title: DEP_High, lung tissue, sRNAseq

city: seoul

first: Youngmin

last: Song

address: 71, Ihwajang-gil, Jongno-gu, Seoul, Republic of Korea

country: South Korea

institute: Seoul National Univeristy College of Medicine

description:
Library name: HIGH
10x Genomics

data_processing:
Sequencing data were processed using Cell Ranger (v3.1.3, 10x Genomics) for alignment to the mm10 reference genome, filtering, and quantification of gene expression. UMAP was used for dimensionality reduction and clustering. Differentially expressed genes (DEGs) were identified with a threshold of |log2FC| > 0.25 and adjusted p-value < 0.05.
Assembly: Mouse mm10
Supplementary files format and content: Processed data files are in Matrix Market Exchange format, consisting of three files: barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz. The matrix.mtx.gz file contains the raw count matrix, while barcodes.tsv.gz and features.tsv.gz provide the corresponding cell barcodes and gene annotations, respectively. These files follow the standard output format of the Cell Ranger pipeline.

source_name: Lung

growth_protocol: Mice were bred and maintained under specific pathogen-free (SPF) conditions at the Seoul National University Hospital and College of Medicine animal facility. Animals were housed with free access to food and water and fed a standard lab chow diet.

extract_protocol:
Lungs were perfused with saline to remove blood, minced, and digested with Collagenase V (1.5 mg/mL) and DNase I (0.1 mg/mL) at 37°C for 30 minutes. The single-cell suspension was filtered, red blood cells were lysed, and immune cells (CD45+) were isolated using fluorescence-activated cell sorting (FACS) with >95% purity.
Single-cell RNA libraries were prepared using the Chromium Next GEM Single Cell 3’ RNA library v3.1 (10x Genomics) following the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 platform.

treatment_protocol: Mice were exposed to diesel exhaust particles (DEP) at 100 µg/m³ or 500 µg/m³ for 1 hour/day, 5 days/week, over 2 weeks using a whole-body inhalation system. Control mice were not exposed to DEP.

value: Lung

value: CD45+ cells

value: DEP exposure (500 µg/m³)


title: DEP_Control, lung tissue, scRNAseq

status: Public on Mar 24 2025

type: SRA

description:
Library name: CTRL
10x Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype

tag: treatment

value: No treatment


title: KO3

city: Nagoya

first: Takashi

last: Yoshimura

address: Furo-cho, Chikusa-ku

country: Japan

institute: Nagoya University

description: Library name: Sample 8

library_source: transcriptomic

data_processing:
Reads were mapped on the Oryzias latipes reference assembly using BWA (v0.7.17-r1188).
The reads per million mapped reads (RPM) was calculated using Salmon (v1.4.0).
Assembly: Oryzias latipes reference assembly
Supplementary files format and content: Excel file include RPM for each sample.

organism: Oryzias latipes

source_name: Liver

growth_protocol: Medaka were kept under long-day conditions.

extract_protocol:
Total RNA of liver were isolated with elimination of DNA contamination using DNase.
Libraries were prepared using the Lasy-Seq v1.1 protocol for 3' RNA sequencing (Kamitani et al., 2019).

treatment_protocol: Liver of wild-type and pd1 knockout medaka kept under long-day conditions were sampled at 12:00.

value: Liver

value: pd1 knockout

value: long-day conditions


title: UNTR+FTY (biol 1)

city: Zürich

first: Hakan

last: Köksal

address: Winterthurerstrasse 190

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zurich

description: control

data_processing:
read alignment, cell barcode demultiplexing, deduplication of reads, generation of expression matrices and quality report were done using the Rhapsody Sequence Analysis Pipeline v2.0 (https://www.bdbiosciences.com/en-us/products/software/rhapsody-sequence-analysis-pipeline)
Assembly: mm39
Supplementary files format and content: Tab-separated value files and matrix files

source_name: tumor

extract_protocol:
Tumors were collected in RPMI with 10% FCS and digested with 1 mg/ml collagenase IV (Thermo Fisher Scientific) and 50 µg/ml DNase I (Roche) for 45 minutes at 37°C using a rotating device. The cells were then washed in PBS with 2 mM EDTA and passed through a 70-µm filter (Biologix). Red blood cells were lysed with a buffer (17 mM Tris pH 7.2, 144 mM NH4Cl) for 2 minutes, followed by a PBS wash.
Library amplification was carried out following the BD Rhapsody System mRNA Whole Transcriptome Analysis (WTA) and Sample Tag Library Preparation Protocol (Doc ID: 23-24119 (02))

value: tumor

tag: Sex

value: female

tag: age

value: 12 weeks old

value: CD8+ T-cells


title: AD_positive  (R-, AD+ and R+, AD+) GEX

city: Los Angeles

first: Richard

last: Ainsworth

address: 8700 Beverly Blvd

country: USA

institute: Cedars-Sinai Medical Center

description:
Library name: SN5_8_mRNA
Sequencing was done on lllumina NovaSeq X plus

data_processing:
mRNA and HTO UMI counts were quantified using Cell Ranger v6.1.2.
Assembly: mm10-2020-A
Supplementary files format and content: CellRanger output files: barcodes.tsv, features.tsv, matrix.mtx
Library strategy: CITE-seq

molecule: polyA RNA

source_name: Forebrain

extract_protocol:
Hash tag antibody (Biolegend) labeled nuclei were isolated using Fluorescence Activated Nuclear sorting (FANs) to enrich for microglia nuclei by preferentially excluding NeuN (neuron), Sox10 (Oligodendroglia) and Sox9 (astrocyte) nuclei and nuclei were mixed in equal proportions to generate Group 1 (SN1-4) and Group 2 (SN5-SN8) samples for nuclear capture
Group1 and Group2 libraries were generated from sample nuclei (SN1-4 and SN5-8) that were mixed together in equal proportions and captured using a Chromium Chip G microfluidics chamber and a Chromium X series processor and the Chromium Next GEM 3’ kit as specified by the manufacturer (10X Genomics). The cDNA libraries were processed for compatibility with Illumina sequencing using the 3’ Feature Barcode Kit, the Dual Index Kit NT Set A, and the Dual Index Kit TT Set A according to the manufacturer’s specifications (10X Genomics)

value: Forebrain

tag: library type

value: mRNA


title: AD_negative (R-, AD- and R+, AD-) HTO

description:
Library name: SN1_4_hto
Sequencing was done on lllumina NovaSeq X plus

library_source: other

molecule: protein

value: HTO

tag: hto

value: TotalSeq-A0451-54 antimouse Hashtag 1. TotalSeq-A0452-antimouse Hashtag 2. TotalSeq-A0453-antimouse Hashtag 3. TotalSeq-A0457-antimouse Hashtag 4.


title: AD_positive  (R-, AD+ and R+, AD+) HTO

description:
Library name: SN5_8_hto
Sequencing was done on lllumina NovaSeq X plus


title: Tissue, Ighasec-/-, SPF, Jejunum, ZE12

city: Chicago

first: Joseph

middle: Joy

last: Sifakis

state: IL

address: 900 East 57th Street

department: Chemistry

institute: The University of Chicago

description: Library name: ZE12

data_processing:
Base calling was performed using the Illumina NovaSeq 6000 platform
Adapters were trimmed using Trim Galore! (0.6.7)
Trimmed sequences were aligned to the reference genome and projected to the transcriptome using STAR (2.7.9a)
Raw gene counts were quantified using Salmon (1.5.2)
Assembly: GRCm38, transcriptome mapped to Gencode Mouse V25 gene annotations
Supplementary files format and content: matrix of raw counts with genes in rows and samples in columns

source_name: Jejunum

extract_protocol:
1 cm of tissue from the beginning of the duodenum, the middle of the jejunum, the end of the ileum, and the middle of the colon was excised and preserved in RNAprotect (Qiagen) overnight at 4°C. The preserved tissue was then stored at -80°C until processing. Tissue was thawed on ice and transferred to a screw-cap tube containing 450 μL of RLT Plus buffer supplemented with 2-mercaptoethanol and equal quantities of 1.0mm and 0.5 mm zirconium oxide beads (Next Advance). Tissue was homogenized three times for 30 sec at a speed of 6 m/s using Bead Ruptor Elite mill homogenizer (Omni), with 1 min incubation on ice between each cycle. RNA from the lysates was purified using RNeasy Plus Mini kit (Qiagen) with the optional on-column DNase I digest step according to manufacturer protocol.
500 ng of RNA was used as input in the TruSeq Stranded mRNA Library Prep (Illumina) according to manufacturer’s specifications.

value: Jejunum

value: Ighasec-/-

value: SPF


title: AD_negative (R-, AD- and R+, AD-) GEX

description:
Library name: SN1_4_mRNA
Sequencing was done on lllumina NovaSeq X plus


title: E14.5_male, ATAC

city: Durham

first: Humphrey

middle: Hung-Chang

last: Yao

state: NC

address: 111 TW Alexander Drive

institute: NIEHS/NIH

library_source: genomic

data_processing:
Raw sequencing data was processed by cellranger-arc v2.0.1 with the default settings.
Assembly: mm10
Supplementary files format and content: CellRanger output files for GEX assay: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CellRanger output files for ATAC assay: atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi
Library strategy: Single Cell Multiome

molecule: genomic DNA

source_name: testis

extract_protocol:
Nuclei isolation was performed using the 10X Genomics Chromium Nuclei Isolation Kit (1000494) following the manufacturer’s protocol.
The 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Library Preparation Kit (1000284) was used to generate a 10X barcoded library of mRNA and transposed DNA from individual nuclei.

value: testis

value: ATAC


title: E14.5_male, GEX


title: KO2

description: Library name: Sample 7


title: RT+FTY (biol1)

description: irradiated


title: Tissue, Ighasec-/-, SPF, Jejunum, ZE11

description: Library name: ZE11


title: WT5

description: Library name: Sample 5

value: wild-type


title: G-3

city: Shanghai

first: Hanjun

last: Li

address: No. 160, Pujian Road, Pudong New Area

department: Renji Hospital

country: China

institute: Shanghai Jiao Tong University

data_processing:
Illumina data collection software
Assembly: GRCm39.108
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: B16F10 tumor

extract_protocol:
Total RNA was extracted by RNeasy Mini Kit (QIAGEN)
RNA was purified by RNAClean XP Kit (Beckman Coulter), DNA was digested by RNase-Free DNase Set (QIAGEN). Paired-end libraries were constructed using TruSeq RNA Sample Preparation Kit (Illumina)

value: B16F10 tumor

tag: cell line

value: CD11b+ Ly6Chi Ly6G- monocytes

value: Monocyte

value: WT

value: LNP-Gsdme


title: WT2

description: Library name: Sample 2

value: Liver

value: long-day conditions


title: WT3

description: Library name: Sample 3


title: G-1


title: WT4

description: Library name: Sample 4


title: WT-3

value: LNP-GFP


title: WT-2


title: WT1

description: Library name: Sample 1


title: WT-1


title: G-2


title: Entrectinib treated well at 0.014 µM, biol repl 4

city: Palo Alto

first: Drishti

last: Guin

state: CA

address: 1804 Embarcadero Rd Ste #201

institute: Transcripta Bio

description:
Library name: F9_CAAGCCAACGCAAGCCAACG
Entrectinib treated well at 0.014 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells

data_processing:
Alignment with Kallisto bus 0.46.1. Bus files were converted to count files using Bustools.
Fold change calculation with DESeq2
Assembly: GRCh38
Supplementary files format and content: counts_entrectinib_ngn2.csv files contain raw gene counts and TPMs for each gene treated with Entrectinib and DMSO. There are 10 entrectinib concentrations each with 4 replicates. Replicates are identified by the well ID.
Supplementary files format and content: fold_changes_entrectinib_ngn2.csv is a comma-separated csv file that contains log2(Fold Change) and significance (p-values and q-values) values per gene from DESeq2 for each treatment. Each treatment consist of Entrectinib at a specific concentration. Each treatment is compared to a set of DMSO control wells.

organism: Homo sapiens

source_name: NGN2-derived glutamatergic neurons

growth_protocol: 10 cm dishes for NGN2-induced neural differentiation were coated with Matrigel according to the manufacturer's manual and incubated overnight at 37°C. On the day of induction, iPSCs were removed using Accutase (StemCell, Cat# 07920), centrifuged at 300 xg for 5 mins and resuspended in NGN2 Neural Induction Media containing 10 µM Y-27632 (StemCell, Cat# 72304). NGN2 Neural Induction Media was made using a base of Knockout DMEM/F12 (Gibco, Cat# 12660012) with the addition of 1x N2 Supplement-B (StemCell, Cat# 07156), 1x MEM Non-Essential Amino Acids (Gibco, Cat# 11140050), 1ug/mL Natural Mouse Laminin (1 mg/mL stock Life Technologies, Cat# 23017-015), 10 ng/mL NT-3 in sterile distilled water (StemCell, Cat# 78074), 10 ng/mL BDNF in sterile distilled water (StemCell, Cat# 78133) and 2 µg/mL doxycycline (stock concentration 20 mg/mL, Fisher Scientific, Cat# AAJ67043AD). Cells were counted using Trypan Blue (Invitrogen, Cat# T10282) on the Invitrogen Countess and plated at 5X106 cells/10 cm dish. Daily media changes were performed on days 2-3 with NGN2 Neural Induction Medium. One day prior to replating cells for neuronal maturation, two 384-well PerkinElmer Pheno Plates were coated with 0.1mg/mL Poly-D-Lysine (Gibco, cat# A3890401) at 37°C overnight. The next morning, the plates were washed 3x with sterile water and dried under a BSC with the fan turned on. At least 2 hours prior to replating, 10 µg/mL Natural Mouse Laminin (Gibco, Cat# 23017015) diluted in DMEM/F12 (Gibco, Cat#11320033) was added to the plates and returned to a 37°C incubator. On day 4, cells were replated at 20000 cells/well in 384-well plates (PerkinElmer Phenoplates) for neuronal maturation in NGN2 Neuronal Medium containing 2 µg/mL doxycycline (Fisher Scientific, Cat# AAJ67043AD) and 5 µM of U-FdU. NGN2 Neuronal Medium was made using 1:1 DMEM/F12 (Gibco, Cat#11320033) and Neurobasal-A Medium (Gibco, Cat# 10888022) as the base with the addition of 1x MEM Non-Essential Amino Acids (Gibco, Cat# 11140050), 0.5x GlutaMAX Supplement (Gibco, Cat# 35050061), 1x N2 Supplement-B (StemCell, Cat# 07156), 1x B-27 Plus Supplement (Gibco, Cat# A3582801), 10 ng/mL NT-3 (StemCell, Cat# 78074), 10ng/mL BDNF (StemCell, Cat# 78133) and 1 µg/mL Natural Mouse Laminin (Gibco, Cat# 23017015). Half media changes were performed every 3-4 days from Day 7-Day 15 using NGN2 Neuronal Medium. Neurons were imaged using an Incucyte for quality control purposes prior to drug treatment using a basic confluence analysis program, followed by a Neurotrack program to identify cell body clusters and neurites.

extract_protocol:
Cell culture media was aspirated using a STARlet liquid handler (Hamilton) and lysis buffer was dispensed directly into each well with a Multidrop Combi Reagent Dispenser (ThermoFisher Scientific) and placed on a shaker for 15 minutes at 900 rpm.
Libraries were prepared using a customized version of the DRUG-seq protocol. Cell lysate was transferred into 384-well PCR plates and reverse transcription (RT) mix was dispensed into each well. Using an Echo 650 Liquid Handler (Beckman Coulter), barcoded RT primers were dispensed into each well. Plates were incubated at 42°C for 2 hours. Following RT, each well was pooled into a single tube and purified using DNA Clean & Concentrator-100 (Zymo Research) followed by concentration with Agencourt RNAClean XP beads (Beckman Coulter). Single-stranded DNA was removed by incubating cDNA with Exonuclease I (New England Biolabs) followed by pre-amplification of the cDNA with DRUG-seq PCR primers. cDNA was fragmented and tagged with Illumina sequencing adapters using Tagmentation DNA Enzyme (TDE1). A final PCR was performed to amplify the libraries and add P7, P5, and index sequences.

treatment_protocol: Neurons were treated with a selection of FDA-approved small molecule compounds added at one-third decreasing dose for 10 doses: 10µM, 3.33µM, 1.11µM, 0.37µM, 0.12µM, 40nM, 14nM, 5nM, 2nM, and 0.5nM in quadruplicate. Additionally, a total of 16 wells were treated with DMSO as control on each 384-well plate. Compounds and DMSO controls were dispensed directly into the 384-well cell culture plates using an Echo 650 Liquid Handler (Beckman Coulter). Cells were held at 37°C for 72 hours following drug treatment.

value: NGN2-derived glutamatergic neurons

value: Neurons

value: Entrectinib treated well at 0.014 µM

tag: treatment time

value: 72 hours


title: Entrectinib treated well at 0.12 µM, biol repl 4

description:
Library name: F7_AGTGCAATGTAGTGCAATGT
Entrectinib treated well at 0.12 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells

value: Entrectinib treated well at 0.12 µM


title: Entrectinib treated well at 0.04 µM, biol repl 4

description:
Library name: F8_ATAAGAGGTCATAAGAGGTC
Entrectinib treated well at 0.04 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells

value: Entrectinib treated well at 0.04 µM


title: Entrectinib treated well at 0.37 µM, biol repl 4

description:
Library name: F6_ACTTCTCCTGACTTCTCCTG
Entrectinib treated well at 0.37 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells

value: Entrectinib treated well at 0.37 µM


title: 18m cortical astrocytes rep3

city: Blacksburg

first: Michelle

middle: Lynne

last: Olsen

state: VA

address: 970 Washington Street SW

department: School of Neuroscience

institute: Virginia Tech

data_processing:
Bases with quality scores less than 30 and adapters were trimmed from raw sequencing reads by Trim Galore (v 0.6.4). After trimming, only reads with lengths greater than 30bp were mapped to mm10 by STAR (v 2.7.1a) with average mapping efficiency of 81.5%.
Raw counts and normalized counts for each gene were outputted by RSEM (v1.2.28). Batch effects were removed with the package sva (v3.46.0). The raw counts were used to identify differentially expressed genes (DEG) by DESeq2 (v 1.36.0). Only genes with adjusted p-value less than 0.05 and at least two-fold change were considered as differentially expressed genes.
Assembly: mm10
Supplementary files format and content: comma-separated values file include TPM values for each Sample

source_name: cortex

extract_protocol:
RNA was isolated from cells with Direct-zol RNA Microprep kit (Zymo Research, #R2060) following the manufacturer’s instructions
Total RNA was reverse transcribed into the first-strand cDNA samples using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA, Mountain View, CA, USA). PolyA enrichment was conducted to enrich all the coding RNA. The cDNA samples were then fragmented, end-repaired, A-tailed, and ligated with adaptors. After size selection and PCR enrichment, sequencing was performed on a NovaSeq instrument (Illumina).

value: cortex

value: astrocyte

tag: developmental stage


title: 18m cortical astrocytes rep2


title: 18m cortical astrocytes rep4


title: 12m cortical astrocytes rep3


title: Entrectinib treated well at 3.33 µM, biol repl 4

description:
Library name: F4_ACAAGCGCGAACAAGCGCGA
Entrectinib treated well at 3.33 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells

value: Entrectinib treated well at 3.33 µM


title: 18m cortical astrocytes rep1


title: Entrectinib treated well at 10.0 µM, biol repl 4

description:
Library name: F3_ACAACCATACACAACCATAC
Entrectinib treated well at 10.0 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells

value: Entrectinib treated well at 10.0 µM


title: Entrectinib treated well at 1.11 µM, biol repl 4

description:
Library name: F5_ACTTCATCACACTTCATCAC
Entrectinib treated well at 1.11 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells

value: Entrectinib treated well at 1.11 µM


title: 12m cortical astrocytes rep2

value: WT


title: Entrectinib treated well at 0.0005 µM, biol repl 4

description:
Library name: F22_TCACCGCCTATCACCGCCTA
Entrectinib treated well at 0.0005 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells

value: Entrectinib treated well at 0.0005 µM


title: 12m cortical astrocytes rep1


title: 6m cortical astrocytes rep5


title: Entrectinib treated well at 0.002 µM, biol repl 4

description:
Library name: F21_TCAAGTGCAGTCAAGTGCAG
Entrectinib treated well at 0.002 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells

value: Entrectinib treated well at 0.002 µM


title: 6m cortical astrocytes rep4


title: 6m cortical astrocytes rep3


title: Entrectinib treated well at 0.014 µM, biol repl 3

description:
Library name: F19_GTCCGCATCAGTCCGCATCA
Entrectinib treated well at 0.014 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: 6m cortical astrocytes rep2


title: Entrectinib treated well at 0.12 µM, biol repl 3

description:
Library name: F17_GCCAAGTACAGCCAAGTACA
Entrectinib treated well at 0.12 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: Entrectinib treated well at 0.04 µM, biol repl 3

description:
Library name: F18_GCCATAGGTTGCCATAGGTT
Entrectinib treated well at 0.04 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: Entrectinib treated well at 0.37 µM, biol repl 3

description:
Library name: F16_GAATTACGGCGAATTACGGC
Entrectinib treated well at 0.37 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: 3m cortical astrocytes rep5


title: 3m cortical astrocytes rep4


title: Entrectinib treated well at 3.33 µM, biol repl 3

description:
Library name: F14_CGGTGACATCCGGTGACATC
Entrectinib treated well at 3.33 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: Entrectinib treated well at 1.11 µM, biol repl 3

description:
Library name: F15_GAATCGAGCCGAATCGAGCC
Entrectinib treated well at 1.11 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: 3m cortical astrocytes rep3


title: Entrectinib treated well at 10.0 µM, biol repl 3

description:
Library name: F13_CGGCTCATCACGGCTCATCA
Entrectinib treated well at 10.0 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: 3m cortical astrocytes rep1


title: Entrectinib treated well at 0.0005 µM, biol repl 3

description:
Library name: F12_CCGGCCAATTCCGGCCAATT
Entrectinib treated well at 0.0005 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: 3m cortical astrocytes rep2


title: Entrectinib treated well at 0.005 µM, biol repl 3

description:
Library name: F10_CACAGTTCATCACAGTTCAT
Entrectinib treated well at 0.005 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells

value: Entrectinib treated well at 0.005 µM


title: Entrectinib treated well at 0.002 µM, biol repl 3

description:
Library name: F11_CCGCTAGCTTCCGCTAGCTT
Entrectinib treated well at 0.002 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: P60 cortical astrocytes rep2


title: P60 cortical astrocytes rep1


title: P60 cortical astrocytes rep3


title: Entrectinib treated well at 0.014 µM, biol repl 2

description:
Library name: E9_CAAGATGAGGCAAGATGAGG
Entrectinib treated well at 0.014 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: P28 cortical astrocytes rep3


title: Entrectinib treated well at 0.005 µM, biol repl 4

description:
Library name: F20_GTCGCTCTCTGTCGCTCTCT
Entrectinib treated well at 0.005 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: P28 cortical astrocytes rep2


title: Entrectinib treated well at 0.04 µM, biol repl 2

description:
Library name: E8_ATAACGCCTCATAACGCCTC
Entrectinib treated well at 0.04 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: Entrectinib treated well at 0.37 µM, biol repl 2

description:
Library name: E6_ACTTCGTTGAACTTCGTTGA
Entrectinib treated well at 0.37 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: P28 cortical astrocytes rep1


title: 6m cortical astrocytes rep1


title: Entrectinib treated well at 1.11 µM, biol repl 2

description:
Library name: E5_ACTTAACTGCACTTAACTGC
Entrectinib treated well at 1.11 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: P21 cortical astrocytes rep3


title: Entrectinib treated well at 3.33 µM, biol repl 2

description:
Library name: E4_ACAACGGAGCACAACGGAGC
Entrectinib treated well at 3.33 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: P21 cortical astrocytes rep2


title: P21 cortical astrocytes rep1


title: Entrectinib treated well at 0.0005 µM, biol repl 2

description:
Library name: E22_TCACAGATACTCACAGATAC
Entrectinib treated well at 0.0005 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: Entrectinib treated well at 0.005 µM, biol repl 2

description:
Library name: E20_GTCCTTCGGTGTCCTTCGGT
Entrectinib treated well at 0.005 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: P14 cortical astrocytes rep2


title: Entrectinib treated well at 0.002 µM, biol repl 2

description:
Library name: E21_TATCGTTACGTATCGTTACG
Entrectinib treated well at 0.002 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: Entrectinib treated well at 0.014 µM, biol repl 1

description:
Library name: E19_GTATTGTGGAGTATTGTGGA
Entrectinib treated well at 0.014 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: P14 cortical astrocytes rep3


title: P14 cortical astrocytes rep1


title: P14 cortical astrocytes rep4


title: Entrectinib treated well at 0.04 µM, biol repl 1

description:
Library name: E18_GCCACGATTCGCCACGATTC
Entrectinib treated well at 0.04 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: P7 cortical astrocytes rep2


title: P7 cortical astrocytes rep4


title: Entrectinib treated well at 0.12 µM, biol repl 2

description:
Library name: E7_AGTCTGTACGAGTCTGTACG
Entrectinib treated well at 0.12 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: Entrectinib treated well at 1.11 µM, biol repl 1

description:
Library name: E15_GAAGGATTAGGAAGGATTAG
Entrectinib treated well at 1.11 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: Entrectinib treated well at 0.37 µM, biol repl 1

description:
Library name: E16_GAATCTTCTCGAATCTTCTC
Entrectinib treated well at 0.37 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: lungs, Control_PR8_rep5, lane2

city: Iowa City

first: Priya

middle: D

last: Issuree

state: IA

address: 431 Newton Road

department: Internal Medicine

institute: University of Iowa

data_processing:
RNA sequencing (paired end reads,100-bp) was performed using Illumina NovaSeq6000 and quality control of the resulting fastq files was assessed using the FastQC program (version 0.11.5). A nextflow pipeline (version 20.01.0) was used to process the fastq files and gene expression was quantitated by alignment of reads with the STAR aligner (version 2.5.3a) to the mouse (build mm10) genome. Raw counts were then imported into R (version 3.5.2) and were normalized and transformed using a variance stabilizing transformation (vst).
Assembly: MM10 reference genome
Supplementary files format and content: txt files

source_name: lungs

extract_protocol:
Total RNA was extracted using Tirzol, following the manufacturer's instructions
Illumina Stranded mRNA protocol

value: lungs

value: bulk

value: wild-type

value: IAV infection


title: Entrectinib treated well at 3.33 µM, biol repl 1

description:
Library name: E14_CGGTCGTATTCGGTCGTATT
Entrectinib treated well at 3.33 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells

value: NGN2-derived glutamatergic neurons

value: Neurons

value: 72 hours


title: Entrectinib treated well at 10.0 µM, biol repl 1

description:
Library name: E13_CGGCAACTTACGGCAACTTA
Entrectinib treated well at 10.0 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: P7 cortical astrocytes rep3


title: Entrectinib treated well at 0.0005 µM, biol repl 1

description:
Library name: E12_CCGGAGTATCCCGGAGTATC
Entrectinib treated well at 0.0005 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: P7 cortical astrocytes rep1


title: Entrectinib treated well at 10.0 µM, biol repl 2

description:
Library name: E3_ACAACAGTCGACAACAGTCG
Entrectinib treated well at 10.0 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: lungs, Control_PR8_rep3, lane2


title: lungs, Control_PR8_rep4, lane2


title: Entrectinib treated well at 0.005 µM, biol repl 1

description:
Library name: E10_CAAGTGGATCCAAGTGGATC
Entrectinib treated well at 0.005 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: DMSO control well, biol repl 28

description:
Library name: N23_TTCTGTACCTTTCTGTACCT
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells

value: DMSO control well


title: lungs, Control_mock_rep2, lane2

value: uninfected (mock)


title: Entrectinib treated well at 0.002 µM, biol repl 1

description:
Library name: E11_CCGCGTTATGCCGCGTTATG
Entrectinib treated well at 0.002 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: lungs, Control_mock_rep3, lane2


title: Entrectinib treated well at 0.12 µM, biol repl 1

description:
Library name: E17_GCATCCGATCGCATCCGATC
Entrectinib treated well at 0.12 µM. Each treated well is a biological replicate, there are 4x biological replicates per condition. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells

value: Entrectinib treated well at 0.12 µM


title: DMSO control well, biol repl 26

description:
Library name: M23_TTCGAGTGATTTCGAGTGAT
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: DMSO control well, biol repl 27

description:
Library name: N2_AATACCGGTAAATACCGGTA
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: DMSO control well, biol repl 25

description:
Library name: M2_AAGTTCCTTGAAGTTCCTTG
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: lungs, CICKO_PR8_rep3, lane2

value: CIC KD


title: lungs, CICKO_PR8_rep4, lane2


title: lungs, CICKO_PR8_rep5, lane2


title: DMSO control well, biol repl 23

description:
Library name: L2_AAGGCATGCGAAGGCATGCG
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: DMSO control well, biol repl 21

description:
Library name: K2_AAGCTCACCTAAGCTCACCT
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: DMSO control well, biol repl 22

description:
Library name: K23_TTATGCCGCGTTATGCCGCG
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: lungs, Control_PR8_rep1, lane2


title: Sibling control

description:
Library name: sibling_control
Sibling whole blood sample as a control.

data_processing:
Alignment with Kallisto 0.46.1 with bootstraps=100
Fold change and TPM calculation with Sleuth
Assembly: GRCh38
Supplementary files format and content: *_tpm.csv files contain TPMS for each gene for each replicate in the comparison
Supplementary files format and content: *_fold_change.csv is a comma-separated csv file that contains log2(Fold Change) and significance values per gene from sleuth.

source_name: Blood

extract_protocol:
Patient n-of-1 trial and data collection was performed in accordance with protocols reviewed and approved by the WGC Institutional Review Board (IRB) (WCG IRB protocol #2001-01). Blood was collected in PAXgene tubes and shipped at room temperature to the sequencing facility (Genewiz, NJ) for processing within 24 hours for RNA sequencing. The RNA was extracted using the PAXgene RNA extraction kit.
Barcoded libraries for RNA-seq were prepared with 100 ng of RNA using NEBNext Ultra II RNA Library Prep Kit (NEB, Ipswich, MA) for Illumina with QIAGEN QIAseq FastSelect -rRNA HMR Kit (QIAGEN, Germany) per manufacturer’s protocol.

value: Blood

value: whole blood


title: DMSO control well, biol repl 20

description:
Library name: J23_TTACTGTGACTTACTGTGAC
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: KO1

description: Library name: Sample 6

value: Liver

value: pd1 knockout

value: long-day conditions


title: lungs, CICKO_PR8_rep2, lane2


title: lungs, CICKO_PR8_rep1, lane2


title: lungs, CICKO_mock_rep1, lane2


title: lungs, CICKO_mock_rep2, lane2


title: DMSO control well, biol repl 19

description:
Library name: J2_AAGCATATGGAAGCATATGG
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: Patient 6 months post treatment biological replicate 2

description:
Library name: patient_post_treat_6mnths_2
Patient whole blood sample 6 months post-treatment with Entrectinib. Fold change file provides gene-level fold changes and significance comparing post-treated sample to pre-treatment.
post_treated_6_months_vs_pre_treat_fold_change.csv.gz

value: 19q12 ASD

value: Entrectinib

value: 6 months


title: Patient 6 months post treatment biological replicate 3

description:
Library name: patient_post_treat_6mnths_3
Patient whole blood sample 6 months post-treatment with Entrectinib. Fold change file provides gene-level fold changes and significance comparing post-treated sample to pre-treatment.
post_treated_6_months_vs_pre_treat_fold_change.csv.gz


title: lungs, Control_PR8_rep5, lane1

value: lungs

value: bulk

value: wild-type


title: Patient 6 months post treatment biological replicate 1

description:
Library name: patient_post_treat_6mnths_1
Patient whole blood sample 6 months post-treatment with Entrectinib. Fold change file provides gene-level fold changes and significance comparing post-treated sample to pre-treatment.
post_treated_6_months_vs_pre_treat_fold_change.csv.gz


title: Patient 3 months post treatment biological replicate 3

description:
Library name: patient_post_treat_3mnths_3
Patient whole blood sample 3 months post-treatment with Entrectinib. Fold change file provides gene-level fold changes and significance comparing post-treated sample to pre-treatment.
post_treated_3_months_vs_pre_treat_fold_change.csv.gz

value: 3 months


title: DMSO control well, biol repl 18

description:
Library name: I23_TTACACACGTTTACACACGT
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells

value: NGN2-derived glutamatergic neurons

value: Neurons

value: 72 hours


title: Patient 3 months post treatment biological replicate 1

description:
Library name: patient_post_treat_3mnths_1
Patient whole blood sample 3 months post-treatment with Entrectinib. Fold change file provides gene-level fold changes and significance comparing post-treated sample to pre-treatment.
post_treated_3_months_vs_pre_treat_fold_change.csv.gz


title: lungs, Control_PR8_rep4, lane1

value: IAV infection


title: DMSO control well, biol repl 17

description:
Library name: I2_AAGATGTCCAAAGATGTCCA
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells

value: DMSO control well


title: lungs, Control_mock_rep1, lane2

value: uninfected (mock)


title: DMSO control well, biol repl 24

description:
Library name: L23_TTCACGGAAGTTCACGGAAG
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: Patient pre-treatment biological replicate 2

description:
Library name: patient_pre_treat_2
Patient whole blood sample pre-treatment with Entrectinib. Fold change file provides gene-level fold changes and significance comparing pre-treatment to sibling control.
pre_treat_vs_sibling_control_fold_change.csv.gz

value: Blood

value: whole blood


title: lungs, Control_PR8_rep1, lane1


title: lungs, Control_PR8_rep3, lane1


title: DMSO control well, biol repl 16

description:
Library name: H23_TGTTCAGGATTGTTCAGGAT
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: Patient pre-treatment biological replicate 1

description:
Library name: patient_pre_treat_1
Patient whole blood sample pre-treatment with Entrectinib. Fold change file provides gene-level fold changes and significance comparing pre-treatment to sibling control.
pre_treat_vs_sibling_control_fold_change.csv.gz


title: Patient 3 months post treatment biological replicate 2

description:
Library name: patient_post_treat_3mnths_2
Patient whole blood sample 3 months post-treatment with Entrectinib. Fold change file provides gene-level fold changes and significance comparing post-treated sample to pre-treatment.
post_treated_3_months_vs_pre_treat_fold_change.csv.gz


title: WDR77_siRNA_R1881_S38

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

description: Library name: Sample24

data_processing:
Basecalls performed using bcl2fastq2 version 2.20
Sequenced reads were mapped to GRCh38 reference GENCODE (p7) annotation (v38) using STAR (v2.7.9a)
Reads counts are obtained using featureCounts from SubRead (v1.6.4)
Assembly: GRCh38.p7 GENCODE r38
Supplementary files format and content: Comma-separated file with raw counts

source_name: prostate cancer

growth_protocol: LNCaP cells were seeded at a density of 300,000 per well of a 6 well plate in RPMI1640 medium supplemented with 9% FBS and without added antibiotics. A day later, cells were transfected.  The next day, medium was changed to androgen-deprived medium. One day later, androgen-deprived medium was refreshed and cells were treated with 5nM of the synthetic androgen R1881 or vehicle (ethanol).  48h later, cells were harvested in Trizol, RNA was extracted and column-purified.

extract_protocol:
Trizol extraction, following by column-purification using RNAeasy columns (Qiagen).
Libraries were constructed at Novogene.  mRNA sequencing libraries were prepared using a polyA enrichment approach.

treatment_protocol: Two days post-transfection, cells were treated with 5nM of the synthetic androgen R1881 or vehicle (ethanol) for  48h.

value: prostate cancer

value: LNCaP

value: prostate adenocarcinoma

tag: cond


title: WDR77_siRNA_R1881_S24

description: Library name: Sample23


title: lungs, Control_mock_rep3, lane1


title: WDR77_siRNA_R1881_S10

description: Library name: Sample22


title: WDR77_siRNA_Veh_S9

description: Library name: Sample21

value: vehicle


title: DMSO control well, biol repl 15

description:
Library name: H2_AACTGTGTCAAACTGTGTCA
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: Contr_siRNA_R1881_S36

description: Library name: Sample17


title: WDR77_siRNA_Veh_S23

description: Library name: Sample19


title: lungs, Control_mock_rep1, lane1


title: Patient pre-treatment biological replicate 3

description:
Library name: patient_pre_treat_3
Patient whole blood sample pre-treatment with Entrectinib. Fold change file provides gene-level fold changes and significance comparing pre-treatment to sibling control.
pre_treat_vs_sibling_control_fold_change.csv.gz

value: 19q12 ASD


title: DMSO control well, biol repl 14

description:
Library name: G23_TGTGCTTCAGTGTGCTTCAG
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: lungs, Control_mock_rep2, lane1

value: lungs


title: DMSO control well, biol repl 13

description:
Library name: G2_AACTCTACACAACTCTACAC
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: lungs, CICKO_PR8_rep5, lane1

value: bulk

value: CIC KD


title: DMSO control well, biol repl 11

description:
Library name: F2_AACCTAGTCCAACCTAGTCC
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: Contr_siRNA_R1881_S22

description: Library name: Sample16


title: DMSO control well, biol repl 12

description:
Library name: F23_TGTCATTCGCTGTCATTCGC
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: Contr_siRNA_Veh_S7

description: Library name: Sample15


title: lungs, CICKO_PR8_rep4, lane1


title: Contr_siRNA_Veh_S35

description: Library name: Sample14


title: DMSO control well, biol repl 10

description:
Library name: E23_TGGAATGGAGTGGAATGGAG
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: Contr_siRNA_R1881_S8

description: Library name: Sample18


title: Contr_siRNA_Veh_S21

description: Library name: Sample13


title: WDR77_siRNA_Veh_S37

description: Library name: Sample20


title: lungs, CICKO_PR8_rep3, lane1


title: P3_R1881_S6

description: Library name: Sample12


title: DMSO control well, biol repl 9

description:
Library name: E2_AACCGGCGTAAACCGGCGTA
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: P3_R1881_S34

description: Library name: Sample11


title: P3_R1881_S20

description: Library name: Sample10


title: lungs, CICKO_PR8_rep2, lane1


title: DMSO control well, biol repl 8

description:
Library name: D23_TGAGTACGTATGAGTACGTA
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: P3_Veh_S5

description: Library name: Sample9


title: lungs, CICKO_PR8_rep1, lane1


title: DMSO control well, biol repl 7

description:
Library name: D2_AACCAGTTGAAACCAGTTGA
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: DMSO control well, biol repl 6

description:
Library name: C23_TGAGCGTTCCTGAGCGTTCC
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: lungs, CICKO_mock_rep1, lane1


title: EmptyVec_R1881_S16

description: Library name: Sample4

value: EmptyVec


title: EmptyVec_R1881_S2

description: Library name: Sample5


title: DMSO control well, biol repl 5

description:
Library name: C2_AACCAGCCAGAACCAGCCAG
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells

value: NGN2-derived glutamatergic neurons


title: B6WT M2

city: Minneapolis

first: Ling

state: MN

address: Mcguire Translational Research Facility, 4-419

department: Experimental and Clinical Pharmacology

institute: University of Minnesota

data_processing:
Raw sequencing reads were evaluated and trimmed using Trimmomatic
Trimmed reads were mapped to the mouse reference genome GRCm38 using HISAT2
RNA-seq raw counts for each gene were extracted using FeatureCounts
Assembly: GRCm38
Supplementary files format and content: xlsx file includes raw counts for each sample

source_name: brain

extract_protocol:
Total RNA was extracted from tissue homogenate using the Aurum Total RNA Fatty and Fibrous Tissue Kit (Bio Rad 7326830) according to the manufacturer’s instructions.
Library preparation was performed using a TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions

value: brain

value: Wild-type C57BL/6

value: male


title: DMSO control well, biol repl 2

description:
Library name: A23_TGAACTAACCTGAACTAACC
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells

value: Neurons

value: DMSO control well

value: 72 hours


title: meso EPC Replicate 3

city: Madison

first: Yunfeng

last: Ding

state: WI

address: 1415 Engineering Dr

department: Chemical and Biological Engineering

institute: University of Wisconsin - Madison

data_processing:
FASTQC v0.12.1
RNA STAR v2.7.11a
featureCounts (subread v 2.0.3)
Assembly: hg38
Supplementary files format and content: Gene counts after alignment for all samples were provided in csv format

extract_protocol:
Tri Reagent and Direct-zol RNA Miniprep kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Endothelial Progenitor Cells

value: Differentiation to EPC


title: meso EC Replicate 1

value: Endothelial Cells

value: hECSR for 2 days


title: meso EC Replicate 3


title: EmptyVect_Veh_S15

description: Library name: Sample2

value: prostate cancer

value: LNCaP

value: prostate adenocarcinoma

value: vehicle

value: EmptyVect


title: B6WT F1

value: female


title: meso EC Replicate 2


title: EmptyVect_Veh_S29

description: Library name: Sample3


title: DMSO control well, biol repl 4

description:
Library name: B23_TGAAGAAGGTTGAAGAAGGT
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells

value: NGN2-derived glutamatergic neurons


title: B6WT M1

value: brain


title: DMSO control well, biol repl 1

description:
Library name: A2_AACACCTAGTAACACCTAGT
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: EmptyVect_Veh_S1

description: Library name: Sample1


title: DMSO control well, biol repl 3

description:
Library name: B2_AACAGGCAATAACAGGCAAT
DMSO control well. Each DMSO well is a biological replicate. Library name contains well id and barcode separated by "_". Read 1 contains barcode provided in library name. Counts file contain gene counts corresponding to well in column "well_id". Fold changes are calculated using DESeq2 by comparing entrectinib wells to DMSO control wells


title: B6WT F2

value: Wild-type C57BL/6


title: unedited IMR90-4

value: Pluripotent Stem Cells


title: IMR90-4 iETV2 hPSC

source_name: IMR90-4 iETV2

value: IMR90-4 iETV2


title: P3_Veh_S19

description: Library name: Sample7


title: SwDI D4F M2

value: Tg-SwDI

value: male


title: A549 cells,si-NC-3+MOI of 0.1 virus(NC-3+),36h

city: Shenzhen

first: Qian

last: Xie

state: Guangdong

address: School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China.

institute: Sun Yat-sen University

description: Library name: siNC3_H7N9

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.
Assembly: GRCh38
Supplementary files format and content: This table contains the RNA count and normalized values for each sample.

extract_protocol:
Total RNA was isolated using TRIZOL reagent. The purity and quantity of the total RNA were assessed using the NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, DE, USA).The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using 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 is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are 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 are 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 library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: lungs

value: Alveolar Basal Epithelial Cells in Lung Cancer

value: WT


title: iETV2 EC expanded in hECSR Replicate 3

value: Endothelial Cells

value: hECSR for 2 days


title: P3_Veh_S33

description: Library name: Sample8

value: prostate cancer

value: LNCaP


title: lungs, CICKO_mock_rep2, lane1

value: bulk

value: CIC KD

value: uninfected (mock)


title: EmptyVec_R1881_S30

description: Library name: Sample6

value: prostate adenocarcinoma

value: EmptyVec


title: meso EPC Replicate 2

value: Endothelial Progenitor Cells

value: Differentiation to EPC


title: SwDI D4F M1

value: brain


title: meso EPC Replicate 1


title: iETV2 EC expanded in hECSR Replicate 1

value: IMR90-4 iETV2


title: iETV2 EC expanded in EGM2 Replicate 3

value: EGM2 for 2 days


title: iETV2 EC expanded in EGM2 Replicate 2


title: A549 cells,si-NC-1+MOI of 0.1 virus(NC-1+),36h

description: Library name: siNC1_H7N9

value: lungs


title: iETV2 EC expanded in EGM2 Replicate 1


title: SwDI D4F F2

value: Tg-SwDI

value: female


title: SwDI D4F M3

value: male


title: SwDI D4F F3


title: iETV2 EPC Replicate 1

value: DMEM/F12 for 3 days


title: A549 cells,si-NC-1(NC-1),36h

description: Library name: siNC1

value: Alveolar Basal Epithelial Cells in Lung Cancer

value: WT


title: SwDI PBS M3

value: PBS


title: A549 cells,si-NC-2(NC-2),36h

description: Library name: siNC2


title: A549 cells,si-NC-3(NC-3),36h

description: Library name: siNC3


title: iETV2 EPC Replicate 3


title: SwDI D4F F1


title: A549 cells, CICKO_PR8_rep2

data_processing:
RNA sequencing (paired end reads,150-bp) was performed using Illumina NextSeq500 and quality control of the resulting fastq files was assessed using the FastQC program (version 0.11.5). A nextflow pipeline (version 20.01.0) was used to process the fastq files and gene expression was quantitated by alignment of reads with the STAR aligner (version 2.5.3a) to the human (build GRCh37) genome. Raw counts were then imported into R (version 3.5.2) and were normalized and transformed using a variance stabilizing transformation (vst).
Assembly: GRCh37/hg19 reference genome
Supplementary files format and content: txt files

source_name: A549 Cell line

value: A549 Cell line

value: Human epithelial cell line

value: IAV infection


title: A549 cells, CICKO_Mock_rep2

value: uninfected (mock)


title: A549 cells, CICKO_PR8_rep1


title: A549 cells,si-GANC-3+MOI of 0.1virus(siGANC-3+),36h

description: Library name: siGANC3_H7N9


title: A549 cells,si-GANC-3(siGANC-3),36h

description: Library name: siGANC3


title: SwDI PBS M2


title: A549 cells, CICKO_Mock_rep1


title: SwDI PBS M1


title: A549 cells,si-NC-2+MOI of 0.1 virus(NC-2+),36h

description: Library name: siNC2_H7N9


title: A549 cells, Control_PR8_rep2

value: Wild-type


title: iETV2 EC expanded in hECSR Replicate 2

value: Endothelial Cells

value: hECSR for 2 days


title: A549 cells,si-GANC-2+MOI of 0.1virus(siGANC-2+),36h

description: Library name: siGANC2_H7N9


title: iETV2 EPC Replicate 2

value: IMR90-4 iETV2

value: Endothelial Progenitor Cells


title: A549 cells, Control_PR8_rep1


title: A549 cells, Control_Mock_rep2


title: A549 cells, Control_Mock_rep1


title: SwDI PBS F1

value: brain


title: A549 cells,si-GANC-1+MOI of 0.1 virus(siGANC-1+),36h

description: Library name: siGANC1_H7N9

value: lungs


title: A549 cells,si-GANC-1(siGANC-1),36h

description: Library name: siGANC1


title: Xenograft tumor from LNCaP OR51E2-KO cells, biological replicate A1

city: Aarhus N

first: Mikkel

middle: Thy

last: Thomsen

state: Midtjylland

address: Palle Juul-Jensens Boulevard 99

department: Department of Clinical Medicine

country: Denmark

institute: Aarhus University

data_processing:
UseGalaxy.org and R package XenofilteR v. 1.6
Sequence reads were trimmed with trimmomatic (remove reads with N > 10% and Qscore<= 5)
Trimmed sequenced were mapped to GRCm38/mm10 and GRCh38/hg38 using HISAT2
XenofilteR was used to remove mouse reads (MM_threshold: 4, Unmapped_penalty: 8)
Read counts and normalization was performed with featureCounts
Assembly: hg38
Supplementary files format and content: Tab-delimited raw counts from each sample with GeneID based on hg38p11 (ncbiRefSeq.2021-12-08)

source_name: LNcaP FGC clone, OR51E2 knockout

growth_protocol: Cell were grown in RPMI 1640 (ATCC modification) supplemented with 10% heat-inactivated FBS at 37 centigrades at 5% CO2 and kept below 90% confluency until injection in mice.

extract_protocol:
Total RNA was extraced using a Qiagen Rneasy mini spin column kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: 4 million cells in 1:1 GelTrex LDEV Free:Growth media was injected subcutaneously into the flank of each mice

value: LNcaP FGC clone, OR51E2 knockout

value: prostate cancer cells

value: OR51E2 KO

value: Xenograft tumor grown in CIEA NOG male mice


title: krbh_treated_d_4l

city: St. Louis

first: Jeongmin

last: Lee

state: Missouri

address: 660 S. Euclid Ave

institute: Washington University in St. Louis

data_processing:
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights function and were fitted using a Limma generalized linear model with additional unknown latent effects as determined by surrogate variable analysis (SVA).  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals.
Assembly: RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.2.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.0.
Supplementary files format and content: Tab-deliminted text file includes gene counts for each sample

source_name: Brown Adipose Tissue

extract_protocol:
RNA has been isolated from brown adipose tissue using RNeasy Lipid Tissue Mini Kit and eluted with water. 10-15ug of RNA was used for RNA-sequencing.
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000.  Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a.

treatment_protocol: NOD mice with blood glucose range between 190mg/dL and 230mg/dL were injected with CB-100 (>100kDa size fraction of brown adipocyte conditioned buffer) for 7 days (subcutaneous, 1.5mg/kg BW)

value: Brown Adipose Tissue

value: NOD/ShiLtJ

value: Sham (KRBH buffer)


title: 1Ping_MDSC_blank_S1

city: Bellinzona

first: Andrea

last: Alimonti

address: Via vela 6

department: Molecular Oncology

institute: Institute of oncology research

description: Library name: Sample1

data_processing:
The overall quality of sequencing reads was evaluated using FastQC. STAR (v.2.7.10a) 61 was used to sequence alignments to the reference mouse genome (GRCm39). Gene Transfer File (GTF) vM27 by Gencode was used to quantify gene expression at gene level.
Further analysis were performed in R Statistical environment (v.4.1.0). Genes without counts were removed for the analysis, and differential expression analysis was performed using DESeq2
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file with raw counts for each samples

source_name: BM-derived MDSC

growth_protocol: Mouse BM-MDSCs were differentiated in vitro as previously described 59. In brief, bone marrow cells were flushed from the legs of C57BL/6 with RPMI 1640 medium. The cell pellets were lysed with ACK buffer (Gibco, A1049201) to prepare the progenitors. For BM-MDSCs, cells are resuspended in complete RPMI containing 40 ng/ml GM-CSF, 40 ng/ml IL-6 for 4 days and PMN-MDSCs were isolated with the MDSCs isolation Kit (Miltenyi Biotec, 130-094-538) according to the reference.

extract_protocol: RNA sequencing was performed at the Institute of Oncology Research using the NEBNext Ultra Directional II RNA library preparation kit for Illumina and sequenced on the Illumina NextSeq2000 with single-end, 75 base pair long reads

treatment_protocol: BM-MDSCs were washed and re-seeded in 24-well plate at 1_106/ml density with fresh culture media after differentiation and either transfected with 250 ng/ml mtDNA by Lipofactamine 2000

value: BM-derived MDSC

value: MDSC

value: blank


title: 2Ping_MDSC_mtDNA_S2

description: Library name: Sample2

value: mtDNA


title: 7Ping_MDSC_blank_S7

description: Library name: Sample5


title: 5Ping_MDSC_mtDNA_S5

description: Library name: Sample4


title: 8Ping_MDSC_mtDNA_S8

description: Library name: Sample6


title: Xenograft tumor from LNCaP OR51E2-KO cells, biological replicate A18


title: imBAT_treated_nd_50r

value: imBAT conditioned buffer (>100kDa)


title: krbh_treated_d_3r


title: Blvra+/+ mouse red blood cells infected with Plasmodium chabaudi chabaudi AS

city: Oeiras

first: Miguel

last: Soares

address: Rua da Quinta Grande, 6

country: Portugal

institute: Instituto Gulbenkian de Ciência

data_processing:
Data was demultiplexed, processed and aggregated into filtered feature-barcode matrices with the CellRanger software (v7.0.0).
Assembly: Reads were mapped agains the Plasmodium chabaudi chabaudi genome annotation: ftp://ftp.ensemblgenomes.org/pub/protists/release-50/protists/
Supplementary files format and content: 10X filtered feature-barcode matrices and count table in tab-separated value format

extract_protocol:
Chromium Next GEM Single Cell 3ʹ protocol (10x Genomics)
Chromium i7 Multiplex Kit (10x Genomics)

value: Blood

value: Red blood cells

value: WT


title: Blvra-/- mouse red blood cells infected with Plasmodium chabaudi chabaudi AS

value: KO


title: pMos_2

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

data_processing:
Raw counts obtained with kallisto version 0.46.1 summing isoforms to obtain counts at the gene level.
Assembly: mm10
Supplementary files format and content: Raw counts in a tab delineated matrix format with samples in columns and genes in rows

source_name: in vitro

extract_protocol:
RNA was extracted using RNAzol according to manufacturer's specifications (Sigma-Aldrich R4533)
Samples were prepped following the standard protocol for the NEBnext Ultra II Stranded mRNA kit (New England Biolabs)

value: in vitro

value: primary

value: patrolling monocyte

value: wt

tag: strain background


title: Xenograft tumor from LNCaP OR51E2-KO cells, biological replicate A17

value: LNcaP FGC clone, OR51E2 knockout

value: prostate cancer cells

value: OR51E2 KO

value: Xenograft tumor grown in CIEA NOG male mice


title: pMos_1


title: imBAT_treated_nd_18r

value: Brown Adipose Tissue

value: NOD/ShiLtJ


title: pMos_0


title: SwDI PBS F2

value: brain

value: Tg-SwDI

value: female

value: PBS


title: intMos_2

value: intermediate monocyte


title: krbh_treated_d_15l

value: Sham (KRBH buffer)


title: intMos_1


title: Xenograft tumor from LNCaP OR51E2-KO cells, biological replicate A15


title: A549 cells,si-GANC-2(siGANC-2),36h

description: Library name: siGANC2

value: lungs

value: Alveolar Basal Epithelial Cells in Lung Cancer

value: WT


title: imBAT_treated_nd_16rl

value: imBAT conditioned buffer (>100kDa)


title: cMos_2

value: in vitro

value: primary

value: conventional monocyte

value: wt


title: imBAT_treated_nd_14r


title: intMos_0


title: cMos_1


title: Xenograft tumor from LNCaP OR51E2-KO cells, biological replicate A14

value: LNcaP FGC clone, OR51E2 knockout

value: prostate cancer cells

value: OR51E2 KO

value: Xenograft tumor grown in CIEA NOG male mice


title: lymph nodes, protein_vaccine

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: 10x Genomics

data_processing:
CellRanger suite (pipeline v7.0.0 https://support.10xgenomics.com) was used with refdata-gex-mm10-2020-A transcriptome as a reference to map reads on the mouse genome.
Assembly: mm10
Supplementary files format and content: 10x Cellranger output with barcodes, features, and matrix

source_name: lymph nodes

extract_protocol:
Live CD45+ CD19- TCR - cells were sorted and subsequently uniquely barcoded using the 10× chromium single-cell platform, and complementary DNA (cDNA) libraries were prepared for Next Generation Sequencing according to the manufacturer’s protocol (Chromium Next GEM Single Cell 3′ Reagent Kits v3.1, 10× Genomics, USA). Cell suspensions of each sample, reverse transcription master mix, and partitioning oil were loaded on a single-cell “G” chip with a targeted cell output of 10,000 cells per library and then run on the Chromium Controller. A total of 4 lanes were used on the G chip, 1 lane/sample. Reverse transcription was performed within the droplets at 53°C for 45 min and newly synthesized cDNA was amplified for 11 cycles on a Veriti Thermal Cycler (Thermofisher, USA). cDNA size selection was performed using SPRIselect beads (Beckman Coulter, USA) following manufacturer’s protocol. cDNA was analyzed on an Agilent Tapestation High Sensitivity D5000 (Agilent, USA) for qualitative and quantitative control purposes.
cDNA was then used to make libraries according to manufacturer’s protocol (Chromium Next GEM Single Cell 3’ Reagent Kit v3.1). cDNA was fragmented using the proprietary fragmentation enzyme blend for 5 min at 32°C, followed by end-repair and A-tailing at 65°C for 30 min. cDNA was double-sided size selected using SPRIselect beads. Sequencing adaptors were ligated to the cDNA at 20°C for 15 min. and after a round of post-ligation SPRIselect bead clean-up, cDNA was amplified for 14 cycles using a sample-specific index oligo as a primer. A final round of double-sided size selection using SPRIselect beads followed. Final library size and quantity was determined using an Agilent Tapestation High Sensitivity D5000 (Agilent, USA) and a Qubit dsDNA High Sensitivity Assay kit (Thermofisher, USA), respectively. Additional library quantification was done using the Kapa Library Quantification kit for Illumina Libraries (Roche, USA).

value: Lymph node

tag: strain

value: BALB/c


title: lymph nodes, mRNA_vaccine

description: 10x Genomics


title: lymph nodes, DNA_vaccine

description: 10x Genomics


title: Xenograft tumor from LNCaP OR51E2-KO cells, biological replicate A13


title: Xenograft tumor from LNCaP WT cells, biological replicate A11

source_name: LNCaP FGC clone

value: LNCaP FGC clone


title: 22rr.(imbat_s)

source_name: inguinal White adipose tissue

extract_protocol:
RNA has been isolated from inguinal white adipose tissue using RNeasy Lipid Tissue Mini Kit and eluted with water. 10-15ug of RNA was used for RNA-sequencing.
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000.  Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a.

value: inguinal White adipose tissue

value: NOD/ShiLtJ


title: Xenograft tumor from LNCaP WT cells, biological replicate A12


title: cMos_0


title: 31rr.(imbat_s)


title: 29ll.(imbat_s)


title: Xenograft tumor from LNCaP OR51E2-KO cells, biological replicate A16


title: CBN 20 μM, biol rep3

city: Laurel

first: Xiugong

last: Gao

state: MD

address: 8301 Muirkirk Rd

department: HFP/OLOAS/OCT/DT

institute: US FDA

description: Library name: CBN21

data_processing:
Concatenated base call files (.cbcl) generated from the sequencing run were converted to a FASTQ file for each sample by the DRAGEN BCL Convert pipeline. The .cbcl files were further analyzed by the DRAGEN RNA pipeline to generate transcript quantification results at the gene level (.quant.genes.sf).
Assembly: Human reference genome hg38-alt-aware
Supplementary files format and content: Files in .sf format containing transcript quantification results at the gene level.

source_name: iPSC-derived hepatocytes

growth_protocol: Commercial iPSC-derived hepatocytes (iCell Hepatocytes 2.0) from FUJIFILM Cellular Dynamics (Madison, WI) were cultured following the manufacturer’s protocols.

extract_protocol:
Cells were lysed in RLT buffer (Qiagen) supplemented with β-mercaptoethanol, homogenized by QIAshredder (Qiagen), and kept in a -80 °C freezer until further processing. Total RNA was isolated on the EZ1 Advanced XL (Qiagen) automated RNA purification instrument using the EZ1 RNA Cell Mini Kit (Qiagen) following the manufacturer’s protocol, including an on-column DNase digestion.
Sequencing libraries were prepared using the Illumina Stranded mRNA Prep, Ligation kit (San Diego, CA) following protocols provided by the manufacturer.

treatment_protocol: Cells cultured at day 6 after seeding were exposed to CBN at varying concentrations (0.1-20 µM) in triplicate for 24 h.

value: iPSC-derived hepatocytes

value: CBN 20 μM


title: 28l.(imbat_s)


title: Xenograft tumor from LNCaP WT cells, biological replicate A10

value: WT


title: CBN 20 μM, biol rep2

description: Library name: CBN20


title: 4Ping_MDSC_blank_S4

description: Library name: Sample3

value: BM-derived MDSC

value: MDSC

value: blank


title: lymph nodes, naïve

description: 10x Genomics

value: naive


title: CBN 20 μM, biol rep1

description: Library name: CBN19


title: 28n.(sham)

value: Sham (KRBH buffer)


title: CBN 10 μM, biol rep3

description: Library name: CBN18

value: CBN 10 μM


title: Xenograft tumor from LNCaP WT cells, biological replicate A9

value: prostate cancer cells


title: CBN 10 μM, biol rep1

description: Library name: CBN16


title: 29l.(sham)


title: Xenograft tumor from LNCaP WT cells, biological replicate A8


title: CBN 5.0 μM, biol rep3

description: Library name: CBN15

value: CBN 5.0 μM


title: 31r..(sham)


title: Xenograft tumor from LNCaP WT cells, biological replicate A7

value: Xenograft tumor grown in CIEA NOG male mice


title: CBN 5.0 μM, biol rep2

description: Library name: CBN14


title: CBN 5.0 μM, biol rep1

description: Library name: CBN13


title: mouse 9-AP806;Liver Male RNA rep2

city: Pittsburgh

first: Irene

middle: Miriam

last: Kaplow

address: 5000 Forbes Avenue, Gates-Hillman 7703

department: Computational Biology

institute: Carnegie Mellon University

data_processing:
We used a custom python script to tally the barcode counts per sample.
For each sequence entry, we searched for the common restriction enzyme site present in both the DNA and the RNA.
Using the location of the enzyme, we identified the sequence of the unique barcode.
We noted cases where the restriction enzyme site or the barcode sequence were not found in sequence entry.
Supplementary files format and content: csv file, where each row is for a bar-code, each column is for a tissue or cell line sample, and each entry is the number of reads for the bar-code in the sample

source_name: liver

growth_protocol: HMC3 cells (ATCC #CRL-3304) were maintained according to manufacturer's specifications

extract_protocol:
We extracted total RNA using RNeasy Mini Kit (Qiagen, cat#74104) and prepared cDNA with a specific reverse transcription primer
MPRA barcodes were amplified from cDNA using Illumina Nextera amlification primers

treatment_protocol:
HMC3 cells were transfected with 250 ug of the MPRA plasmid library with FuGENE6 and allowed to incubate for 72 hours
C57BL6/J mice were transduced with 7.73x1011 to 2.28x1012 vector genomes (vg) total into the retro-orbital cavity

value: liver

value: AAV transduction

tag: time

value: 21 days


title: CBN 1.0 μM, biol rep3

description: Library name: CBN12

value: CBN 1.0 μM


title: Xenograft tumor from LNCaP WT cells, biological replicate A5

value: LNCaP FGC clone


title: CBN 1.0 μM, biol rep2

description: Library name: CBN11

value: iPSC-derived hepatocytes


title: CBN 1.0 μM, biol rep1

description: Library name: CBN10


title: CBN 0.5 μM, biol rep3

description: Library name: CBN09

value: CBN 0.5 μM


title: mouse 9-AP806:Kidney Male RNA rep2

source_name: kidney

value: kidney


title: mouse 9-AP806;Hypothalamus Male RNA rep2

source_name: brain (hypothalamus)

value: brain (hypothalamus)


title: mouse 8-AP802:Liver Female RNA rep2

value: 20 days


title: CBN 0.5 μM, biol rep1

description: Library name: CBN07


title: Xenograft tumor from LNCaP WT cells, biological replicate A3

value: WT


title: CBN 0.5 μM, biol rep2

description: Library name: CBN08


title: mouse 8-AP802;CTX Female RNA rep2

source_name: brain (cortex)

value: brain (cortex)


title: CBN 0.1 μM, biol rep3

description: Library name: CBN06

value: CBN 0.1 μM


title: CBN 0.1 μM, biol rep2

description: Library name: CBN05


title: CBN 0.1 μM, biol rep1

description: Library name: CBN04


title: Xenograft tumor from LNCaP WT cells, biological replicate A2


title: CBN 0.0 μM (control), biol rep2

description: Library name: CBN02

value: CBN 0.0 μM (control)


title: CBN 0.0 μM (control), biol rep3

description: Library name: CBN03


title: CBN 10 μM, biol rep2

description: Library name: CBN17

value: CBN 10 μM


title: mouse 5-AP796:Liver Male RNA rep2


title: CBN 0.0 μM (control), biol rep1

description: Library name: CBN01


title: PCD Subject 2, Airway cells, scRNAseq

city: St Louis

first: Amjad

last: Horani

address: 660S Euclid Ave

institute: Washington University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Primary airway cells

growth_protocol: Cells were diffrentiated and maintained at ALI conditions

extract_protocol:
Airway cells were isolated after incubation in trypsin for 5 minutes and mechanical dissociation. The isolated cells were resuspended in tryspin for  and incubated at 37 °C for 5 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (PBS+0.04% BSA).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains a primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up, amplified, and the apropiated sized fragments were selected for subsequent library construction.

value: Primary airway cells


title: Xenograft tumor from LNCaP WT cells, biological replicate A4

value: prostate cancer cells

value: Xenograft tumor grown in CIEA NOG male mice


title: CBC 40 μM, biol rep2

description: Library name: CBC23

treatment_protocol: Cells cultured at day 6 after seeding were exposed to CBC at varying concentrations (0.1-40 µM) in triplicate for 24 h.

value: CBC 40 μM


title: mouse 5-AP796;Hp Male RNA rep2

source_name: brain (hippocampus)

value: brain (hippocampus)

value: AAV transduction

value: 19 days


title: mouse 5-AP796;STR Male RNA rep2

source_name: brain (striatum)

value: brain (striatum)


title: CBC 40 μM, biol rep1

description: Library name: CBC22

value: iPSC-derived hepatocytes


title: PCD Subject 1, Airway cells, scRNAseq

description: 10x Genomics


title: CBC 20 μM, biol rep3

description: Library name: CBC21

value: CBC 20 μM


title: mouse 2-AP683;Hp Female RNA rep2


title: CBC 20 μM, biol rep2

description: Library name: CBC20


title: CBC 20 μM, biol rep1

description: Library name: CBC19


title: mouse 2-AP683;CTX Female RNA rep2


title: CBC 10 μM, biol rep3

description: Library name: CBC18

value: CBC 10 μM


title: Healthy Subject 4, Airway cells, scRNAseq

description: 10x Genomics


title: CBC 10 μM, biol rep2

description: Library name: CBC17


title: mouse 1-AP669;STR Male RNA rep2


title: Healthy Subject 3, Airway cells, scRNAseq

description: 10x Genomics


title: H9 iETV2 hPSC

source_name: H9 iETV2

value: H9 iETV2

value: Pluripotent Stem Cells


title: Healthy Subject 2, Airway cells, scRNAseq

description: 10x Genomics


title: mouse 1-AP669;CTX Male RNA rep2

value: brain (cortex)


title: mouse 10-AP804;Lung Female RNA rep2

source_name: lung

value: lung

value: 21 days


title: CBC 5.0 μM, biol rep2

description: Library name: CBC14

value: CBC 5.0 μM


title: Healthy Subject 1, Airway cells, scRNAseq

description: 10x Genomics

value: Primary airway cells


title: CBC 5.0 μM, biol rep3

description: Library name: CBC15


title: CBC 5.0 μM, biol rep1

description: Library name: CBC13


title: CBC 10 μM, biol rep1

description: Library name: CBC16


title: CBC 1.0 μM, biol rep3

description: Library name: CBC12

value: CBC 1.0 μM


title: CBC 1.0 μM, biol rep2

description: Library name: CBC11


title: CBC 0.5 μM, biol rep3

description: Library name: CBC09

value: CBC 0.5 μM


title: mouse 10-AP804:Liver Female RNA rep2

value: liver


title: Healthy Subject 6, Airway cells, scRNAseq

description: 10x Genomics


title: CBC 1.0 μM, biol rep1

description: Library name: CBC10


title: Patient_20151223, Binet_A, IgHV_N

city: Taipei

first: Ho-Yang

last: Tsai

address: No. 128, Sec. 2, Academia Rd., Nangang Dist.

department: Genomics research center

country: Taiwan

institute: Academia Sinica

data_processing:
Trimmomatic（v.0.38）
Raw reads were trimmed for adaptor sequence. And low-qualilty sequence were trimmed off on the basis of (1) nucelotides on both ends of sequence (parameter_quality<3); (2) accumulated  score of 4 successive  nucleotides (parameter_quality<20; the following sequences and these 4 nucleotides were trimmed); (3) read length less than 36.
Assembly: Clean reads were mapped to hsa_GRCh38 using HISAT2 and the number of reads to individual genes was counted using featureCounts (v1.6.3).
Supplementary files format and content: Tab-delimited text files includes raw counts, TPM and FPKM values for all samples

source_name: Blood

extract_protocol:
Total RNA was prepared from 5×10^6 purified B cells with RNeasy Mini Kit (Qiagen)
Sequencing library was prepared with KAPA mRNA HyperPrep Kit (Roche)

value: Blood

value: CD19+ B cells


title: mouse 10-AP804;Hypothalamus Female RNA rep2

value: brain (hypothalamus)

value: AAV transduction


title: Healthy Subject 5, Airway cells, scRNAseq

description: 10x Genomics


title: CBC 0.5 μM, biol rep2

description: Library name: CBC08

value: iPSC-derived hepatocytes


title: Patient_20180118, Binet_C, IgHV_M


title: mouse 10-AP804;Muscle Female RNA rep2

source_name: muscle

value: muscle


title: CBC 0.5 μM, biol rep1

description: Library name: CBC07


title: PCD Subject 3, Airway cells, scRNAseq

description: 10x Genomics


title: CBC 0.1 μM, biol rep3

description: Library name: CBC06

value: CBC 0.1 μM


title: Patient_20170111, Binet_A, IgHV_N


title: mouse 10-AP804:Kidney Female RNA rep2

value: kidney


title: CBC 0.1 μM, biol rep1

description: Library name: CBC04


title: CBC 0.1 μM, biol rep2

description: Library name: CBC05


title: Patient_20161207, Binet_A, IgHV_M


title: Patient_20161130, Binet_A, IgHV_N


title: mouse 8-AP802;PFC FeMale RNA rep1

source_name: brain (pre-frontal cortex)

value: brain (pre-frontal cortex)

value: 20 days


title: Patient_20161027, Binet_A, IgHV_N


title: CBC 0.0 μM (control), biol rep1

description: Library name: CBC01

value: CBC 0.0 μM (control)


title: CBC 0.0 μM (control), biol rep2

description: Library name: CBC02