title: benign lung disease 4

city: xi'an

first: qian

last: zhang

address: Xinsi Road

institute: Tangdu Hospital

description: the microRNA expression in plasma exosome

data_processing:
In order to  obtain high-quality clean reads,  raw sequencing  reads were trimmed for 3' adaptor sequence and filtered for low-quality sequence using cutadapt v1.14.
Clean reads were mapped against the reference genome (GRCh38) using bowtie. Then miRdeep2 v0.0.8 was used to estimate the expression levels of all transcripts and perform the expression abundance of miRNAs by calculating CPM (counts per million reads) value.
MiRNAs differential expression analysis was performed by edgeR v3.18.1 between two groups. The miRNAs with the parameter of |log2 (fold change) | ≥ 1.5 and P-value < 0.05 were considered differentially expressed exosomal miRNAs.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include the ID of  mature miRNAs and the CPM value of miRNA for each sample

source_name: plasma from patient with benign lung disease

extract_protocol:
1.5ml of plasma was diluted in PBS to 10ml. The sample underwent differential centrifugation at 500×g for 5 min at 4 ℃ and 2000×g for 30 min at 4 ℃, followed by 10000×g for 45 min at 4 ℃. After that, the supernatant was filtered through a 0.45 um membrane filter and ultracentrifuged at 100000×g for 70 min at 4 ℃, then resuspended in PBS and underwent a second ultracentrifugation at 100000×g for 70 min at 4 ℃. The obtained exosomes were resuspended in PBS. The miRNAs were isolated from plasma-derived exosomes using TRIzol LS Reagent (Invitrogen) according to the manufacturer’ s instruction. During RNA precipitation with isopropanol, glycogen was added for co-precipitation to improve the yield of RNA. The yield and quality of extracted RNA were evaluated by NanoDrop 1000 Spectrophotometer (NanoDrop Technologies, Delaware, USA).
RNA samples were used to prepare the miRNA sequencing library, which included the following steps: (1) 3′-adaptor ligation, (2) 5′-adaptor ligation, (3) cDNA synthesis, (4) PCR amplification, and (5) size selection of ~135–155 bp PCR amplified fragments (corresponding to ~15–35 nt small RNAs). The sequencing library was determined by an Agilent 2100 Bioanalyzer using an Agilent DNA 1000 chip kit (part # 5067-1504, Agilent, Santa Clara, CA, USA). And then the libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells (Illumina), amplified in situ as clusters and finally sequenced for 50 cycles on an Illumina NextSeq per the manufacturer’s instructions.

tag: gender

value: female

tag: age

value: benign lung disease

tag: disease state

tag: Stage


title: hiPSC_WT_Rep1

status: Public on Feb 04 2025

type: SRA

city: Philadelphia

first: Phillip

last: Wulfridge

state: Pennsylvania

address: 3601 Spruce St

country: USA

institute: The Wistar Institute

library_source: transcriptomic

data_processing:
RNA-Seq reads were aligned with STAR.
RNA expected counts were generated with RSEM.
Assembly: hg38
Supplementary files format and content: TXT file (RSEM gene counts)

molecule: total RNA

organism: Homo sapiens

source_name: patient derived hiPSC

growth_protocol: Human iPSCs were cultured on Geltrex (ThermoFisher, A14133020) coated plates in StemMACS iPS Brew-XF medium (Miltenyi Biotec, 130-104-368).

extract_protocol:
Total RNA was collected using Trizol (Invitrogen) and digested with Turbo Dnase (Ambion). rRNA was selectively depleted using FastSelect (Qiagen).
rRNA-depleted RNA was converted to cDNA using the Ultra II Directional RNA kit for Illumina (NEB #E7760).
DNA samples were end-repaired using End-Repair Mix (Enzymatics), A-tailed using Klenow exonuclease minus (Enzymatics), purified with MinElute columns (Qiagen), and ligated to Illumina adapters (NEB E7600) with T4 DNA ligase (Enzymatics).  Size selection for fragments >150 bp was performed with AMPure XP (Beckman Coulter).  Libraries were PCR amplified with dual index barcode primers for Illumina sequencing (NEB E7600) using Q5 DNA polymerase (NEB M0491) and purified with MinElute.

tag: cell line

value: patient derived hiPSC

tag: genotype

value: Wildtype

tag: cell type

value: hiPSC

value: WT


title: benign lung disease 2

country: China

value: male

tag: tissue


title: lung cancer 4

source_name: plasma from lung cancer patient

value: primary lung adenocarcinoma

value: ⅣB


title: benign lung disease 1


title: lung cancer 1


title: benign lung disease 3


title: lung cancer 2


title: hiPSC_S763P_fs9_Rep1


title: tumor_106

type: RNA

city: chapel hill

first: michael

middle: francis

last: coleman

state: North Carolina

address: 235 dauer drive

institute: UNC

hyb_protocol: Labeled cDNA was hybridized to the plate using GeneTitan Hybridization Wash and Stain Kit for WT Arrays (Affymetrix)

scan_protocol: arrays were scanned using GeneTitan

data_processing: Quality control and differential gene expression was conducted using TAC4 software (Affymetrix)

label: Biotin

organism: Mus musculus

source_name: tumor

label_protocol: The GeneChip® WT PLUS Reagent Kit (Affymetrix, Santa Clara, CA) was used to prepare the samples

growth_protocol: E0771 cells were cultured in DMEM with 10% FBS and 2mM glutamine, then orthotopically transplanted into C57BL6 mice. Tumors were removed and RNA extracted for analysis

extract_protocol: RNA extracted with trizol reagent then isolated with EZNA HP Total RNA kit (omega bio-tek)

treatment_protocol: no treatments were applied to injected cells

tag: treatment

value: ICR


title: hiPSC_WT_Rep2


title: tumor_114


title: tumor_120


title: tumor_116


title: lung cancer 3

value: ⅣA


title: tumor_74

value: CCR


title: tumor_78


title: tumor_69


title: tumor_112


title: tumor_103


title: tumor_64


title: 4T1 tumors K2-KO

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

description:
Library name: Sample 2
10X genomics

library_source: transcriptomic single cell

data_processing:
The multiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software V2.1.1 (HTTPS://support.10xgenomics.com/single-cell-gene-expression/re/pipelines/what-is-cell-ranger)
Assembly: mouse mm10
Supplementary files format and content: Tab-separated vaules files and matrix files (in barcodes.tsv, barcode-1 represents control cells, barcode-2 represents K2-KO cells)

source_name: Breast tumors

extract_protocol:
Tumors cut into small pieces were digested in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml Dnase I) and incubated at 37C for 45 min. cells were washed and resuspended in PBS and stained with Viability Dye, washed and resuspended in FACSbuffer (HBSSwo, 2% v/v FCS, 5 mM EDTA). Live cells were sorted using FACs Jazz (Becton Dickinson) according to the presence or absence of the mCherry signal. 4T1 cells were used as negative control. Sorted cells were  washed in HBSS-?- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
Library construction was performed according to the manufacturer's instructions )single cell 3' v2 protocol, 10x genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier  (UMI) and the 10X Barcode. The pooled barcoded cDNA was then cleaned up with Silan DynaBeads, amplified by PCR and the appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction of Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added

value: Breast tumors

value: TNBC cells

value: K2 sgRNA


title: tumor_60

value: LFD


title: tumor_63


title: tumor_57


title: tumor_46


title: 4T1 tumors control sgRNA

description:
Library name: Sample 1
10X genomics

value: Ctrl sgRNA


title: tumor_40

value: DIO


title: tumor_23


title: tumor_35


title: tumor_38


title: tumor_28


title: tumor_24


title: tumor_66


title: tumor_5

value: Con


title: tumor_18


title: tumor_2


title: tumor_13


title: tumor_10


title: hPCSK9 tg mouse liver, dCas9-TET, 1

city: Boston

first: Frederic

last: Tremblay

state: MA

address: 201 Brookline Ave, Suite 1101

institute: Chroma Medicine

library_source: genomic

data_processing:
We used the Nextflow Methyl-Seq pipeline (https://zenodo.org/badge/latestdoi/124913037) to map sequencing reads to the human reference genome (GRCh38) using Bismark v0.24.0 with the following parameters: igenomes_ignore = true, clip_r1 = 10, clip_r2 = 10, three_prime_clip_r1 = 10, three_prime_clip_r2 = 10, cytosine_report = true.
Multi-QC (10.1093/bioinformatics/btw354) reports were then generated from the stats files resulting from the Methyl-Seq pipeline.
IGV was used to visualize methylation in the region of the human PCSK9 TSS.
Assembly: GRCh38
Supplementary files format and content: bedgraph of CpG methylation
Library strategy: EM-seq

molecule: genomic DNA

source_name: Liver

extract_protocol:
Genomic DNA was extracted from mouse liver tissue samples or HeLa cells using simultaneous RNA and DNA extraction from cultured cells without splitting lysate protocol and reagents or DNAdvance kit (Beckman Coulter).
Genomic DNA was sheared to a target size of 350bp using a Covaris 96 AFA-Tube TPX plate. Sequencing libraries were then constructed from the sheared genomic DNA using the NEBNext Enzymatic Methyl-seq (EM-seq) kit plus NEBNext Multiplex Oligos for Enzymatic Methyl-seq, After methylation conversion, we performed hybridization capture target enrichment using a custom designed panel and manufacturer recommendations (Twist). Libraries were sequenced using an Illumina MiSeq, 150 bp paired-end reads.

value: Liver


title: hPCSK9 tg mouse liver, dCas9-TET, 2


title: hPCSK9 tg mouse liver, dCas9-TET, 4


title: hPCSK9 tg mouse liver, dCas9-TET, 3


title: hPCSK9 tg mouse liver, dCas9-TET, 5


title: hPCSK9 tg mouse liver, PCSK9-EE, 4


title: hPCSK9 tg mouse liver, PCSK9-EE, 3


title: tumor_53


title: tumor_59


title: hPCSK9 tg mouse liver, PCSK9-EE, Regenerated, 4

value: PCSK9-EE, regenerated


title: hPCSK9 tg mouse liver, PCSK9-EE, 1


title: tumor_1


title: hPCSK9 tg mouse liver, PCSK9-EE, Regenerated, 3


title: hPCSK9 tg mouse liver, PCSK9-EE, 2


title: hPCSK9 tg mouse liver, PCSK9-EE, Regenerated, 1


title: tumor_48


title: hPCSK9 tg mouse liver, PCSK9-EE, Sham, 4

value: PCSK9-EE, sham


title: hPCSK9 tg mouse liver, PCSK9-EE, Regenerated, 2


title: hPCSK9 tg mouse liver, PCSK9-EE, Sham, 3


title: hPCSK9 tg mouse liver, PCSK9-EE, 5


title: hPCSK9 tg mouse liver, PCSK9-EE, Sham, 2


title: hPCSK9 tg mouse liver, PCSK9-EE, Sham, 1


title: hPCSK9 tg mouse liver, PCSK9-EE, Resected, 3

value: PCSK9-EE, resected


title: hPCSK9 tg mouse liver, PCSK9-EE, Resected, 1


title: hPCSK9 tg mouse liver, Cas9, Regenerated, 3

value: Cas9, regenerated


title: hPCSK9 tg mouse liver, PCSK9-EE, Resected, 4


title: hPCSK9 tg mouse liver, Cas9, Regenerated, 2


title: P3_pSer_VDJ

city: Cambridge

first: Darrell

middle: J.

last: Irvine

address: 77 Massachusetts Ave

institute: Massachusetts Institute of Technology

description:
Library name: P3_VDJ
B3E-Seq

data_processing:
scRNA-seq libraries were sequenced by Illumina NovaSeq and aligned to the GRCm39 reference genome using the STARsolo pipeline (version 2.4.0). The gene expression count matrix and cell hashing sequence reads were processed and analyzed using Seurat v5.0.1, ggplot2 v3.5.1, CITE-seq-Count v1.4.2, Scanpy v1.10.4, and scVelo v0.3.3.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: lymph node

extract_protocol:
Draining inguinal lymph nodes were isolated, and lymph node cells were filtered through 70 μm cell strainers. Antigen-specific germinal center cells were sorted by fluorescent-activated cell sorting.
The libraries were prepared using the SeqWell S3 protocol followed by the B3E-seq protocol.

treatment_protocol: Mice were immunized with 5 μg of antigen MD39 and 50 μg of alum and/or 5 μg SMNP in 100 μL sterile tris-buffered saline (TBS, Sigma Aldrich) per mouse.

value: lymph node

value: Germinal center B cell

value: Alum-pSer


title: P1_pSer_VDJ

description:
Library name: P1_VDJ
B3E-Seq


title: AQ3_both_VDJ

description:
Library name: AQ3_VDJ
B3E-Seq

value: Alum-pSer/SMNP


title: P4_pSer_VDJ

description:
Library name: P4_VDJ
B3E-Seq


title: AQ2_pSer_VDJ

description:
Library name: AQ2_VDJ
B3E-Seq


title: AQ4_both_VDJ

description:
Library name: AQ4_VDJ
B3E-Seq


title: hPCSK9 tg mouse liver, Cas9, Sham, 3

value: Cas9, sham


title: hPCSK9 tg mouse liver, Cas9, Sham, 4


title: AQ1_SMNP_VDJ

description:
Library name: AQ1_VDJ
B3E-Seq

value: SMNP


title: AG2_VDJ

description:
Library name: AG2_VDJ
B3E-Seq


title: hPCSK9 tg mouse liver, Cas9, Regenerated, 1


title: AG3_both_VDJ

description:
Library name: AG3_VDJ
B3E-Seq


title: hPCSK9 tg mouse liver, Cas9, Sham, 2


title: AG1_VDJ

description:
Library name: AG1_VDJ
B3E-Seq. The heavy chain of AG1 and AG2 are multiplexed, sequenced together, and named AG2H_*.fastq.gz. They can be demultiplexed during processing by their corresponding cellular barcodes found in their gene expression libraries.


title: P4_pSer_HTO

description:
Library name: P4_HTO
SeqWell


title: P3_pSer_HTO

description:
Library name: P3_HTO
SeqWell


title: hPCSK9 tg mouse liver, Cas9, Resected, 4

value: Cas9, resected


title: hPCSK9 tg mouse liver, Cas9, Sham, 1


title: P2_pSer_VDJ

description:
Library name: P2_VDJ
B3E-Seq


title: hPCSK9 tg mouse liver, Cas9, Regenerated, 4


title: P2_pSer_HTO

description:
Library name: P2_HTO
SeqWell


title: hPCSK9 tg mouse liver, Cas9, Resected, 1


title: hPCSK9 tg mouse liver, Cas9, Resected, 3


title: P1_pSer_HTO

description:
Library name: P1_HTO
SeqWell


title: hPCSK9 tg mouse liver, Cas9, Resected, 2


title: AQ4_both_HTO

description:
Library name: AQ4_HTO
SeqWell


title: hPCSK9 tg mouse liver, Vehicle, Regenerated, 3

value: Vehicle, regenerated


title: AQ2_pSer_HTO

description:
Library name: AQ2_HTO
SeqWell


title: hPCSK9 tg mouse liver, Vehicle, Sham, 3

value: Vehicle, sham


title: AG3_both_HTO

description:
Library name: AG3_HTO
SeqWell


title: AQ3_both_HTO

description:
Library name: AQ3_HTO
SeqWell


title: hPCSK9 tg mouse liver, Vehicle, Regenerated, 1


title: AQ1_SMNP_HTO

description:
Library name: AQ1_HTO
SeqWell


title: hPCSK9 tg mouse liver, Vehicle, Regenerated, 2


title: hPCSK9 tg mouse liver, Vehicle, Sham, 2


title: hPCSK9 tg mouse liver, Vehicle, Resected, 3

value: Vehicle, resected


title: hPCSK9 tg mouse liver, Vehicle, Sham, 1


title: hPCSK9 tg mouse liver, PCSK9-EE, Resected, 2


title: P4_pSer

description:
Library name: P4
SeqWell


title: AG2_pSer_HTO

description:
Library name: AG2_HTO
SeqWell


title: hPCSK9 tg mouse liver, Vehicle, Resected, 2


title: AG1_SMNP_HTO

description:
Library name: AG1_HTO
SeqWell


title: hPCSK9 tg mouse liver, Vehicle, Resected, 1


title: hPCSK9 tg mouse liver, PCSK9-EE, day365, 6


title: P1_pSer

description:
Library name: P1
SeqWell


title: hPCSK9 tg mouse liver, PCSK9-EE, day365, 5


title: P2_pSer

description:
Library name: P2
SeqWell


title: AQ4_both

description:
Library name: AQ4
SeqWell


title: hPCSK9 tg mouse liver, PCSK9-EE, day365, 4


title: wt_hog1_NaCl_t30

city: Barcelona

first: Francesc

last: Posas

address: Carrar Baldiri Reixac 10

country: Spain

institute: Cell Signaling Group, IRB Barcelona

description: 10X genomics

data_processing:
Raw FASTQ files were processed with cellranger-4.0.0 to perform sample demultiplexing, cell barcode extraction and gene counting.
Assembly: Reference genome was obtained from (Nadal-Ribelles, Mariona, et al. "Control of Cdc28 CDK1 by a stress-induced lncRNA." Molecular cell 53.4 (2014): 549-561.)
Supplementary files format and content: Tab separated values files and matrix files

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown individually in rich medium. At mid exponential growth phase cells were pooled at a 1:1 ratio  before treatment.

extract_protocol:
Fixed cells were rehydrated follwoing manufacturer's protocol
Library was performed according to manufacturer's protocol (10X v3.2) except for a minor modification, by which zymoliase was added to the enzyme mix to perform an in drop cell wall digestion.
scRNA-seq 3' end

treatment_protocol: Cells were treated or not (control) with osmotic stress 0.4M NaCl at the indicated times. Cells were harvested and fixed with methanol using 10X methanol fixation protocol.

tag: group

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0

value: NaCl 0.4M

tag: time


title: AQ3_both

description:
Library name: AQ3
SeqWell


title: AQ1_SMNP

description:
Library name: AQ1
SeqWell


title: AQ2_pSer

description:
Library name: AQ2
SeqWell


title: hPCSK9 tg mouse liver, PCSK9-EE, day365, 3

value: Liver


title: wt_hog1_NaCl_t05

description: 10X genomics


title: AG2_pSer

description:
Library name: AG2
SeqWell


title: AG3_both

description:
Library name: AG3
SeqWell


title: Muscle,9,Sucrose+JNK_D2

city: Solna

first: Hong

last: Yang

state: Stockholm

address: Tomtebodavägen 23A

department: Systems Biology

country: Sweden

institute: KTH Royal Institute of Technology/Science For Life Laboratory

description: Library name: Muscle,9,Sucrose+JNK_D2

data_processing:
Raw sequencing data (.bcl) was converted to FASTQ with the Dragen Bio-IT platform (v3.9.5).
The quality of RNA-seq data was assessed by FastQC (v0.11.9).
Tissue bulk RNA-seq data were aligned and quantified using a standard protocol of Kallisto (v0.46.2) against Rattus norvegicus genome (mRatBN7.2)  downloaded from Ensembl official website
The output of Kallisto, both estimated counts and TPM (transcript per kilobase million)-based transcript-level expressions were then transformed into gene-level expressions using the Bioconductor package tximport (v1.22.0) with the tx2gene option set to connect transcripts to genes.
Assembly: mRatBN7.2
Supplementary files format and content: Tab-delimited Raw counts for every gene and samples

organism: Rattus norvegicus

source_name: Muscle

extract_protocol: RNA sequencing library was prepared with Illumina Stranded Total RNA Prep and Ligation with Ribo-Zero Plus kit was used by following the standard protocol provided by the manufacturer

treatment_protocol: Total RNA is extracted from the snap-frozen rat tissues with Zymo Research Quick RNA Miniprep kit (California USA) by following the protocol provided on the manufacturer’s website with slight modifications made to improve the quality and quantity of RNA from each tissue.

value: Muscle

value: 10% Sucrose in drinking water

tag: diet

value: Chow


title: hPCSK9 tg mouse liver, PCSK9-EE, day365, 2


title: hPCSK9 tg mouse liver, PCSK9-EE, day365, 1


title: Mouse E11.5 Mboat7-/- cortex, biiol rep 1

city: Tokyo

first: Nozomu

last: Kono

address: Hongo 7-3-1, Bunkyo-ku

country: Japan

institute: Universtiy of Tokyo

description:
Library name: Sample3
Column name in Mboat7_KO_E11_count_table.txt; KO-E11-5-cortex-1
E11_5No_3

data_processing:
For E11.5 samples, sequence reads were trimmed for adaptor sequence/low-quality sequence using Fastp.Trimmed seqence reads were mapped to mm10 using Hisat2 and read counts were generated using the feature-counts option from the subRead package. For E12.5 samples. For E12.5 samples, read counts were generated using the nf-core/rnaseq pipeline with the GRCm39 reference genome.
Assembly: mm10/GRCm39
Supplementary files format and content: Tab-delimited text file include raw counts for each sample.

source_name: cortex

extract_protocol:
RNA was harvested using RNeasy mini plus kit (QIAGEN).
Poly(A) selection was performed using NEBNext® Poly(A) mRNA Magnetic Isolation Module. RNA libraries for RNA-seq were prepared using NEB NEXT Directional Ultra RNA Library Prep Kit for Illumina.

value: cortex

tag: batch


title: Liver,9,Sucrose+JNK_D2

description: Library name: Liver,9,Sucrose+JNK_D2


title: Mouse E11.5 Mboat7+/- cortex, biol rep 1

description:
Library name: Sample1
Column name in Mboat7_KO_E11_count_table.txt; HT-E11-5-cortex-1
E11_5No_1


title: Mouse E11.5 Mboat7-/- cortex, biiol rep 2

description:
Library name: Sample4
Column name in Mboat7_KO_E11_count_table.txt; KO-E11-5-cortex-2
E11_5No_4


title: P3_pSer

description:
Library name: P3
SeqWell

value: lymph node


title: wt_hog1_control

description: 10X genomics

value: control


title: WAT.T0_8

first: Sinisa

last: Hrvatin

address: 455 Main Street

department: Whitehead Institute

institute: MIT

description: Library name: L511_145

data_processing:
The following command was used to align reads to the mm10 reference mouse genome using STAR v2.7.10: for fq1 in `/bin/ls *R1_001.fastq.gz` do    name=`basename $fq1 | perl -pe 's/_R1_001.fastq.gz//'`    fq2=`basename $fq1 | perl -pe 's/R1_001.fastq.gz/R2_001.fastq.gz/'`    echo Processing $name ...    # Slurm cluster call    # echo sbatch --partition=20 --job-name=STAR --mem=32G --wrap "STAR --genomeDir /nfs/genomes/mouse_mm10_dec_11_no_random/STAR/GRCm38.102.canonical_overhang_100 --sjdbScore 2 --runThreadN 8 --outSAMtype BAM SortedByCoordinate  --readFilesCommand zcat --readFilesIn $fq1 $fq2 --outFileNamePrefix ../STAR/$name."    sbatch --partition=20 --job-name=STAR --mem=32G --wrap "STAR --genomeDir /nfs/genomes/mouse_mm10_dec_11_no_random/STAR/GRCm38.102.canonical_overhang_100 --sjdbScore 2 --runThreadN 8 --outSAMtype BAM SortedByCoordinate  --readFilesCommand zcat --readFilesIn $fq1 $fq2 --outFileNamePrefix ../STAR/$name." done After alignment, data was processed through the DESeq2 pipeline. In brief, data was separated by tissue-type and processed independently. DESeq() was run to normalize counts using con-trast of treatment (TLS vs. Con). DESeq results were transformed to variance stabilized expres-sion levels using the vst() function followed by log fold change shrinkage with the lfcShrink() function using apelgm. Data was visualized using the EnhancedVolcano() function with the fol-lowing thresholds, (-log10(Pval) < 10-6 and Log2 fold change > 1.
Assembly: mm10 reference mouse genome
Supplementary files format and content: processed data is displayed in a matrix of raw transcript counts per sample on the x-axis and genomic location on the y-axis.

source_name: WAT

extract_protocol:
Mice were anesthetized via inhalation of isoflurane and euthanized by cervical dislocation. Blood was collected via cardiac puncture followed by transcardial perfusion of 10 mL PBS to wash tissues. Tissues were removed and washed in PBS twice before being flash frozen in liquid nitrogen. Following collection, tissues were stored at -80ºC before further processing. For RNA extraction, RNeasy Mini kits were used (QIAGEN #74104). After extraction, RNA was stored at -80ºC until further processing.
Libraries were prepared using the NEBNext UltraTM II kit. In brief 500 ng of RNA per sample un-derwent Poly(A) selection before fragmentation and random priming followed by first and second strand cDNA synthesis. Following cDNA synthesis, NEBNext Multiplex Oligos for Illumina (E6440S) were ligated before PCR enrichment. All libraries were pooled to a final concentration of 1nM and sequenced on a NovaSeq 6000.

treatment_protocol: Tissues were collected from time-0 mice, control mice, and experimental mice after 3 months of TLS.

value: WAT

value: M


title: Mouse E11.5 Mboat7+/- cortex, biol rep 2

description:
Library name: Sample2
Column name in Mboat7_KO_E11_count_table.txt; HT-E11-5-cortex-2
E11_5No_2


title: AG1_SMNP

description:
Library name: AG1
SeqWell

value: Germinal center B cell


title: hPCSK9 tg mouse liver, PCSK9-EE, day28, 3


title: hPCSK9 tg mouse liver, PCSK9-EE, day28, 4


title: WAT.5A66

description: Library name: L511_144

value: Con


title: Brain,9,Sucrose+JNK_D2

description: Library name: Brain,9,Sucrose+JNK_D2

source_name: Brain

value: Brain


title: hPCSK9 tg mouse liver, PCSK9-EE, day28, 2


title: WAT.9916

description: Library name: L511_143

value: F


title: Kidney.T0_8

description: Library name: L511_142

source_name: Kidney

value: Kidney


title: wt_hog1_NaCl_t15

description: 10X genomics


title: Adipose,9,Sucrose+JNK_D2

description: Library name: Adipose,9,Sucrose+JNK_D2

source_name: Adipose

value: Adipose


title: Kidney.5A66

description: Library name: L511_141


title: Kidney.9916

description: Library name: L511_140


title: Cortex.T0_8

description: Library name: L511_139

source_name: Cortex

value: Cortex


title: hPCSK9 tg mouse liver, PCSK9-EE, day28, 1


title: hPCSK9 tg mouse liver, CRISPRi, day28, 4

value: CRISPRi


title: Cortex.5A66

description: Library name: L511_138


title: Liver,8,Sucrose+JNK_D2

description: Library name: Liver,8,Sucrose+JNK_D2

value: Liver


title: hPCSK9 tg mouse liver, CRISPRi, day28, 3


title: Liver.T0_8

description: Library name: L511_137


title: Liver.5A66

description: Library name: L511_136


title: Liver.9916

description: Library name: L511_135


title: Cortex.9916

description: Library name: L511_134


title: WAT.E329

description: Library name: L511_132


title: WAT.D215

description: Library name: L511_131


title: hPCSK9 tg mouse liver, CRISPRi, day28, 2


title: Liver,7,Sucrose+JNK_D2

description: Library name: Liver,7,Sucrose+JNK_D2


title: WAT.T0_7

description: Library name: L511_133


title: Kidney.T0_7

description: Library name: L511_130


title: Adipose,8,Sucrose+JNK_D2

description: Library name: Adipose,8,Sucrose+JNK_D2


title: hPCSK9 tg mouse liver, WTCas9, day28, 3

value: WT Cas9


title: Brain,8,Sucrose+JNK_D2

description: Library name: Brain,8,Sucrose+JNK_D2

value: 10% Sucrose in drinking water


title: Muscle,7,Sucrose+JNK_D2

description: Library name: Muscle,7,Sucrose+JNK_D2

value: Muscle

value: Chow


title: Cortex.T0_7

description: Library name: L511_127


title: Kidney.D215

description: Library name: L511_128


title: hPCSK9 tg mouse liver, CRISPRi, day28, 1


title: Muscle,8,Sucrose+JNK_D2

description: Library name: Muscle,8,Sucrose+JNK_D2


title: hPCSK9 tg mouse liver, WTCas9, day28, 2


title: Brain,7,Sucrose+JNK_D2

description: Library name: Brain,7,Sucrose+JNK_D2


title: Cortex.E329

description: Library name: L511_126


title: Adipose,7,Sucrose+JNK_D2

description: Library name: Adipose,7,Sucrose+JNK_D2


title: hPCSK9 tg mouse liver, WTCas9, day28, 1


title: Liver.T0_7

description: Library name: L511_125


title: Muscle,6,Sucrose+JNK_D2

description: Library name: Muscle,6,Sucrose+JNK_D2


title: Liver.E329

description: Library name: L511_124


title: Liver.D215

description: Library name: L511_123


title: hPCSK9 tg mouse liver, WTCas9, day28, 4


title: hPCSK9 tg mouse liver, Vehicle, day28, 4

value: Vehicle


title: Liver,6,Sucrose+JNK_D2

description: Library name: Liver,6,Sucrose+JNK_D2


title: WAT.T0_6

description: Library name: L511_121


title: Cortex.D215

description: Library name: L511_122


title: Brain,6,Sucrose+JNK_D2

description: Library name: Brain,6,Sucrose+JNK_D2


title: hPCSK9 tg mouse liver, Vehicle, day28, 3


title: WAT.A123

description: Library name: L511_119


title: Kidney.9BA4

description: Library name: L511_117


title: Adipose,6,Sucrose+JNK_D2

description: Library name: Adipose,6,Sucrose+JNK_D2


title: Kidney.E329

description: Library name: L511_129


title: Kidney.T0_6

description: Library name: L511_118


title: Cortex.T0_6

description: Library name: L511_115


title: hPCSK9 tg mouse liver, Vehicle, day28, 1


title: Muscle,5,Sucrose+JNK_D2

description: Library name: Muscle,5,Sucrose+JNK_D2


title: Cortex.9BA4

description: Library name: L511_114


title: Liver.9BA4

description: Library name: L511_112


title: Kidney.A123

description: Library name: L511_116


title: Liver,5,Sucrose+JNK_D2

description: Library name: Liver,5,Sucrose+JNK_D2


title: Liver.A123

description: Library name: L511_111


title: KMS-27 sh NTC 30h Rep2

city: South San Francisco

first: Ioanna

last: Oikonomidi

state: California

address: 1 DNA Way

department: Research Biology

institute: Genentech Inc

description: Library name: SAM24430511

data_processing:
Sequenced reads were aligned to the genome using gsnap-based NGS workflow that runs the BCB endorsed RNASeq workflows via sunrise v1.182718.1
RNA-sequencing data were analyzed using HTSeqGenie (Pau and Reeder, 2012) in BioConductor (Huber et al., 2015) as follows: first, reads with low nucleotide qualities (70% of bases with quality <23) or matches to rRNA and adapter sequences were removed. The remaining reads were aligned to the human reference genome (human: GRCh38.p10) using GSNAP (PMID:20147302, 27008021) version ‘2013-10-10-v2’, allowing maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap'). Transcript annotation was based on the Gencode genes data base (human: GENCODE 27). To quantify gene expression levels, the number of reads mapping unambiguously to the exons of each gene was calculated.
Assembly: Genome_build: GRCh38
Supplementary files format and content: "Raw_counts" tab delimited file contains raw counts for all samples
Supplementary files format and content: "Norm_counts" tab delimited file contains normalized counts [ log2((counts + 1*SF)/(N/10^6) ]

source_name: Plasmacytoma

growth_protocol: Cells grown in biological triplicates in T-75 flasks in RPMI 10% FBS

extract_protocol:
RNA from 1x10^6 cell was first extracted with RNeasy Plus Mini kit (Qiagen), per manufacturer’s protocol. Total RNA was quantified with Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and quality was assessed using RNA ScreenTape on 4200 TapeStation (Agilent Technologies).
Truseq Stranded mRNA kit (Illumina) was used with an input of 100 nanograms of total RNA. Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on 4200 TapeStation (Agilent Technologies). Libraries were pooled and sequenced on HISeq 1000 (Illumina) to generate 30 million single-end 50-base pair reads for each sample.

treatment_protocol: 0.2 ug/ml Doxycycline (Dox) for the indicated times vs Mock treatment

value: Plasmacytoma

value: Tumor plasma cell

value: Dox 30h


title: Brain,5,Sucrose+JNK_D2

description: Library name: Brain,5,Sucrose+JNK_D2


title: KMS-27 sh NTC Mock Rep3

description: Library name: SAM24430510

value: Mock


title: Cortex.A123

description: Library name: L511_110

value: Con


title: Liver.T0_6

description: Library name: L511_113

value: M


title: Adipose,5,Sucrose+JNK_D2

description: Library name: Adipose,5,Sucrose+JNK_D2


title: KMS-27 sh NTC Mock Rep2

description: Library name: SAM24430509


title: WAT.A367

description: Library name: L511_108

value: WAT


title: WAT.983B

description: Library name: L511_107

value: F


title: Muscle,4,Sucrose+JNK_D2

description: Library name: Muscle,4,Sucrose+JNK_D2


title: hPCSK9 tg mouse liver, Vehicle, day28, 2


title: Kidney.T0_5

description: Library name: L511_106

value: Kidney


title: Kidney.A367

description: Library name: L511_105


title: KMS-27 shIRF4 Clone 20 30h Rep3

description: Library name: SAM24430508


title: Kidney.983B

description: Library name: L511_104


title: Cortex.T0_5

description: Library name: L511_103

value: Cortex


title: KMS-27 sh NTC 30h Rep3

description: Library name: SAM24430512


title: KMS-27 shIRF4 Clone 20 30h Rep2

description: Library name: SAM24430507


title: Cortex.A367

description: Library name: L511_102


title: Adipose,4,Sucrose+JNK_D2

description: Library name: Adipose,4,Sucrose+JNK_D2

value: Adipose


title: Liver.T0_5

description: Library name: L511_101

value: Liver


title: Liver.A367

description: Library name: L511_100


title: Muscle,3,Sucrose+JNK_D2

description: Library name: Muscle,3,Sucrose+JNK_D2


title: KMS-27 shIRF4 Clone 20 20h Rep2

description: Library name: SAM24430505

value: Dox 20h


title: KMS-27 shIRF4 Clone 20 Mock Rep3

description: Library name: SAM24430504


title: KMS-27 shIRF4 Clone 20 20h Rep3

description: Library name: SAM24430506


title: WAT.47BE

description: Library name: L511_96

value: Stim


title: WAT.T0_5

description: Library name: L511_109


title: WAT.T0_4

description: Library name: L511_97


title: Liver,3,Sucrose+JNK_D2

description: Library name: Liver,3,Sucrose+JNK_D2

value: 10% Sucrose in drinking water


title: Liver.983B

description: Library name: L511_99


title: Cortex.983B

description: Library name: L511_98


title: KMS-27 shIRF4 Clone 20 Mock Rep2

description: Library name: SAM24430503


title: Brain,3,Sucrose+JNK_D2

description: Library name: Brain,3,Sucrose+JNK_D2

value: Brain

value: Chow


title: Kidney.T0_4

description: Library name: L511_94


title: WAT.B03E

description: Library name: L511_95


title: Brain,4,Sucrose+JNK_D2

description: Library name: Brain,4,Sucrose+JNK_D2


title: Liver,4,Sucrose+JNK_D2

description: Library name: Liver,4,Sucrose+JNK_D2


title: Adipose,3,Sucrose+JNK_D2

description: Library name: Adipose,3,Sucrose+JNK_D2


title: AMO-1 shNTC 24h Rep3

description: Library name: SAM24430502

value: Plasmacytoma

value: Dox 24h


title: Cortex.T0_4

description: Library name: L511_91


title: AMO-1 shNTC 24h Rep2

description: Library name: SAM24430501

value: Tumor plasma cell


title: Liver,2,Sucrose+JNK_D2

description: Library name: Liver,2,Sucrose+JNK_D2


title: Cortex.47BE

description: Library name: L511_90


title: AMO-1 shNTC Mock Rep2

description: Library name: SAM24430499

value: Mock


title: Liver.B03E

description: Library name: L511_87


title: Brain,2,Sucrose+JNK_D2

description: Library name: Brain,2,Sucrose+JNK_D2


title: Cortex.B03E

description: Library name: L511_86


title: AMO-1 shNTC Mock Rep3

description: Library name: SAM24430500


title: Liver.T0_4

description: Library name: L511_89


title: WAT.B23B

description: Library name: L511_83


title: WAT.T0_3

description: Library name: L511_85


title: Liver.47BE

description: Library name: L511_88


title: Adipose,2,Sucrose+JNK_D2

description: Library name: Adipose,2,Sucrose+JNK_D2


title: AMO-1 shIRF4 Cl. 4-3 24h Rep3

description: Library name: SAM24430496


title: WAT.E46E

description: Library name: L511_84


title: AMO-1 shIRF4 Cl. 4-3 24h Rep2

description: Library name: SAM24430495


title: HeLa cell, baseline, 1

source_name: HeLa

value: HeLa


title: AMO-1 shIRF4 Cl. 4-3 16h Rep3

description: Library name: SAM24430494

value: Dox 16h


title: Kidney.T0_3

description: Library name: L511_82


title: Kidney.47BE

description: Library name: L511_93

value: M


title: Muscle,2,Sucrose+JNK_D2

description: Library name: Muscle,2,Sucrose+JNK_D2

value: Muscle


title: Brain,11,Sucrose+JNK_D2

description: Library name: Brain,11,Sucrose+JNK_D2


title: AMO-1 shIRF4 Cl. 4-3 16h Rep2

description: Library name: SAM24430493


title: AMO-1 shIRF4 Cl. 4-3 8h Rep3

description: Library name: SAM24430492

value: Dox 8h


title: Kidney.E46E

description: Library name: L511_81

value: Kidney


title: A21_9_234F_4

city: Palo Alto

first: Ishita

last: Jain

address: 3801 Miranda Avenue

institute: Stanford University

description:
Library name: A21_9_234F_4
Cells cultured on 2D surface

data_processing:
To estimate gene expression levels, the fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM) was quantified for each aligned read. This accounted for both sequencing depth and gene length on counting of fragments.
Assembly: fatsq files for each sample
Supplementary files format and content: FPKM in CSV combined for all samples

source_name: Bone Marrow

extract_protocol:
Short term gene changes were assessed in MSCs seeded on tissue chips on 4, 234 and 234F ECM combinations at 150kPa and 900 kPa, following the proliferation protocol. After 48 hours in growth media, cells were lysed and RNA was extracted using GeneJET RNA isolation kit (Fisher Scientific) followed by RNA sequencing by Novogene Corporation (n=4).
CASAVA base recognition (Base Calling) was used to convert original image data files from Illumina sequencing platform to sequenced reads in FASTQ format. A series filtration criteria was applied based on uncertain nucleotides constituting more than 10% of either read (n>10%) and with low-quality nucleotides (base quality less than 5) constituting more than 50 per cent of the read. Next, alignment of raw reads was performed to reference genome using HISAT2. To estimate gene expression levels, the fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM) was quantified for each aligned read. This accounted for both sequencing depth and gene length on counting of fragments.

value: Bone Marrow

value: Mesenchymal Stem Cells

value: Stiffness 900kPa ECM C2+C3+C4+F


title: A21_9_234F_3

description:
Library name: A21_9_234F_3
Cells cultured on 2D surface


title: Kidney.B03E

description: Library name: L511_92

value: F

value: Stim


title: AMO-1 shIRF4 Cl. 4-3 8h Rep2

description: Library name: SAM24430491


title: A21_9_234F_2

description:
Library name: A21_9_234F_2
Cells cultured on 2D surface


title: Kidney.B23B

description: Library name: L511_80


title: Cortex.T0_3

description: Library name: L511_79

value: Cortex


title: Muscle,10,Sucrose+JNK_D2

description: Library name: Muscle,10,Sucrose+JNK_D2

value: 10% Sucrose in drinking water

value: Chow


title: A21_9_234F_1

description:
Library name: A21_9_234F_1
Cells cultured on 2D surface


title: AMO-1 shIRF4 Cl. 4-3 Mock Rep3

description: Library name: SAM24430490

value: Plasmacytoma


title: Muscle,11,Sucrose+JNK_D2

description: Library name: Muscle,11,Sucrose+JNK_D2


title: Liver,11,Sucrose+JNK_D2

description: Library name: Liver,11,Sucrose+JNK_D2

value: Liver


title: Cortex.E46E

description: Library name: L511_78


title: Liver.T0_3

description: Library name: L511_77


title: AMO-1 shIRF4 Cl. 4-3 Mock Rep2

description: Library name: SAM24430489

value: Tumor plasma cell

value: Mock


title: Brain,10,Sucrose+JNK_D2

description: Library name: Brain,10,Sucrose+JNK_D2

value: Brain


title: A19_9_234_3

description:
Library name: A19_9_234_3
Cells cultured on 2D surface

value: Stiffness 900kPa ECM C2+C3+C4


title: AMO-1 shIRF4 Cl. 1 24h Rep3

description: Library name: SAM24430488

value: Dox 24h


title: Adipose,10,Sucrose+JNK_D2

description: Library name: Adipose,10,Sucrose+JNK_D2

value: Adipose


title: Liver.E46E

description: Library name: L511_76

value: M


title: A18_9_234_2

description:
Library name: A18_9_234_2
Cells cultured on 2D surface

value: Bone Marrow


title: Liver.B23B

description: Library name: L511_75


title: AMO-1 shIRF4 Cl. 1 24h Rep2

description: Library name: SAM24430487


title: Muscle,9,Sucrose+JNK_D1

description: Library name: Muscle,9,Sucrose+JNK_D1

value: Muscle


title: A17_9_234_1

description:
Library name: A17_9_234_1
Cells cultured on 2D surface

value: Mesenchymal Stem Cells


title: Cortex.B23B

description: Library name: L511_74

value: F


title: Adipose,11,Sucrose+JNK_D2

description: Library name: Adipose,11,Sucrose+JNK_D2


title: Liver,9,Sucrose+JNK_D1

description: Library name: Liver,9,Sucrose+JNK_D1


title: WAT.T0_2

description: Library name: L511_73

value: WAT


title: AMO-1 shIRF4 Cl. 1 8h Rep3

description: Library name: SAM24430484

value: Dox 8h


title: WAT.A5DA

description: Library name: L511_72

value: Stim


title: AMO-1 shIRF4 Cl. 1 16h Rep2

description: Library name: SAM24430485

value: Dox 16h


title: Adipose,9,Sucrose+JNK_D1

description: Library name: Adipose,9,Sucrose+JNK_D1

value: 10% Sucrose in drinking water

value: Chow


title: A20_9_234_4

description:
Library name: A20_9_234_4
Cells cultured on 2D surface


title: A14_9_4_2

description:
Library name: A14_9_4_2
Cells cultured on 2D surface

value: Stiffness 900kPa ECM Collagen 4


title: AMO-1 shIRF4 Cl. 1 8h Rep2

description: Library name: SAM24430483

value: Plasmacytoma

value: Tumor plasma cell


title: A13_9_4_1

description:
Library name: A13_9_4_1
Cells cultured on 2D surface


title: Liver,10,Sucrose+JNK_D2

description: Library name: Liver,10,Sucrose+JNK_D2

value: Liver


title: Kidney.T0_2

description: Library name: L511_70

value: Kidney


title: Liver,8,Sucrose+JNK_D1

description: Library name: Liver,8,Sucrose+JNK_D1


title: WAT.B4B9

description: Library name: L511_71


title: Muscle,8,Sucrose+JNK_D1

description: Library name: Muscle,8,Sucrose+JNK_D1


title: A12_1_234F_4

description:
Library name: A12_1_234F_4
Cells cultured on 2D surface

value: Stiffness 150kPa ECM C2+C3+C4+F


title: AMO-1 shIRF4 Cl. 1 Mock Rep3

description: Library name: SAM24430482

value: Mock


title: Kidney.A5DA

description: Library name: L511_69

value: M


title: AMO-1 shIRF4 Cl. 1 Mock Rep2

description: Library name: SAM24430481


title: Brain,8,Sucrose+JNK_D1

description: Library name: Brain,8,Sucrose+JNK_D1

value: Brain


title: A16_9_4_4

description:
Library name: A16_9_4_4
Cells cultured on 2D surface

value: Bone Marrow

value: Mesenchymal Stem Cells


title: A11_1_234F_3

description:
Library name: A11_1_234F_3
Cells cultured on 2D surface


title: KMS-27 shNTC 30h Rep1

description: Library name: SAM24430071

value: Dox 30h


title: Kidney.B4B9

description: Library name: L511_68

value: F


title: A10_1_234F_2

description:
Library name: A10_1_234F_2
Cells cultured on 2D surface


title: Adipose,8,Sucrose+JNK_D1

description: Library name: Adipose,8,Sucrose+JNK_D1

value: Adipose


title: A15_9_4_3

description:
Library name: A15_9_4_3
Cells cultured on 2D surface


title: AMO-1 shIRF4 Cl. 1 16h Rep3

description: Library name: SAM24430486

value: Dox 16h


title: KMS-27 shNTC Mock Rep1

description: Library name: SAM24430070


title: Brain,9,Sucrose+JNK_D1

description: Library name: Brain,9,Sucrose+JNK_D1

value: 10% Sucrose in drinking water


title: KMS-27 shIRF4 Clone 20 30h Rep1

description: Library name: SAM24430069


title: Cortex.A5DA

description: Library name: L511_66

value: Cortex

value: Stim


title: A9_1_234F_1

description:
Library name: A9_1_234F_1
Cells cultured on 2D surface


title: Liver,7,Sucrose+JNK_D1

description: Library name: Liver,7,Sucrose+JNK_D1

value: Chow


title: A8_1_23_4

description:
Library name: A8_1_23_4
Cells cultured on 2D surface

value: Stiffness 150kPa ECM C2+C3+C4


title: KMS-27 shIRF4 Clone 20 20h Rep1

description: Library name: SAM24430068

value: Plasmacytoma

value: Tumor plasma cell

value: Dox 20h


title: Brain,7,Sucrose+JNK_D1

description: Library name: Brain,7,Sucrose+JNK_D1


title: A7_1_23_3

description:
Library name: A7_1_23_3
Cells cultured on 2D surface


title: KMS-27 shIRF4 Clone 20 Mock Rep1

description: Library name: SAM24430067

value: Mock


title: Liver.T0_2

description: Library name: L511_65

value: Liver


title: Adipose,7,Sucrose+JNK_D1

description: Library name: Adipose,7,Sucrose+JNK_D1


title: Liver.A5DA

description: Library name: L511_64

value: M


title: Liver.B4B9

description: Library name: L511_63


title: A6_1_23_2

description:
Library name: A6_1_23_2
Cells cultured on 2D surface

value: Bone Marrow


title: AMO-1 shNTC 24h Rep1

description: Library name: SAM24430066

value: Dox 24h


title: WAT.T0_1

description: Library name: L511_61

value: WAT


title: AMO-1 shIRF4 Cl. 4-3 24h Rep1

description: Library name: SAM24430063


title: Cortex.B4B9

description: Library name: L511_62

value: F


title: AMO-1 shNTC Mock Rep1

description: Library name: SAM24430065


title: A4_1_4_4

description:
Library name: A4_1_4_4
Cells cultured on 2D surface

value: Mesenchymal Stem Cells

value: Stiffness 150kPa ECM Collagen 4


title: Cortex.T0_2

description: Library name: L511_67


title: Liver,5,Sucrose+JNK_D1

description: Library name: Liver,5,Sucrose+JNK_D1

value: 10% Sucrose in drinking water


title: Adipose,5,Sucrose+JNK_D1

description: Library name: Adipose,5,Sucrose+JNK_D1

value: Adipose


title: Muscle,7,Sucrose+JNK_D1

description: Library name: Muscle,7,Sucrose+JNK_D1

value: Muscle


title: A5_1_234_1

description:
Library name: A5_1_234_1
Cells cultured on 2D surface


title: Brain,5,Sucrose+JNK_D1

description: Library name: Brain,5,Sucrose+JNK_D1

value: Brain

value: Chow


title: AMO-1 shIRF4 Cl. 4-3 16h Rep1

description: Library name: SAM24430062

value: Plasmacytoma

value: Dox 16h


title: AMO-1 shIRF4 Cl. 4-3 8h Rep1

description: Library name: SAM24430061

value: Tumor plasma cell

value: Dox 8h


title: WAT.B51B

description: Library name: L511_59

value: Stim


title: A3_1_4_3

description:
Library name: A3_1_4_3
Cells cultured on 2D surface


title: A2_1_4_2

description:
Library name: A2_1_4_2
Cells cultured on 2D surface


title: WAT.DDF3

description: Library name: L511_60

value: M


title: Muscle,4,Sucrose+JNK_D1

description: Library name: Muscle,4,Sucrose+JNK_D1


title: A1_1_4_1

description:
Library name: A1_1_4_1
Cells cultured on 2D surface

value: Bone Marrow


title: AMO-1 shIRF4 Cl. 4-3 Mock Rep1

description: Library name: SAM24430060

value: Mock


title: Liver,4,Sucrose+JNK_D1

description: Library name: Liver,4,Sucrose+JNK_D1

value: Liver


title: Kidney.T0_1

description: Library name: L511_58

value: Kidney

value: F


title: AMO-1 shIRF4 Cl. 1 24h Rep1

description: Library name: SAM24430059

value: Dox 24h


title: Kidney.DDF3

description: Library name: L511_57


title: Muscle,5,Sucrose+JNK_D1

description: Library name: Muscle,5,Sucrose+JNK_D1

value: 10% Sucrose in drinking water


title: Brain,4,Sucrose+JNK_D1

description: Library name: Brain,4,Sucrose+JNK_D1


title: AMO-1 shIRF4 Cl. 1 16h Rep1

description: Library name: SAM24430058


title: Adipose,4,Sucrose+JNK_D1

description: Library name: Adipose,4,Sucrose+JNK_D1

value: Adipose


title: Muscle,3,Sucrose+JNK_D1

description: Library name: Muscle,3,Sucrose+JNK_D1

value: Muscle


title: Subject 13

city: Denver

first: Camille

last: Moore

state: CO

address: 1400 Jackson St.

institute: National Jewish Health

description:
Library name: Subject 13
Bronchoalveolar lavage cells from healthy adult

data_processing:
Initial pre-processing of the 10 subjects’ 10X scRNA-seq data, including demultiplexing, alignment to the hg38 human genome, and UMI-based gene expression quantification, was performed using Cell Ranger (version 3.0, 10X Genomics)
Assembly: hg38
Supplementary files format and content: comma separated (.csv) matrix of raw counts. Rows are features and columns are cells.

source_name: Bronchoalveolar lavage cells

extract_protocol:
Enrolled subjects underwent flexible fiberoptic bronchoscopy and bronchoalveolar lavage with serial installation and aspiration of normal saline. Lavage fluid was centrifuged to pellet cells. Cell pellet was resuspended  at 1x10^6 cells per ml in PBS containing 0.04% bovine serum albumin.
Single cells were captured using The Chromium Box (10x Genomics, Pleasanton, CA). The Chromium Single Cell 3’ GEM, library, and gel bead kit PN-1000075 were used along with Bead Chip B PN-1000092 for cell capture and library construction. Libraries were sequenced with the Illumina NovaSEQ 6000 sequencer (Illumina, Inc., San Diego, CA) using an S4 flow cell.

tag: Sex

value: female

value: Bronchoalveolar lavage cells

tag: diagnosis

value: healthy


title: AMO-1 shIRF4 Cl. 1 8h Rep1

description: Library name: SAM24430057

value: Plasmacytoma


title: AMO-1 shIRF4 Cl. 1 Mock Rep1

description: Library name: SAM24430056

value: Tumor plasma cell


title: Cortex.T0_1

description: Library name: L511_55

value: Cortex


title: Cortex.DDF3

description: Library name: L511_54

value: Stim


title: Liver,3,Sucrose+JNK_D1

description: Library name: Liver,3,Sucrose+JNK_D1

value: Chow


title: Subject 12

description:
Library name: Subject 12
Bronchoalveolar lavage cells from healthy adult

value: male


title: Liver.T0_1

description: Library name: L511_53


title: Brain,3,Sucrose+JNK_D1

description: Library name: Brain,3,Sucrose+JNK_D1

value: Brain


title: O4, female, BPA, ATAC, rep5

city: Paris

first: Anne-Laure

last: Schang

state: Select Option

address: 4, Avenue de l'Observatoire

department: Faculté de Pharmacie

country: France

institute: Université Paris Cité

description: library name: Sample_19

data_processing:
Data were processed on the Galaxy platform (The Galaxy community, 2022).
After read trimming using Trimmomatic (Galaxy Version 0.36.5), the reads were aligned to the mm10 genome using Bowtie 2, (Galaxy Version 2.3.4.3+galaxy0) and duplicates were removed with RmDup (Galaxy Version 2.0.1).
Peak calling was carried out with MACS2 (Galaxy Version 2.2.7.1+galaxy0) for each group using pooled (n=4) bam files. The resulting four bed files were then merged.
After removing the mm10 blacklist (https://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/), 151,033 DNA regions (peaks) detected in at least one group were identified.
The number of reads per peak for each sample was determined using Bedtools MultiCovBed (Galaxy Version 2.29.0) and normalized to the library sizes.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Brain O4+ oligodendrocytes

extract_protocol:
Brain O4+ oligodendrocytes were isolated by magnetic cell sorting (Miltenyi). Nuclei were isolated from 50,000 cells and chromatin was tagmented during 30 min at 37°C using Tn5 (Illumina). DNA fragments were purified using MinElute columns (Qiagen).
Purified DNA fragements were subjected to a two-step amplification and tagging process with NEBnext High-Fidelity 2× PCR master mix (New England Biolabs). The resulting amplified DNA underwent double purification using 1.8 volumes of NucleoMag NGS Clean-up and Size Select beads (Macherey Nagel). The final libraries were checked for quality, quantified, multiplexed and sequenced on an Illumina NextSeq500 system (Illumina, San Diego, California, USA) at IGenSeq Platform (ICM, Paris, France).

tag: mouse strain

value: Brain O4+ oligodendrocytes

value: Post-natal day 16

value: BPA (40 µg.kg-1.day-1) from gestational day 7


title: Liver.DDF3

description: Library name: L511_52

value: Liver

value: M


title: O4, female, BPA, ATAC, rep4

description: library name: Sample_18


title: Healthy donor 2 fetal liver HSC

city: Seattle

first: Brandon

last: Hadland

state: WA

address: 1100 Fairview Avenue N., D2-115, P.O. Box 19024

institute: Fred Hutchinson Cancer Center

description:
Library name: Sample6
10x Genomics

data_processing:
The Cell Ranger 2.1.1 pipeline (10X Genomics) was used to align reads to the mm10 reference genome and generate feature barcode matrix, filtering low-quality cells using default parameters.
The Monocle (v.3.1.2.9) platform was used for downstream analysis, combining read-depth normalized data across samples where applicable.
Assembly: mm10/hg38
Supplementary files format and content: 10X Cell Ranger output files in filtered feature-barcode matrix: "genes.tsv" contains gene information, "barcodes.tsv" contains cellular barcodes, and "matrix.mtx" contains a sparse matrix of UMIs.
Supplementary files format and content: Monocle cell data set files: "SampleX.RDS" contains monocle cell data sets for sample(s) X imported from 10Xoutput files; "SampleX_P.RDS" contains cell data set for sample(s) X following pre-processing, dimensionality reduction, and clustering steps.

source_name: Fetal Liver

extract_protocol:
FACS-isolated primary cells or cultured cells harvested by trypsinization (for FL-EC) or pipetting (for co-cultured hematopoietic cells) were washed with PBS/0.04% ultrapure BSA, and resuspended in PBS/BSA for loading into the 10X Genomics Chromium Single Cell B Chip, and processed in the Chromium single cell controller.
The 10X Genomics Version 3.1 single cell 3’ kit was used to prepare single cell mRNA libraries for freshly isolated primary cells or FL-EC, while the 10X Genomics Version 3.1 with Feature Barcoding technology for Cell Surface Protein Sequencing was used for co-cultured cells. Both kits were used according to manufacturer protocols with the Index Kit T Set A. Sequencing was performed for pooled libraries from each sample on an Illumina NextSeq 500 using the 75 cycle, high output kit. For the human fetal liver samples, sorted cells were prepped via the 10X Genomics version 2 single cell 5' kit in accordance with manufacturers protocol with the Dual Index plate TT Set A. Samples were sequenced on an Illumina NovaSeq.

value: Hematopoietic cells, primary

value: Fetal Liver

tag: cell fraction


title: Adipose,3,Sucrose+JNK_D1

description: Library name: Adipose,3,Sucrose+JNK_D1

value: Adipose

value: 10% Sucrose in drinking water


title: Liver.B51B

description: Library name: L511_51

value: F


title: O4, female, BPA, ATAC, rep3

description: library name: Sample_17

value: female


title: Muscle,2,Sucrose+JNK_D1

description: Library name: Muscle,2,Sucrose+JNK_D1

value: Muscle


title: Subject 15

description:
Library name: Subject 15
Bronchoalveolar lavage cells from healthy adult

value: Bronchoalveolar lavage cells

value: healthy


title: Liver,2,Sucrose+JNK_D1

description: Library name: Liver,2,Sucrose+JNK_D1

value: Chow


title: O4, female, BPA, ATAC, rep2

description: library name: Sample_16


title: Subject 14

description:
Library name: Subject 14
Bronchoalveolar lavage cells from healthy adult


title: Kidney.B51B

description: Library name: L511_56

value: Kidney

value: Stim


title: Cortex.B51B

description: Library name: L511_50

value: Cortex


title: O4, female, BPA, ATAC, rep1

description: library name: Sample_15

value: Brain O4+ oligodendrocytes

value: Post-natal day 16


title: HT1080IFNb302

city: Fuzhou

first: Jun

last: Lu

address: Xierhuan Road No.156

institute: The 900th Hospital of Chinese PLA Logistic Support Forces

description:
Library name: sample5
Column name in fpkm_merged_count.xls: HT1080IFNb302

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: Trimmed sequence reads were mapped to Homo sapiens GRCh38 using HISAT2.
Supplementary files format and content: tab-delimited text file includes raw counts.

source_name: Tumor

growth_protocol: HT1080 were cultured in DMEM (high glucose) containing 10% fetal bovine serum, 100 units/mL penicillin, and 100 µg/mL streptomycin (Thermo Fisher Scientific) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen). 1 μg of total RNA was used for the construction of sequencing libraries.
Paired-end RNA-seq sequencing library was sequenced with the NovaSeq 6000 sequencer (2 × 150bp read length).

treatment_protocol: HT1080 cells were treated with human IFNβ at a concentration of 20 ng/mL (Sinobiological, China) for 24 hours.

value: Tumor

value: human fibrosarcoma cells


title: Brain,2,Sucrose+JNK_D1

description: Library name: Brain,2,Sucrose+JNK_D1

value: Brain


title: Subject 11

description:
Library name: Subject 11
Bronchoalveolar lavage cells from healthy adult

value: male


title: HT1080IFNb301

description:
Library name: sample4
Column name in fpkm_merged_count.xls: HT1080IFNb301


title: Adipose,2,Sucrose+JNK_D1

description: Library name: Adipose,2,Sucrose+JNK_D1

value: Adipose


title: Control exp 2 replicate 1

city: Leuven

first: Samantha

last: Pretto

address: ON4 Herestraat 49

department: Center for Cancer Biology

country: Belgium

institute: VIB-KU Leuven

description: Library name: SP_NT_8

data_processing:
Reads were aligned to the mus musculus reference genome GRCm39 using STAR (v2.7.10b) with default parameters.
Aligned reads were quantified using featureCounts (v2.0.1) in R (v4.3.3) with options -t gene and -s 2.
To reduce mice-to-mice variability, counts from replicate mice from the same experiment were merged prior to subsequent analyses.
Subsequent analyses were performed using DESeq2 package (v1.42.0).
Assembly: mm39; GRCm39
Supplementary files format and content: csv file of matrix containing all samples with raw counts after merging replicate samples (not normalized by library size)

source_name: CD90.1+ OT-I T cells in vitro activated

extract_protocol:
OT-I Cas9 knockin T cells where transduced with a lentiviral vector containing a non-targeting guide or a sgRNA targeting Elovl1. 3 days post transduction, transduced cells were sorted based on CD90.1 expression. Total RNA was isolated using the RNeasy Minikit (Qiagen) following the manufacturer's protocol and resuspended in RNase-free water.
Frozen RNA was shipped to Novogene for the Plant and Animal Eukaryotic Strand Specific mRNA (WOBI) service.

value: CD90.1+ OT-I T cells in vitro activated

tag: condition

value: Control


title: HT1080con3

description:
Library name: sample3
Column name in fpkm_merged_count.xls: HT1080con3


title: O4, male, BPA, ATAC, rep5

description: library name: Sample_14

value: BPA (40 µg.kg-1.day-1) from gestational day 7


title: Control exp 1 replicate 2

description: Library name: SP_NT_3


title: Control exp 2 replicate 2

description: Library name: SP_NT_9


title: Healthy donor 1 fetal liver HSC

description:
Library name: Sample5
10x Genomics

value: Hematopoietic cells, primary

value: Fetal Liver


title: O4, male, BPA, ATAC, rep4

description: library name: Sample_13


title: Control exp 1 replicate 1

description: Library name: SP_NT_2


title: HT1080con2

description:
Library name: sample2
Column name in fpkm_merged_count.xls: HT1080con2


title: O4, male, BPA, ATAC, rep3

description: library name: Sample_12


title: Muscle,1,Sucrose+JNK_D1

description: Library name: Muscle,1,Sucrose+JNK_D1

value: Muscle

value: 10% Sucrose in drinking water


title: Liver,1,Sucrose+JNK_D1

description: Library name: Liver,1,Sucrose+JNK_D1

source_name: Liver

value: Liver

value: Chow


title: HT1080IFNb303

description:
Library name: sample6
Column name in fpkm_merged_count.xls: HT1080IFNb303


title: Elovl1 KO exp 2 replicate 2

description: Library name: SP_ELO_13


title: HT1080con1

description:
Library name: sample1
Column name in fpkm_merged_count.xls: HT1080con1


title: O4, male, BPA, ATAC, rep2

description: library name: Sample_11


title: Brain,1,Sucrose+JNK_D1

description: Library name: Brain,1,Sucrose+JNK_D1


title: PXB Cells, PCSK9-EE, 3

description: Library name: NGSWGM009

data_processing:
A nf-core methyl-seq pipeline was used for initial read alignment and estimation of methylation calls using Bismark.
Initial quality control and low coverage filtering was performed using Methrix (DOI: 10.18129/B9.bioc.methrix). Here, we assessed genome-wide coverage for each sequencing sample and replicate concordance. At least two samples were included in each condition, which were then used for downstream differential CpG and methylated region analysis.
DSS (DOI: 10.18129/B9.bioc.DSS) was run to aggregate nearby differentially methylated CpGs into differentially methylated regions, with the following parameters: p_threshold = 1e-10, minCG = 3.
IGV was used to visualize methylation bedgraphs in the region surrounding selected DMRs.
Assembly: GRCh38
Supplementary files format and content: bedgraph, genome-wide CpG methylation
Library strategy: EM-seq

growth_protocol: Primary human hepatocytes isolated from mice with a chimeric humanized liver (PXB cells®) were obtained from Phoenix Bio. Pre-plated cells were kept in hepatocyte growth medium.

extract_protocol:
Genomic DNA was extracted from primary liver cells using simultaneous RNA and DNA extraction from cultured cells without splitting lysate protocol and reagents (Beckman Coulter).
Genomic DNA (gDNA) quality and quantification assessment was done using Qubit fluorometric quantification and fragment analyzer to measure DNA fragment lengths. Sequencing library was prepared using NEBNext® Enzymatic Methyl-seq Kit with input gDNA (200 ng) was sheared using Bioruptor Pico to an average fragment size of ~300bp. Sequencing was performed on an Illumina NovaSeq6000 using 150bp paired-end reads, resulting in at least 600 million read pairs per library. Two sequencing runs were merged for analysis.

treatment_protocol: LNP formulations were mixed with recombinant human ApoE3 (R&D Systems) and added onto cells at the desired concentration. The next day, Matrigel Basement Membrane Matrix (Corning) was overlayed on hepatocytes to a final concentration of 0.25 mg/ml.

value: PXB Cells

value: Primary Human Hepatocyte


title: Elovl1 KO exp 2 replicate 1

description: Library name: SP_ELO_12


title: PXB Cells, PCSK9-EE, 2

description: Library name: NGSWGM008


title: O4, male, BPA, ATAC, rep1

description: library name: Sample_10

value: Brain O4+ oligodendrocytes

value: Post-natal day 16


title: Elovl1 KO exp 1 replicate 2

description: Library name: SP_ELO_6


title: Adipose,1,Sucrose+JNK_D1

description: Library name: Adipose,1,Sucrose+JNK_D1


title: O4, female, control, ATAC, rep4

description: library name: Sample_09

value: female


title: Muscle,11,Sucrose+JNK_D1

description: Library name: Muscle,11,Sucrose+JNK_D1


title: PXB Cells, PCSK9-EE, 1

description: Library name: NGSWGM007


title: O4, female, control, ATAC, rep3

description: library name: Sample_08


title: Elovl1 KO exp 1 replicate 1

description: Library name: SP_ELO_5


title: PXB Cells, Effector only, 3

description: Library name: NGSWGM015

value: Effector Only


title: Brain,11,Sucrose+JNK_D1

description: Library name: Brain,11,Sucrose+JNK_D1

value: Brain


title: E9.5 Yolk Sac Trim71-KO

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: 10x Genomics

data_processing:
Cell Ranger 7.1
Assembly: Mm10 2020a
Supplementary files format and content: Seurat object, .rds format

source_name: E9.5 yolk sac

extract_protocol:
For developmental stage E7.5, one whole embryo of each genotype was used for sequencing. Single cells were isolated by digestion of E7.5 embryos with 0.25% Trypsin (Sigma-Aldrich) and 0.5 mM EDTA in PBS for 10 min at 37 °C, followed by mechanical dissociation by gentle resuspension through a 200 µl pipette tip and filtering through a 40 µm strainer into a 1.5 mL reaction tube. For E9.5 stage yolk sacs, cells isolated from two organs per genotype were pooled into one sample. Yolk sacs were digested with 100 mg/mL Collagenase D and 100 U/mL DNase I in 3% FCS/PBS for 30 min at 37 °C, diluted to 1.5 mL with PBS, minced through a 100 µm pore strainer and filtered through a 70 µm pore strainer into a 1.5 mL reaction tube. Cells isolated from E7.5 whole embryos or E9.5 yolk sacs in 1.5 mL reaction tubes were centrifuged (400g, 4 °C, 5 min) and completely loaded onto the Next GEM Chip G.
The 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) kit was used according to the manufacturer’s instructions. After GEM-RT cleanup, the cDNA amplification step was performed with 12 PCR cycles for all samples. The Sample Index PCR was performed with 16 cycles for E7.5 whole embryo samples or 10 cycles for E9.5 yolk sac samples.

value: E9.5 yolk sac


title: O4, female, control, ATAC, rep2

description: library name: Sample_07


title: Liver,11,Sucrose+JNK_D1

description: Library name: Liver,11,Sucrose+JNK_D1


title: Adipose,11,Sucrose+JNK_D1

description: Library name: Adipose,11,Sucrose+JNK_D1

value: Adipose


title: PXB Cells, Effector only, 2

description: Library name: NGSWGM014


title: Muscle,10,Sucrose+JNK_D1

description: Library name: Muscle,10,Sucrose+JNK_D1

source_name: Muscle


title: PXB Cells, PCSK9-EE, 2

data_processing:
We used the nf-core Methyl-Seq pipeline (https://zenodo.org/badge/latestdoi/124913037) to map sequencing reads to the reference genome (GRCh38) using Bismark v0.24.0 47, with the following parameters: igenomes_ignore = true, clip_r1 = 10, clip_r2 = 10, three_prime_clip_r1 = 10, three_prime_clip_r2 = 10, cytosine_report = true.
Multi-QC (10.1093/bioinformatics/btw354) reports were then generated from the stats files resulting from the Methyl-Seq pipeline.
Next, we used the R packages Methrix (DOI: 10.18129/B9.bioc.methrix) and DSS (DOI: 10.18129/B9.bioc.DSS) to filter the results from the Methyl-seq pipeline, and to call DMRs. We loaded the Bismark coverage files into Methrix objects using methrix::read_bedgraphs with the following parameters: pipeline = “bismark_cov”, stranded = FALSE, zero_based = FALSE, collapse_strands = FALSE, and filtered to keep only CpGs that meet a minimum 5x coverage threshold, across all libraries in the dataset. CpGs that are in the top 99.9% of coverage were also filtered out of the dataset, as these may represent mapping artifacts or repetitive regions.
Next, we used DSS::DMLTest to call significantly differentially methylated CpGs between the experimental and reference conditions, with the following parameter: smoothing = true.
Then we ran DSS::callDMR to aggregate nearby differentially methylated CpGs into differentially methylated regions, with the following parameters: p_threshold = 1e-10, minCG = 10. DMRs were further filtered by the average methylation difference between control and experimental conditions, with greater than 20% average difference DMRs retained.
Assembly: GRCh38
Supplementary files format and content: bedgraph of CpG methylation
Library strategy: EM-seq

extract_protocol:
Genomic DNA was extracted from primary liver cells using simultaneous RNA and DNA extraction from cultured cells without splitting lysate protocol and reagents (Beckman Coulter).
Genomic DNA was sheared to a target size of 350bp using a Covaris 96 AFA-Tube TPX plate. Sequencing libraries were then constructed from the sheared genomic DNA using the NEBNext Enzymatic Methyl-seq (EM-seq) kit plus NEBNext Multiplex Oligos for Enzymatic Methyl-seq, After methylation conversion, the Twist Human Methylome Hybrid Capture panel was used to enrich for regions of interest, following the recommended Twist protocol and libraries were then amplified and sequenced using an Illumina NovaSeq 6000 instrument to a read-depth of ~70 million read pairs per sample.


title: E9.5 Yolk Sac Trim71-WT

description: 10x Genomics


title: O4, female, control, ATAC, rep1

description: library name: Sample_06

value: Control


title: PXB Cells, Effector only, 1

description: Library name: NGSWGM013


title: O4, male, control, ATAC, rep5

description: library name: Sample_05

value: male


title: E7.5 Whole Embryo Trim71-WT

description: 10x Genomics

source_name: whole E7.5 embryo

value: whole E7.5 embryo


title: E7.5 Whole Embryo Trim71-KO

description: 10x Genomics


title: PXB Cells, PCSK9-EE, 1


title: O4, male, control, ATAC, rep4

description: library name: Sample_04


title: O4, male, control, ATAC, rep3

description: library name: Sample_03


title: cell_surface_protein, WT d7 rep 3 + Mr1KO d7 rep 3

city: Oxford

first: Shuailin

last: Li

address: Old Road Campus Research Building

country: United Kingdom

institute: University of Oxford

data_processing:
10x Genomics cellranger analysis pipelines were used to generate single cell gene counts. Reads from gene expression and TCR library were aligned to the mouse mm10 reference genome (version 2020-A) and GRCm38 Mouse V(D)J Reference-7.0.0 (May 17, 2022), respectively, and quantified using cellranger multi pipeline together with those from ADT library.
Assembly: mm10 (refdata-gex-mm10-2020-A from 10x Genomics)
Supplementary files format and content: CITE-seq: h5 files with raw counts and h5ad for processed data by scanpy
Supplementary files format and content: scTCR-seq: csv files with clonotype and TCR information

source_name: Lung

extract_protocol:
Sequencing libraries were generated using 10x Genomics Chromium Next GEM Single Cell 5’ Reagent kit v2 (Dual Index) following manufacturer’s instructions (CG000330 Rev D). ADT-labelled (BioLegend, Cat. No. 155861, 155863 and 199903) cells were loaded onto the Chromium iX (10x Genomics) at a concentration of ~1 x 106 cells/mL, with 50,000 cells loaded per channel. One channer was loaded per 2 mice lung samples.
Library generation was performed using Biomek FXP Laboratory Automation Workstation (Beckman Coulter) at MRC Weatherall Institute of Molecular Medicine Single-Cell Facility (WIMM, University of Oxford). Library quality and concentration was assessed using a Bioanalyzer (Agilent) and Qubit 2.0 Fluorometer (Thermo Fisher Scientific), respectively. Libraries were sequenced on an Illumina NovaSeq 6000 to a mean depth of 40,000 read pairs/cell for scRNA-seq, 10,000 read pairs/cell for Cite-seq and TCR-seq, performed at Novogene.
CITE-seq

value: Lung


title: cell_surface_protein, WT d3 rep 3 + Mr1KO d3 rep 3


title: PXB Cells, Effector only, 2


title: O4, male, control, ATAC, rep2

description: library name: Sample_02


title: Brain,10,Sucrose+JNK_D1

description: Library name: Brain,10,Sucrose+JNK_D1

source_name: Brain


title: Adipose,10,Sucrose+JNK_D1

description: Library name: Adipose,10,Sucrose+JNK_D1


title: Muscle,9,Sucrose

description: Library name: Muscle,9,Sucrose

value: Muscle


title: cell_surface_protein, WT d0 rep 3 + Mr1KO d0 rep 3


title: PXB Cells, Effector only, 1


title: cell_surface_protein, Mr1KO d7 rep 1 + Mr1KO d7 rep 2


title: Liver,9,Sucrose

description: Library name: Liver,9,Sucrose

value: 10% Sucrose in drinking water


title: Liver_PD1_biol_rep3

data_processing:
MAGeCK-VISPR (version 0.5.3) was used to process CRISPR/Cas9 screen sequencing data. MAGeCK ‘count’ module generated raw count table with sgRNA as rows and samples as columns. This table was normalized by 250 non-targeting control sgRNAs, and corrected for batches effects between different organs by Combat. Two samples were excluded after initial quality control. MAGeCK ‘mle’ module calculated beta score for each targeted gene to measure positive or negative selection.
Assembly: Lentiviral CRISPR gRNA Library
Supplementary files format and content: MAGeCK output containing batch corrected gRNA counts in each sample

source_name: PDAC (KPC_OVA ) Liver

extract_protocol:
OT-I Cas9 knockin T cells where transduced with a lentiviral metabolic CRISPR library for NGS. Transduced cells were selected based on CD90.1 expression and injected tail vein into recipient mice bearing hortotopic KPC_OVA tumors. The same day treatment with aPD-1 was started. 7 days post adoptive T cells transfer (ACT), mice were sacrificed and CD90.1+ OT-I T cells were sorted from the primary tumor, metastatic sites (Lung, Lver and peritoneal metastasis), lymphoid organs (draining and non-draining lymph nodes and spleen).
Illumina NextSeq500 Medium Output 150
Next generation sequencing (NGS) on sgRNA sequence integrated in the genomic DNA

value: PDAC (KPC_OVA ) Liver

value: CD90.1+ OT-I T cells

value: Cas9 Knockin OT-I transduced with CRISPR library


title: DS2U_NPC

first: Suraj

last: Upadhya

address: 415 Main St

institute: Broad Institute

data_processing:
Paired-end read FASTQ files were aligned to GRCh38 Genome Reference Consortium Human Reference 38 (hg38) using the ‘count’ method of CellRanger v8.0.1. 4
Assembly: GRCh38
Supplementary files format and content: Tab-separeted values files and matrix files

source_name: Neural Progenitor Cell

extract_protocol:
Three wells of NPCs per genotype were lifted off plates using accutase and pooled together to obtain 1-1.5 million cells for scRNA-seq cell preparation, following instructions from Illumina.
The cDNA library was made using the 10X Genomics Chromium Single Cell 3′ Library and Bead Kit v3.

value: Neural Progenitor Cell

value: Euploid


title: Liver,10,Sucrose+JNK_D1

description: Library name: Liver,10,Sucrose+JNK_D1

value: Liver

value: Chow


title: DS1_NPC

value: Trisomy 21


title: cell_surface_protein, Mr1KO d3 rep 1 + Mr1KO d3 rep 2


title: Lungs_PD1_biol_rep3

source_name: PDAC (KPC_OVA ) Lung

value: PDAC (KPC_OVA ) Lung


title: Brain,9,Sucrose

description: Library name: Brain,9,Sucrose

value: Brain


title: Liver_IgG_biol_rep3

value: IgG


title: Non-Sibling_T21_CA_3

city: Boulder

first: Meaghan

last: Courvan

address: 596 UCB

department: Biofrontiers

institute: University of Colorado, Boulder

description:
Cells treated with CDK8 inhibitor for 4.5 hours
T21_counts_combined.txt
sva_corrected_counts_NonSiblingT21.csv

data_processing:
Read trimming using bbduk (options: ktrim=r qtrim=r1, trimq=10, k=23 mink=11 hdist=1 maq=10 minlen=25 tpe tbo literal=AAAAAAAAAAAAAAAAAAAAAAA)
Reads were mapped to hg38 using hisat2
Reads over hg38 refseq gene annotations and ERCC "genome" were counted using featurecounts and then RPKM normalized. Highest average RPKM isoform (across replicates and treatments) was retained in cases where multiple isoform annotations existed
Tdfs were generated from trimmed BAM files using igvtools
SVA correction (Leek et al. Bionformatics 2012) was used to correct for batch effects in gene count data
Assembly: hg38
Supplementary files format and content: TDF files for gene count visualization were generated using igvtools
Supplementary files format and content: featurecounts output file containing both human (hg38) and ERCC gene counts
Supplementary files format and content: .csv files containing gene counts that have been corrected using SVA

source_name: EBV immortalized suspension cells

growth_protocol: Lymphoblastoid suspension cells were grown in RPMI medium supplemented with 20% fetal bovine serum, pennicilin/strep, and L-glutamine, in 37C incubators with 5% CO2

extract_protocol:
4.5 hours after vehicle or CA treatment, cells were collected, spun down, washed once in PBS, then resuspended in TRIzol reagent (Invitrogen, 15596026) and snap frozen. After all 3 biological replicates were collected, cell lysates in TRIzol were thawed and total RNA was extracted according to the manufacturer's protocol. RNA concentration was measured by Qubit and quality was verified using a TapeStation
Libraries prepped using 200 ng total RNA spiked with ERCC spike-in mix (Invitrogen #4456740) and the Zymo-Seq RiboFree Total RNA Library Kit (Zymo Research). Paired-end sequencing reads of 150 nucleotides were generated on a NovaSeq X.

treatment_protocol: Cells were split and plated on T75 flasks, allowed to recover for 24 hours, then media containing either vehicle (final concentration 0.01% DMSO) or Cortistatin A (100 nM) was added to each flask

value: EBV immortalized suspension cells

value: Non-sibling T21 (TIC0001672)

value: Lymphoblastoid cell line

value: 100 nM Cortistatin A


title: Adipose,9,Sucrose

description: Library name: Adipose,9,Sucrose

data_processing:
Raw sequencing data (.bcl) was converted to FASTQ with the Dragen Bio-IT platform (v3.9.5).
The quality of RNA-seq data was assessed by FastQC (v0.11.9).
Tissue bulk RNA-seq data were aligned and quantified using a standard protocol of Kallisto (v0.46.2) against Rattus norvegicus genome (mRatBN7.2)  downloaded from Ensembl official website
The output of Kallisto, both estimated counts and TPM (transcript per kilobase million)-based transcript-level expressions were then transformed into gene-level expressions using the Bioconductor package tximport (v1.22.0) with the tx2gene option set to connect transcripts to genes.
Assembly: mRatBN7.2
Supplementary files format and content: Tab-delimited Raw counts for every gene and samples

source_name: Adipose

extract_protocol: RNA sequencing library was prepared with Illumina Stranded Total RNA Prep and Ligation with Ribo-Zero Plus kit was used by following the standard protocol provided by the manufacturer

value: Adipose


title: cell_surface_protein, Mr1KO d0 rep 1 + Mr1KO d0 rep 2

value: Lung


title: Lungs_IgG_biol_rep3


title: cell_surface_protein, WT d7 rep 1 + WT d7 rep 2


title: Non-Sibling_T21_CA_1


title: Muscle,8,Sucrose

description: Library name: Muscle,8,Sucrose

value: Muscle

value: 10% Sucrose in drinking water


title: Mets_PD1_biol_rep3

source_name: PDAC (KPC_OVA ) Peritoneal metastasis

value: PDAC (KPC_OVA ) Peritoneal metastasis

value: CD90.1+ OT-I T cells

value: Cas9 Knockin OT-I transduced with CRISPR library


title: cell_surface_protein, WT d3 rep 1 + WT d3 rep 2


title: Liver,8,Sucrose

description: Library name: Liver,8,Sucrose

value: Liver


title: O4, male, control, ATAC, rep1

description: library name: Sample_01

value: Brain O4+ oligodendrocytes

value: Post-natal day 16

value: male

value: Control


title: Non-Sibling_T21_V_3

description:
Cells treated with vehicle for 4.5 hours
T21_counts_combined.txt
sva_corrected_counts_NonSiblingT21.csv

value: Trisomy 21

value: 0.1% DMSO


title: Brain,8,Sucrose

description: Library name: Brain,8,Sucrose

value: Brain

value: Chow


title: Mets_IgG_biol_rep3

value: IgG


title: Non-Sibling_T21_V_2

value: EBV immortalized suspension cells

value: Non-sibling T21 (TIC0001672)

value: Lymphoblastoid cell line


title: NDL_PD1_biol_rep3

source_name: PDAC (KPC_OVA ) Non-Draining Lymphnodes

value: PDAC (KPC_OVA ) Non-Draining Lymphnodes


title: Adipose,8,Sucrose

description: Library name: Adipose,8,Sucrose

value: Adipose

value: 10% Sucrose in drinking water


title: scTCR-seq, WT d7 rep 3 + Mr1KO d7 rep 3

value: Lung


title: NDL_IgG_biol_rep3

value: CD90.1+ OT-I T cells

value: Cas9 Knockin OT-I transduced with CRISPR library


title: Non-Sibling_T21_V_1


title: cell_surface_protein, WT d0 rep 1 + WT d0 rep 2


title: Muscle,7,Sucrose

description: Library name: Muscle,7,Sucrose

value: Muscle


title: Non-Sibling_T21_CA_2

value: 100 nM Cortistatin A


title: Liver,7,Sucrose

description: Library name: Liver,7,Sucrose

value: Liver


title: Sibling_T21_CA_3

description:
Cells treated with CDK8 inhibitor for 24 hours
T21_counts_combined.txt
sva_corrected_counts_SiblingT21_24h.csv

value: Sibling T21 (TIC001678)

value: Trisomy 21


title: DL_PD1_biol_rep3

source_name: PDAC (KPC_OVA ) Draining Lymphnodes

value: PDAC (KPC_OVA ) Draining Lymphnodes


title: scTCR-seq, WT d0 rep 3 + Mr1KO d0 rep 3


title: DL_IgG_biol_rep3


title: Brain,7,Sucrose

description: Library name: Brain,7,Sucrose

value: Brain

value: Chow


title: scTCR-seq, Mr1KO d7 rep 1 + Mr1KO d7 rep 2


title: Sibling_T21_CA_1

value: EBV immortalized suspension cells


title: Sibling_T21_CA_2


title: Sibling_T21_V_3

description:
Cells treated with vehicle for 24 hours
T21_counts_combined.txt
sva_corrected_counts_SiblingT21_24h.csv

value: 0.1% DMSO


title: scTCR-seq, Mr1KO d3 rep 1 + Mr1KO d3 rep 2


title: Spleen_IgG_biol_rep3

source_name: PDAC (KPC_OVA ) Spleen

value: PDAC (KPC_OVA ) Spleen

value: IgG


title: Adipose,7,Sucrose

description: Library name: Adipose,7,Sucrose

value: Adipose


title: Spleen_PD1_biol_rep3


title: scTCR-seq, Mr1KO d0 rep 1 + Mr1KO d0 rep 2


title: Tumor_PD1_biol_rep3

source_name: PDAC (KPC_OVA ) Primary tumor

value: PDAC (KPC_OVA ) Primary tumor


title: Sibling_T21_V_2

value: Lymphoblastoid cell line


title: scTCR-seq, WT d7 rep 1 + WT d7 rep 2

value: Lung


title: Muscle,6,Sucrose

description: Library name: Muscle,6,Sucrose

value: 10% Sucrose in drinking water


title: Sibling_T21_V_1


title: Tumor_IgG_biol_rep3

value: CD90.1+ OT-I T cells

value: Cas9 Knockin OT-I transduced with CRISPR library


title: Liver,6,Sucrose

description: Library name: Liver,6,Sucrose

value: Liver


title: scTCR-seq, WT d3 rep 1 + WT d3 rep 2


title: Brain,6,Sucrose

description: Library name: Brain,6,Sucrose


title: scTCR-seq, WT d3 rep 3 + Mr1KO d3 rep 3


title: LSEC5

city: Montreal

first: Alain

last: Pacis

state: QC

address: 1010 Sherbrooke #1800

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

data_processing:
Adaptor sequences and low quality score bases (Phred score < 30) were first trimmed using Trimmomatic (Bolger et al., 2014).
The resulting reads were aligned to the GRCh38 human reference genome assembly, using STAR (Dobin et al., 2012).
Read counts were obtained using HTSeq (Anders et al., 2015) with parameters -m intersection-nonempty -stranded=reverse.
Assembly: GRCh38
Supplementary files format and content: rawCountMatrix.tsv

source_name: DR-LSCC

growth_protocol: LSCC were maintained in complete media containing DMEM media supplemented with 10% fetal bovina serum, non-essential aminoacids, and antibiotics in a humidifed atmposphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNeasy mini Kit (Qiagen) was used to isolate and purify the RNA from cells according to the manufacturer’s guidelines
The TruSeq Stranded Total RNA with Illumina Ribo-Zero Plus rRNA Depletion protocol is optimized for 100 ng  of intact RNA
RNA libraries for RNA-seq were prepared using the TruSeq rRNA Depletion protocol (Illumina) according to the manufacturer's guidelines

treatment_protocol:
LSCC were monthly exposed to escalating doses of docetaxel. LSCC were exposed to increasing doses (50nM, 100nm, 200nM and 400nM) for up to 4 months.
LSCC were exposed to docetaxel-enriched complete media for 3 days followed by a 3-day exposure of complete media with no docetaxel.

value: DR-LSCC

value: LSEC


title: T0_biol_rep3

source_name: in vitro T cells day of adoptive T cell transfer


title: Adipose,6,Sucrose

description: Library name: Adipose,6,Sucrose


title: scTCR-seq, WT d0 rep 1 + WT d0 rep 2


title: LSEC4


title: T0_biol_rep2

value: in vitro T cells day of adoptive T cell transfer


title: Muscle,5,Sucrose

description: Library name: Muscle,5,Sucrose

value: Muscle


title: scRNA-seq, WT d7 rep 3 + Mr1KO d7 rep 3


title: scRNA-seq, WT d3 rep 3 + Mr1KO d3 rep 3


title: LSEC2


title: Liver,5,Sucrose

description: Library name: Liver,5,Sucrose

source_name: Liver

value: Chow


title: Tumor_PD1_biol_rep2


title: LSEC3


title: LSEC1


title: Adipose,5,Sucrose

description: Library name: Adipose,5,Sucrose


title: Spleen_PD1_biol_rep2


title: scRNA-seq, Mr1KO d7 rep 1 + Mr1KO d7 rep 2


title: Lungs_IgG_biol_rep2

value: PDAC (KPC_OVA ) Lung


title: LSCC5

value: LSCC


title: LSCC4


title: scRNA-seq, Mr1KO d3 rep 1 + Mr1KO d3 rep 2


title: Spleen_IgG_biol_rep2

value: PDAC (KPC_OVA ) Spleen


title: Muscle,4,Sucrose

description: Library name: Muscle,4,Sucrose

source_name: Muscle


title: scRNA-seq, Mr1KO d0 rep 1 + Mr1KO d0 rep 2


title: Mets_IgG_biol_rep2

value: PDAC (KPC_OVA ) Peritoneal metastasis

value: IgG


title: scRNA-seq, WT d7 rep 1 + WT d7 rep 2


title: Brain,4,Sucrose

description: Library name: Brain,4,Sucrose

value: Brain


title: LSCC2


title: Liver,4,Sucrose

description: Library name: Liver,4,Sucrose


title: Tumor_IgG_biol_rep2

value: PDAC (KPC_OVA ) Primary tumor


title: scRNA-seq, WT d3 rep 1 + WT d3 rep 2

value: Lung


title: Liver_IgG_biol_rep2

value: PDAC (KPC_OVA ) Liver


title: Adipose,4,Sucrose

description: Library name: Adipose,4,Sucrose

value: Adipose

value: 10% Sucrose in drinking water


title: DL_IgG_biol_rep2

value: PDAC (KPC_OVA ) Draining Lymphnodes

value: CD90.1+ OT-I T cells

value: Cas9 Knockin OT-I transduced with CRISPR library


title: LSCC1

value: DR-LSCC


title: Muscle,3,Sucrose

description: Library name: Muscle,3,Sucrose

value: Muscle


title: DL_PD1_biol_rep2


title: lung mait cells, PR8 IAV d13, rep 3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. 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 the clean data were calculated. All the downstream analyses were based on the clean data with high quality. mm10 was used as the reference genome. Index of the reference genome was built usingHisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: mm10
Supplementary files format and content: comma-delimited csv file with raw counts for each sample and gene annotation for each gene

extract_protocol:
RNA extraction was performed by single column centrifugation using the RNeasy® Plus Micro Kit (Qiagen, Cat No. 74034) following the manufacturer’s protocol. RNA integrity was assessed by Agilent High Sensitivity RNA ScreenTape Assay on an Agilent 4200 TapeStation following the manufacturer’s protocol (Agilent, Cat. No. 5067-5579, 5580 and 5581).
Total RNA was subsequently submitted to Novogene following their sample preparation and shipping instructions. All further laboratory work was performed by Novogene using their commercial protocol. RNA was reverse transcribed and cDNA amplified by in vitro transcription with the TaKaRa SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TaKaRa, Cat. No. 634889, for MAIT cell after PR8 IAV challenge), or a low input method using NEB Next® Ultra RNA Library Prep Kit for Illumina® (NEB, Cat. No. 7530, for MAIT cell after bleomycin challenge), or NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, Cat. No. 7770, for total lung RNA-seq).

value: MAIT cell


title: DR_LSCC5


title: scRNA-seq, WT d0 rep 3 + Mr1KO d0 rep 3


title: Brain,5,Sucrose

description: Library name: Brain,5,Sucrose

value: Chow


title: Liver,3,Sucrose

description: Library name: Liver,3,Sucrose

value: Liver


title: lung mait cells, PR8 IAV d13, rep 2


title: DR_LSCC4


title: DR_LSCC3


title: NDL_IgG_biol_rep2

value: PDAC (KPC_OVA ) Non-Draining Lymphnodes


title: lung mait cells, PR8 IAV d13, rep 1


title: NDL_PD1_biol_rep2


title: LSCC3

value: LSCC


title: Brain,3,Sucrose

description: Library name: Brain,3,Sucrose


title: lung mait cells, PR8 IAV d7, rep 3


title: DR_LSCC1


title: Mets_PD1_biol_rep2

value: PDAC (KPC_OVA ) Spleen


title: lung mait cells, PR8 IAV d7, rep 2


title: DR_LSCC2


title: Liver_PD1_biol_rep2

description:
Liver_PD1_rep2
sample excluded after initial quality control


title: Muscle,2,Sucrose

description: Library name: Muscle,2,Sucrose


title: scRNA-seq, WT d0 rep 1 + WT d0 rep 2


title: Liver,2,Sucrose

description: Library name: Liver,2,Sucrose


title: 22ALA-CART CD8, (+) Antigen, 30 min, biol rep 3

city: AURORA

first: Etienne

last: Danis

department: Cancer Center

institute: University of Colorado, Denver - Anschutz Medical Campus

data_processing:
The quality of the fastq files was accessed using FastQC  (v.0.11.8), , FastQ Screen (v.0.13.0), and MultiQC (v.1.8)
Illumina adapters and low-quality reads were filtered out using BBDuk (v. 38.87).
Trimmed fastqc files were aligned to the hg38 human reference genome and aligned counts per gene were quantified using STAR (v.2.7.9a)
Differential gene expression analysis was performed using the DESeq2 package.
Pathway enrichment analysis was performed using GSEA and IPA.
Assembly: hg38
Supplementary files format and content: Text file containing raw data matrix

source_name: blood

growth_protocol: CAR T cells were maintained in AIM-V medium supplemented with 5% heat-inactivated FBS, 100 U/mL penicillin, 100 U/mL streptomycin, 5 mL GlutaMax, 10mM HEPES, and 40IU/mL IL-2.

extract_protocol:
RNA was extracted using Qiagen RNeasy mini kit according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using Tecan Universal Plus mRNA-Seq according to the manufactuer's protocol.

treatment_protocol: CAR4 and CAR8 cells were stimulated with 22Fc-antigen at 3ug/mL coated 24-well plates for 30mins.

value: blood

value: CD4 T cell

value: (+) Antigen


title: Lungs_PD1_biol_rep2

value: PDAC (KPC_OVA ) Lung


title: Brain,2,Sucrose

description: Library name: Brain,2,Sucrose

value: Brain


title: Lungs_PD1_biol_rep1


title: lung mait cells, PR8 IAV d7, rep 1

source_name: Lung

value: Lung


title: Adipose,2,Sucrose

description: Library name: Adipose,2,Sucrose

value: Adipose

value: 10% Sucrose in drinking water


title: lung mait cells, PR8 IAV d5, rep 3


title: Lungs_IgG_biol_rep1

value: CD90.1+ OT-I T cells

value: Cas9 Knockin OT-I transduced with CRISPR library

value: IgG


title: 22ALA-CART CD8, (+) Antigen, 30 min, biol rep 1


title: lung mait cells, PR8 IAV d5, rep 2

value: MAIT cell


title: Mets_PD1_biol_rep1

value: PDAC (KPC_OVA ) Peritoneal metastasis


title: Muscle,1,Sucrose

description: Library name: Muscle,1,Sucrose

value: Muscle

value: Chow


title: Adipose,3,Sucrose

description: Library name: Adipose,3,Sucrose


title: lung mait cells, PR8 IAV d3, rep 3


title: 22ALA-CART CD4, (+) Antigen, 30 min, biol rep 2


title: Brain,1,Sucrose

description: Library name: Brain,1,Sucrose

source_name: Brain


title: 22ALA-CART CD4, (+) Antigen, 30 min, biol rep 1


title: Adipose,1,Sucrose

description: Library name: Adipose,1,Sucrose


title: 22BBz CD8, (+) Antigen, 30 min, biol rep 3


title: NDL_IgG_biol_rep1

value: PDAC (KPC_OVA ) Non-Draining Lymphnodes


title: NDL_PD1_biol_rep1


title: Muscle,11,Sucrose

description: Library name: Muscle,11,Sucrose


title: lung mait cells, PR8 IAV d3, rep 2


title: lung mait cells, PR8 IAV d3, rep 1


title: 22ALA-CART CD8, (+) Antigen, 30 min, biol rep 2


title: 22BBz CD8, (+) Antigen, 30 min, biol rep 2


title: lung mait cells, PR8 IAV d0, rep 3


title: Liver,11,Sucrose

description: Library name: Liver,11,Sucrose

value: Liver


title: Liver,1,Sucrose

description: Library name: Liver,1,Sucrose


title: 22ALA-CART CD4, (+) Antigen, 30 min, biol rep 3

value: blood


title: 22BBz CD8, (+) Antigen, 30 min, biol rep 1

value: CD4 T cell


title: DL_IgG_biol_rep1

value: PDAC (KPC_OVA ) Draining Lymphnodes


title: lung mait cells, PR8 IAV d0, rep 2


title: lung mait cells, PR8 IAV d5, rep 1


title: Spleen_PD1_biol_rep1

value: PDAC (KPC_OVA ) Spleen


title: DL_PD1_biol_rep1


title: 22BBz CD4, (+) Antigen, 30 min, biol rep 2

value: (+) Antigen


title: Brain,11,Sucrose

description: Library name: Brain,11,Sucrose

value: Brain


title: 22BBz CD4, (+) Antigen, 30 min, biol rep 3


title: lung mait cells, PR8 IAV d0, rep 1

value: Lung


title: Spleen_IgG_biol_rep1


title: Mets_IgG_biol_rep1

description:
Mets_IgG_rep1
sample excluded after initial quality control


title: lung mait cells, bleomycin d28, rep 3


title: Muscle,10,Sucrose

description: Library name: Muscle,10,Sucrose

value: 10% Sucrose in drinking water


title: lung mait cells, bleomycin d28, rep 2


title: 22BBz CD4, (+) Antigen, 30 min, biol rep 1


title: Tumor_PD1_biol_rep1

value: PDAC (KPC_OVA ) Primary tumor

value: CD90.1+ OT-I T cells


title: 22ALA-CART CD8, (-) Antigen, 30 min, biol rep 3

value: CD8 T cell

value: (-) Antigen


title: Brain,10,Sucrose

description: Library name: Brain,10,Sucrose


title: Adipose,10,Sucrose

description: Library name: Adipose,10,Sucrose

value: Adipose


title: 22ALA-CART CD8, (-) Antigen, 30 min, biol rep 1


title: lung mait cells, bleomycin d28, rep 1

value: MAIT cell


title: lung mait cells, bleomycin d21, rep 3


title: T0_biol_rep1

value: in vitro T cells day of adoptive T cell transfer

value: Cas9 Knockin OT-I transduced with CRISPR library


title: Muscle,9,Control

description: Library name: Muscle,9,Control

value: Muscle

value: Tap water

value: Chow


title: lung mait cells, bleomycin d21, rep 2


title: Adipose,11,Sucrose

description: Library name: Adipose,11,Sucrose


title: Well P1-12G

city: Worcester

first: Summer

middle: B

last: Thyme

address: 55 N Lake Ave

institute: UMass Chan

description: Library name: P1-12G

data_processing:
Demultiplexing, trimming, alignment, filtering, and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci-RNA-seq3_pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 (Lawson et al. 2020).
Assembly: GRCz11
Supplementary files format and content: RDS containing Seurat object with cell-level features, counts, and barcodes
Library strategy: sci-RNA-seq

organism: Danio rerio

source_name: 6 dpf head

growth_protocol: Sci-RNA-seq was conducted following the “Tiny-Sci” protocol (Martin et al. 2023). Briefly, Tg(elavl3:KalTA4) fish were crossed with Tg(4xUAS-hmgn6) fish to produce wildtype, elavl3:KalTA4, 4xUAS-hmgn6, and elavl3:KalTA4; 4xUAS-hmgn6 offspring. At 6 dpf, larvae were anesthetized with MS-222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.

extract_protocol:
tiny sci sci-RNA-seq protocol
Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl lysis buffer B in DNA LowBind tubes (Eppendorf, 002431021). Heads were homogenized with a tissue homogenizer at 1 second intervals for 30-45 seconds until no clumps remained. Following fixation with ice-cold methanol and dithiobis (succinimidyl propionate) (DSP, Thermo Fisher, 22586), nuclei were resuspended in sucrose PBS TritonX MgCl2 (SPBSTM) and sonicated for 12 seconds on low at 4°C using a Bioruptor® Pico (Diagenode). Nuclei were resuspended in SPBSTM with dNTPs, and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate (Eppendorf, 0030129512).
Reverse transcription, ligation, final distribution, second-strand synthesis, protease digestion, tagmentation, PCR amplification, and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes (Martin et al. 2023). Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription, ligation, and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1, 10 cycles for Index, and 48 cycles for Read2.

value: 6 dpf head

tag: well

tag: rtindex

value: GGTACCGGCA


title: lung mait cells, bleomycin d21, rep 1


title: 22ALA-CART CD4, (-) Antigen, 30 min, biol rep 2

value: blood


title: Well P1-12F

description: Library name: P1-12F

value: CATTCGACGG


title: Brain,9,Control

first: Hong

last: Yang

institute: KTH Royal Institute of Technology/Science For Life Laboratory

description: Library name: Brain,9,Control

value: Brain


title: lung mait cells, bleomycin d14, rep 3

value: Lung


title: 22ALA-CART CD4, (-) Antigen, 30 min, biol rep 1


title: lung mait cells, bleomycin d14, rep 2


title: Well P1-12E

description: Library name: P1-12E

value: AACCATTGGA


title: 22BBz CD8, (-) Antigen, 30 min, biol rep 3


title: Adipose,9,Control

description: Library name: Adipose,9,Control


title: Tumor_IgG_biol_rep1

value: PDAC (KPC_OVA ) Primary tumor

value: CD90.1+ OT-I T cells

value: IgG


title: Muscle,8,Control

description: Library name: Muscle,8,Control


title: 22ALA-CART CD8, (-) Antigen, 30 min, biol rep 2

value: CD8 T cell

value: (-) Antigen


title: Well P1-12D

description: Library name: P1-12D

value: CGAACGCCGG


title: Well P1-12H

description: Library name: P1-12H

value: TAACTGGTTA


title: lung mait cells, bleomycin d14, rep 1

value: MAIT cell


title: Liver,10,Sucrose

description: Library name: Liver,10,Sucrose

value: Liver

value: 10% Sucrose in drinking water


title: lung mait cells, bleomycin d7, rep 3


title: Well P1-12C

description: Library name: P1-12C

value: 6 dpf head

value: GACCTTGATA


title: Liver,8,Control

description: Library name: Liver,8,Control

value: Tap water

value: Chow


title: Well P1-12B

description: Library name: P1-12B

value: TGGTCAGCCA


title: 22BBz CD8, (-) Antigen, 30 min, biol rep 2

value: blood


title: Liver,9,Control

description: Library name: Liver,9,Control


title: Brain,8,Control

description: Library name: Brain,8,Control

value: Brain


title: 22BBz CD8, (-) Antigen, 30 min, biol rep 1


title: 22ALA-CART CD4, (-) Antigen, 30 min, biol rep 3


title: 22BBz CD4, (-) Antigen, 30 min, biol rep 3


title: Well P1-12A

description: Library name: P1-12A

value: TTATTCATTC


title: lung mait cells, bleomycin d7, rep 2

value: Lung


title: 22BBz CD4, (-) Antigen, 30 min, biol rep 2


title: lung mait cells, bleomycin d3, rep 3


title: Well P1-11H

description: Library name: P1-11H

value: ACCTGGCCAA


title: lung mait cells, bleomycin d3, rep 2


title: Well P1-11G

description: Library name: P1-11G

value: AACCTGGTCT