultured AML Cell Line

growth_protocol: Culture human AML cells were cultured in 20% FBS containing alpha-MEM 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.
Libraries were constructed following standard Illumina protocols for RNA sequencing in a sequencing and microarray core facility.

treatment_protocol: 1 x 10^6 Human AML cells were treated for 8 hours with DMSO or 100 nM of HHT. Cells were harvested by centrifugation and lysed with a Beta-mercaptoethanol containing RNA lysis buffer.

tag: treatment


title: MPA.TNA_ControlSi_AEW

source_name: Patient 3 amnion Control siRNA MPA+TNF


title: MPA_GRkd_AEU

source_name: Patient 2 amnion GR siRNA MPA


title: MPA.TNF_ControlSi_AEN

source_name: Patient 1 amnion Control siRNA MPA+TNF


title: OCIAML2 Runx1R174*/wt 100nM HHT replicate 3


title: MPA_GRkd_AEW

source_name: Patient 3 amnion GR siRNA MPA


title: MPA_GRkd_AEN

source_name: Patient 1 amnion GR siRNA MPA


title: MPA.TNF_GRkd_AEN

source_name: Patient 1 amnion GR siRNA MPA+TNF


title: OCIAML2 Runx1R174*/wt 100nM HHT replicate 1


title: OCIAML2 Runx1R174*/wt Control replicate 4


title: OCIAML2 Runx1R174*/wt 100nM HHT replicate 2


title: OCIAML2 Runx1R174*/wt Control replicate 3


title: OCIAML2 Runx1R174*/wt Control replicate 2


title: OCIAML2 Runx1R174*/wt RiboLace replicate 2


title: MPA.TNF_GRkd_AEU

source_name: Patient 2 amnion GR siRNA MPA+TNF


title: OCIAML2 Runx1R174*/wt RiboLace replicate 1


title: OCIAML2 Runx1wt/wt RiboLace replicate 2


title: OCIAML2 Runx1wt/wt replicate 2


title: OCIAML2 Runx1wt/wt RiboLace replicate 1


title: OCIAML2 Runx1R174*/wt 100nM HHT ChIP-P300

data_processing:
cut adapter by trim_galore (0.6.5)
aligment by bowtie2 (2.3.4.2)
remove duplicates by PICARD (2.9.0)
peak calling by MACS2 (2.1.2)
differential open region by diffReps.pl (5.28.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: macs2 called peaks

extract_protocol:
AML cells (10 million) were treated with 1% formaldehyde for 10 minutes with rotation. The crosslinking reaction was quenched with 2.5 M Glycine for 5 minutes. Chromatin lysates were clarified from ultra-sonicated nuclei and histone-DNA complexes or BRD4-containing complexes were isolated with H3K27Ac or BRD4 antibody, respectively. Following ChIP washes, the  immunoprecipitated DNA fragments were treated with mutant Tn5 transposase for 10 minutes at 37°C to attach sequencing adapters to the DNA. Tagmented DNA was eluted and formaldehyde-induced crosslinks were reversed. Tagmented, eluted DNA was purified over a column and utilized for library preparation.
ChIP-Seq libraries were prepared according to Illumina's instructions accompanying the Nextera DNA Library Prep Kit (Cat. No. FC-121-1030). After adapter ligation, DNA was PCR amplified with Illumina universal primer for 12-15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated utilizing AMP-XP beads. The purified DNA was captured on an Illumina NExt-Seq 500 flow cell for cluster generation. Libraries were sequenced following the manufacturer's protocols.

treatment_protocol: 1 x 10^7 Human AML cells were treated for 16 hours with DMSO or 100 nM of HHT.

value: 100 nM HHT, 16hr

tag: tissue

value: human Acute Myelogenous Leukemia (AML), M4

value: Rabbit anti-p300 Antibody, Affinity Purified Bethyl Cat# A300-358A, RRID:AB_185565


title: CRISPRi_sgRNA-walA1_low xyl_biol rep3

city: Iowa City

first: Craig

last: Ellermeier

state: IA

address: 431 Newton Road

department: Microbiology and Immunology

institute: University of Iowa

description: High Output 75cyc

data_processing:
Fastq files were trimmed and filtered using a combination of Trimmomatic and FastQC
Alignment, normalization and differential expression were analyzed with SeqMan NGen® Version 17.2. DNASTAR, Madison, WI.
Annotation was imported from NCBI with additional information obtained from proGenomes v2.1.
All subsequent analysis was performed in Excel.
Assembly: AM180355
Supplementary files format and content: Comma separated values (csv) file contains linear rlog reads, log2 fold change and adjusted P-value

organism: Clostridioides difficile

source_name: Bacterial

growth_protocol: All cultures were grown in tryptone-yeast exract broth at 37C under anaerobic conditions

extract_protocol:
Cultures were fixed by mixing with an equal volume of cells with ice-cold 1:1 ethanol:acetone. Cells were lysed with a FastPrep-24 homogenizer and RNA was extracted with the Qiagen RNeasy kit. All samples had a RIN of 9.4 or higher (Agilent Bioanalyzer).
Illumina Stranded RNA library preparation paired with RiboZero Plus  was prepared per manufacturer's specifications.

treatment_protocol:
Overexpression: strains were subcultured to OD600=0.05, grown to 0.2, induced with 3% xylose, grown for an additional 3h and fixed.
No xylose: strains were subcultured to OD600=0.03 and grown to 0.7 (~5-6h) and fixed.
Low xylose: strains were subcultured to OD600=0.03, grown to 0.3, back-diluted to 0.1 and induced with 0.1% xylose. They were then grown for an additional 2.5h and fixed.

value: Bacterial

tag: cell line

tag: genotype

value: Low (0.1%) xylose, 2.5h


title: OCIAML2 Runx1wt/wt replicate 1


title: CRISPRi_neg con_low xyl_biol rep3

description: High Output 75cyc

value: sgRNA-neg


title: OCIAML2 Runx1R174*/wt Control ChIP-P300

value: Control, 16hr


title: CRISPRi_neg con_no xyl_biol rep3

description: High Output 75cyc

value: No xylose


title: OCIAML2 Runx1R174*/wt Control replicate 1

value: Control, 8hr


title: OCIAML2 Runx1R174*/wt Control ChIP-Brd4

value: BRD4 rabbit monoclonal [ clone BL-149-2H5] (Bethyl Labs)  catalog #A700-004 RRID:AB_2631885


title: CRISPRi_sgRNA-walA1_no xyl_biol rep3

description: High Output 75cyc


title: OCIAML2 Runx1R174*/wt 100nM HHT ChIP-H3K27Ac

value: H3K27Ac (Active Motif) RRID:AB_2793305


title: CRISPRi_sgRNA-walA1_low xyl_biol rep2

description: High Output 75cyc


title: OCIAML2 Runx1R174*/wt 100nM HHT ChIP-Input


title: CRISPRi_neg con_no xyl_biol rep2

description: High Output 75cyc


title: OCIAML2 Runx1R174*/wt Control ChIP-Input


title: CRISPRi_sgRNA-walA1_no xyl_biol rep2

description: High Output 75cyc


title: OCIAML2 Runx1R174*/wt 100nM HHT ChIP-Brd4


title: CRISPRi_neg con_low xyl_biol rep2

description: High Output 75cyc


title: CRISPRi_sgRNA-walA1_low xyl_biol rep1

description: High Output 75cyc


title: BKS-DB, scRNAseq

city: Beijing

first: Kai

last: Chen

address: 8th Xishiku Street

department: General Surgery

institute: Peking University First Hospital

description: 10x Genomics

data_processing:
The Cell Ranger software was downloaded from 10x Genomics website (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest). Alignment (mm10 reference for mouse samples), filtering, barcode counting, and UMI counting were performed with cell ranger count module to generate gene-cell matrix (v3.0.1, 10x Genomics).
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, genes.tsv, matrix.mtx)

source_name: Pancreatic islet

extract_protocol:
Both BKS_DB (n = 3) and BKS_WT (n = 3) mice were euthanized with cervical dislocation at 9 weeks of age. Tape the limbs of the mouse in supine position, spray the skin of the abdominal area with 75% ethanol. Make a vertical incision to fully expose organs in abdominal cavity. Find the bile duct and ampulla of Vater, which is located at the duodenal papilla, under a dissection microscope. Carefully insert the syringe with 10 mL of the collagenase Type V solution (Sigma-Aldrich, Cat. no. C9263, 0.5 mg/ml) into the ampulla of Vater, and steadily inject 2-3 mL of the collagenase solution when the common bile duct was clamped. Stop injection until the head, neck, body and tail region of the pancreas are all fully inflated. Carefully dissect out the inflated pancreas and place it in a 50 mL tube containing 2 mL of ice-cold collagenase solution. After completing pancreas isolation of six mice, place the tube in a rack in 37 °C water bath for about 15 minutes. Shake gently the tube every five minutes. Take out tube from water bath and shake vigorously for 30 seconds. Then, place the tubes on ice and add 45 mL of ice-cold Hank’s Balanced Salt Solution (HBSS) supplemented with 5% fetal bovine serum (Gibco, Cat. no. 10099-141) to stop the enzymatic digestion. Filter out undigested tissues with the mesh sieve. Centrifuge the tube in a swinging-bucket centrifuge at 300g for 2 minutes. Discard the supernatant and rinse twice with HBSS. After the last centrifugation remove all HBSS and add 10 ml room temperature Histopaque-1077 solution (Sigma-Aldrich, Cat. no. 10771). Vortex briefly and slowly add another 10 ml Histopaque-1077 and room temperature RPMI-1640 (Gibco, Cat. no. C11875500BT). Centrifuge the tube in a swinging-bucket centrifuge at 900g with no brake for 20 minutes. Pipette out the layer of islets (5–10 mL) into the new 50 mL collection tube. Add 20 mL of ice cold HBSS and repeat washing and centrifuging three times. Pipette out the complete RPMI-1640 containing pancreatic islets into a Petri dish (NEST Biotechnology). Incubate the islets in a sterile incubator at 37 °C with 5% CO2 overnight. Transfer cultured islets overnight to a new 15 ml tube and centrifuge at 200g for 3 minutes. Discard the supernatant and rinse twice with PBS. After the last centrifugation, remove all PBS and add 3 ml room temperature Accutase solution (Gibco, Cat. no. A1110501). Incubate the tube in 37 °C water bath for 20 minutes. Pipette up and down every 2 minutes. Terminate the digestion by adding 5 ml complete RPMI-1640. Centrifuge at 200g for 3 minutes and discard the supernatant. The pellet was resuspended with 2 ml RPMI-1640 and filtered with 35 um cell strainer (Falcon, Cat. no. 352235).
The concentration of single cell suspension was determined using the Count Star instrument and adjusted to 1000 cells/ul. Using single cell 3’ Library and Gel Bead Kit v3.1 (10x Genomics, Cat. No. 1000121) and Chromium Next GEM Chip G Single Cell Kit (10x Genomics, Cat. No. 1000120), the cell suspension was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In brief, single cells were suspended in PBS containing 0.04% BSA. About 6,000 cells were added to each channel, and the target cell will be recovered (about 3000 cells). Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed in 200 ul tube (NEST Biotechnology, Cat. No. 401001) on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 minutes, followed by 85°C for 5 min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using the Agilent 4200. The cDNA libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with paired-end 150 bp (PE150) reading strategy.

value: Pancreatic islet

value: Pancreatic islet cells

tag: disease state

value: type 2 diabetes

value: No treatment


title: OCIAML2 Runx1R174*/wt Control ChIP-H3K27Ac


title: OCIAML2 Runx1R174*/wt 100nM HHT ATAC replicate 4

data_processing:
cut adapter by trim_galore (0.6.5)
aligment by bowtie2 (2.3.4.2)
remove duplicates by PICARD (2.9.0)
peak calling by MACS2 (2.1.2)
differential open region by diffReps.pl (5.28.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: macs2 called open peaks

extract_protocol:
AML cells (75,000 cells) were treated with nuclear isolation buffer and centrifuged for 10 minutes. Following this, mutant Tn5 transposase was added to the nuclei preparation. Tagmentation reactions were carried out at 37°C for 30 minutes to fragment the accessible genomic DNA and simultaneously add sequencing adapter sequences. Tagmentation reactions were stopped by the addition of binding buffer from a PCR purification kit and the tagmented DNA fragments were purified over a column. The eluted DNA fragments were utilized for library preparation and amplification. PCR Amplified libraries were size selected with AMPure XP beads to remove unbound Illumina index primers. Finished libraries were pooled and paired-end sequenced on a NextSeq 500 sequencer with a 150 cycle mid-output kit.
ATAC-Seq Libraries were prepared according to Illumina's instructions accompanying the Nextera DNA Library Prep Kit (Cat. No. FC-121-1030). After adapter ligation, DNA was PCR amplified with Illumina universal primer for 12-15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated utilizing AMP-XP beads. The purified DNA was captured on an Illumina NExt-Seq 500 flow cell for cluster generation. Libraries were sequenced following the manufacturer's protocols.

treatment_protocol: 1 x 10^6 Human AML cells were treated for 16 hours with DMSO or 100 nM of HHT.


title: CRISPRi_neg con_low xyl_biol rep1

description: High Output 75cyc


title: S3_2_NS

city: 大连

first: 张

last: 疆雨

address: 甘井子区凌工路2号

institute: 大连理工大学

description: Gene expression data from hBMSCs

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit in Hybridization Oven 645 and Fluidics Station 450 followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000.

data_processing: Raw data were normalized by MAS 5.0/RMA algorithm, Affy packages in R

label: biotin

source_name: Human bone marrow mesenchymal stem cells

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip  3' IVT PLUS Reagent Kit followed the manufacturer’s instructions to obtain biotin labeled cRNA

growth_protocol: The cells were cultured in Human MSC Basal Medium (Cyagen) containing 10% fetal bovine serum (FBS), 1% L-glutamine and 1% penicillin-streptomycin at 37 ℃with 5% humidified CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The cells were treated with 125 μg/mL nicotine or  25 μg/mL NEOs  for 7 d.

tag: Sex

value: male

value: bone marrow mesenchymal stem cells

value: treated with 25 ug/mL NIT for 7 d


title: BKS-WT, scRNAseq

description: 10x Genomics

value: control


title: S2_3_NS

description: Gene expression data from hBMSCs

value: treated with 25 ug/mL IMI for 7 d


title: CRISPRi_sgRNA-walA1_no xyl_biol rep1

description: High Output 75cyc

value: Bacterial


title: S3_1_NS

description: Gene expression data from hBMSCs


title: S4_2_NS

description: Gene expression data from hBMSCs

value: treated with 25 ug/mL ACE for 7 d


title: CRISPRi_neg con_no xyl_biol rep1

description: High Output 75cyc

value: sgRNA-neg


title: OCIAML2 Runx1R174*/wt 100nM HHT ATAC replicate 1

value: 100 nM HHT, 16hr

value: human Acute Myelogenous Leukemia (AML), M4


title: S2_1_NS

description: Gene expression data from hBMSCs


title: S3_3_NS

description: Gene expression data from hBMSCs


title: S2_2_NS

description: Gene expression data from hBMSCs


title: OCIAML2 Runx1R174*/wt 100nM HHT ATAC replicate 2


title: Overexpression-WalR-D54E_biol rep3

description: High Output 75cyc

value: Overexpression (3% xylose, 3h)


title: kai2-24-Heat-3

city: El Sokhna

first: MOSTAFA

middle: ABDELWAHED

last: Abdelrahman

state: SUZE

address: Suze

country: Egypt

institute: GALALA UNNIVERSITY

description: Gene expression inkai2-24-Heat-3

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized for 17 hours at 65C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: ly after washing on the Agilent DNA Microarray Scanner G2505C using one color scan setting

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

source_name: whole seedling

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions,

growth_protocol: 10-day-old plants (45 plants from each genotype per tray) were grown on plastic trays ((21×30×5 cm in width, length and height, respectively) containing dry soil and saturated with water

extract_protocol: Aerial tissues of 10-day-old WT and kai2-2 mutant plants grown on soil under control and 6h and 24h heat stress conditions were detached and collected in four biological replicates for transcriptome analysis

treatment_protocol: Plant samples were divided into two groups and each group contained three trays. One group set were subjected to continuous 40°C heat stress, while control group was grown at 23°C using growth chamber

value: whole seedling

tag: genotype/variation

value: heat

tag: age

value: 10-day old


title: S1_2_NS

description: Gene expression data from hBMSCs

tag: cell type

value: treated with 125 ug/mL nicotine for 7 d


title: kai2-24-Heat-2

description: Gene expression inkai2-24-Heat-2


title: kai2-24-Heat-4

description: Gene expression inkai2-24-Heat-4


title: S4_1_NS

description: Gene expression data from hBMSCs


title: S4_3_NS

description: Gene expression data from hBMSCs


title: S1_3_NS

description: Gene expression data from hBMSCs


title: kai2-24-Heat-1

description: Gene expression inkai2-24-Heat-1


title: AngII heart 2

city: Wenzhou

first: guang

last: liang

state: Wenzhou

address: Wenzhou medical university of  higher education park  chashan town

department: School of Pharmaceutical Sciences

institute: Wenzhou Medical University

data_processing:
Illumina novaseq 6000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Heart

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

tag: strain

value: heart

value: 6-8 weeks

value: AngII induced


title: AngII heart 3


title: S1_1_NS

description: Gene expression data from hBMSCs

value: male

value: bone marrow mesenchymal stem cells


title: Overexpression-WalR-biol rep3

description: High Output 75cyc


title: AngII heart 1


title: WT-24-Heat-4

description: Gene expression inWT-24-Heat-4

value: WT

tag: time point


title: OCIAML2 Runx1R174*/wt Control ATAC replicate 4

value: Control, 16hr


title: OCIAML2 Runx1R174*/wt Control ATAC replicate 3


title: CON heart 1

value: control


title: OCIAML2 Runx1R174*/wt Control ATAC replicate 2


title: OCIAML2 Runx1R174*/wt Control ATAC replicate 1


title: Overexpression-WalR-D54E_biol rep2

description: High Output 75cyc

value: Bacterial


title: WT-24-Heat-3

description: Gene expression inWT-24-Heat-3


title: WT-24-Heat-2

description: Gene expression inWT-24-Heat-2


title: CON heart 2


title: OCIAML2 Runx1wt/wt 100nM HHT ATAC replicate 2


title: Grem1∆/∆ tumour_5 [IE01_abmk40-1a]

city: Sutton

first: Anguraj

last: Sadanandam

state: Surrey

address: 15 Cotswold Road

department: Molecular Pathology

institute: Institute of Cancer Research (ICR), London

description: Bulk tumour tissue

data_processing:
bcl2fastq (version 2.0) was used to convert BCL files to fastq
Raw reads were quality checked using FastQC (version 0.11.9) before alignment. Reads were mapped to the mouse genome using RSEM (version 1.3.3) and HISAT2 (version 2.2.1). Ensembl 102 GTF file was used as annotation source.
Normalisation of raw count data was performed with the DESeq2 package (version 1.32.0)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalised count values  for each sample .
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Grem1∆/∆ tumour

growth_protocol: KPF mice in C57BL/6J background were bred and maintained in the BRF unit at the Francis Crick Institute; mice at 6-12 weeks of age were used for experiments.

extract_protocol:
RNA from FACS-sorted cells was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
Samples were prepared with KAPA mRNA HyperPrep Kit (Roche) and sequenced using Illumina NovaSeq 6000 platform.

treatment_protocol: Mice at the age of 5 weeks were treated with vehicle (peanut oil, Grem1wt/wt tumours) or tamoxifen (100 mg/kg body weight, Grem1∆/∆ tumours), once a day for 5 days.

tag: strain background

value: Pancreatic tumour


title: Grem1∆/∆ tumour_4 [IE01_abmk39-1d]

description: Bulk tumour tissue


title: OCIAML2 Runx1wt/wt 100nM HHT ATAC replicate 1

value: 100 nM HHT, 16hr


title: Overexpression-reference-biol rep2

description: High Output 75cyc

value: Wildtype


title: WT-24-Heat-1

description: Gene expression inWT-24-Heat-1


title: CON heart 3


title: Overexpression-WalR-biol rep1

description: High Output 75cyc

value: Overexpression (3% xylose, 3h)


title: OCIAML2 Runx1wt/wt Control ATAC replicate 2

value: human Acute Myelogenous Leukemia (AML), M4


title: Overexpression-reference-biol rep3

description: High Output 75cyc


title: OCIAML2 Runx1wt/wt Control ATAC replicate 1


title: Overexpression-reference-biol rep1

description: High Output 75cyc


title: Grem1∆/∆ tumour_2 [IE01_abmk36-3a]

description: Bulk tumour tissue


title: Grem1∆/∆ tumour_1 [IE01_abmk25-2f]

description: Bulk tumour tissue


title: Grem1wt/wt tumour_5 [IE01_abmk40-3g]

description: Bulk tumour tissue

source_name: Grem1wt/wt tumour

value: wild type


title: Grem1∆/∆ tumour_3 [IE01_abmk38-1d]

description: Bulk tumour tissue


title: OCIAML2 Runx1R174*/wt 100nM HHT ATAC replicate 3


title: CD36_null_2

city: san francisco

first: Kamran

last: Atabai

state: California

address: 555 Mission bay Blvd

institute: UCSf

description: CD36 Intestine null2

data_processing:
Trimmomatic 0.38.1: to trimmed the files
umitools: remove low quality reads and adapter contamination
HISAT2 v2.1.0: To align with mouse genome (mm10
Htseq-count v0.91: Read count
DESEQ2 V2.11.40: Differentially express genes
Assembly: mm10/GCRm38

source_name: Intestine

extract_protocol:
RNA from primary enterocytes were isolated using Qiagen RNeasy plus micro kit. RNA from small intestinal tissues were isolated using Qiagen RNeasy lipid tissue mini kit.
Barcoded sequencing libraries were prepared using the QuantSeq FWD kit (Lexogen, Vienna, Austria) for multiplexed sequencing according to the recommendations of the manufacturer using the UDI-adapter and UMI Second-Strand Synthesis modules (Lexogen).  High integrity total RNA samples were processed according to the QuantSeq default protocol. The fragment size distribution of the libraries was verified via micro-capillary gel electrophoresis on a LabChip GX system (PerkinElmer, Waltham, MA).   The libraries were quantified by fluorometry on a Qubit fluorometer (LifeTechnologies, Carlsbad, CA), and pooled in equimolar ratios. The library pool was Exonuclease VII (NEB, Ipswich, MA) treated, SPRI-bead purified with KapaPure beads (Kapa Biosystems / Roche, Basel, Switzerland) , quantified via qPCR with a Kapa Library Quant kit (Kapa Biosystems) on a QuantStudio 5 RT-PCR system (Applied Biosystems, Foster City, CA). Up to 48 libraries were sequenced per lane on a HiSeq 4000 sequencer (Illumina, San Diego, CA) with single-end 100 bp reads.

value: Intestine

value: Cd36 KO


title: CD36_null_3

description: CD36 Intestine null3


title: kai2-control-3

description: Gene expression inkai2-control-3

value: whole seedling

value: 10-day old


title: Grem1wt/wt tumour_4 [IE01_abmk40-3d]

description: Bulk tumour tissue


title: A549 cells, COMBO, rep 2

city: Amsterdam

first: Rodrigo

last: Leite de Oliveira

address: De Boelelaan 1118

country: Netherlands

institute: Amsterdam UMC / location VUmc

data_processing:
Reads were aligned to the prebuilt reference GRCh38 genome_snp_tran using HiSAT2 version 2.2.1
Genecounts were generated by counting mapped reads overlapping genes defined in Ensembl GTF release 100 using a Htseq-count union strategy
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files with genecounts for Ensembl gene id's

source_name: lung cancer

growth_protocol: A549 cells were grown in RPMI (Gibco) supplemented with 10% FBS

extract_protocol:
Total RNA was extracted with RNeasy mini kit (Qiagen, cat# 74106) including a column DNase digestion (Qiagen, cat#79254).
polyA+ stranded RNA library prep

treatment_protocol: A549 cells were treated with 2µM Indisulam for 18 hours.

value: lung cancer

value: indisulam + sphinx 31


title: A549 cells, COMBO, rep 1


title: A549 cells, SP, rep 2

value: sphinx 31


title: Grem1wt/wt tumour_3 [IE01_abmk38-4f]

description: Bulk tumour tissue


title: CD36_WT_4

description: CD36 Intestine WT4

value: WT


title: A549 cells, SP, rep 1


title: CD36_WT_3

description: CD36 Intestine WT3


title: Grem1wt/wt tumour_2 [IE01_abmk38-2e]

description: Bulk tumour tissue


title: kai2-control-1

description: Gene expression inkai2-control-1


title: A549 cells, IN, rep 2

value: indisulam


title: CD36_WT_2

description: CD36 Intestine WT2


title: WT-control-4

description: Gene expression inWT-control-4

value: control


title: Grem1wt/wt tumour_1 [IE01_abmk36-3d]

description: Bulk tumour tissue


title: kai2-control-2

description: Gene expression inkai2-control-2


title: WT-control-3

description: Gene expression inWT-control-3


title: kai2-control-4

description: Gene expression inkai2-control-4


title: WT-control-2

description: Gene expression inWT-control-2


title: WT-control-1

description: Gene expression inWT-control-1


title: A549 cells, IN, rep 1


title: kai2-6-Heat-4

description: Gene expression inkai2-6-Heat-4

value: heat


title: CD36_null_1

description: CD36 Intestine null1


title: A549 cells, UT, rep 2

value: untreated


title: pRPS3-mCherry-tRPS3, modNNN, 4

city: Edinburgh

first: Edward

last: Wallace

address: Waddington 2.18, Max Born Crescent, King’s Buildings

department: School of Biological Sciences

institute: University of Edinburgh

description:
QS_processed_polyAconstructs.tsv
QS_processed_polyAcontrols.tsv
QS_all_sample_gene_counts.tsv

data_processing:
Read quality was checked with fastqc=0.11.9
Adapters were removed with cutadapt=1.18 (Options = --trim-n -O 1 -m 20)
Alignment was completed with hisat2=2.1.0 (Options = --no-spliced-alignment --no-unal --maxins 1500 -k 2)
Reads per gene were counted with featureCounts=2.00 (Options = -p -s 2 -R BAM)
Bed files were created with bedtools=2.30.0
Alignment quality was checked with multiQC=1.9
Bam files were create with samtools=1.11
Analysis was conducted using the Nextflow pipeline available here: https://github.com/DimmestP/nextflow_paired_reads_pipeline
The custom 3’UTR gff file used in this analysis was created by the code available here: https://github.com/ewallace/yeastutrgff
Assembly: sacCer3 (R64-2)
Supplementary files format and content: Format: tsv, Content: quantified reads ending in 3'-UTR region of reporter constructs, per construct
Supplementary files format and content: Format: tsv, Content: raw read counts mapped to each gene across the genome, one file per sample.
Supplementary files format and content: Format: tsv, Content: quantified reads ending in 3'-UTR region of control gene, per construct

organism: Saccharomyces cerevisiae

source_name: S.cerevisiae expressing plasmid with reporter gene pRps3-mCherry-tRps3_modNNN

growth_protocol: Yeast cultures were grown for 4h at 30degC, 200rpm, in liquid SC-Ura medium up to OD600=0.7

extract_protocol:
RNA extraction protocol: dx.doi.org/10.17504/protocols.io.beetjben
QuantSeq REV (Lexogen)
3'-end sequencing

tag: parent strain

tag: plasmid

value: pRPS3-mCherry-tRPS3_modNNN (pJA0068)


title: kai2-6-Heat-2

description: Gene expression inkai2-6-Heat-2


title: kai2-6-Heat-3

description: Gene expression inkai2-6-Heat-3


title: pRPS3-mCherry-tRPS3, modNNN, 3


title: A549 cells, UT, rep 1


title: MFGE8_null_5

description: MFGE8 Enterocytes null5

source_name: Enterocytes

value: Enterocytes

value: Mfge8 KO


title: Overexpression-WalR-biol rep2

description: High Output 75cyc

value: Bacterial

value: Overexpression (3% xylose, 3h)


title: pPGK1-mCherry-tRPS3, modHTH, 2

source_name: S.cerevisiae expressing plasmid with reporter gene pPgk1-mCherry-tRps3_modHTH

value: pPGK1-mCherry-tRPS3_modHTH (pJA0079)


title: kai2-6-Heat-1

description: Gene expression inkai2-6-Heat-1


title: pPGK1-mCherry-tRPS3, modHTH, 1


title: MFGE8_null_3

description: MFGE8 Enterocytes null3


title: Perfusate_d10_CD56loCD16+ [000008514669_F04]

city: Maynooth

first: Mark

last: Robinson

state: Co. Kildare

address: Department of Biology, Maynooth University

department: Department of Biology

country: Ireland

institute: Maynooth University

data_processing:
Sequencing data quality was assessed using FastQC
Reads were aligned to the hg38 human genome build using the HISAT2 with parameters --score-min L,0,-2 --no-mixed --no-discordant --no-unal
Multimapping reads were removed and BAM files were generated using samtools view with parameters -h -q 50 -b
BAM file alignments were loaded into Qlucore Omics Explorer 3.2 using the UCSC hg38 genome gtf file. The BAM files were loaded with a minimum of one read count across all samples was required for inclusion of each specific variable. Expression values were calculated using the "TMM" approach. Differential expression was assessed using t-test and ANOVA, controlling for the false discovery rate using the Benjamini-Hochberg method.
Assembly: hg38
Supplementary files format and content: CSV text file containing expression values calculated using the TMM approach. Differential expression was assessed using ANOVA, controlling for the false discovery rate using the Benjamini-Hochberg method.

source_name: Liver Perfusate

extract_protocol:
NK cell subpopulations cells were stained with the following antibodies: CD56, clone NCAM16.2; CD16, clone 3G8; CD3, clone UCHT1; CD45, clone HI30 (all BD Biosciences); CD127, clone REA614 (Miltenyi Biotec); with propidium iodide (ThermoFischer Scientific, Massachusetts, USA) for live/dead discrimination. NK cell subpopulations were then sorted to >98% purity using either a FACS Aria or a FACS Melody (BD Biosciences). A total of 1,500 cells of each sub-population of interest was FACS sorted into 1x TCL buffer (Qiagen, Manchester, UK) with 1% b-mercaptoethanol (molecular biology grade, v/v; Sigma-Aldrich, Missouri, USA). Sorted samples were frozen on dry-ice and stored at -80°C until library preparation.
Libraries were constructed using a modified version of the SMART-Seq2 protocol (as described in Picelli et. al., 2013 and Picelli et. al., 2014). Polyadenylated transcripts were captured, reverse transcribed, then template switching was performed and pre-amplification used to increase both yield and length of cDNA inserts generated. The generated libraries were sequenced on an Illumina NextSeq 500using a High Output kit to generate 2 x 25 bp indexed reads.

value: Liver Perfusate

tag: donor id


title: pPGK1-mCherry-tRPS3, modNAA, 2

source_name: S.cerevisiae expressing plasmid with reporter gene pPgk1-mCherry-tRps3_modNAA

value: pPGK1-mCherry-tRPS3_modNAA (pJA0076)


title: Perfusate_d10_CD56hiCD16+ [000008514669_G04]


title: MFGE8_null_2

description: MFGE8 Enterocytes null2


title: pPGK1-mCherry-tRPS3, modNAA, 1


title: CD36_WT_1

description: CD36 Intestine WT1

value: Intestine


title: Perfusate_d9_CD56loCD16+ [000008514669_B04]


title: MFGE8_null_1

description: MFGE8 Enterocytes null1


title: pPGK1-mCherry-tRPS3, modNTN, 2

source_name: S.cerevisiae expressing plasmid with reporter gene pPgk1-mCherry-tRps3_modNTN

value: pPGK1-mCherry-tRPS3_modNTN (pJA0075)


title: MFGE8_WT_4

description: MFGE8 Enterocytes WT4


title: Perfusate_d10_CD56hiCD16-  [000008514669_H04]


title: MFGE8_null_4

description: MFGE8 Enterocytes null4


title: pPGK1-mCherry-tRPS3, modNTN, 1


title: WT-6-Heat-2

description: Gene expression inWT-6-Heat-2

value: whole seedling

value: 10-day old


title: MFGE8_WT_3

description: MFGE8 Enterocytes WT3

value: WT


title: WT-6-Heat-1

description: Gene expression inWT-6-Heat-1


title: Normal KO2 B

city: CHANDIGARH

first: Dibyendu

last: Sarkar

address: SECTOR 39A

country: India

institute: CSIR-IMTECH

data_processing:
Basecalling, demultiplication and adaptor trimming was performed by Illumina HiSeq control software
Quality of raw reads was assessed by using FastQC tool
Clean reads that passed the quality filter were mapped to the reference genome (Mycobacterium tuberculosis H37Rv accession number NC_000962.3) using Hisat2.
Differential gene expression analysis of samples with respect to control was performed using Cuffdiff program (v2.2.1).
Genome_build: NC_000962.3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Mycobacterium tuberculosis

source_name: ∆sigH Mtb H37Rv Normal condition

growth_protocol: M. tuberculosis H37Rv strains were grown at 37°C in Middlebrook 7H9 broth (Difco) containing 0.2% glycerol, 0.05% Tween-80 and 10% Middlebrook ADC (albumin-dextrose-catalase).

extract_protocol:
RNA was extracted from exponentially growing mycobacterial cells in Middlebrook 7H9 media. Briefly, 25 ml of bacterial culture was grown to mid-log phase (OD600= 0.4 to 0.6) and combined with 40 ml of 5 M guanidinium thiocyanate solution containing 1% β-mercaptoethanol and 0.5% Tween 80. Cells were pelleted by centrifugation, and lysed by re-suspending in 1 ml Trizol (Ambion) in the presence of Lysing Matrix B (100 µm silica beads; MP Bio) using a FastPrep-24 bead beater (MP Bio) at a speed setting of 6.0 for 30 seconds. The procedure was repeated for 2-3 cycles with incubation on ice in between pulses. Next, cell lysates were centrifuged at 13000 rpm for 10 minutes; supernatant was collected and processed for RNA isolation using Direct-ZolTM RNA isolation kit (ZYMO) as per manufacturer’s recommendation. Following extraction, RNA was treated with DNAse I (Promega) to degrade contaminating DNA, and integrity was assessed using a Nanodrop (ND-1000, Spectrophotometer). RNA samples were further checked for intactness of 23S and 16S rRNA using formaldehyde-agarose gel electrophoresis, and Qubit fluoremeter (Invitrogen).
Total RNA was isolated using Direct-zol RNA MiniPrep kit (Zymo Research Corporation), the purity of isolated RNA was determined using the NanoDrop (Thermo Scientific), quantified using Qubit (Invitrogen), and RNA integrity was checked using Agilent 2200 Tape Station system (Agilent Technologies).  Library construction, RNA-sequencing and data analysis have been carried out by Agrigenome Labs Private Limited (Cochin), India. Briefly, The rRNA was removed using ‘si-tools Pan-prokaryote ribopool probes,’ and further library preparation was carried out using TruSeq Stranded RNA library prep kit. Prepared libraries were sequenced using Illumina HiSeq x10 platform, and 150-bp paired-end reads were generated. Thereads that passed quality control were mapped onto the reference genome of M. tuberculosis H37Rv using Hisat2 (version-2.0.5).  The abundance of transcripts in individual samples was estimated using Cufflinks (v2.2.1).

treatment_protocol: Cultures were grown till mid log phase and then divided into two halves. One part was exposed to 5 mM Diamide (Redox stress) and other one with equal volume of DMSO (Normal condition) for 2 hours. RNA was isolated and processed for RNA sequencing.

tag: agent

value: Normal


title: WT-6-Heat-3

description: Gene expression inWT-6-Heat-3


title: WT-6-Heat-4

description: Gene expression inWT-6-Heat-4


title: Perfusate_d9_CD56hiCD16+ [000008514669_C04]


title: Normal KO2 A


title: Perfusate_d9_CD56hiCD16-  [000008514669_D04]


title: MFGE8_WT_2

description: MFGE8 Enterocytes WT2


title: pPGK1-mCherry-tRPS3, modNNN, 2

source_name: S.cerevisiae expressing plasmid with reporter gene pPgk1-mCherry-tRps3_modNNN

value: pPGK1-mCherry-tRPS3_modNNN (pJA0074)


title: Diamide KO2 B

description: For growth under redox stress, mycobacterial strains were grown to mid log phase (OD600 0.4-0.6) and exposed to 5 mM diamide for 2 hours at 37°C.

source_name: ∆sigH Mtb H37Rv Redox stress

value: 5 mM Diamide (Redox stress)


title: MFGE8_WT_1

description: MFGE8 Enterocytes WT1


title: pPGK1-mCherry-tRPS3, modNNN, 1


title: Diamide KO2 A


title: pPGK1-mCherry-tRPS3, WT, 1

source_name: S.cerevisiae expressing plasmid with reporter gene pPgk1-mCherry-tRps3_WT

value: pPGK1-mCherry-tRPS3_WT (pJA0149)


title: Perfusate_d8_CD56hiCD16+ [000008514669_D03]


title: Perfusate_d8_CD56hiCD16-  [000008514669_B03]


title: Perfusate_d7_CD56loCD16+ [000008514669_C02]


title: Normal KO1 A

source_name: ∆phoP Mtb H37Rv Normal condition


title: Normal KO1 B


title: pTSA1-mCherry-tTSA1, modNTN, 2

source_name: S.cerevisiae expressing plasmid with reporter gene pTsa1-mCherry-tTsa1_modNTN

value: pTSA1-mCherry-tTSA1_modNTN (pJA0090)


title: NAc test [L09]

city: shijiazhuang

first: xiaojie

address: 361 Zhongshan East Road, Chang'an District, Shijiazhuang, Hebei Province

institute: Hebei Medical University

data_processing: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC-content of the clean data were calculated. All the downstream analyses were based on clean data with high quality

source_name: nucleus accumben

extract_protocol:
nucleus accumbens were removed, flash frozen on dry ice, and RNA was harvest using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: nucleus accumben

value: Morphine injection


title: NAc test [L07]


title: Diamide KO1 B

source_name: ∆phoP Mtb H37Rv Redox stress


title: Perfusate_d8_CD56loCD16+ [000008514669_C03]


title: NAc saline [L03]

value: Saline injection


title: Perfusate_d7_CD56hiCD16+ [000008514669_D02]


title: pTSA1-mCherry-tTSA1, modNTN, 1


title: pRPS3-mCherry-tRPS3, modNTN, 2

source_name: S.cerevisiae expressing plasmid with reporter gene pRps3-mCherry-tRps3_modNTN

value: pRPS3-mCherry-tRPS3_modNTN (pJA0069)


title: NAc saline [L01]


title: NAc saline [L02]


title: pPGK1-mCherry-tRPS3, WT, 2


title: Normal WT A

source_name: WT Mtb H37Rv Normal condition


title: Perfusate_d7_CD56hiCD16-  [000008514669_F02]


title: Diamide KO1 A


title: Diamide WT B

source_name: WT Mtb H37Rv Redox stress


title: Perfusate_d6_CD56hiCD16+ [000008514669_H01]


title: POT1-ccdB, 2

source_name: S.cerevisiae expressing control plasmid without reporter gene

value: POT1-ccdB (pJA0004)


title: pRPS3-mCherry-tRPS3, modNTN, 1


title: Perfusate_d6_CD56hiCD16-  [000008514669_B02]

value: Liver Perfusate


title: Recipient-chimeric-lung

data_processing:
cellranger V4.0.0 mkfastq
cellranger V4.0.0 count
reads are mapped to mm10
UMI counts are summarized are gene expression levels
Genome_build: mm10
Supplementary_files_format_and_content: filtered feature matrix, barcodes, features

source_name: lung cells

growth_protocol: Freshly isolated FACS purified cells

extract_protocol:
Freshly isolated FACS purified cells
The lungs from three chimeric mice were enzymatically treated, dissociated into single cells, pooled, and FACS sorted for CD45- td-tomato positive and CD45- - td-tomato negative cells. The single cell RNA transcriptome analysis was performed at the MD Anderson core lab, using 10x Genomics platform. The Cell Ranger Single Cell Software Suite v3.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome) was used for sample demultiplexing, alignment to the mm10 mouse reference genome and transcriptome, and generating filtered unique molecular identifier (UMI) count matrices, which were used for downstream analyses. The R package Seurat (Satija et al., 2015, Butler et al., 2018, Stuart et al., 2019) v3.1.1 was used to perform data QC, normalization, and integration of the three datasets. Cells with dataset-specific outliers of high mitochondria percentage, extremely high or low number of genes, or high RNA content were filtered out as potential dead cells or doublets. LogNormalize was used for normalization. Integration was based on 2000 anchor genes as a default. The R package monocle3 (Trapnell et al., 2014, Qiu et al., 2017, Cao et al., 2019) v0.2.0 was used for dimension reduction of the integrated dataset using the uniform manifold approximation and projection (UMAP) method (McInnes, Healy & Melville, 2018) and unsupervised clustering of cells was performed using Louvain/Leiden community detection (Traag, Waltman & Van Eck, 2019). Marker genes of each cluster were identified using Seurat by comparing the gene expression profile of each cluster to all others using Wilcoxon rank sum test. A single-sample gene set variation analysis was performed to calculate cluster-wise gene set enrichment scores using R package GSVA (Hänzelmann, Castelo & Guinney, 2013) v1.32.0 on MSigDB (Liberzon et al., 2015) hallmark gene sets (v7.0) and curated lung gene sets (https://research.cchmc.org/pbge/lunggens/mainportal.html). The resulting clusters were manually curated and/or merged based on marker genes and gene set analysis results.

treatment_protocol: Single-cell RNAseq analysis of the chimeric lungs.  Chimeric lungs were harvested from C57Bl mice transplanted with TdTom single cell suspension, 6 months post-transplant. The lungs from three chimeric mice were enzymatically treated, dissociated into single cells, pooled, and FACS sorted for CD45- td-tomato positive and CD45- td-tomato negative cells. The single cell RNA transcriptome analysis was performed at the MD Anderson core lab, using 10x Genomics platform.

value: C57BL cells recipient cells

tag: cell subtype

value: FACS purified CD45- live cells


title: NAc test [L08]

tag: treatment


title: Diamide WT A


title: Donor-chimeric-lung

value: td-tomato fluorescent  donor lung cells


title: POT1-ccdB, 1


title: pTSA1-mCherry-tTSA1, modHTH, 2

source_name: S.cerevisiae expressing plasmid with reporter gene pTsa1-mCherry-tTsa1_modHTH

value: pTSA1-mCherry-tTSA1_modHTH (pJA0094)


title: Panc10.05 cells, Resistant indisulam, rep 2

data_processing:
Reads were aligned to the prebuilt reference GRCh38 genome_snp_tran using HiSAT2 version 2.2.1
PCR duplcates were marked using a UMI barcode sequence using Picard version UmiAwareMarkDuplicatesWithMateCigar
Genecounts were generated by counting non PCR duplicated mapped reads overlapping genes defined in Ensembl GTF release 100 using a Htseq-count union strategy
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files with genecounts for Ensembl gene id's

tag: tissue

value: pancreatic cancer

tag: phenotype

value: indisulam-resistant

value: indisulam


title: Panc10.05 cells, Resistant untreated, rep 2

tag: cell line

value: untreated


title: Normal WT B

tag: genotype

value: WT

value: Normal


title: PBMC_d5_CD56loCD16+  [000008514669_E05]

source_name: PBMC

value: PBMC


title: pTSA1-mCherry-tTSA1, modHTH, 1


title: Perfusate_d6_CD56loCD16+ [000008514669_G01]

source_name: Liver Perfusate


title: PBMC_d3_CD56loCD16+  [000008514669_F03]


title: pTSA1-mCherry-tTSA1, modNNN, 2

source_name: S.cerevisiae expressing plasmid with reporter gene pTsa1-mCherry-tTsa1_modNNN

value: pTSA1-mCherry-tTSA1_modNNN (pJA0089)


title: Panc10.05 cells, Resistant indisulam, rep 1