title: Batch1_Patient11600-15149_BF10_2

description:
BF10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BF11_1

status: Public on Nov 01 2023

type: SRA

city: Oxford

first: Ahmed

middle: Ashour

last: Ahmed

state: Oxfordshire

address: John Radcliffe Hospital, Headley way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
BF11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv

library_source: transcriptomic single cell

data_processing:
Paired-end reads from Illumina NextSeq 500 were processed and mapped using STAR
The following filters were used to eliminate cells with (1) UMI counts < 10,000 and (2) gene counts < 200
Removed genes detected in < 3 cells
Assembly: UCSC hg19
Supplementary files format and content: Gene-cell matrix table containing transcript counts for every gene in every cell for each sample in batch1
Supplementary files format and content: Gene-cell matrix table containing transcript counts for every gene in every cell for each sample in batch2

molecule: polyA RNA

organism: Homo sapiens

source_name: Fallopian tube

growth_protocol: Fallopian tube WNT/β-catenin signaling reporter organoids were established from patient-derived cells, and expanded for 4-7 passages (each passage ~ 12 days). Endogenous WβA and non-WβA cells were isolated by FACS into RNA lysis buffer.

extract_protocol:
Isolated WβA or non-WβA cells were sorted into 96-well plates containing 4 μl lysis buffer supplemented with 0.1 μl RNase inhibitor (Clonetech), 1.9 μl 0.4% Triton X-100, 1 μl 10 μM 5‘-biotinylated oligo-dT30VN (IDT) and 1 μl 10 mM dNTP (Thermo Scientific). Cells were sorted at one cell per well, with bulk controls (10 cells) and empty well controls (0 cells) included for each plate. Plates were snap frozen on dry ice and stored at - 80 degrees C for less than 4 weeks.
Single cell cDNA synthesis and library generation were performed according to the SMART-seq2 protocol (Picelli et al., 2014), as previously described (Hu et al., 2020). Briefly, cells were lysed by removing plates from  -80 0C and heating at 72 0C for 3 min. Plates were then placed at 4 0C before adding the reverse transcription mix containing 5’-biotinylated TSO (Qiagen). PCR products were cleaned up using 0.8:1 Ampure XP beads (Beckman Coulter) with Biomek FxP Laboratory Automation Workstation (Biomek). Quality of single-cell cDNA was tested using TapeStation, as well as by single cell qPCR for GAPDH or ACTB using the QuantiNova SYBR Green PCR Kit (Qiagen). cDNA concentration was measured using Quant-iTTM PicoGreenTM dsDNA Assay Kit (Invitrogen) on the CLARIOstar Plate Reader (BMG Labtech). Wells with CT values of GAPDH or ACTB below 20 were selected as wells with good quality cDNA. Libraries from single cell cDNA were generated using miniaturized Nextera XT (Illumina) protocol (Mora-Castilla et al., 2016) with Mosquito HTS (TTP LabTech), in 384-well Endure plate (Life Technology). Library sequencing was performed by Novogene.

tag: tissue

value: Fallopian tube


title: Donor 9429 endogenous GIRK2, alcohol-chronic, batch a, bio rep 3

city: New York

first: Paul

last: Slesinger

state: NY

address: 1425 Madison Ave

department: Neuroscience

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic

data_processing:
Raw reads were assessed for quality using FastQC (version 0.11.8) before and after adapter sequence trimming by Cutadapt (version 4.1).
Reads were pseudoaligned using Salmon (version 0.13.1) for estimation of normalized gene expression (TPM, i.e. transcript per million).
Reads were also aligned to the human reference genome (Gencode version 28) and quantified for gene read counts, both in STAR (version 2.5.3a).
For differential gene expression analyses, read counts were modelled in the linear mixed model using batch, sex and donor information as the random effect terms by the R (version 4.1.0) package "variancePartition" (version 1.28.0).
Assembly: hg38
Supplementary files format and content: "star_gene.tsv" includes reads counts for genes (in rows) across samples (in columns)
Supplementary files format and content: salmon_gene.tsv includes TPM values for genes (in rows) across samples (in columns)

molecule: total RNA

growth_protocol: Doxycycline-inducible transcription factor NGN2 with neuomycin selection and rt-TA lentiviruses were used on neural progenitor cells. After dox-induction and antibiotic selection, cells were grown in Neurobasal medium with B27 supplement up to 14 days post-induction, then transitioned to Neurobasal Plus medium.

extract_protocol:
Total RNA was extracted from fresh frozen cell pellet samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions

treatment_protocol: 17 mM ethanol exposure began at 21 days post-induction, through harvest at 42 days post-induction. EtOH was supplemented daily to account for evaporation.

tag: cell line

tag: cell type

value: NGN2 neurons

tag: genotype

value: isoCTL

tag: treatment

value: Chronic

tag: upregmethod

value: Lenti


title: shKras,dox,10days,HTO

first: ZHUXUAN

last: LI

address: 417 E 68th St

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
FASTQ files of single-cell RNA-sequencing data generated on the 10X Chromium platform were processed using the standard CellRanger pipeline (version 5.0.0). Reads were aligned to a custom GRCm38 / mm10 reference including the tdTomato, GFP, and mKate transgenes used in this study. Cell-gene count matrices were analyzed using a combination of published packages and custom scripts centered around the scanpy / AnnData ecosystem. Single-cell RNA-sequencing datasets from GFPshRNA KP LUAD tumors, MRTX1133-treated KP LUAD tumors, and lung regeneration experiments were analyzed separately using the same workflows.  Single-cell RNA-sequencing data from treated and control replicates were dehashed and compiled into a combined count matrix. Cells with less than 500 UMIs, more than 20% mitochondrial UMIs, and low complexity based on the number of detected genes vs. number of UMIs were removed. Doublets were filtered using scrublet. UMI counts were normalized using the size factor approach described by Lun et al. .  Highly variable features were selected using a variance stabilizing transformation and dimensionality reduction was performed on normalized, log2-transformed count data using principal component analysis. The dimensionality reduced count matrices were used as input for UMAP-embedding and unsupervised clustering with the leiden algorithm; bbknn was used to control for batch effects.
Supplementary files format and content: mm10
Supplementary files format and content: matrix files

organism: Mus musculus

source_name: lung

extract_protocol:
To dissociate tumors into single-cell suspensions, primary tumors were finely chopped with scissors and incubated with digestion buffer containing collagenase IV (#17104019, ThermoFisher Scientific, 0.1 U/ml), dispase (#354235, Corning, 0.6 U/ml), and DNase I (#69182–3; Sigma Aldrich, 10 U/ml). For dissociating normal lung epithelial cells, digestion buffer was administrated intratracheally into the lung as described before (27). Following enzymatic dissociation, samples were washed with 2% heat-inactivated FBS in S-MEM (#11380037, Thermo Fisher Scientific), filtered through a 100 μm cell strainer (#431752, Corning), and centrifuged at 1500 rpm for 5 min at 4 °C. The supernatant was removed, and the pellet was resuspended in lysis buffer (#555899, BD Biosciences) to remove red blood cells. Cells were passed through a 40 μm strainer (#431750, Corning) and centrifuged at 1500 rpm for 5 min at room temperature. Cells were resuspended in 2% of heat-inactivated FBS in PBS. Cell suspensions were blocked for 5 min at 4 °C with rat anti-mouse CD16/CD32 (#553142, Mouse BD Fc Block, BD Biosciences) in FACS buffer, and incubated for 30 min with a mix of four APC-conjugated antibodies binding CD45 (#103112, Biolegend), CD31 (#102410, Biolegend), CD11b (#101212, Biolegend), F4/80 (#123116, BioLegend), CD19 (#115512, Biolegend), and TER-119 (#116212, Biolegend). 300 nM DAPI was added as a live-cell marker. Individual cancer cell suspensions were incubated for 30 min with hashtag oligonucleotide-conjugated antibodies in addition to FACS antibodies.
Sorted cell suspensions were prepared for scRNA-seq using the 3′ v3 10X Genomics Chromium platform according to manufacturer’s instructions. Briefly, sorted cells were washed once with PBS containing 1% bovine serum albumin (BSA) and resuspended in PBS containing 1% BSA to a final concentration of 700–1,300 cells per μl. The viability of cells in all experiments was above 80%, as confirmed with 0.2% (w/v) Trypan Blue staining (Countess II, Invitrogen). Cells were captured in droplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken, and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification as per manufacturer’s instructions. Between 20,000 to 25,000 cells were targeted for each droplet formulation lane. Samples were multiplexed together in the lanes following the TotalSeq B cell hashing protocol. Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles).

value: lung

value: primary lung tumor cells


title: shKras,dox,3days,HTO


title: Batch1_Patient11600-15149_BF10_1

description:
BF10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: subq,MRTX,BFPpos

source_name: subcutanous tumors

value: subcutanous tumors

value: KP tumor cells


title: Donor 9492 endogenous GIRK2, alcohol-chronic, batch a, bio rep 1


title: subq,MRTX,BFPneg


title: Batch1_Patient11600-15149_BF09_2

description:
BF09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 553 upregulated GIRK2, alcohol-naïve, batch b, bio rep 3

value: Naïve

value: CRISPRa


title: Donor 553 upregulated GIRK2, alcohol-naïve, batch b, bio rep 2


title: Batch1_Patient11600-15149_BF08_2

description:
BF08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BF09_1

description:
BF09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BF08_1

description:
BF08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: shKras,dox,7days

value: primary lung epithelial cells


title: KP,mrtx,20days


title: Batch1_Patient11600-15149_BF07_2

description:
BF07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 553 upregulated GIRK2, alcohol-naïve, batch a, bio rep 2


title: shKras,dox,20days


title: Donor 553 upregulated GIRK2, alcohol-naïve, batch b, bio rep 1


title: shKras,dox,10days


title: Donor 553 upregulated GIRK2, alcohol-naïve, batch a, bio rep 1


title: Donor 9429 endogenous GIRK2, alcohol-chronic, batch a, bio rep 2


title: Donor 553 upregulated GIRK2, alcohol-chronic, batch b, bio rep 3


title: KP,mrtx,5days


title: Batch1_Patient11600-15149_BF06_1

description:
BF06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: shKras,dox,3days


title: Donor 553 upregulated GIRK2, alcohol-chronic, batch b, bio rep 2


title: shKras,dox,5days


title: Batch1_Patient11600-15149_BF07_1

description:
BF07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 553 upregulated GIRK2, alcohol-chronic, batch b, bio rep 1


title: lung tumor, cisplatin, rep 5

data_processing: PDXes and autochthonous KP LUAD tumors were FACS-isolated, RNA was extracted, and libraries were prepared for SMARTerSeq2, n = 3 mice/group. FASTQ files were processed using the standard DESeq2 pipeline (version 1.24.0). Reads were aligned to the GRCm38 mouse genome. Count matrices were generated was performed using DESeq2. Data were filtered to only include genes with 10 or more counts in 2 or more samples. The significance of differential expression between vehicle and treatment groups was quantified by one-way ANOVA.

source_name: Lung

value: Lung

value: lung tumor

value: cisplatin


title: Batch1_Patient11600-15149_BF05_1

description:
BF05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: lung tumor, cisplatin, rep 4


title: Donor 553 upregulated GIRK2, alcohol-chronic, batch a, bio rep 2


title: Batch1_Patient11600-15149_BF04_2

description:
BF04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 553 upregulated GIRK2, alcohol-chronic, batch a, bio rep 1


title: Batch1_Patient11600-15149_BF04_1

description:
BF04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 553 endogenous GIRK2, alcohol-naïve, batch b, bio rep 3


title: lung tumor, vehicle, rep 3

value: vehicle


title: Batch1_Patient11600-15149_BF03_2

description:
BF03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: lung tumor, vehicle, rep 2


title: Batch1_Patient11600-15149_BF03_1

description:
BF03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 553 endogenous GIRK2, alcohol-naïve, batch b, bio rep 1


title: lung tumor, vehicle, rep 1


title: Batch1_Patient11600-15149_BF06_2

description:
BF06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BF02_2

description:
BF02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BF05_2

description:
BF05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BF02_1

description:
BF02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 553 endogenous GIRK2, alcohol-naïve, batch a, bio rep 3


title: lung tumor, cisplatin, rep 3


title: Donor 553 endogenous GIRK2, alcohol-naïve, batch a, bio rep 2


title: Donor 553 endogenous GIRK2, alcohol-naïve, batch a, bio rep 1


title: Batch1_Patient11600-15149_BF01_2

description:
BF01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: lung tumor, cisplatin, rep 2


title: lung tumor, cisplatin, rep 1


title: Donor 553 endogenous GIRK2, alcohol-chronic, batch b, bio rep 3


title: Batch1_Patient11600-15149_BE12_2

description:
BE12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: lung tumor, vehicle, rep 4


title: Batch1_Patient11600-15149_BF01_1

description:
BF01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 553 endogenous GIRK2, alcohol-chronic, batch b, bio rep 1


title: SS2iTregCsA_2

city: Beijing

first: Huiyun

last: Lyu

address: Tsinghua University, Zhengyutong Building D301

department: Institute for Immunology

country: China

institute: Tsinghua University

data_processing:
RNA-seq analysis: Raw fastq reads were trimmed by Cutadapt (version 1.18) to trim adapter and low quality sequence.  Reads were aligned to the mouse genome (mm10) using STAR (version 2.5.3). The number of reads within each gene in each single cell were counted using RSEM (version 1.3.0) with gene annotation file from GENCODE (GRCm38.m23).  Differential expression was estimated by using DESeq2 package (version 1.26) with absolute log2 Fold change > 0.5 and adjusted P value < 0.05. Functional enrichment analysis were performed by using the clusterProfiler R package (v3.14.3) with default parameters (P value < 0.05) and the functional annotations terms in Gene Ontology (GO)
Assembly: mm10

source_name: Treg

extract_protocol:
Live cells were sorted using PI staining, then 5 × 104 cells were transferred to a low-binding centrifuge tube and resuspended in 50 μL of pre-chilled Lysis Buffer. After 20 times pipetting, cells were incubated on ice for 10 minutes for lysis.
RNA-seq The RNA-seq library preparation was performed by a modified SMART-seq2 protocol49,51. Briefly, RNA was added into 4 µl elution mix made of 1 µl RT primer (10 µM), 1 µl dNTP mix (10 mM each), 1 µl RNase inhibitor (4 U/µl), and 1 µl H2O. Eluted samples were incubated at 72 °C for 3 min and immediately placed on ice. Each sample was added with 7 µl reverse transcription (RT) mix made of 0.75 µl H2O, 0.1 µl Maxima RNase-minus RT (Thermo Fisher Scientific, #EP0741), 2 µl 5x Maxima RT buffer, 2 µl Betaine (5 M, Sigma-Aldrich, B0300), 0.9 µl MgCl2 (100 mM), 1 µl TSO primer (10 µM), 0.25 µl RNase inhibitor (40 U/µl).The RT reaction was incubated at 42 °C for 90 min and followed by 10 cycles of (50 °C for 2 min, 42 °C for 2 min), then heat inactivated at 70 °C for 15 min. Samples were then amplified with an addition of 14 µl PCR mix made of 1 µl H2O, 0.5 µl ISPCR primer (10 µM), 12.5 µl KAPA HiFi HotStart ReadyMix (KAPA Biosystems, KK2602). The PCR reaction was performed as follows: 98 °C for 3 min, 22 cycles of (98 °C for 15 sec, 67 °C for 20 sec, 72 °C for 6 min), and final extension at 72 °C for 5 min.  The amplified cDNA product was purified using VAHTS DNA Clean Beads. Sequencing libraries were prepared using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503-02).  Primer sequences: RT primer (Sangon), 5’Biotin-AAGCAGTGGTATCAACGCAGAGTACTTTTTT TTTTTTTTTTTTTTTTTTTTTTTTVN; TSO primer (Sangon), 5’Biotin-AAGCAGTGGTATCAAC CAGAGTACAT/rG//rG//iXNA_G/; ISPCR primer (Sangon), 5’Biotin-AAGCAGTGGTATCAACGC AGA*G*T. ATAC-sequencing ATAC-seq were performed using TruePrep DNA Library Prep Kit V2 for Illumina according to the manufacturer’s recommendation. Briefly, live cells were sorted using PI staining, then 5 × 104 cells were transferred to a low-binding centrifuge tube and resuspended in 50 μL of pre-chilled Lysis Buffer. After 20 times pipetting, cells were incubated on ice for 10 minutes for lysis. Subsequently, cells were pelleted by centrifugation at 4°C 500 g for 5 minutes, and suspended in a mixture consisting of 10 μL of 5× TTBL, 5 μL of TTE Mix V50, and 35 μL of ddH2O. The mixture was gently mixed by pipetting 20 times, and incubated at 37°C for 30 minutes for fragmentation. The products were purified using 2× VAHTS DNA Clean Beads, eluted with 26 μL of water, and collected for the subsequent amplification. 24 μl of the eluted samples were amplified with different combination of i7 index and i5 index primers. QPCR were performed to determine the cycle number for PCR amplification.0.55×VAHTS DNA Clean Beads was employed for size selection of the PCR product. Finally, 30 ng of each sample were pooled for subsequent second-generation sequencing, on the Illumina NovaSeq 6000 with read length of 150 bp.
RNA: smartSeq-2.

value: Treg


title: SS2iTregCsA_1


title: Donor 553 endogenous GIRK2, alcohol-chronic, batch b, bio rep 2


title: Batch1_Patient11600-15149_BE12_1

description:
BE12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv

value: Fallopian tube


title: Donor 553 endogenous GIRK2, alcohol-chronic, batch a, bio rep 3

value: NGN2 neurons


title: Donor 553 endogenous GIRK2, alcohol-naïve, batch b, bio rep 2

value: isoCTL


title: Batch1_Patient11600-15149_BE11_1

description:
BE11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BE11_2

description:
BE11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: sample10_spag7_KO

city: Cambridge

first: Mary

last: Piper

state: Massachusetts

address: 1 Portland St

institute: Pfizer Inc

data_processing:
The raw FASTQ files were processed using an internal pipeline, Rnaseq Experiment DAshboard, utilizing STAR (v2.7.3a)  and Salmon (v1.5.2) to map reads to the mouse genome and transcriptome (GRCm39, Ensembl release 106), respectively.
The Salmon transcript abundance estimates were aggregated to the gene level using tximport (v1.22.0) and rounded to the nearest integer
Differential expression analysis was performed with DESeq2 (v1.34.0)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes DESeq2-normalized counts for each sample combined with the differential expression results

source_name: gastrocnemius muscle

extract_protocol:
Tissue was pulverized and total RNA was extracted using Qiagen Rneasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany). The RNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked using TapeStation (Agilent Technologies, Palo Alto, CA, USA)
RNA sequencing libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: gastrocnemius muscle

value: Spag7 KO


title: Donor 553 endogenous GIRK2, alcohol-chronic, batch a, bio rep 2

value: Chronic


title: sample9_spag7_KO


title: sample8_spag7_WT

value: WT


title: Batch1_Patient11600-15149_BE10_1

description:
BE10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: SS2iTregCsA_3


title: Batch1_Patient11600-15149_BE09_2

description:
BE09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: sample6_spag7_WT


title: sample7_spag7_KO


title: Donor 3440 upregulated GIRK2, alcohol-naïve, batch b, bio rep 3

value: Lenti


title: Donor 3440 upregulated GIRK2, alcohol-naïve, batch b, bio rep 1


title: Donor 3440 upregulated GIRK2, alcohol-naïve, batch b, bio rep 2


title: Batch1_Patient11600-15149_BE09_1

description:
BE09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: sample5_spag7_WT


title: Batch1_Patient11600-15149_BE08_2

description:
BE08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 3440 upregulated GIRK2, alcohol-naïve, batch a, bio rep 2


title: Donor 3440 upregulated GIRK2, alcohol-naïve, batch a, bio rep 1


title: Batch1_Patient11600-15149_BE08_1

description:
BE08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 3440 upregulated GIRK2, alcohol-naïve, batch a, bio rep 3


title: sample3_spag7_KO


title: sample4_spag7_WT


title: Batch1_Patient11600-15149_BE07_1

description:
BE07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 3440 upregulated GIRK2, alcohol-chronic, batch b, bio rep 3


title: Donor 3440 upregulated GIRK2, alcohol-chronic, batch b, bio rep 2


title: Donor 3440 upregulated GIRK2, alcohol-chronic, batch b, bio rep 1


title: Batch1_Patient11600-15149_BE06_1

description:
BE06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BE06_2

description:
BE06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: 3T3L1 D7 Rep2

city: Riyadh

first: Sameer

last: Mohammad

address: Ali Al Arini, Ar Rimayah, P.O. Box 3660, Mail code 1515

country: Saudi Arabia

institute: KAIMRC, KSAU-HS

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore (version 0.6.7)
Trimmed sequence reads were mapped to GRCm38 using STAR (version 2.7.10a)
Gene-level counts were generated from the aligned reads using Salmon (version 1.9.0)

growth_protocol: 3T3-L1 cells were differentiated into adipocytes using adipogenic cocktail (IBMX, Insulin, Dexamethasone and roziglitazone)

extract_protocol:
The RNeasy mini kit was purchased from Qiagen, (Maryland, USA) and utilized to isolate RNA from cell adipocytes.
The library was created using the Illumina Stranded Total RNA Prep protocol.
The library was amplified using PCR and cleaned with Agencourt AMPureXP (Beckman, CA,USA). The final library was then normalized, pooled, and loaded into an SP flow cell for up to 400 million reads of coverage. On an Illumina NovaSeq 6000 platform, the library was sequenced (200 cycles).

treatment_protocol: 3T3-L1 cells were harvested without differentiation (Day 0) or after differentiation (Day 7) and used for RNA sequencing.

value: Fibroblats

value: Adipogenic Differentiation


title: 3T3L1 D7 Rep3


title: Batch1_Patient11600-15149_BE10_2

description:
BE10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: 3T3L1 D7 Rep1


title: Batch1_Patient11600-15149_BE05_2

description:
BE05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 3440 upregulated GIRK2, alcohol-chronic, batch a, bio rep 3


title: Donor 3440 upregulated GIRK2, alcohol-chronic, batch a, bio rep 2


title: 3T3L1 D0 Rep3

value: No differentiation


title: 3T3L1 D0 Rep2


title: Batch1_Patient11600-15149_BE05_1

description:
BE05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 3440 endogenous GIRK2, alcohol-naïve, batch b, bio rep 3

value: Naïve


title: 3T3L1 D0 Rep1


title: Batch1_Patient11600-15149_BE04_1

description:
BE04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BE07_2

description:
BE07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 3440 endogenous GIRK2, alcohol-naïve, batch b, bio rep 1


title: sample2_spag7_WT


title: Donor 3440 endogenous GIRK2, alcohol-naïve, batch a, bio rep 3


title: Donor 3440 endogenous GIRK2, alcohol-naïve, batch b, bio rep 2


title: CX3CR1hi T cells, BCG 4

city: Montreal

first: Maziar

last: Divangahi

state: QC

address: 1001 Decarie Bvld

country: Canada

institute: McGill University

data_processing:
fastp (version 0.20.1)
Raw RNA-seq reads were subjected to preliminary quality control and trimming using fastp (version 0.20.1)
Processed reads were mapped to the reference genome using HISAT2 (version 2.2.1). Mapped reads were preserved in a Sequence Alignment/Map (SAM) format.
Aligned reads were quantified using HTSeq-count (version 0.13.5)
Count data from HTSeq-count served as the input for the DESeq2 (version 1.30.1) R package
Assembly: mm10
Supplementary files format and content: Counts file include raw counts of each sample.

source_name: Spleen

extract_protocol:
RNA was extracted by Spin-column with GENEzol TriRNA Pure kit (Geneaid).
Libraries were prepared using SMARter Pico v2 kit (Takara Bio) according to manufacturer's protocol.

treatment_protocol: Splenic T cells isolated from PBS-iv or BCG-iv mice 4 weeks after vaccination, then enriched by EasySep magnetic separation (StemCell). T cell were sorted for CX3CR1lo or CX3CR1hi (BD FACSAria Fusion) for a total of 30 000 cells per sample directly into TRIzol Reagent (ThermoFisher).

value: Spleen

tag: sorted fraction

value: Purified T cells

value: BCG-IV vaccination

tag: time

value: Day 28


title: CX3CR1hi T cells, BCG 3


title: Donor 3440 endogenous GIRK2, alcohol-naïve, batch a, bio rep 2


title: CX3CR1hi T cells, BCG 2


title: Donor 3440 endogenous GIRK2, alcohol-naïve, batch a, bio rep 1


title: Batch1_Patient11600-15149_BE03_2

description:
BE03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: CX3CR1hi T cells, BCG 1


title: Donor 3440 endogenous GIRK2, alcohol-chronic, batch b, bio rep 3


title: Batch1_Patient11600-15149_BE01_2

description:
BE01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: CX3CR1lo T cells, BCG 4


title: Donor 3440 endogenous GIRK2, alcohol-chronic, batch b, bio rep 2


title: Batch1_Patient11600-15149_BE01_1

description:
BE01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: CX3CR1lo T cells, BCG 3


title: Batch1_Patient11600-15149_BE04_2

description:
BE04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: CX3CR1lo T cells, BCG 2


title: Batch1_Patient11600-15149_BD12_2

description:
BD12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BD12_1

description:
BD12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BE03_1

description:
BE03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BE02_2

description:
BE02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BD11_2

description:
BD11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: CX3CR1hi T cells, Control 3

value: PBS-IV vaccination


title: Donor 2607 upregulated GIRK2, alcohol-naïve, batch b, bio rep 3

value: CRISPRa


title: CX3CR1hi T cells, Control 2


title: Batch1_Patient11600-15149_BD10_1

description:
BD10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv

value: Fallopian tube


title: Donor 2607 upregulated GIRK2, alcohol-naïve, batch b, bio rep 1

value: NGN2 neurons


title: Batch1_Patient11600-15149_BD10_2

description:
BD10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 2607 upregulated GIRK2, alcohol-naïve, batch b, bio rep 2


title: Batch1_Patient11600-15149_BE02_1

description:
BE02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BD09_2

description:
BD09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 2607 upregulated GIRK2, alcohol-naïve, batch a, bio rep 3


title: Donor 3440 endogenous GIRK2, alcohol-chronic, batch b, bio rep 1

value: isoCTL


title: Batch1_Patient11600-15149_BD11_1

description:
BD11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BD09_1

description:
BD09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: CX3CR1lo T cells, Control 2


title: CX3CR1lo T cells, BCG 1


title: Donor 3440 endogenous GIRK2, alcohol-chronic, batch a, bio rep 3


title: Donor 3440 endogenous GIRK2, alcohol-chronic, batch a, bio rep 2


title: CX3CR1hi T cells, Control 4


title: Batch1_Patient11600-15149_BD08_2

description:
BD08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 3440 endogenous GIRK2, alcohol-chronic, batch a, bio rep 1


title: CX3CR1lo T cells, Control 1


title: Batch1_Patient11600-15149_BD08_1

description:
BD08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 2607 upregulated GIRK2, alcohol-chronic, batch b, bio rep 1


title: CX3CR1hi T cells, Control 1


title: Organoid pool3 HTO

city: Portland

first: Timothy

middle: J

last: Nice

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Molecular Microbiology and Immunology

institute: Oregon Health & Science University

description:
TotalSeq-A0301 anti-mouse hashtag 1, TotalSeq-A0302 anti-mouse hashtag 2, TotalSeq-A0303 anti-mouse hashtag 3, TotalSeq-A0304 anti-mouse hashtag 4, TotalSeq-A0305 anti-mouse hashtag 5, TotalSeq-A0306 anti-mouse hashtag 6, TotalSeq-A0307 anti-mouse hashtag 7, TotalSeq-A0308 anti-mouse hashtag 8, TotalSeq-A0309 anti-mouse hashtag 9
hashtag oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains hashtag-derived reads

library_source: other

data_processing: mm10-2020-A cellranger reference with "MNV-CR6-VP1CW3" viral transcript

molecule: protein

source_name: Small intestine

growth_protocol: Organoid derivation, transduction, culture, and maintenance was performed as previously described (Miyoshi et al., 2013; 10.1038/nprot.2013.153).

extract_protocol: Single cells were isolated from 3D matrigel cultures using Trypsin/EDTA

treatment_protocol: Recombinant cytokines purchased from the following suppliers were added to culture media: IFN-β (PBL, #12405-1); IFN-λ3 (PBL, #12820-1)

value: Small intestine

value: epithelial

value: B6.Cg-Mx1tm1.1Agsa /J

value: mixed sample (+/- Irf6 KO; +/- IFN treatments)

value: CD300lf transduced

value: Murine Norovirus infection


title: Donor 2607 upregulated GIRK2, alcohol-chronic, batch b, bio rep 3

value: Chronic


title: Batch1_Patient11600-15149_BD07_2

description:
BD07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Organoid pool3

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Batch1_Patient11600-15149_BD07_1

description:
BD07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 2607 upregulated GIRK2, alcohol-chronic, batch b, bio rep 2


title: Batch1_Patient11600-15149_BD06_2

description:
BD06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Organoid pool2 HTO


title: Donor 2607 upregulated GIRK2, alcohol-chronic, batch a, bio rep 2


title: Organoid pool2


title: Donor 2607 upregulated GIRK2, alcohol-chronic, batch a, bio rep 3


title: CX3CR1lo T cells, Control 4

value: WT


title: CX3CR1lo T cells, Control 3

value: Spleen


title: Donor 2607 upregulated GIRK2, alcohol-chronic, batch a, bio rep 1


title: Organoid pool1_2 HTO


title: Donor 2607 upregulated GIRK2, alcohol-naïve, batch a, bio rep 2

value: Naïve


title: Batch1_Patient11600-15149_BD05_2

description:
BD05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 2607 endogenous GIRK2, alcohol-naïve, batch b, bio rep 3


title: Organoid pool1_2


title: Batch1_Patient11600-15149_BD05_1

description:
BD05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 2607 endogenous GIRK2, alcohol-naïve, batch b, bio rep 2


title: Batch1_Patient11600-15149_BD04_2

description:
BD04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Organoid pool1_1 HTO


title: Organoid pool1_1


title: Batch1_Patient11600-15149_BD04_1

description:
BD04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 2607 endogenous GIRK2, alcohol-naïve, batch b, bio rep 1


title: Donor 2607 endogenous GIRK2, alcohol-naïve, batch a, bio rep 3


title: NU8

data_processing:
Reads were aligned to the mouse reference genome using STAR version 2.7.9a
Total read counts for annotated genes were determined using the featureCounts program.
Assembly: GRCm39
Supplementary files format and content: count matrix output from featureCounts program

source_name: Colon

growth_protocol: Cell culture and maintenance was performed as previously described (Robinson et al., 2019; doi: 10.1371/journal.ppat.1007940).

extract_protocol:
RNA was isolated from cells using Trizol
mRNA sequencing libraries were prepared using the Ilumina Stranded polyA+ Library Prep Kit

value: Colon

value: Irf6 WT

value: NoIFN


title: Batch1_Patient11600-15149_BD03_1

description:
BD03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 2607 endogenous GIRK2, alcohol-naïve, batch a, bio rep 1

value: CRISPRa


title: NU3


title: Batch1_Patient11600-15149_BD06_1

description:
BD06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv

value: Fallopian tube


title: NU5


title: Donor 2607 endogenous GIRK2, alcohol-naïve, batch a, bio rep 2

value: NGN2 neurons


title: Batch1_Patient11600-15149_BD02_2

description:
BD02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 2607 endogenous GIRK2, alcohol-chronic, batch b, bio rep 3

value: isoCTL


title: NL5

value: IFNL


title: Donor 2607 endogenous GIRK2, alcohol-chronic, batch b, bio rep 2


title: NL8

value: epithelial


title: Batch1_Patient11600-15149_BD01_1

description:
BD01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BD03_2

description:
BD03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 2607 endogenous GIRK2, alcohol-chronic, batch a, bio rep 3


title: Batch1_Patient11600-15149_BD01_2

description:
BD01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BD02_1

description:
BD02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 2607 endogenous GIRK2, alcohol-chronic, batch b, bio rep 1


title: NL3


title: NB8

value: IFNB


title: NB5


title: Batch1_Patient11600-15149_BC12_1

description:
BC12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 2607 endogenous GIRK2, alcohol-chronic, batch a, bio rep 2


title: NB3


title: Batch1_Patient11600-15149_BC11_2

description:
BC11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BC12_2

description:
BC12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 12455 upregulated GIRK2, alcohol-naïve, batch b, bio rep 3

value: Lenti


title: Donor 2607 endogenous GIRK2, alcohol-chronic, batch a, bio rep 1


title: FU8

value: Irf6 KO2


title: Batch1_Patient11600-15149_BC11_1

description:
BC11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 12455 upregulated GIRK2, alcohol-naïve, batch b, bio rep 2


title: FU5


title: Batch1_Patient11600-15149_BC10_2

description:
BC10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 12455 upregulated GIRK2, alcohol-naïve, batch b, bio rep 1


title: FL8


title: FU3


title: Donor 12455 upregulated GIRK2, alcohol-naïve, batch a, bio rep 3


title: Batch1_Patient11600-15149_BC10_1

description:
BC10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 12455 upregulated GIRK2, alcohol-naïve, batch a, bio rep 2


title: Batch1_Patient11600-15149_BC09_2

description:
BC09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BC09_1

description:
BC09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: FL5


title: Batch1_Patient11600-15149_BC08_2

description:
BC08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 12455 upregulated GIRK2, alcohol-chronic, batch b, bio rep 3


title: Batch1_Patient11600-15149_BC08_1

description:
BC08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 12455 upregulated GIRK2, alcohol-naïve, batch a, bio rep 1


title: FL3


title: Batch1_Patient11600-15149_BC07_2

description:
BC07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: FB5


title: Donor 12455 upregulated GIRK2, alcohol-chronic, batch b, bio rep 2


title: Donor 12455 upregulated GIRK2, alcohol-chronic, batch b, bio rep 1


title: FB3


title: Donor 12455 upregulated GIRK2, alcohol-chronic, batch a, bio rep 3


title: Batch1_Patient11600-15149_BC07_1

description:
BC07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: EU8

value: Irf6 KO1


title: Batch1_Patient11600-15149_BC06_1

description:
BC06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: EU5


title: Donor 12455 upregulated GIRK2, alcohol-chronic, batch a, bio rep 2

value: Chronic


title: Donor 12455 upregulated GIRK2, alcohol-chronic, batch a, bio rep 1


title: Batch1_Patient11600-15149_BC05_2

description:
BC05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: EU3


title: Donor 12455 endogenous GIRK2, alcohol-naïve, batch b, bio rep 3


title: Batch1_Patient11600-15149_BC05_1

description:
BC05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: EL8


title: Donor 12455 endogenous GIRK2, alcohol-naïve, batch b, bio rep 2


title: EL5


title: EL3


title: FB8


title: Donor 12455 endogenous GIRK2, alcohol-naïve, batch b, bio rep 1


title: Batch1_Patient11600-15149_BC04_1

description:
BC04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: EB8


title: Batch1_Patient11600-15149_BC03_2

description:
BC03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: EB5


title: Donor 12455 endogenous GIRK2, alcohol-naïve, batch a, bio rep 3


title: Donor 12455 endogenous GIRK2, alcohol-naïve, batch a, bio rep 2


title: Batch1_Patient11600-15149_BC03_1

description:
BC03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: EB3


title: Batch1_Patient11600-15149_BC06_2

description:
BC06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 12455, endogenous GIRK2, alcohol-naïve, batch a, bio rep 1


title: Batch1_Patient11600-15149_BC02_2

description:
BC02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BC02_1

description:
BC02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 12455 endogenous GIRK2, alcohol-chronic, batch b, bio rep 3


title: Batch1_Patient11600-15149_BC01_2

description:
BC01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: BRQ_3

city: xi'an

first: Wei

last: Gaofei

state: Shaanxi

address: beilin

institute: Northwestern Polytechnical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Supplementary files format and content: genes_fpkm_expression.txt

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: BRQ


title: Donor 12455 endogenous GIRK2, alcohol-chronic, batch b, bio rep 2


title: BRQ_2


title: Donor 12455 endogenous GIRK2, alcohol-chronic, batch b, bio rep 1


title: BRQ_1


title: Batch1_Patient11600-15149_BC01_1

description:
BC01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 12455 endogenous GIRK2, alcohol-chronic, batch a, bio rep 3


title: Cont_3

value: control


title: Batch1_Patient11600-15149_BB12_2

description:
BB12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BC04_2

description:
BC04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor 12455 endogenous GIRK2, alcohol-chronic, batch a, bio rep 2


title: Batch1_Patient11600-15149_BB12_1

description:
BB12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BB11_2

description:
BB11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Cont_1


title: Cont_2


title: Donor BJ upregulated GIRK2, alcohol-naïve, batch b, bio rep 3

source_name: BJ

value: BJ

value: Naïve


title: Sample 2

city: Brooklyn

first: Ngoc

last: Luu

address: 6 Metrotech Center

institute: New York University

description: 10x Genomics

data_processing:
Cell Ranger Single Cell Software was used to perform de-multiplexing, barcode and UMI processing, and single-cell 3′ gene counting, Seurat package was used for quality control, data filtering, dimensionality reduction, differential gene expression analysis, and uniform manifold approximation.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Vascular smooth muscle cells

extract_protocol:
Four groups of vascular smooth muscle cells  cultured on 6-well plate different conditions (Young, Old, Young + Angiotensin II, Old + siPiezo1) were harvested by 0.25% Trypsin-EDTA (Gibco) and cell viability was confirmed using an automated cell counter (Biorad, TC20).
Cell hashing with anti-mouse oligo-tagged antibodies (TotalSeq A, Biolegend) were performed according to the manufacturer’s protocol before mixing them in single-cell suspension. The libraries were prepared using Chromium Single Cell 3′ Library & Gel Bead Kit v3.1, PN-1000268, the Chromium Next GEM Chip G Single Cell Kit PN-1000120 and theDual Index Kit TT, Set A PN-1000215,(10x Genomics). Amplified cDNA was evaluated on a Agilent BioAnalyzer 2100 using a High Sensitivity DNA Kit (Agilent Technologies) and final libraries on a Agilent TapeStation 4200 using High Sensitivity D1000 ScreenTape (Agilent Technologies).

treatment_protocol:
Young vascular smooth muscle cells were treated with 10-7 M Angiotensin II (AngII) for 48 hours in Young + AngII group
Knockdown of Piezo1 was performed by siRNA transfection with 20 nM of either ON-TARGETplus Piezo1 siRNA Reagents (L-061455-00-0005, Horizon Discovery) or ON-TARGETplus non-targeting control pool (D-001810-10-05, Horizon Discovery) using Lipofectamine™ 3000 Transfection Reagent (L3000001, Invitrogen).

value: Vascular smooth muscle cells

tag: age


title: Batch1_Patient11600-15149_BB10_2

description:
BB10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BB10_1

description:
BB10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: B9

city: New Haven

first: In-Jung

last: Kim

state: CT

address: 300 George Street

department: Ophthalmology

institute: Yale University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fqTrim2.py
Trimmed sequence reads were mapped to GRCm38.p5/mm10 using Tophat2/Bowtie2
Raw read counts per gene were calculated using HTSeq
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Dorsal Midbrain

extract_protocol:
Total RNA was prepared using the Rneasy PowerLyzer Tissue & Cell Kit (Qiagen). 1 μg of total RNA per sample was used to generate cDNA libraries.
Libraries were generated using the Kapa mRNA Hyper Prep Kit for Illumina Platforms (KAPA Biosystems) following manufacturer's protocol

value: Dorsal Midbrain

tag: developmental stage

value: Homozygote


title: Donor BJ upregulated GIRK2, alcohol-naïve, batch b, bio rep 1


title: Donor BJ upregulated GIRK2, alcohol-naïve, batch b, bio rep 2


title: Batch1_Patient11600-15149_BB11_1

description:
BB11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv

value: Fallopian tube


title: Sample 1

description: 10x Genomics

value: two control and two experimental group

value: 12-78 weeks old


title: Donor BJ upregulated GIRK2, alcohol-naïve, batch a, bio rep 3

value: NGN2 neurons


title: Batch1_Patient11600-15149_BB09_2

description:
BB09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: B8


title: Donor BJ upregulated GIRK2, alcohol-naïve, batch a, bio rep 2


title: Donor BJ upregulated GIRK2, alcohol-naïve, batch a, bio rep 1


title: B7


title: Batch1_Patient11600-15149_BB09_1

description:
BB09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: B1


title: Batch1_Patient11600-15149_BB08_2

description:
BB08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BB08_1

description:
BB08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor BJ upregulated GIRK2, alcohol-chronic, batch b, bio rep 3


title: A6

value: Heterozygote


title: Batch1_Patient11600-15149_BB07_2

description:
BB07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: A4


title: Donor 12455 endogenous GIRK2, alcohol-chronic, batch a, bio rep 1

value: isoCTL


title: Donor BJ upregulated GIRK2, alcohol-chronic, batch b, bio rep 1

value: Lenti


title: A2


title: Batch1_Patient11600-15149_BB06_2

description:
BB06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Mtb_pcaA_W8_4_S13

city: Lausanne

first: Maxime

last: Jan

state: Suisse

address: University of Lausanne

department: CIG

country: Switzerland

institute: University of Lausanne

data_processing:
Reads were mapped to C3H/HeJ version 1 using STAR (version 2.7.10b) with default parameters.
Count data was generated directly from STAR using the option --quantMode GeneCounts.
Gene features were taken from ensembl, using version 108 (Mus_musculus_c3hhej.C3H_HeJ_v1.108.gtf)
EdgeR was then used to normalize read counts by library size. Genes with a mean raw read count below 10 were excluded from the analysis.
The raw read counts were normalized using the TMM normalization, and converted to log counts per million (CPM)
Assembly: C3H_HeJ_v1, INSDC Assembly GCA_001632575.1
Supplementary files format and content: Tab-delimited text file includes raw count per samples
Supplementary files format and content: Tab-delimited text file includes normalized log2 CPM per samples

growth_protocol: Mixed-sex C3HeB/FeJ mice aged between 8 and 12 weeks were infected with between 50 and 100 CFU of WT and cording-deficient bacteria. The animals were sacrificed at 8 weeks post infection by CO2 overdose.

extract_protocol:
After euthanasia, the lungs were extracted, washed with PBS to remove excess blood. Ca. 60 mg of tissue was added to 1 mL of Trizol and maintained on ice. The samples were then homogenized using zirconia beads and a Precellys Beadbeater and the nucleic acids were isolated after addition of chloroform and precipitation of the resulting acqeous layer with an equal volume of 70% ethanol. Thhereafter the samples were removed from the BSL-3 laboratory and RNA extracted using the Qiagen RNeasy Mini Kit with on-column DNase treatment
Libraries were prepared from ribodepleted RNA isolated from lung tissue taken from Mtb-infected mice and sequenced using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (New England Biolabs) as per the manufacturer’s instructions. A mean of 51.9 million 60 base-pairs paired-end reads were obtained among the 9 samples (39.2 – 69.3 million reads).

value: Lung

tag: infection

tag: batch


title: Donor BJ upregulated GIRK2, alcohol-chronic, batch a, bio rep 2


title: Donor BJ upregulated GIRK2, alcohol-chronic, batch a, bio rep 3


title: Batch1_Patient11600-15149_BB05_2

description:
BB05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Mtb_pcaA_W8_1_S11


title: Batch1_Patient11600-15149_BB06_1

description:
BB06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Mtb_pcaA_W8_3_S12


title: Mtb_wt_W8_3_S10

value: Mtb


title: Batch1_Patient11600-15149_BB05_1

description:
BB05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor BJ upregulated GIRK2, alcohol-chronic, batch a, bio rep 1

value: Chronic


title: Donor BJ endogenous GIRK2, alcohol-naïve, batch b, bio rep 3


title: Batch1_Patient11600-15149_BB04_2

description:
BB04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BB04_1

description:
BB04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor BJ endogenous GIRK2, alcohol-naïve, batch b, bio rep 1


title: Donor BJ endogenous GIRK2, alcohol-naïve, batch b, bio rep 2


title: Mtb_wt_W8_1_S8


title: Mtb_wt_W8_2_S9


title: Batch1_Patient11600-15149_BB03_2

description:
BB03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BB07_1

description:
BB07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor BJ upregulated GIRK2, alcohol-chronic, batch b, bio rep 2


title: uninfected_control_5_S7

value: CTR


title: Donor BJ endogenous GIRK2, alcohol-naïve, batch a, bio rep 2


title: uninfected_control_4_S6


title: Donor BJ endogenous GIRK2, alcohol-naïve, batch a, bio rep 1


title: Batch1_Patient11600-15149_BB03_1

description:
BB03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: uninfected_control_2_S5


title: Batch1_Patient11600-15149_BB02_2

description:
BB02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor BJ endogenous GIRK2, alcohol-chronic, batch b, bio rep 3


title: Batch1_Patient11600-15149_BB01_2

description:
BB01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor BJ endogenous GIRK2, alcohol-chronic, batch b, bio rep 2


title: Mtb_pcaA_W8_4_S12


title: Mtb_pcaA_W8_3_S11


title: Batch1_Patient11600-15149_BB02_1

description:
BB02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Donor BJ endogenous GIRK2, alcohol-chronic, batch b, bio rep 1


title: Donor BJ endogenous GIRK2, alcohol-chronic, batch a, bio rep 2


title: Donor BJ endogenous GIRK2, alcohol-chronic, batch a, bio rep 1


title: Mtb_wt_W8_5_S8


title: Batch1_Patient11600-15149_BA12_2

description:
BA12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BB01_1

description:
BB01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BA11_2

description:
BA11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Mtb_pcaA_W8_5_S13


title: Batch1_Patient11600-15149_BA12_1

description:
BA12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: 15149-inactive [S3]

data_processing:
Fastq files were trimmed for adapter sequences and quality withTrim Galore! (v0.6.5)
Sequencing reads were mapped to the UCSC hg19 human genome assembly using STAR (v2.7.3a)
Read counts were obtained using subread FeatureCounts (v2.0.0)
Assembly: hg19
Supplementary files format and content: tab-delimited file containing gene features and the count matrix

growth_protocol: WNT/β-catenin signaling reporter organoids were established from patient-derived cells, and expanded for 4-7 passages (each passage ~ 12 days). Endogenous WβA and non-WβA cells were isolated by FACS into RNA lysis buffer.

extract_protocol:
RNAqueous-Micro Total RNA Isolation Kit (Thermo Fisher Scientific)
SMARTer Stranded Total RNA-seq kit v2 - Pico Input (Takara)

tag: patient no.

tag: wnt signaling_status

value: inactive


title: Donor BJ endogenous GIRK2, alcohol-naïve, batch a, bio rep 3

value: BJ


title: Mtb_pcaA_W8_2_S10


title: Batch1_Patient11600-15149_BA10_1

description:
BA10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: 15149-active [S4]

value: active


title: Batch1_Patient11600-15149_BA11_1

description:
BA11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BA10_2

description:
BA10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: 11600-active [S2]


title: Mtb_wt_W8_1_S4


title: Mtb_wt_W8_2_S5


title: Mtb_wt_W8_3_S6


title: Mtb_pcaA_W8_1_S9


title: Mtb_wt_W8_4_S7


title: Batch1_Patient11600-15149_BA09_2

description:
BA09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: uninfected_control_2_S2


title: uninfected_control_3_S3


title: Batch1_Patient11600-15149_BA08_2

description:
BA08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: uninfected_control_1_S1


title: Batch1_Patient11600-15149_BA08_1

description:
BA08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BA09_1

description:
BA09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: 11600-inactive [S1]


title: BCGiv_aIFNg

city: Bethesda

first: Sivaranjani

last: Namasivayam

address: 33 North Drive

department: NIAID

institute: NIH

data_processing:
Alignment, tagging, gene and transcript counting, and clustering analysis was performed using Cellranger 6.1.2
Supplementary files format and content: Tab sepearated value files and matrix files

extract_protocol:
Lung lobes were diced into small pieces and incubated in RPMI containing 0.33mg/mL Liberase TL and 0.1mg/mL DNase I at 37°C for 45 minutes under agitation (200rpm). Enzymatic activity was stopped by adding FCS. Digested lung was filtered through a 70µm cell strainer and washed with RPMI. Red blood cells were lysed with the addition of ammonium-chloride-potassium buffer for 3 minutes at room temperature. Cells were then washed with RPMI supplemented with 10% FCS. Live cell numbers were enumerated using AOPI staining on a Cellometer Auto 2000 Cell Counter
Equal number of cells were pooled from all mice in a group. 10,000 cells from each group were loaded on a 10X Genomics Next GEM chip and single-cell GEMs were generated on a 10X Chromium Controller. Subsequent steps and library construction was performed as manufacterer's instructions (10X Genomics v3.1)

tag: group

tag: agent

value: Wild type


title: PBSiv_aIFNg


title: Desmoid,B 1uM,2

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s reverse -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, version 1.22.1, which is used to both normalize the full dataset and analyze differential expression between sample groups.
Assembly: hg19
Supplementary files format and content: tab-delimited file containing normalized counts

source_name: Desmoid Tumor

growth_protocol: Desmoid 9525 cells were maintained in DMED supplemented with 20% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37 degree

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen), 1ug RNA was used for constructing RNA libraries.
Library preparation used the TruSeq Stranded Total RNA LT Kit (Illumina catalog # RS-122-1202) according to instructions provided by the manufacturer with 8 cycles of PCR.

treatment_protocol: 20ng/ml PDGFBB or 1uM, 10uM sorafenib were used to treat cells for 24h.

value: Desmoid Tumor

value: Desmoid 9525

value: Desmoid

value: WT

value: PDGFBB&1uM sorafenib


title: Desmoid,Bnt,2

value: PDGFBB


title: Desmoid,B10uM,2

value: PDGFBB&10uM sorafenib


title: Desmoid, nt, 2


title: Batch1_Patient11600-15149_BA06_2

description:
BA06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv

data_processing:
Paired-end reads from Illumina NextSeq 500 were processed and mapped using STAR
The following filters were used to eliminate cells with (1) UMI counts < 10,000 and (2) gene counts < 200
Removed genes detected in < 3 cells
Assembly: UCSC hg19
Supplementary files format and content: Gene-cell matrix table containing transcript counts for every gene in every cell for each sample in batch1
Supplementary files format and content: Gene-cell matrix table containing transcript counts for every gene in every cell for each sample in batch2

value: Fallopian tube


title: Batch1_Patient11600-15149_BA07_2

description:
BA07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Desmoid,B10uM,1


title: Batch1_Patient11600-15149_BA06_1

description:
BA06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Desmoid, 10uM,2

value: 10uM sorafenib


title: Batch1_Patient11600-15149_BA07_1

description:
BA07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Desmoid,B 1uM,1


title: Desmoid,Bnt,1


title: Batch1_Patient11600-15149_BA05_2

description:
BA05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: PBSiv

value: Lung

value: PBSiv


title: intracolorectal and intrahepatic injection - Sample 2 - Blood - TCR

city: Toulouse

first: Christel

last: Devaud

address: 2 Avenue Hubert Curien

country: France

institute: INSERM

description: Single-cell RNA

data_processing:
The Cell Ranger output of single-cell RNA sequencing data were analyzed using Seurat in R-program (https://satijalab.org/seurat/).
Assembly: mm10
Supplementary files format and content: Archive with barcodes, genes, matrix and clonotypes of each sample

source_name: Blood

growth_protocol: 250 000 MC38-luciferase (luc) expressing cells (colorectal (CRC) tumor cell line, from c57Black/6 mice background, that express luciferase reporter gene for in vivo tumor growth monitoring) were injected intra-hepatic (IH) in the liver of B6 mice (by microsurgery procedure). Only IH implantation were performed in the mice (group IH alone) or they were performed concomitantly with intra-colon (IC) injection of 500 000 MC38 (parental) cells (by microsurgery procedure) (group IH+IC). At day 10, mice were sacrificed and colorectal and hepatic tumors and blood samples were harvested.

extract_protocol:
CD4/CD8 T cells were enriched by positive selection from tumor cell suspension by magnetic cell sorting.
Samples were processed on the Chromium Controller using the Chromium NextGEM Single Cell 5' reagents kits v2 (Dual Index) protocol from 10x Genomics. Starting with 16000 cells per sample, 5' gene expression libraries and VDJ immune repertoire from TCR libraries were prepared according to the manufacturer's instructions. The quality of cDNA and final libraries were assessed on the 5200 Fragment Analyzer system using the HS NGS Fragment kit (1-6000bp). Libraries were quantified using the Qubit 4 fluorometer and the KAPA library quantification kit for qPCR amplification on the QuantStudio5 system. The libraries were pooled at a 1:4 ratio (VDJ library: gene expression library) per sample reaching an equimolarity of the different samples in the final sequencing pool including 1% PhiX sequencing control. The paired-end sequencing was performed on the NovaSeq 6000 system with the NovaSeq S1 Reagent kit v1.5 (100 cycles) following the cycling parameters: 26bp (read1), 10bp (index 1), 10bp (index2), 90bp (read2).

value: day 10 of in vivo tumor development

value: Blood

tag: library type

value: TCR


title: Desmoid, 10uM,1

tag: tissue


title: Desmoid, 1uM, 2

tag: cell line

value: 1uM sorafenib


title: intracolorectal and intrahepatic injection - Sample 2 - Liver - TCR

description: Single-cell RNA

source_name: Liver metastases

value: Liver metastases


title: Desmoid, nt, 1

tag: cell type


title: intracolorectal and intrahepatic injection - Sample 2 - Colon - TCR

description: Single-cell RNA

source_name: Colon tumors

value: Colon tumors


title: Batch1_Patient11600-15149_BA05_1

description:
BA05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv

extract_protocol:
Isolated WβA or non-WβA cells were sorted into 96-well plates containing 4 μl lysis buffer supplemented with 0.1 μl RNase inhibitor (Clonetech), 1.9 μl 0.4% Triton X-100, 1 μl 10 μM 5‘-biotinylated oligo-dT30VN (IDT) and 1 μl 10 mM dNTP (Thermo Scientific). Cells were sorted at one cell per well, with bulk controls (10 cells) and empty well controls (0 cells) included for each plate. Plates were snap frozen on dry ice and stored at - 80 degrees C for less than 4 weeks.
Single cell cDNA synthesis and library generation were performed according to the SMART-seq2 protocol (Picelli et al., 2014), as previously described (Hu et al., 2020). Briefly, cells were lysed by removing plates from  -80 0C and heating at 72 0C for 3 min. Plates were then placed at 4 0C before adding the reverse transcription mix containing 5’-biotinylated TSO (Qiagen). PCR products were cleaned up using 0.8:1 Ampure XP beads (Beckman Coulter) with Biomek FxP Laboratory Automation Workstation (Biomek). Quality of single-cell cDNA was tested using TapeStation, as well as by single cell qPCR for GAPDH or ACTB using the QuantiNova SYBR Green PCR Kit (Qiagen). cDNA concentration was measured using Quant-iTTM PicoGreenTM dsDNA Assay Kit (Invitrogen) on the CLARIOstar Plate Reader (BMG Labtech). Wells with CT values of GAPDH or ACTB below 20 were selected as wells with good quality cDNA. Libraries from single cell cDNA were generated using miniaturized Nextera XT (Illumina) protocol (Mora-Castilla et al., 2016) with Mosquito HTS (TTP LabTech), in 384-well Endure plate (Life Technology). Library sequencing was performed by Novogene.


title: Batch1_Patient11600-15149_BA04_2

description:
BA04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BA03_2

description:
BA03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: intracolorectal and intrahepatic injection - Sample 1 - Blood - TCR

description: Single-cell RNA


title: BCGiv

value: BCGiv

tag: genotype

value: Wild type


title: intracolorectal and intrahepatic injection - Sample 1 - Liver - TCR

description: Single-cell RNA


title: Batch1_Patient11600-15149_BA04_1

description:
BA04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BA03_1

description:
BA03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: intrahepatic injection alone - Control - Liver - TCR

description: Single-cell RNA


title: Desmoid 9525, shControl, 3

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s reverse -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, version 1.22.1, which is used to both normalize the full dataset and analyze differential expression between sample groups. Output is tab delimited file containing normalized counts for each sample - one row per feature.
Assembly: hg19
Supplementary files format and content: tab-delimited file containing normalized counts

treatment_protocol: Cells were treated with lentiORF carrying shRNA directed against CTNNB1, selected with antibiotics and RNA harvested after 3-4 days

value: Desmoid Tumor

value: Desmoid 9525

value: Desmoid

tag: treatment


title: Desmoid 9525, shCTNNB1, 2

value: CTNNB1 KD


title: Batch1_Patient11600-15149_BA02_2

description:
BA02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Desmoid 9525, shCTNNB1, 3


title: Desmoid 9525, shControl, 2

value: WT


title: intracolorectal and intrahepatic injection - Sample 1 - Colon - TCR

description: Single-cell RNA


title: intracolorectal and intrahepatic injection - Sample 2 - Blood

description: Single-cell RNA

value: Gene Expression


title: intrahepatic injection alone - Control - Blood - TCR

description: Single-cell RNA


title: Desmoid 9525, shCTNNB1, 1


title: Desmoid 9525, shControl, 1


title: intracolorectal and intrahepatic injection - Sample 2 - Liver

description: Single-cell RNA


title: Batch1_Patient11600-15149_BA01_1

description:
BA01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv

value: Fallopian tube


title: Desmoid, 1uM, 1


title: X6306_11.206402_GGCTAC_L003

city: La Jolla

first: Emily

last: Wang

state: CA

address: 9500 Gilman Dr

department: Vc-health Sciences-schools

institute: UC San Diego

data_processing:
Sequenced reads were processed to remove 3-bp at 5'-end and any adapters at 3'-end using cutadapt
Trimmed reads were aligned to hg19 genome using Bowtie with default settings
miRNAs in miRBase v21 were counted using customized R scripts
Assembly: hg19
Supplementary files format and content: tab delimited files containing raw expression count

source_name: serum

growth_protocol: MDA-MB-231 (HTB-26) cells were obtained from American Type Culture Collection (ATCC; Manassas, VA) and cultured in Dulbecco's Modified Eagle's medium (DMEM; Gibco, Waltham, MA) supplemented with 10% fetal bovine serum (FBS; Sigma-Aldrich, St. Louis, MO).  The brain-tropic subline MDA-MB-231-BR3 (AKA MDA-231-brain) was developed from the MDA-231BR brain-seeking clone previously generated by Dr. Yoneda et al.  To further enhance brain tropism, MDA-231BR cells were inoculated into the left ventricle of the heart in female NSG mice and brain metastases were isolated and cultured in vitro to generate MDA-MB-231-BR2, which subsequently underwent another round of in vivo selection and explant culture to generated MDA-MB-231-BR3 from the brain metastases.  MDA-MB-231-BR3 cells were cultured same as MDA-MB-231.

extract_protocol:
Total RNA was extracted using Trizol Reagent for cell lysate or Trizol LS (ThermoFisher Scientific) for EVs and sera following manufacturer's instructions.  RNA was extracted from ~0.5 mL of serum and the final RNA pellet was dissolved in 10 μL of RNase-free water and subjected to small RNA-seq.
Turseq small RNA library stragety with some modificatons: 1) add "NNN" at 3' of 5' adatpor, and "TCT" at 5' of 3' adaptor; 2) add RT primer after 3' adaptor ligtation to block free 3' adptors

treatment_protocol: EVs were purified from conditioned medium by ultracentrifugation.  Cells were cultured in serum-free medium containing 1% BSA for 24 h before conditioned medium was collected.  The conditioned medium was pre-cleared by centrifugation at 500 g for 15 min and then at 10,000 g for 20 min.  The supernatant underwent ultracentrifugation at 110,000 g for 70 min and the EV-containing pellet was washed once in PBS under the same ultracentrifugation conditions.

value: serum

tag: disease state

value: case


title: Batch1_Patient11600-15149_AH12_2

description:
AH12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv

source_name: Fallopian tube


title: intracolorectal and intrahepatic injection - Sample 2 - Colon

description: Single-cell RNA

value: day 10 of in vivo tumor development


title: X6305_10.181149_TAGCTT_L001


title: intracolorectal and intrahepatic injection - Sample 1 - Liver

description: Single-cell RNA


title: Batch1_Patient11600-15149_AH12_1

description:
AH12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: intracolorectal and intrahepatic injection - Sample 1 - Blood

description: Single-cell RNA

value: Blood


title: Batch1_Patient11600-15149_AH11_2

description:
AH11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: X6303_8.193384_ACTTGA_L001

value: control


title: intracolorectal and intrahepatic injection - Sample 1 - Colon

description: Single-cell RNA


title: Batch1_Patient11600-15149_BA02_1

description:
BA02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AH11_1

description:
AH11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_BA01_2

description:
BA01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: intrahepatic injection alone - Control - Blood

description: Single-cell RNA


title: X6302_7.217367_CAGATC_L001


title: Batch1_Patient11600-15149_AH10_2

description:
AH10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AH10_1

description:
AH10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: X6298_3.189343_TTAGGC_L001


title: Batch1_Patient11600-15149_AH09_2

description:
AH09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: intrahepatic injection alone - Control - Liver

description: Single-cell RNA


title: X6297_2.181631_CGATGT_L001


title: K2

city: BEIJING

address: Malianwa street

institute: China Agriculture University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: testis

extract_protocol:
Trizol
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: testis

value: CKO

value: no


title: Batch1_Patient11600-15149_AH09_1

address: John Radcliffe Hospital, Headley way

institute: University of Oxford

description:
AH09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: K1


title: K3


title: Batch1_Patient11600-15149_AH08_2

description:
AH08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: X6296_1.199853_ATCACG_L001


title: X5787_201780_GTGGCC_L004_19.X5787_201780_GTGGCC_L005_19


title: Batch1_Patient11600-15149_AH08_1

description:
AH08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: X6304_9.161384_GATCAG_L001


title: C2


title: X5786_292252_GTGAAA_L004_18.X5786_292252_GTGAAA_L005_18


title: Batch1_Patient11600-15149_AH07_2

description:
AH07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: X5783_179853_CCGTCC_L004_15.X5783_179853_CCGTCC_L005_15


title: X5782_226228_ATGTCA_L004_13.X5782_226228_ATGTCA_L005_13


title: Batch1_Patient11600-15149_AH06_2

description:
AH06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: renal fibroblasts, Ad-Cre, rep4

city: nanjing

first: li

state: Jiangsu

address: Longmian Avenue

department: Basic Medicine College

institute: nanjing medical university

data_processing:
Reading data through Linux system
Removing reads containing sequencing adapter
Removing reads containing low-quality base ratio
Trimmed sequence reads were mapped to GrCM38/mm10
Read count extraction and normalization were performed
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes counts and FPKM values for each Sample

source_name: kidney

growth_protocol: Primary renal fibroblasts were maintained in DMEM/F12 supplemented with 10% fetal bovine serum  and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Trizol. Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared  following manufacturer's protocols.

treatment_protocol: Fibroblast activation was induced by treatment of 48h  with 5ng/ml TGF-β

value: kidney

value: primary renal fibroblasts

value: suv39h1 knockdown

value: TGF-β


title: X6301_6.215519_GCCAAT_L001


title: Batch1_Patient11600-15149_AH06_1

first: Ahmed

description:
AH06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: renal fibroblasts, Ad-Cre, rep3


title: X5779_97098_CTTGTA_L004_10.X5779_97098_CTTGTA_L005_10


title: renal fibroblasts, Ad-Cre, rep1


title: Batch1_Patient11600-15149_AH05_2

description:
AH05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: renal fibroblasts, Ad-Cre, rep2


title: C3


title: Batch1_Patient11600-15149_AH04_2

description:
AH04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: X5703_37970_ACTTGA_L004


title: renal fibroblasts, Ad-GFP, rep3


title: renal fibroblasts, Ad-GFP, rep2


title: X5702_215269_CAGATC_L004_7.X5702_215269_CAGATC_L005_7


title: Batch1_Patient11600-15149_AH04_1

description:
AH04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AH03_2

description:
AH03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: X5699_294701_TGACCA_L004_6.X5699_294701_TGACCA_L005_6


title: renal fibroblasts, Ad-GFP, rep1


title: C1


title: X5785_255140_GTCCGC_L004_17.X5785_255140_GTCCGC_L005_17


title: Batch1_Patient11600-15149_AH07_1

description:
AH07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: X5781_93368_AGTTCC_L004_12.X5781_93368_AGTTCC_L005_12


title: renal fibroblasts,siprune2 TGFβ-2

first: LI

address: longmian avenue

data_processing:
Reading data through Linux system
Removing reads containing sequencing adapter
Removing reads containing low-quality base ratio
Trimmed sequence reads were mapped to GrCM38/mm10
Read count extraction and normalization were performed
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: tab-delimited text files include log2fold change and FDR values

value: prune2 konckdown


title: Batch1_Patient11600-15149_AH02_2

description:
AH02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: X5697_254609_CGATGT_L004_2.X5697_254609_CGATGT_L005_2


title: Batch1_Patient11600-15149_AH02_1

description:
AH02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: renal fibroblasts, Ad-GFP, rep4


title: Batch1_Patient11600-15149_AH05_1

description:
AH05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: X226907_AGTCAA_L006


title: X5704_149674_GATCAG_L004_8.X5704_149674_GATCAG_L005_8


title: Batch1_Patient11600-15149_AH01_2

description:
AH01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: renal fibroblasts,siprune2 TGFβ-1


title: renal fibroblasts,NC TGFβ-3


title: X148665_TTAGGC_L006


title: renal fibroblasts,NC TGFβ-2


title: Batch1_Patient11600-15149_AH01_1

description:
AH01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AH03_1

description:
AH03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: renal fibroblasts,NC TGFβ-1


title: X268813_9_GTAGAG_L002


title: Batch1_Patient11600-15149_AG12_1

description:
AG12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: X5698_270470_TTAGGC_L004_4.X5698_270470_TTAGGC_L005_4


title: normal pancreas, Paf1 knockout rep2

first: Xiangzheng

last: Liu

address: Tsinghua University, Haidian  District, Beijing

data_processing:
The paired-end reads were trimmed and quality checked using trim-galore (v.0.6.7).
Trimmed reads were aligned to the mouse genome (GRCm38.p6) from GENCODE using STAR(v.2.7.7a)
Reads in BAM files were counted using featureCounts(v.2.0.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include counts numbers of all samples generated by featureCounts

source_name: pancreas

extract_protocol:
Mouse pancreas was triturated under the protection of liquid nitrogen and RNA was extracted with TRIzol (Invitrogen, 15596018) according to the manual
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, NR604) following manufacturer's protocols.

treatment_protocol: Paf1 KO was performed with intraperitoneal (i.p.) injections of AAV8 with sgRNAs targeting Rosa26 (CACATTGCATGGATTATACA) or Paf1 (GAAACACTAAAGAAACGAAAG).

tag: strain

value: pancreas

value: Acinar cell

value: Paf1 knockout

value: Knockout Paf1 using AAV8


title: Batch1_Patient11600-15149_AG11_2

last: Ahmed

description:
AG11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv

value: Fallopian tube


title: X214191_1_CCGTCC_L002

value: serum


title: normal pancreas, Paf1 knockout rep1


title: renal fibroblasts,siprune2 TGFβ-3


title: X149144_1_ATGTCA_L002


title: Batch1_Patient11600-15149_AG11_1

description:
AG11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: normal pancreas, Rosa26 knockout rep2

value: Rosa26 kuockout

value: Knockout Rosa26 using AAV8


title: X140813_5_AGTTCC_L001

value: control


title: X256538_2_AGTCAA_L001


title: Batch1_Patient11600-15149_AG10_1

description:
AG10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: X79065_1_CTTGTA_L001


title: Batch1_Patient11600-15149_AG10_2

description:
AG10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AG09_2

description:
AG09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: X304618_ACTTGA_L006


title: normal pancreas, Rosa26 knockout rep1


title: Batch1_Patient11600-15149_AG09_1

description:
AG09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Normal pancreas, Rosa-KO H3K27ac Input

library_source: genomic

data_processing:
The paired-end reads were trimmed and quality checked using trim-galore (v.0.6.7).
Bowtie2 (v.2.4.4) was used to map the trimmed reads to the mouse genome (GRCm38.p6) from GENCODE
Mapped reads were stored in SAM format and used to generate the BAM files using Samtools(v.1.13) with parameter ‘samtools view –b –h –F 1028 –f 3’
MASC2 were used for peak-calling with parameters as ‘macs2 callpeak -B -f BAMPE -g mm --broad’
Bigwig files were generated using deepTools(bamCoverage, v.3.5.0) with bins per million normalization
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

extract_protocol:
Cut the pancreas with razor blades on ice, then the tissue was crosslinked at room temperature for 10 min with 1% formaldehyde. After quenching,pellets were washed twice with PBS and sonicated in lysis buffer (50 mM HEPES/KOH (pH 7.5), 140 mM NaCl, 0.1% Na-deoxycholate, 1% Triton X-100, 1 mM EDTA, 0.5mM PMSF).
DNA libraries for ChIP-seq were prepared using VAHTS Universal Pro DNA Library Prep Kit for Illumina (Vazyme, ND608) following manufacturer's protocols.

value: Rosa26 knockout

tag: chip antibody


title: Normal pancreas, Paf1-KO H3K27ac Input


title: X264105_9_GGCTAC_L001


title: X306120_5_GTCCGC_L002


title: Normal pancreas, Paf1-KO H3K27ac ChIP

value: H3K27ac (Abcam, ab4729)


title: X185485_1_TAGCTT_L001

value: case


title: Batch1_Patient11600-15149_AG08_2

description:
AG08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AG07_2

description:
AG07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AG08_1

description:
AG08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: X43072_2_2_GATCAG_L001


title: X202490_4_GCCAAT_L001


title: X267470_4_ACTTGA_L001


title: Lumbar, mut, E12.5, rep2

city: Gwangju

first: Mi-Ryoung

last: Song

address: 123, Cheomdangwagi-ro

department: School of Life Sciences

country: South Korea

institute: Gwangju Institute of Science and Technology

data_processing:
FastQC (FastQC v0.11.7)
Sequence reads were trimmed for adaptor sequence and low-quality sequence (Trimmomatic 0.38)
The processed reads were mapped to the mm10 mouse reference genome (HISAT2 version 2.1.0, Bowtie2 2.3.4.1)
Assemble a potential transcript using sequencing information mapped to a reference genome (StringTie version 2.1.3b)
Assembly: mm10
Supplementary files format and content: tab files include gene ID, FPKM and TPM values for each sample

source_name: Lumbar spinal cord

extract_protocol:
RNA was extraced using NucleoSpin RNA XS, Micro kit for RNA purification (MACHEREY-NAGEL). 500 ng of total RNA was used for the construction of sequencing libraries. RNA QC using a 2100 Bioanalyzer System (Agilent). All samples acquired high-quality scores between 9.6 and 10 RIN.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA with Ribo-Zero library kit following manufacturer's protocols.

value: Lumbar spinal cord


title: Batch1_Patient11600-15149_AG07_1

city: Oxford

description:
AG07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Lumbar, mut, E12.5, rep3


title: Lumbar, mut, E12.5, rep1


title: Batch1_Patient11600-15149_AG06_2

description:
AG06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AG12_2

description:
AG12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Lumbar, cnt, E12.5, rep3


title: X213878_8_ACAGTG_L001


title: Batch1_Patient11600-15149_AG06_1

description:
AG06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: X195300_11_TGACCA_L001


title: Normal pancreas, Rosa-KO H3K27ac ChIP

institute: Tsinghua University


title: Batch1_Patient11600-15149_AG05_2

description:
AG05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Lumbar, cnt, E12.5, rep2


title: X136100_11_TTAGGC_L001


title: Batch1_Patient11600-15149_AG05_1

description:
AG05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AG04_2

description:
AG04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Brachial, mut, E12.5, rep3

source_name: Brachial spinal cord

value: Brachial spinal cord


title: Lumbar, cnt, E12.5, rep1


title: X217445_1_CGATGT_L001


title: X294747_1_ATCACG_L001


title: Brachial, mut, E12.5, rep2


title: MDA-231 exo

source_name: breast

value: breast

value: MDA-MB-231 EV

value: breast cancer - EV

value: EV collection


title: Batch1_Patient11600-15149_AG04_1

description:
AG04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Brachial, mut, E12.5, rep1


title: MDA-231 cell

value: MDA-MB-231 Cell

value: breast cancer - cell


title: Batch1_Patient11600-15149_AG03_1

description:
AG03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: MDA-231-brain exo

value: MDA-MB-231-brain EV


title: Batch1_Patient11600-15149_AG02_2

description:
AG02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv

value: Fallopian tube


title: Batch1_Patient11600-15149_AG03_2

description:
AG03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: MDA-231-brain cell

value: MDA-MB-231-brain Cell


title: Brachial, cnt, E12.5, rep3


title: Brachial, cnt, E12.5, rep2


title: Brachial, cnt, E12.5, rep1


title: Batch1_Patient11600-15149_AG02_1

description:
AG02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: renal tissues, DMXAA, rep2

city: Nanjing

first: Lingling

last: Lu

state: State...

address: Guangzhou Road 72

institute: Children's hospital of Nanjing Medical University

data_processing:
Illumina Casava2.19 software used for basecalling.
HISAT2 was used to align the clean reads to the reference genome.
The expression of each gene was calculated with the featureCounts tool in subread.
DESeq2 R package (1.16.1) was used to perform differential expression analysis. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution.
The resulting P-values were adjusted using Benjamini and Hochberg’s approach for controlling the false discovery rate (FDR).
Assembly: mm10
Supplementary files format and content: gene_read count txt file includes gene read count values for each sample

growth_protocol: Wild type C57BL/6J mice were maintained under standard environmental conditions. The mice were allowed free access to food and water.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 0.4 ug of total RNA for the construction of sequencing libraries.
Sequencing libraries were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations.

treatment_protocol: The mice received 10 mg/kg of DMXAA or vehicle via intraperitoneal injection daily for three days.

value: WT

tag: age

value: 8 weeks

tag: Sex

value: male

value: kidney

value: DMXAA injection (10 mg/kg, i.p.) daily for 3 days

tag: time

value: Day 3


title: renal tissues, DMXAA, rep1


title: Batch1_Patient11600-15149_AG01_2

description:
AG01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: renal tissues, vehicle, rep3

value: vehicle injection (i.p.) daily for 3 days


title: Batch1_Patient11600-15149_AF12_2

description:
AF12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AG01_1

description:
AG01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: GW24_cerebellum

city: Beijing

first: xiaoqun

last: wang

state: Beijing

address: 15 Datun Road, Chaoyang District

department: Institute of Biophysics

institute: Chinese Academy of Sciences

description: Sample 13

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned to hg19 human genome by Cellranger(v2.0.1)
Filtered count matrix was merged by Seurat R Package(v2.1.0)
Genome_build: hg19
Supplementary_files_format_and_content: Filtered count matrix was formatted by mtx, and barcode and gene information was with tsv format

source_name: human embryonic cerebellum

extract_protocol: Fetal retina tissue samples were collected in ice-cold artificial cerebrospinal fluid (ACSF)

tag: gestational week

value: cerebellum


title: GW27_cerebellum

description: Sample 14


title: GW21-03_cerebellum

description: Sample 11


title: GW21-04_cerebellum

description: Sample 12


title: renal tissues, vehicle, rep2


title: GW21-02_cerebellum

description: Sample 10


title: Batch1_Patient11600-15149_AF11_2

description:
AF11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: GW21-01_cerebellum

description: Sample 9


title: Batch1_Patient11600-15149_AF10_2

description:
AF10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AF11_1

description:
AF11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: GW18-02_cerebellum

description: Sample 8


title: GW18-01_cerebellum

description: Sample 7


title: dHep_TCDD_16

city: Saltlake city

first: Michael

last: Jurynec

state: UT

institute: University of Utah

description: AhRΔHep

data_processing:
The libraries were sequenced on an Illumina Nova 6000 platform, and 150 bp paired-end reads were generated with a read depth of ~20M per sample. Raw data were analyzed for the per-base sequence quality (>30), per sequence GC content, adapter presence (universal Illumina adapter), and adapter removal using FASTQC v0.11.9.
Reads were mapped to the mouse reference genome (GRCm38 release 96) using HISAT2 v2.1.0. Aligned reads were counted using HTSeq v0.11.3.
The obtained counts were analyzed for differential expression using the Median-Ratio-Normalization method  with Deseq2 v1.22.2. Fold-change was calculated relative to counts in vehicle-treated AhRfl/fl mice. Genes were considered differentially expressed if the adjusted p-value was < 0.05. The enrichment analysis of the differentially expressed genes (DEGs) was performed in Cytoscape v3.7.0 using ClueGo2.5.1.
Assembly: GRCm38 release 96
Supplementary files format and content: .txt files for Deseq2 counts

source_name: Liver

growth_protocol: Mice were housed in microisolator cages with a 12:12 hour light/dark cycle. Food and water were available ad libitum.

extract_protocol:
Liver tissue was submitted to Novogene Corporation Inc. (Sacramento, CA) for mRNA extraction, library preparation, and RNA sequencing. Briefly, mRNA was isolated from 10 mg of liver tissue using poly-T oligonucleotide-magnetic beads. RNA quality was determined using a Nano 6000 assay kit and Bioanalyzer 2100 (Agilent Technologies, CA, USA), and samples with an RNA integrity number (RIN) > 6.8 were used for library preparation.
Transcriptome libraries were prepared using NEBNext® Ultra™ RNA Library Prep Kit (New England Biolabs. Ipswich, MA), and library quality was determined using a Qubit2.0 fluorimeter and Biolanalyzer 2100 (Agilent).

treatment_protocol: Female C57BL/6 mice were gavaged once with peanut vehicle or 100 ug/kg TCDD every four days for 92 days and then euthanized and liver were collected.

value: Liver

tag: strain background

value: AhR{delta}Hep

value: TCDD


title: dHSC_Veh_17

description: AhRΔHSC

value: AhR{delta}HSC

value: Vehicle


title: Batch1_Patient11600-15149_AF10_1

description:
AF10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: dHep_Veh_15

description: AhRΔHep


title: GW16-02_cerebellum

description: Sample 6


title: GW16-01_cerebellum

description: Sample 5


title: Batch1_Patient11600-15149_AF09_2

description:
AF09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AF09_1

description:
AF09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: WT_TCDD_14

description: WT


title: GW14-02_cerebellum

description: Sample 4


title: WT_Veh_13

description: WT


title: GW14-01_cerebellum

description: Sample 3


title: Batch1_Patient11600-15149_AF12_1

description:
AF12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AF08_1

description:
AF08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: GW12-02_cerebellum

description: Sample 2


title: dHSC_TCDD_12

description: AhRΔHSC


title: dHSC_Veh_11

description: AhRΔHSC


title: Batch1_Patient11600-15149_AF08_2

description:
AF08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AF07_2

description:
AF07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: GW12-01_cerebellum

description: Sample 1


title: dHSC_TCDD_18

description: AhRΔHSC


title: dHep_Veh_09

description: AhRΔHep


title: Batch1_Patient11600-15149_AF07_1

description:
AF07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: dHep_TCDD_10

description: AhRΔHep


title: renal tissues, vehicle, rep1


title: WT_TCDD_08

description: WT


title: PAMs, Infection 12hr replicate 1

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) .
Assembly: Sscrofa11.1
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

organism: Sus scrofa

source_name: Porcine alveolar macrophage

extract_protocol:
For in vivo study, PAM cell were collected directly from infected or control pigs by lung lavage. For in vitro study, cells were collected from culture. All cells were washed, and resuspended in 1X PBS to a final concentration of about 1,200 cell/uL before performing library construction.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs 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 Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Porcine alveolar macrophage

tag: infection

value: PRRSV-FL12 GFP


title: PAMs, Infection 12hr replicate 2

description: 10x Genomics


title: Batch1_Patient11600-15149_AF05_2

description:
AF05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv

value: Fallopian tube


title: WT_Veh_07

description: WT


title: dHSC_TCDD_06

description: AhRΔHSC


title: Batch1_Patient11600-15149_AF06_2

description:
AF06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AF06_1

description:
AF06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AF05_1

description:
AF05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: PAMs, Mock replicate 2

description: 10x Genomics

value: Mock


title: PAMs, Infection 6hr replicate 1

description: 10x Genomics


title: Batch1_Patient11600-15149_AF04_2

description:
AF04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: PAMs, Mock replicate 1

description: 10x Genomics


title: dHSC_Veh_05

description: AhRΔHSC


title: dHep_TCDD_04

description: AhRΔHep


title: Batch1_Patient11600-15149_AF04_1

description:
AF04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AF03_2

description:
AF03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: PAMs, Control

description: 10x Genomics

value: Control


title: WT_Veh_01

description: WT

value: WT


title: dHep_Veh_03

description: AhRΔHep


title: PAMs, Infection 4 days

description: 10x Genomics

value: 4 days


title: PAMs, Infection 7 days

description: 10x Genomics

value: 7 days


title: Batch1_Patient11600-15149_AF03_1

description:
AF03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AF02_2

description:
AF02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: WT_TCDD_02

description: WT