title: CTCF, CHIP, shYTHDC1

description:
Library name: shYTHDC1-CTCF-ChIP-seq
shYTHDC1-CTCF-ChIP-seq


title: RAD21, CHIP, Control

status: Public on Feb 11 2026

type: SRA

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

country: China

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

description:
Library name: Ctrl-RAD21-ChIP-seq
Ctrl-RAD21-ChIP-seq

library_source: genomic

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq, ATAC-seq, DRIP-seq, DRIPc-seq, RIP-seq, 4C-seq, ChIP-seq, and HiC-seq from MOLM13 AML cells were aligned to the hg19  genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks and visualization files were created using deepTools version 3.0
Peak annotation was performed with HOMER(version 4.10)
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include FPKM values for RNA-seq Samples, and bigwig and bed peaks for DRIPseq, DRIPc-seq, RIP-seq, ATAC-seq, MeRIP-seq, ChIP-seq, 4C-seq and HiC-seq.

molecule: genomic DNA

organism: Homo sapiens

source_name: leukemia cells

growth_protocol: Human MOLM13 leukemia cells were culture at RMPI1640 medium with 10% FBS media.

extract_protocol:
Total RNA was purified from cells using the TRIzol reagent (TIANGEN, cat# DP424), followed by standard chloroform phase separation and alcohol precipitation. cDNA was synthesized from 1 μg total RNA, and reverse transcription was performed using the HiScript II Q RT SuperMix kit (Vazyme, cat#R222-01) according to the manufacturer’s instructions. The ATAC-seq assay was performed as described previously. Brieﬂy, 5x104 cells were washed twice with PBS and lysed in lysis buffer containing 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.1 % NP-40. The lysate was washed in PBS and treated with Tn5 transposase at 37°C for 30 minutes. DNA was puriﬁed using the DNA purification Kit (TIANGEN, Cat# DP214). DNA library was then generated by Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, cat# TD711-01).
RNA sequencing libraries were prepared from 1 μg of total RNA using the VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, cat# NR605-01/02) following the manufacturer instructions.  ChIP-DNA libraries were prepared using the Illumina’s VAHTS Universal Pro DNA Library Prep Kit according to the manufacturer’s instructions (Vazyme, cat# ND608-01/02).  The ATAC-seq DNA was puriﬁed using the DNA purification Kit (TIANGEN, Cat# DP214). ATAC chromatin DNA library was then generated by Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, cat# TD711-01). Hi-C assay was performed to generate a genome-wide interaction as described previously with Arima-HiC Kit (Cat: A410030) (https://arimagenomics.com/) with minor modifications.

treatment_protocol: Immediately extract RNA from MOLM13 AML cells without any treatment

tag: tissue

value: leukemia cells

tag: cell line

value: MOLM13 cells

tag: cell type

value: acute myeloid leukemia

tag: genotype

value: WT

tag: chip antibody


title: H3K27ac, CHIP, RNase

description:
Library name: RNase-H3K27ac-ChIP-seq
RNase-H3K27ac-ChIP-seq

value: H3K27ac (Abclonal, Cat#A7253)


title: CTCF, CHIP, Control

description:
Library name: Ctrl-CTCF-ChIP-seq
Ctrl-CTCF-ChIP-seq

value: CTCF (CST, Cat# 2899)


title: CTCF, CHIP, RNase

description:
Library name: RNase-CTCF-ChIP-seq
RNase-CTCF-ChIP-seq


title: METTL3, CHIP, Control

description:
Library name: METTL3-ChIP-seq
METTL3-ChIP-seq

value: METTL3 (Abclonal, Cat#A26858)


title: H2BO Treated-3

city: Grand Rapids

first: Yvonne

middle: Nsokika

last: Fondufe-Mittendorf

state: MI

address: 333 Bostwick Ave NE

department: Epigenetics

country: USA

institute: Van Andel Institute

description: Library name: H2BOTR3

library_source: transcriptomic

data_processing:
Base calling was performed using Illumina RTA3, and the NCS output was demultiplexed and converted to FastQ format using Illumina Bcl2fastq v2.20.0.
To trim reads and remove low-quality bases and adapter sequences, we used TrimGalore v0.6.10 and parameters ‘--paired -q 20’.
Trimmed reads were aligned to the hg38 reference genome using STAR v2.7.10a.
Bigwig files were generated using bamCoverage from DeepTools v3.5.2 with the parameters, '--minMappingQuality 30 --normalizeUsing "None" --binSize 10', and using "--scaleFactor" to set the scaling factor, which was the reciprocal of the scaling factor calculated using DESeq2.
Assembly: hg38
Supplementary files format and content: BigWig

molecule: total RNA

source_name: cell line

growth_protocol: Human breast epithelial cells, MCF10A, were cultured in DMEM/F12 media supplemented with 5% horse serum, 1X penicillin-streptomycin, 20 ng/mL EGF, 0.5 ug/mL hydrocortisone, 100 ng/mL cholera toxin, and 10 μg/mL insulin. Cells were mainted in humidified incubator at 37C with 5% CO2.

extract_protocol:
Total RNA was extracted from washed and pelleted cells using the Quick-RNA Miniprep Kit per the manufacturer’s protocol (Zymo Research #R1054), and eluted in RNase-free water
Total RNA was depleted of ribosomal RNA with the QIAseq FastSelect –rRNA HMR Kit, libraries were contructed using the KAPA RNA HyperPrep Kit following manufacturers protocols.

treatment_protocol: MCF10A cells were electroporated with either constructs stably expressing mRNA of H2B variants under their own promoter or empy vector control constructs.

value: cell line

value: breast epithelial

value: H2BO-2xHA mRNA overexpression

tag: treatment

value: nucleofection+TNFalpha and TGFB


title: H2BO Treated-1

description: Library name: H2BOTR1


title: H2BH Treated-2

description: Library name: H2BHTR2

value: H2BH-2xHA mRNA overexpression


title: H2BO Treated-2

description: Library name: H2BOTR2


title: H2BH Treated-1

description: Library name: H2BHTR1


title: H2BC Treated-2

description: Library name: H2BCTR2

value: H2BC-2xHA mRNA overexpression


title: H2BC Treated-3

description: Library name: H2BCTR3


title: H2BH Treated-3

description: Library name: H2BHTR3


title: EV Treated-1

description: Library name: EVTR1

value: Empty vector control


title: Treated-4

description: Library name: Treated4

value: TNFalpha and TGFB


title: EV Treated-2

description: Library name: EVTR2


title: H2BC Treated-1

description: Library name: H2BCTR1


title: EV Treated-3

description: Library name: EVTR3


title: Treated-3

description: Library name: Treated3


title: Treated-2

description: Library name: Treated2


title: H2BO-2xHA-1

description: Library name: H2BO1

value: nucleofection


title: H2BH-2xHA-3

description: Library name: H2BH3


title: H2BH-2xHA-2

description: Library name: H2BH2


title: H2BH-2xHA-1

description: Library name: H2BH1


title: H2BO-2xHA-3

description: Library name: H2BO3


title: H2BC-2xHA-2

description: Library name: H2BC2


title: H2BC-2xHA-3

description: Library name: H2BC3


title: EV-2

description: Library name: EV2


title: H2BC-2xHA-1

description: Library name: H2BC1


title: EV-1

description: Library name: EV1


title: EV-3

description: Library name: EV3


title: Treated-1

description: Library name: Treated1


title: 2_O_HA

description: Library name: 2_O_HA

data_processing:
Read quality was assessed using FastQC, and high-quality reads were subsequently aligned to the reference genome (hg38) using Bowtie2.
Genome coverage profiles were generated using bedtools genomecov, and peak calling was performed with MACS2.
Peaks were kept only if the q-value was < 0.01, and the enrichment was > 2.
FeatureCounts in Subread 2.0.0 was then used to count reads mapped to each consensus peak
Assembly: hg38
Supplementary files format and content: bigWig, narrow peaks for H3K4me3 target, broad peaks for H3K27me3 target, and broad peaks for HA target.
Library strategy: CUT&RUN

extract_protocol:
MCF10A cells (empty plasmid vector, or H2B variants expressing cells) were grown to 70-90% confluency. A total of 5 × 10⁵ cells were used per reaction. The cells were washed and subsequently incubated with the target antibody according to the protocol provided in the CUTANA CUT&RUN (version 3) kit. Nuclei bound to ConA beads were then sent to Fred Hutchinson Cancer Research Center (Seattle, WA) for genomic DNA extraction and sequencing.
CUT&RUN seq libraries were prepared in Fred Hutch Cancer center Genomics core. The end repair, A-tailing, adapter ligation, post-ligation cleanup, library amplification, and post-amplification cleanup steps were carried out using the KAPA HyperPrep Kit (Kapa Biosystems, Wilmington, MA, USA), following the manufacturer's protocol.


title: 2_O_H3K4me3

description: Library name: 2_O_H3K4me3


title: 1_O_H3K4me3

description: Library name: 1_O_H3K4me3


title: 3_O_HA

description: Library name: 3_O_HA


title: 1_O_HA

description: Library name: 1_O_HA


title: 2_O_H3K27me

description: Library name: 2_O_H3K27me


title: O_IgG

description: Library name: O_IgG


title: 1_H_HA

description: Library name: 1_H_HA


title: 2_H_H3K4me3

description: Library name: 2_H_H3K4me3


title: 3_H_HA

description: Library name: 3_H_HA


title: 1_H_H3K4me3

description: Library name: 1_H_H3K4me3


title: 1_O_H3K27me

description: Library name: 1_O_H3K27me


title: H_IgG

description: Library name: H_IgG


title: 3_C_HA

description: Library name: 3_C_HA


title: 2_H_H3K27me

description: Library name: 2_H_H3K27me


title: 2_H_HA

description: Library name: 2_H_HA


title: 2_C_H3K4me3

description: Library name: 2_C_H3K4me3


title: 2_C_HA

description: Library name: 2_C_HA


title: 1_C_H3K4me3

description: Library name: 1_C_H3K4me3


title: 1_C_HA

description: Library name: 1_C_HA


title: C_IgG

description: Library name: C_IgG


title: 1_C_H3K27me

description: Library name: 1_C_H3K27me


title: 2_EV_HA

description: Library name: 2_EV_HA


title: 3_EV_HA

description: Library name: 3_EV_HA


title: 2_EV_H3K4me3

description: Library name: 2_EV_H3K4me3


title: 1_H_H3K27me

description: Library name: 1_H_H3K27me


title: 2_EV_H3K27me

description: Library name: 2_EV_H3K27me


title: 1_EV_H3K4me3

description: Library name: 1_EV_H3K4me3


title: EV_IgG

description: Library name: EV_IgG


title: 2_C_H3K27me

description: Library name: 2_C_H3K27me


title: H2BO-2xHA-2

description: Library name: H2BO2


title: NC_EDC_2

city: Bergen

first: Simona

last: Chera

address: Haukelandsbakken 15

country: Norway

institute: University of Bergen

description: Library name: Sample 5

data_processing:
CLC Genomic Workbench version 24.0
Assembly: hg38 (Refseq)
Supplementary files format and content: Geneexpression Track for each sample als xlsx file

source_name: Differentiating cells

extract_protocol:
RNA was extracted using QIAGEN RNeasy mini
Performed by UiB Genomic Core Facility

value: Differentiating cells

value: induced pluripotent stem cells

value: non carrier

value: 1 mM EDC mix for 14 days


title: 1_EV_HA

description: Library name: 1_EV_HA


title: 1_EV_H3K27me

description: Library name: 1_EV_H3K27me


title: NC_EDC_1

description: Library name: Sample 4


title: NC_NT_3

description: Library name: Sample 3

value: Non treated


title: NC_NT_2

description: Library name: Sample 2


title: NC_EDC_3

description: Library name: Sample 6


title: pA_RNA-Low-Exp1-RepC

city: Durham

first: Brian

last: Bennett

address: 111 T.W. Alexander Drive

institute: NIEHS

data_processing:
Aligned using STAR
Counts generated with featureCounts and GENCODE v44.basic
Assembly: hg38
Supplementary files format and content: tab-delimited text: column 1 = gene, column 2 = counts

source_name: Cell Line

growth_protocol: MCF7 cells were cultured in DMEM supplemented with 10% FBS, 1% Pen/Strep and 1% L-Glutamine and hormone depleted in Phenol-red free DMEM supplemented with 10% Charcoal-stripped FBS, 1% Pen/Strep and 1% L-Glutamine.

extract_protocol:
For total RNA extraction :  cell pellets were resuspended in 1 mL of Trizol and RNA was extracted following manufacturer's instructions. For Nascent RNA extraction :  cell pellets were lysed in a hypotonic buffer, nuclei were purified on sucrose cushion, the chromatin fraction was then extracted using a high-salt high-urea concentration buffer (300mM NaCl, 1M Urea, 1% NP-40) and chromatin-bound nascent RNA was further extracted using Trizol according to manufacturer´s instructions.
Total RNA or  Nascent RNA were processed using NEBNext Ultra II directional RNA library prep kit for Illumina (#E7760) using section 1 “Protocol for use with NEBNext Poly(A) mRNA Magnetic Isolation Module” or section 4 “Protocol for use with purified mRNA”, respectively.

treatment_protocol: MCF7 cells were hormone depleted for 72 hours before Estrogen stimulation using 1nM E2 for 24 hours, or ethanol for the control condition.

value: Cell Line

value: ER+ Breast Cancer

value: 48h 1nM E2 TFF1low


title: pA_RNA-Low-Exp1-RepB


title: pA_RNA-High-Exp1-RepC

value: 48h 1nM E2 TFF1high


title: NUN-High-Exp2-RepC

library_source: other

data_processing:
Aligned using STAR
Counts generated with featureCounts and GENCODE v44.basic
Assembly: hg38
Supplementary files format and content: tab-delimited text: column 1 = gene, column 2 = counts
Library strategy: Nascent RNA-seq

molecule: other


title: pA_RNA-High-Exp1-RepA


title: NC_NT_1

description: Library name: Sample 1


title: pA_RNA-Low-Exp1-RepA


title: NUN-Low-Exp2-RepB


title: NUN-High-Exp2-RepB


title: pA_RNA-High-Exp1-RepB


title: NUN-High-Exp1-RepC


title: NUN-Low-Exp2-RepC


title: NUN-Low-Exp1-RepB


title: NUN-High-Exp1-RepB


title: NUN-Low-Exp1-RepC


title: NUN-Low-Exp1-RepA


title: NUN-High-Exp2-RepA


title: NUN-High-Exp1-RepA


title: H3K27ac-Low-RepB

data_processing:
Data were processed using an adapted pipeline from Hoffman et al., eLife, 2018 (PMID: 29792595)
Assembly: hg38
Supplementary files format and content: bigWig: read coverage
Library strategy: CUT&Tag

extract_protocol:
Fresh nuclei were extracted  according to the Bench top CUT&Tag V.3 protocol (PMID: 31036827)
Extracted DNA was PCR amplified using unique primer sets (Nextera XT v2 Full Set (N7-S5).

treatment_protocol: MCF7 cells were hormone depleted for 72 hours before Estrogen stimulation using 1nM E2 for 48 hours of treatment.


title: H3K27ac-High-RepA


title: H3K27ac-High-RepB


title: NUN-Low-Exp2-RepA


title: WCH_NC04

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

institute: Sichuan University

library_source: transcriptomic single cell

data_processing:
The raw single-cell RNA sequencing (scRNA-seq) data were preprocessed, which included demultiplexing cellular barcodes, aligning reads, and generating a gene count matrix, using Cell Ranger (version 4.0.0) software from 10X Genomics. Quality control (QC) metrics for all cells were generated and assessed to ensure high-quality data for subsequent analysis. In brief, cells exhibiting fewer than 200 or more than 6,000 unique molecular identifier (UMI) counts, or having over 50 counts of mitochondrial RNAs, were excluded. The remaining count data were normalized using the “LogNormalize” method with a scale factor of 10,000. The “ScaleData” function was applied to standardize the gene count numbers and the percentage of mitochondrial content in the normalized data. The “FindVariableFeatures” function was then used to identify the top 2,000 variable features, which were subsequently analyzed using principal component analysis (PCA). To mitigate potential batch effects among samples, the “RunHarmony” function from the “Harmony” package was employed 85. Following these preprocessing steps, cell clusters were delineated using the shared nearest neighbor (SNN) modularity optimization based on the original Louvain algorithm. The resulting clusters were visualized using Uniform Manifold Approximation and Projection (UMAP).
Assembly: GRCh38
Supplementary files format and content: rds files

molecule: polyA RNA

source_name: Normal adjacent tissue

extract_protocol:
The tissues were digested by collagenase I (2 mg/ml) (Gibco 1710-0017), collagenase IV (1 mg/ml) (Gibco 1710-4019), and 0.25% pancreatic enzymes (Gibco 25200-056) for 1 hour at 37°C. The digested tissues were filtered through 40-mm strainer to remove cell debris and large clumps. The suspensions were pelleted at 500gfor 5 min at 4°C. After lysis of the red blood cells with 10× RBC Lysis Buffer (Thermo Fisher Scientific, 00-4300-54), the pellets were resuspended in HBSS with 0.04% bovine serum albumin (BSA) to count cell viability and concentration (Counting Star, Aber Instruments Ltd.). The remaining cells were pelleted at 500gfor 5 min at 4°C and preserved at −80°C. Single-cell suspensions were finally diluted to 5 × 106cells per milliliter.
The Chromium Single Cell 3′ Library & Gel Bead Kit v2 (PN- 120237), Chromium Single Cell 3’ Chip Kit v2 (PN-120236), and Chromium i7 Multiplex Kit (PN-120262) were used according to the manufacturer’s instructions in the Chromium Single Cell 3′ Reagents Kits v2 User Guide. The single-cell suspension was washed twice with 1× phosphate-buffered saline (PBS) + 0.04% BSA. Cell number and concentration were confirmed with TC20 Automated Cell Counter. Cells were subjected immediately onto a 10× Genomics Chromium Controller machine for gel beads-in-emulsion (GEM) generation. Barcoded complementary DNAs (cDNAs) were prepared using a 10× Genomics Chromium Single Cell 3′ reagent kit (V2 chemistry), which was subsequently recovered, purified, and amplified to generate sufficient quantities for library preparation. Library quality and concentration were assessed using Agilent Bioanalyzer 2100.

value: Normal adjacent tissue

tag: Sex

value: Male

tag: age

tag: diagnosis

value: Advanced Gastric Cancer (AGC)


title: WCH_NC03


title: H3K27ac-Low-RepA


title: WCH_NC02


title: WCH_GC06

source_name: Primary tumor

value: Primary tumor

value: Female


title: WCH_NC01


title: WCH_GC07


title: WCH_GC04


title: WCH_GC05


title: WCH_GC03


title: WCH_GC01


title: WCH_GC02


title: J084

city: Moncton

first: Eric

middle: P

last: Allain

state: New Brunswick

address: 330 University ave

department: Medical Genetics

country: Canada

institute: Vitalité Health Network

data_processing:
TrimGalore-0.6.6/trim_galore -a TGGAATTCTCGGGTGCCAAGG --clip_R1 4 --three_prime_clip_R1 4 --length 18 {input.fq_in} --output_dir {output.trimdir}
STAR-2.7.9a/bin/Linux_x86_64/STAR --runThreadN 16 --genomeDir {input.ref} --readFilesIn {input.trim_in} --readFilesCommand gunzip -c --outFileNamePrefix {params.pr} --outFilterScoreMinOverLread 0 --outFilterMatchNmin 16 --outFilterMatchNminOverLread 0 --outFilterMismatchNoverLmax 0.025 --alignIntronMax 1 --alignEndsType EndToEnd --outSAMtype BAM Unsorted"
Quantification with derfinder - see https://github.com/acri-nb/sRNA_Seq_pipeline/blob/main/Step2_derfinder_script_v3.R
DGE with edgeR - see https://github.com/acri-nb/sRNA_Seq_pipeline/blob/main/Step3_DE_edgeR.Rmd
Assembly: hg38
Supplementary files format and content: Excel table with read counts, alignment coordinates and statistics such as fold-change, annotation, % annotation covered.

source_name: Blood

extract_protocol:
miRVana Total RNA kit
NEXTFlex small RNA v3

value: Blood

value: Primary human samples

value: Human Plasma Evs

value: GBM


title: J082


title: J077


title: J087


title: J079


title: J053


title: J037


title: Control Plasma EV 4

description: Yellow

value: Control


title: J045


title: J066


title: Control Plasma EV 3

description: Orange


title: Control Plasma EV 2

description: Green


title: Kidney cyst 1

city: Milan

first: Giulia

middle: Maria

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

country: Italy

institute: Fondazione Human Technopole

data_processing:
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.39)
Retained reads were mapped to the reference human genome, GRCh38, using STAR (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using featureCounts (version 1.6.4). Only reads mapped to exons were considered in the counting procedure. Genomic features were annotated according to Gencode basic annotations, version 31.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: kidney

extract_protocol:
Immediately after surgery, samples were harvested by a dedicated pathologist, flash-frozen in liquid nitrogen and then kept at -80°C before RNA extraction.
RNA was extracted using a miRNeasy kit (Qiagen) according to the manufacturer's instructions. RNA purity was determined by NanoDrop spectrophotometer and integrity, and concentration of isolated RNA was assessed using the Tape Station 4100 (Agilent). RNA samples with RIN values <7 were excluded.
RNA libraries for bulk RNA-seq were prepared using the Illumina Stranded mRNA kit starting from 100 ng of good quality RNA.

value: kidney

value: renal cyst

tag: disease state

value: VHL disease


title: J070


title: Lesion 10 of ccRCC from the right kidney

value: ccRCC


title: Kidney cyst 2


title: Lesion 7 of ccRCC from the left kidney


title: Control Plasma EV 1

description: Blue


title: Normal epithelial cells from renal parenchyma

description: LN

value: renal epithelial cell


title: Lesion 5.1 of ccRCC from the left kidney


title: Normal epithelial cells from renal parenchyma [scRNA-Seq]

data_processing:
FASTQ files were demultiplexed from the raw base call (BCL) files using 10x Genomics 'cellranger demux' (CellRanger v3.0.2).
The whitelists of cell barcodes wwere identified with the 'umi_tools whitelist' command, then reads of the whitelisted cells were extracted with the 'umi_tools extract' command (UMI-tools version 1.0.0).
Extracted reads were aligned with STAR aligner (v2.5.3a) to the primary assembly of human genome GRCh38
Uniquely mapped reads were assigned to gene_name attributes from GENCODE basic annotation (v. 31) using featureCounts (v1.6.4).
Per gene counts were summarized for each cell using the 'umi_tools count' command
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes mRNA molecule count values for all the samples

extract_protocol:
Immediately after surgery, five independent tumors (i.e., L1, L2, L4, L5.1 and L7) and one sample of normal parenchyma were harvested by a dedicated pathologist and transfered to a storage buffer (Miltenyi Biotech).
Each sample was dissociated with a Tumor dissociation kit (Miltenyi Biotec) using a gentleMACS Dissociator according to the manufacturer’s instructions. For each sample, around 2000 cells were isolated and captured using the droplet-based Chromium 10X platform.
Chromium Single Cell 3′ Library & Gel Bead Kit v3 kit (10xGenomics).


title: Lesion 5.1 of ccRCC from the left kidney  [scRNA-Seq]


title: Lesion 7 of ccRCC from the left kidney  [scRNA-Seq]


title: Lesion 2 of ccRCC from the left kidney  [scRNA-Seq]


title: Lesion 4 of ccRCC from the left kidney  [scRNA-Seq]


title: Lesion 2 of ccRCC from the left kidney


title: Lesion 1 of ccRCC from the left kidney  [scRNA-Seq]


title: Sorted CD8 CXCR3+ TCM from healthy donor R53799

type: genomic

city: Kyoto

first: Hiroyuki

last: Matsui

state: Kyoto

address: 54 Shogoin-Kawahara-cho

department: Hematology

country: Japan

institute: Kyoto University Graduate School of Medicine

description:
208125100005_R04C01
Sorted CD8 CXCR3+ TCM from healthy donor

hyb_protocol: Bisulfite-converted DNA was then amplified, fragmented, and hybridized to the Illumina Infinium HumanMethylationEPIC BeadChip following the standard Illumina protocol.

scan_protocol: Raw image intensities were taken by using Illumina iScan SQ instrument.

data_processing:
IDAT files were further converted into beta values by using the minfi R package, with a functional normalization pre-processing step.
normalized beta values

label: Cy3 and Cy5

source_name: Peripheral blood

label_protocol: Extracted DNA was bisulfite-converted by using EZ DNA Methylation kit (Zymo Research) following manufacturer’s protocol.

extract_protocol: Genomic DNA was extracted from the FACS sorted CD8 T cells using Quick-DNA Microprep kit (Zymo Research, D3020) per manufacturer’s protocol.

value: Peripheral blood

value: CD8+ CXCR3+ CM T cell


title: HeLaS3-NT-Rep2

city: Toulouse

first: Claire

last: Vargas

address: 2 Avenue Hubert Curien

country: France

institute: Centre de Recherches en Cancérologie de Toulouse

data_processing:
All analysis were made with Genotoul-Sigenae Galaxy servers.
Read alignements were done on Genome Reference Consortium Human GRCh38.p14 (hg38) with HISAT2 (v.2.2.1 ; unstranded)
Read count extraction and normalization were performed using htseq (v.1.0.0 , overlapping : intersection-non empty)
Read count < 20 were excluded from this analysis using SARTools DESeq2 (v.0.99.2)
Assembly: hg38
Supplementary files format and content: count

source_name: Cervical adenocarcinoma

extract_protocol:
Total RNA was isolated from HeLaS3 cells transfected or not with IDR-GFP constructs from the same experiment as ATAC-seq experiments, using TRIzol® Reagent (Life Technologies) according to supplier’s recommendations. Quality and quantity of total mRNA was ensured by Agilent 5400 Fragment Analyzer system
mRNA libraries were constructed using poly A enrichment preparation. 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. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount

value: Cervical adenocarcinoma

tag: transfection


title: Sorted CD8 CXCR3+ TCM from healthy donor R53269

description:
208125100005_R02C01
Sorted CD8 CXCR3+ TCM from healthy donor


title: Kidney cyst 4


title: Lesion 1 of ccRCC from the left kidney


title: HeLaS3-NT-Rep1


title: HeLaS3-IDRGFP-Rep2


title: HeLaS3-IDRGFP-Rep1


title: Sorted CD8 CXCR3+ TCM from healthy donor R53739

description:
208125090028_R08C01
Sorted CD8 CXCR3+ TCM from healthy donor


title: Sorted CD8 CXCR3+ TCM from healthy donor R53230

description:
208125090028_R04C01
Sorted CD8 CXCR3+ TCM from healthy donor


title: Sorted CD8 CXCR3+ TCM from healthy donor R51312

description:
208125090026_R04C01
Sorted CD8 CXCR3+ TCM from healthy donor


title: Sorted CD8 CXCR3+ TCM from healthy donor R50108 [2]

description:
208125090028_R02C01
Sorted CD8 CXCR3+ TCM from healthy donor


title: Sorted CD8 CXCR3+ TCM from healthy donor R51330

description:
208125090026_R06C01
Sorted CD8 CXCR3+ TCM from healthy donor


title: Sorted CD8 CXCR3+ TCM from healthy donor R50108

description:
208125090026_R02C01
Sorted CD8 CXCR3+ TCM from healthy donor


title: Sorted CD8 CXCR3- TCM from healthy donor R53799

description:
208125100005_R03C01
Sorted CD8 CXCR3- TCM from healthy donor

value: CD8+ CXCR3- CM T cell


title: Sorted CD8 CXCR3- TCM from healthy donor R53269

description:
208125100005_R01C01
Sorted CD8 CXCR3- TCM from healthy donor


title: Sorted CD8 CXCR3+ TCM from healthy donor R53231

description:
208125090028_R06C01
Sorted CD8 CXCR3+ TCM from healthy donor


title: Sorted CD8 CXCR3+ TCM from healthy donor R53645

description:
208125090026_R08C01
Sorted CD8 CXCR3+ TCM from healthy donor


title: Sorted CD8 CXCR3- TCM from healthy donor R50108 [2]

description:
208125090028_R01C01
Sorted CD8 CXCR3- TCM from healthy donor


title: Sorted CD8 CXCR3- TCM from healthy donor R53645

description:
208125090026_R07C01
Sorted CD8 CXCR3- TCM from healthy donor


title: Sorted CD8 CXCR3- TCM from healthy donor R51330

description:
208125090026_R05C01
Sorted CD8 CXCR3- TCM from healthy donor


title: Sorted CD8 CXCR3- TCM from healthy donor R53739

description:
208125090028_R07C01
Sorted CD8 CXCR3- TCM from healthy donor


title: Sorted CD8 CXCR3- TCM from healthy donor R51312

description:
208125090026_R03C01
Sorted CD8 CXCR3- TCM from healthy donor


title: Sorted CD8 CXCR3- TCM from healthy donor R53230

description:
208125090028_R03C01
Sorted CD8 CXCR3- TCM from healthy donor


title: Sorted CD8 CXCR3- TCM from healthy donor R50108

description:
208125090026_R01C01
Sorted CD8 CXCR3- TCM from healthy donor


title: Sadash Day 21 Bio-rep 2

city: Saskatoon

first: Morgan

middle: W

last: Kirzinger

state: Saskatchewan

address: 110 Gymnasium Place

institute: National Research Council Canada

description: Library name: Sample 17

data_processing:
Sequencing adapters, low-quality reads and reads shorter than 75 bp were trimmed using Trimmomatic (v0.39) with default settings.
Filtered reads for each sample were aligned to the wheat reference genome (IWGSC v1.1)  using STAR (v2.7.5a).
Relative gene abundance was estimated using the IWGSC v1.1 annotation and the RSEM (v1.3.3) algorithm.
Assembly: wheat reference genome (IWGSC v1.1)
Supplementary files format and content: wheat_embryogenesis_tpm.xlsx file includes TPM normalized counts for each sample
Supplementary files format and content: wheat_embryogenesis_readCount.xlsx file includes raw read counts for each sample

organism: Triticum aestivum

source_name: microspore cultures

growth_protocol: Seeds were sown in 8-inch pots filled with Sunshine LA4 (Sungro Horticulture, AB, Canada) with 4.5 g slow-release Nutricote fertilizer, 14-13-13. Plants were thinned to three plants per pot after seedling emergence. They were grown under the conditions of 18/6 h photoperiod, 20/18 °C day/night temperatures, and 350-420 μmol/m2/s light intensity in a growth chamber (PGW40, Conviron, Winnipeg, MB, Canada) at the Aquatic and Crop Resource Development Research Centre (ACRD), National Research Council Canada (NRC) in Saskatoon.

extract_protocol:
RNAqueous™-Micro Total RNA Isolation Kit (Thermo Fisher) was used to extract total RNA from pooled microspores.
RNA libraries for RNA-seq were prepared using Illumina TruSeq RNA library kits following the manufacturer’s instructions.

treatment_protocol: Spikes were harvested when microspores reached the mid- to late-uninucleate stage (staged using acetocarmine staining), and microspores were extracted after spikes were exposed to 4°C cold pre-treatment. Microspores were isloated as described previously (Wang et al., 2019. Plant Cell, Tissue and Organ Culture (PCTOC) 139, 589–599).

value: microspore cultures


title: Sorted CD8 CXCR3- TCM from healthy donor R53231

description:
208125090028_R05C01
Sorted CD8 CXCR3- TCM from healthy donor


title: Sadash Day 7 Bio-rep 2

description: Library name: Sample 14


title: Sadash Day 21 Bio-rep 1

description: Library name: Sample 16


title: Sadash Day 21 Bio-rep 3

description: Library name: Sample 18


title: Sadash Day 7 Bio-rep 3

description: Library name: Sample 15


title: Sadash Day 7 Bio-rep 1

description: Library name: Sample 13


title: Sadash Day 0 Bio-rep 3

description: Library name: Sample 12


title: Nanda Day 21 Bio-rep 1

description: Library name: Sample 7


title: Nanda Day 21 Bio-rep 2

description: Library name: Sample 8


title: Sadash Day 0 Bio-rep 2

description: Library name: Sample 11


title: Sadash Day 0 Bio-rep 1

description: Library name: Sample 10


title: Nanda Day 7 Bio-rep 3

description: Library name: Sample 6


title: Nanda Day 7 Bio-rep 1

description: Library name: Sample 4


title: Nanda Day 0 Bio-rep 2

description: Library name: Sample 2


title: Nanda Day 0 Bio-rep 3

description: Library name: Sample 3


title: Nanda Day 0 Bio-rep 1

description: Library name: Sample 1


title: Nanda Day 21 Bio-rep 3

description: Library name: Sample 9


title: rat Schwann cells - mouse dorsal root ganglia myelinated cocultures treated with DMSO (biol repl 1)

city: Milano

first: Luca

last: Massimino

address: Via Olgettina, 58

department: Gastroenterology

institute: Ospedale San Raffaele

data_processing:
Trimming reads with Trimmomatic 0-36
Alignment with Kallisto
Differential Expression analysis with DESeq2
Assembly: mm10, rn5
Supplementary files format and content: xls file with raw counts generated using DESeq2 R-package.

organism:
Mus musculus
Rattus norvegicus

source_name: Primary cell culture, dorsal root ganglia neurons  from E.14.5 C56/Bl6 mouse embryonic development. Rat Schwann cells from P2 Sprague Dawley sciatic nerves

growth_protocol: Mouse dorsal root ganglia (DRG) neurons were isolated from E14.5 embryos and established on rat collagen I (Cultrex) coated glass coverslips or 6–well plates as previously described (Taveggia et al., Neuron 2005)

extract_protocol:
Cell cultures and sciatic nerves were homogenized in TriPure Reagent (Roche) using Precellys Lysing Kit CK14 and homogenizer (8000 rpm, 60 sec at 0°C, twice). RNA extraction was performed according to manufacturer's instruction.
RNAseq libraries were prepared from 2500 ng total RNA using the TruSeq RNA Library Preparation Kit v2 (Illumina, San Diego, CA, USA) after poly(A) capture, according to manufacturer’s instructions.  Quality and size of RNAseq libraries were assessed by capillary electrophoretic analysis with the Agilent 4200 Tape station (Agilent). Libraries were quantified by real–time PCR against a standard curve with the KAPA Library Quantification Kit (KapaBiosystems, Wilmington, MA, USA). After barcoding, the RNA libraries were pooled, denatured, and diluted to equimolar concentration for further analyses.
RNA sequencing was performed by using NextSeq 500 (Illumina) set for 150 cycles in single end (SE). On average 42 million fragments were produced for each sample.

treatment_protocol: Once established, Schwann cells neuronal cocultures were treated with 50ug/ml ascorbic acid to induce myeliantion for 14 days and then treated with AT-56 or DMSO as vehicle control for additional 7 days.

value: wild type

value: DMSO


title: rat Schwann cells - mouse dorsal root ganglia myelinated cocultures treated with AT56 (biol repl 1)

value: Primary cell culture, dorsal root ganglia neurons  from E.14.5 C56/Bl6 mouse embryonic development. Rat Schwann cells from P2 Sprague Dawley sciatic nerves


title: rat Schwann cells - mouse dorsal root ganglia myelinated cocultures treated with AT56 (biol repl 2)


title: rat Schwann cells - mouse dorsal root ganglia myelinated cocultures treated with DMSO (biol repl 2)


title: Nanda Day 7 Bio-rep 2

description: Library name: Sample 5


title: 15_S11723_neurotypical_replicate4

city: Salt Lake City

first: Philip

middle: J

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

description:
Library name: 24149X10
10X genomics

data_processing:
10x genomics Cell Ranger was used to process raw sequencing data, and produce counts
MEX data were further processed and merged with Seurat (4.1), the Seurat object was reanalyzed with Seurat (5.2)
Assembly: GRCh38, hg38
Supplementary files format and content: counts matrix in csv format - counts_matrix_24149.csv
Supplementary files format and content: metadata in csv format - metadata_24149.csv

molecule: nuclear RNA

source_name: prefrontal cortex BA9

growth_protocol: no growth

extract_protocol:
Dissected prefrontal cortex was preserved at -80C until processing. The specimens were gently thawed in 2 ml of ice-cold phosphate-buffered saline (PBS, devoid of Ca2+ and Mg2+). This solution was supplemented with various compounds to preserve the quality of the sample: 0.54 μM Nectostatin (Inc. #J65341, ThermoFisher Scientific Chemicals, Waltham, MA), 1 μM HPN-07 (SML2163, Sigma-Aldrich), 0.32 μM sodium hydroxybutyrate (A1161314, ThermoFisher Scientific Chemicals), 78 nM Q-VD-Oph (SML0063, Sigma-Aldrich), and 0.2 U/ml of Ribolock RNase inhibitor (EO0381, Life Technologies Corporation, Carlsbad, CA). The tissue, held over dry ice in a 60-mm Petri dish, was methodically minced into fragments smaller than 2 mm using a razor blade. Subsequently, this tissue was transitioned to a 2 ml Dounce homogenizer containing 1.5 ml of nuclei extraction buffer (130-128-024, Miltenyi Biotec, Bergisch Gladbach, Germany) along with 0.2 U/ml Ribolock RNase inhibitor.  Samples were then centrifuged at 600×g for 5 min, resuspended in 400 μL of PBS enriched with 2% BSA, passed through a 70-μm FLOWMI for clarification, and strained via a 40-μm FLOWMI. Specimens were then entrusted to the Hunstman Cancer Institute High Throughput Genomics Core for 10X Genomics library construction and sequencing.
Libraries were prepped according to the 10X Genomics scRNA-seq 3’ v3.1 Next GEM protocol, NovaSeq Reagent Kit Series 10B_150x150 bp Sequencing.

treatment_protocol: no treatment

value: prefrontal cortex BA9

value: neurotypical


title: 22_S19192_TD_replicate5

description:
Library name: 24149X12
10X genomics

value: Tourette disease


title: rat Schwann cells - mouse dorsal root ganglia myelinated cocultures treated with AT56


title: 9_S08454_neurotypical_replicate3

description:
Library name: 24149X7
10X genomics


title: rat Schwann cells - mouse dorsal root ganglia myelinated cocultures treated with DMSO


title: Lesion 4 of ccRCC from the left kidney


title: 10_S05076_TD_replicate3

description:
Library name: 24149X8
10X genomics


title: 7_S04804_neurotypical_replicate2

description:
Library name: 24149X6
10X genomics


title: 6_S04269_TD_replicate2

description:
Library name: 24149X5
10X genomics


title: 20_S19007_TD_replicate4

description:
Library name: 24149X11
10X genomics


title: 4_S03667_TD_replicate1

description:
Library name: 24149X3
10X genomics


title: PETER001_THP1_6H_X1.A2_B46:H21

type: RNA

city: New York

first: Avi

last: Ma'ayan

state: NY

address: One Gustave L. Levy Place, Box 1603

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

description: L1000 inferred profile; pert_id: DMSO

scan_protocol: Following treatment and lysis, gene expression was profiled using the L1000 platform, a high-throughput assay that measures the expression of ∼1,000 landmark genes and computationally infers the expression of nonmeasured transcripts.

data_processing: The data was normalized relative to the expression of 80 invariant landmark control genes. The expression of additional genes was inferred via a linear model trained on thousands of Affymetrix gene expression datasets from the gene expression omnibus (GEO). In this study, we utilized the L1000 data with the 12,328 measured and inferred mRNAs.

label: biotin

source_name: THP1 treated with DMSO 0.5 uM for 6.0 h

label_protocol: biotin labeling. Processing was done by th Broad Institute as previously described (10.1016/j.cell.2017.10.049)

growth_protocol:
HepG2 cells (5000 cells/well; ATCC, HB-8065) were cultured in Eagle's Minimum Essential Medium (EMEM; ATCC, cat. no.  30-2003), supplemented with 10% FBS and 1% P/S  at 37°C, 5% CO2.
HK-2 cells (5000 cells/well; ATCC, cat. no. CRL-2190) were cultured in Keratinocyte Serum Free Medium (K-SFM), Kit (Gibco, cat. no. 17005-042)  at 37°C, 5% CO2.
THP-1 cells (10,000 cells/well; ATCC, cat. no. TIB-202) were cultured in RPMI-40 medium (Gibco, cat. no. 11875-093) supplemented with 10% fetal bovine serum (FBS, Gibco, cat. no. 10438026) and 1% penicillin/streptomycin (P/S, Corning, cat. no. 30-002) at 37°C, 5% CO2. Macrophage differentiation was induced in vitro with phorbol-12-myristate-13-acetate (PMA, 50 ng/mL; Sigma) for 72 hours at 37°C in 5% CO2

extract_protocol: After treatment, cells were lysed using the TCL Buffer (Qiagen, cat. no. 1031576) and incubated for 30 minutes at 37°C. The lysates were then stored at -80°C. RNA was extracted by the Broad Institute, according to their protocol.

treatment_protocol: After 24 hours of culture for HepG2 and HK-2 cells, and 72 hours for THP-1 macrophages, the cells were placed in their respected culture media supplemented with 2% FBS for 16 hours. Subsequently, they were treated for 6 or 24 hours with either vehicle (DMSO) or with ART medications at a concentration of 0.1, or 0.5 µM.

value: DMSO 0.5 uM

tag: duration

tag: plate

tag: well


title: PETER001_THP1_6H_X1.A2_B46:H20

description: L1000 inferred profile; pert_id: DMSO


title: PETER001_THP1_6H_X1.A2_B46:H19

description: L1000 inferred profile; pert_id: DMSO


title: Calf-rep1-4

city: Yinchuan

first: Jin

last: Haoyan

state: NingXia

address: No. 489, West Helanshan Road

department: colllege of animal science and technology

institute: NingXia University

description: Library name: calves

data_processing:
The raw data generated by sequencing was fastq sequence. The BGI SAW ( version 5. 5. 4 ) software package was used to process the spatial transcriptome data and the bright field microscope slice images, and to compare them with the bovine reference genome (ARS-UCD2.0).
Assembly: ARS-UCD2.0
Supplementary files format and content: The spatial expression location information of the gene was recorded, including calf testicular tissue and adult bovine testicular tissue.
Library strategy: Spatial Transcriptomics

organism: Bos taurus

source_name: testis

extract_protocol:
The testicular tissue was placed in a low-temperature PBS laboratory. OCT embedding agent was used to complete the embedding of the treated testicular tissue on ice, and the Stereo-seq library was created according to the manufacturer 's scheme.
OCT-embedded tissues were cut into 10μm frozen sections, which were affixed to Stereo-seq T vector microarrays (BGI;201ST114), incubated at 37℃ for 4min, followed by methanol fixation, H&E staining, image scanning, tissue permeabilization, reverse transcription, tissue removal, cDNA recovery and purification with the STOmics Stereo-seq transcription kit. Finally, DNA libraries were constructed using Stereo-seq library construction kit

value: testis

value: testis cell

value: germ cells and somatic cells


title: PETER001_THP1_6H_X1.A2_B46:H18

description: L1000 inferred profile; pert_id: Darunavir

source_name: THP1 treated with Darunavir 0.1 uM for 6.0 h

value: Darunavir 0.1 uM


title: Adult-rep1-3

description: Library name: adult bovine


title: PETER001_THP1_6H_X1.A2_B46:H17


title: 5_S03639_neurotypical_replicate1

description:
Library name: 24149X4
10X genomics


title: PETER001_THP1_6H_X1.A2_B46:H12

description: L1000 inferred profile; pert_id: Darunavir|Tenofovir Disoproxil Fumarate

source_name: THP1 treated with Darunavir|Tenofovir Disoproxil Fumarate 0.1|0.1 uM for 6.0 h


title: PETER001_THP1_6H_X1.A2_B46:H16


title: PETER001_THP1_6H_X1.A2_B46:H14

description: L1000 inferred profile; pert_id: Emtricitabine|Ritonavir

source_name: THP1 treated with Emtricitabine|Ritonavir 0.1|0.5 uM for 6.0 h

value: Emtricitabine|Ritonavir 0.1|0.5 uM


title: PETER001_THP1_6H_X1.A2_B46:H11

value: Darunavir|Tenofovir Disoproxil Fumarate 0.1|0.1 uM


title: PETER001_THP1_6H_X1.A2_B46:H10


title: PETER001_THP1_6H_X1.A2_B46:H09

description: L1000 inferred profile; pert_id: Ritonavir|Tenofovir Disoproxil Fumarate

source_name: THP1 treated with Ritonavir|Tenofovir Disoproxil Fumarate 0.5|0.1 uM for 6.0 h


title: PETER001_THP1_6H_X1.A2_B46:H06

description: L1000 inferred profile; pert_id: Darunavir|Emtricitabine

source_name: THP1 treated with Darunavir|Emtricitabine 0.1|0.1 uM for 6.0 h

value: Darunavir|Emtricitabine 0.1|0.1 uM


title: PETER001_THP1_6H_X1.A2_B46:H08

value: Ritonavir|Tenofovir Disoproxil Fumarate 0.5|0.1 uM


title: PETER001_THP1_6H_X1.A2_B46:H04


title: PETER001_THP1_6H_X1.A2_B46:H02

description: L1000 inferred profile; pert_id: Water

source_name: THP1 treated with Water 0.01 uM for 6.0 h

value: Water 0.01 uM


title: PETER001_THP1_6H_X1.A2_B46:H07


title: PETER001_THP1_6H_X1.A2_B46:H13


title: PETER001_THP1_6H_X1.A2_B46:H03

description: L1000 inferred profile; pert_id: Water


title: PETER001_THP1_6H_X1.A2_B46:G21

description: L1000 inferred profile; pert_id: DMSO


title: PETER001_THP1_6H_X1.A2_B46:H15


title: PETER001_THP1_6H_X1.A2_B46:H01

description: L1000 inferred profile; pert_id: Water


title: PETER001_THP1_6H_X1.A2_B46:G20

description: L1000 inferred profile; pert_id: DMSO


title: PETER001_THP1_6H_X1.A2_B46:H05


title: PETER001_THP1_6H_X1.A2_B46:G18

description: L1000 inferred profile; pert_id: Tenofovir Alafenamide Fumarate

source_name: THP1 treated with Tenofovir Alafenamide Fumarate 0.5 uM for 6.0 h

value: Tenofovir Alafenamide Fumarate 0.5 uM


title: PETER001_THP1_6H_X1.A2_B46:G19

description: L1000 inferred profile; pert_id: DMSO


title: PETER001_THP1_6H_X1.A2_B46:G16


title: PETER001_THP1_6H_X1.A2_B46:G15

description: L1000 inferred profile; pert_id: Darunavir|Emtricitabine|Tenofovir Disoproxil Fumarate

source_name: THP1 treated with Darunavir|Emtricitabine|Tenofovir Disoproxil Fumarate 0.1|0.1|0.1 uM for 6.0 h


title: PETER001_THP1_6H_X1.A2_B46:G17


title: PETER001_THP1_6H_X1.A2_B46:G13

value: Darunavir|Emtricitabine|Tenofovir Disoproxil Fumarate 0.1|0.1|0.1 uM


title: PETER001_THP1_6H_X1.A2_B46:G10

description: L1000 inferred profile; pert_id: Darunavir|Ritonavir|Tenofovir Disoproxil Fumarate

source_name: THP1 treated with Darunavir|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.5|0.1 uM for 6.0 h


title: PETER001_THP1_6H_X1.A2_B46:G12

value: Darunavir|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.5|0.1 uM


title: PETER001_THP1_6H_X1.A2_B46:G11


title: PETER001_THP1_6H_X1.A2_B46:G09

description: L1000 inferred profile; pert_id: Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate

source_name: THP1 treated with Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.5|0.1 uM for 6.0 h


title: PETER001_THP1_6H_X1.A2_B46:G05

description: L1000 inferred profile; pert_id: Darunavir|Emtricitabine|Ritonavir

source_name: THP1 treated with Darunavir|Emtricitabine|Ritonavir 0.1|0.1|0.5 uM for 6.0 h


title: PETER001_THP1_6H_X1.A2_B46:G08

value: Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.5|0.1 uM


title: PETER001_THP1_6H_X1.A2_B46:G04


title: PETER001_THP1_6H_X1.A2_B46:G03

description: L1000 inferred profile; pert_id: Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: THP1 treated with Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM for 6.0 h


title: PETER001_THP1_6H_X1.A2_B46:G14


title: PETER001_THP1_6H_X1.A2_B46:F20

description: L1000 inferred profile; pert_id: Wortmannin

source_name: THP1 treated with Wortmannin 5 uM for 6.0 h

value: Wortmannin 5 uM


title: PETER001_THP1_6H_X1.A2_B46:G06


title: PETER001_THP1_6H_X1.A2_B46:G07


title: PETER001_THP1_6H_X1.A2_B46:F21


title: PETER001_THP1_6H_X1.A2_B46:F17

description: L1000 inferred profile; pert_id: Bictegravir

source_name: THP1 treated with Bictegravir 0.5 uM for 6.0 h

value: Bictegravir 0.5 uM


title: PETER001_THP1_6H_X1.A2_B46:G01

value: Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM


title: PETER001_THP1_6H_X1.A2_B46:F19


title: PETER001_THP1_6H_X1.A2_B46:F18


title: PETER001_THP1_6H_X1.A2_B46:F15

description: L1000 inferred profile; pert_id: Elvitegravir

source_name: THP1 treated with Elvitegravir 0.1 uM for 6.0 h

value: Elvitegravir 0.1 uM


title: PETER001_THP1_6H_X1.A2_B46:F12

description: L1000 inferred profile; pert_id: Elvitegravir|Tenofovir Alafenamide Fumarate

source_name: THP1 treated with Elvitegravir|Tenofovir Alafenamide Fumarate 0.1|0.5 uM for 6.0 h


title: PETER001_THP1_6H_X1.A2_B46:F16


title: PETER001_THP1_6H_X1.A2_B46:F13


title: PETER001_THP1_6H_X1.A2_B46:F11

value: Elvitegravir|Tenofovir Alafenamide Fumarate 0.1|0.5 uM


title: PETER001_THP1_6H_X1.A2_B46:F10


title: PETER001_THP1_6H_X1.A2_B46:F09

description: L1000 inferred profile; pert_id: Darunavir|Ritonavir

source_name: THP1 treated with Darunavir|Ritonavir 0.1|0.5 uM for 6.0 h

value: Darunavir|Ritonavir 0.1|0.5 uM


title: PETER001_THP1_6H_X1.A2_B46:F07


title: PETER001_THP1_6H_X1.A2_B46:F14


title: PETER001_THP1_6H_X1.A2_B46:F06

description: L1000 inferred profile; pert_id: Dolutegravir|Tenofovir Alafenamide Fumarate

source_name: THP1 treated with Dolutegravir|Tenofovir Alafenamide Fumarate 0.1|0.5 uM for 6.0 h


title: PETER001_THP1_6H_X1.A2_B46:F08


title: PETER001_THP1_6H_X1.A2_B46:G02


title: PETER001_THP1_6H_X1.A2_B46:F05

value: Dolutegravir|Tenofovir Alafenamide Fumarate 0.1|0.5 uM


title: PETER001_THP1_6H_X1.A2_B46:F04


title: PETER001_THP1_6H_X1.A2_B46:E20

description: L1000 inferred profile; pert_id: Rapamycin

source_name: THP1 treated with Rapamycin 5 uM for 6.0 h

value: Rapamycin 5 uM


title: PETER001_THP1_6H_X1.A2_B46:F02

description: L1000 inferred profile; pert_id: Cobicistat|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: THP1 treated with Cobicistat|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM for 6.0 h


title: PETER001_THP1_6H_X1.A2_B46:E19


title: PETER001_THP1_6H_X1.A2_B46:F03

value: Cobicistat|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM


title: PETER001_THP1_6H_X1.A2_B46:F01


title: PETER001_THP1_6H_X1.A2_B46:E18

description: L1000 inferred profile; pert_id: Tenofovir Disoproxil Fumarate

source_name: THP1 treated with Tenofovir Disoproxil Fumarate 0.1 uM for 6.0 h

value: Tenofovir Disoproxil Fumarate 0.1 uM


title: PETER001_THP1_6H_X1.A2_B46:E09

description: L1000 inferred profile; pert_id: Bictegravir|Emtricitabine

source_name: THP1 treated with Bictegravir|Emtricitabine 0.5|0.1 uM for 6.0 h

value: Bictegravir|Emtricitabine 0.5|0.1 uM


title: PETER001_THP1_6H_X1.A2_B46:E14

description: L1000 inferred profile; pert_id: Cobicistat

source_name: THP1 treated with Cobicistat 0.1 uM for 6.0 h

value: Cobicistat 0.1 uM


title: PETER001_THP1_6H_X1.A2_B46:E12

description: L1000 inferred profile; pert_id: Bictegravir|Tenofovir Alafenamide Fumarate

source_name: THP1 treated with Bictegravir|Tenofovir Alafenamide Fumarate 0.5|0.5 uM for 6.0 h


title: PETER001_THP1_6H_X1.A2_B46:E15


title: PETER001_THP1_6H_X1.A2_B46:E07


title: PETER001_THP1_6H_X1.A2_B46:E04

description: L1000 inferred profile; pert_id: Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: THP1 treated with Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.5 uM for 6.0 h


title: PETER001_THP1_6H_X1.A2_B46:E03

description: L1000 inferred profile; pert_id: Cobicistat|Elvitegravir|Emtricitabine

source_name: THP1 treated with Cobicistat|Elvitegravir|Emtricitabine 0.1|0.1|0.1 uM for 6.0 h


title: PETER001_THP1_6H_X1.A2_B46:E11

value: Bictegravir|Tenofovir Alafenamide Fumarate 0.5|0.5 uM


title: PETER001_THP1_6H_X1.A2_B46:E17


title: PETER001_THP1_6H_X1.A2_B46:E02


title: PETER001_THP1_6H_X1.A2_B46:E01


title: PETER001_THP1_6H_X1.A2_B46:E16


title: PETER001_THP1_6H_X1.A2_B46:E08


title: PETER001_THP1_6H_X1.A2_B46:D19

description: L1000 inferred profile; pert_id: Vorinostat

source_name: THP1 treated with Vorinostat 5 uM for 6.0 h

value: Vorinostat 5 uM


title: PETER001_THP1_6H_X1.A2_B46:E13


title: PETER001_THP1_6H_X1.A2_B46:E10


title: PETER001_THP1_6H_X1.A2_B46:D20


title: PETER001_THP1_6H_X1.A2_B46:E06

value: Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.5 uM


title: PETER001_THP1_6H_X1.A2_B46:D18

description: L1000 inferred profile; pert_id: Efavirenz

source_name: THP1 treated with Efavirenz 0.5 uM for 6.0 h

value: Efavirenz 0.5 uM


title: PETER001_THP1_6H_X1.A2_B46:D16


title: PETER001_THP1_6H_X1.A2_B46:E05


title: PETER001_THP1_6H_X1.A2_B46:D14

description: L1000 inferred profile; pert_id: Cobicistat|Tenofovir Alafenamide Fumarate

source_name: THP1 treated with Cobicistat|Tenofovir Alafenamide Fumarate 0.1|0.5 uM for 6.0 h


title: PETER001_THP1_6H_X1.A2_B46:D21


title: PETER001_THP1_6H_X1.A2_B46:D13

value: Cobicistat|Tenofovir Alafenamide Fumarate 0.1|0.5 uM


title: PETER001_THP1_6H_X1.A2_B46:D15


title: PETER001_THP1_6H_X1.A2_B46:D10

description: L1000 inferred profile; pert_id: Efavirenz|Tenofovir Disoproxil Fumarate

source_name: THP1 treated with Efavirenz|Tenofovir Disoproxil Fumarate 0.5|0.1 uM for 6.0 h


title: PETER001_THP1_6H_X1.A2_B46:D12

value: Efavirenz|Tenofovir Disoproxil Fumarate 0.5|0.1 uM


title: PETER001_THP1_6H_X1.A2_B46:D06

description: L1000 inferred profile; pert_id: Efavirenz|Emtricitabine

source_name: THP1 treated with Efavirenz|Emtricitabine 0.5|0.1 uM for 6.0 h

value: Efavirenz|Emtricitabine 0.5|0.1 uM


title: PETER001_THP1_6H_X1.A2_B46:D11


title: PETER001_THP1_6H_X1.A2_B46:D05


title: PETER001_THP1_6H_X1.A2_B46:D03


title: PETER001_THP1_6H_X1.A2_B46:D01


title: PETER001_THP1_6H_X1.A2_B46:D07

description: L1000 inferred profile; pert_id: Emtricitabine|Tenofovir Disoproxil Fumarate

source_name: THP1 treated with Emtricitabine|Tenofovir Disoproxil Fumarate 0.1|0.1 uM for 6.0 h


title: PETER001_THP1_6H_X1.A2_B46:D02


title: PETER001_THP1_6H_X1.A2_B46:C20

description: L1000 inferred profile; pert_id: Genistein

source_name: THP1 treated with Genistein 5 uM for 6.0 h

value: Genistein 5 uM


title: PETER001_THP1_6H_X1.A2_B46:D08

value: Emtricitabine|Tenofovir Disoproxil Fumarate 0.1|0.1 uM


title: PETER001_THP1_6H_X1.A2_B46:C18

description: L1000 inferred profile; pert_id: Emtricitabine

source_name: THP1 treated with Emtricitabine 0.1 uM for 6.0 h

value: Emtricitabine 0.1 uM


title: PETER001_THP1_6H_X1.A2_B46:D04


title: PETER001_THP1_6H_X1.A2_B46:C17


title: PETER001_THP1_6H_X1.A2_B46:C19


title: PETER001_THP1_6H_X1.A2_B46:C16


title: PETER001_THP1_6H_X1.A2_B46:C21


title: PETER001_THP1_6H_X1.A2_B46:C15

description: L1000 inferred profile; pert_id: Elvitegravir|Emtricitabine

source_name: THP1 treated with Elvitegravir|Emtricitabine 0.1|0.1 uM for 6.0 h

value: Elvitegravir|Emtricitabine 0.1|0.1 uM


title: PETER001_THP1_6H_X1.A2_B46:D09


title: PETER001_THP1_6H_X1.A2_B46:D17


title: PETER001_THP1_6H_X1.A2_B46:C14


title: PETER001_THP1_6H_X1.A2_B46:C13


title: PETER001_THP1_6H_X1.A2_B46:C12

description: L1000 inferred profile; pert_id: Abacavir|Emtricitabine

source_name: THP1 treated with Abacavir|Emtricitabine 0.5|0.1 uM for 6.0 h

value: Abacavir|Emtricitabine 0.5|0.1 uM


title: PETER001_THP1_6H_X1.A2_B46:C06

description: L1000 inferred profile; pert_id: Abacavir|Dolutegravir

source_name: THP1 treated with Abacavir|Dolutegravir 0.5|0.1 uM for 6.0 h

value: Abacavir|Dolutegravir 0.5|0.1 uM


title: PETER001_THP1_6H_X1.A2_B46:B20

description: L1000 inferred profile; pert_id: Water

source_name: THP1 treated with Water 0.01 uM for 6.0 h

value: Water 0.01 uM


title: PETER001_THP1_6H_X1.A2_B46:B21

description: L1000 inferred profile; pert_id: Water


title: PETER001_THP1_6H_X1.A2_B46:C09

description: L1000 inferred profile; pert_id: Dolutegravir|Emtricitabine

source_name: THP1 treated with Dolutegravir|Emtricitabine 0.1|0.1 uM for 6.0 h

value: Dolutegravir|Emtricitabine 0.1|0.1 uM


title: PETER001_THP1_6H_X1.A2_B46:B11

description: L1000 inferred profile; pert_id: Cobicistat|Emtricitabine

source_name: THP1 treated with Cobicistat|Emtricitabine 0.1|0.1 uM for 6.0 h

value: Cobicistat|Emtricitabine 0.1|0.1 uM


title: PETER001_THP1_6H_X1.A2_B46:B19

description: L1000 inferred profile; pert_id: Water


title: PETER001_THP1_6H_X1.A2_B46:C11


title: PETER001_THP1_6H_X1.A2_B46:C03

description: L1000 inferred profile; pert_id: DMSO

source_name: THP1 treated with DMSO 0.5 uM for 6.0 h

value: DMSO 0.5 uM


title: PETER001_THP1_6H_X1.A2_B46:C05


title: PETER001_THP1_6H_X1.A2_B46:C04


title: PETER001_THP1_6H_X1.A2_B46:C10


title: PETER001_THP1_6H_X1.A2_B46:C02

description: L1000 inferred profile; pert_id: DMSO


title: PETER001_THP1_6H_X1.A2_B46:B17

description: L1000 inferred profile; pert_id: Dolutegravir

source_name: THP1 treated with Dolutegravir 0.1 uM for 6.0 h

value: Dolutegravir 0.1 uM


title: PETER001_THP1_6H_X1.A2_B46:B15

description: L1000 inferred profile; pert_id: Cobicistat|Elvitegravir

source_name: THP1 treated with Cobicistat|Elvitegravir 0.1|0.1 uM for 6.0 h

value: Cobicistat|Elvitegravir 0.1|0.1 uM


title: PETER001_THP1_6H_X1.A2_B46:C08


title: PETER001_THP1_6H_X1.A2_B46:B14


title: PETER001_THP1_6H_X1.A2_B46:B13


title: PETER001_THP1_6H_X1.A2_B46:C07


title: PETER001_THP1_6H_X1.A2_B46:C01

description: L1000 inferred profile; pert_id: DMSO


title: PETER001_THP1_6H_X1.A2_B46:B18


title: PETER001_THP1_6H_X1.A2_B46:B12


title: PETER001_THP1_6H_X1.A2_B46:B16


title: PETER001_THP1_6H_X1.A2_B46:B10


title: PETER001_THP1_6H_X1.A2_B46:B08

description: L1000 inferred profile; pert_id: Cobicistat|Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: THP1 treated with Cobicistat|Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.1|0.5 uM for 6.0 h


title: PETER001_THP1_6H_X1.A2_B46:B07

value: Cobicistat|Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.1|0.5 uM


title: PETER001_THP1_6H_X1.A2_B46:B06

description: L1000 inferred profile; pert_id: Darunavir|Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate

source_name: THP1 treated with Darunavir|Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.1|0.5|0.1 uM for 6.0 h


title: MLC, IL-1β+LOXL2, Replicate2

city: Boston

first: Manish

middle: V.

last: Bais

state: MA

address: W216, 700 Albany street

department: Translational Dental Medicine

institute: Boston University

data_processing:
Proprietary perl script developed by NOVOGENE bioinformatics facility.
Reference genome alignment using HISAT2.
Gene expression quantification using featureCounts.
Assembly: ncbi_capra_hircus_gcf_001704415_2_ars1_2
Supplementary files format and content: tab-delimited text file includes raw count for each samples

organism: Capra hircus

source_name: TMJ

growth_protocol: Both SLC and MLC cells were maintained in DMEM supplemented 10% FBS, 1% PenStrep, and 5% CO2 at 37°C.

extract_protocol:
RNA was islated using Rneasy Mini kit (Qiagen). Around 400 nanogram of RNA was used for sequencing at NOVOGENE facility.
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.

treatment_protocol: Treated with IL-1β or IL-1β+LOXL2

value: TMJ

value: MLC


title: PETER001_THP1_6H_X1.A2_B46:B04

value: Darunavir|Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.1|0.5|0.1 uM


title: MLC, IL-1β+LOXL2, Replicate3


title: MLC, IL-1β, Replicate2


title: PETER001_THP1_6H_X1.A2_B46:B05


title: PETER001_THP1_6H_X1.A2_B46:A17

description: L1000 inferred profile; pert_id: Abacavir

source_name: THP1 treated with Abacavir 0.5 uM for 6.0 h

value: Abacavir 0.5 uM


title: PETER001_THP1_6H_X1.A2_B46:A16


title: SLC, IL-1β+LOXL2, Replicate3

value: SLC


title: PETER001_THP1_6H_X1.A2_B46:A18


title: PETER001_THP1_6H_X1.A2_B46:A19

description: L1000 inferred profile; pert_id: Ritonavir

source_name: THP1 treated with Ritonavir 0.5 uM for 6.0 h

value: Ritonavir 0.5 uM


title: SLC, IL-1β, Replicate2


title: PETER001_THP1_6H_X1.A2_B46:A21


title: MLC, IL-1β, Replicate1


title: PETER001_THP1_6H_X1.A2_B46:A20


title: MLC, IL-1β, Replicate3


title: PETER001_THP1_6H_X1.A2_B46:A15

description: L1000 inferred profile; pert_id: Dolutegravir|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: THP1 treated with Dolutegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM for 6.0 h


title: SLC, IL-1β, Replicate3


title: SLC, IL-1β+LOXL2, Replicate2


title: SLC, IL-1β+LOXL2, Replicate1


title: SLC, IL-1β, Replicate1


title: PETER001_THP1_6H_X1.A2_B46:A14

value: Dolutegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM


title: PETER001_THP1_6H_X1.A2_B46:B09


title: MLC, IL-1β+LOXL2, Replicate1


title: PETER001_THP1_6H_X1.A2_B46:A13


title: Cnga2_P65_M_ctrl_2_scATAC

city: Cambridge

first: Harris

last: Kaplan

address: 16 Divinity Ave., Room 4019

department: MCB

institute: Harvard University

description: Library name: Sample 91

library_source: genomic single cell

data_processing:
Illumina sequencing reads were aligned to the mouse genome using the 10x Genomics CellRanger ARC pipeline with default parameters.
Assembly: mm10
Supplementary files format and content: BED-like tabular file, where each line represents a unique ATAC-seq fragment captured by the assay

organism: Mus musculus

source_name: age: P65 sex: male strain: Cnga2+/y rep: ctr_2

extract_protocol:
At each age, we dissected the anterior portion of the mouse hypothalamus containing the POA and surrounding regions, pooling tissue from three brains per sample, and performed nuclei isolation and library preparation for two biological replicates per sex per age (samples always contained only male or only female brains).Except for experiments on mutant strains affecting sensory input, C57BL/6J mice were used for all sequencing experiments. Mothers of all C57BL/6J experiments subjects were placed in a fresh cage when embryos were ~E12. For samples collected at P28 and P65, animals were separated from parents and opposite-sex siblings at P21, and group-housed, and kept separated from the opposite sex until dissection. C57BL/6J brains were collected during the first three hours of the dark cycle. Cnga2, Trpc2, and Trpm8 mutants were treated the same, whereas Piezo2 cKO and Gabrb3 cKO animals and littermate controls were raised in another facility (Harvard Medical School) and thus brains were collected over a wider time window (2-7 hours into the start of the light phase of 12h:12h light cycle).Brains were dissected (P10+) or whole heads were removed (E14 to P4) and frozen in Optimal Cutting Temperature medium and placed at -80℃. The preoptic area and surrounding regions were dissected on a cryostat at -15℃ using the Paxinos Developing and Adult Brain Atlases to determine locations for dissection based on landmarks. At all ages, tissue was collected from the anterior-most portion of MnPO to the posterior-most portion of the POA. To achieve this, after slicing away anterior material, thin (10-20µm) sections were collected and examined under a dissecting microscope to identify landmarks. At E16 to P65, the anterior commissure on each brain hemisphere is distinctly visible and moves medially as the brain is sliced from anterior to posterior. When the medial edge of the anterior commissure lined up underneath the ventral tip of the lateral ventricle, we began collecting tissue for sequencing. At E14, the anterior commissure is not clearly visible; we instead began collecting tissue when we first saw the ventral tips of lateral ventricles reach their full extents. To collect tissue, we first used a razor blade to remove large blocks of tissue lateral to the lateral ventricles, and then sliced 200µm-thick sections to collect approximately the ventral-most 1/3rd of the brain into a 2-mL tube. At E14, we collected 800µm; at E16 to P4, we collected 1.2mm; and at P10 to P65, we collected 1.4mm. Dissected tissue was placed in a 2-mL tube and kept at -80℃ until the day of library preparation.  For library preparation, 4-8 samples were prepared simultaneously, pairing mutant/control and male/female samples on the same day. Dissected tissues from 3 mice (C57BL6/J samples) or 2-3 mice (mutant/control samples) were pooled for each sample. 2 female and 2 male samples were collected at each of the 8 ages, except for E16, where only 1 female and 1 male sample were collected. Nuclei preparation was modified from 10x Genomics demonstrated protocol CG000375.
Libraries were sequenced on an Illumina NovaSeq 6000 S4 200 flowcell (8 samples per flowcell of either RNA-seq only or ATAC-seq only, targeting 200,000 reads per cell) using instructions provided by 10x Genomics Multiome protocol (GEX: read 1=26bp, i1=10bp, i2=10bp, read 2=90bp; ATAC: read 1=50bp, i1=8bp, i2=24bp, read 2=49bp), to a saturation of at least 70% for each run. Paired-end sequencing with read lengths of 100 nt was performed for all samples.  In our initial submission to GEO, we are uploading only GEX (i.e. snRNA-seq) data; ATAC-seq data will follow.

value: Preoptic area of the hypothalamus and surrounding tissue

value: male

tag: strain

tag: batch


title: PETER001_THP1_6H_X1.A2_B46:A12

description: L1000 inferred profile; pert_id: Bictegravir|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: THP1 treated with Bictegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.5|0.1|0.5 uM for 6.0 h


title: Cnga2_P65_M_ctrl_1_scATAC

description: Library name: Sample 90

source_name: age: P65 sex: male strain: Cnga2+/y rep: ctr_1


title: PETER001_THP1_6H_X1.A2_B46:A11

value: Bictegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.5|0.1|0.5 uM


title: Cnga2_P65_M_mut_2_scATAC

description: Library name: Sample 89

source_name: age: P65 sex: male strain: Cnga2-/y rep: mut_2


title: PETER001_THP1_6H_X1.A2_B46:A09

description: L1000 inferred profile; pert_id: Efavirenz|Emtricitabine|Tenofovir Disoproxil Fumarate

source_name: THP1 treated with Efavirenz|Emtricitabine|Tenofovir Disoproxil Fumarate 0.5|0.1|0.1 uM for 6.0 h


title: PETER001_THP1_6H_X1.A2_B46:A07

value: Efavirenz|Emtricitabine|Tenofovir Disoproxil Fumarate 0.5|0.1|0.1 uM


title: PETER001_THP1_6H_X1.A2_B46:A05

description: L1000 inferred profile; pert_id: Abacavir|Dolutegravir|Emtricitabine

source_name: THP1 treated with Abacavir|Dolutegravir|Emtricitabine 0.5|0.1|0.1 uM for 6.0 h


title: PETER001_THP1_6H_X1.A2_B46:A10


title: PETER001_THP1_6H_X1.A2_B46:A08


title: Cnga2_P10_M_ctrl_1_scATAC

description: Library name: Sample 82

source_name: age: P10 sex: male strain: Cnga2+/y rep: ctr_1


title: Cnga2_P18_M_ctrl_2_scATAC

description: Library name: Sample 87

source_name: age: P18 sex: male strain: Cnga2+/y rep: ctr_2


title: Cnga2_P18_M_ctrl_1_scATAC

description: Library name: Sample 86

source_name: age: P18 sex: male strain: Cnga2+/y rep: ctr_1


title: Cnga2_P65_M_mut_1_scATAC

description: Library name: Sample 88

source_name: age: P65 sex: male strain: Cnga2-/y rep: mut_1


title: Cnga2_P10_M_ctrl_2_scATAC

description: Library name: Sample 83

source_name: age: P10 sex: male strain: Cnga2+/y rep: ctr_2


title: PETER001_THP1_6H_X1.A2_B46:A04


title: Cnga2_P18_M_mut_1_scATAC

description: Library name: Sample 84

source_name: age: P18 sex: male strain: Cnga2-/y rep: mut_1


title: Cnga2_P10_M_mut_2_scATAC

description: Library name: Sample 81

source_name: age: P10 sex: male strain: Cnga2-/y rep: mut_2


title: PETER001_THP1_6H_X1.A2_B46:A06


title: PETER001_THP1_24H_X1_B46:H21

description: L1000 inferred profile; pert_id: DMSO

source_name: THP1 treated with DMSO 0.5 uM for 24.0 h


title: Cnga2_P18_M_mut_2_scATAC

description: Library name: Sample 85

source_name: age: P18 sex: male strain: Cnga2-/y rep: mut_2


title: PETER001_THP1_24H_X1_B46:H20

description: L1000 inferred profile; pert_id: DMSO


title: Cnga2_P10_M_mut_1_scATAC

description: Library name: Sample 80

source_name: age: P10 sex: male strain: Cnga2-/y rep: mut_1


title: Trpm8_P18_M_mut_scATAC

description: Library name: Sample 79

source_name: age: P18 sex: male strain: Trpm8-/- rep: mut


title: PETER001_THP1_24H_X1_B46:H19

description: L1000 inferred profile; pert_id: DMSO


title: PETER001_THP1_24H_X1_B46:H18

description: L1000 inferred profile; pert_id: Darunavir

source_name: THP1 treated with Darunavir 0.1 uM for 24.0 h

value: Darunavir 0.1 uM


title: Trpm8_P18_F_mut_scATAC

description: Library name: Sample 78

source_name: age: P18 sex: female strain: Trpm8-/- rep: mut

value: female


title: Trpm8_P10_M_mut_scATAC

description: Library name: Sample 77

source_name: age: P10 sex: male strain: Trpm8-/- rep: mut


title: PETER001_THP1_24H_X1_B46:H17


title: PETER001_THP1_24H_X1_B46:H16


title: PETER001_THP1_24H_X1_B46:H14

description: L1000 inferred profile; pert_id: Emtricitabine|Ritonavir

source_name: THP1 treated with Emtricitabine|Ritonavir 0.1|0.5 uM for 24.0 h

value: Emtricitabine|Ritonavir 0.1|0.5 uM


title: PETER001_THP1_24H_X1_B46:H15


title: Gabrb3_P65_F_mut_scATAC

description: Library name: Sample 72

source_name: age: P65 sex: female strain: Advillin-Cre ; Gabrb3-fl/+ rep: mut

value: Advillin-Cre ; Gabrb3-fl/+


title: Trpm8_P10_F_mut_scATAC

description: Library name: Sample 76

source_name: age: P10 sex: female strain: Trpm8-/- rep: mut


title: PETER001_THP1_24H_X1_B46:H12

description: L1000 inferred profile; pert_id: Darunavir|Tenofovir Disoproxil Fumarate

source_name: THP1 treated with Darunavir|Tenofovir Disoproxil Fumarate 0.1|0.1 uM for 24.0 h


title: Gabrb3_P65_F_ctrl_scATAC

description: Library name: Sample 74

source_name: age: P65 sex: female strain: Advillin-Cre(-/+) ; Gabrb3-fl(-/+)/+ rep: ctrl

value: Advillin-Cre(-/+) ; Gabrb3-fl(-/+)/+


title: Gabrb3_P65_M_ctrl_scATAC

description: Library name: Sample 75

source_name: age: P65 sex: male strain: Advillin-Cre(-/+) ; Gabrb3-fl(-/+)/+ rep: ctrl


title: Gabrb3_P65_M_mut_scATAC

description: Library name: Sample 73

source_name: age: P65 sex: male strain: Advillin-Cre ; Gabrb3-fl/+ rep: mut


title: PETER001_THP1_24H_X1_B46:H09

description: L1000 inferred profile; pert_id: Ritonavir|Tenofovir Disoproxil Fumarate

source_name: THP1 treated with Ritonavir|Tenofovir Disoproxil Fumarate 0.5|0.1 uM for 24.0 h


title: PETER001_THP1_24H_X1_B46:H13


title: PETER001_THP1_24H_X1_B46:H11

value: Darunavir|Tenofovir Disoproxil Fumarate 0.1|0.1 uM


title: Piezo2_P18_F_mut_2_scATAC

description: Library name: Sample 68

source_name: age: P18 sex: female strain: Cdx2-Cre ; Piezo2-fl/fl rep: mut_2

value: Cdx2-Cre ; Piezo2-fl/fl


title: PETER001_THP1_24H_X1_B46:H10


title: Piezo2_P18_F_ctrl_2_scATAC

description: Library name: Sample 70

source_name: age: P18 sex: female strain: Cdx2-Cre(-/+) ; Piezo2-fl/(-/+) rep: ctr_2


title: Piezo2_P18_F_ctrl_3_scATAC

description: Library name: Sample 71

source_name: age: P18 sex: female strain: Cdx2-Cre(-/+) ; Piezo2-fl/(-/+) rep: ctr_3


title: Piezo2_P18_M_ctrl_1_scATAC

description: Library name: Sample 67

source_name: age: P18 sex: male strain: Cdx2-Cre(-/+) ; Piezo2-fl/(-/+) rep: ctr_1


title: Piezo2_P18_F_mut_3_scATAC

description: Library name: Sample 69

source_name: age: P18 sex: female strain: Cdx2-Cre ; Piezo2-fl/fl rep: mut_3


title: PETER001_THP1_24H_X1_B46:H08

value: Ritonavir|Tenofovir Disoproxil Fumarate 0.5|0.1 uM


title: Piezo2_P18_F_ctrl_1_scATAC

description: Library name: Sample 66

source_name: age: P18 sex: female strain: Cdx2-Cre(-/+) ; Piezo2-fl/(-/+) rep: ctr_1


title: PETER001_THP1_24H_X1_B46:H06

description: L1000 inferred profile; pert_id: Darunavir|Emtricitabine

source_name: THP1 treated with Darunavir|Emtricitabine 0.1|0.1 uM for 24.0 h

value: Darunavir|Emtricitabine 0.1|0.1 uM


title: PETER001_THP1_24H_X1_B46:H05


title: Piezo2_P18_M_mut_1_scATAC

description: Library name: Sample 65

source_name: age: P18 sex: male strain: Cdx2-Cre ; Piezo2-fl/fl rep: mut_1


title: Piezo2_P18_F_mut_1_scATAC

description: Library name: Sample 64

source_name: age: P18 sex: female strain: Cdx2-Cre ; Piezo2-fl/fl rep: mut_1


title: PETER001_THP1_24H_X1_B46:H03

description: L1000 inferred profile; pert_id: Water

source_name: THP1 treated with Water 0.01 uM for 24.0 h

value: Water 0.01 uM


title: PETER001_THP1_24H_X1_B46:H04


title: PETER001_THP1_24H_X1_B46:H01

description: L1000 inferred profile; pert_id: Water


title: PETER001_THP1_24H_X1_B46:G20

description: L1000 inferred profile; pert_id: DMSO

source_name: THP1 treated with DMSO 0.5 uM for 24.0 h

value: DMSO 0.5 uM


title: Trpc2_P65_M_ctrl_scATAC

description: Library name: Sample 59

source_name: age: P65 sex: male strain: Trpc2-/+ rep: ctrl


title: PETER001_THP1_24H_X1_B46:H02

description: L1000 inferred profile; pert_id: Water


title: PETER001_THP1_24H_X1_B46:G21

description: L1000 inferred profile; pert_id: DMSO


title: Piezo2_P10_F_mut_scATAC

description: Library name: Sample 60

source_name: age: P10 sex: female strain: Cdx2-Cre ; Piezo2-fl/fl rep: mut


title: PETER001_THP1_24H_X1_B46:G19

description: L1000 inferred profile; pert_id: DMSO


title: PETER001_THP1_24H_X1_B46:G18

description: L1000 inferred profile; pert_id: Tenofovir Alafenamide Fumarate

source_name: THP1 treated with Tenofovir Alafenamide Fumarate 0.5 uM for 24.0 h

value: Tenofovir Alafenamide Fumarate 0.5 uM


title: PETER001_THP1_24H_X1_B46:G17


title: Piezo2_P10_M_ctrl_scATAC

description: Library name: Sample 63

source_name: age: P10 sex: male strain: Cdx2-Cre(-/+) ; Piezo2-fl/(-/+) rep: ctrl


title: Piezo2_P10_M_mut_scATAC

description: Library name: Sample 61

source_name: age: P10 sex: male strain: Cdx2-Cre ; Piezo2-fl/fl rep: mut


title: Piezo2_P10_F_ctrl_scATAC

description: Library name: Sample 62

source_name: age: P10 sex: female strain: Cdx2-Cre(-/+) ; Piezo2-fl/(-/+) rep: ctrl


title: Trpc2_P65_F_ctrl_scATAC

description: Library name: Sample 58

source_name: age: P65 sex: female strain: Trpc2-/+ rep: ctrl


title: Trpc2_P18_M_ctrl_scATAC

description: Library name: Sample 55

source_name: age: P18 sex: male strain: Trpc2-/+ rep: ctrl


title: Trpc2_P65_M_mut_scATAC

description: Library name: Sample 57

source_name: age: P65 sex: male strain: Trpc2-/- rep: mut


title: Trpc2_P65_F_mut_scATAC

description: Library name: Sample 56

source_name: age: P65 sex: female strain: Trpc2-/- rep: mut


title: PETER001_THP1_24H_X1_B46:H07

source_name: THP1 treated with Ritonavir|Tenofovir Disoproxil Fumarate 0.5|0.1 uM for 24.0 h


title: PETER001_THP1_24H_X1_B46:G15

description: L1000 inferred profile; pert_id: Darunavir|Emtricitabine|Tenofovir Disoproxil Fumarate

source_name: THP1 treated with Darunavir|Emtricitabine|Tenofovir Disoproxil Fumarate 0.1|0.1|0.1 uM for 24.0 h


title: PETER001_THP1_24H_X1_B46:G16


title: Trpc2_P18_F_ctrl_scATAC

description: Library name: Sample 54

source_name: age: P18 sex: female strain: Trpc2-/+ rep: ctrl


title: Trpc2_P18_M_mut_scATAC

description: Library name: Sample 53

source_name: age: P18 sex: male strain: Trpc2-/- rep: mut


title: PETER001_THP1_24H_X1_B46:G14

value: Darunavir|Emtricitabine|Tenofovir Disoproxil Fumarate 0.1|0.1|0.1 uM


title: PETER001_THP1_24H_X1_B46:G13


title: Trpc2_P18_F_mut_scATAC

description: Library name: Sample 52

source_name: age: P18 sex: female strain: Trpc2-/- rep: mut

value: Preoptic area of the hypothalamus and surrounding tissue


title: PETER001_THP1_24H_X1_B46:G12

description: L1000 inferred profile; pert_id: Darunavir|Ritonavir|Tenofovir Disoproxil Fumarate

source_name: THP1 treated with Darunavir|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.5|0.1 uM for 24.0 h


title: Trpc2_P10_F_ctrl_2_V1_scATAC

description: Library name: Sample 50

source_name: age: P10 sex: female strain: Trpc2-/+ rep: ctr_2_V1

value: Visual cortex


title: Trpc2_P10_M_ctrl_2_V1_scATAC

description: Library name: Sample 51

source_name: age: P10 sex: male strain: Trpc2-/+ rep: ctr_2_V1

value: male


title: PETER001_THP1_24H_X1_B46:G09

description: L1000 inferred profile; pert_id: Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate

source_name: THP1 treated with Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.5|0.1 uM for 24.0 h


title: PETER001_THP1_24H_X1_B46:G10

value: Darunavir|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.5|0.1 uM


title: PETER001_THP1_24H_X1_B46:G11


title: PETER001_THP1_24H_X1_B46:G08

value: Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.5|0.1 uM


title: Trpc2_P10_F_mut_2_V1_scATAC

description: Library name: Sample 48

source_name: age: P10 sex: female strain: Trpc2-/- rep: mut_2_V1

value: female


title: Trpc2_P10_M_mut_2_V1_scATAC

description: Library name: Sample 49

source_name: age: P10 sex: male strain: Trpc2-/- rep: mut_2_V1


title: PETER001_THP1_24H_X1_B46:G07


title: Trpc2_P10_M_mut_2_scATAC

description: Library name: Sample 45

source_name: age: P10 sex: male strain: Trpc2-/- rep: mut_2


title: PETER001_THP1_24H_X1_B46:G06

description: L1000 inferred profile; pert_id: Darunavir|Emtricitabine|Ritonavir

source_name: THP1 treated with Darunavir|Emtricitabine|Ritonavir 0.1|0.1|0.5 uM for 24.0 h


title: Trpc2_P10_F_ctrl_2_scATAC

description: Library name: Sample 46

source_name: age: P10 sex: female strain: Trpc2-/+ rep: ctr_2


title: PETER001_THP1_24H_X1_B46:G04


title: PETER001_THP1_24H_X1_B46:G05


title: PETER001_THP1_24H_X1_B46:G03

description: L1000 inferred profile; pert_id: Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: THP1 treated with Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM for 24.0 h


title: Trpc2_P10_M_ctrl_1_scATAC

description: Library name: Sample 43

source_name: age: P10 sex: male strain: Trpc2-/+ rep: ctr_1


title: Trpc2_P10_F_ctrl_1_scATAC

description: Library name: Sample 42

source_name: age: P10 sex: female strain: Trpc2-/+ rep: ctr_1


title: Trpc2_P10_M_mut_1_scATAC

description: Library name: Sample 41

source_name: age: P10 sex: male strain: Trpc2-/- rep: mut_1


title: Trpc2_P10_M_ctrl_2_scATAC

description: Library name: Sample 47

source_name: age: P10 sex: male strain: Trpc2-/+ rep: ctr_2


title: PETER001_THP1_24H_X1_B46:G02

value: Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM


title: Trpc2_P10_F_mut_2_scATAC

description: Library name: Sample 44

source_name: age: P10 sex: female strain: Trpc2-/- rep: mut_2


title: PETER001_THP1_24H_X1_B46:G01


title: PETER001_THP1_24H_X1_B46:F21

description: L1000 inferred profile; pert_id: Wortmannin

source_name: THP1 treated with Wortmannin 5 uM for 24.0 h

value: Wortmannin 5 uM


title: Trpc2_P10_F_mut_1_scATAC

description: Library name: Sample 40

source_name: age: P10 sex: female strain: Trpc2-/- rep: mut_1


title: Trpc2_P0_M_ctrl_scATAC

description: Library name: Sample 39

source_name: age: P0 sex: male strain: Trpc2-/+ rep: ctrl


title: PETER001_THP1_24H_X1_B46:F20


title: Trpc2_P0_M_mut_scATAC

description: Library name: Sample 37

source_name: age: P0 sex: male strain: Trpc2-/- rep: mut


title: Trpc2_P0_F_mut_scATAC

description: Library name: Sample 36

source_name: age: P0 sex: female strain: Trpc2-/- rep: mut


title: PETER001_THP1_24H_X1_B46:F19


title: Trpc2_P0_F_ctrl_scATAC

description: Library name: Sample 38

source_name: age: P0 sex: female strain: Trpc2-/+ rep: ctrl


title: PETER001_THP1_24H_X1_B46:F16

description: L1000 inferred profile; pert_id: Bictegravir

source_name: THP1 treated with Bictegravir 0.5 uM for 24.0 h

value: Bictegravir 0.5 uM


title: PETER001_THP1_24H_X1_B46:F17


title: PETER001_THP1_24H_X1_B46:F15

description: L1000 inferred profile; pert_id: Elvitegravir

source_name: THP1 treated with Elvitegravir 0.1 uM for 24.0 h

value: Elvitegravir 0.1 uM


title: E14_M_1_scATAC

description: Library name: Sample 34

source_name: age: E14 sex: male strain: C57Bl6/j rep: 1


title: E14_M_2_scATAC

description: Library name: Sample 35

source_name: age: E14 sex: male strain: C57Bl6/j rep: 2


title: E14_F_2_scATAC

description: Library name: Sample 33

source_name: age: E14 sex: female strain: C57Bl6/j rep: 2


title: PETER001_THP1_24H_X1_B46:F18


title: E14_F_1_scATAC

description: Library name: Sample 32

source_name: age: E14 sex: female strain: C57Bl6/j rep: 1


title: PETER001_THP1_24H_X1_B46:F14


title: P65_M_2_scATAC

description: Library name: Sample 31

source_name: age: P65 sex: male strain: C57Bl6/j rep: 2


title: P65_M_1_scATAC

description: Library name: Sample 30

source_name: age: P65 sex: male strain: C57Bl6/j rep: 1


title: P65_F_2_scATAC

description: Library name: Sample 29

source_name: age: P65 sex: female strain: C57Bl6/j rep: 2


title: PETER001_THP1_24H_X1_B46:F13


title: PETER001_THP1_24H_X1_B46:F10

description: L1000 inferred profile; pert_id: Elvitegravir|Tenofovir Alafenamide Fumarate

source_name: THP1 treated with Elvitegravir|Tenofovir Alafenamide Fumarate 0.1|0.5 uM for 24.0 h


title: PETER001_THP1_24H_X1_B46:F11

value: Elvitegravir|Tenofovir Alafenamide Fumarate 0.1|0.5 uM


title: PETER001_THP1_24H_X1_B46:F09

description: L1000 inferred profile; pert_id: Darunavir|Ritonavir

source_name: THP1 treated with Darunavir|Ritonavir 0.1|0.5 uM for 24.0 h

value: Darunavir|Ritonavir 0.1|0.5 uM


title: P65_F_1_scATAC

description: Library name: Sample 28

source_name: age: P65 sex: female strain: C57Bl6/j rep: 1


title: PETER001_THP1_24H_X1_B46:F08


title: P28_M_2_scATAC

description: Library name: Sample 27

source_name: age: P28 sex: male strain: C57Bl6/j rep: 2


title: P28_M_1_scATAC

description: Library name: Sample 26

source_name: age: P28 sex: male strain: C57Bl6/j rep: 1


title: PETER001_THP1_24H_X1_B46:F05

description: L1000 inferred profile; pert_id: Dolutegravir|Tenofovir Alafenamide Fumarate

source_name: THP1 treated with Dolutegravir|Tenofovir Alafenamide Fumarate 0.1|0.5 uM for 24.0 h


title: PETER001_THP1_24H_X1_B46:F06

value: Dolutegravir|Tenofovir Alafenamide Fumarate 0.1|0.5 uM


title: P28_F_2_scATAC

description: Library name: Sample 25

source_name: age: P28 sex: female strain: C57Bl6/j rep: 2


title: PETER001_THP1_24H_X1_B46:F04


title: PETER001_THP1_24H_X1_B46:F12


title: P18_M_2_scATAC

description: Library name: Sample 23

source_name: age: P18 sex: male strain: C57Bl6/j rep: 2


title: PETER001_THP1_24H_X1_B46:F07


title: PETER001_THP1_24H_X1_B46:F02

description: L1000 inferred profile; pert_id: Cobicistat|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: THP1 treated with Cobicistat|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM for 24.0 h


title: P18_M_1_scATAC

description: Library name: Sample 22

source_name: age: P18 sex: male strain: C57Bl6/j rep: 1


title: P18_F_2_scATAC

description: Library name: Sample 21

source_name: age: P18 sex: female strain: C57Bl6/j rep: 2


title: PETER001_THP1_24H_X1_B46:F01

value: Cobicistat|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM


title: PETER001_THP1_24H_X1_B46:E21

description: L1000 inferred profile; pert_id: Rapamycin

source_name: THP1 treated with Rapamycin 5 uM for 24.0 h

value: Rapamycin 5 uM


title: P10_M_2_scATAC

description: Library name: Sample 19

source_name: age: P10 sex: male strain: C57Bl6/j rep: 2


title: P18_F_1_scATAC

description: Library name: Sample 20

source_name: age: P18 sex: female strain: C57Bl6/j rep: 1


title: P10_F_2_scATAC

description: Library name: Sample 17

source_name: age: P10 sex: female strain: C57Bl6/j rep: 2


title: PETER001_THP1_24H_X1_B46:F03


title: P28_F_1_scATAC

description: Library name: Sample 24

source_name: age: P28 sex: female strain: C57Bl6/j rep: 1


title: P10_M_1_scATAC

description: Library name: Sample 18

source_name: age: P10 sex: male strain: C57Bl6/j rep: 1


title: PETER001_THP1_24H_X1_B46:E20


title: P10_F_1_scATAC

description: Library name: Sample 16

source_name: age: P10 sex: female strain: C57Bl6/j rep: 1


title: PETER001_THP1_24H_X1_B46:E18

description: L1000 inferred profile; pert_id: Tenofovir Disoproxil Fumarate

source_name: THP1 treated with Tenofovir Disoproxil Fumarate 0.1 uM for 24.0 h

value: Tenofovir Disoproxil Fumarate 0.1 uM


title: PETER001_THP1_24H_X1_B46:E19


title: P4_M_2_scATAC

description: Library name: Sample 15

source_name: age: P4 sex: male strain: C57Bl6/j rep: 2


title: P4_M_1_scATAC

description: Library name: Sample 14

source_name: age: P4 sex: male strain: C57Bl6/j rep: 1


title: PETER001_THP1_24H_X1_B46:E17


title: P4_F_1_scATAC

description: Library name: Sample 12

source_name: age: P4 sex: female strain: C57Bl6/j rep: 1


title: PETER001_THP1_24H_X1_B46:E16


title: P4_F_2_scATAC

description: Library name: Sample 13

source_name: age: P4 sex: female strain: C57Bl6/j rep: 2


title: PETER001_THP1_24H_X1_B46:E14

description: L1000 inferred profile; pert_id: Cobicistat

source_name: THP1 treated with Cobicistat 0.1 uM for 24.0 h

value: Cobicistat 0.1 uM


title: PETER001_THP1_24H_X1_B46:E13


title: PETER001_THP1_24H_X1_B46:E12

description: L1000 inferred profile; pert_id: Bictegravir|Tenofovir Alafenamide Fumarate

source_name: THP1 treated with Bictegravir|Tenofovir Alafenamide Fumarate 0.5|0.5 uM for 24.0 h


title: PETER001_THP1_24H_X1_B46:E15


title: P0_M_2_scATAC

description: Library name: Sample 11

source_name: age: P0 sex: male strain: C57Bl6/j rep: 2

value: Preoptic area of the hypothalamus and surrounding tissue


title: PETER001_THP1_24H_X1_B46:E08

description: L1000 inferred profile; pert_id: Bictegravir|Emtricitabine

source_name: THP1 treated with Bictegravir|Emtricitabine 0.5|0.1 uM for 24.0 h

value: Bictegravir|Emtricitabine 0.5|0.1 uM


title: PETER001_THP1_24H_X1_B46:E09


title: P0_F_2_scATAC

description: Library name: Sample 9

source_name: age: P0 sex: female strain: C57Bl6/j rep: 2


title: E18_M_1_scATAC

description: Library name: Sample 5

source_name: age: E18 sex: male strain: C57Bl6/j rep: 1

value: male


title: P0_F_1_techrep2_scATAC

description: Library name: Sample 8

source_name: age: P0 sex: female strain: C57Bl6/j rep: techrep2


title: E18_M_2_scATAC

description: Library name: Sample 6

source_name: age: E18 sex: male strain: C57Bl6/j rep: 2


title: PETER001_THP1_24H_X1_B46:E07


title: P0_M_1_scATAC

description: Library name: Sample 10

source_name: age: P0 sex: male strain: C57Bl6/j rep: 1


title: P0_F_1_techrep1_scATAC

description: Library name: Sample 7

source_name: age: P0 sex: female strain: C57Bl6/j rep: techrep1


title: PETER001_THP1_24H_X1_B46:E10

value: Bictegravir|Tenofovir Alafenamide Fumarate 0.5|0.5 uM


title: PETER001_THP1_24H_X1_B46:E06

description: L1000 inferred profile; pert_id: Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: THP1 treated with Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.5 uM for 24.0 h


title: PETER001_THP1_24H_X1_B46:E05

value: Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.5 uM


title: E18_F_2_scATAC

description: Library name: Sample 4

source_name: age: E18 sex: female strain: C57Bl6/j rep: 2

value: female


title: E18_F_1_scATAC

description: Library name: Sample 3

source_name: age: E18 sex: female strain: C57Bl6/j rep: 1


title: PETER001_THP1_24H_X1_B46:E04


title: PETER001_THP1_24H_X1_B46:E03

description: L1000 inferred profile; pert_id: Cobicistat|Elvitegravir|Emtricitabine

source_name: THP1 treated with Cobicistat|Elvitegravir|Emtricitabine 0.1|0.1|0.1 uM for 24.0 h


title: E16_M_scATAC

description: Library name: Sample 2

source_name: age: E16 sex: male strain: C57Bl6/j rep: 1


title: E16_F_scATAC

description: Library name: Sample 1

source_name: age: E16 sex: female strain: C57Bl6/j rep: 1


title: PETER001_THP1_24H_X1_B46:E02


title: PETER001_THP1_24H_X1_B46:E01


title: Mouse spinal cord Chrna7-cKO male vehicle rep3

city: Richmond

first: Imad

last: Damaj

state: Virginia

address: 1201 E Marshall St

department: Department of Pharmacology and Toxicology

institute: Virginia Commonwealth University

description:
Library name: Sample_24
Male myeloid-specific Chrna7 knockout mouse, vehicle treated

data_processing:
Reads were trimmed for quality, then aligned to the mm10 mouse reference genome using STAR aligner.
Gene-level counts were generated using featureCounts v1.6.2 with Ensembl annotation (Mus_musculus.GRCm38.96.gtf).
Assembly: mm10 (GRCm38)
Supplementary files format and content: Tab-delimited text file containing raw gene counts. Rows are genes (gene names), columns are samples (1-24).

source_name: spinal cord

growth_protocol: Male and female C57BL/6J mice ≥8 weeks of age (Jackson Laboratory, Bar Harbor, ME) were 8-10 weeks of age at the start of experimentation and were group-housed (4 per cage) in a 21°C humidity-controlled AAALAC-approved animal care facility with free access to food and water. Experiments were performed during the light cycle and were approved by the Institutional Animal Care and Use Committee of Virginia Commonwealth University.

extract_protocol:
On day 7 after the first paclitaxel injection, RNA was extracted from L4-L6 spinal cord tissue. RNA extractions were performed identically as in Beierle et al. (2022).
RNA-seq libraries were prepared and sequenced using an Illumina NovaSeq 6000 by the University of Chicago Genomics facility.

treatment_protocol: Mice were treated with paclitaxel (1 mg/kg, 4 injections every other day) or vehicle (n=6/group). Paclitaxel (Athenex, NDC 70860-200-50, Richmond, VA, USA) was dissolved in a 1:1:18 mixture of Kolliphor (Sigma-Aldrich, St. Louis, MO, USA), ethanol (Sigma-Aldrich), and distilled water.

value: spinal cord

value: myeloid-specific Chrna7 knockout

value: vehicle


title: PETER001_THP1_24H_X1_B46:D21

description: L1000 inferred profile; pert_id: Vorinostat

source_name: THP1 treated with Vorinostat 5 uM for 24.0 h

value: Vorinostat 5 uM


title: Mouse spinal cord WT female paclitaxel rep3

description:
Library name: Sample_23
Female wild-type mouse, paclitaxel treated

value: wild-type

value: paclitaxel


title: Mouse spinal cord Chrna7-cKO female paclitaxel rep3

description:
Library name: Sample_22
Female myeloid-specific Chrna7 knockout mouse, paclitaxel treated


title: PETER001_THP1_24H_X1_B46:D20


title: Mouse spinal cord Chrna7-cKO male vehicle rep2

description:
Library name: Sample_20
Male myeloid-specific Chrna7 knockout mouse, vehicle treated


title: Mouse spinal cord WT male vehicle rep3

description:
Library name: Sample_21
Male wild-type mouse, vehicle treated


title: PETER001_THP1_24H_X1_B46:D17

description: L1000 inferred profile; pert_id: Efavirenz

source_name: THP1 treated with Efavirenz 0.5 uM for 24.0 h

value: Efavirenz 0.5 uM


title: Mouse spinal cord Chrna7-cKO female paclitaxel rep2

description:
Library name: Sample_18
Female myeloid-specific Chrna7 knockout mouse, paclitaxel treated


title: PETER001_THP1_24H_X1_B46:D19


title: Mouse spinal cord WT female paclitaxel rep2

description:
Library name: Sample_19
Female wild-type mouse, paclitaxel treated


title: PETER001_THP1_24H_X1_B46:D16


title: PETER001_THP1_24H_X1_B46:D18


title: PETER001_THP1_24H_X1_B46:D15

description: L1000 inferred profile; pert_id: Cobicistat|Tenofovir Alafenamide Fumarate

source_name: THP1 treated with Cobicistat|Tenofovir Alafenamide Fumarate 0.1|0.5 uM for 24.0 h


title: Mouse spinal cord Chrna7-cKO male vehicle rep1

description:
Library name: Sample_16
Male myeloid-specific Chrna7 knockout mouse, vehicle treated


title: Mouse spinal cord WT male vehicle rep2

description:
Library name: Sample_17
Male wild-type mouse, vehicle treated


title: PETER001_THP1_24H_X1_B46:D14

value: Cobicistat|Tenofovir Alafenamide Fumarate 0.1|0.5 uM


title: Mouse spinal cord WT female paclitaxel rep1

description:
Library name: Sample_15
Female wild-type mouse, paclitaxel treated


title: PETER001_THP1_24H_X1_B46:D13


title: Mouse spinal cord WT male vehicle rep1

description:
Library name: Sample_13
Male wild-type mouse, vehicle treated


title: PETER001_THP1_24H_X1_B46:D12

description: L1000 inferred profile; pert_id: Efavirenz|Tenofovir Disoproxil Fumarate

source_name: THP1 treated with Efavirenz|Tenofovir Disoproxil Fumarate 0.5|0.1 uM for 24.0 h


title: Mouse spinal cord Chrna7-cKO female paclitaxel rep1

description:
Library name: Sample_14
Female myeloid-specific Chrna7 knockout mouse, paclitaxel treated


title: Mouse spinal cord Chrna7-cKO female vehicle rep3

description:
Library name: Sample_12
Female myeloid-specific Chrna7 knockout mouse, vehicle treated


title: PETER001_THP1_24H_X1_B46:D11

value: Efavirenz|Tenofovir Disoproxil Fumarate 0.5|0.1 uM


title: PETER001_THP1_24H_X1_B46:D09

description: L1000 inferred profile; pert_id: Emtricitabine|Tenofovir Disoproxil Fumarate

source_name: THP1 treated with Emtricitabine|Tenofovir Disoproxil Fumarate 0.1|0.1 uM for 24.0 h


title: Mouse spinal cord WT male paclitaxel rep3

description:
Library name: Sample_11
Male wild-type mouse, paclitaxel treated


title: PETER001_THP1_24H_X1_B46:D10


title: Mouse spinal cord WT female vehicle rep3

description:
Library name: Sample_9
Female wild-type mouse, vehicle treated


title: Mouse spinal cord Chrna7-cKO male paclitaxel rep3

description:
Library name: Sample_10
Male myeloid-specific Chrna7 knockout mouse, paclitaxel treated


title: PETER001_THP1_24H_X1_B46:D07

value: Emtricitabine|Tenofovir Disoproxil Fumarate 0.1|0.1 uM


title: PETER001_THP1_24H_X1_B46:D08


title: PETER001_THP1_24H_X1_B46:D06

description: L1000 inferred profile; pert_id: Efavirenz|Emtricitabine

source_name: THP1 treated with Efavirenz|Emtricitabine 0.5|0.1 uM for 24.0 h

value: Efavirenz|Emtricitabine 0.5|0.1 uM


title: PETER001_THP1_24H_X1_B46:D05


title: PETER001_THP1_24H_X1_B46:D04


title: Mouse spinal cord Chrna7-cKO male paclitaxel rep2

description:
Library name: Sample_6
Male myeloid-specific Chrna7 knockout mouse, paclitaxel treated


title: Mouse spinal cord WT female vehicle rep2

description:
Library name: Sample_5
Female wild-type mouse, vehicle treated


title: PETER001_THP1_24H_X1_B46:D03

description: L1000 inferred profile; pert_id: Cobicistat|Elvitegravir|Emtricitabine


title: PETER001_THP1_24H_X1_B46:C21

description: L1000 inferred profile; pert_id: Genistein

source_name: THP1 treated with Genistein 5 uM for 24.0 h

value: Genistein 5 uM


title: Mouse spinal cord WT male paclitaxel rep2

description:
Library name: Sample_7
Male wild-type mouse, paclitaxel treated


title: Mouse spinal cord Chrna7-cKO female vehicle rep2

description:
Library name: Sample_8
Female myeloid-specific Chrna7 knockout mouse, vehicle treated


title: Mouse spinal cord Chrna7-cKO female vehicle rep1

description:
Library name: Sample_4
Female myeloid-specific Chrna7 knockout mouse, vehicle treated


title: Mouse spinal cord WT male paclitaxel rep1

description:
Library name: Sample_3
Male wild-type mouse, paclitaxel treated


title: PETER001_THP1_24H_X1_B46:D02


title: PETER001_THP1_24H_X1_B46:D01


title: Mouse spinal cord Chrna7-cKO male paclitaxel rep1

description:
Library name: Sample_2
Male myeloid-specific Chrna7 knockout mouse, paclitaxel treated


title: Mouse spinal cord WT female vehicle rep1

description:
Library name: Sample_1
Female wild-type mouse, vehicle treated


title: Kidney ECs from I-PpoI mouse 1 on HFD

city: tokyo

first: akihito

last: hishikawa

address: Shinanomachi35, shinjyukuku

country: Zimbabwe

institute: keio university

description: Library name: Tg_kidneyEC_1

data_processing:
DEGs, heatmaps, and PCAs were analyzed using the DESeq2 package version 1.28.13. The enrichment of GO biological processes and the correlation network of enriched GO terms were analyzed with the clusterProfiler package, version 3.16.14, with p values of 0.01 and 0.05 and q-values of 0.05 (BH methods).
Assembly: mm10 (GRCm38)
Supplementary files format and content: Processed data files include a gene-level count matrix generated from RNA-seq data. The matrix contains raw and normalized read counts for each gene across all samples. Differential expression analysis was performed using DESeq2, and result tables include gene symbols, log2 fold changes, p-values, and adjusted p-values (BH method).

source_name: kidney

growth_protocol: Mice were maintained under a 12-h light/dark cycle with ad libitum access to food and water. At 8 weeks of age, mice were switched from a standard chow diet to a high-fat diet (HFD; 60% kcal fat) and were maintained on this diet for 4 weeks before tissue collection for RNA-sequencing.

extract_protocol:
Endothelial cells (ECs) were isolated from collagenase-digested whole kidneys via magnetic-activated cell sorting (MACS) using a CD31 antibody. Total RNA was subsequently extracted from the purified ECs using ISOGEN reagent for library preparation.
The libraries were sequenced for 100 cycles (paired ends) using a NovaSeq

value: kidney

value: endothelial cell

value: VE-cadherin Cre; ROSA26-STOP-I-PpoI

value: High-fat diet


title: PETER001_THP1_24H_X1_B46:C20


title: Kidney ECs from I-PpoI mouse 3 on HFD

description: Library name: Tg_kidneyEC_3

value: VE-cadherin Cre; ROSA28-STOP-I-PpoI


title: PETER001_THP1_24H_X1_B46:C19


title: Kidney ECs from I-PpoI mouse 2 on HFD

description: Library name: Tg_kidneyEC_2

value: VE-cadherin Cre; ROSA27-STOP-I-PpoI


title: PETER001_THP1_24H_X1_B46:C17

description: L1000 inferred profile; pert_id: Emtricitabine

source_name: THP1 treated with Emtricitabine 0.1 uM for 24.0 h

value: Emtricitabine 0.1 uM


title: PETER001_THP1_24H_X1_B46:C16


title: PETER001_THP1_24H_X1_B46:C18


title: PETER001_THP1_24H_X1_B46:C12

description: L1000 inferred profile; pert_id: Abacavir|Emtricitabine

source_name: THP1 treated with Abacavir|Emtricitabine 0.5|0.1 uM for 24.0 h

value: Abacavir|Emtricitabine 0.5|0.1 uM


title: PETER001_THP1_24H_X1_B46:C15

description: L1000 inferred profile; pert_id: Elvitegravir|Emtricitabine

source_name: THP1 treated with Elvitegravir|Emtricitabine 0.1|0.1 uM for 24.0 h

value: Elvitegravir|Emtricitabine 0.1|0.1 uM


title: cLNs_ BCG+Mtb+aCD4_14_Lesion_rep3

city: Cairns

first: Andreas

last: Kupz

state: Queensland

address: McGregor Road, Smithfield

department: Australian Institute of Tropical Health and Medicine

country: Australia

institute: James Cook University

description:
Library name: DSP-1001510800105-F-C10_S300_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue

data_processing:
Slides were stained with barcoded probes and fluorescent markers
ROIs were selected on the GeoMx instrument and UV light releases barcodes from chosen areas
The released barcodes were quantified
FASTQfiles.gz
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatia bar codes
Supplementary files format and content: Feature.tsv.gz: List of gene ID
Library strategy: Spatial Transcriptomics

source_name: Cervical Lymph Nodes (cLNs)

growth_protocol: C57BL/6 mice were 1) untreated mice (Normal); 2) unvaccinated and Mtb-infected (Mtb); 3)  unvaccinated, immunosuppressed with anti-CD4 mAb and Mtb-infected (Mtb+aCD4); 4) vaccinated with BCG,  immunosuppressed with anti-CD4 mAb and Mtb-infected (BCG+aCD4+Mtb); 5) vaccinated with PE25,  immunosuppressed with anti-CD4 mAb and Mtb-infected (PE25+aCD4+Mtb). Mice were unvaccinated or vaccinated, 60 days post-vaccination some mice were Mtb-infected and/or immunosupressed with weekly intra-peritoneal injections of aCD4 mAb for 120 days.

extract_protocol:
Samples were Fixed in 4% paraformaldehyde for 24 hours, transfer to 70% ethanol and embbeding in parafin. Then slides were cut and sent to Nanostring (Seattle) where they were stained and data was generated
Sample transcriptome sequence libraries were done following the manufacturer products by Nanstring Seattle.

treatment_protocol: After treatment period mice cLNs were collected

value: Cervical Lymph Nodes (cLNs)

value: C57BL/6 mice


title: Kidney ECs from Control mouse 2 on HFD

description: Library name: WT_kidneyEC_2

value: wild-type littermate


title: cLNs_ Mtb+aCD4_17_Normal in disease__rep1

description:
Library name: DSP-1001510800105-F-D01_S303_001.fastq.gz
Paraformaldehyde-fixed and paraffin-embedded tissue


title: Kidney ECs from Control mouse 3 on HFD

description: Library name: WT_kidneyEC_3


title: PETER001_THP1_24H_X1_B46:C13


title: PETER001_THP1_24H_X1_B46:C10