title: HEK293T, WT, rep2

city: Austin

first: Yan

middle: Jessie

address: 100 E. 24th Street

institute: University of Texas-Austin

data_processing:
Sequence reads were trimmed using Trimmomatic v.0.38  to omit adaptor sequences
trimmed sequences were mapped to hg38 using HISAT2 v.2.2.1 (parameter: -unstranded)
read count extraction was conducted using featurecounts v.2.0.1
Assembly: hg38
Supplementary files format and content: text file including raw counts for each sample

growth_protocol: HEK293T cells were maintained in DMEM supplemented in 10% FBS and antibiotics in a humidified chamber with 5% CO2 at 37°C

extract_protocol:
RNA was isolated from HEK293T cells (at least ~106 cells per sample) using DirectZol RNA Miniprep kit (Zymo Research).
Libraries were prepared at Novogene Co. according to manufacturer’s instructions for the NEBNext Ultra RNA Library kit for Illumina.

treatment_protocol: Cells were transfected with an alpha amanitin-resistant RPB1 construct with a wild-type or T4A sequence. After 1 day the cells were supplemented with 2.5μg/ml of alpha amanitin for 48 hours

value: human embryonic kidney cells

value: transfected with RPB1 construct containing the wild-type CTD sequence


title: Cal27 cell, NC-2

status: Public on Jul 31 2024

type: SRA

city: Nanjing

first: Jiayi

last: Zhang

address: Hanzhong Road 140#

country: China

institute: Nanjing Medical University

library_source: transcriptomic

data_processing:
The sequencing reads were mapped onto the reference gene set by using Bowtie1 software . A Perl script program was used to process the mapping results and the gene expression profile was generated.
Assembly: GRCh38.p13_104
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cal27 cells were cultured in high-glucose DMEM (Gibco) containing 10% FBS and 1% penicillin/streptomycin at 37 ℃ in the 5% CO2-humidifed incubator.

extract_protocol:
RNA was harvested using TRIzol (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The lentivirus was transfected to knockdown DAZAP1, and the empty vector was co-transfected as a negative control.

tag: cell line

tag: cell type

value: oral cancer cell line

tag: genotype

value: control


title: HEK293T_ChIP_H3K9me3_Input_NC_ASO_rep1

city: Xi'an

first: Wei

last: Sun

state: Shaanxi

address: No. 229 Taibai North Road, Beilin District

department: College of Life Sciences and Medicine

institute: Northwest University

description:
HEK293T_ChIP_H3K9me3_Input_NC_ASO_rep1
HEK293T_H3K9me3_Input_NC.bigwig

library_source: genomic

data_processing:
The raw sequencing reads were Quality Controled by FastQC(v0.11.8).
The sequencing reads were subject to removal of adapter and quality filter using Cutadapt (v3.3).
The trimmed reads were aligned to hg19 genome using Bowtie2 (v2.4.2) with the parameters: bowtie2 --no-unal.
PCR duplicates were removed using GATK MarkDuplicates (v4.1.9.0) with the parameters: gatk MarkDuplicates --REMOVE_DUPLICATES true.
Peak calling was performed using MACS2 (v2.2.7.1) with the parameters: macs2 callpeak -f BAMPE -g hs.
Assembly: hg19
Supplementary files format and content: bigwig, all samples
Supplementary files format and content: narrowPeak, all samples

molecule: genomic DNA

growth_protocol: Antisense oligonucleotides (ASOs) including ASOSETD5-AS1, ASOLINC00641 and ASO LINC00662 were transfected into HEK293T cells grown on the 6-well plates, and incubated for 48h.

extract_protocol:
1% Formaldehyde (Sigma, F8775) was added into each well to crosslink the cells for 10 min with a slight shaking at room temperature.chromtin was sonicated using Covaris M220 sonicator.
DNA was isolated by performing a phenol/chloroform/isoamyl alcohol extraction to prepare the ChIP-seq library using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645).

value: Human embryonic kidney


title: HEK293T,WT, rep1

country: USA

molecule: polyA RNA

tag: treatment


title: HEK293T, T4A, rep2

value: transfected with RPB1 construct containing the T4A mutation


title: HEK293T, T4A, rep1


title: HEK293T_ChIP_H3K9me3_LINC00662_ASO_rep3

description:
HEK293T_ChIP_H3K9me3_LINC00662_ASO_rep3
HEK293T_H3K9me3_LINC00662ASOMIX.bigwig
HEK293T_H3K9me3_LINC00662ASO_vs_Input_peaks.narrowPeak


title: HEK293T_ChIP_H3K9me3_NC_ASO_rep2

description:
HEK293T_ChIP_H3K9me3_NC_ASO_rep2
HEK293T_H3K9me3_NC_ASO.bigwig
HEK293T_H3K9me3_NC_ASO_vs_Input_peaks.narrowPeak


title: HEK293T_ChIP_H3K9me3_Input_NC_ASO_rep3

description:
HEK293T_ChIP_H3K9me3_Input_NC_ASO_rep3
HEK293T_H3K9me3_Input_NC.bigwig


title: HEK293T_ChIP_H3K9me3_NC_ASO_rep3

description:
HEK293T_ChIP_H3K9me3_NC_ASO_rep3
HEK293T_H3K9me3_NC_ASO.bigwig
HEK293T_H3K9me3_NC_ASO_vs_Input_peaks.narrowPeak


description:
HEK293T_ChIP_H3K9me3_Input_LINC00662_ASO_rep1
HEK293T_H3K9me3_Input_LINC00662ASOMIX.bigwig


title: HEK293T_ChIP_H3K9me3_Input_NC_ASO_rep2

description:
HEK293T_ChIP_H3K9me3_Input_NC_ASO_rep2
HEK293T_H3K9me3_Input_NC.bigwig


description:
HEK293T_ChIP_H3K9me3_Input_LINC00662_ASO_rep3
HEK293T_H3K9me3_Input_LINC00662ASOMIX.bigwig


description:
HKE293T_ChIP_H3K27me3_Input_SETD5-AS1_ASO_rep2
HEK293T_H3K27me3_SETD5_AS1_ASO_Input.bigwig


title: HEK293T_ChIP_H3K9me3_LINC00662_ASO_rep1

description:
HEK293T_ChIP_H3K9me3_LINC00662_ASO_rep1
HEK293T_H3K9me3_LINC00662ASOMIX.bigwig
HEK293T_H3K9me3_LINC00662ASO_vs_Input_peaks.narrowPeak


description:
HKE293T_ChIP_H3K27me3_Input_SETD5-AS1_ASO_rep1
HEK293T_H3K27me3_SETD5_AS1_ASO_Input.bigwig


description:
HKE293T_ChIP_H3K27me3_Input_SETD5-AS1_ASO_rep3
HEK293T_H3K27me3_SETD5_AS1_ASO_Input.bigwig


title: HEK293T_ChIP_H3K9me3_NC_ASO_rep1

description:
HEK293T_ChIP_H3K9me3_NC_ASO_rep1
HEK293T_H3K9me3_NC_ASO.bigwig
HEK293T_H3K9me3_NC_ASO_vs_Input_peaks.narrowPeak


description:
HKE293T_ChIP_H3K27me3_Input_LINC00641_ASO_rep3
HEK293T_H3K27me3_LINC00641_ASO_Input.bigwig


title: HKE293T_ChIP_H3K27me3_Input_NC_ASO_rep1

description:
HKE293T_ChIP_H3K27me3_Input_NC_ASO_rep1
HEK293T_H3K27me3_NC_ASO_Input.bigwig


description:
HKE293T_ChIP_H3K27me3_Input_LINC00641_ASO_rep2
HEK293T_H3K27me3_LINC00641_ASO_Input.bigwig


description:
HKE293T_ChIP_H3K27me3_SETD5-AS1_ASO_rep3
HEK293T_H3K27me3_SETD5_AS1_ASO.bigwig
HEK293T_H3K27me3_SETD5_AS1_ASO_vs_Input_peaks.narrowPeak


title: HKE293T_ChIP_H3K27me3_Input_NC_ASO_rep3

description:
HKE293T_ChIP_H3K27me3_Input_NC_ASO_rep3
HEK293T_H3K27me3_NC_ASO_Input.bigwig


description:
HKE293T_ChIP_H3K27me3_Input_LINC00641_ASO_rep1
HEK293T_H3K27me3_LINC00641_ASO_Input.bigwig


description:
HKE293T_ChIP_H3K27me3_SETD5-AS1_ASO_rep1
HEK293T_H3K27me3_SETD5_AS1_ASO.bigwig
HEK293T_H3K27me3_SETD5_AS1_ASO_vs_Input_peaks.narrowPeak


description:
HKE293T_ChIP_H3K27me3_SETD5-AS1_ASO_rep2
HEK293T_H3K27me3_SETD5_AS1_ASO.bigwig
HEK293T_H3K27me3_SETD5_AS1_ASO_vs_Input_peaks.narrowPeak


description:
HKE293T_ChIP_H3K27me3_LINC00641_ASO_rep1
HEK293T_H3K27me3_LINC00641_ASO.bigwig
HEK293T_H3K27me3_LINC00641_ASO_vs_Input_peaks.narrowPeak


description:
HKE293T_ChIP_H3K27me3_LINC00641_ASO_rep2
HEK293T_H3K27me3_LINC00641_ASO.bigwig
HEK293T_H3K27me3_LINC00641_ASO_vs_Input_peaks.narrowPeak


description:
HKE293T_ChIP_H3K27me3_LINC00641_ASO_rep3
HEK293T_H3K27me3_LINC00641_ASO.bigwig
HEK293T_H3K27me3_LINC00641_ASO_vs_Input_peaks.narrowPeak


title: HEK293T_Chromseq_CBX7_rep2

description:
HEK293T_NLS_CBX7_rep2
Chromseq_allsamples_raw_counts.txt

data_processing:
The raw sequencing reads were Quality Controled by FastQC(v0.11.8).
Then, raw reads were trimmed using fastp(v0.23.1) with the options: fastp -A -f 11 -F 0 -t 0 -T 11.
Clean reads were aligned using HISAT2(v.2.1.0) to the hg19 genome with the options: hisat2 -q -t --no-unal.
The aligned reads were quantified by featureCounts(v2.0.1) using the options: featureCounts -t gene -g gene_id --extraAttributes gene_name,gene_type -s 1 -p -C
Differential expression analysis using DESeq2 (v1.34.0).
Assembly: hg19
Supplementary files format and content: tab-delimited text file include Chromseq three biological replicates raw counts for each sample
Supplementary files format and content: tab-delimited text file include RNAseq three biological replicates raw counts for each sample
Library strategy: Chrom-seq

growth_protocol: Plate HEK293T cells co-expressing the corresponding GCN4 and APEX2 fusion constructs for 48 hours.

extract_protocol:
The total RNA was isolated by using the NEB Next Poly A+Isolation Kit (NEB, #E7490S/L).1-5 μg of total RNA was used for the construction of sequencing libraries.
Libraries were built using the Smart-seq protocol.

treatment_protocol: Cells were changed the medium to fresh medium containing 500 µM biotin-aniline and incubate at 37℃ under 5% CO2 for 30 min. Then, H2O2 was then added to each well to a final concentration of 1 mM, and the plate gently agitated for 1 min.


title: HEK293T_RNAseq_CBX7_rep3

description:
HEK293T_RNAseq_CBX7_rep3
RNAseq_allsamples_raw_counts.txt

data_processing:
The raw sequencing reads were Quality Controled by FastQC(v0.11.8).
Then, raw reads were trimmed using fastp(v0.23.1) with the options: fastp -A -f 11 -F 0 -t 0 -T 11.
Clean reads were aligned using HISAT2(v.2.1.0) to the hg19 genome with the options: hisat2 -q -t --no-unal.
The aligned reads were quantified by featureCounts(v2.0.1) using the options: featureCounts -t gene -g gene_id --extraAttributes gene_name,gene_type -s 1 -p -C
Differential expression analysis using DESeq2 (v1.34.0).
Assembly: hg19
Supplementary files format and content: tab-delimited text file include Chromseq three biological replicates raw counts for each sample
Supplementary files format and content: tab-delimited text file include RNAseq three biological replicates raw counts for each sample


title: HKE293T_ChIP_H3K27me3_Input_NC_ASO_rep2

description:
HKE293T_ChIP_H3K27me3_Input_NC_ASO_rep2
HEK293T_H3K27me3_NC_ASO_Input.bigwig


title: HEK293T_RNAseq_CBX7_rep2

description:
HEK293T_RNAseq_CBX7_rep2
RNAseq_allsamples_raw_counts.txt


title: HKE293T_ChIP_H3K27me3_NC_ASO_rep2

description:
HKE293T_ChIP_H3K27me3_NC_ASO_rep2
HEK293T_H3K27me3_NC_ASO.bigwig
HEK293T_H3K27me3_NC_ASO_vs_Input_peaks.narrowPeak


title: HEK293T_Chromseq_dPC_rep3

description:
HEK293T_NLS_dPC_rep3
Chromseq_allsamples_raw_counts.txt


title: HEK293T_Chromseq_CBX7_rep1

description:
HEK293T_NLS_CBX7_rep1
Chromseq_allsamples_raw_counts.txt


title: HKE293T_ChIP_H3K27me3_NC_ASO_rep1

description:
HKE293T_ChIP_H3K27me3_NC_ASO_rep1
HEK293T_H3K27me3_NC_ASO.bigwig
HEK293T_H3K27me3_NC_ASO_vs_Input_peaks.narrowPeak


title: HEK293T_RNAseq_Control_rep2

description:
HEK293T_RNAseq_Control_rep2
RNAseq_allsamples_raw_counts.txt


title: HEK293T_RNAseq_CBX7_rep1

description:
HEK293T_RNAseq_CBX7_rep1
RNAseq_allsamples_raw_counts.txt


title: HEK293T_RNAseq_Control_rep1

description:
HEK293T_RNAseq_Control_rep1
RNAseq_allsamples_raw_counts.txt


title: HEK293T_Chromseq_CBX7_rep3

description:
HEK293T_NLS_CBX7_rep3
Chromseq_allsamples_raw_counts.txt


title: HEK293T_RNAseq_Control_rep3

description:
HEK293T_RNAseq_Control_rep3
RNAseq_allsamples_raw_counts.txt


title: TFN Low Rep8

city: Toulouse

first: Thomas

last: FARGE

state: Occitanie

address: 1 Avenue jean pouilles

country: France

institute: INSERM

data_processing:
Data were extracted and annotated using Galaxy and following the procedure described in Batut et al 2021 in RNA Bioinformatics
Batut B, van den Beek M, Doyle MA, Soranzo N. RNA-Seq Data Analysis in Galaxy. Methods Mol Biol. 2021;2284:367-392. doi: 10.1007/978-1-0716-1307-8_20. PMID: 33835453.
Assembly: HG18
Supplementary files format and content: CSV (FPM)

source_name: Bone Marrow

growth_protocol: hbmMSCs were obtained from healthy bone marrow by culturing cells through a collaboration with EFS Occitanie. Cells were incubated at 37 ◦C and 5% CO2 in EGM2 media after adherence. At 70% of confluence, the cells were detached using 0.05% Trypine EDTA (Sigma-Aldrich, St Louis, MO, USA)

extract_protocol:
Promega reliaPrep
RNA librairies for RNA sequencing were prepared with Illumina TruSeq Stranded mRNA kit following the manufacturer's instructions

treatment_protocol: bmMSC were incubated at 37 ◦C for 30 min with 200 nM Tetramethylrhodamine (TMRM) (CMXRos Mitotracker, Thermo Fisher Scientific, Walthman, MS, USA). After cell resuspension in PBS with 1% FBS and 0,5mM EDTA, cells were sorted using a BD Influx cell sorter (BD Biosciences) to identify and separate High-TMRM from Low-TMRM subpopulations. Sorting setup, based on the scatter and fluorescent parameters, and appropriate gating, to exclude dead and double cells, were established using unlabeled cells.

tag: tissue

value: Bone Marrow

value: Mesenchymal stromal cells

value: TMRM Low


title: HEK293T_Chromseq_dPC_rep1

description:
HEK293T_NLS_dPC_rep1
Chromseq_allsamples_raw_counts.txt


title: TFN High Rep7

value: TMRM High


title: HEK293T_Chromseq_dPC_rep2

description:
HEK293T_NLS_dPC_rep2
Chromseq_allsamples_raw_counts.txt


title: TFN Low Rep6


title: HHT VMO

city: Irvine

first: Christopher

middle: J

last: Hatch

state: CA

address: 2400 Biological Sciences III

institute: University of California, Irvine

description:
10x Genomics
IPTGD10

library_source: transcriptomic single cell

data_processing:
The barcoded processing, gene counting, and aggregation were made using the Cell Ranger software v6.0.0
Count matrices were imported into R and analyzed using the standard Seurat SCT pipeline
Assembly: GRCh38
Supplementary files format and content: Seurat objects from processed datasets
Supplementary files format and content: Count matrices output from cell ranger

source_name: Human umbilical cord endothelial cells + normal human lung fibroblast

extract_protocol:
The thin transparent membrane was carefully removed from the bottom of the PDMS layer to expose the tissue chambers for two microfluidic devices containing 24 device units. The chambers were washed with HBSS prior to adding TrypLE express enzyme in a drop-wise manner. After incubation at 37°C for 5 minutes, the chambers were flushed with a micropipette to collect ~10,000 cells into a centrifuge tube. Cells were then quenched with EGM-2. Next, cells were centrifuged (340xg for 3 min) and resuspended in an HBSS/collagenase type III solution (1 mg mL-1) to digest the matrix fully. The cells were then washed with EGM-2 and pushed through a 70 μm filter to create a single-cell suspension. Finally, a propidium iodide stain was used to remove dead and dying cells by FACS on a BD Flow-assisted cell sorting AriaII
The cellular suspensions were then loaded onto a Chromium Single Cell Instrument (10X genomics) and processed to generate cDNA using 10X Genomics v2 chemistry according to the Chromium Single Cell 3' Reagents kits v2 user guide

tag: time

value: Day 10

value: IPTG 3 mm


title: TFN Low Rep7


title: TFN High Rep5


title: TFN High Rep8


title: HEK293T_ChIP_H3K9me3_LINC00662_ASO_rep2

description:
HEK293T_ChIP_H3K9me3_LINC00662_ASO_rep2
HEK293T_H3K9me3_LINC00662ASOMIX.bigwig
HEK293T_H3K9me3_LINC00662ASO_vs_Input_peaks.narrowPeak


title: TFN Low Rep5


title: TFN Low Rep4


title: TFN High Rep6


title: HKE293T_ChIP_H3K27me3_NC_ASO_rep3

description:
HKE293T_ChIP_H3K27me3_NC_ASO_rep3
HEK293T_H3K27me3_NC_ASO.bigwig
HEK293T_H3K27me3_NC_ASO_vs_Input_peaks.narrowPeak


title: TFN High Rep4


title: TFN Low Rep3


title: TFN High Rep3


title: Control VMO

description:
10x Genomics
ControlD10

value: Human umbilical cord endothelial cells + normal human lung fibroblast


title: TFN High Rep2


title: TFN Low Rep2


title: MN_20

city: Oxford

first: Georgios

last: Baskozos

address: NDCN, Level 6, West Wing, John Radcliffe Hospital

country: United Kingdom

institute: University of Oxford

data_processing:
Reads were mapped to the GRCh38 human genome by the STAR aligner with standard ENCODE options,and gene counts were determined using HTSeq.
Supplementary files format and content: Raw gene counts table in csv format.

source_name: plantar digital nerves

extract_protocol:
Total RNA extraction was done using a hybrid method of phenol extraction (TriPure; Roche, Welwyn Garden City, United Kingdom) combined with column purification (High Pure RNA tissue Kit; Roche). The aqueous liquid phase containing the nucleic acids was removed and added to the columns of the High Pure RNA tissue kit (Roche Diagnostics). RNA was purified using repeated wash steps and DNAse treatment. The concentration of RNA in the samples was measured using a nanodrop. Total RNA was provided to the sequencing center, and the poly-adenylated fraction was selected for sequencing.
RNAseq was performed at the Wellcome Centre for Human Genetics. Polyadenylated transcript enrichment and strand specific library preparation was done using the NEBNext® UltraTM II RNA Library Prep kit (NEB, E7770) following manufacturer’s instructions. Libraries were amplified using unique dual indexing primers, based on Lamble, et al. Paired end sequencing was performed on an Illumina NovaSeq6000 system

value: plantar digital nerves

tag: disease state

value: Morton’s neuroma

tag: Sex

value: F


title: TFN High Rep1


title: TFN Low Rep1


title: MN_19


title: MN_17


title: MN_22

value: M


title: MN_21


title: MN_18


title: MN_15


title: MN_16


title: MN_14


title: MN_10


title: MN_13


title: MN_11


title: MN_5


title: MN_4


title: MN_3


title: MN_9


title: MN_1


title: CON_10

source_name: nerves of the upper and lower limbs

value: nerves of the upper and lower limbs

value: Control nerves


title: CON_11


title: CON_9


title: CON_8


title: CON_6


title: CON_4


title: CON_3


title: MN_12


title: EPCART_WT_2

city: Tampere

first: Tapio

last: Visakorpi

address: Kalevantie 4

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

data_processing:
The quality of raw RNA-seq reads was evaluated using FastQC v0.11.8 and the reads were trimmed with Trim Galore! v.0.6.5. Reads were aligned to GRCh38 using STAR v2.71a and indexed with Samtools v1.8. Read counts of protein coding transcripts were calculated using BEDTools v. 2.27.1 sub-command multicov and GENCODE v.38 annotation was used for gene calls.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw read counts for each sample

source_name: LNCaP

growth_protocol: All cells were cultured in RPMI 1640 medium with 10% FBS, 1% glutamine, and 1% penicillin-streptomycin for 48h.

extract_protocol:
RNA from cells was isolated using Trizol (Invitrogen, Thermo Fisher Scientific), treated with RNase-free DNase set (Qiagen), and purified by Monarch RNA Cleanup Kit (New England Biolabs) according to manufacturers’ protocols. The purified RNA was quantified by Qubit 4 Fluorometer (Invitrogen, Thermo Fisher Scientific) and Qubit RNA Broad Range Assay Kit (Invitrogen, Thermo Fisher Scientific), and its purity assessed by the 260nm/280nm ratio. RNA integrity was checked using 5300 Fragment Analyzer System (Agilent Technologies).
Library preparation was performed using standard polyA enrichment and strand-specific library protocol, and sequencing was performed with a Novaseq6000 (Illumina) in Novogene (Hong Kong, China) for 150 bp pairedend reads. On average, 105 million cleaned reads per sample were obtained in strand-specific RNA-seq.

treatment_protocol: EPCART-deletion and WT clones were created by CRIPR-Cas9 as previously described (Kohvakka et al., Oncogene, 2020, 39:5241-5251).

value: LNCaP

value: prostate cancer cells

value: EPCART wild-type


title: EPCART_WT_1


title: CON_1


title: EPCART_WT_3


title: MN_8


title: MN_7


title: MN_6


title: EPCART_del-56_2

value: EPCART knockout


title: EPCART_del-56_1


title: EPCART_del-4_3


title: EPCART_del-4_2


title: MN_2


title: EPCART_del-4_1


title: N4-RT12-190

city: Philadelphia

first: Huasheng

last: Yu

state: PENNSYLVANIA

address: 3610 Hamilton Walk

department: Neuroscience

institute: University of Pennsylvania

data_processing:
Raw sequencing data was demultiplexed with bcl2fastq2 v.2.20 (Illumina)
Demultiplexed data was trimmed with Cutadapt to remove Tn5 transposon adapter sequences.
The trimmed data were aligned to human genome using STAR v.2.7.9a49.
STAR quantMode GeneCounts was used to quantify unique mapped reads to gene counts.
Gene counts file was used for the downstream analysis
Assembly: human genome (GRCh38 GENCODE as the reference genome, and GRCh38.104. GTF as the annotation)
Supplementary files format and content: Comma-separated file includes raw counts for each Sample

source_name: Dorsal root ganglia

extract_protocol:
Human DRG tissues were procured from National Disease Research Interchange (NDRI). The research application was approved by the NDRI Feasibility Committee (RLUW1 01). Six DRGs between T11 to L5 of three human donors aged from 23- 61 years were used in this study. The dissected DRG tissues from human donors were immediately imbedded in OCT, shipped to the Luo lab on dry ice and stored in -80 ℃ until use. The information of DRGs and dis-identified donors and screening criteria are summarized in the manuscript Supplementary Tables 1 & 2. The hDRGs imbedded in OCT were cryosectioned (Cryostat Leica Cm1950) into 20 μm sec-tions and mounted onto Arcturus PEN Membrane Frame Slides (Applied biosystems, LCM0521). One of every five consecutive sections was collected for laser capture microdissec-tion to avoid repeated dissection of the soma from the same neuron in different sections. The slides were stored in -80 ℃ until further use.On the day of laser capture microdissection, the slides were transferred to the SBDRC laser capture microdissection (LCM) core on dry ice. Before dissection, the section was briefly stained with RNase free Arcturus™ Histogene™ staining solution (Applied biosystems, 12241-05) for better visualization of neuronal soma: 70% cold EtOH for 30s; Histogene™ staining for 10s; 70% cold EtOH for 30s; 95% cold EtOH for 30s; 100% cold EtOH for 30s and air dry for 2min. Then, the slide was put onto laser capture microdissection microscope system (Leica LMD6) for the neuronal soma dissection. The laser was calibrated, and the laser intensity was adjusted to achieve best dissection efficiency. The dissected individual neuronal soma was col-lected in the cap of a 200 μl PCR tube containing 4 μl lysis buffer.
The sequencing library was generated following Smart-seq2 workflow. The libraries passing through all quality con-trols were selected for the final sequencing.

value: Dorsal root ganglia

tag: donor id

tag: age(years)

tag: race

value: Caucasian

tag: gender

value: Male

tag: region

value: thoracic 12

tag: sequencing batch

tag: dissected soma size

tag: cell identity


title: CON_7


title: CON_5


title: N4-RT12-186


title: N4-RT12-188


title: CON_2


title: N4-RT12-192

value: hPropr


title: N4-RT12-191


title: N4-RT12-193


title: N4-RT12-187


title: N4-RT12-189


title: N4-RT12-194


title: N4-RT12-183


title: N4-RT12-179


title: N4-RT12-178


title: EPCART_del-56_3


title: N4-RT12-177


title: N4-RT12-176


title: N4-RT12-182


title: N4-RT12-173


title: N4-RT12-171


title: N4-RT12-175


title: N4-RT12-170


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value: thoracic 11


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title: N4-RT12-32


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title: N4-RT12-8


title: N4-RT12-9


title: N4-RT12-7


title: N4-RT12-6


title: N4-RT12-5


title: N4-RT12-3


title: N4-RT12-4


title: N4-RT12-2


title: N4-RL3-132


title: N4-RT12-1


title: N4-RT12-15


title: 30min_pi_60_Jvpna-1308_PHIKZ151

city: Würzburg

first: Jörg

last: Vogel

address: Josef-Schneider-Straße 2

department: Institute for Molecular Infection Biology

country: Germany

institute: Würzburg University

data_processing:
The library was sequenced on the NextSeq2000 (Illumina) with a P1-seq kit (single-end 1x100 bp, Illumina). RNA-seq analysis for the ChmA knockdown and the screen was conducted with READemption 2.0.4 (Förstner et al. 2014, Sauerwein et al. 2022). Reads were aligned for PAO1 and ΦKZ to NC_002516 and NC_004629, respectively. Enrichment of transcripts was calculated with the DeSeq2 module in READemption. Read-coverage was illustrated with the Integrated Genomics Viewer (IGV, Robinson et al. 2011).
Assembly: NC_002516, NC_004629
Supplementary files format and content: reads (fq.gz)
Supplementary files format and content: coverage files (wig)
Supplementary files format and content: counts table (csv)

organism: Pseudomonas aeruginosa PAO1

growth_protocol: PAO1 was grown o/n in LB at 37 °C 220 rpm. Cells were inoculated 1:100 in MH media at 37 °C and grown until OD600 0.3.

extract_protocol:
RNA was isolated from 200 µl of cells using the RNAsnap procedure (Stead et al. 2012). Two volumes of RNAprotect (Qiagen) were added and cells were incubated for 5 min. Cells were pelleted at full-speed for 20 min at 4 °C and the supernatant was removed. The pellet was resuspended in 100 µl SNAP buffer (0.025% SDS, 18 mM EDTA, 1% β-mercaptoethanol, 95% formamide (RNA-grade)). Samples were incubated for 7 min at 95 °C, cell debris was pelleted at full-speed for 5 min at room-temperature, and the supernatant was transferred to a new tube. 1.5 volumes of ethanol was added to the supernatant and the sample was mixed by pipetting. The sample was loaded onto a miRNeasy mini column (Qiagen) two times and spun at full-speed for 20 s at room-temperature. Columns were washed two times with 500 µl RPE buffer (Qiagen) and spun at 8k×g for one minute at room-temperature. One final spin was used to dry the column in an empty tube. 30 µl RNase-free water was added to the column and the RNA eluted at 8k×g for one minute at room-temperature. The elution was repeated with the flow-through to recover more RNA. The RNA concentration was determined by absorption at 260 nm. RNA was stored at -80 °C.
RNA-sequencing was performed at the CoreUnit SysMed at the University of Würzburg. DNA was digested with DNaseI and the rRNA was depleted with the Lexogen RiboCOP META depletion kit. RNA library was prepared with the CORALL Total RNA-Seq Library Prep Kit V1 (Lexogen).

treatment_protocol: 4 µM AS molecules were added to 1.6 ml of cell culture and incubated for 30 min at 37 °C 220 rpm. Cells were infected  with ΦKZ at an MOI of 5. At indicated time points, 250 µl were removed and put on ice. Infection efficiency was independently validated by confocal microscopy and CFU spotting with 50 µl of cells.

tag: strain

value: bacteria

value: wt


title: 30min_pi_59_Jvpna-1307_PHIKZ064


title: 30min_pi_61_Jvpna-1312_PHIKZ169


title: N4-RL3-129


title: N4-RT12-42


title: 30min_pi_63_inf__water_repl3


title: 30min_pi_57_Jvpna-1303_PHIKZ305


title: N4-RL3-131


title: 30min_pi_58_Jvpna-1304_PHIKZ126


title: N4-RL3-128


title: 30min_pi_62_uninf__water


title: N4-RL3-126


title: 30min_pi_56_Jvpna-1301_PHIKZ042


title: N4-RL3-125


title: 30min_pi_55_Jvpna-1299_PHIKZ059


title: N4-RL3-127


title: 30min_pi_54_Jvpna-1295_PHIKZ_p46


title: N4-RL3-122


title: N4-RL3-124


title: N4-RL3-121


title: N4-RL3-119


title: N4-RL3-120


title: 30min_pi_50_Jvpna-1286_PHIKZ004


title: 30min_pi_53_Jvpna-1293_PHIKZ203


title: 30min_pi_52_Jvpna-1290_PHIKZ144


title: 30min_pi_48_Jvpna-1281_PHIKZ235


title: 30min_pi_51_Jvpna-1288_PHIKZ_p17


title: 30min_pi_49_Jvpna-1284_PHIKZ286


title: N4-RT12-57


title: N4-RL3-117


title: N4-RL3-115


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title: 30min_pi_46_Jvpna-1275_PHIKZ283


title: N4-RL3-114


title: N4-RL3-113


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title: 30min_pi_47_Jvpna-1278_PHIKZ208


title: 30min_pi_44_Jvpna-1271_PHIKZ104


title: 30min_pi_43_Jvpna-1269_PHIKZ177


title: 30min_pi_42_Jvpna-1265_PHIKZ_p49


title: N4-RL3-110


title: N4-RL3-111


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title: 30min_pi_41_Jvpna-1262_PHIKZ147


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title: 30min_pi_39_Jvpna-1258_PHIKZ186


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title: 30min_pi_37_Jvpna-1252_PHIKZ176


title: N4-RL3-103


title: 30min_pi_34_Jvpna-1240_PHIKZ120


title: 30min_pi_35_Jvpna-1239_PHIKZ089


title: N4-RL3-104


title: 30min_pi_36_Jvpna-1247_PHIKZ122


title: N4-RL3-101


title: N4-RL3-102


title: 30min_pi_35_Jvpna-1242_PHIKZ171


title: 30min_pi_45_Jvpna-1272_PHIKZ124


title: N4-RL3-100


title: 30min_pi_29_Jvpna-1225_PHIKZ_p16


title: 30min_pi_31_Jvpna-1229_PHIKZ066


title: N4-RL3-98


title: 30min_pi_34_Jvpna-1233_PHIKZ_p27


title: N4-RL3-96


title: 30min_pi_27_Jvpna-1221_PHIKZ068


title: N4-RL3-97


title: N4-RL3-99


title: N4-RL3-95


title: 30min_pi_26_Jvpna-1218_PHIKZ075


title: 30min_pi_28_Jvpna-1222_PHIKZ049


title: N4-RL3-107


title: N4-RL3-94


title: N4-RL3-106


title: 30min_pi_25_JVpna-1217_PHIKZ082


title: N4-RL3-92


title: N4-RL3-91


title: 30min_pi_23_JVpna-1212_PHIKZ025


title: 30min_pi_24_JVpna-1214_PHIKZ165


title: 30min_pi_22_JVpna-1210_PHIKZ072


title: N4-RL3-93


title: 30min_pi_21_JVpna-1209_PHIKZ179


title: 30min_pi_20_JVpna-1207_PHIKZ050


title: 30min_pi_19_JVpna-1183_PHIKZ296


title: N4-RL3-87


title: N4-RL3-89


title: 30min_pi_18_JVpna-1181_PHIKZ272


title: N4-RL3-88


title: 30min_pi_17_JVpna-1178_PHIKZ155


title: N4-RL3-85


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title: 30min_pi_16_JVpna-1175_PHIKZ065


title: 30min_pi_30_Jvpna-1227_PHIKZ062


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title: 30min_pi_13_Jvpna-970_PHIKZ067


title: N4-RL3-84


title: N4-RL3-80


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title: N4-RL3-90


title: N4-RL3-79


title: 30min_pi_11_Jvpna-964_PHIKZ069


title: 30min_pi_10_JVpna-962_PHIKZ002_ChmB


title: N4-RL3-78


title: 30min_pi_8_Jvpna-958_PHIKZ037_Dip


title: N4-RL3-76


title: 30min_pi_9_Jvpna-960_PHIKZ039_PhuZ


title: N4-RL3-74


title: N4-RL3-75


title: N4-RL3-73


title: 30min_pi_4_JVpna-79_ctrl


title: 30min_pi_6_Jvpna-127_PHIKZ073


title: N4-RL3-71


title: N4-RL3-82


title: 30min_pi_2_inf__water_repl2


title: 30min_pi_3_JVpna-72_PHIKZ054_ChmA


title: N4-RL3-68


title: 15min_pi_62_uninf__water_repl1


title: 15min_pi_61_Jvpna-1312_PHIKZ169


title: 15min_pi_63_inf__water


title: 15min_pi_60_Jvpna-1308_PHIKZ151


title: N4-RL3-67


title: N4-RL3-64


title: N4-RL3-77


title: 30min_pi_1_inf__water_repl1


title: N4-RL3-65


title: N4-RL3-66


title: 30min_pi_7_Jvpna-134_PHIKZ145


title: 15min_pi_58_Jvpna-1304_PHIKZ126


title: N4-RL3-62


title: N4-RL3-61


title: 15min_pi_57_Jvpna-1303_PHIKZ305


title: 15min_pi_56_Jvpna-1301_PHIKZ042


title: N4-RL3-72


title: N4-RL3-70


title: N4-RL3-63


title: N4-RL3-60


title: N4-RL3-58


title: 15min_pi_53_Jvpna-1293_PHIKZ203


title: 15min_pi_51_Jvpna-1288_PHIKZ_p17


title: N4-RL3-69


title: N4-RL3-56


title: N4-RL3-55


title: 15min_pi_59_Jvpna-1307_PHIKZ064


title: N4-RL3-57


title: N4-RL3-54


title: 15min_pi_50_Jvpna-1286_PHIKZ004


title: N4-RL3-53


title: 15min_pi_55_Jvpna-1299_PHIKZ059


title: 15min_pi_47_Jvpna-1278_PHIKZ208


title: N4-RL3-52


title: 15min_pi_48_Jvpna-1281_PHIKZ235


title: 15min_pi_46_Jvpna-1275_PHIKZ283


title: 15min_pi_49_Jvpna-1284_PHIKZ286


title: N4-RL3-50


title: 30min_pi_5_JVpna-126_PHIKZ055


title: N4-RL3-49


title: N4-RL3-59


title: 15min_pi_54_Jvpna-1295_PHIKZ_p46


title: N4-RL3-48


title: 15min_pi_52_Jvpna-1290_PHIKZ144


title: N4-RL3-47


title: 15min_pi_42_Jvpna-1265_PHIKZ_p49


title: 15min_pi_43_Jvpna-1269_PHIKZ177


title: 15min_pi_44_Jvpna-1271_PHIKZ104


title: N4-RL3-46


title: N4-RL3-44


title: 15min_pi_40_Jvpna-1260_PHIKZ153


title: N4-RL3-43


title: 15min_pi_38_Jvpna-1254_PHIKZ174


title: 15min_pi_39_Jvpna-1258_PHIKZ186


title: 15min_pi_37_Jvpna-1252_PHIKZ176


title: N4-RL3-45


title: 15min_pi_35_Jvpna-1242_PHIKZ171


title: N4-RL3-42


title: N4-RL3-41


title: N4-RL3-39


title: 15min_pi_35_Jvpna-1239_PHIKZ089


title: 15min_pi_34_Jvpna-1240_PHIKZ120


title: 15min_pi_36_Jvpna-1247_PHIKZ122


title: N4-RL3-38


title: 15min_pi_45_Jvpna-1272_PHIKZ124


title: N4-RL3-51


title: N4-RL3-40


title: 15min_pi_31_Jvpna-1229_PHIKZ066


title: 15min_pi_34_Jvpna-1233_PHIKZ_p27


title: 15min_pi_41_Jvpna-1262_PHIKZ147


title: N4-RL3-36


title: N4-RL3-35


title: 15min_pi_30_Jvpna-1227_PHIKZ062


title: N4-RL3-37


title: 15min_pi_29_Jvpna-1225_PHIKZ_p16


title: 15min_pi_28_Jvpna-1222_PHIKZ049


title: N4-RL3-34


title: N4-RL3-32


title: N4-RL3-31


title: 15min_pi_26_Jvpna-1218_PHIKZ075


title: 15min_pi_27_Jvpna-1221_PHIKZ068


title: 15min_pi_25_JVpna-1217_PHIKZ082


title: N4-RL3-29


title: N4-RL3-28


title: N4-RL3-27


title: 15min_pi_24_JVpna-1214_PHIKZ165


title: 15min_pi_22_JVpna-1210_PHIKZ072


title: N4-RL3-25


title: N4-RL3-26


title: N4-RL3-23


title: 15min_pi_18_JVpna-1181_PHIKZ272


title: 15min_pi_19_JVpna-1183_PHIKZ296


title: 15min_pi_23_JVpna-1212_PHIKZ025


title: 15min_pi_17_JVpna-1178_PHIKZ155


title: N4-RL3-21


title: N4-RL3-24


title: N4-RL3-22


title: N4-RL3-20


title: N4-RL3-33


title: N4-RL3-19


title: 15min_pi_14_JVpna-1170_PHIKZ137


title: 15min_pi_15_JVpna-1171_PHIKZ056


title: 15min_pi_20_JVpna-1207_PHIKZ050


title: 15min_pi_16_JVpna-1175_PHIKZ065


title: N4-RL3-17


title: N4-RL3-16


title: 15min_pi_13_Jvpna-970_PHIKZ067


title: 15min_pi_12_Jvpna-969_PHIKZ129


title: 15min_pi_11_Jvpna-964_PHIKZ069


title: 15min_pi_10_JVpna-962_PHIKZ002_ChmB


title: N4-RL3-30


title: N4-RL3-14


title: 15min_pi_21_JVpna-1209_PHIKZ179


title: 15min_pi_7_Jvpna-134_PHIKZ145


title: N4-RL3-18


title: 15min_pi_8_Jvpna-958_PHIKZ037_Dip


title: N4-RL3-13


title: N4-RL3-12


title: 15min_pi_9_Jvpna-960_PHIKZ039_PhuZ


title: N4-RL3-15


title: N4-RL3-9


title: 15min_pi_5_JVpna-126_PHIKZ055


title: N4-RL3-10


title: 15min_pi_4_JVpna-79_ctrl


title: N4-RL3-6


title: N4-RL3-8


title: 15min_pi_3_JVpna-72_PHIKZ054_ChmA


title: 15min_pi_2_inf__water_repl2


title: 15min_pi_1_inf__water_repl1


title: Bp-II1561 expression (RNA-seq)

city: Honolulu

first: Ian

middle: A

last: McMillan

state: HI

address: 1800 East-west road

institute: University of Hawaii

data_processing:
Rockhopper tool designed specifically for analysis of bacterial RNA-Seq was used for the analysis
Assembly: GCF_000260515.1
Supplementary files format and content: Combined rockhopper transcript outputs from chromosome I and chromosome II are in the included excel file

organism: Burkholderia pseudomallei

source_name: gram negative bacterium

growth_protocol: Bp 82 pAM3G-3xTY1/empty vector and Bp 82 pAM3G-3xTY1-BP1026B_II1561 were grown overnight and sub-cultured to midlog phase in LB+adenine+0.1mM IPTG for RNA and DNA extraction (RNA-seq and ChIP-seq respectively)

extract_protocol:
Total RNA from 12 ml culture of each strain was isolated using TRIzol® reagent and purify through QIAGEN RNeasy plus mini kit according to the manufacturer’s instructions.
Sequencing was performed by the Tufts University Core Facility Genomics on the Illumina HiSeq 2500 platform after rRNA depletion and library generation.

value: gram negative bacterium

value: overnight growth, and subcultured and induced with IPTG to expoenential phase


title: N4-RL3-5


title: Bp-empty vector (RNA-seq)

value: empty vector


title: N4-RL3-3


title: N4-RL3-4


title: Bp-empty vector (ChIP-seq)

data_processing:
Alignments were generated using Bowtie2 and peaks were called using MACS2
Assembly: GCF_000260515.1
Supplementary files format and content: Excel file contains output from MACS2 and peak calling.

extract_protocol:
Samples were fixed with 4% (w/v) paraformaldehyde in PBS, followed by shearing of DNA-protein complexes with the Covaris M220 ultrafocused sonicator. Cell debris was removed and DNA-protein complexes were immunoprecipitated with anti-TY1-tag monoclonal antibody (Diagenode C15200054) and secondary antibodies conjugated to magnetic beads (Diagenode C03010022). DNA-protein complexes were washed, decrosslinked, treated with RNaseA and proteinase K, and purified with QIAquick PCR purification kit.
Immunoprecipitated DNA was sent to TUCF Genomics where DNA libraries were prepped and 50 bp single-end reads were sequenced with the Illumina HiSeq 2500.


title: TOP3A_YF, HEK293, CUT&Tag

city: BESTHESDA

first: Hongliang

state: MD

address: 37 Convent Dr

department: DTB

institute: NCI

data_processing:
The generated fastq files were quality controlled with FastQC, aligned to hg19 or hg38 reference genome (as indicated in the bigWig files) with bwa-mem2, deduplicated, sorted and indexed using Samtools and Picard. BigWig files were generated with BAMscale. The profiles were smoothed using the sliding window algorithm.
Assembly: Hg19 or hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
DNA was generated from un-fixed nuclei with antibody-lead-transposon-complex.
The libraries were prepared with Illumina Nextera prep.

treatment_protocol: Aphidicolin treatment was 1mM (microM)for 1 hour.

tag: cell line

value: Human embryonic kidney

tag: cut&tag antibody

value: Flag M2(Cell Signaling, #14793)


title: N4-RL3-2

value: Dorsal root ganglia


title: TOP3A_RW, HEK293, CUT&Tag

tag: cell type


title: N3-RT11-128

value: Caucasian


title: 15min_pi_6_Jvpna-127_PHIKZ073

tag: genotype

tag: treatment


title: TOP3A_WT, HEK293, CUT&Tag


title: N3-RT11-126

tag: tissue


title: TOP3B, HEK293, CUT&Tag


title: N3-RT11-124


title: N3-RT11-123


title: TOP3A, HEK293_1_Aph, CUT&Tag

value: Aphidicolin


title: N3-RT11-122


title: N3-RT11-121


title: TOP3A, HEK293_1, CUT&Tag


title: TOP3A, HEK293_2_Aph, CUT&Tag


title: TOP2B, HEK293_Aph, CUT&Tag


title: Bp-II1561 expression (ChIP-seq)


title: N4-RL3-11

value: Male


title: N4-RL3-7


title: TOP2B, HEK293, CUT&Tag


title: N3-RT11-119


title: N3-RT11-118


title: TOP2A, HEK293, CUT&Tag


title: N4-RL3-1


title: TOP3B, HEK293_Aph, CUT&Tag


title: N3-RT11-127


title: N3-RT11-117


title: N3-RT11-125


title: TOP1, HEK293_Aph, CUT&Tag


title: N3-RT11-116


title: N3-RT11-115


title: N3-RT11-114


title: TOP3A, HEK293_2, CUT&Tag


title: HEK_FHPKM2NES_dsScramble_B

city: Bethesda

first: Markus

last: Hafner

address: 50 South Drive

department: NIAMS

institute: NIH

data_processing:
bcl2fastq/2.20.0 was used to convert bcl to fastq
For RNA-Seq fastq files were aligned using star/2.7.2b.
differential expression was done using cuffdiff (cufflinks/2.2.1)
PARCLIP was analysed using Parpipes (https://github.com/ohlerlab/PARpipe)
Genome_build: hg38

source_name: Flp-In™ 293 T-REx

growth_protocol: HEK293 T-Rex Flp-In cells (Thermo Fisher Scientific, Cat# R78007) were cultured in DMEM medium (Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS), 100 μg/ml zeocin, and 10 μg/ml blasticidin (Gibco)

extract_protocol:
Trizol for RNA-Seq, For PARCLIP, the cytoplasm was extracted by resuspending cells in a modified hypotonic lysis buffer (10 mM Tris-HCl pH 7.5, 50 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 10% glycerol) for 2 min. The nuclear pellet was washed twice with the same buffer and lysed in NP-40 buffer(20 mM Tris, pH 7.5, 150 mM NaCl, 2 mM EDTA, 1% (v/v) NP40, 0.5 mM DTT), followed by sonication.
NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®

treatment_protocol: 2ug/ml Doxycycline

value: HEK293 T-Rex Flp-In

tag: molecule

value: rRNA depleted total RNA


title: TOP1, HEK293, CUT&Tag


title: N3-RT11-113

value: Female


title: HEK_FHPKM2NES_dsScramble_A


title: N3-RT11-112

value: thoracic 11


title: N3-RT11-111


title: N3-RT11-120


title: N3-RT11-110


title: HEK_FHPKM2NLS_2ug_DOX_72H_B


title: HEK_FHPKM2NLS_2ug_DOX_72H_A


title: HEK_FHPKM2NES_dsPKM2_B


title: TOP2A, HEK293_Aph, CUT&Tag


title: N3-RT11-109


title: N3-RT11-107


title: HEK_FHPKM2NLS_0_DOX_72H_A


title: HEK_FHPKM2NLS_0_DOX_72H_B


title: N3-RT11-106


title: N3-RT11-108


title: N3-RT11-105


title: N3-RT11-104


title: N3-RT11-102


title: N3-RT11-101


title: N3-RT11-100


title: HEK_FHPKM2NES_dsPKM2_A


title: N3-RT11-99


title: N3-RT11-103


title: N3-RT11-98


title: N3-RT11-97


title: N3-RL2-124

value: lumbar 2

value: hPropr


title: N3-RL2-121


title: N3-RL2-123


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H33

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
The raw data containing reads of low quality, connector contamination and excessively high leveles of unknown base N were removed before data analysis. . The clean reads thus generated were aligned to the reference genome using HISAT, mapped to reference genes using Bowtie2. The mapped genes were  subjected to differential expression analysis using DEseq2.
Assembly: hg19_UCSC_20180822
Supplementary files format and content: The processed file is in Excel format and contains FPKM
Supplementary files format and content: The processed file is in Excel format and contains  log2fc, qvalue, p value for the respetive genes with their gene symbol, gene ID and other gene related informations.

source_name: Blood

extract_protocol:
Peripheral Blood samples (2.5 ml) were drawn from each volunteer in a PAXgene tube (Qiagen cat# 762165) followed by total RNA isolation using an RNA isolation kit (Qiagen cat# 763134) according to the manufacturer instruction. Total RNA concentration and quality were evaluated using a nanodrop system (ThermoFisher Scientific).
After Sample QC was by qubit and Agilent Bioanalyzer, a certain amount of RNA samples were denatured at suitable temperatures to open-up their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads followed by mRNA fragmentation and cDNA Synthesis. The double-stranded cDNA fragments were subjected to end-repair, the addition of a single ‘A’ nucleotide to the 3’ ends of the blunt fragments and ligated to adaptors before amplification. After quality control of the prepared library, the amplified products were denatured to generate single stranded PCR products which was then circularized to replicate using rolling cycle amplification yielding a DNA nanoball (DNB).   containing multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: Blood

value: Peripheral blood mono nuclear cells


title: N3-RL2-120


title: N3-RL2-119


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H32


title: Adult Dele1 KO BAT, cold, biological rep6

type: RNA

first: Narendra

last: Derek

address: 35 Convent Drive, Room 2A215

department: National Institute of Neurological Disorders and Stroke

institute: National Institutes of Health

hyb_protocol: Samples were hybridized using Hybridization Control Kit (Applied Biosystems) according to manufacturer's instructions.

scan_protocol: not provided

data_processing: Raw data was processed with Transcriptome Analysis Console (TAC v4.0.3) using the default settings, which uses a one-way ANOVA corrected with the Benjamini-Hochberg procedure for multiple procedures..

label: biotin

organism: Mus musculus

source_name: Dele1 KO

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Applied Biosystems) according to manufacturer's instructions.

growth_protocol: Mice were maintained on a 12-hour light/dark cycle with normal chow.

extract_protocol: Mice were genotyped beforehand. All samples were snap frozen in liquid N2. Total RNA were extracted from the frozen samples.

treatment_protocol: Adult mice in the experimental group were transferred to individual plastic cages with pre-chilled water but without bedding or food in a 4 °C cold room while mice in the control group remain room temperature. After 9 hours of exposure, mice were anesthetized with isoflurane and euthanized by cervical dislocation. Interscapular BATs were harvested immediately.

value: BAT

tag: cold stress

value: cold

value: Dele1 KO


title: N3-RL2-118

tag: donor id


title: Adult WT BAT, cold, biological rep6

source_name: WT

value: WT


title: N3-RL2-117

tag: age(years)


title: Adult WT BAT, cold, biological rep5


title: Adult Dele1 KO BAT, cold, biological rep5


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H31


title: Adult WT BAT, cold, biological rep2


title: Adult WT BAT, cold, biological rep3


title: Adult Dele1 KO BAT, RT, biological rep7

value: RT


title: Adult WT BAT, cold, biological rep1


title: Adult Dele1 KO BAT, cold, biological rep3


title: N3-RL2-116

value: Dorsal root ganglia

tag: race


title: Adult WT BAT, cold, biological rep7


title: Adult Dele1 KO BAT, cold, biological rep1


title: Adult Dele1 KO BAT, cold, biological rep4


title: Adult Dele1 KO BAT, cold, biological rep7


title: Adult Dele1 KO BAT, RT, biological rep5


title: Adult Dele1 KO BAT, RT, biological rep6


title: Adult Dele1 KO BAT, cold, biological rep2


title: Adult WT BAT, RT, biological rep7


title: Adult WT BAT, RT, biological rep6


title: N3-RL2-115

value: Caucasian

tag: gender


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H29


title: Adult WT BAT, RT, biological rep5


title: Adult WT BAT, RT, biological rep4


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H28


title: Adult WT BAT, cold, biological rep4


title: Adult Dele1 KO BAT, RT, biological rep4


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H30


title: N3-RL2-114

tag: region


title: N3-RL2-113

tag: sequencing batch


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H25


title: N3-RL2-112

tag: dissected soma size


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H27


title: Adult WT BAT, RT, biological rep2


title: N3-RL2-111

tag: cell identity


title: Adult WT BAT, RT, biological rep3


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H24


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H23


title: N3-RL2-110


title: Adult Dele1 KO BAT, RT, biological rep2


title: Adult Dele1 KO BAT, RT, biological rep3


title: N3-RL2-109


title: Adult OMA1 KO BAT, RT, biological rep7

source_name: OMA1 KO

value: OMA1 KO


title: Adult OMA1 KO BAT, cold, biological rep7


title: N3-RL2-108


title: Adult Dele1 KO BAT, RT, biological rep1


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H21


title: Adult OMA1 KO BAT, RT, biological rep5


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H22


title: N3-RL2-107


title: Adult OMA1 KO BAT, cold, biological rep6


title: Adult OMA1 KO BAT, RT, biological rep4


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H20


title: Adult OMA1 KO BAT, RT, biological rep2


title: N3-RL2-106


title: Adult OMA1 KO BAT, cold, biological rep5


title: Adult OMA1 KO BAT, RT, biological rep6


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H19


title: N3-RL2-105


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H18


title: N3-RL2-104


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H17


title: Adult OMA1 KO BAT, cold, biological rep1


title: Adult OMA1 KO BAT, RT, biological rep3


title: Adult OMA1 KO BAT, cold, biological rep4


title: Adult OMA1 KO BAT, cold, biological rep2


title: C10WT Dele + gastrocnemius at P28, biological rep4

description: gastrocnemius from mouse ID#5398

source_name: C10WT Dele +

growth_protocol: Mice were maintained on a 12-hour light/dark cycle with normal chow. Mouse gastrocnemius dissected from postnatal day 28 mice.

extract_protocol: Mice were genotyped beforehand. All samples were snap frozen in liquid N2. Total RNA were extracted from the frozen samples using Direct-zol RNA Miniprep Kit (Zymo, catalog R2051) according to manufacturer's instructions.

treatment_protocol: not applicable

tag: age

value: gastrocnemius

value: C10WT Dele +


title: G58R Dele1 KO gastrocnemius at P28, biological rep4

description: gastrocnemius from mouse ID#5399

source_name: G58R Dele1 KO

value: G58R Dele1 KO


title: N3-RL2-103

value: Female


title: C10WT Dele KO gastrocnemius at P28, biological rep4

description: gastrocnemius from mouse ID#5397

source_name: C10WT Dele KO

value: C10WT Dele KO


title: Adult OMA1 KO BAT, RT, biological rep1


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H26


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H15


title: N3-RL2-101

value: lumbar 2


title: N3-RL2-102


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H14


title: G58R Dele1 + gastrocnemius at P28, biological rep4

description: gastrocnemius from mouse ID#5395

source_name: G58R Dele1 +

value: G58R Dele1 +


title: G58R Dele1 KO gastrocnemius at P28, biological rep3

description: gastrocnemius from mouse ID#5394


title: C10WT Dele + gastrocnemius at P28, biological rep3

description: gastrocnemius from mouse ID#5392


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H13

value: Blood


title: G58R Dele1 KO gastrocnemius at P28, biological rep2

description: gastrocnemius from mouse ID#5365


title: G58R Dele1 + gastrocnemius at P28, biological rep3

description: gastrocnemius from mouse ID#5393


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H16

value: Peripheral blood mono nuclear cells


title: N3-RL2-98

value: hPropr


title: C10WT Dele + gastrocnemius at P28, biological rep2

description: gastrocnemius from mouse ID#5363


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H11


title: C10WT Dele + gastrocnemius at P28, biological rep1

description: gastrocnemius from mouse ID#4938


title: N3-RL2-99


title: C10WT Dele KO gastrocnemius at P28, biological rep2

description: gastrocnemius from mouse ID#4939


title: N3-RL2-100


title: G58R Dele1 + gastrocnemius at P28, biological rep2

description: gastrocnemius from mouse ID#5362


title: N3-RL2-96


title: G58R Dele1 KO gastrocnemius at P28, biological rep1

description: gastrocnemius from mouse ID#4935


title: Ckmm-cretg/+; Tfamf/f; Dele1-/- heart at P56, biological rep4

source_name: Ckmm-cretg/+; Tfamf/f; Dele1-/-

growth_protocol: Mice were maintained on a 12-hour light/dark cycle with normal chow. Mouse hearts dissected from postnatal day 56 mice.

value: heart

value: Ckmm-cretg/+; Tfamf/f; Dele1-/-


title: N3-RL2-97


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H9


title: N3-RL2-95


title: G58R Dele1 + gastrocnemius at P28, biological rep1

description: gastrocnemius from mouse ID#4936


title: Ckmm-cretg/+; Tfamf/f; Dele+/-  heart at P56, biological rep4

source_name: Ckmm-cretg/+; Tfamf/f; Dele+/-

value: Ckmm-cretg/+; Tfamf/f; Dele+/-


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H8


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H12


title: Ckmm-cretg/+; Tfamf/f; Dele1-/- heart at P56, biological rep3


title: N3-RL2-94


title: Adult OMA1 KO BAT, cold, biological rep3

value: BAT

value: cold


title: Ckmm-cretg/+; Tfamf/f; Dele+/-  heart at P56, biological rep3


title: Ckmm-cre+/+; Tfamf/+; Dele1-/- heart at P56, biological rep4

source_name: Ckmm-cre+/+; Tfamf/+; Dele1-/-

value: Ckmm-cre+/+; Tfamf/+; Dele1-/-


title: N3-RL2-93

value: Dorsal root ganglia

value: Caucasian


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H10


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H7


title: Ckmm-cre+/+; Tfamf/+; Dele1-/- heart at P56, biological rep3


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H6


title: C10WT Dele KO gastrocnemius at P28, biological rep1

description: gastrocnemius from mouse ID#4937

value: gastrocnemius


title: N2-RT12-128

value: thoracic 12


title: Ckmm-cretg/+; Tfamf/f; Dele1-/- heart at P56, biological rep2


title: N2-RT12-126

value: Female


title: Ckmm-cretg/+; Tfamf/f; Dele+/-  heart at P56, biological rep2


title: Ckmm-cre+/+; Tfamf/+; Dele1+/- heart at P56, biological rep4

source_name: Ckmm-cre+/+; Tfamf/+; Dele1+/-

value: Ckmm-cre+/+; Tfamf/+; Dele1+/-


title: Ckmm-cretg/+; Tfamf/f; Dele+/-  heart at P56, biological rep1


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H4


title: N2-RT12-125


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H3


title: Ckmm-cretg/+; Tfamf/f; Dele1-/- heart at P56, biological rep1


title: Ckmm-cre+/+; Tfamf/+; Dele1-/- heart at P56, biological rep2


title: C10WT Dele KO gastrocnemius at P28, biological rep3

description: gastrocnemius from mouse ID#5361

value: C10WT Dele KO


title: Ckmm-cre+/+; Tfamf/+; Dele1-/- heart at P56, biological rep1


title: Ckmm-cre+/+; Tfamf/+; Dele1+/- heart at P56, biological rep1


title: Ckmm-cre+/+; Tfamf/+; Dele1+/- heart at P56, biological rep2


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H5


title: N2-RT12-124


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, HT1


title: N2-RT12-127


title: N2-RT12-123


title: PBMC RNA, bulk RNA-Seq, Mid/Elevated Blood Pressure, E13


title: N2-RT12-122


title: C10WT Dele + heart at P28, biological rep4

description: heart from mouse ID#5398

growth_protocol: Mice were maintained on a 12-hour light/dark cycle with normal chow. Mouse hearts dissected from postnatal day 28 mice.

value: C10WT Dele +


title: PBMC RNA, bulk RNA-Seq, High Blood Pressure, H2

value: Blood


title: C10WT Dele KO heart at P28, biological rep4

description: heart from mouse ID#5397


title: PBMC RNA, bulk RNA-Seq, Mid/Elevated Blood Pressure, E12

value: Peripheral blood mono nuclear cells


title: G58R Dele1 KO heart at P28, biological rep3

description: heart from mouse ID#5394

value: G58R Dele1 KO


title: PBMC RNA, bulk RNA-Seq, Mid/Elevated Blood Pressure, E11


title: Ckmm-cre+/+; Tfamf/+; Dele1+/- heart at P56, biological rep3

value: heart


title: G58R Dele1 KO heart at P28, biological rep4

description: heart from mouse ID#5399


title: G58R Dele1 + heart at P28, biological rep3

description: heart from mouse ID#5393

value: G58R Dele1 +


title: PBMC RNA, bulk RNA-Seq, Mid/Elevated Blood Pressure, E9


title: G58R Dele1 KO heart at P28, biological rep2

description: heart from mouse ID#5365


title: PBMC RNA, bulk RNA-Seq, Mid/Elevated Blood Pressure, E10


title: N2-RT12-118


title: Adult WT BAT, RT, biological rep1

value: RT

value: WT


title: C10WT Dele KO heart at P28, biological rep3

description: heart from mouse ID#5361


title: G58R Dele1 + heart at P28, biological rep2

description: heart from mouse ID#5362


title: N2-RT12-119


title: N2-RT12-117


title: C10WT Dele + heart at P28, biological rep1

description: heart from mouse ID#4938


title: N2-RT12-121


title: PBMC RNA, bulk RNA-Seq, Mid/Elevated Blood Pressure, E8


title: C10WT Dele KO heart at P28, biological rep2

description: heart from mouse ID#4939


title: N2-RT12-116


title: C10WT Dele KO heart at P28, biological rep1

description: heart from mouse ID#4937


title: G58R Dele1 + heart at P28, biological rep4

description: heart from mouse ID#5395


title: N2-RT12-115


title: N2-RT12-120


title: N2-RT12-114


title: PBMC RNA, bulk RNA-Seq, Mid/Elevated Blood Pressure, E5


title: C10WT Dele1+ heart at P140, biological rep2

growth_protocol: Mice were maintained on a 12-hour light/dark cycle with normal chow. Mouse hearts dissected from postnatal day 140 mice.

tag: chchd10 genotype

value: wt/wt

tag: dele1 genotype

value: wt/-


title: PBMC RNA, bulk RNA-Seq, Mid/Elevated Blood Pressure, E6

tag: cell type


title: C10WT Dele1+ heart at P140, biological rep4


title: C10WT Dele1+ heart at P140, biological rep3


title: C10WT Dele + heart at P28, biological rep2

description: heart from mouse ID#5363

tag: genotype


title: S59L Dele1 KO heart at P140, biological rep4

source_name: S59L Dele1 KO


title: C10WT Dele1 KO heart at P140, biological rep3


title: G58R Dele1 KO heart at P28, biological rep1

description: heart from mouse ID#4935


title: PBMC RNA, bulk RNA-Seq, Mid/Elevated Blood Pressure, E3


title: G58R Dele1 + heart at P28, biological rep1

description: heart from mouse ID#4936


title: PBMC RNA, bulk RNA-Seq, Mid/Elevated Blood Pressure, E4


title: S59L Dele1+ heart at P140, biological rep4

source_name: S59L Dele1 +


title: N2-RT12-113

source_name: Dorsal root ganglia

value: Dorsal root ganglia


title: S59L Dele1+ heart at P140, biological rep3


title: PBMC RNA, bulk RNA-Seq, Mid/Elevated Blood Pressure, E1


title: PBMC RNA, bulk RNA-Seq, Mid/Elevated Blood Pressure, E7


title: C10WT Dele1 KO heart at P140, biological rep1


title: C10WT Dele1 KO heart at P140, biological rep2


title: S59L Dele1 KO heart at P140, biological rep3


title: S59L Dele1+ heart at P140, biological rep2


title: N2-RT12-111

value: Caucasian


title: C10WT Dele + heart at P28, biological rep3

description: heart from mouse ID#5392


title: S59L Dele1 KO heart at P140, biological rep2


title: SINV_control

first: Linzhen

last: Kong

address: University of Oxford Old Road Campus Research Building

department: Nuffield Department of Medicine

institute: Ludwig Institute for Cancer Research

library_source: other

data_processing:
Raw sequencing reads were processed by Cutadapt (v.4.2) to remove low-quality bases (-q 20) and short reads (-m 18), as well as to trim adaptors. 6mer UMI were extracted by UMI-tools extract (v.1.0.1) and used for deduplication. Paired reads were then merged into single reads using fastp (v.1.0.1).
Cleaned reads were first mapped to synthetic spike-ins and rRNA references using bowtie2 (v.2.4.4). The key parameters are as follows: bowtie2 -p 2 --no-unal --local -L 16 -N 1 --mp 4. The unaligned reads were subsequently mapped to snoRNA references and then to tRNA references, using the same parameters. Human snoRNA sequences that belong to HGNC “Small nucleolar RNAs” gene group were downloaded from RefSeq. Duplicate snoRNA sequences were removed. High-confidence human tRNA sequences (hg38) were downloaded from GtRNAdb. Only non-redundant tRNA sequences were kept and appended with a “3’-CCA” end. Finally, unmapped reads were aligned to human genome (hg38) with GENCODE v.43 annotation by STAR (v.2.7.9a)
The aligned reads were then filtered and sorted using samtools (v.1.16.1). For synthetic spike-ins and rRNA, only reads with MAPQ ≥10 were kept. For snoRNA and tRNA, only reads with MAPQ ≥1 were kept. For mRNA, only uniquely mapped reads (-q 30) with a maximum of 3 mutation counts were kept. Deduplication was performed using UMI-tools dedup (v.1.0.1).. Finally, mutations are counted by samtools mpileup (v.1.16.1) and cpup (v.0.1.0) (https://github.com/y9c/cpup).
Assembly: hg38
Supplementary files format and content: Excel tables show the ψ list

molecule: other

growth_protocol: HeLa cells were cultured in DMEM medium (Gibco) supplemented with 10% (v/v) FBS (Gibco) and 1% penicillin/streptomycin (Gibco) at 37 °C with 5% CO2. For isolation of RNA, cells were harvested by centrifugation for 5 min at 1,000× g and room temperature.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) and Direct-zol RNA Miniprep Plus (Zymo Research) according to the manufacturer’s protocol. Ribo– RNA was isolated using RiboMinus Eukaryote System v2 (Invitrogen) according to the manufacturer’s protocol. PolyA+ RNA was isolated by two rounds of polyA-tailed selection using Dynabeads mRNA DIRECT Purification Kit (Invitrogen) according to the manufacturer’s protocol. To remove genomic DNA contamination, RNA was then treated with Turbo DNase and purified by Zymo-IC Column with RNA binding buffer.
50–100 ng ribo– or polyA+ RNA was fragmented by NEBNext Magnesium RNA Fragmentation Module at 94 °C for 4 min according to the manufacturer’s protocol and purified by Zymo-IC Column with RNA binding buffer. The fragmented RNA was mixed with 5 μl 10× T4 PNK reaction buffer (NEB), 5 μl T4 PNK (NEB), and 2.5 μl SUPERase.In RNase Inhibitor (Invitrogen) in a 50 µL final solution and incubated at 37 °C for 1 h. The 3’-repaired RNA was purified by Zymo-IC Column with RNA binding buffer and eluted with 10 μl nuclease-free H2O. The eluted RNA was then mixed with 1 μl synthetic 30mer spike-ins (2%) and 1 μl of 20 μM RNA adapter (5’-/5rApp/AGATCGGAAGAGCGTCGTG/3SpC3/-3’), incubated at 70 °C for 2 min and immediately placed on ice. Next, 2.5 μl 10× T4 RNA Ligase reaction buffer (NEB), 1 μl SUPERase.In RNase Inhibitor, 7.5 μl 50% PEG 8000 (NEB), and 2 μl T4 RNA Ligase 2, truncated KQ (NEB) were added to the mixture and the reaction was incubated at 25 °C for 2 h followed by 16 °C for 14 h. To digest excess adapters, the solution was further diluted to 47 μl with nuclease-free H2O and treated with 2 μl 5’-Deadenylase (NEB) at 30 °C for 1 h followed by adding 1 μl RecJf (NEB) and incubating at 37 °C for 1 h. The 3’-ligated RNA was purified by Zymo-IC Column with RNA binding buffer and eluted with 10 μl nuclease-free H2O. A 7 μl aliquot was subjected to BACS library construction, while the rest 3 μl was saved as control sample and diluted to 12.5 μl with nuclease-free H2O. For BACS, 1 M 2-bromoacrylamide (Enamine) was prepared by dissolving the solid in DMSO. 7 μl 3’-ligated RNA was added into a 20 μl solution containing 250 mM 2-bromoacrylamide and 625 mM phosphate buffer (pH 8.5) and incubated at 85 °C for 30 min. The treated RNA was double purified by Micro Bio-Spin P-6 Tris Column (Bio-Rad) and Zymo-IC Column with RNA binding buffer and finally eluted with 12.5 μl nuclease-free H2O. Both treated and control RNA samples were mixed with 1 μl of 2 μM RT primer (5’-ACACGACGCTCTTCCGATCT-3’) and 1 μl of 10 mM dNTP mix (NEB), incubated at 70 °C for 2 min and immediately placed on ice. Next, 4 μl 5× Maxima H– RT buffer (Thermo), 0.5 μl RiboLock RNase Inhibitor (Thermo), and 1 μl Maxima H– Reverse Transcriptase (Thermo) were added to the mixture and the reaction was incubated at 50 °C for 1 h. To digest excess RT primers, the solution was treated with 1 μl Exo I (NEB) and incubated at 37 °C for 30 min followed by adding 1 μl of 0.5 M EDTA (Sigma) to quench the reaction. To hydrolyze the RNA, 2.5 µl of 1 M NaOH (Sigma) was added and the solution was then incubated at 70 °C for 12 min followed by adding 2.5 µl of 1 M HCl (Sigma) to neutralize NaOH. The cDNA was finally purified with Dynabeads MyOne Silane (Invitrogen) and eluted with 13 µl nuclease-free H2O. The eluted cDNA was then mixed with 2 µl of 25 μM cDNA adapter (5’-/5Phos/NNNNNNAGATCGGAAGAGCACACGTCTG/3SpC3/-3’), incubated at 70 °C for 2 min and immediately placed on ice. Next, 5 μl 10× T4 RNA Ligase reaction buffer, 25 μl 50% PEG 8000, 0.5 μl of 100 mM ATP (NEB), 3.5 μl DMSO (Thermo), and 1 μl T4 RNA Ligase 1, high concentration (NEB) were added to the mixture and the reaction was incubated at 25 °C for 16 h. The ligated cDNA was purified with Dynabeads MyOne Silane and eluted with 15 µl nuclease-free H2O. The eluted DNA was amplified with NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) and NEBNext Ultra II Q5 Master Mix for 10 cycles according to the manufacturer’s protocol. The PCR products were purified with 0.8× AMPure XP beads and quantified with Qubit dsDNA HS Assay Kit (Thermo) according to the manufacturer’s protocol. BACS and control libraries were sequenced on NextSeq 2000 (60 bp paired end) with no PhiX added.

tag: cell line

tag: treatment

value: control


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N43

tag: tissue


title: N2-RT12-109

value: thoracic 12


title: SINV_BACS

value: bacs


title: S59L Dele1 KO heart at P140, biological rep1


title: PBMC RNA, bulk RNA-Seq, Mid/Elevated Blood Pressure, E2


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N42


title: N2-RT12-112

value: Female


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N41


title: N2-RT12-107


title: N2-RT12-110


title: S59L Dele1+ heart at P140, biological rep1


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N40


title: N2-RT12-106


title: PT1|012|Full.ROI

type: other

city: London

first: Dimitra

last: Peppa

address: Pond Street

institute: University College London

data_processing: Quality control checks and data analysis were performed in the GeoMx DSP Data Analysis suite. All regions of interest (ROI) had acceptable sequencing quality metrics after examination of the raw, trimmed, stitched, aligned and deduplicated reads, and the sequencing saturation (>60%). An expression value per gene target per ROI was generated in GeoMx DSP Analysis Suite through the compilation of multiple probes, within the NanoString GeoMx Human Whole Transcriptome Atlas probe mix, for each transcript.   The manufacturer’s recommended threshold for the detection of genes in referred to as the Limit of Quantification (LOQ); the LOQ is 2 geometric standard deviations above the geometric mean. The AOI from PT2, PT1 and PT3 tissues were filtered to include only the genes detected over the LOQ in 3 or more AOI: 9672 genes. The data were then quantile normalised and the performance of the normalisation was assessed by the standardisation of housekeeping genes and distribution of total gene expression between ROI

label_protocol: Tissue sections were loaded into the GeoMx platform and scanned for an immunofluorescent signal. A geometric strategy was employed for selection of regions of interest (ROIs) which were segmented on the basis of HBsAg staining and presence of immune cell infiltrate


title: PT1|011|Full.ROI


title: PT1|009|Full.ROI


title: PT1|008|Full.ROI


title: PT1|010|Full.ROI


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N39


title: PT1|007|Full.ROI


title: N2-RT12-105


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N38


title: N2-RT12-108


title: N2-RT12-104


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N36


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N37


title: PT1|005|Full.ROI


title: PT1|006|Full.ROI


title: PT1|002|Full.ROI


title: PT3|011|Full.ROI


title: PT1|004|Full.ROI


title: PT1|003|Full.ROI


title: C10WT Dele1+ heart at P140, biological rep1


title: N2-RT12-101

value: hPropr


title: N2-RT12-102


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N35


title: PT3|012|Full.ROI


title: PT3|013|Full.ROI


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N34


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N33


title: PT3|010|Full.ROI


title: PT3|009|Full.ROI


title: PT3|008|Full.ROI


title: N2-RT12-103


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N32


title: PT3|007|Full.ROI


title: PT3|006|Full.ROI


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N31


title: PT1|001|Full.ROI


title: PT3|005|Full.ROI


title: PT3|004|Full.ROI


title: N2-RT12-97


title: PT3|003|Full.ROI


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N30


title: N2-RT12-100


title: PT3|001|Full.ROI


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N29


title: N2-RL5-128

value: lumbar 5


title: N2-RT12-99


title: N2-RT12-98


title: PT3|002|Full.ROI


title: N2-RL5-127


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N28

value: Blood


title: PT2|012|Full.ROI


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N27

value: Peripheral blood mono nuclear cells


title: PT2|011|Full.ROI


title: N2-RL5-125


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N26


title: PT2|010|Full.ROI


title: PT2|006|Full.ROI


title: PT2|009|Full.ROI


title: N2-RL5-124


title: PT2|008|Full.ROI


title: PT2|005|Full.ROI


title: N2-RL5-123


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N24


title: PT2|004|Full.ROI


title: N2-RL5-122


title: N2-RL5-126


title: PT2|001|Full.ROI


title: PT2|003|Full.ROI


title: Rat Ileocecal valve,vB+Probiotics group,Number-4

city: nanjing

first: Lan

last: Sang

address: Longmian Avenue 639

institute: China Pharmaceutical University

data_processing:
Data was analysed on the Meta Amplicon Analysis platform in BGI Genomics Co., Ltd (Shenzhen, China)
Assembly: Not collected
Supplementary files format and content: include the format of fq.gz and fasta.gz files for each sample

organism: Rattus norvegicus

source_name: Ileocecal valve content

extract_protocol:
DNA extraction was executed using the MagPure Stool DNA KF Kit B  in strict adherence to the manufacturer's protocol
Meta amplicon library preparation was based on BGI-NGS-JK-meta-004 A0 in BGI Genomics Co., Ltd (Shenzhen, China)

value: Ileocecal valve content


title: PT2|002|Full.ROI


title: PT2|007|Full.ROI


title: Rat Ileocecal valve,vB+Probiotics group,Number-1


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N22


title: Rat Ileocecal valve,vB+Probiotics group,Number-3


title: Rat Ileocecal valve,vB+Probiotics group,Number-5


title: N2-RL5-120


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N23


title: Rat Ileocecal valve,vB+Probiotics group,Number-2


title: Rat Ileocecal valve,Probiotics group,Number-3


title: Rat Ileocecal valve,Probiotics group,Number-5


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N25


title: Rat Ileocecal valve,Probiotics group,Number-2


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N20


title: N2-RL5-121


title: Rat Ileocecal valve,Probiotics group,Number-1


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N19


title: Rat Ileocecal valve,VB group,Number-5


title: N2-RL5-118


title: Rat Ileocecal valve,VB group,Number-4


title: Rat Ileocecal valve,VB group,Number-3


title: N2-RL5-117


title: N2-RL5-116


title: Rat Ileocecal valve,VB group,Number-1


title: Rat Ileocecal valve,VB group,Number-2


title: Rat Ileocecal valve,Model group,Number-5


title: N2-RL5-114


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N21


title: Rat Ileocecal valve,Model group,Number-2


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N17


title: N2-RL5-115


title: Rat Ileocecal valve,Model group,Number-4


title: Rat Ileocecal valve,Control group,Number-5


title: Rat Ileocecal valve,Probiotics group,Number-4


title: N2-RL5-113


title: Rat Ileocecal valve,Model group,Number-1


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N15


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N14


title: Rat Ileocecal valve,Control group,Number-4


title: N2-RL5-119


title: N2-RL5-112


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N13


title: Rat Ileocecal valve,Control group,Number-2


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N12


title: N2-RL5-111


title: Rat Ileocecal valve,Control group,Number-1


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N18


title: N2-RL5-110


title: Rat Ileocecal valve,Control group,Number-3


title: TSL-9, summer, liver mitochondria

city: Waterloo

first: Karyn

last: Robichaud

state: ON

address: 200 University Ave West, B1 171B

department: Biology

country: Canada

institute: University of Waterloo

data_processing:
A quality control check on the raw data was completed using FastQC (version 0.11.9), then Cutadapt (version 1.3) was used to remove adapters, low-quality bases and reads, and to exclude any reads shorter than 18 nucleotides or longer than 35 nucleotides. A second quality control check using FastQC was completed after Cutadapt trimming.
Reads were analyzed using the miARma-seq pipeline (version 1.7.2). Reads were then mapped to the reference Ensembl genome for Ictidomys tridecemlineatus using Bowtie (version 1.1.1).
Assembly: Ensembl SpeTri2.0 (GCA_000236235.1)
Supplementary files format and content: Readcount file generated from the miARma-seq pipeline in .TAB format.

organism: Ictidomys tridecemlineatus

source_name: Liver mitochondria

growth_protocol: All squirrels were trapped in Carman, MB, CAN, or bred in captivity at Western University.

extract_protocol:
Total RNA was extracted using the Qiagen miRNeasy kit.
Libraries were generated using the New England Biolabs (NEB) Small RNA Library Prep.

treatment_protocol: Squirrels were sampled during summer, torpor, and interbout euthermia to collect livers for mitochondrial isolation. Torpid squirrels were euthanized by cervical dislocation, while summer and interbout euthermia squirrels were euthanized using Euthanyl (0.5 ml of 240 mg/ml; Bimeda-MTC, Cambridge, ON, CAN) followed by cervical dislocation. Liver mitochondria were isolated using differential centrifugation and a Percoll density gradient, then stored at - 80 C.

value: Liver mitochondria

value: summer


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N16

source_name: Blood


title: TSL-7, summer, liver mitochondria


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N11


title: TSL-8, summer, liver mitochondria


title: Rat Ileocecal valve,Model group,Number-3


title: N2-RL5-109


title: TSL-6, summer, liver mitochondria


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N9


title: TSL-5, summer, liver mitochondria


title: N2-RL5-108


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N10


title: TSL-3, summer, liver mitochondria


title: N2-RL5-106


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N8


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N7


title: TSL-1, summer, liver mitochondria


title: TSL-2, summer, liver mitochondria


title: N2-RL5-107


title: TTL-7, torpor, liver mitochondria

value: torpor


title: TTL-5, torpor, liver mitochondria


title: N2-RL5-104


title: TTL-4, torpor, liver mitochondria


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N5


title: N2-RL5-105


title: TTL-3, torpor, liver mitochondria


title: TTL-2, torpor, liver mitochondria


title: N2-RL5-103


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N6


title: TTL-1, torpor, liver mitochondria


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N4


title: TAL-8, interbout euthermia, liver mitochondria

value: interbout euthermia


title: N2-RL5-102


title: TAL-6, interbout euthermia, liver mitochondria


title: TAL-7, interbout euthermia, liver mitochondria


title: N2-RL5-101


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N3


title: TTL-9, torpor, liver mitochondria


title: TAL-5, interbout euthermia, liver mitochondria


title: TTL-8, torpor, liver mitochondria


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N2


title: N2-RL5-100


title: TAL-3, interbout euthermia, liver mitochondria


title: TAL-4, interbout euthermia, liver mitochondria


title: TAL-2, interbout euthermia, liver mitochondria


title: PBMC RNA, bulk RNA-Seq, Low Blood Pressure, N1


title: PBMC RNA, High Blood Pressure, H37

data_processing:
The bioinformatic pipeline for the samples sequenced using BGI500 includes, (i) the elimination of the low-quality reads, adaptors and other contaminants to get clean reads. The elimination includes 5' primer contaminants, no-insert tags, oversized insertion tags, low-quality tags, poly A tags, and small tags, tags without 3' primer. The low-quality tags are those which have more than four bases and whose quality is less than ten, or those which have more than six bases and have a quality less than thirteen. (ii) Next the length distribution of clean tags is then summarized. Normally, the length distribution of small RNA is between 18nt and 30nt (miRNA -21nt or 22nt, siRNA -24nt, and piRNA - 30nt). (iii)After filtering, the remaining tags are called clean tags and stored in FASTQ format. (iv) Bowtie was used to map clean reads to the reference genome and to other sRNA databases (cmsearch was used for Rfam)19,20. In the annotation information of different RNAs, to avoid mapping of sRNA to multiple categories, priority rule was followed: miRNA > piRNA > snoRNA > Rfam > other sRNA. The small RNA expression level was calculated by using Transcripts Per Kilobase Million (TPM).  The TPM method eliminates the influence of sequencing discrepancy on the calculation of small RNA expression level. Therefore, the calculated gene expression level data can be used directly to compare the difference in gene expression between the samples. To calculate the TPM the following formula is used: TPM=(C*106 )/N. DESeq2 based on the negative binomial distribution, was performed as described at Michael I, et al. We used 'Adjusted Pvalue ≤ 0.1 and the absolute value of Log2Ratio ≥ 1' as the default threshold to judge the significance of gene expression difference.
Assembly: hg19_UCSC_20180822
Supplementary files format and content: The processed file is in Excel format and contains TPM.
Supplementary files format and content: The processed file is in Excel format and contains  log2fc, qvalue, p value for the respetive genes with their gene symbol, gene ID and other gene related informations.

extract_protocol:
Peripheral Blood samples (2.5 ml) were drawn from each volunteer in a PAXgene tube (Qiagen cat# 762165) followed by total RNA (including miRNA) isolation using a commercial kit (Qiagen cat# 763134) according to the manufacturer instruction. Total RNA concentration and quality were evaluated using a nanodrop system (ThermoFisher Scientific).
The experiment pipeline for library preparation for small RNA sequencing includes (i) separation of 18-30nt RNA segment by PAGE gel, (ii)3' adaptor ligation to link 5-adenylated 3-blocked single-stranded DNA adapter to 3' end of selected small RNAs, (iii)reverse primer annealing using a RT primer which is cross-linked to the 3’-adapter sequence of RNA and excess 3’adapter followed by (iv) 5' adaptor ligation, (v) cDNA synthesis, (vi)PCR amplification to enrich cDNA with both 3' and 5' adaptor, (vii)library fragment selection by separation of the PCR product of 100~120bp by PAGE gel to eliminate primer-dimer and other byproducts, (viii) library quantitative and pooling cyclization followed by (ix)sequencing using BGISEQ-500 technology.


title: TAL-1, interbout euthermia, liver mitochondria


title: N2-RL5-98


title: N2-RL5-99


title: PBMC RNA, High Blood Pressure, H36


title: CD4+ T cells with IgG treatment#2

city: Shanghai

first: Jianli

last: He

address: 280 South Chongqing Road,

department: Department of Biochemistry and Molecular Cell Biology

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Ballgown (2.10.0)
CPAT (1.2.4)
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus

source_name: spleen CD4+ T cells

growth_protocol: CD4+ T were cultured in T cell media (RPMI 1640 + 10% FBS + 100 U/mL penicillin/ streptomycin + 2 mM L-glutamine + 55 μM β-mercaptoethanol).

extract_protocol:
total RNA extracted by TRIzol reagent.
KAPA Stranded RNA-Seq Library Prep Kit (Illumina) was used for cDNA construction.

treatment_protocol: CD4+ naïve T cells were activated by anti-CD3 (5 μg/mL) and anti-CD28 (2 μg/mL) plus IL-2 (100 U/mL) with the treatment of anti-VEGF-B (1 μg/mL) or normal IgG control (1 μg/mL) for 3 days.

value: spleen CD4+ T cells

value: WT

value: IgG


title: CD4+ T cells with aVEGFB treatment#2

value: aVEGFB


title: CD4+ T cells with IgG treatment#1


title: CD4+ T cells with IgG treatment#3


title: N2-RL5-97

value: Dorsal root ganglia

value: Caucasian


title: PBMC RNA, High Blood Pressure, H35


title: N3-RT11-96

value: thoracic 11


title: CD4+ T cells with aVEGFB treatment#3


title: CD4+ T cells with aVEGFB treatment#1


title: PBMC RNA, High Blood Pressure, H34


title: N3-RT11-95

value: Female


title: N3-RT11-94


title: PBMC RNA, High Blood Pressure, H32


title: PBMC RNA, High Blood Pressure, H33


title: N3-RT11-93


title: PBMC RNA, High Blood Pressure, H31


title: N3-RT11-92


title: PBMC RNA, High Blood Pressure, H30


title: N3-RT11-90


title: AssayA_Pilot_GFP_IP2,Jurkat Trex cells,anti-FLAG

city: Gent

first: Wim

last: Trypsteen

state: East-Flanders

address: Corneel Heymanslaan 10

department: Internal Medicine

country: Belgium

institute: UGent

data_processing:
high performance computing RNAseq analysis pipeline
QC via FASTQC 0..11.8, bad read removal (min quality phred score >20) and adapter trimming (cutadap 3.4)
read mapping via STAR 2.6.0
count tables generated via HTSeq 0.11.0
count table normalization via deseq2
Assembly: hg38/enbsembl v91
Supplementary files format and content: tab-delimited text files including raw count tables

source_name: Jurkat Trex cells

growth_protocol: Trex cell lines were cultured in RPMI (Gibco) , supplemented with 10% FCS (HyClone), Pen/Strep, sodium-pyruvate (1 mM; Gibco), HEPES (15 mM; Gibco), Blasticidine (10 µg/mL; InvivoGen), Zeocin (300 µg/mL; InvivoGen), at 5% CO2 and 37°C

extract_protocol:
miRNEasy micro kit (Qiagen) with on-column RNAse free DNAse set (Qiagen)
Total RNA library preparation was performed using the SMARTer Stranded Total RNA-Seq Mamalian Pico v2 Kit (Takara) using the manufacturer’s instructions with 8 µL RNA input, 4 min fragmentation and 16 PCR2 cycles.

treatment_protocol: Doxycyline induction was performed either constitutively or with 1 µg/mL for 16h

value: Jurkat Trex cells

value: T cell line

value: Doxycyline inducible

tag: treatment doxycyline

value: yes

tag: treatment doxycyline_time

tag: treatment rip_antibody

value: anti-FLAG

tag: treatment infection

value: no


title: AssayA_Pilot_GFP_IP3,Jurkat Trex cells,anti-FLAG


title: N3-RT11-89

tag: donor id

tag: age(years)

tag: race

tag: gender


title: AssayA_Pilot_GFP_IP1,Jurkat Trex cells,anti-FLAG


title: NI_Donor2_ART

city: Jupiter

first: Susana

middle: T

last: Valente

state: FL

address: 130 Scripps Way

department: Immunology and Microbiology

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

description: Not infected with HIV

data_processing:
FastQC
Read trimming using trim-galore version 0.6.1: trim_galore --paired --length 24 --stringency 3
Alignment by Salmon v 0.14.1 using the --validateMappings flag
Raw counts were imported using the DESeqDataSetFromTximport function from DESeq2, and differential expression analysis performed using DESeq2. Variation in the data was accounted for in the design formula using “~ donor + treatment” for the Kessing study samples and “~ infection + donor + treatment” for the Mori study samples.
Transcripts per million (TPMs) were determined by normalizing counts to gene length (in kb) and then by library size.
Assembly: A custom genome was created by merging the human genome (GRCh38.p14), and the HIV-1 genome (NL4-3: GenBank: AF324493.2, or PLWH autologous virus – a consensus sequence was constructed from the DNA methylation sequencing).
Supplementary files format and content: Salmon quantification files in a .sf format
Supplementary files format and content: TPM table in a .txt format

source_name: memory CD4+ T cells

growth_protocol: Human PBMCs from 3 healthy donors were obtained from Buffy coats by density centrifugation as previously described (Takata et al., 2019). Primary memory CD4+ T cells were isolated by negative selection and activated with 1:2 ratio with Dynabeads™ Human T-Activator in the presence of 6 ng/ml IL-2, 36 ng/ml IL-7 and 36 ng/ml IL-15. The cells were cultured in RPMI 1640 media supplemented with 1xMEM vitamin solution, 1xNEAA, 1x Sodium Pyruvate , 1xPen/Strep/L-glut, 0.01M HEPES pH 8.0, 1xL-Asp/L-Arg/Folic acid mix (house-made), and 10% FBS.

extract_protocol:
Total RNA was extracted from cells using the Qiagen RNeasy kit. RNA was DNase treated using the TURBO DNA-free kit. Total RNA was quantified using a Qubit 2.0 Fluorometer and evaluated on an Agilent 2100 Bioanalyzer Nano chip for quality assessment.
The DNase-treated total RNA (350ng input) was depleted of ribosomal RNA using probes provided by the NEBNext rRNA depletion module according to the manufacturer’s recommendations. The library preparation from the rRNA-depleted RNA was conducted according to NEBNext Ultra II Directional RNA kit guidelines. Briefly, the samples were chemically fragmented in a buffer containing divalent cations by heating to 94°C for 15 minutes. The fragmented RNA was random hexamer primed and reverse transcribed to generate the first strand cDNA. The second strand was synthesized after removing RNA template and incorporating dUTP in place of dTTP. The double-stranded cDNA was then end repaired and adenylated at their 3’ ends.  A corresponding T nucleotide on the adaptors was utilized for ligating the adaptor sequences to cDNA. The adaptor loop contains a dUTP that is removed along with all other incorporated U’s in the second strand by treatment with USER enzyme (Uracil-Specific Excision Reagent). The degradation of the second strand in this step preserves directional sequencing of the intact first strand thus preserving strand information of the RNA. The adaptor ligated DNA was purified using magnetic beads and PCR amplified using 9 cycles to incorporate a unique barcode and generate the final libraries. The final libraries were purified using magnetic beads to remove any remaining primers and adaptors, validated on a TapeStation D1000 tape, normalized to 4nM and pooled equally. The final pool was loaded onto the NextSeq 500 (PLWH samples – Exp630) or NextSeq 2000 (NL4-3 and NI samples – Exp711) P3 flow cell at 750 pM final concentration and sequenced using 2 x 50bp paired-end chemistry. On average, we generated 39 to 53 million reads pass filter per sample.

treatment_protocol: Infection and drug treatment of memory CD4+ T cells. Three days post activation cells were infected with 5 ng p24 NL4-3 per million cells at a cell density of 2 million/ml, note that half of the donor cells were left uninfected for control. Virus was added to the media, cells were mixed every 20 min for 2 h and then left overnight. Cells were then pelleted by centrifugation after 12 h and resuspended in fresh T cell media (uninfected controls were treated the same), at a concentration of 1 million/ml. Cells were then divided into ART+dCA or ART alone treatments (including the uninfected controls). ART cocktail = 200 nM lamivudine, 200 nM raltegravir, and 100 nM efavirenz. Didehydro-Cortistatin A (dCA) was synthesized by Dr. Ravi Natarajan, Thimble Therapeutics, and was used at a concentration of 50 nM. Half media changes were performed every 3-4 days as needed, with fresh drug being added to maintain the concentration. Every 7 days, supernatant was collected for p24 ELISA, cells were counted, reseeded at a concentration of 1.5 million/ml. After 5 weeks of treatment (33 days), cells were collected for RNA-sequencing analysis.

value: memory CD4+ T cells

value: Non-infected + ART


title: HIV_Donor1_ART

description: Infected with NL4.3 HIV in vitro

value: HIV infected + ART


title: HIV_Donor2_ART

description: Infected with NL4.3 HIV in vitro


title: HIV_Donor3_ART+dCA

description: Infected with NL4.3 HIV in vitro

value: HIV infected + ART + 50 nM dCA


title: HIV_Donor3_ART

description: Infected with NL4.3 HIV in vitro


title: N3-RT11-88

tag: region

tag: sequencing batch

tag: dissected soma size

tag: cell identity

value: hPropr


title: HIV_Donor1_ART+dCA

description: Infected with NL4.3 HIV in vitro

tag: cell type


title: NI_Donor2_ART+dCA

description: Not infected with HIV

value: Non-infected + ART + 50nM dCA


title: NI_Donor3_ART

description: Not infected with HIV


title: HIV_Donor2_ART+dCA

description: Infected with NL4.3 HIV in vitro


title: AssayA_Pilot_Tat_IgG3,Jurkat Trex cells,anti-FLAG

tag: genotype


title: PBMC RNA, High Blood Pressure, H26

value: Blood

value: Peripheral blood mono nuclear cells


title: NI_Donor3_ART+dCA

description: Not infected with HIV


title: N3-RT11-87

value: Dorsal root ganglia

value: Caucasian


title: NI_Donor1_ART

description: Not infected with HIV


title: PBMC RNA, High Blood Pressure, H29


title: NI_Donor1_ART+dCA

description: Not infected with HIV


title: PBMC RNA, High Blood Pressure, H25


title: N3-RT11-86

value: Female

value: thoracic 11


title: AssayA_Pilot_Tat_IgG1,Jurkat Trex cells,anti-FLAG

tag: cell line

value: Jurkat Trex cells

value: T cell line


title: N3-RT11-91


title: AssayA_Pilot_Tat_IP2,Jurkat Trex cells,anti-FLAG

value: Doxycyline inducible

value: yes


title: PBMC RNA, High Blood Pressure, H24


title: AssayA_Pilot_Tat_IP3,Jurkat Trex cells,anti-FLAG

value: anti-FLAG

value: no


title: AssayA_Pilot_Tat_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Pilot_Tat_IgG2,Jurkat Trex cells,anti-FLAG