title: HOXB13_TCCSUP_48h_NC3_a

value: Treated with negative control siRNA

tag: time point

value: 48 hours post transfection


title: WT3 BMDM, 6 h, PAM3CSK4

status: Public on Jul 31 2024

type: SRA

city: Saint Louis

first: Hannah

last: Dorando

state: Missouri

address: 660 South Euclid Avenue, Campus Box 8118-0020-07

country: USA

institute: Washington University in St. Louis

description: Sample 6

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the Ensembl release 101 primary assembly with STAR (v 2.7.9a1).
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount (v 2.0.32).
Isoform expression of known Ensembl transcripts were quantified with Salmon (v 1.5.23).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: bone marrow-derived macrophages

growth_protocol: Bone marrow-derived macrophages (BMDMs) were produced by treating bone marrow cells with the equivalent of 10 ng/mL M-CSF from CMG14-12 cells for 6 days.

extract_protocol:
RNA was isolated using an RNeasy Plus Mini kit (Qiagen, 74134).
Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

treatment_protocol: Bone marrow-derived macrophages were plated at 200,000 cells/mL and treated with PBS or 500 ng/mL PAM3CSK4 (Tocris Bioscience, 4633) for 6 hours.

tag: cell type

value: bone marrow-derived macrophages

tag: genotype

value: WT

tag: treatment

value: PAM3CSK4 6 hours


title: PBMC RNA, High Blood Pressure High LVMI, 10

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

library_source: other

data_processing:
The samples  sequenced on the Illumina MiSeq platform rendering 50 bp single end reads underwent removal of  Adapter sequences followed by trimming of low-quality reads using Cutadapt (v. 1.11). The resulting reads were mapped to the human reference genome from Ensembl, GRCh38, using Bowtie2 (v. 2.1.0). The aligned sequencing reads and a list of mature miRNA genomic coordinates from miRBase (v. 21) were used as input for the Python package HTSeq (v. 0.6.1p1) to count the mapped miRNAs and generate a table of raw counts. The DESeq2 package (v. 1.14.1) was used to determine differential expression between sample groups using the raw count table by fitting the negative binomial generalized linear model for each miRNA and then using the Wald test for significance testing. Count outliers were detected using Cook’s distance and were removed from further analysis. The Wald test p-values from the subset of genes that passed an independent filtering step were then adjusted for multiple testing using the Benjamin-Hochburg procedure.
Assembly: GRCh38 (Illumina seq)
Supplementary files format and content: The processed file is in Excel format and contains read counts.
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.

molecule: other

organism: Homo sapiens

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 (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 NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA) and the concentration of the input material required for library preparation was determined using the Qubit Fluorometer (Invitrogen, Carlsbad, CA).  was used to convert small RNA transcripts present in the total RNA into barcoded cDNA libraries. The samples were sequenced on the Illumina MiSeq platform rendering 50 bp single end reads.

tag: tissue

value: Blood

value: Peripheral blood mono nuclear cells


title: HOXB13_TCCSUP_48h_NC2_b

city: Bandar Sunway

first: Abhi

last: Veerakumarasivam

state: Selangor

address: Jalan Universiti

country: Malaysia

institute: Sunway University

data_processing:
Base calling was performed using Illumina HiSeq Control Software.
Paired-end reads were trimmed for adaptor sequence and rRNA sequence using BBDuk software.
The clean reads were mapped to the human reference genome, GRCh37.75
Quantification of transcripts abundance from the reads was performed using Salmon’s quasi-mapping.
Genome_build: GRCh37.75
Supplementary_files_format_and_content: sf files include TPM value for each sample.

source_name: Bladder

extract_protocol:
RNA was extracted using miRNeasy Mini Kit (Qiagen, Germany) according to the manufacturer's instructions.
Libraries were prepared using TruSeq Stranded mRNA Sample Prep LS Kit (Illumina, USA) according to the manufacturer's instructions.

treatment_protocol: One group was treated with HOXA13 or HOXB13 siRNA (T), another group was treated with negative control siRNA (NC).

value: Bladder

tag: cell line

value: Bladder cancer TCCSUP cells

tag: replicate


title: N2-RT12-51

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: Female

tag: region

value: thoracic 12

tag: sequencing batch

tag: dissected soma size

tag: cell identity


title: Mononuclear cells, diagnosis, MBD, S15

city: Old Al rayyan

first: Nisar

last: Ahmed

state: Doha

address: LAS Building, Education city

department: College of Health and Life Sciences

country: Qatar

institute: Hamad Bin Khalifa University

description: ATAC-seq

library_source: genomic

data_processing:
ATAC-seq libraries underwent FastQC testing for quality assessment. Trimmomatic was employed with default parameters to filter low-quality reads and remove TruSeq adaptors. The processed reads were aligned to the hg38 human genome using Bowtie2, and SAM files were converted to BAM format using samtools. Mitochondrial, duplicate, and blacklisted reads were subsequently removed. Reads were adjusted for tn5 binding using the alignmentSieve tool. Finally, peaks were called on the processed BAM files using the callpeak and BAMPE commands of the MACS2 peak calling algorithm.
Assembly: Hg38
Supplementary files format and content: NarrowPeak

molecule: genomic DNA

source_name: Diagnosis

growth_protocol: Flash-frozen mononuclear cells from bone marrow and/or peripheral blood of adult AML diagnosis and relapse pair samples were maintained in IMDM supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
The Active Motif ATAC-seq kit was used to perform ATAC-seq on MNCs. 1 × 10^5 cells were first pelleted and washed with ice-cold PBS. Subsequently, the cells were re-suspended in an ice-cold ATAC-Lysis buffer. Next, for tagmentation the isolated nuclei were incubated at 37°C for precisely 30 minutes.
In ATAC-seq, treated DNA was purified using the Zymo DNA Clean and Concentrator-5 Kit. Subsequently, tagmented libraries underwent PCR amplification with 10 cycles and were size-selected using 60µl SPRI beads.

treatment_protocol: Cryopreserved bone marrow samples were slowly thawed using IMDM supplemented  with 10% FBS and DNAse. Viability was calculated under a hemocytometer with trypan blue – samples with a viability <80% were subjected to a dead cell sort using MACS dead cell removal kit (cat: 130-090-101)

value: Diagnosis

tag: disease

value: AML

value: Mononuclear cells


title: WT2 BMDM, 6 h, PAM3CSK4

description: Sample 4


title: PBMC RNA, High Blood Pressure High LVMI, 9


title: HOXB13_TCCSUP_48h_NC2_a


title: N2-RT12-49


title: WT1 BMDM, 6 h, PAM3CSK4

description: Sample 2


title: N2-RT12-50


title: HOXB13_TCCSUP_48h_NC1_b


title: HOXB13_TCCSUP_48h_NC1_a


title: WT1 BMDM, 6 h, PBS

description: Sample 1

value: PBS 6 hours


title: PBMC RNA, High Blood Pressure High LVMI, 7


title: N2-RT12-48


title: PBMC RNA, High Blood Pressure High LVMI, 6


title: WT3 BMDM, 6 h, PBS

description: Sample 5


title: Lair1_KO2_abscess_48h

description: Sample 4

data_processing:
RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR (v 2.7.9a1).
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount (v 2.0.32).
Isoform expression of known Ensembl transcripts were quantified with Salmon (v 1.5.23).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: skin punch biopsy

extract_protocol:
RNA was isolated from homogenized mouse skin punch biopsies using a Direct-zol RNA MiniPrep Plus kit (Zymo research, R2072).
Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

value: skin punch biopsy

value: Lair1 KO

value: 48 hours S. aureus infection


title: HOXB13_TCCSUP_48h_T3_b

value: Treated with HOXB13 siRNAs

value: 48 hours post transfection


title: PBMC RNA, High Blood Pressure High LVMI, 5

value: Blood


title: HOXB13_TCCSUP_48h_T3_a


title: N2-RT12-46


title: N2-RT12-45


title: Lair1_KO1_abscess_48h

description: Sample 3


title: WT2_abscess_48h

description: Sample 2

value: WT


title: PBMC RNA, High Blood Pressure High LVMI, 8

value: Peripheral blood mono nuclear cells


title: WT2 BMDM, 6 h, PBS

description: Sample 3

value: bone marrow-derived macrophages


title: PBMC RNA, High Blood Pressure High LVMI, 3


title: N2-RT12-44

value: Dorsal root ganglia


title: HOXB13_TCCSUP_48h_T2_a

value: Bladder

value: Bladder cancer TCCSUP cells


title: N2-RT12-43

value: Caucasian

value: Female

value: thoracic 12


title: HOXB13_TCCSUP_48h_T1_b


title: PBMC RNA, High Blood Pressure High LVMI, 4


title: N2-RT12-47


title: CON_VEH_VTA_DA_neuron_0021

city: Biberach an der Riss

first: Gregorio

last: Alanis-Lobato

address: Birkendorfer Str 65

department: Global Computational Biology and Digital Sciences

country: Germany

institute: Boehringer Ingelheim Pharma

data_processing:
Sequencing reads were mapped to the Mus musculus reference genome (mm10) using STAR v2.5.2b allowing for soft clipping of adapter sequences. An average of 13 million reads per sample was obtained , from which approximately 10 million reads were assigned to genomic features. Transcript quantification was conducted with RSEM v1.3.0 and feature Counts v1.5.1. QC and downstream bioinformatics analyses were performed with R v4.1.0 and Bioconductor v3.12 tools, respectively.
Assembly: mm10
Supplementary files format and content: SummExp_1191_CSS_CON_VEH_VTA_DA_neurons_Pryce.rds: R data storage file (rds) with a SummarizedExperiment object containing all sample metadata, gene metadata, raw and normalized gene expression matrices

source_name: Ventral tegmental area

extract_protocol:
At 3 days after completion of CSS/CON, mice were deeply anaesthetized and then perfused with PBS (20 mL) at RT. The brain was removed and placed in a cryo-mould (E6032-ICS, Sigma) with embedding medium (Tissue-TEK OCT Compound). The cryo-mould was then placed on dry ice, wrapped in aluminium foil and a polythene bag and stored at -80°C. Frozen brains were processed using RNA- and RNAse-free conditions throughout. Using a cryostat set at -18°C, coronal sections that included the VTA at AP -2.9 to -3.3 mm were cut at 10 µm and mounted (3 sections/slide) on RNAse-free PET membrane slides (50102, Molecular Machines & Industries, MMI). Sections then underwent fixation and dehydration: 100% ETOH at RT for 20 s and xylene at RT for 20 s. Slides/sections were placed on their edge in a covered boy at RT for 10 min or until completely dried, and then in a capped 50 ml Falcon tube for storage at -80°C for 3 days maximum. Tissue samples that were EGFP+ were collected from these coronal sections using a laser capture microdissection (LCM) system (CellCut, MMI). Fluorescence settings were optimized for visualization of EGFP+ tissue (channel FITC) or mScarlet-I+ tissue (channel TRITC). The membrane slide was positioned and using 4x magnification, VTA tissue areas that were EGFP+ were each encircled at Ø=35 µm using the MMI CellTools software. Selected EGFP+ areas that were also mScarlet-I+ were deselected. There were 20-30 EGFP+/m-Scarlet-I- samples per VTA hemisphere/section; these were encircled for both hemispheres for each of the 3 sections on the membrane slide. An MMI Universal UV laser (355 nm, 2 µJ, 4 kHz frequency, 500 pico-s pulse-duration) at 88% laser power was activated (velocity=51 µm/s, focus=2233 µm) and the designated tissue areas were collected on the adhesive cap of an MMI isolation tune (0.5 ml). The procedure was conducted with 3 membrane slides (7-9 sections) and isolation tubes per mouse, to yield a total of 500 EGFP+/mScarlet-I- tissue samples per mouse; this was with the exception of one CSS mouse in which the EGFP/mScarlet-I signals were weak (likely due to misplaced injection), and this mouse was excluded from the experiment. Following tissue collection, tissue lysis was conducted by adding QIAzol (100 µl) to the tube, triturating the tissue on the cap with 20 µl volumes and returning this volume to the tube; the tube was closed, inverted for 15 min at RT, and vortexed for 1 min, inverted for 5 min and centrifuged for 5 s. The tube was then sealed with Parafilm and frozen at -80°C until RNA extraction.
Per mouse sample, lysate aliquots (3 x 100 µl per sample) were pooled to give a final lysis volume of 300 µL. Samples were transferred to 2 mL PhaseLock tubes (QuantaBio). A half volume of chloroform:isoamyl alcohol (24:1 v:v) was added before shaking, 3 min RT incubation and centrifugation at 4°C. The aqueous phase was then transferred to a 1.5mL Eppendorf tube and mixed with a 1.5 volume of isopropanol (Sigma). After thorough pipette mixing, the isopropanol mixture was applied to a RNeasy MinElute spin column and total RNA was extracted using the miRNeasy Micro Kit (Qiagen) with a DNase treatment. Samples were eluted in 14 µL nuclease-free water. RNA samples were assessed both quantitatively and qualitatively using the High Sensitivity Total RNA 15nt Analysis DNF-472 Kit on a 48-channel Fragment Analyzer (Agilent). Total RNA yield was 1.14 ± 0.20 ng; RNA integrity could often not be computed due to low input. Up to 1.4 ng of total RNA was used for cDNA synthesis, conducted with the SMART-Seq® v4 Ultra Low Input RNA kit (Takara Bio); 12 amplification cycles were conducted. After clean-up, up to 10 ng of cDNA was used to generate the final sequencing libraries with the tagmentation-based DNA Prep Kit (#20018705) and the IDT® DNA/RNA UD Indexes Set A (#20026121), both Illumina®. The index PCR was performed with 9 cycles, while the final library was eluted in 30 µL EB Buffer. Low input mRNA libraries were then quantified using the High Sensitivity dsDNA Quanti-iT Assay Kit (ThermoFisher) on a Synergy HTX (BioTek). Library molarity averaged 42 nM. Libraries were also assessed for size distribution and adapter dimer presence (10, Rd3: 10, Rd4: 101), reaching an average depth of 26 million Pass-Filter reads per sample (14.2% CV).

treatment_protocol: To enable identification of VTA DA neurons, mice were injected with a cocktail of 2 AAV vectors, each in a volume of 300 nl per hemisphere: ssAAV-9/2-mTH-EGFP-WPRE-SV40p(A) (AAV mTH-EGFP, 7.0 x 1011 vg/ml; Viral Vector Facility, ETH and University of Zurich), to achieve EGFP expression in DA neurons; ssAAV-9/2-hGAD67-chI-mScarlet-I-SV40p(A) (AAV hGAD67-mScarlet-I, 8.0 x 1011 vg/ml; Viral Vector Facility, ETH and University of Zurich), to achieve m-Scarlet-I expression in GABA interneurons. In each vector, expression of a specific fluorescent protein was therefore dependent on a promoter-region sequence of a neuron type-specific marker gene: EGFP under the control of tyrosine hydroxylase (Th) promoter for DA neurons, and monomeric bright red fluorescent protein under the control of glutamate decarboxylase 67 (Gad1) promoter for GABA (inter)neurons. Stereotactic coordinates were set to inject into VTA at AP -3.1 mm, ML ±0.5 mm, DV -4.9 mm. Mice were weighed and wound healing was controlled for 10 days post-surgery. Littermate pairs were allocated to CSS (n=5 mice) and CON (n=6 mice) by counterbalancing on body weight. Mean cumulative duration of daily attack experienced by CSS mice was 49.6±5.4 s (range: 43.0-55.5 s); all CSS mice displayed submissive behaviour and vocalization during the proximal stressor. From day 15 of CSS until the end of the experiment, each CSS mouse remained in the same divided cage with the same CD-1 mouse without further attacks.

value: Ventral tegmental area

tag: strain

value: Dopaminergic neuron

tag: experimental group

value: Control

value: AAV mTH-EGFP+AAV hGAD67-mScarlet-I


title: N2-RT12-42


title: HOXB13_TCCSUP_48h_T1_a

tag: time point


title: CON_VEH_VTA_DA_neuron_0020

tag: cell type


title: PBMC RNA, High Blood Pressure High LVMI, 2


title: N2-RT12-41


title: PBMC RNA, Low Blood Pressure Low LVMI, 10


title: CSS_VEH_VTA_DA_neuron_0018

value: CSS

tag: treatment


title: HOXB13_TCCSUP_48h_T2_b

tag: tissue

value: Treated with HOXB13 siRNAs


title: HOXB13_5637_72h_NC3_a

tag: cell line

value: Bladder cancer 5637 cells

value: Treated with negative control siRNA

value: 72 hours post transfection


title: N2-RT12-40


title: PBMC RNA, Low Blood Pressure Low LVMI, 9

value: Blood

value: Peripheral blood mono nuclear cells


title: WT1_abscess_48h

description: Sample 1

value: skin punch biopsy

tag: genotype

value: WT

value: 48 hours S. aureus infection


title: CSS_VEH_VTA_DA_neuron_0017


title: HOXB13_5637_72h_NC1_b

value: Bladder

tag: replicate


title: N2-RT12-39

value: Dorsal root ganglia

tag: donor id

tag: age(years)

value: Caucasian

value: Female


title: CON_VEH_VTA_DA_neuron_0016

value: Ventral tegmental area

value: Dopaminergic neuron


title: PBMC RNA, Low Blood Pressure Low LVMI, 8


title: PBMC RNA, High Blood Pressure High LVMI, 1


title: HOXB13_5637_72h_NC1_a


title: N2-RT12-38

tag: race

tag: gender

value: thoracic 12


title: PBMC RNA, Low Blood Pressure Low LVMI, 7


title: CON_VEH_VTA_DA_neuron_0015

value: Control

value: AAV mTH-EGFP+AAV hGAD67-mScarlet-I


title: HOXB13_5637_72h_T3_b

value: Bladder cancer 5637 cells

value: Treated with HOXB13 siRNAs


title: HOXB13_5637_72h_NC3_b

value: Treated with negative control siRNA

value: 72 hours post transfection


title: HOXB13_5637_72h_T3_a


title: CSS_VEH_VTA_DA_neuron_0011

value: CSS


title: PBMC RNA, Low Blood Pressure Low LVMI, 6

value: Blood

value: Peripheral blood mono nuclear cells


title: HOXB13_5637_72h_T2_b


title: PBMC RNA, Low Blood Pressure Low LVMI, 4


title: N2-RT12-34

tag: region

tag: sequencing batch


title: CSS_VEH_VTA_DA_neuron_0009


title: N2-RT12-35

tag: dissected soma size

tag: cell identity


title: PBMC RNA, Low Blood Pressure Low LVMI, 3


title: HOXB13_5637_72h_T1_a


title: CON_VEH_VTA_DA_neuron_0002

tag: strain


title: HOXB13_5637_72h_T2_a


title: CSS_VEH_VTA_DA_neuron_0005

tag: experimental group


title: N2-RT12-33


title: PBMC RNA, Low Blood Pressure Low LVMI, 2


title: CON_VEH_VTA_DA_neuron_0001


title: N2-RT12-32


title: HOXB13_5637_24h_NC3_a

tag: time point

value: 24 hours post transfection


title: PBMC RNA, Low Blood Pressure Low LVMI, 1

tag: cell type


title: N2-RT12-36


title: N2-RT12-31


title: N2-RT12-30


title: PBMC RNA, repeat, High Blood pressure with High LVMI , 10

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: GRCh38
Supplementary files format and content: The processed file is in Excel format and contains sequencing normalised read counts of individual genes
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 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, the Illumina TruSeq Stranded mRNA Library Prep kit (Illumina, San Diego, CA) was used, the mRNA in the total RNA was converted into a library of template molecules of known strand origin. Specifically, mRNA molecules were isolated using poly-T oligo attached magnetic beads. The resulting mRNA was fragmented and reverse transcribed using random primers. The cDNA product was then amplified, incorporating sequencing adapters and barcodes to create a final double-stranded cDNA library ready for sequencing. The samples were sequenced on the Illumina HiSeq platform rendering 50 bp single-end reads.


title: PBMC RNA, Low Blood Pressure Low LVMI, 5


title: HOXB13_5637_24h_NC2_a

value: Bladder

tag: treatment


title: N2-RT12-29

tag: tissue

value: Dorsal root ganglia


title: IgG_Cg1_control

city: Chicago

first: Vipul

last: Shukla

state: Illinois

address: 303 E. Superior Street

department: Department of Cell and Developmental Biology

institute: Northwestern University

data_processing:
Single-end reads (50bp) were mapped to the mm10 GRCm38 (Dec. 2011) from UCSC using Bowtie 1.0.052 ("--p 8).
Duplicated reads were marked and kept with picard-tools-2.21.4 MarkDuplicates (https://broadinstitute.github.io/picard/).
Subsequent These fragments were used to call peaks using HOMER (v4.9.1) (F)  findPeaks function for each replicate (-center -style dnase "). The intersected peaks from the same condition were obtained with HOMER mergePeaks and filtered with grep.
Peaks were called using macs2 (“callpeak --keep-dup all” using IgG samples as input.). The intersected peaks from the same condition were obtained using HOMER mergePeaks and filtered with grep.
Assembly: mm10
Supplementary files format and content: bw bigwig files with counts per million
Supplementary files format and content: bed file contains chromosome start end of peaks
Library strategy: CUT&TAG

source_name: B cells

growth_protocol: Naïve B cells were co cultured with 40 LB and IL4 for 4 days. Expanded B cells were harvested and 300,000 B cells were processed for Cut and Tag analysis

extract_protocol:
B cells were enriched by depleting 40LB cells after 4 days of co culture
The epicypher CUT & Tag protocol was employed with slight modifications. Approximately 300,000 B cells obtained from 4 days of 40LB+ IL4 stimulation were used for CUT & Tag assay. Briefly, isolated nuclei from Cg1 Arid1a KO and control B cells were mixed with activated ConA beads and incubated for 10 minutes at room temperature. The nuclei-conjugated ConA bead complexes were incubated overnight at 4 ℃ with primary antibody Arid1a/BAF250A (1:50; cell signaling # 12354S) or control IgG (1:100; cell signaling #2729S) in digitonin 150 buffer. After primary incubation, nuclei-bead complexes were incubated with secondary antibody in digitonin 150 buffer for 1 hour at room temperature followed by the tagmentation step using CUTANA pAG-Tn5. Targeted chromatin tagmented products were column purified and libraries were amplified with 18 PCR cycles. Purified libraries were sequenced on Illumina NovaSeq 6000.
Kaya-Okur, H.S., Wu, S.J., Codomo, C.A., Pledger, E.S., Bryson, T.D., Henikoff, J.G., Ahmad, K., and Henikoff, S. (2019). CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat. Commun. 10, 1930. https://doi.org/10.1038/s41467-019-09982-5.

treatment_protocol: No treatment

value: Hematopoietic

value: ex vivo activated B cells

value: Cg1 cre

tag: chip antibody

value: anti-IgG (1:100; cell signaling #2729S)

value: 40LB + IL4


title: IgG_Cg1_ko

tag: genotype

value: Cg1 Arid1a KO


title: HOXB13_5637_24h_T3_b

tag: cell line

tag: replicate


title: N2-RT12-28

tag: donor id

tag: age(years)

value: Caucasian

value: Female

value: thoracic 12


title: HOXB13_5637_24h_T3_a

value: Bladder cancer 5637 cells

value: Treated with HOXB13 siRNAs


title: PBMC RNA, repeat, High Blood pressure with High LVMI , 9


title: Arid1a_Cg1_ko_rep1

value: anti-Arid1a/BAF250A (1:50; cell signaling # 12354S)


title: Arid1a_Cg1_ko_rep2


title: N2-RT12-27

tag: race

tag: gender


title: HOXB13_5637_24h_T2_b


title: PBMC RNA, repeat, High Blood pressure with High LVMI , 7

value: Blood


title: HOXB13_5637_24h_T2_a


title: N2-RT12-26

tag: region

tag: sequencing batch


title: Arid1a_Cg1_ctrl_rep2

value: Arid1a fl/fl


title: Arid1a_Cg1_ctrl_rep1


title: HOXB13_5637_24h_T1_b

value: 24 hours post transfection


title: PBMC RNA, repeat, High Blood pressure with High LVMI , 5

value: Peripheral blood mono nuclear cells


title: N2-RT12-25

value: Dorsal root ganglia

tag: dissected soma size

tag: cell identity


title: PBMC RNA, repeat, High Blood pressure with High LVMI , 6


title: HOXB13_5637_24h_T1_a

value: Bladder


title: N2-RT12-24


title: PBMC RNA, repeat, High Blood pressure with High LVMI , 8


title: PTBP1_KO_3

city: URBANA

first: Ullas

middle: Valiya

last: Chembazhi

address: 600 S Mathews Avenue

department: Biochemistry

institute: UIUC

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).
Adaptors were trimmed from the reads using trimmomatic V0.38
Reads were mapped to the genome using STAR_2.6.1d
Differential splicing analysis was performed using rMATs v4.0.2(turbo)
FPKM/TPM values were calculated and compared between sets of samples using Cufflinks package
Assembly: mm10
Supplementary files format and content: Cuffdiff and rMATs output

molecule: polyA RNA

source_name: Testis

extract_protocol:
RNAs were extracted from whole testes of mice at postnatal day 35 using the PureLink RNA Mini Kit (Ambion, Cat. 12183025)
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina).

value: Testis

tag: strain

value: mixed

tag: age

value: 35 days

value: Ptbp1fl/fl; Amh-Cre+/-


title: PBMC RNA, repeat, High Blood pressure with High LVMI , 4

tag: cell type


title: PTBP1_KO_2


title: HOXA13_UMUC5_48h_NC3_c

value: Bladder cancer UMUC5 cells

tag: treatment

value: Treated with negative control siRNA

tag: time point

value: 48 hours post transfection


title: PTBP1_KO_1

tag: tissue


title: PBMC RNA, repeat, High Blood pressure with High LVMI , 3


title: WT_3

tag: genotype


title: N2-RT12-23

value: Caucasian

value: Female

value: thoracic 12


title: PBMC RNA, repeat, High Blood pressure with High LVMI , 1


title: N2-RT12-21


title: N2-RT12-22


title: HOXA13_UMUC5_48h_NC3_b

tag: cell line


title: HOXA13_UMUC5_48h_NC3_a

tag: replicate


title: HOXA13_UMUC5_48h_NC2_b


title: PBMC RNA, repeat, High Blood pressure with High LVMI , 2


title: WT_2


title: N2-RT12-20

tag: donor id


title: HOXA13_UMUC5_48h_T3_b

value: Treated with HOXA13 siRNAs


title: HOXA13_UMUC5_48h_NC2_a


title: PBMC RNA, repeat, Low Blood pressure with Low LVMI , 9

value: Blood


title: N2-RT12-17

tag: age(years)


title: Mouse kidney tissue_Diabetic (Sample F)

city: Shenzhen

first: qiu

middle: zhong

last: guo

state: Guangdong

address: No. 53 Aixin Rd, Longgang Central City

country: China

institute: Longgang District People's Hospital

library_source: transcriptomic single cell

data_processing:
The data processing workflow for 10X Genomics single-cell sequencing starts with Base Calling, utilizing software Illumina bcl2fastq, working with default parameters
Quality Control and Data Filtering follow, aimed at removing low-quality reads and sequences containing adapters or poly-N stretches. For this purpose, FastQC serves for quality evaluation, while Trimmomatic or Cutadapt take on read trimming. Specific parameters include SLIDINGWINDOW:4:20 MINLEN:36 for Trimmomatic, tailored to the dataset’s quality requirements, and -a ADAPTER_SEQUENCE -m 20 for Cutadapt, denoting the adapter sequence and minimum length threshold.
Processing moves to Barcode Processing and UMI Extraction, where the 10X Genomics Cell Ranger software plays a central role. The recommended practice is to engage the latest software version to ensure full compatibility with ongoing 10X Genomics kit releases. Typically, Cell Ranger is operated with default settings; however, manual adjustments can be made as dictated by peculiar experimental demands.
Read Alignment is inherently facilitated within the Cell Ranger pipeline, employing STAR as the internal alignment engine. This step necessitates the selection of a reference genome that aligns with the mouse organism
During Gene Expression Quantification, also conducted by Cell Ranger within its processing pipeline, transcripts undergo counting. Unique Molecular Identifiers (UMIs) aid in duplicity correction, leading to the establishment of a digital gene expression matrix. This automated process encapsulates the essence of deriving quantitative insights into gene expression on a single-cell level, facilitated by the comprehensive, streamlined capabilities of the Cell Ranger software suite.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: kidney tissue

growth_protocol: The 4-week-old male C57BL/6J mice ( weight 18-20 g ) were randomly divided into two groups: normal group ( n=1 ) and diabetic group ( n=2 ) fed with ordinary diet and drinking water;

extract_protocol:
Then mice were anesthetized with intraperitoneal injections of sodium pentobarbital (70 mg/kg) and sacrificed by cervical dislocation. The kidneys were taken out.
Perform end repair, A-Tailing, adapter ligation, and further amplification steps to attach sequencing adapters to the amplified cDNA. Conduct final library cleanup and quality validation, such as quantification with qPCR and evaluation of library size.

treatment_protocol: A type 1 diabetic mice model was established after 1 week. The mice were fasted for 12 hours but watered in the model group. STZ was dissolved in sodium citrate buffer ( pH=4.5 ) at a concentration of 6 mg/ml. Intraperitoneal injection was given to mice at 40 mg/kg for 5 consecutive days. On the 7th day after the last injection, the mouse’s blood was collected by tail-cutting method. If the mouse’s fasting blood glucose was≥16.7 mmol/L, it indicated that a type 1 diabetes model was successfully replicated.

value: kidney tissue

value: C57BL/6J mice

value: streptozotocin -induced diabetic


title: PBMC RNA, repeat, Low Blood pressure with Low LVMI , 8

value: Peripheral blood mono nuclear cells


title: WT_1


title: PBMC RNA, repeat, Low Blood pressure with Low LVMI , 10


title: N2-RT12-16

value: Dorsal root ganglia

tag: race


title: HOXA13_UMUC5_48h_T3_a

value: Bladder


title: PBMC RNA, repeat, Low Blood pressure with Low LVMI , 7


title: HOXA13_UMUC5_48h_T2_b


title: N2-RT12-14

tag: gender


title: Treat-6 [B6]

city: Chongqing

first: Xia

last: Chen

address: Jiangbei

institute: The 958th Army Hospital of the Chinese People's Liberation Army

data_processing:
After filtering out splice sequences, N-containing reads and reads with Qphred ≤ 20 using fastp, raw data was aligned to the mus musculus reference genome (GRCm38) by HISAT2 software.
FeatureCounts was used to calculate the number of reads mapped to each gene. Fragments Per Kilobase per Million reads (FPKM) was then calculated for each gene based on the length of the gene and the number of reads mapped to the reference.
Assembly: mm10
Supplementary files format and content: excel file

source_name: Lung

extract_protocol:
Total RNA was extracted from lung tissue samples using the TRIzol method.
Sequencing libraries were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer's recommendations and RNA sequencing (RNA‒seq) was performed on the NovaSeq 6000 platform

value: Lung

value: acute lung injury (ALI)


title: PBMC RNA, repeat, Low Blood pressure with Low LVMI , 5


title: Treat-5 [B5]


title: N2-RT12-13

tag: region


title: HOXA13_UMUC5_48h_T2_a


title: HOXA13_UMUC5_48h_T1_a


title: PBMC RNA, repeat, Low Blood pressure with Low LVMI , 4


title: N2-RT12-12

tag: sequencing batch


title: Treat-4 [B4]


title: Treat-3 [B3]


title: PBMC RNA, repeat, Low Blood pressure with Low LVMI , 2


title: PBMC RNA, repeat, Low Blood pressure with Low LVMI , 3


title: Mouse kidney tissue_normal (Sample C)


title: N2-RT12-10

tag: dissected soma size


title: Treat-2 [B2]


title: N2-RT12-15

tag: cell identity


title: PBMC RNA, repeat, Low Blood pressure with Low LVMI , 1


title: HOXA13_UMUC5_24h_NC2_a

value: 24 hours post transfection


title: Mouse kidney tissue_Diabetic (Sample A)

value: streptozotocin-induced diabetic


title: N2-RT12-9


title: Treat-1 [B1]


title: Control-6 [A6]

value: control


title: HOXA13_UMUC5_24h_NC1_a

value: Bladder cancer UMUC5 cells

value: Treated with negative control siRNA


title: PBMC RNA, High Blood pressure with High LVMI , 10


title: PBMC RNA, repeat, Low Blood pressure with Low LVMI , 6


title: N2-RT12-8

value: Caucasian

value: Female


title: HOXA13_UMUC5_24h_T3_b

value: Treated with HOXA13 siRNAs


title: N2-RT12-6

value: thoracic 12

value: hPropr


title: HOXA13_UMUC5_24h_T3_a


title: N2-RT12-11


title: Control-5 [A5]


title: PBMC RNA, High Blood pressure with High LVMI , 9

value: Blood


title: HOXA13_UMUC5_24h_NC2_b


title: N2-RT12-7


title: Control-4 [A4]


title: HOXA13_UMUC5_24h_NC3_a


title: PBMC RNA, High Blood pressure with High LVMI , 8


title: HOXA13_UMUC5_24h_T2_c


title: N2-RT12-5


title: PBMC RNA, High Blood pressure with High LVMI , 7


title: HOXA13_UMUC5_24h_T2_b


title: N2-RT12-3


title: Control-3 [A3]


title: PBMC RNA, High Blood pressure with High LVMI , 6


title: N2-RT12-2


title: Control-1 [A1]


title: PBMC RNA, High Blood pressure with High LVMI , 5


title: PBMC RNA, High Blood pressure with High LVMI , 4


title: HOXA13_UMUC5_24h_T1_b


title: HOXA13_UMUC5_24h_T2_a


title: N2-RT12-1


title: Control-2 [A2]


title: N2-RL5-96

value: lumbar 5


title: MC57G, MHV68-R443I-infected rep 3, 50-200 bp insert

city: Santa Cruz

first: Todd

last: Lowe

state: CA

address: 1156 High Street

department: Biomolecular Engineering and Bioinformatics

institute: University of California Santa Cruz

data_processing:
Sequencing adaptors were trimmed from raw reads using cutadapt, v1.18, and read counts were generated for host and viral small RNA types using tRAX (Holmes et al. 2022). Briefly, trimmed reads were mapped to a combined mouse (GRCm38/mm10) and gammaherpesvirus (MHV68) reference containing mature tRNAs obtained from GtRNAdb (Lowe and Chan 2016) and their corresponding genomic sequences using Bowtie2 in very-sensitive mode with the following parameters to allow for a maximum of 100 alignments per read: --very-sensitive --ignore-quals --np 5 -k 100. Mapped reads were filtered to retain only the “best mapping” alignments. Raw read counts of tRNAs and other small RNA types were computed using tRNA annotations from GtRNAdb, and annotations from  GENCODE M23 and miRBase v22 (Koomara et al. 2014). Raw read counts were then normalized using DESeq2.
Assembly: Mus musculus GRCm38/mm10
Supplementary files format and content: Processed data files are in bigwig format and can be visualized by uploading them into the UCSC Genome Browser. They contain the read coverage aligned to the reference genome.
Library strategy: OTTR-seq

source_name: cell line

growth_protocol: NIH 3T3 murine fibroblasts, NIH 3T12 murine fibroblasts, and MC57G fibrosarcoma cells (ATCC) were maintained in high-glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS). Cultures were screened regularly for mycoplasma and cultured in the absence of antibiotics.

extract_protocol:
Total RNA was isolated from cells using TRIzol (Invitrogen). For RT-qPCR analysis, total RNA was treated with Turbo DNase (Ambion) and reverse transcribed with AMV RT (Promega) primed with random 9-mer (IDT) for total RNA measurements or stem-loop primers for 5’ tDR measurements. Gene expression was measured by amplifying cDNA using iTaq SYBR Green Supermix (Biorad) and the primers listed in Table 2 on a QuantStudio 3 (Applied Biosystems). RT-qPCR was analyzed using the delta delta CT (ΔΔCT) method. Average fold changes were calculated relative to 18S or U6 internal controls. For Northern blot analysis, total RNA was loaded onto 8 to 12% PAGE–7 M urea gels and transferred to Hybond-N+ (GE) membranes using a Trans-Blot Turbo Transfer system (Bio-Rad) in 1X TBE. Blots were crosslinked using the auto-crosslink setting on a UV Crosslinker FB-UV-XL-1000 (1,200 μJ × 100) (Fisher Scientific) and prehybridized in ULTRAhyb buffer (Thermo Fisher) at 42°C for 1hr before adding radiolabeled probe. Probes were generated by end labeling oligonucleotides specific for Tyr or 5S as a loading control using T4 PNK and [γ-32P] ATP. Blots were probed overnight at 55°C and washed 3 times for 10 minutes in 0.5× SSC (1× SSC is 0.15 M NaCl plus 0.015 M sodium citrate) and 0.1% SDS. Blots were imaged using a Typhoon imager and processed on Photoshop (Adobe). Densitometry was performed using BioRad ImageLab software.
OTTR-seq libraries were generated as previously described (Upton et al. 2021). Briefly, total PNK-treated RNA was 3’ tailed using mutant BoMoC RT in buffer containing only ddATP for 90 minutes at 30 ̊C, with the addition of ddGTP for another 30 minutes at 30 ̊C. This was then heat-inactivated at 65 ̊C for 5 minutes, and unincorporated ddATP/ddGTP were hydrolyzed by incubation in 5 mM MgCl2 and 0.5 units of shrimp alkaline phosphatase (rSAP) at 37 ̊C for 15 minutes. 5 mM EGTA was added and incubated at 65 ̊C for 5 minutes to stop this reaction. Reverse transcription was then performed at 37 ̊C for 30 minutes, followed by heat inactivation at 70 ̊C for 5 minutes. The remaining RNA and RNA/DNA hybrids were then degraded using 1 unit of RNase A at 50 ̊C for 10 minutes. cDNA was then cleaned up using a MinElute Reaction CleanUp Kit (Qiagen). To reduce adaptor dimers, cDNA was run on a 9% UREA page gel, and the size range of interest was cut out and eluted into gel extraction buffer (300mM NaCl, 10mM Tris; pH 8.0, 1mM EDTA, 0.25% SDS) and concentrated using EtOH precipitation. Size-selected cDNA was then PCR amplified for 12 cycles using Q5 High-fidelity polymerase (NEB #M0491S). Amplified libraries were then run on a 6% TBE gel, and the size range of interest was extracted to reduce adaptor dimers further. Gel slices were eluted into gel extraction buffer (300mM NaCl, 10mM Tris; pH 8.0, 1mM EDTA) followed by concentration using EtOH precipitation. Final libraries were pooled and sequenced on an Illumina NovaSeq 6000.

treatment_protocol: Green fluorescent protein (GFP) expressing MHV6817 and the R443I derivative (CITE) was amplified in NIH 3T12s. MHV68-infected NIH 3T12 cells and media were subjected to two freeze-thaws, then cellular material was pelleted and discarded. Viruses present in the supernatant were pelleted at high-speed (12K x g) for 2h, then treated with DNase (Fisher #EN0523) for 1h at 37 °C. Media was added and virus was pelleted at high-speed (12K x g) for 2h. Virus pellet was dissolved in DMEM +10% FBS media, aliquoted, and stored at -80 °C. MHV68-GFP titer was measured on NIH 3T3 cells for the 50% tissue culture infective dose (TCID50). For high MOI/single-step infection, MHV68 virus was added to ½ culture volume of media, placed on NIH 3T3 or MC57G cells for 1 h at multiplicity of infection (MOI) of 5 to allow viral entry, then replaced with fresh DMEM +10% FBS medium. Pooled siRNA purchased from Dharmacon was nucleofected into 5x105 NIH 3T3 cells. The Neon™ Transfection System (Thermo Fisher), with buffer E2 and 100uL tips, was used to perform the nucleofection (1400 volts/20 ms/2 pulses). Cells were infected 24h r post-nucleofection and harvested 24 hr post-infection (hpi). Total RNA was analyzed via RT-qPCR.

value: cell line

value: fibrosarcoma

value: WT


title: Input_Cdca7_RH_10

city: Houston

first: Bin

last: Liu

state: TX

address: 1515 Holcombe BLVD

department: epigenetics and molecular carcinogenesis

institute: University of Texas MD Anderson Cancer Center

description: input sample

data_processing:
For each ChIP sample, peaks were identified using MACS2 (version V2.1.1.20160309). MACS2 was configured to call peaks from the pile-up of 150bp around the midpoints of fragments, and a q-value cutoff of 0.05 was applied. The peaks that overlapped with ENCODE blacklisted regions were removed. Cdca7_RH_10 and Cdca7_WT_4 had no peak found, thus no peak file is provided
Assembly: GRCm38/mm10
Supplementary files format and content: Peak locations in bed format

source_name: CDCA7 KO mESCs reconstituted with R285H mutant mCDCA7 clone 10

growth_protocol: mESCs were maintained in DMEM medium containing serum and LIF

extract_protocol:
Cells were fixed with 1% formaldehyde, chromatin was sonicated, and ChIP was done using HA antibody.
ChIP libraries were constructed using a KAPA Hyper Library Preparation Kit

treatment_protocol: CDCA7 KO mESC lines were generated by CRISPR/Cas9, plasmids encoding HA-tagged WT or R285H (RH) mutant mCDCA7 were transfected into CDCA7 KO mESCs, and stable clones were obtained after blasticidin selection.

value: Cell line

value: J1 mESC

value: embryonic stem cell

value: CDCA7 KO, expressing exogenous ICF mutant CDCA7

value: Reconstituted with HA-tagged R285H mutant mCDCA7


title: HOXA13_UMUC5_24h_T1_a

value: Bladder

value: Bladder cancer UMUC5 cells

value: 24 hours post transfection


title: MC57G, MHV68-R443I-infected rep 2, 50-200 bp insert


title: PBMC RNA, High Blood pressure with High LVMI , 2

value: Peripheral blood mono nuclear cells


title: N2-RL5-95

value: Dorsal root ganglia

value: Caucasian

value: Female


title: Chip_Cdca7_RH_10

description:
ChIP was done using HA antibody
no peaks found for this sample


title: N2-RL5-94

value: hPropr


title: PBMC RNA, High Blood pressure with High LVMI , 1

value: Blood


title: MC57G, MHV68-R443I-infected rep 1, 50-200 bp insert

value: cell line


title: PBMC RNA, Low Blood pressure with Low LVMI , 10


title: N2-RL5-92

value: lumbar 5


title: Input_Cdca7_RH_5

description: input sample

source_name: CDCA7 KO mESCs reconstituted with R285H mutant mCDCA7 clone 5


title: PBMC RNA, Low Blood pressure with Low LVMI , 9


title: MC57G, MHV68-MR-infected, rep 2, 50-200 bp insert

value: fibrosarcoma

value: WT

value: MHV68-MR, MOI=5, 24h


title: N2-RL5-91


title: MC57G, MHV68-MR-infected, rep 1, 50-200 bp insert


title: PBMC RNA, High Blood pressure with High LVMI , 3


title: N2-RL5-90


title: PBMC RNA, Low Blood pressure with Low LVMI , 8


title: Chip_Cdca7_WT_9

description: ChIP was done using HA antibody

source_name: CDCA7 KO mESCs reconstituted with WT mCDCA7 clone 9

value: Cell line

value: J1 mESC

value: embryonic stem cell

value: CDCA7 KO, expressing exogenous WT CDCA7

value: Reconstituted with HA-tagged WT mCDCA7


title: MC57G, mock-infected, rep 2, 50-200 bp insert

value: mock-infected


title: N2-RL5-89


title: PBMC RNA, Low Blood pressure with Low LVMI , 7

value: Peripheral blood mono nuclear cells


title: Input_Cdca7_WT_4

description: input sample

source_name: CDCA7 KO mESCs reconstituted with WT mCDCA7 clone 4


title: N2-RL5-93

value: Dorsal root ganglia


title: Chip_Cdca7_WT_4


title: PBMC RNA, Low Blood pressure with Low LVMI , 5


title: MC57G, MHV68-MR-infected, rep 3, 50-200 bp insert


title: MC57G, mock-infected, rep 1, 50-200 bp insert


title: Chip_Cdca7_RH_5

description: ChIP was done using HA antibody

value: CDCA7 KO, expressing exogenous ICF mutant CDCA7

value: Reconstituted with HA-tagged R285H mutant mCDCA7


title: N2-RL5-87

value: Caucasian

value: Female


title: MC57G, MHV68-R443I-infected rep 3, 15-50 bp insert

value: cell line


title: PBMC RNA, Low Blood pressure with Low LVMI , 4

value: Blood


title: BMDMs, ST_2, Salmonella infection

city: Hangzhou

first: Pinanong

last: Na Phatthalung

address: Department of Nutrition Yuhangtang Road 866, Hangzhou, Zhejiang Province Zijingang Campus, Zhejiang University

country: Thailand

institute: Zhejiang University

data_processing:
The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions.
After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated.
The cluster generation and sequencing were performed on Novaseq 6000 S4 platform ,using NovaSeq 6000 S4 Reagent kit V1.5.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: Bone marrow-derived macrophages

growth_protocol: BMDMs differentiated from bone marrow cells of C57BL/6 mice were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
The purity of the sample was determined by NanoPhotometer ®（IMPLEN, CA, USA). The concentration and integrity of RNA samples were detected by Agilent 2100 RNA nano 6000 assay kit.
A total amount of 1-3μg RNA per sample was used as input material for the RNA sample preparations.
RNA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 3.0 to preliminary quantify and then dilute to 1ng/μl.
Insert size was assessed using the Agilent Bioanalyzer 2100 system.
After the insert size met the expectation, the Bio-RAD CFX 96 fluorescence quantitative PCR instrument was used to accurately quantify the library effective concentration.

treatment_protocol:
BMDMs were infected with Salmonella enterica serovar Typhimurium (MOI = 1) for 2 hrs.
BMDMs were washed with sterile PBS, then BMDM RNA was harvested using a RNeasy kit (Qiagen).

tag: strain

tag: Sex

value: Male

value: Bone marrow-derived macrophages

value: Salmonella infection

value: 2 hr


title: Input_Cdca7_WT_9

description: input sample

value: Cell line

value: J1 mESC

tag: cell type


title: MC57G, MHV68-R443I-infected rep 2, 15-50 bp insert

value: fibrosarcoma

value: WT

tag: treatment


title: BMDMs, ST_3, Salmonella infection

tag: age


title: MC57G, mock-infected, rep 3, 50-200 bp insert

tag: tissue

value: mock-infected


title: N2-RL5-86

value: lumbar 5


title: BMDMs, ST_1, Salmonella infection

tag: genotype


title: PBMC RNA, Low Blood pressure with Low LVMI , 2

value: Peripheral blood mono nuclear cells


title: N2-RL5-85

value: Dorsal root ganglia


title: PBMC RNA, Low Blood pressure with Low LVMI , 3


title: MC57G, MHV68-R443I-infected rep 1, 15-50 bp insert

tag: cell line


title: BMDMs, Control_3, Uninfection

value: Uninfection

value: 0 hr


title: PBMC RNA, Low Blood pressure with Low LVMI , 6


title: BMDMs, Control_2, Uninfection


title: N2-RL5-84

value: Caucasian

value: Female


title: PBMC RNA, Low Blood pressure with Low LVMI , 1

value: Blood


title: N2-RL5-83

value: hPropr


title: N2-RL5-88


title: snRNASeq_BA30_and_BA31

city: Orlando

first: Lauren

last: Sparks

state: Florida

address: 301 E Princeton St, 301

institute: AdventHealth

description:
Mixed Sample of BA30_BA31
Mixed Sample of BA30_BA31

data_processing:
FASTQ files are processed with the CogentAP pipeline using appropriate sample WellList.TXT files. Due to two samples with primer A and primer B sex indexes being sequenced on the same pair-end sequencing lane, each pair of FASTQ files will be processed through cogentAP twice, once with the first sample wellList.TXT file and secondly with the second sample WellList.TXT file.
Following trimming, data was aligned to the GRCh38 reference genome and sample count matrices were generated that contain counts for all the single nuclei analyzed for that sample
Assembly: GRCh38
Supplementary files format and content: CSV files include raw read count values  all the single nuclei profiles for that sample

source_name: subcutaneous abdominal fat

extract_protocol:
Adipose tissue biopsies were collected from subcutaneous abdominal adipose tissue.  Frozen adipose tissue (~100mg) was pulverized under liquid nitrogen and homogenized in 2mL of homogenization buffer (5mM MgCl2, 25mM Tris Buffer pH 8.0, 25mM KCL, 250mM sucrose, 1µm DDT, 1 x protease inhibitor, 0.2 U/µL SUPERase•In RNase Inhibitor (Thermofisher Scientific) in nuclease-free water) with a glasscol homogenizer. The homogenate was incubated for 30 minutes on ice with the addition of Triton-X100 (0.1% v/v) with regular vortexing. Samples were filtered through a 100µm and 40µm strainer (BD Falcon), centrifuged at 2,700g for 10 min at 4°C, resuspended in homogenization buffer and recentrifuged again at 2,700g for 10 min at 4°C. The pellet was then re-suspended in 1mL nuclei isolation medium (5mM MgCl2, 25mM Tris Buffer pH 8.0, 25mM KCL, 1 mM EDTA, 0.2 U/µL Ribolock RNAase inhibitor, 1% BSA in nuclease-free water) and centrifuged at 2,700g for 10 min at 4°C. Following re-suspension in 500µL nuclei isolation medium, sample was filtered 10 x with a 25g syringe prior to being counted. Single-nuclei suspension (40K/mL)  was distributed into eight wells of a 384-well source plate (Takara) and dispensed onto a ICELL8® 350v Chip (Takara) using an ICELL8 MultiSample NanoDispenser (MSND, Takara). Following dispense, the chip nanowells were imaged using the ICELL8 Imaging Station to identify nanowells containing a single nucleus. Only these nanowells were subjected for downstream dispenses. After imaging, the chip was subjected to freeze-thaw to lyse the cells/nuclei, followed by a 3 min incubation at 72oC to denature the RNA.
Selected nuclei were subjected to first-strand cDNA synthesis initiated by oligo dT primer (SMART-Seq ICELL8 CDS), followed by template switching with template switching oligo (SMART-Seq ICELL8 oligonucleotide) for 2nd strand cDNA synthesis, prior to unbiased amplification of full-length cDNA. Synthesized full-length cDNA was tagmented by TDE1 (Illumina Tagment DNA enzyme) and amplified using forward (i5) and reverse (i7) indexing primers. Each single nucleus was indexed by a unique combination of 1 of 72 forward and 1 of 72 reverse indexing primers allowing for downstream identification. Collected cDNA was purified twice using a 1:1 proportion of AMPure XP beads (Beckman, A63880), further amplified according to manufacturer’s instructions and purified again at a 1:1 proportion of AMPure XP beads. The resultant sequencing-ready cDNA library was assessed for concentration by fluorometer (Qubit) and quality by electrophoresis (Agilent Bioanalyzer high sensitivity DNA chips) respectively. Libraries were sequenced with Illumina HiSeq 4000.

value: Adipose Tissue


title: BMDMs, Control_1, Uninfection

value: Male

value: Bone marrow-derived macrophages


title: N2-RL5-82


title: MC57G, mock-infected, rep 3, 15-50 bp insert

value: cell line


title: N2-RL5-81


title: TCR P5.Day3

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

description: total RNA + tVDJ

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices and VDJ output generated using the Cellranger count and vdj pipelines 6.0.0
Assembly: hg38
Supplementary files format and content: gzipped folder containing cellranger generated barcodes, features, and matrix files
Supplementary files format and content: gzipped folder containing cellranger generated filtered contig annotations for tVDJ
Library strategy: 5' RNAseq + VDJ

source_name: CSF

extract_protocol:
10x Genomics Chromium single-cell preparation
NGS Illumina Next Seq

value: CSF


title: snRNASeq_BA26_and_BA27

description:
Mixed Sample of BA26_BA27
Mixed Sample of BA26_BA27


title: snRNASeq_BA20_and_BA22

description:
Mixed Sample of BA20_BA22
Mixed Sample of BA20_BA22


title: TCR P5.Day5

description: total RNA + tVDJ


title: N2-RL5-80


title: MC57G, mock-infected, rep 2, 15-50 bp insert

value: fibrosarcoma


title: TCR P5.Day1

description: total RNA + tVDJ


title: N2-RL5-79


title: N2-RL5-78


title: MC57G, MHV68-MR-infected, rep 2, 15-50 bp insert

value: WT

value: MHV68-MR, MOI=5, 24h


title: snRNASeq_BA19_and_BA24

description:
Mixed Sample of BA19_BA24
Mixed Sample of BA19_BA24


title: TCR P4.Day5

description: total RNA + tVDJ


title: MC57G, mock-infected, rep 1, 15-50 bp insert

value: mock-infected


title: TCR P4.Day1

description: total RNA + tVDJ


title: snRNASeq_BA17_and_BA18

description:
Mixed Sample of BA17_BA18
Mixed Sample of BA17_BA18


title: endo_t4_ko_M00509904

city: Cambridge

first: Kevin

middle: Richard

last: Costello

state: Cambridgeshire

address: Genetics Building Downing St.

department: Department of Genetics

country: United Kingdom

institute: Univerity of Cambridge

data_processing:
The Illumina sequencing reads were pre-processed by removing adapters and trimming low-quality bases (phred score < 20) using cutadapt v3.4. To account for the Pico v2 SMART Adapter, we also trimmed the last 4 bp of read 1 (preceding the Illumina adapter, if it was detected in the read) and the first 4 bp of read 2. Read quality was assessed before and after trimming with FastQC v0.11.9. Further quality control metrics were obtained by aligning the reads to the GRCm38/mm10 mouse reference genome (Ensembl release 102) using STAR v2.7.9a, followed by rseqc v4.0.0 to estimate junction saturation and percentages of reads aligning to annotated features such as exons, introns or UTRs. These quality metrics were compiled using multiqc v1.10.1.  Transcript quantification was done using salmon v1.5.0 against the reference transcriptome annotation (GRCm38/mm10, Ensembl release 102). Differential expression analysis between WT/KO was performed using DESeq2 v1.32.0.
Assembly: GRCm38
Supplementary files format and content: Processed data provided are quant.sf files generated using Salmon. File includes gene name, gene legnth , effective Lenth, TPM, and Number of reads mapping to each transcript

source_name: Mammary Gland

extract_protocol: Libraries for RNA sequencing (RNA-seq) from sorted mammary cells were generated using SMARTer stranded total RNA-seq kit V2   Pico input mammalian (TaKaRa bio, 634414) according to the manufacturer's instructions. The quality and RNA integrity number were assessed using Bioanalyzer 2100 (Agilent), Qubit fluorometer (Thermo Fisher) and sequenced using the NovaSeq 6000 system (Illumina)

value: Mammary Gland

value: endothelial

tag: timepoint

value: Lacation day 2


title: MC57G, MHV68-MR-infected, rep 1, 15-50 bp insert


title: N2-RL5-76

source_name: Dorsal root ganglia

value: Dorsal root ganglia

tag: donor id

value: lumbar 5


title: snRNASeq_BA23_and_BA06

description:
Mixed Sample of BA23_BA06
Mixed Sample of BA23_BA06


title: snRNASeq_BA10_and_BA15

description:
Mixed Sample of BA10_BA15
Mixed Sample of BA10_BA15


title: basal_t4_ko_M00471543

value: basal


title: lumhi_t4_ko_M00490577

value: luminal progenitor cells


title: N2-RL5-75

tag: age(years)

value: Caucasian

value: Female


title: snRNASeq_BA14_and_BA16

description:
Mixed Sample of BA14_BA16
Mixed Sample of BA14_BA16

value: Adipose Tissue


title: TCR P4.Day3

description: total RNA + tVDJ


title: stromal_t4_wt_M00483956

value: stromal

value: wt


title: TCR P2.Day5

description: total RNA + tVDJ

value: CSF


title: TCR P3.Day5

description: total RNA + tVDJ


title: N2-RL5-74

tag: race


title: snRNASeq_BA07_and_BA09

description:
Mixed Sample of BA07_BA09
Mixed Sample of BA07_BA09


title: MC57G, MHV68-MR-infected, rep 3, 15-50 bp insert

value: cell line

value: fibrosarcoma


title: N2-RL5-73

tag: gender


title: TCR P2.Day3

description: total RNA + tVDJ


title: snRNASeq_BA01_and_BA08

description:
Mixed Sample of BA01_BA08
Mixed Sample of BA01_BA08


title: lumhi_t4_wt_M00460359


title: TCR P1.Day5

description: total RNA + tVDJ


title: lumlo_t4_ko_M00504337

value: luminal differentiated  cells


title: lumlo_t4_wt_M00460358


title: TCR P1.Day3

description: total RNA + tVDJ


title: endo_t4_wt_M00467006


title: N2-RL5-70

tag: region


title: N2-RL5-77

tag: sequencing batch


title: TCR P1.Day1

description: total RNA + tVDJ


title: stromal_t2_ko_M00439062

value: Gestation day 9.5


title: Pca_04_N

city: Seoul

first: BYULA

last: JEE

address: 81 Irwon-Ro Gangnam-gu

department: Urology

country: South Korea

institute: Samsung medical center

description: 10x Genomics

data_processing:
FASTQ files were processed with cellranger v3.1
Doublets and low-quality cells were excluded from subsequent analysis (< 500 or >8000 genes and > 15% expression of the percentage from mitochondrial gene). For the remaining cells, gene expression data were normalized using NormalizeData function and were scaled with the ScaleData function in Seurat package. The batch effects were removed by RunHarmony function using Seurat package (version 4.1.1).
TSV files containing detected cellular barcodes (barcodes.tsv) and correspondig genes (features.tsv) as returned from Cell Ranger.
MTX sparse matrix containing counts as returned from Cell Ranger
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: prostate cancer

extract_protocol:
Tissue biopsies were extracted within one hour after surgery from prostate specimens. The biopsies were rinsed with PBS, minced into 1mm3 pieces and transferred to the 5 ml of digestion solution ((DMEM high glucose (Sigma-Aldrich) supplemented with with L-glutamine-penicillin-streptomycin (100 U/ml) (Sigma-Aldrich), 20 uL DNase (Quiagen) (75 U/ml), 2 mL Collagenase V (2 %) (Sigma-Aldrich) and Dispase II (2.5 U/mL) (Gibco)) for 45 minutes in water bath (37 °C).
To perform scRNA sequencing, 10X Chromium Chip Single-cell library generation and preparation were performed on the single-cell suspension according to 10X Chromium 3'solution (V2 kit) as per manufacturer’s instructions with an aim to capture 5000-10000 cells/channel. Sequencing was performed using the Illumina HiSeq 4000 platform. Raw sequencing data was processed by Cell Ranger software (10X Genomics, version 3.1) and aligned to the human reference genome (GRCh38).

value: prostate cancer

tag: disease status

value: Normal

tag: batch

tag: sample id


title: N2-RL5-69

tag: dissected soma size

tag: cell identity


title: RNA-Seq P5.Day5

description: total RNA + tVDJ

tag: cell type


title: Pca_03_TB

description: 10x Genomics

value: Tumor


title: N2-RL5-67

value: Dorsal root ganglia


title: Pca_04_T1

description: 10x Genomics


title: RNA-Seq P5.Day3

description: total RNA + tVDJ


title: Pca_03_TA

description: 10x Genomics


title: RNA-Seq P5.Day1

description: total RNA + tVDJ


title: N2-RL5-66

value: lumbar 5


title: Pca_06_T

description: 10x Genomics


title: RNA-Seq P4.Day5

description: total RNA + tVDJ


title: N2-RL5-65


title: N2-RL5-71


title: endo_t2_wt_M00439079

value: Mammary Gland

value: endothelial


title: basal_t2_wt_M00433264

value: basal


title: N2-RL5-68

value: Caucasian

value: Female


title: N2-RL5-64


title: basal_t2_ko_M00438677


title: Pca_06_N

description: 10x Genomics


title: RNA-Seq P4.Day3

description: total RNA + tVDJ


title: Pca_01_T2

description: 10x Genomics


title: Pca_01_T1

description: 10x Genomics


title: stromal_t2_wt_M00424114

value: stromal


title: N2-RL5-63


title: RNA-Seq P4.Day1

description: total RNA + tVDJ


title: RNA-Seq P3.Day5

description: total RNA + tVDJ


title: N2-RL5-62

value: hPropr


title: mHSPC_03

description: 10x Genomics

value: mHSPC


title: Pca_01_N

description: 10x Genomics


title: lumhi_t0_ko_M00398657

value: luminal progenitor cells

value: Nulliparous


title: mHSPC_02

description: 10x Genomics


title: N2-RL5-60


title: Pca_02_T

description: 10x Genomics


title: lumlo_t2_ko_AFGK78

value: luminal differentiated  cells


title: endo_t0_ko_M00395206


title: RNA-Seq P2.Day3

description: total RNA + tVDJ

value: CSF


title: RNA-Seq P2.Day5

description: total RNA + tVDJ


title: RNA-Seq P1.Day5

description: total RNA + tVDJ


title: N2-RL5-59


title: basal_t0_ko_M00384810


title: RNA-Seq P1.Day3

description: total RNA + tVDJ


title: stromal_t0_ko_M00373634


title: N2-RL5-58


title: COLLAB6and7_02

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Takes output from raw files.  Run to trim off both 5’ and 3’ adapters on both reads. Command: quality-cutoff 6  -m 18  -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGT  AGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.metrics
Takes output from cutadapt round 1. Run to trim off the 3’ adapters on read 2, to control for double ligation events. Command: cutadapt -f fastq --match-read-wildcards  --times 1  -e 0.1  -O 5  --quality-cutoff 6  -m 18  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.metrics
Takes output from cutadapt round 2.  Maps to human specific version of RepBase used to remove repetitive elements, helps control for spurious artifacts from rRNA (& other) repetitive reads.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir /path/to/RepBase_human_database_file --genomeLoad LoadAndRemove  --readFilesIn /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz --outSAMunmapped Within  --outFilterMultimapNmax 30  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam --outSAMattributes All  --readFilesCommand zcat  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam
Takes output from STAR rmRep.  Maps unique reads to the human genome.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir  /path/to/STAR_database_file --genomeLoad LoadAndRemove  --readFilesIn  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate1  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate2  --outSAMunmapped Within  --outFilterMultimapNmax 1  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --outSAMattributes All  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam
takes output from STAR genome mapping.  Custom random-mer-aware script for PCR duplicate removal. Command: barcode_collapse_pe.py  --bam /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --out_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  --metrics_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.metrics
Takes output from barcode collapse PE.  Sorts resulting bam file for use downstream.  Command: java  -Xmx2048m  -XX:+UseParallelOldGC  -XX:ParallelGCThreads=4  -XX:GCTimeLimit=50  -XX:GCHeapFreeLimit=10  -Djava.io.tmpdir=/full/path/to/files/.queue/tmp  -cp /path/to/gatk/dist/Queue.jar  net.sf.picard.sam.SortSam  INPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  TMP_DIR=/full/path/to/files/.queue/tmp  OUTPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  VALIDATION_STRINGENCY=SILENT  SO=coordinate  CREATE_INDEX=true
Takes output from sortSam, makes bam index for use downstream.  Command: samtools index  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam.bai
Takes inputs from multiple final bam files.  Merges the two technical replicates for further downstream analysis.  Command: samtools  merge  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam /full/path/to/files/file_R1.D08.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam
Takes output from sortSam, makes bam index for use downstream.  Command: samtools  index  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/CombinedID.merged.bam.bai
Takes output from sortSam.  Only outputs the second read in each pair for use with single stranded peak caller.  This is the final bam file to perform analysis on.  Command: samtools view -hb -f 128  /full/path/to/files/CombinedID.merged.bam  >  /full/path/to/files/CombinedID.merged.r2.bam
Takes results from samtools view.  Calls peaks on those files.  Command: clipper  -b /full/path/to/files/CombinedID.merged.r2.bam  -s hg19  -o /full/path/to/files/CombinedID.merged.r2.peaks.bed  --bonferroni  --superlocal  --threshold-method binomial  --save-pickle
Genome_build: hg19
Supplementary_files_format_and_content: bed format, contains clusters of predicted RBP binding

growth_protocol: Tissues

extract_protocol:
Cells were lysed in iCLIP lysis buffer, followed by limited digestion with RNase I (Ambion), immunoprecipitation of RBP-RNA complexes with a specific antibody of interest (Protein G sheep anti-rabbit Dynabeads), and stringent washes.
After dephosphorylation with FastAP (Thermo Fisher) and T4 PNK (NEB), a barcoded RNA adapter is ligated to the 3’ end (T4 RNA Ligase, NEB). Ligations are performed on-bead (to allow washing away unincorporated adapter) in high concentration of PEG8000. Samples are then run on standard protein gels and transferred to nitrocellulose membranes, and a region 75 kDa (~150 nt of RNA) above the protein size is isolated and proteinase K (NEB) treated to isolate RNA. RNA is reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter (containing a random-mer of 10 (N10) random bases at the 5’ end) is then ligated to the cDNA fragment 3’ end (T4 RNA Ligase, NEB), performed with high concentration of PEG8000 (to improve ligation efficiency) and DMSO (to decrease inhibition of ligation due to secondary structure). After cleanup (Dynabeads MyOne Silane, ThermoFisher), an aliquot of each sample is first subjected to qPCR (to identify the proper number of PCR cycles), and then the remainder is PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis.

treatment_protocol: Flash-frozen brain tissue was cryo-ground in pestles pre-chilled with liquid nitrogen, spread out in standard tissue culture plates pre-chilled to -80 C, and UV crosslinked twice at 254 nM (400 mJ/cm2). 50 mg of crosslinked tissue was then used for each eCLIP experiment.

value: barodes:X2A, X2B

tag: antibody

value: Anti-A1CF, Abcam ab89050

value: brain


title: COLLAB6and7_02_INPUT

tag: tissue


title: lumlo_t2_wt_M00424115

tag: genotype

value: wt

value: Gestation day 9.5


title: RNA-Seq P1.Day1

city: Saint Louis

description: total RNA + tVDJ


title: COLLAB6and7_01

value: barcodes:X1A, X1B


title: lumlo_t0_wt_M00399832

value: Mammary Gland


title: COLLAB6and7_01_INPUT


title: lumhi_t0_wt_M00394900


title: PLWH_DonorE_ART+dCA

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:
Autologous HIV - Kessing Study
Kessing_Study_Exp630_tpms.txt

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

tag: treatment

value: ART+50nM dCA


title: N2-RL5-56

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

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

value: Caucasian

value: Female

value: lumbar 5


title: N2-RL5-61


title: endo_t0_wt_M00381049

value: endothelial

tag: timepoint


title: N2-RL5-55

tag: donor id


title: PLWH_DonorE_ART

value: ART


title: Sinus node,alectinib, replicate 3

city: Jinan

first: Guoxuan

address: qingdao road 6699

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: mRatBN7.2
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample

organism: Rattus norvegicus

source_name: Sinus node

extract_protocol:
Total RNA was extracted from tissues using Trizol (Invitrogen).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified  (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Male SD rats aged 7-8 weeks were given alectinib (10 mg/kg/day) by gavage for 7 days. The control rats were given solvent only by gavage.

value: Sinus node

tag: strain

value: SD

tag: Sex

value: male

value: Wild type

value: alectinib gavage


title: N2-RL5-54

city: Philadelphia

first: Huasheng

address: 3610 Hamilton Walk

institute: University of Pennsylvania

tag: age(years)

tag: race

tag: gender


title: Sinus node,alectinib, replicate 2


title: PLWH_DonorD_ART+dCA


title: basal_t0_wt_M00373181

value: basal

value: wt

value: Nulliparous


title: PLWH_DonorD_ART


title: stromal_t4_ko_M00504337

value: Mammary Gland

value: stromal

value: Lacation day 2


title: N2-RL5-53

value: Dorsal root ganglia

tag: region

tag: sequencing batch


title: lumlo_t4_ko_M00490577

value: luminal differentiated  cells


title: Sinus node,control, replicate 4

value: vehicle gavage


title: PLWH_DonorC_ART

value: memory CD4+ T cells


title: N2-RL5-57

value: Caucasian

value: Female

value: lumbar 5


title: N2-RL5-52


title: N2-RL5-51


title: PLWH_DonorC_ART+dCA

value: ART+50nM dCA


title: Sinus node,control, replicate 3

value: Sinus node

value: SD

value: male


title: PLWH_DonorB_ART+dCA


title: endo_t4_ko_M00471543

value: endothelial


title: basal_t4_wt_M00483956

value: basal

value: wt


title: Sinus node,alectinib, replicate 4

value: Wild type

value: alectinib gavage


title: PLWH_DonorB_ART

value: ART


title: N2-RL5-49

value: Dorsal root ganglia


title: Sinus node,control, replicate 2


title: Sinus node,control, replicate 1

value: Vehicle gavage


title: stromal_t4_wt_M00460358

value: Mammary Gland

value: stromal

value: Lacation day 2


title: PLWH_DonorA_ART+dCA

value: memory CD4+ T cells


title: Sinus node,alectinib, replicate 1


title: lumlo_t4_wt_M00460359

value: luminal differentiated  cells


title: J774_cells_UAL3

city: Medellin

first: alejandro

last: mejia

state: Antioquia

address: carrera 56A #61-24

country: Colombia

institute: University of antioquia

description:
21_1_filtered.bam
adipocytes_mice_counts.txt

data_processing:
quality control with FASTQC
Trimming of adapters and bad quality nucleotides with trimmomatic
Trimmed sequences were aligned to the reference human genome (hg19) or mm38 mouse genome using STAR
Raw counts were obtained using FeatureCounts
Normalization and gene expression analysis was performed using Deseq2 R package
Assembly: GRCh38 for human and GRCm39 for mouse
Supplementary files format and content: raw counts per sample

growth_protocol: 3T3-L1(CL-173TM) mouse pre-adipocytes were purchased from ATCC (Manassas, VA, USA). Cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) with 10% fetal bovine serum (FBS), 2mM glutamine, 1% penicillin/streptomycin, and 25 mM glucose (Growth Medium 2 – GM2) at 37°C and 5% CO2. Differentiation was induced two days postconfluence by adding GM2 containing 0.5 mM 3-isobutyl-1-methylxanthine (IBMX), 0.25 μM dexamethasone, 2 μM Rosiglitazone, and 1 μg/ml insulin. After two days of incubation, the medium was replaced with GM2 containing 1 μg/ml insulin. Two days later, the medium was replaced by GM2 and incubated for 24 hours with the different treatments. Human primary adipocyte culture was obtained from the abdominal fat of young women. Pre-adipocytes were induced into adipocytes after 100% confluence cultured in a differentiation medium (DMEM 25 mM glucose, 10% FBS, 0.5 mM IBMX, 5 μM dexamethasone, 10 μM insulin, and 2 μM Rosiglitazone) for 7 days. The cells were incubated with DMEM, 25 mM glucose, 10% SFB, and different treatments for another 24 hours.

extract_protocol: total RNA was extracted from cells with the RNeasy kit (QIAGEN, Valencia, CA, USA). RNA quality control, library construction, and RNA sequencing using the DNBseq platform were performed by BGI Americas Corporation (Cambridge, MA, USA).

treatment_protocol: Crude extract OBE100, M1, UA, OA, and UAL were reconstituted in dimethyl sulfoxide (DMSO) at 25 mg/ml (stock solution). The final concentration of the compounds in the culture medium was OBE100 50 µg/ml, M1 39 µg/ml (UA+OA+UAL mix), UA 23.8 µg/ml, OA 7 µg/ml, and UAL 8.2 µg/ml. The concentration used for the three different triterpenes, both in the mixture called M1 and individually, were those determined in the fraction called OBE100. Three independent experiments were performed, each in triplicate.

tag: cell line

value: Pre-adipocyte

value: WT

value: UAL


title: N2-RL5-48

last: Yu

value: Caucasian

value: Female

value: lumbar 5

tag: dissected soma size


title: N2-RL5-47

tag: cell identity

value: hPropr


title: PLWH_DonorA_ART

tag: cell type


title: lumhi_t4_ko_M00509904

value: luminal progenitor cells


title: lumhi_t4_wt_M00467006

value: wt


title: N2-RL5-45


title: SKUT1B-MGD-3-3

city: Neward

first: Nataki

middle: C.

last: Douglas

state: NJ

address: 185 S Orange Ave, MBS E569

department: Ob-Gyn and Women's Health

institute: Rutgers-New Jersey Medical

data_processing:
Trim galore v0.3.7
Trimmed fastq files were then aligned against human genome hg38 using STAR aligner v2.7.9a
Ribosomal RNA was detected and removed using SortMeRNA v4.3.4.
Differential analysis were performed using R package DESeq2 v1.42.0, genes with more than 2 fold change and below 0.05 adjusted pvalue were considered significant differential.
Gene set enrichment analysis was done using R package fgsea v1.28.0 against KEGG and GO database.
Heatmap was generated using R package heatmap v1.0.12.
Assembly: hg38
Supplementary files format and content: Excel spreadsheet with raw counts for each sample

growth_protocol: SK-UT-1B and SK-LMS-1 cells were maintained in EMEM with 10% fetal bovine serum (FBS) and 1% pen/strep in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested usin Rneasy mini kit (Qiagen)
Purified total RNA was used to prepare libraries following the protocol using Qiaseq Stranded RNA Library Kit with UDIand QIAseq FastSelect -rRNA HMR Kit (Qiagen INC.)for Illumina sequencing.

treatment_protocol: Cells were exposed to either MK-0752 alone, MK-0752+Gemcitabine+Docetaxel at the IC30 for 72 hours or the equivalent volume of DMSO

value: uterine leiomyosarcoma cell line

value: MK-0752, Gemcitabine, Docetaxel


title: J774_cells_UA3

description:
19_1_filtered.bam
adipocytes_mice_counts.txt

value: UA


title: endo_t2_ko_M00438677

value: Mammary Gland

value: endothelial

value: Gestation day 9.5


title: SKUT1B-MGD-3-1


title: J774_cells_M13

description:
18_1_filtered.bam
adipocytes_mice_counts.txt


title: N2-RL5-50

value: Dorsal root ganglia


title: N2-RL5-43


title: J774_cells_OBE3

description:
17_1_filtered.bam
adipocytes_mice_counts.txt

value: OBE


title: SKUT1B-DMSO-4-2

value: DMSO


title: SKUT1B-DMSO-4-1

value: WT


title: J774_cells_CONTROL ACTIVADO3

description:
16_1_filtered.bam
adipocytes_mice_counts.txt

value: Pre-adipocyte

value: Adipocyte with fat


title: N2-RL5-42

value: Caucasian

value: Female


title: N2-RL5-41

value: lumbar 5


title: stromal_t2_ko_AFGK78

value: stromal


title: lumlo_t2_ko_AFGK76

value: luminal differentiated  cells


title: SKLMS1-MK-2-3

value: uterine leiomyosarcoma cell line


title: N2-RL5-40

value: hPropr


title: J774_cells_UAL2

description:
14_1_filtered.bam
adipocytes_mice_counts.txt

value: UAL


title: SKLMS1-MK-2-2


title: endo_t2_wt_M00433264

value: Mammary Gland

value: wt


title: lumhi_t2_wt_M00439079

value: luminal progenitor cells

value: Gestation day 9.5


title: J774_cells_OA3

description:
20_1_filtered.bam
adipocytes_mice_counts.txt

value: OA


title: SKLMS1-MGD-4-2

value: MK-0752, Gemcitabine, Docetaxel


title: N2-RL5-39

value: Dorsal root ganglia


title: basal_t2_wt_M00424114

value: basal


title: SKLMS1-MGD-4-1

value: WT


title: N2-RL5-44

value: Caucasian


title: J774_cells_OA2

description:
13_1_filtered.bam
adipocytes_mice_counts.txt

value: Pre-adipocyte


title: stromal_t2_wt_M00424115


title: SKLMS1-DMSO-4-2

value: DMSO


title: N2-RL5-37

value: Female

value: lumbar 5


title: N2-RL5-38


title: J774_cells_UA2

description:
12_1_filtered.bam
adipocytes_mice_counts.txt

value: UA


title: lumlo_t0_ko_M00398657

value: luminal differentiated  cells

value: Nulliparous


title: J774_cells_M12

description:
11_1_filtered.bam
adipocytes_mice_counts.txt


title: SKLMS1-DMSO-4-1

value: uterine leiomyosarcoma cell line


title: J774_cells_CONTROL3

description:
15_1_filtered.bam
adipocytes_mice_counts.txt

value: adipocyte without fat


title: lumhi_t0_ko_M00395206

value: Mammary Gland

value: luminal progenitor cells


title: SKLMS1-DMSO-2-3


title: J774_cells_OBE2

description:
10_1_filtered.bam
adipocytes_mice_counts.txt

value: OBE


title: N2-RL5-35

value: hPropr


title: endo_t0_ko_M00384810

value: endothelial


title: J774_cells_CONTROL ACTIVADO2

description:
9_1_filtered.bam
adipocytes_mice_counts.txt

value: Adipocyte with fat


title: SKLMS1-DMSO-2-1

value: WT


title: basal_t0_ko_M00373634

value: basal


title: N2-RL5-33

value: Dorsal root ganglia

value: Caucasian


title: J774_cells_CONTROL2

description:
8_1_filtered.bam
adipocytes_mice_counts.txt

value: Pre-adipocyte


title: AML sample2, 5uM DB2115, 12hr

city: Bronx

first: Samuel

middle: John

last: Taylor

state: NY

address: 1300 Morris Park Ave, Chanin building 601

institute: Albert Einstein College of Medicine

data_processing:
library strategy: CUT&Tag (ChIP Seq)
Cleaned and trimmed reads were analyzed by FastQC for base sequence quality, GC content, N content, and sequence duplication levels.
Sequencing reads passing quality control criteria were aligned to the Homo Sapiens transcriptome (hg38) using bowtie2 aligner using the options --end-to-end --very-sensitive --no-mixed --no-discordant --phred -I 10 -X 700.
Normalized bedgraphs were generated using genomecov with a normalization factor of 1,000,000/ number of total reads.
Assembly: hg38
Supplementary files format and content: Bedgraph of each sample

source_name: hematopoietic

growth_protocol: MOLM13 & JURKAT cells were maintained in 10% FBS, 1% Pen Strep, RPMI media. Primary AML samples were maintained in StemSpan SFEMII media plus 1xCC100 growth cocktail plus 50ng/ml TPO

extract_protocol:
CUT&Tag was performed as follows, 5×10^5 cells per cell line were harvested and lightly fixed with 0.5% formaldehyde for 2 minutes. The cells were bound to Concavalin A-coated beads (Bangs laboratories) and incubated with the primary antibody at 4°C overnight. Samples were then incubated with a secondary antibody (guinea pig α-rabbit (Antibodies Online, ABIN101961)) followed by adding pre-loaded pA-Tn5 adapter complex (generated in house). Tagmentation buffer with magnesium was used to induce transposase fragmentation. And PCR based library preparation was conducted (see below).
DNA was extracted by phenol/chloroform/isoamyl alcohol and fragments were amplified with NEBNext HiFi 2x PCR Master mix and universal i5 and barcoded i7 primers for 13 cycles. AMPure XP beads (#A63880) were used for post-PCR clean-up of the libraries. Libraries were subject to 35 bp paired-end sequencing using Illumina NextSeq 500 platform with 35bp paired end reads on high output mode at the Einstein Epigenomics core. Fastq files were generated using Picard tools v2.17.1 with adapter trimming by TrimGalore v0.3.7 and QC assessment using FASTQC v0.11.4.

treatment_protocol: Cells were maintained at 1mill/ml before treatment with 5uM DB compound, or Vehicle (0.001% DMSO) for 12hrs

value: hematopoietic

value: Primary AML

value: Acute myeloid leukemia

tag: antibody

value: PU.1 antibody


title: N2-RL5-34

tag: tissue

value: Female

value: lumbar 5


title: N2-RL5-36


title: J774_cells_UAL1

description:
7_1_filtered.bam
adipocytes_mice_counts.txt

tag: genotype

value: UAL


title: J774_cells_OA1

description:
6_1_filtered.bam
adipocytes_mice_counts.txt

tag: treatment

value: OA


title: stromal_t0_wt_M00399832

value: Mammary Gland

value: stromal

value: wt

tag: timepoint

value: Nulliparous


title: AML sample2, VEH, 12hr

value: VEH


title: N2-RL5-32

tag: donor id

value: hPropr


title: lumlo_t0_wt_M00394900

value: luminal differentiated  cells


title: N2-RL5-31

value: Dorsal root ganglia

value: Caucasian


title: AML sample1, 5uM DB2115, 12hr

value: hematopoietic


title: J774_cells_UA1

description:
5_1_filtered.bam
adipocytes_mice_counts.txt

value: Pre-adipocyte

value: WT

value: UA


title: lumhi_t0_wt_M00381049

value: luminal progenitor cells


title: J774_cells_M11

description:
4_1_filtered.bam
adipocytes_mice_counts.txt


title: endo_t0_wt_M00373181

value: endothelial


title: AML sample1, VEH, 12hr

value: Primary AML

value: Acute myeloid leukemia

value: PU.1 antibody


title: MOLM13, 5uM DB2115, 12hr, GABPA

value: GABPA antibody


title: N2-RL5-29

value: Female

value: lumbar 5


title: basal_t4_ko_M00504337

value: Mammary Gland

value: basal

value: Lacation day 2


title: J774_cells_CONTROL ACTIVADO1

description:
2_1_filtered.bam
adipocytes_mice_counts.txt

value: Adipocyte with fat


title: MOLM13, VEH, 12hr, GABPA

value: VEH


title: J774_cells_OBE1

description:
3_1_filtered.bam
adipocytes_mice_counts.txt

value: OBE


title: MOLM13, 5uM DB2115, 12hr, ELF1

value: hematopoietic

value: ELF1 antibody


title: N2-RL5-26

value: Dorsal root ganglia

value: Caucasian


title: lumlo_t4_ko_M00509904

value: luminal differentiated  cells


title: stromal_t4_ko_M00490577

value: stromal


title: N2-RL5-25


title: lumhi_t4_ko_M00471543

value: luminal progenitor cells


title: JURKAT, 5uM DB2115, 12hr, FLI1

value: JURKAT

value: T cell lymphoblast

value: FLI1 antibody


title: N2-RL5-30

value: Female

value: lumbar 5


title: intestinal crypts, KO_1mo_2

city: London

first: Vivian

last: Li

address: 1 Midland Road

institute: The Francis Crick Institute

description:
ANG958A7_R1
VLDC 8.3b

data_processing:
Processed using NFCore RNASeq pipeline version 3.0, using STAR-RSEM
Generate fold-changes using DESeq2
Assembly: GRCm38/release-95
Supplementary files format and content: .genes.results' files are RSEM-STAR-quantified raw counts
Supplementary files format and content: differential' file is an excel spreadsheets of all inferential properties
Supplementary files format and content: vst' file is variance stabilised normalised counts from DESeq2

source_name: intestinal crypts

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using polyA_KAPA_mRNA_Hyper_Prep kit following manufacturer's protocols.

treatment_protocol: WT and Arid3a conditional KO animals were injected with tamoxifen for 3 consecutive days and animals were culled by S1K at 1 month after the first tamoxifen injection. Intestinal crypts were collected as previously described (Baulies et al., 2020)

value: intestinal crypts

value: KO

value: 1 month after tamoxifen


title: N2-RL5-23


title: basal_t2_ko_M00439062

value: Mammary Gland

value: basal

value: Gestation day 9.5


title: intestinal crypts, KO_1mo_4

description:
ANG958A9_R1
VLDC 10.1a


title: basal_t4_wt_M00460358

value: wt

value: Lacation day 2


title: JURKAT, VEH, 12hr, FLI1

value: hematopoietic

value: VEH


title: endo_t4_wt_M00483956

value: endothelial


title: intestinal crypts, KO_1mo_3

description:
ANG958A8_R1
VLDC 9.2a


title: JURKAT, 5uM DB2115, 12hr, GATA3

value: GATA3 antibody


title: intestinal crypts, KO_1mo_1

description:
ANG958A6_R1
VLDC 8.3a


title: N2-RL5-22

value: Dorsal root ganglia

value: Caucasian


title: N2-RL5-28

value: hPropr


title: stromal_t4_wt_M00460359

value: stromal


title: JURKAT, VEH, 12hr, GATA3

value: JURKAT

value: T cell lymphoblast


title: N2-RL5-21

value: Female

value: lumbar 5


title: lumhi_t2_ko_AFGK76

value: Mammary Gland

value: luminal progenitor cells


title: MOLM13, VEH, 12hr, ELF1

value: Acute myeloid leukemia

value: ELF1 antibody


title: intestinal crypts, WT_1mo_5

description:
ANG958A5_R1
BRGU 81.1d

value: intestinal crypts

value: WT

value: 1 month after tamoxifen


title: J774_cells_CONTROL1

description:
1_1_filtered.bam
adipocytes_mice_counts.txt

value: Pre-adipocyte

value: adipocyte without fat


title: JURKAT, 5uM DB2115, 12hr, ELF1

value: hematopoietic


title: N2-RL5-20

value: Dorsal root ganglia

value: Caucasian


title: lumhi_t2_ko_M00438677

value: Gestation day 9.5


title: N2-RL5-19


title: intestinal crypts, WT_1mo_4

description:
ANG958A4_R1
BRGU 81.1a


title: JURKAT, VEH, 12hr, ELF1

value: JURKAT

value: VEH


title: N2-RL5-24

value: Female

value: hPropr


title: endo_t2_ko_M00439062

value: Mammary Gland

value: endothelial