title: CRC05_L2_CRC08_L2

description:
Library name: CRC05_L2_CRC08_L2
HRS995185
HRX1128569
HRR1451157
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: Y0304

status: Public on Jul 29 2025

type: SRA

city: Hong Kong

first: Wing Tung

last: Lee

address: Room Y934, 9/F, Lee Shau Kee Building, The Hong Kong Polytechnic University, Hung Hom, Kowloon

department: Department of Health Technology and Informatics

country: Hong Kong

institute: The Hong Kong Polytechnic University (PolyU)

description: without MSC co-culture

library_source: transcriptomic

data_processing:
Raw reads from both RNA-seq were checked by FastQC (v0.11.8, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed by Trim Galore (v0.4.5, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
For RNA-seq data, trimmed reads were mapped to the mouse reference genome (mm10) by TopHat (v2.1.1) [68] with default parameters and Cufflinks was employed to quantify gene expression level with gene annotation obtained from Ensembl GRCm38.p5 [69].
Gene expression level was calculated in the form of fragments per kilobase million (FPKM). Genes with undetected expression level in all the samples were excluded in the following analysis.
Genome_build: mm10
Supplementary_files_format_and_content: text files include expected_count, TPM, FPKM.

molecule: total RNA

organism: Mus musculus

extract_protocol:
7 µl of soft lysis buffer containing 500 mM KCl (Sigma), 100mM pH 8.0 Tris-HCl (Sigma), 1.35 mM MgCl2 (Sigma), 4.5 mM DTT (Thermo Fisher Scientific), 0.45% Nonidet P-40 (Sigma), 0.18U SUPERase-In (Thermo Fisher) and 0.36U recombination RNase-inhibitor (Thermo Fisher) were added into each PCR tube containing a single oocyte and were incubated at 4˚C for 30 min. Then, the lysate was vortexed at room temperature for 1 min and centrifuged at 1000g for 5 min to allow the nucleus to sink to the bottom of the tube. 6.5 µl of supernatant containing RNA was carefully transferred to a new PCR tube for generating scRNA-seq library.
TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) was used for library construction.

tag: cell type

value: in vitro-matured metaphase II (IVM-MII) oocyte

tag: strain

tag: age

value: 6 weeks

tag: genotype

value: wild type

tag: co-culture

value: without MSC co-culture


title: CRC04_L4_CRC08_L1

city: Beijing

first: Ping

last: Lu

address: 5 Yiheyuan Road

country: China

institute: Peking University

description:
Library name: CRC04_L4_CRC08_L1
HRS995183
HRX1128567
HRR1451155
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz

library_source: transcriptomic single cell

data_processing:
The electronic raw signals (FAST5 data) were translated into bases (FASTQ data) using Guppy. Nanoplexer was performed on the FASTQ data to generate individual cell data of SCAN-seq based on the 24 bp barcode information. Reads with barcode mapping score below 31 were discarded. Low-quality reads (read quality score < 7) and short reads (read length < 100) were then filtered using NanoFilt. In order to obtain full-length reads, PCR anchor sequence and cell barcode sequence were identified and trimmed using Pychopper, and polyA tail was trimmed using trim_isoseq_polyA command. The full-length reads were aligned to the human reference genome (GRCh38, Ensembl, release-108) using minimap2 (v2.17) (-ax splice -uf -k14 --secondary=no --junc-bed). All bam files were consolidated into a single bam file, followed by transcriptome assembly conducted by StringTie. Transcript isoforms with coverage below 3 were subsequently eliminated.
Assembly: GRCh38
Supplementary files format and content: CRC_NewRef_LongRead_assembled_Sorted.gtf.gz includes gene/transcript annotations that have beed assembled from the long-read scRNA-seq data.
Supplementary files format and content: CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz includes the categorizaation of isoforms from SQANTI3.
Supplementary files format and content: Counts.csv.gz files include gene/isoform-level expression counts in human colorectal cancer or human colorectal cancer cell lines.
Supplementary files format and content: CRC_Metadata_Cell_Info.csv.gz includes the detailed information about each cell.

molecule: polyA RNA

organism: Homo sapiens

source_name: colorectum

extract_protocol:
Dissected tumor samples and matched normal mucosa were digested into single-cell suspension via 1.5 mg/ml collagenase type II and 1.5 mg/ml collagenase type IV, All samples treated at 37°C for 30-60 min, depending on viscosity. We used CD45 antibody and EPCAM antibody in FACS to collect CD45-EPCAM+ epithelial cells. Cells were sorted into 96-well plates containing SCAN-seq lysis buffer and stored at -80°C.
Plates were thawed and thoroughly vortexed for 60 s, and incubated at 72˚C for 3 minutes to release the linearized RNA molecules and immediately transferred them on ice. Reverse transcription and PCR amplification were performed as described before. Then, we pooled the cDNAs of different cell barcodes together and purified twice with 0.4X Ampure XP beads and 0.8X Ampure XP beads separately. A total of 500 ng to 1 ug cDNA products were used for further library construction.

tag: tissue

value: colorectum

tag: cell line

tag: crc patient_tissue_type

value: PT


title: CRC04_L3_CRC07_L4

description:
Library name: CRC04_L3_CRC07_L4
HRS995182
HRX1128566
HRR1451154
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz

value: NT


title: CRC09_L2

description:
Library name: CRC09_L2
HRS995179
HRX1128577
HRR1451165
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: CRC04_L2_CRC07_L3

description:
Library name: CRC04_L2_CRC07_L3
HRS995182
HRX1128565
HRR1451153
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: Y0303

description: without MSC co-culture


title: S3_RHI

city: Boston

first: Single Cell

last: Sequencing Core

address: 72 E. Concord St

country: USA

institute: BU Single Cell Sequencing Core

description: 10x Genomics

data_processing:
CellRanger v6.0.1 was used to align reads to the GRCH38 reference and generate filtered count matrices provided in the processed data files
Assembly: GRCH38
Supplementary files format and content: Tab-separated and matrix files with counts, feature (gene), and barcode data.
Supplementary files format and content: Tab-separated and matrix files with unfiltered counts, feature (gene), and barcode data.

molecule: nuclear RNA

source_name: Dorsolateral Frontal Cortex - Brain

extract_protocol:
Nuclei isolation and sorting were performed on two donor samples per day, randomizing for diagnosis and age. Tissue was kept on ice throughout nuclei isolation. Tissue was homogenized and lysed in NST Buffer with DAPI (146mM NaCl, 10mM Tris, 1mM CaCl2, 21mM MGCl2, 0.1%BSA, 0.1% NP-40, 40U/ml Protector RNase Inhibitor, DAPI) and snipped with scissors on ice for 10 minutes. Debris was removed using a 70μm filter. Cells were spun down and resuspended in nuclei storage buffer (2% BSA, 400U/mL Protector RNase Inhibitor) to reach a concentration of 500-1000 nuclei/μL. Nuclei were purified for DAPI positive cells with a FACS-Aria flow cytometer to remove debris
Library was performed according to the manufacturer's instructions (single cell 3' V2 protocol, 10xGenomics). Briefly, nuclei were combined with the master mix at the correct dilution and loaded with partitioning oil and gell beads into the chip to generate the gel bead emulsion or GEMs. Retrotranscription was performed to create cDNA from the RNA in the beads, with primer sequences and unique molecular identifier (UMI) barcodes, and the 10x genomics barcode included. Pooled barcoded cDNA was put through the 10x library prep protocol which includes amplification with PCR, SPRI bead cleanups for size selections and addition of paired end constructs and sample indices.
single nucleus RNA sequencing

value: Dorsolateral Frontal Cortex - Brain

value: RHI


title: S2_CTE

description: 10x Genomics

value: CTE


title: S8_Control

description: 10x Genomics

value: Control


title: CRC04_L1_CRC07_L2

description:
Library name: CRC04_L1_CRC07_L2
HRS995182
HRX1128564
HRR1451152
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: Y0103

description: without MSC co-culture


title: Y0301

description: without MSC co-culture

value: germinal vesicle (GV) oocyte


title: S1_CTE

description: 10x Genomics


title: CRC03_L3_CRC07_L1

description:
Library name: CRC03_L3_CRC07_L1
HRS995181
HRX1128563
HRR1451151
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: GL_BM

city: Bronx

first: Jinan

last: Behnan

state: New York

address: 1300 Morris Park Avenue

department: The Leo M. Davidoff Department of Neurological Surgery, Department of Microbiology & Immunology

institute: Albert Einstein College of Medicine

data_processing:
Data demultiplexing, barcode processing, gene counting and aggregating was performed on Cell Ranger version v.7.0.1. The generated .h5 matrices were subsequently processed in Scanpy and Seurat.
Assembly: mm10
Supplementary files format and content: comma-separated matrix file

source_name: Bone Marrow

extract_protocol:
Skull marrow and Bone marrow samples from i.c. GL261 or SB28 injected mouse were harvested by immediate decapitation posterior to the occipital bone after perfusion with ice-cold HBSS. The drilling site for the intracranial surgery was discarded to avoid mechanical disruption or contamination related to tumor induction.  Bone Marrow was chopped into fine pieces on a glass slide. For both types of samples, single cell suspensions were prepared using enzymatic digestion (50% TrypLE (ThermoFisher), 50% Collagenase Type VII-S (Sigma-Aldrich)). Samples were incubated for 10 minutes at 37 degree C, pipetted gently using wide tips, and filtered onto 70 micron cell strainer. Cold Hibernate-E medium (ThermoFisher) with 4% BSA was used for sample collection, washing and resuspension. Cells were sorted using FACS Aria-II to clear debris and dead cells. Sorted cells with viability >70% were kept on ice until processed for library within 1-3 hours.
scRNAseq libraries were constructed by the Albert Einstein Genomics Core using the 3’ kit protocols of 10X Genomics processed on a Chromium Chip B microfluidic apparatus (10X Genomics).

value: Bone Marrow


title: S5_RHI

description: 10x Genomics


title: MGG4 input, BRD9, ChIP

city: Hangzhou

first: Zhilin

last: Long

address: No. 600 Dunyu Road Sandun Town

institute: Westlake University

library_source: genomic

data_processing:
Raw sequencing reads were trimmed using fastp (v0.23.2) to remove adapters and then aligned to the GRCh38 human genome using Bowtie2 (v2.4.5). All reads with MAPQ < 30 or mapping to the mitochondrial were removed using samtools (v1.16.1). PCR duplicates were removed using PicardTools MarkDuplicates (v2.27.4). Peaks were identified using MACS2 (v2.2.7.1). Normalized BigWig files were generated by DeepTools (v3.5.2), and the genome tracks were visualized in IGV.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

growth_protocol: Neurobasal™-A Medium without phenol red supplemented with B-27™ supplement , 20 ng/mL recombinant human EGF protein , 20 ng/mL recombinant human FGF basic protein, 1% penicillin/streptomycin, 1% sodium pyruvate, and 1% GlutaMax™ supplement at 37°C in an incubator with 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using Bioruptor Pico (Diagenode).
ChIP-seq libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina complemented with the NEBNext Multiplex Oligos for Illumina. 2-5 ng of DNA was used as starting material for input and IP sample. Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were purified using AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

tag: chip antibody

value: input

value: Human glioblastoma cell line

tag: treatment


title: CRC05_L1_CRC07_L5

description:
Library name: CRC05_L1_CRC07_L5
HRS995184
HRX1128568
HRR1451156
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: Y0102

description: without MSC co-culture


title: GL_sk

source_name: Skull Marrow

value: Skull Marrow


title: CRC03_L2_CRC06_L5

description:
Library name: CRC03_L2_CRC06_L5
HRS995174
HRX1128562
HRR1451150
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: MGG4 sgBRD9, BRD9, ChIP

value: BRD9 (Active motif, #91413)


title: MGG4 sgNT, BRD9, ChIP

value: sgNT


title: CRC03_L1_CRC06_L4

description:
Library name: CRC03_L1_CRC06_L4
HRS995174
HRX1128561
HRR1451149
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: Immortalized HCASMC cell line, siRNA IFIH1, calcification 7 days, replicate 3

city: Stanford

first: Chad

middle: S

last: Weldy

state: CA

address: 870 Quarry Road, CVRC Falk

department: Medicine, Cardiovascular Medicine

institute: Stanford University

description:
C12_1
featureCountsCalcification.txt

data_processing:
RNAseq data were processed using a workflow starting from fastq files and code is available on github (https://github.com/zhaoshuoxp/Pipelines-Wrappers/blob/master/RNAseq.sh). In brief, the quality control was performed using FastQC, mapping to the human genome hg19/GRCh37 was performed using STAR second pass mapping to increase the percentage of mapped reads, and counting was done with featureCounts using GENCODE gtf annotation. Next, differential analysis was performed using DESeq2.
Assembly: hg19
Supplementary files format and content: tab-delimited text file including raw featureCounts for each sample

source_name: 2105 hTert HCASMC

growth_protocol: Cells were cultured in smooth muscle growth medium (Lonza; catalog number: CC-3182) supplemented with human epidermal growth factor, insulin, human basic fibroblast growth factor and 5% FBS, according to the manufacturer’s instructions. All HCASMC lines were used at passages 4–8. HCASMCs immortalized with hTert transgene were acquired from Dr. Clint Miller (UVA) were used for all calcification assays with HCASMCs between passages 31 and 35.

extract_protocol:
RNA was isolated from disrupted HCASMC cells using standard RNeasy mini kit protocol (Qiagen).
Isolated RNA underwent quality assessment, cDNA conversion, and library construction by Novogene (San Jose, CA).

treatment_protocol: siRNA knockdowns were performed using Lipofectamine RNAiMax (Life Technologies) using manufacturer’s recommended protocol at 50pg siRNA / 100,000cells.

value: 2105 hTert HCASMC

value: Human coronary artery SMC

value: IFIH1 KD

value: Calcification medium

tag: time point

value: 7 days


title: CRC02_L4_CRC06_L3

description:
Library name: CRC02_L4_CRC06_L3
HRS995173
HRX1128560
HRR1451148
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz

value: colorectum

value: NT


title: Myobacterium tuberculosis, UNT, 24 hrs, Biological Replicate 3, Technical Replicate 3

first: Bree

last: Aldridge

state: Massachusetts

address: 136 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts University

data_processing:
Reads were aligned to GCF_000350205.1 using BWA. Aligned reads were then sorted and indexed with samtools (v1.9) using the commands “samtools sort -l 0” and “samtools index”. Gene-level counts were obtained from the sorted, genome-mapped reads using the python-based package HTSeq (v0.13.5).
Assembly: GCF_000350205.1
Supplementary files format and content: tab-deliminated text file of raw counts for each Mycobacterium tuberculosis Erdman locus tag

organism: Mycobacterium tuberculosis

source_name: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

growth_protocol: Mtb strain Erdman with plasmid pMV306hsp+LuxG13 were adapted to a cholesterol in-vitro growth condition prior to drug exposure and RNA extraction. Briefly, Mtb were first cultured in standard growth medium consisting of 7H9 broth, (ThermoFisher; DF0713-17-9), 0.2% glycerol, 10% OADC (0.5g/L oleic acid, 50g/L albumin, 20g/L dextrose and 0.04g/L catalase), and 0.05% Tween-80 and then subcultured at least once prior to cholesterol adaptation. Once the bacterial cultures reached an OD600nm ~0.5, the cultures were diluted to an OD600nm of 0.05 in cholesterol growth medium consisting of 7H9 powder (4.7g/L), fatty acid-free BSA (0.5g/L), NaCl (100mM) and tyloxapol (0.05%). Cultures were then subcultured once more in the same media after reaching mid-log phase (OD600nm ∼0.5-0.7). Then, the cultures were subcultured to 0.05 OD in 50ml conical tubes containing the cholesterol growth media and their respective drug. All cultures were buffered with 100 mM 3-(N-morpholino)propanesulfonic acid at pH 7.

extract_protocol:
Drug-treated cultures and untreated controls were then harvested by centrifugation at timepoints 4, and 24 hours post drug treatment. To halt transcriptional responses during the RNA extraction process, GTC buffer was added to the cultures and they were washed twice in GTC buffer. The resulting pellets were stored in Eppendorf tubes containing ~1ml of GTC buffer (4M guanidinium thiocyanate) + 0.5% sarcosyl, 25 mM sodium citrate and 0.1M beta-mercaptoethanol. Samples were stored in aerosol tight O-ring caps at -80°C until RNA extractions were performed. On the day of extraction, the frozen GTC treated pellets were thawed at 37 degrees, harvested by centrifugation, resuspended in prewarmed triazole and transferred to 2ml O-ring tubes containing sterile zirconia beads. The triazole mixture was then bead beaten twice followed by the addition of chloroform and vigorous shaking for one minute. The samples were then centrifuged, and the aqueous layer was removed and placed in Qiagen RNeasy columns for RNA cleanup. Genomic DNA was removed from all samples through a DNAse digest on the columns prior to elution in pre-warmed RNase free water. The resulting RNA was then removed from the BSL-3 facility. Concentration and quality of RNA (260nm/280nm absorbance) was assessed using a nanodrop spectrophotometer and stored at -80°C until sample submission.
Samples were submitted to the Broad Institute MOCP for sequencing, where they performed QC, library preparation, ribodepletion and paired-end sequencing on the Illumina NovaSeq 6000 following a modified version of the RNAtag-Seq method.

treatment_protocol: Cultures were treated with 1x the IC90 of the drug. Cells were then harvested by centrifugation at timepoints 4, and 24 hours post drug treatment.

value: 24 hrs

value: UNT


title: rep3-MonocultureTTX2

first: Carlos Alberto

middle: Oliveira de

last: Biagi Junior

state: MA

address: 360 Longwood Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

data_processing:
Fastq files were generated using bcl2fastq software (Illumina) as part of CellRanger v7.1.0 pipeline (10x Genomics) using mkfastq command
Fastq files processed using CellRanger v7.1.0 pipeline (10x Genomics), mapping was done to a customized mm10 version of mouse genome including GFP sequence.
Assembly: mm10
Supplementary files format and content: tab-delimited text files with filtered_gene_bc_matrices

source_name: SCLC cell lines single-cell

extract_protocol:
A single-cell suspension from cultured 16T-mGFP SCLC neurospheres was prepared in sterile HBSS immediately before surgery. Animals at postnatal day (P) 21–35 were anaesthetized with 1–4% isoflurane and placed in a stereotactic apparatus. The cranium was exposed via midline incision under aseptic conditions. 70,000 cells in 3 μL sterile HBSS were stereotactically injected into the M2 region of the cortex through a 31-gauge burr hole using a digital pump at infusion rate of 0.4 μL min−1 and 31-gauge Hamilton syringe. Stereotactic coordinates for Thy1-Chr2 animal allografts used were as follows: 0.5 mm lateral to midline, 1.0 mm anterior to bregma, −1.5 mm deep to cortical surface. At the completion of infusion, the syringe needle was allowed to remain in place for a minimum of 2 min, then withdrawn at a rate of 0.875 mm min−1 to minimize backflow of the injected cell suspension. To generate animals with interneuron-specific expression of light-sensitive ion channels, 1 μl of AAV8-Dlx-ChRmine-p2A-mCherry (virus titer=6.9E+12) (a gift from Dr. Karl Deisseroth from Stanford University; Chen et al., 449 2020, Nature Biotech) was unilaterally injected using Hamilton Neurosyringe and 450 Stoelting stereotaxic injector over 5 minutes. These animals then received allografts of 16T-mGFP SCLC cells as described above at 0.8 mm lateral to midline, 1.0 mm anterior to bregma, -1.2 mm deep to the cortical surface. Allografts of 16T-mGFP-ChR2 SCLC cells were performed following the procedure as above with exception for the following alterations: 15,000 cells were injected in 1 μL sterile HBSS 0.8 mm lateral to midline, 1.0 mm anterior to bregma, −1.2 mm deep to cortical surface. For electrophysiology experiments and EM tissue analysis, 16T-mGFP cells were allografted into the CA1 region of the hippocampus at the following coordinates: 1.5 mm lateral to midline, 1.8 mm posterior to bregma, -1.35 mm deep to the cortical surface. The cells were harvested and processed FACS for single cells, then lysed and combined into droplets with barcoded beads which captured the mRNA then used for reverse transcription with the The Chromium Single Cell Gene Expression platform (10x Genomics) per manufacturer's instructions.
We then followed the rest of the 10x standard or high-throughput protocols and used the Dual Index Kit TT Set A for library production. 16T SCLC cells were cultured alone or in neuron co-cultures with or without 1 μM TTX for 24 hours per protocol below and harvested in PBS 0.5% BSA, 1mM EDTA (Invitrogen), 1x DNAse (Worthington Biochemical). GFP-negative cells were harvested in parallel to serve as negative control during FACS sorting. Calcein violet (Thermo Fisher) was used to label live cells. GFP+ Calcein+ cells were sorted and collected and processed for scRNA sequencing.

value: SCLC cell lines single-cell

tag: replicate

tag: culture

value: MonocultureTTX


title: Myobacterium tuberculosis, UNT, 4 hrs, Biological Replicate 3, Technical Replicate 3

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: 4 hrs


title: CRC02_L3_CRC06_L2

description:
Library name: CRC02_L3_CRC06_L2
HRS995173
HRX1128559
HRR1451147
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz

value: PT


title: CRC02_L2_CRC06_L1

description:
Library name: CRC02_L2_CRC06_L1
HRS995173
HRX1128558
HRR1451146
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: Y0101

description: without MSC co-culture

value: germinal vesicle (GV) oocyte

value: 6 weeks

value: wild type

value: without MSC co-culture


title: Myobacterium tuberculosis, UNT, 0 hrs, Biological Replicate 3, Technical Replicate 3

value: 0 hrs


title: rep3-MonocultureTTX1


title: SB_BM

value: Bone Marrow


title: Immortalized HCASMC cell line, siRNA IFIH1, calcification 7 days, replicate 2

description:
C11_1
featureCountsCalcification.txt

value: 2105 hTert HCASMC

value: Human coronary artery SMC

value: IFIH1 KD

value: Calcification medium


title: rep3-CocultureTTX2

value: CocultureTTX


title: Immortalized HCASMC cell line, siRNA IFIH1, calcification 7 days, replicate 1

description:
C10_1
featureCountsCalcification.txt

value: 7 days


title: rep3-CocultureTTX1

value: SCLC cell lines single-cell


title: CRC01_L3

description:
Library name: CRC01_L3
HRS995172
HRX1128555
HRR1451143
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz

value: colorectum


title: Myobacterium tuberculosis, UNT, 24 hrs, Biological Replicate 2, Technical Replicate 3

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: 24 hrs

value: UNT


title: CRC01_L4

description:
Library name: CRC01_L4
HRS995172
HRX1128556
HRR1451144
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz

value: PT


title: Immortalized HCASMC cell line, siRNA ADAR1 IFIH1, calcification 7 days, replicate 3

description:
C09_1
featureCountsCalcification.txt

value: ADAR1 & IFIH1 KD


title: Immortalized HCASMC cell line, siRNA ADAR1 IFIH1, calcification 7 days, replicate 2

description:
C08_1
featureCountsCalcification.txt


title: Myobacterium tuberculosis, UNT, 0 hrs, Biological Replicate 2, Technical Replicate 3


title: rep3-Monoculture

value: Monoculture


title: rep3-Coculture

value: Coculture


title: Myobacterium tuberculosis, UNT, 4 hrs, Biological Replicate 2, Technical Replicate 3

value: 4 hrs


title: CRC01_L2

description:
Library name: CRC01_L2
HRS995172
HRX1128554
HRR1451142
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: Myobacterium tuberculosis, UNT, 24 hrs, Biological Replicate 1, Technical Replicate 3


title: Immortalized HCASMC cell line, siRNA ADAR1 IFIH1, calcification 7 days, replicate 1

description:
C07_1
featureCountsCalcification.txt


title: Immortalized HCASMC cell line, siRNA ADAR1, calcification 7 days, replicate 3

description:
C06_1
featureCountsCalcification.txt

value: ADAR1 KD


title: rep2-MonocultureTTX

value: MonocultureTTX


title: rep2-CocultureTTX


title: CRC01_L1

description:
Library name: CRC01_L1
HRS995172
HRX1128553
HRR1451141
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz

value: NT


title: rep2-Monoculture


title: Immortalized HCASMC cell line, siRNA ADAR1, calcification 7 days, replicate 1

description:
C04_1
featureCountsCalcification.txt

value: 2105 hTert HCASMC

value: Human coronary artery SMC


title: Immortalized HCASMC cell line, siRNA ADAR1, calcification 7 days, replicate 2

description:
C05_1
featureCountsCalcification.txt

value: Calcification medium


title: Myobacterium tuberculosis, UNT, 0 hrs, Biological Replicate 1, Technical Replicate 3

value: 0 hrs


title: rep2-Coculture

value: SCLC cell lines single-cell


title: Myobacterium tuberculosis, UNT, 4 hrs, Biological Replicate 1, Technical Replicate 3


title: Germ line_yki RNAi_Late_3

city: Cambridge

first: Shreeharsha

last: Tarikere

address: 16 Divinity Avenue, Biolabs

department: Organismic and Evolutionary Biology

institute: Harvard University

data_processing:
Reads from multiplexed samples pooled in a lane were demultiplexed and trimmed (of adapters) using the bcl2fastq2 v2.2 pipeline to yield final fastq files.
The reads in the fastq files were aligned with RSEM (v1.3.3) using STAR aligner (v2.7.6a)
Differential Expression analysis: Gene counts in each dataset were normalized with the variance stabilizing transformation (vst) method implemented in the DESeq2 (v1.26.0)
Assembly: Drosophila melanogaster FlyBase version dmel_r6.36_FB2020_05
Supplementary files format and content: Tab-delimited text files include the number of raw counts for each biological sample. Files with long-format and metadata information are provided.

organism: Drosophila melanogaster

source_name: Ovary: Germ line Tissue 120h AEL

growth_protocol: Drosophila larvae and adult were reared at 25°C at 60% humidity with food containing yeast.

extract_protocol:
sorted cells in Trizol were processed through Zymo RNA Micro-Prep kit (Zymo Research R2060) for RNA extraction.
Poly A selection was done using Takara PrepX mRNA-8 (Takara 640098) protocol. cDNA libraries were prepared with Takara PrepX mRNA-8 (Takara 640096) protocol. Libraries were amplified for 15 cycles in PCR with sample specific PrepX Index primers and sequenced in 50bp single end runs on a Illumina HiSeq 2500.

treatment_protocol: hpo and yki RNAi knockdowns in three stages (early, mid, late ) of somatic and germ line cells of ovaries. Each stage/treatment has three replicates except early germline knockdowns, which only have one replicate. Ovaries were dissociated with a sequential lysis using 0.25% Trypsin (Thermo Fisher 25200056) and 2.5% Liberase (Sigma 5401119001) for ten minutes each. GFP positive somatic and germline cells were sorted using FACS directly into 100-200µl of Trizol.

value: Ovary:Germ line Tissue 120h AEL

tag: developmental stage

value: White Pupae 120h AEL

value: Germ line tissue

value: nos:GAL4>UAS yki RNAi, UAS GFP

value: _rnai:yki RNAi


title: CRC02_L1

description:
Library name: CRC02_L1
HRS995173
HRX1128557
HRR1451145
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz

value: colorectum

value: PT


title: Immortalized HCASMC cell line, siRNA control, calcification 7 days, replicate 3

description:
C03_1
featureCountsCalcification.txt

value: Control

value: 7 days


title: Germ line_yki RNAi_Late_2


title: Myobacterium tuberculosis, SAN, 24 hrs, Biological Replicate 3

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: 24 hrs

value: SAN


title: rep1-Monoculture

value: Monoculture


title: Myobacterium tuberculosis, GSK286, 24 hrs, Biological Replicate 3


title: SB_sk

extract_protocol:
Skull marrow samples from Sham and i.c. SB28 injected mouse were harvested by immediate decapitation posterior to the occipital bone after perfusion with ice-cold HBSS. The drilling site for the intracranial surgery was discarded to avoid mechanical disruption or contamination related to tumor induction.  Single cell suspension was prepared using enzymatic digestion (50% TrypLE (ThermoFisher), 50% Collagenase Type VII-S (Sigma-Aldrich)). Samples were incubated for 10 minutes at 37 degree C, pipetted gently using wide tips, and filtered onto 70 micron cell strainer. Cold Hibernate-E medium (ThermoFisher) with 4% BSA was used for sample collection, washing and resuspension. Cells were sorted using FACS Aria-II to clear debris and dead cells. Sorted cells with viability >70% were kept on ice until processed for library within 1-3 hours.
scRNAseq libraries were constructed by the Albert Einstein Genomics Core using the 3’ kit protocols of 10X Genomics processed on a Chromium Chip B microfluidic apparatus (10X Genomics).

value: Skull Marrow


title: Myobacterium tuberculosis, GSK839, 24 hrs, Biological Replicate 3


title: Immortalized HCASMC cell line, siRNA control, calcification 7 days, replicate 1

description:
C01_1
featureCountsCalcification.txt

value: 2105 hTert HCASMC

value: Human coronary artery SMC

value: Calcification medium


title: Germ line_yki RNAi_Mid_4

source_name: Ovary: Germ line Tissue 96h AEL

value: Ovary:Germ line Tissue 96h AEL

value: III instar Larvae 96h AEL


title: rep1-Coculture

value: SCLC cell lines single-cell

value: Coculture


title: Germ line_yki RNAi_Late_1

value: Ovary:Germ line Tissue 120h AEL

value: White Pupae 120h AEL

value: Germ line tissue

value: nos:GAL4>UAS yki RNAi, UAS GFP

value: _rnai:yki RNAi


title: Immortalized HCASMC cell line, siRNA control, calcification 7 days, replicate 2

description:
C02_1
featureCountsCalcification.txt

value: Control

value: 7 days


title: Germ line_yki RNAi_Mid_3


title: Immortalized HCASMC cell line, siRNA IFIH1, control 7 days, replicate 3

description:
A12_1
featureCountsCalcification.txt

value: IFIH1 KD

value: Control medium


title: Myobacterium tuberculosis, KRS, 24 hrs, Biological Replicate 3

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: 24 hrs

value: KRS


title: Myobacterium tuberculosis, TBI, 24 hrs, Biological Replicate 3

value: TBI


title: Sham_sk

value: Skull Marrow


title: Germ line_yki RNAi_Mid_2

value: Ovary:Germ line Tissue 96h AEL

value: III instar Larvae 96h AEL


title: Immortalized HCASMC cell line, siRNA IFIH1, control 7 days, replicate 2

description:
A11_1
featureCountsCalcification.txt

value: 2105 hTert HCASMC

value: Human coronary artery SMC


title: Myobacterium tuberculosis, TBA, 24 hrs, Biological Replicate 3

value: TBA


title: Germ line_yki RNAi_Early_1

source_name: Ovary: Germ line Tissue 72h AEL

value: Ovary:Germ line Tissue 72h AEL

value: III instar Larvae 72h AEL

value: Germ line tissue


title: Normal_2nd_001

city: Montreal

first: Fiona

last: Chan Pak Choon

state: QC

address: 3755 Côte-Sainte-Catherine

department: Human Genetics

country: Canada

institute: McGill University

description:
Library name: Normal_2nd_001_E-A02
FFPE spatial transcriptome sequencing

data_processing:
Data collected from the selected 28 PanCK+ areas of illumination (AOIs) was filtered, normalized (Q3), and analysed on the GeoMx DSP data analysis platform (GeomxTools 3.10.0 and GeoMxWorkflows 1.12.0)
Assembly: GRCh38.p13
Supplementary files format and content: Sample.dcc: Raw digital count data file generated by GeoMx DSP for each ROI
Supplementary files format and content: Hs_R_NGS_WTA_v1.0.pkc: Annotation file for the Whole Transcriptome Atlas (WTA v1.0) panel (GRCh38)
Supplementary files format and content: Sample_APC_Q3_matrix.xlsx: Processed expression matrix containing gene-level Q3-normalized counts across ROIs
Library strategy: Spatial Transcriptomics

extract_protocol:
4um sections from three FFPE blocks containing the proband’s BCACs (parotid and submandibular), BCA, IDH and normal salivary tissue were mounted on a single glass slide
Spatial transcriptome sequencing libraries were prepared using the NanoString GeoMx Digital Spatial Profiler (DSP) platform according to the manufacturer's protocol.


title: S11_RHI

description: 10x Genomics

value: Dorsolateral Frontal Cortex - Brain

value: RHI


title: Germ line_hpo RNAi_Late_4

value: Ovary:Germ line Tissue 120h AEL

value: White Pupae 120h AEL

value: nos:GAL4>UAS hpo RNAi, UAS GFP

value: _rnai:hpo RNAi


title: Immortalized HCASMC cell line, siRNA IFIH1, control 7 days, replicate 1

description:
A10_1
featureCountsCalcification.txt

value: IFIH1 KD

value: Control medium

value: 7 days


title: Myobacterium tuberculosis, SAN, 4 hrs, Biological Replicate 3

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: 4 hrs

value: SAN


title: Myobacterium tuberculosis, SFN, 24 hrs, Biological Replicate 3

value: 24 hrs

value: SFN


title: Normal_027

description:
Library name: Normal_027_F-C11
FFPE spatial transcriptome sequencing


title: Immortalized HCASMC cell line, siRNA ADAR1 IFIH1, control 7 days, replicate 3

description:
A09_1
featureCountsCalcification.txt

value: 2105 hTert HCASMC

value: Human coronary artery SMC

value: ADAR1 & IFIH1 KD


title: Germ line_hpo RNAi_Late_2

value: Germ line tissue


title: Normal_026

description:
Library name: Normal_026_F-C09
FFPE spatial transcriptome sequencing


title: Normal_025

description:
Library name: Normal_025_F-C07
FFPE spatial transcriptome sequencing


title: Normal_024

description:
Library name: Normal_024_F-C05
FFPE spatial transcriptome sequencing


title: Myobacterium tuberculosis, GSK286, 4 hrs, Biological Replicate 3


title: Germ line_hpo RNAi_Late_1


title: Immortalized HCASMC cell line, siRNA ADAR1 IFIH1, control 7 days, replicate 1

description:
A07_1
featureCountsCalcification.txt


title: Germ line_hpo RNAi_Mid_4

value: Ovary:Germ line Tissue 96h AEL

value: III instar Larvae 96h AEL


title: Myobacterium tuberculosis, GSK839, 4 hrs, Biological Replicate 3


title: Myobacterium tuberculosis, KRS, 4 hrs, Biological Replicate 3

value: KRS


title: BCAC_submand_022

description:
Library name: BCAC_submand_022_F-C03
FFPE spatial transcriptome sequencing


title: Myobacterium tuberculosis, TBI, 4 hrs, Biological Replicate 3

value: TBI


title: Immortalized HCASMC cell line, siRNA ADAR1 IFIH1, control 7 days, replicate 2

description:
A08_1
featureCountsCalcification.txt


title: Germ line_hpo RNAi_Mid_1

value: nos:GAL4>UAS hpo RNAi, UAS GFP

value: _rnai:hpo RNAi


title: Immortalized HCASMC cell line, siRNA ADAR1, control 7 days, replicate 2

description:
A05_1
featureCountsCalcification.txt

value: ADAR1 KD

value: Control medium


title: Immortalized HCASMC cell line, siRNA ADAR1, control 7 days, replicate 1

description:
A04_1
featureCountsCalcification.txt

value: 7 days


title: Germ line_hpo RNAi_Early_1

value: Ovary:Germ line Tissue 72h AEL

value: III instar Larvae 72h AEL


title: BCAC_submand_021

description:
Library name: BCAC_submand_021_F-C02
FFPE spatial transcriptome sequencing


title: Immortalized HCASMC cell line, siRNA control, control 7 days, replicate 3

description:
A03_1
featureCountsCalcification.txt

value: Control


title: Myobacterium tuberculosis, SFN, 4 hrs, Biological Replicate 3

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: 4 hrs

value: SFN


title: Immortalized HCASMC cell line, siRNA control, control 7 days, replicate 2

description:
A02_1
featureCountsCalcification.txt

value: 2105 hTert HCASMC

value: Human coronary artery SMC


title: Somatic_yki RNAi_Late_3

source_name: Ovary: Somatic Tissue 120h AEL

value: Ovary:Somatic Tissue 120h AEL

value: White Pupae 120h AEL

value: Somatic tissue

value: bab:GAL4>UAS yki RNAi, UAS GFP

value: _rnai:yki RNAi


title: BCAC_submand_020

description:
Library name: BCAC_submand_020_F-C01
FFPE spatial transcriptome sequencing


title: BCAC_parotid_019

description:
Library name: BCAC_parotid_019_F-B12
FFPE spatial transcriptome sequencing


title: Myobacterium tuberculosis, UNT, 24 hrs, Biological Replicate 3, Technical Replicate 2

value: 24 hrs

value: UNT


title: Somatic_yki RNAi_Late_2


title: BCAC_parotid_018

description:
Library name: BCAC_parotid_018_F-B11
FFPE spatial transcriptome sequencing


title: Immortalized HCASMC cell line, siRNA control, control 7 days, replicate 1

description:
A01_1
featureCountsCalcification.txt

value: Control medium


title: BCAC_submand_023

description:
Library name: BCAC_submand_023_F-C04
FFPE spatial transcriptome sequencing


title: Immortalized HCASMC cell line, siRNA ADAR1, control 7 days, replicate 3

description:
A06_1
featureCountsCalcification.txt

value: ADAR1 KD

value: 7 days


title: Germ line_hpo RNAi_Mid_3

value: Ovary:Germ line Tissue 96h AEL

value: III instar Larvae 96h AEL

value: Germ line tissue

value: nos:GAL4>UAS hpo RNAi, UAS GFP

value: _rnai:hpo RNAi


title: Somatic_yki RNAi_Late_1


title: Myobacterium tuberculosis, UNT, 4 hrs, Biological Replicate 3, Technical Replicate 2

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: 4 hrs


title: BCAC_parotid_017

description:
Library name: BCAC_parotid_017_F-B10
FFPE spatial transcriptome sequencing


title: Myobacterium tuberculosis, UNT, 0 hrs, Biological Replicate 3, Technical Replicate 2

value: 0 hrs


title: Somatic_yki RNAi_Mid_3

source_name: Ovary: Somatic Tissue 96h AEL

value: Ovary:Somatic Tissue 96h AEL


title: Myobacterium tuberculosis, TBA, 4 hrs, Biological Replicate 3

value: TBA


title: Primary HCASMC cells, siRNA ADAR1 IFIH1, serum stimulated  48 hrs, replicate 2

description:
B8
featureCountsPhenotypic.txt

source_name: 1508 HCASMC

value: 1508 HCASMC

value: Human coronary artery SMC

value: ADAR1 & IFIH1 KD

value: Serum stimulated

value: 48 hrs


title: Myobacterium tuberculosis, UNT, 24 hrs, Biological Replicate 2, Technical Replicate 2

value: 24 hrs

value: UNT


title: BCAC_parotid_016

description:
Library name: BCAC_parotid_016_F-B09
FFPE spatial transcriptome sequencing


title: Somatic_yki RNAi_Mid_2

value: Somatic tissue

value: bab:GAL4>UAS yki RNAi, UAS GFP

value: _rnai:yki RNAi


title: Primary HCASMC cells, siRNA ADAR1 IFIH1, serum stimulated 48 hrs, replicate 1

description:
B7
featureCountsPhenotypic.txt


title: BCAC_parotid_015

description:
Library name: BCAC_parotid_015_F-B08
FFPE spatial transcriptome sequencing


title: Somatic_yki RNAi_Mid_1

value: III instar Larvae 96h AEL


title: Myobacterium tuberculosis, UNT, 0 hrs, Biological Replicate 2, Technical Replicate 2


title: Somatic_yki RNAi_Early_3

source_name: Ovary: Somatic Tissue 72h AEL

value: Ovary:Somatic Tissue 72h AEL

value: III instar Larvae 72h AEL


title: BCAC_parotid_014

description:
Library name: BCAC_parotid_014_F-B07
FFPE spatial transcriptome sequencing


title: Primary HCASMC cells, siRNA ADAR1, serum stimulated  48 hrs, replicate 3

description:
B6
featureCountsPhenotypic.txt

value: ADAR1 KD


title: Primary HCASMC cells, siRNA ADAR1, serum stimulated  48 hrs, replicate 2

description:
B5
featureCountsPhenotypic.txt


title: BCAC_parotid_013

description:
Library name: BCAC_parotid_013_F-B06
FFPE spatial transcriptome sequencing


title: Myobacterium tuberculosis, UNT, 24 hrs, Biological Replicate 1, Technical Replicate 2

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13


title: Primary HCASMC cells, siRNA ADAR1 IFIH1, serum stimulated  48 hrs, replicate 3

description:
B9
featureCountsPhenotypic.txt


title: Primary HCASMC cells, siRNA ADAR1, serum stimulated  48 hrs, replicate 1

description:
B4
featureCountsPhenotypic.txt


title: Somatic_yki RNAi_Early_1


title: BCAC_parotid_012

description:
Library name: BCAC_parotid_012_F-B05
FFPE spatial transcriptome sequencing


title: Myobacterium tuberculosis, UNT, 4 hrs, Biological Replicate 1, Technical Replicate 2

value: 4 hrs


title: Somatic_yki RNAi_Early_2


title: BCAC_submand_011

description:
Library name: BCAC_submand_011_F-B04
FFPE spatial transcriptome sequencing


title: Primary HCASMC cells, siRNA control, serum stimulated  48 hrs, replicate 3

description:
B3
featureCountsPhenotypic.txt

value: Control


title: Somatic_hpo RNAi_Late_3

value: Ovary:Somatic Tissue 120h AEL

value: White Pupae 120h AEL

value: bab:GAL4>UAS hpo RNAi, UAS GFP

value: _rnai:hpo RNAi


title: Myobacterium tuberculosis, UNT, 0 hrs, Biological Replicate 1, Technical Replicate 2

value: 0 hrs


title: Myobacterium tuberculosis, UNT, 4 hrs, Biological Replicate 2, Technical Replicate 2


title: CRC07_L8

description:
Library name: CRC07_L8
HRS995177
HRX1128574
HRR1451162
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz

value: colorectum

value: PT


title: Primary HCASMC cells, siRNA control, serum stimulated  48 hrs, replicate 2

description:
B2
featureCountsPhenotypic.txt

value: 1508 HCASMC

value: Human coronary artery SMC

value: Serum stimulated

value: 48 hrs


title: BCAC_submand_010

description:
Library name: BCAC_submand_010_F-B03
FFPE spatial transcriptome sequencing


title: Somatic_hpo RNAi_Late_2

value: Somatic tissue


title: Myobacterium tuberculosis, SAN, 24 hrs, Biological Replicate 2

value: 24 hrs

value: SAN


title: Primary HCASMC cells, siRNA control, serum stimulated 48 hrs, replicate 1

description:
B1
featureCountsPhenotypic.txt


title: BCAC_submand_009

description:
Library name: BCAC_submand_009_F-B02
FFPE spatial transcriptome sequencing


title: Somatic_hpo RNAi_Late_1


title: Myobacterium tuberculosis, GSK286, 24 hrs, Biological Replicate 2

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13


title: Primary HCASMC cells, siRNA ADAR1 IFIH1, serum starved 48 hrs, replicate 3

description:
A9
featureCountsPhenotypic.txt

value: ADAR1 & IFIH1 KD

value: Serum starved


title: Myobacterium tuberculosis, GSK839, 24 hrs, Biological Replicate 2


title: Somatic_hpo RNAi_Mid_3

value: Ovary:Somatic Tissue 96h AEL

value: III instar Larvae 96h AEL


title: Primary HCASMC cells, siRNA ADAR1 IFIH1, serum starved 48 hrs, replicate 2

description:
A8
featureCountsPhenotypic.txt


title: Primary HCASMC cells, siRNA ADAR1 IFIH1, serum starved 48 hrs, replicate 1

description:
A7
featureCountsPhenotypic.txt


title: BCA_007

description:
Library name: BCA_007_F-A11
FFPE spatial transcriptome sequencing


title: Somatic_hpo RNAi_Mid_2

value: bab:GAL4>UAS hpo RNAi, UAS GFP


title: BCAC_submand_008

description:
Library name: BCAC_submand_008_F-B01
FFPE spatial transcriptome sequencing


title: Myobacterium tuberculosis, TBI, 24 hrs, Biological Replicate 2

value: TBI


title: Myobacterium tuberculosis, KRS, 24 hrs, Biological Replicate 2

value: KRS


title: Somatic_hpo RNAi_Mid_1

value: _rnai:hpo RNAi


title: BCA_005

description:
Library name: BCA_005_F-A07
FFPE spatial transcriptome sequencing


title: BCA_006

description:
Library name: BCA_006_F-A09
FFPE spatial transcriptome sequencing


title: Somatic_hpo RNAi_Early_4

value: Ovary:Somatic Tissue 72h AEL

value: III instar Larvae 72h AEL


title: Primary HCASMC cells, siRNA ADAR1, serum starved 48 hrs, replicate 3

description:
A6
featureCountsPhenotypic.txt

value: 1508 HCASMC

value: Human coronary artery SMC

value: ADAR1 KD


title: Myobacterium tuberculosis, TBA, 24 hrs, Biological Replicate 2

value: TBA


title: Myobacterium tuberculosis, SFN, 24 hrs, Biological Replicate 2

value: 24 hrs

value: SFN


title: BCA_004

description:
Library name: BCA_004_F-A05
FFPE spatial transcriptome sequencing


title: Primary HCASMC cells, siRNA ADAR1, serum starved 48 hrs, replicate 2

description:
A5
featureCountsPhenotypic.txt

value: 48 hrs


title: Primary HCASMC cells, siRNA ADAR1, serum starved 48 hrs, replicate 1

description:
A4
featureCountsPhenotypic.txt


title: Hyperplasia_003

description:
Library name: Hyperplasia_003_F-A04
FFPE spatial transcriptome sequencing


title: Myobacterium tuberculosis, SAN, 4 hrs, Biological Replicate 2

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: 4 hrs

value: SAN


title: Somatic_hpo RNAi_Early_1

value: Somatic tissue


title: Hyperplasia_002

description:
Library name: Hyperplasia_002_F-A03
FFPE spatial transcriptome sequencing


title: Primary HCASMC cells, siRNA control, serum starved 48 hrs, replicate 3

description:
A3
featureCountsPhenotypic.txt

value: Control

value: Serum starved


title: Myobacterium tuberculosis, GSK286, 4 hrs, Biological Replicate 2


title: Hyperplasia_001

description:
Library name: Hyperplasia_001_F-A02
FFPE spatial transcriptome sequencing


title: Myobacterium tuberculosis, GSK839, 4 hrs, Biological Replicate 2


title: Somatic_hpo RNAi_Early_3

value: bab:GAL4>UAS hpo RNAi, UAS GFP


title: Primary HCASMC cells, siRNA control, serum starved 48 hrs, replicate 1

description:
A1
featureCountsPhenotypic.txt


title: BG2_RPMI_FLUC_C

city: Edinburgh

first: Edward

middle: William Joseph

last: Wallace

address: Waddington Building, Max Born Crescent

department: Institute for Cell Biology, School of Biological Sciences

country: United Kingdom

institute: University of Edinburgh

data_processing:
RNA-Seq FASTQ files were processed using a Nextflow a pipeline for QuantSeq data which is available online in GitHub repository (https://github.com/DimmestP/nextflow_paired_reads_pipeline). Software versions used were (Nextflow 3.1, FastQC 0.12.1, Cutadapt 4.3, HISAT2 2.2.1, SAMtools 1.17, MultiQC 1.14, BEDTools 2.30.0, Subread /FeatureCounts 3.11.3, DESeq2 1.40.2, Python 3.11.3, R 4.3.2, NCBI Datasets CLI 16.0.0). The reads were aligned to genome sequence. Differential gene expression was performed using DESeq2, and code is shared in GitHub (https://github.com/daneckaw/cglab_rnaseq/).
Assembly: For strain BG2:  GCA_014217725.1, downloaded from NCBI.  For CBS138, GCF_000002545.3, downloaded from NCBI.
Supplementary files format and content: RNA-seq counts per gene from Feature Counts, one file per strain covering all measured conditions.

organism: Nakaseomyces glabratus

growth_protocol: Candida glabrata strains were streaked to single colonies on YPDA agar plates for 2 days, then a single colony inoculated for each biological replicate into 5mL mL RPMI-1640 with 2% glucose and grown overnight. The next day, 1x10^8 cells were pelleted and inoculated into 50 mL of RPMI-1640 media with 2% glucose pre-warmed to 37°C with drug or DMSO (mock) treatment. After inoculation, cells were grown for 4 hours at 37°C with 200 rpm shaking, and harvested by pelleting cells for 3 min at 4000 rpm, the supernatant was decanted, and the cells were pelleted for 2 min at 3000 g to remove all supernatant, and the pellet frozen in liquid nitrogen, and stored at -80°C.

extract_protocol:
RNA was extracted using a modified Zymo kit protocol following bead-beating with zirconia beads. RNA extraction was performed using silica columns purification method using Zymo reagents. The yeast pellets were thawed briefly on ice, then transferred to a screw cap tube and 200 μL of zirconia beads were added. 400 μL of RNA binding buffer (Zymo) was added, and the mixture was kept on ice for 1 minute. The tubes were transferred to PreCellys homogenizer (Bertin), and lysed using the following protocol: 10 seconds vortexing, followed by 10 seconds of waiting repeated 3 times. The cells were then transferred to ice for 1 minute. Vortexing and incubation on ice were repeated a total of 6 times. The tubes were then centrifuged at 12,000 × g for 2 minutes. The supernatant was transferred to a Zymo Spin IIIC column (Zymo) and centrifuged at 12,000 × g for 1 minute. 400 μL of ethanol was added to the flow through, mixed, transferred to a Zymo Spin IICG column (Zymo) and centrifuged for 1 minute. The column was washed with DNA/RNA Prep buffer (Zymo) and centrifuged for 1 minute, and then washed with DNA/RNA Wash buffer (Zymo) and centrifuged for 1 minute twice. The column was then transferred to a clean 1.5 mL tube, and RNA was eluted by adding 30 μL of water and centrifuging at 10,000 × g for 1 minute. The concentration of the samples was measured using Denovix. The quality and integrity of RNA was assessed on Fragment Analyzer (Agilent) using High Sensitivity RNA Kit DNF-472-1000 (Agilent). RQN and 28S/18S ratio were used to determine the quality of the sample.
Lexogen QuantSeq Rev: RNA sequencing libraries were prepared from 500 ng total RNA using QuantSeq 3’ mRNA-Seq V2 Library Prep Kit REV (Lexogen)

treatment_protocol: Voriconazole was added at 1 ug/mL or 0.5 ug/mL for BG2 and CBS138, respectively (RPMI_VORI). Fluconazole was added at 64 ug/mL or 32 ug/mL for BG2 and CBS138, respectively (RPMI_FLUC). Mock-treatment was performed using 0.004% DMSO (RPMI_DMSO). For drug addition, stock solutions of voriconazole or fluconazole were prepared in DMSO, and the solution mixed with RPMI media imediately before inoculation. DMSO was added to voriconazole and fluconazole treatments to the final concentration of 0.004%.

value: C


title: Primary HCASMC cells, siRNA control, serum starved 48 hrs, replicate 2

description:
A2
featureCountsPhenotypic.txt


title: Myobacterium tuberculosis, KRS, 4 hrs, Biological Replicate 2

value: KRS


title: BG2_RPMI_VORI_C


title: Rabbit Vocal Fold, 107R, VFLP (man), rep2-2

city: Raleigh

first: Xinxia

last: Peng

address: 1060 William Moore Drive

institute: North Carolina State University

description:
Library name: VF94
DNBSEQ-G400C

data_processing:
RNA-seq data in the FASTQ file format was generated and demultiplexed on the DNBSEQ-G400C sequencer. Raw RNA-seq data was quality-controlled during and after sequencing to identify potential technical issues. Raw RNA-seq sequencing reads were mapped to the rabbit reference genome (assembly UM_NZW_1.0,  RefSeq annotation GCF_009806435.1-RS_2023_02) using STAR v2.7.10b to generate read counts for each of the annotated genes. RefSeq transcript annotations were supplied to facilitate mapping reads spanning known splicing junctions.
Assembly: UM_NZW_1.0
Supplementary files format and content: tab-delimited text file includes raw counts for each sample as generated by STAR

organism: Oryctolagus cuniculus

source_name: Vocal Fold

extract_protocol:
Frozen tissue (0.5-3mg) previously stored in RNALater ICE (Invitrogen) was homogenized in 1ml of buffer RLT+βME (Qiagen) using a Bead Mill 4 (Fisherbrand) for three cycles of 30s at a speed of 4m/s with 2min ice rests interspersed between cycles.  Total RNA was isolated using the RNeasy Plus (Qiagen) extraction kit with the protocol adjusted proportionally for an input of 825µL of homogenized solution. RNA quality (RIN) and quantity was assessed on the Bioanalyzer 2100 instrument using the RNA 6000 Pico Kit (Agilent).
mRNA-seq libraries were prepared using a target input of 100ng of intact (RIN>7) RNA with the KAPA mRNA HyperPrep kit implementing a fragmentation step of 94C for 6min and 15 cycles of final amplification (Roche). Library conversion and deep sequencing were performed using the App-A Universal Library Conversion kit and App-D Primer kit on a DNBSEQ-G400C sequencer with the FCL PE100 sequencing set (Complete Genomics).

treatment_protocol: New Zealand white rabbits were randomized into five groups (n = 6 each)—four subjected to bilateral superficial vocal fold mucosal stripping under ketamine/dexmedetomidine sedation (with isoflurane supplementation as needed) and topical lidocaine, and one uninjured control. Seven days post injury, the injury groups received 20 µL bilateral injections—collagen type I, VFLP (man), VFLP (au), or no injection. For each condition, three larynges (both folds analyzed separately) were allocated to transcriptome profiling and three (one fold per animal to preserve the anterior commissure) to mechanical testing. Twenty eight days after treatment, rabbits were euthanized with intravenous sodium pentobarbital, larynges were excised, mucosa meticulously dissected under stereomicroscopy, flash frozen, and stored at –80 °C until further analysis.

value: Vocal Fold

value: VFLP (man)

tag: batch

value: D

tag: animal

tag: side

value: right


title: RNAseq_ILC2_Ctrl_3

city: Jinan

first: Jing

last: Shen

address: Wenhua West Road 44

institute: Shandong University

description: Library name: Ctrl_3

data_processing:
The raw reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version: cutadapt-1.9).
Filtered reads were mapped against the mm10 assembly of the Mus musculus genome (National Center for Biotechnology Information) using hisat2 (Version 2.2.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Ctrl, replicate 3, RNA_seq

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
Full-length cDNA was generated using SMART-Seq HT Kit (Takara), paired-end DNA libraries was generated and indexed using NexteraTM XT Library Prep Kit and then NexteraTM XT Index Kit.

value: colon

tag: cell type

value: immune cell


title: RNAseq_ILC2_DSS_3

description: Library name: DSS_3

source_name: DSS, replicate 3, RNA_seq

value: DSS


title: RNAseq_ILC2_DSS_1

description: Library name: DSS_1

source_name: DSS, replicate 1, RNA_seq


title: Myobacterium tuberculosis, TBA, 4 hrs, Biological Replicate 2

value: TBA


title: CBS138_RPMI_FLUC_C

tag: strain


title: Rabbit Vocal Fold, 113L, Col1, rep2-1

description:
Library name: VF91
DNBSEQ-G400C

value: left


title: RNAseq_ILC2_Ctrl_2

description: Library name: Ctrl_2

source_name: Ctrl, replicate 2, RNA_seq


title: RNAseq_ILC2_Ctrl_1

description: Library name: Ctrl_1

source_name: Ctrl, replicate 1, RNA_seq


title: Myobacterium tuberculosis, SFN, 4 hrs, Biological Replicate 2

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: 4 hrs

value: SFN


title: Myobacterium tuberculosis, UNT, 24 hrs, Biological Replicate 3, Technical Replicate 1

value: 24 hrs

value: UNT


title: Rabbit Vocal Fold, 108R, VFLP (man), rep3-2

description:
Library name: VF90
DNBSEQ-G400C


title: CBS138_RPMI_DMSO_C


title: 1110

city: Geneva

first: Ivan

last: Rodriguez

address: 30 quai Ernest Anrsermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

description:
Library name: Sample 12
10x Genomics Chromium Single Cell 3â€² v3.1

data_processing:
Demultiplexing of Illumina indices was performed on the raw Illumina data using bcl2fastq2 Conversion Software version 2.20.0 (Illumina), which generated a pair of fastq files per sample (i.e. reads 1 and 2).
Digital gene expression matrices (i.e. matrices with genes in rows, cells in columns, and gene counts as matrix entries) were generated using Cell Ranger version 6.0.0. Fastq files were mapped to the Mus musculus genome primary assembly reference 38 (GRCm38) using STAR, implemented in Cell Ranger. A modified version of Ensembl release 102 of the Mus musculus GTF annotation was used, with the Gm45623 annotation replaced by a custom annotation for Smim32, as described in Tuberosa et al. (https://doi.org/10.7554/eLife.99168.1). Mapping, UMI counting, and barcode filtering were performed using the count function of Cell Ranger. The expected number of recovered cells (--expect-cells argument) was customized for each sample and set to the targeted cell recovery of the sample.
Assembly: GRCm38
Supplementary files format and content: Tab-separated Cell Ranger filtered output files

source_name: brain

growth_protocol: Mice were group-housed in standard type II cages with ad libitum food and water, maintained on a 12/12h dark/light cycle, at 21–22°C and 45–55% humidity.

extract_protocol:
Mice were anesthetized with isoflurane and sacrificed by decapitation. Brains were immediately extracted and placed in ice-cold oxygenated artificial cerebro-spinal fluid (ACSF) with an osmolarity of 300 mOsm and pH at 7.4. Coronal sections of the brain spanning the antero-posterior localization of the claustrum were cut at a thickness of 300 μm using a vibrating-blade microtome. Immediately after sectioning, the claustrum and adjacent brain regions were microdissected under a stereomicroscope. Tissues from each mouse were processed individually, with no pooling across different animals. Tissue dissociations were performed using the Papain Dissociation System (ref. LK003150; Worthington® Biochemical Corporation) according to the manufacturer’s protocol with slight modifications, using EBSS and medium with serum solutions adapted from Saxena et al. (DOI: 10.2144/0000113878). To ensure the exclusive isolation of live nucleated cells, cell suspensions were incubated with 2 μg/ml of Hoechst 33342 (a UV fluorescent adenine-thymine binding dye; ref. H1399, Life Technologies) at 37°C for 15 min. In order to exclude dead cells, 1 μM of DRAQ7 (a far-red fluorescent DNA intercalating dye; ref. DR71000, BioStatus) was added to the cell suspensions before fluorescence activated cell sorting (FACS). Between 11’000-25’000 Hoechst+/DRAQ7- cells were collected from each sample. Single-cell capture, reverse transcription, cDNA amplification, and library preparation were performed using the 10x Genomics Chromium Controller instrument and the Single Cell 3′ v3.1 reagent kit with dual indexes, following the manufacturer’s protocol (CG000315 Rev B User Guide). Cells were loaded on the 10x Genomics Chromium Controller instrument at a concentration of 400 cells/μl, and the targeted cell recovery was adjusted for each sample based on the number of sorted cells. For a detailed description of the protocol, please refer to the methods section of Fodoulian et al. (2024) bioRxiv (https://doi.org/10.1101/2024.11.05.622016).
Libraries from mice of the same age were pooled and each loaded at 2 nM on 4 lanes for clustering on a paired-end Illumina Flow Cell using the HiSeq 4000 PE Cluster Kit (ref. PE-410-1001; Illumina) and sequenced on an Illumina HiSeq 4000 sequencer using the HiSeq 4000 SBS Kit (ref. FC-410-1001; Illumina) chemistry. Read 1 consisted of 28 bases, while read 2 was either 90 or 100 bases. An average of 5’171 cells were sequenced with 42’199 mean reads, 1’125 median genes, and 1’999 median UMI counts per cell.

tag: age

tag: Sex

value: female

value: brain

tag: brain region

value: claustro-insular region

tag: targeted cell_recovery


title: 1113

description:
Library name: Sample 13
10x Genomics Chromium Single Cell 3â€² v3.1

tag: genotype

tag: tissue


title: Rabbit Vocal Fold, 117L, VFLP (au), rep2-1

description:
Library name: VF89
DNBSEQ-G400C

value: Vocal Fold

value: VFLP (au)


title: CBS138_RPMI_VORI_C

value: C


title: RNAseq_ILC2_DSS_2

description: Library name: DSS_2

source_name: DSS, replicate 2, RNA_seq

tag: cell line


title: Rabbit Vocal Fold, 115R, Col1, rep3-2

description:
Library name: VF87
DNBSEQ-G400C

tag: treatment

value: D

value: right


title: Myobacterium tuberculosis, UNT, 4 hrs, Biological Replicate 3, Technical Replicate 1

source_name: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

tag: time point


title: BG2_RPMI_FLUC_B

tag: replicate

value: B


title: Myobacterium tuberculosis, UNT, 0 hrs, Biological Replicate 3, Technical Replicate 1

value: 0 hrs


title: BG2_RPMI_DMSO_C


title: BG2_RPMI_VORI_B


title: Rabbit Vocal Fold, 109R, Col1, rep1-2

description:
Library name: VF85
DNBSEQ-G400C


title: Rabbit Vocal Fold, 116L, VFLP (au), rep1-1

description:
Library name: VF93
DNBSEQ-G400C


title: 1109

description:
Library name: Sample 11
10x Genomics Chromium Single Cell 3â€² v3.1

value: male


title: 1108

description:
Library name: Sample 10
10x Genomics Chromium Single Cell 3â€² v3.1


title: BG2_RPMI_DMSO_B


title: Rabbit Vocal Fold, 108L, VFLP (man), rep3-1

description:
Library name: VF84
DNBSEQ-G400C

value: VFLP (man)

value: left


title: CBS138_RPMI_FLUC_B


title: Rabbit Vocal Fold, 115L, Col1, rep3-1

description:
Library name: VF82
DNBSEQ-G400C


title: Myobacterium tuberculosis, UNT, 4 hrs, Biological Replicate 2, Technical Replicate 1

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: 4 hrs


title: 1105

description:
Library name: Sample 8
10x Genomics Chromium Single Cell 3â€² v3.1


title: Myobacterium tuberculosis, UNT, 0 hrs, Biological Replicate 2, Technical Replicate 1


title: CBS138_RPMI_VORI_B


title: Rabbit Vocal Fold, 79R, injury only, rep1-2

description:
Library name: VF81
DNBSEQ-G400C

value: injury only


title: Myobacterium tuberculosis, UNT, 24 hrs, Biological Replicate 1, Technical Replicate 1

value: 24 hrs

value: UNT


title: CBS138_RPMI_DMSO_B


title: Myobacterium tuberculosis, UNT, 4 hrs, Biological Replicate 1, Technical Replicate 1


title: Rabbit Vocal Fold, 119R, VFLP (au), rep3-2

description:
Library name: VF79
DNBSEQ-G400C


title: Myobacterium tuberculosis, UNT, 24 hrs, Biological Replicate 2, Technical Replicate 1


title: 1104

description:
Library name: Sample 7
10x Genomics Chromium Single Cell 3â€² v3.1

value: female

value: brain


title: BG2_RPMI_FLUC_A

value: A


title: 1106

description:
Library name: Sample 9
10x Genomics Chromium Single Cell 3â€² v3.1

value: claustro-insular region


title: BG2_RPMI_VORI_A


title: 1096

description:
Library name: Sample 4
10x Genomics Chromium Single Cell 3â€² v3.1


title: Rabbit Vocal Fold, 106L, VFLP (man), rep1-1

description:
Library name: VF76
DNBSEQ-G400C

value: Vocal Fold


title: Myobacterium tuberculosis, SAN, 24 hrs, Biological Replicate 1

value: SAN


title: BG2_RPMI_DMSO_A


title: Rabbit Vocal Fold, 107L, VFLP (man), rep2-1

description:
Library name: VF77
DNBSEQ-G400C

value: D


title: 1093

description:
Library name: Sample 3
10x Genomics Chromium Single Cell 3â€² v3.1


title: CBS138_RPMI_FLUC_A


title: Myobacterium tuberculosis, GSK286, 24 hrs, Biological Replicate 1


title: Rabbit Vocal Fold, 119L, VFLP (au), rep3-1

description:
Library name: VF75
DNBSEQ-G400C

value: VFLP (au)


title: Rabbit Vocal Fold, 106R, VFLP (man), rep1-2

description:
Library name: VF80
DNBSEQ-G400C

value: right


title: Myobacterium tuberculosis, GSK839, 24 hrs, Biological Replicate 1


title: 1103

description:
Library name: Sample 6
10x Genomics Chromium Single Cell 3â€² v3.1


title: 1091

description:
Library name: Sample 2
10x Genomics Chromium Single Cell 3â€² v3.1

value: male


title: Myobacterium tuberculosis, KRS, 24 hrs, Biological Replicate 1

value: KRS


title: Rabbit Vocal Fold, 116R, VFLP (au), rep1-2

description:
Library name: VF72
DNBSEQ-G400C


title: 1099

description:
Library name: Sample 5
10x Genomics Chromium Single Cell 3â€² v3.1


title: Myobacterium tuberculosis, UNT, 0 hrs, Biological Replicate 1, Technical Replicate 1

value: 0 hrs


title: bHLH35_S+HL+HS_Rep3

city: Columbia

first: Ron

last: Mittler

state: Missouri

address: University of Missouri,1201 Rollins St

department: Division of Plant Science and Technology

institute: University of Missouri - Columbia

data_processing:
Sequencing was performed by Novogene, Inc.
Bioinformatic analysis was performed by Joshi Lab in University of Missouri
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence. Subsequently, the processed reads were mapped to the Arabidopsis thaliana TAIR10.57 version whole genome using Hisat2 V2.2.1.
Assembly: Arabidopsis thaliana TAIR10.54
Supplementary files format and content: Matrix table FPKM values for all samples

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Arabidopsis thaliana wild-type (Col0), and mutants of bHLH35  gene plants were subjected to salt stress (S; 50mM), high light stress (HL; 700 µE), heat stress (HS; 33 °C) and different combinations of these three stresses (S+HL, S+HS, HL+HS, S+HL+HS). Sterilized seeds of above-mentioned genotypes were germinated on ½ MS (murashige and Skoog media) with or without salt, at 21°C temperature and 150 µE light intensity. 7 days old seedling were subjected to HL and HS for 3 days (in combinations mentioned above) to determine the impact of stresses on survival. Seedlings for control were grown on ½ MS media without salt at 21°C temperature and 150 µE light intensity. To study the transcriptomic response of Arabidopsis genotypes, 7 days old seedling growing on ½ MS with or without salt were exposed to HS and HL stress (in combinations mentioned above) for 1.5 hrs.

extract_protocol:
Total RNA from the seedlings were isolated using Qiagen RNeasy® Plant Mini Kit.
RNA libraries for sequencing were prepared using standard Illumina protocols.

value: Seedlings

value: bHLH35 mutant in Col0 background

value: Salt, high light and heat stress together


title: Myobacterium tuberculosis, TBA, 24 hrs, Biological Replicate 1

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: 24 hrs

value: TBA


title: A549 spike addition after 48h 2

type: RNA

city: Tokyo

first: Yoichi

last: Teratake

country: Japan

institute: National Center for Global Health and Medicine

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: The probe cell intensity data computation and a CEL file generation was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

label: biotin

source_name: spike protein addition for 48 h

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling ki

growth_protocol: Samples were taken 48 hours after adding spike protein.

extract_protocol: qiagen RNA extruction kit accoding to manufacture's protocol

treatment_protocol: spike protein was added to A549 cells cultured in 10% FCS DMEM, and RNA was collected using an RNA extraction kit at each time point.

value: A549 cell line


title: bHLH35_S+HS_Rep3

value: Salt and heat stress together


title: Rabbit Vocal Fold, 117R, VFLP (au), rep2-2

description:
Library name: VF68
DNBSEQ-G400C


title: A549 spike addition after 48h 1


title: 1090

description:
Library name: Sample 1
10x Genomics Chromium Single Cell 3â€² v3.1

value: brain

value: claustro-insular region


title: Myobacterium tuberculosis, SFN, 24 hrs, Biological Replicate 1

value: SFN


title: bHLH35_S+HL_Rep3

value: Salt and high light stress together


title: Rabbit Vocal Fold, 83R, injury only, rep3-2

description:
Library name: VF65
DNBSEQ-G400C

value: Vocal Fold

value: injury only

value: C


title: Rabbit Vocal Fold, 113R, Col1, rep2-2

description:
Library name: VF73
DNBSEQ-G400C

value: D

value: right


title: bHLH35_S_Rep3

value: Seedlings

value: Salt stress


title: Myobacterium tuberculosis, GSK286, 4 hrs, Biological Replicate 1

value: 4 hrs


title: A549 delta psudo 6h 2

source_name: Delta covid19 psudovirus addition for 6 h

growth_protocol: Samples were taken 4 and 6 hours after adding each pseudotyped virus.

treatment_protocol: Pseudotyped viruses were added to A549 cells cultured in 10% FCS DMEM, and RNA was collected using an RNA extraction kit at each time point.


title: CBS138_RPMI_DMSO_A

value: A


title: bHLH35_HL+HS_Rep3

value: bHLH35 mutant in Col0 background

value: High light and heat stress together


title: Rabbit Vocal Fold, 84R, no injury/control, rep2-2

description:
Library name: VF61
DNBSEQ-G400C

value: no injury/control


title: A549 delta psudo 6h 1

value: A549 cell line


title: Rabbit Vocal Fold, 85L, no injury/control, rep3-1

description:
Library name: VF60
DNBSEQ-G400C

value: left


title: Myobacterium tuberculosis, GSK839, 4 hrs, Biological Replicate 1

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13


title: Myobacterium tuberculosis, KRS, 4 hrs, Biological Replicate 1

value: KRS


title: bHLH35_HS_Rep3

value: Heat stress


title: Myobacterium tuberculosis, TBI, 24 hrs, Biological Replicate 1

value: 24 hrs

value: TBI


title: Rabbit Vocal Fold, 82L, injury only, rep2-1

description:
Library name: VF58
DNBSEQ-G400C

value: Vocal Fold

value: injury only

value: C


title: Rabbit Vocal Fold, 109L, Col1, rep1-1

description:
Library name: VF70
DNBSEQ-G400C

value: D


title: WTC11_neuron_dTAG_R2_HiC

city: La Jolla

first: Jesse

middle: R

last: Dixon

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute for Biological Studies

description: Library name: TP647

data_processing:
HiC data was first aligned to the hg38 reference genome using BWA-MEM and processed with in-house perl scripts (see https://github.com/dixonlab/HiC_alignment_basic_scripts).
Aligned data was de-duplicated using Picard MarkDuplicates.
Contact files were generated from bam files using in-house perl scripts (see https://github.com/dixonlab/HiC_alignment_basic_scripts).
Juicer was used to create .hic files from contact files, while cooler was used to create multi-resolution cool (mcool) files.
Assembly: hg38
Supplementary files format and content: Multi-resolution cool file
Supplementary files format and content: hic file

source_name: hTERT RPE-1

growth_protocol: hTERT RPE-1 were maintained in DMEM/F12 supplemented with 10% FBS and 1% penicillin/streptomycin, and grown at 37°C with 5% CO2. Prior to differentiation, WTC11 iNgn2 hiPSC cells  were maintained on Cultrex-coated plates in either Essential 8 Flex Medium (Gibco #A2858501) or mTeSR Plus (StemCell Technologies #100-0276). WTC11 iNgn2 hiPSC cells were differentiated into neurons using SMAD inhibition or into cardiomyocytes using STEMdiff Ventricular Cardiomyocyte Differentiation Kit (StemCell Technologies #05010).

extract_protocol:
Cells were fixed and processed according to the Arima Genomics HiC+ Kit protocol.
Proximity-ligated DNA was first sonicated to ~400 bp using a Covaris M220 with 50 W power, 10% duty factor and 200 cycles per burst for 78 seconds, and then size-selected using AMPure beads. Lbrary preparation was performed using KAPA HyperPrep (Roche #KK8502) according to instructions provided with the Arima Genomics HiC+ Kit, with library preparation done on streptavidin beads.

treatment_protocol: Asynchronous hTERT RPE-1 cells or post-mitotic hiPSC-derived cells were treated with DMSO or dTAGV-1 for the stated times.

value: hTERT RPE-1

value: dTAG 4hr


title: Myobacterium tuberculosis, TBI, 4 hrs, Biological Replicate 1

value: 4 hrs


title: Myobacterium tuberculosis, SAN, 4 hrs, Biological Replicate 1

value: SAN


title: A549 not treatment 48 h 1

source_name: not treatment sample


title: bHLH35_Control_Rep3

value: Seedlings

value: bHLH35 mutant in Col0 background

value: No treatment


title: Rabbit Vocal Fold, 80L, no injury/control, rep1-1

description:
Library name: VF64
DNBSEQ-G400C

value: no injury/control

value: left


title: Rabbit Vocal Fold, 82R, injury only, rep2-2

description:
Library name: VF56
DNBSEQ-G400C

value: right


title: Myobacterium tuberculosis, TBA, 4 hrs, Biological Replicate 1

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: TBA


title: bHLH35_S+HL+HS_Rep2

value: Salt, high light and heat stress together


title: WTC11_neuron_DMSO_R2_HiC

description: Library name: TP645

value: DMSO 4hr


title: Myobacterium tuberculosis, SFN, 4 hrs, Biological Replicate 1

value: SFN


title: Rabbit Vocal Fold, 83L, injury only, rep3-1

description:
Library name: VF55
DNBSEQ-G400C

value: Vocal Fold

value: injury only

value: C


title: bHLH35_HL_Rep3

value: High light


title: bHLH35_S+HL_Rep2

value: Salt and high light stress together


title: Rabbit Vocal Fold, 85R, no injury/control, rep3-2

description:
Library name: VF54
DNBSEQ-G400C


title: Rabbit Vocal Fold, 79L, injury only, rep1-1

description:
Library name: VF53
DNBSEQ-G400C


title: WTC11_neuron_dTAG_R1_HiC

description: Library name: TP646

value: hTERT RPE-1

value: dTAG 4hr


title: Myobacterium tuberculosis, UNT, 24 hrs, Biological Replicate 3, Standard growth control

value: 24 hrs

value: UNT


title: WTC11_neuron_DMSO_R1_HiC

description: Library name: TP644


title: WTC11_cardio_dTAG_R2_HiC

description: Library name: TP643


title: bHLH35_S_Rep2

value: Seedlings

value: bHLH35 mutant in Col0 background

value: Salt stress


title: bHLH35_HL+HS_Rep2

value: High light and heat stress together


title: Rabbit Vocal Fold, 84L, no injury/control, rep2-1

description:
Library name: VF51
DNBSEQ-G400C

value: no injury/control

value: left


title: Rabbit Vocal Fold, 80R, no injury/control, rep1-2

description:
Library name: VF50
DNBSEQ-G400C

value: right


title: Myobacterium tuberculosis, UNT, 24 hrs, Biological Replicate 1, Standard growth control

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13


title: WTC11_cardio_dTAG_R1_HiC

description: Library name: TP642


title: Myobacterium tuberculosis, UNT, 0 hrs, Biological Replicate 1, Plate Control

value: 0 hrs


title: bHLH35_HS_Rep2

value: Heat stress


title: WTC11_cardio_DMSO_R1_HiC

description: Library name: TP640

value: DMSO 4hr


title: bHLH35_HL_Rep2

value: High light


title: bHLH35_S+HS_Rep2

value: Salt and heat stress together


title: Myobacterium tuberculosis, UNT, 24 hrs, Biological Replicate 3


title: NIPBL-D7_STAG2-KO-B8_dTAG_4hr_HiC

description: Library name: AP101

value: hTERT RPE-1


title: bHLH35_Control_Rep2

value: No treatment


title: Myobacterium tuberculosis, UNT, 24 hrs, Biological Replicate 2, Standard growth control

value: 24 hrs


title: WTC11_cardio_DMSO_R2_HiC

description: Library name: TP641


title: Myobacterium tuberculosis, TBI, 4 hrs, Biological Replicate 2

value: 4 hrs

value: TBI


title: Myobacterium tuberculosis, RFP, 24 hrs, Biological Replicate 3

value: RFP


title: NIPBL-D7_STAG2-KO-B8_DMSO_4hr_HiC

description: Library name: AP100


title: bHLH35_S+HL+HS_Rep1

value: Seedlings

value: bHLH35 mutant in Col0 background

value: Salt, high light and heat stress together


title: NIPBL-D7_STAG2-KO-A2_dTAG_4hr_HiC

description: Library name: AP99

value: dTAG 4hr


title: bHLH35_S+HS_Rep1


title: Myobacterium tuberculosis, RIF, 24 hrs, Biological Replicate 3

value: RIF


title: Myobacterium tuberculosis, PZA, 24 hrs, Biological Replicate 3

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: PZA


title: bHLH35_S+HL_Rep1

value: Salt and high light stress together


title: NIPBL-D7_STAG1-KO-C5_dTAG_4hr_HiC

description: Library name: AP97


title: Myobacterium tuberculosis, PRE, 24 hrs, Biological Replicate 3

value: PRE


title: NIPBL-D7_STAG2-KO-A2_DMSO_4hr_HiC

description: Library name: AP98

value: DMSO 4hr


title: Myobacterium tuberculosis, MOX, 24 hrs, Biological Replicate 3

value: MOX


title: Jurkat_IgG

city: Marseille

first: Delphine

last: Potier

address: 27 boulevard Lei Roure

country: France

institute: CRCM

description: Library name: Sample14

data_processing:
Raw reads were processed using the nextflow nf-core ChIP-seq pipeline (Next- flow version: 25.04.2 build 5947; nf-core/chipseq v2.1.0-g76e2382) adapted for cut & tag experiments. The different steps are listed below
Raw reads were first quality- and adapter-trimmed using Trim Galore!
Trimmed reads were aligned to the human reference genome (GRCh38) using BWA
BigWigs were generated via deepTools
Peak calling was performed with MACS3. The ‘macs3 callpeak’ step was modified (in nf- core/macs3/callpeak/main.nf) to include the ‘--no-model’ option to be adapted to CUT&Tag analysis. For broad histone mark (H3K4me1), the pipeline’s default broad calling was applied, while peaks for H3K4me3 and H3K27ac were called using the ‘--narrow_peak TRUE’ option.
Peak quantification was performed using featureCounts on the consensus peak files corresponding to each histone mark, resulting in the generation of '*_raw_counts.txt' files
Normalized count data were extracted from the DESeq2 object using the function counts() with the argument 'normalized = TRUE', providing read counts adjusted for library size differences.
Variance-stabilized counts were obtained using the vst() function from DESeq2 with the argument 'blind = FALSE', applied to the DESeqDataSet object used for differential analysis. The transformed expression matrix is provided as *_vst_counts.txt.
Assembly: GRCh38
Supplementary files format and content: A bigWig per sample for each histone mark (H3K27ac, H3K4me1, H3K4me3, and for each histone mark, three tab-delimited files are provided containing: raw counts ; library-size normalized counts; variance-stabilized counts (vst) per consensus peak and sample extracted from the DESeq2 object.  Each tab-delimited file has consensus peaks as rows and samples as columns.
Library strategy: CUT&Tag

source_name: Jurkat

extract_protocol:
For nuclei preparation, cells were permeabilized for 10 min at 4°C in NE1 buffer (20 mM Hepes-KOH pH 7.9, 10 mM KCL, 0.5 mM Spermidine, 0.1% Triton-X100, 20 % Glycerol, protease inhibitor cocktail). Then nuclei were washed with 20 mM Hepes pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, protease inhibitor cocktail).
The protocol was adapted from Carter et al (PMID: 31431618). The protein A (pA) fused to Tn5 Transposase (pA-Tn5) was first loaded with DNA duplexes (pMENTS oligonucleotide with either I’5 or I7’ adapter oligonucleotides) and then incubated with antibodies targeting H3K27Ac, H3K4Me1 or H3K4Me3. Next, pA-Tn5-Antibody complexes were incubated with nuclei at RT for 1 h. Tagmentation was initiated by adding MgCl2 (incubation 1 h, 37°C). The reaction was stopped by adding EDTA, SDS and Proteinase K (55°C for 1 h) and DNA was purified using Zymo-Spin IC Columns. For library preparation, DNA (250 ng) were amplified with i’7 and i’5 primers and  NEBNext High-Fidelity 2X PCR Master Mix; the following PCR programwas used: 72°C for 5 min; 98°C for 45 sec; 22 cycles of [98°C for 15 sec, 63°C for 10 sec]; 72°C for 1 min; hold at 8°C. PCR products (CUT&Tag libraries) were separated by gel electrophoresis and DNA fragments between ~250-1000 bp were excised and purified.

value: Jurkat

value: Thymocyte

value: WT


title: Jurkat_WT_H3K4me3

description:
Library name: Sample12
column name in  K4Me3_normalized_counts.txt = JKT_K4Me3

tag: chip antibody

value: H3K4me3 (Invitrogen, #711958)


title: Jurkat_3B6_TripleKO_H3K4me1

description:
Library name: Sample7
column name in K4Me1_normalized_counts.txt = 3B6_K4Me1

value: Triple KO BEX1 | BEX2 | BEX5

value: H3K4me1 (Invitrogen, #710795)


title: Myobacterium tuberculosis, LIN, 24 hrs, Biological Replicate 3

value: 24 hrs

value: LIN


title: NIPBL-D7_STAG1-KO-A7_dTAG_4hr_HiC

description: Library name: AP95

value: hTERT RPE-1


title: Jurkat_3B6_TripleKO_H3K4me3

description:
Library name: Sample11
column name in  K4Me3_normalized_counts.txt = 3B6_K4Me3


title: Jurkat_1D9_TripleKO_H3K4me3

description:
Library name: Sample9
column name in  K4Me3_normalized_counts.txt = 1D9_K4Me3


title: NIPBL-D7_STAG1-KO-C5_DMSO_4hr_HiC

description: Library name: AP96


title: Jurkat_WT_H3K4me1

description:
Library name: Sample8
column name in K4Me1_normalized_counts.txt = JKT_K4Me1


title: bHLH35_S_Rep1

value: Seedlings

value: bHLH35 mutant in Col0 background

value: Salt stress


title: Jurkat_2G5_TripleKO_H3K4me3

description:
Library name: Sample10
column name in  K4Me3_normalized_counts.txt = 2G5_K4Me3


title: bHLH35_HL+HS_Rep1

value: High light and heat stress together


title: 3B6_IgG

description: Library name: Sample13


title: Myobacterium tuberculosis, INH, 24 hrs, Biological Replicate 3

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: INH


title: bHLH35_HS_Rep1

value: Heat stress


title: Jurkat_2G5_TripleKO_H3K4me1

description:
Library name: Sample6
column name in K4Me1_normalized_counts.txt = 2G5_K4Me1


title: Jurkat_1D9_TripleKO_H3K4me1

description:
Library name: Sample5
column name in K4Me1_normalized_counts.txt = 1D9_K4Me1


title: bHLH35_HL_Rep1

value: High light


title: NIPBL-D7_STAG1-KO-A7_DMSO_4hr_HiC

description: Library name: AP94

value: DMSO 4hr


title: NIPBL-D7_STAG1-2-WT_dTAG_4hr_R2_HiC

description: Library name: AP93

value: dTAG 4hr


title: bHLH35_Control_Rep1

value: No treatment


title: Myobacterium tuberculosis, BDQ, 24 hrs, Biological Replicate 3

value: BDQ


title: NIPBL-D7_STAG1-2-WT_DMSO_4hr_R2_HiC

description: Library name: AP92


title: Myobacterium tuberculosis, CLZ, 24 hrs, Biological Replicate 3

value: CLZ


title: Col0_S+HL+HS_Rep3

value: Columbia 0

value: Salt, high light and heat stress together


title: Jurkat_WT_H3K27ac

description:
Library name: Sample4
column name in H3K27Ac_normalized_counts.txt = JKT_K27Ac

value: Jurkat

value: Thymocyte

value: WT

value: H3K27ac (Abcam, #AB4729)


title: Jurkat_3B6_TripleKO_H3K27ac

description:
Library name: Sample3
column name in H3K27Ac_normalized_counts.txt = 3B6_K27Ac

value: Triple KO BEX1 | BEX2 | BEX5


title: Col0_S+HL_Rep3

value: Seedlings

value: Salt and high light stress together


title: Jurkat_1D9_TripleKO_H3K27ac

description:
Library name: Sample1
column name in H3K27Ac_normalized_counts.txt = 1D9_K27Ac


title: NIPBL-D7_STAG1-2-WT_dTAG_4hr_R1_HiC

description: Library name: AP91

value: hTERT RPE-1


title: Col0_S_Rep3

value: Salt stress


title: Jurkat_Wtbis

description:
Library name: Sample7
column name in normalized_count_CRISPR.txt =Jktbis

data_processing:
Sequence read were trimmed of adapters with Trimmomatic using ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:8:TRUE
Read were mapped with Hisat2 with default parameters
Mapped read were counted using FeatureCount with the following parameters : -t exon -C -g gene_id -p -s 2
Assembly: hg38
Supplementary files format and content: tab delimited text included normalized count from Deseq2 object.

extract_protocol:
RNA extraction was done with RNeasy mini kit from Qiagen
Libraries were prepared using the Illumina Stranded mRNA Prep, Ligation kit, according to the manufacturer’s protocol (Illumina, Document #1000000124518 v04)


title: MPN-BP_patient_SCR-shRNA_rep2

city: Hannover

first: Florian

last: Perner

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

description: Library name: MPN-BP_patient_SCR-shRNA_rep2

data_processing:
Data processing and analysis was perfomed in a Galaxy environment (version: 24.2.3) hosted at Hannover Medical School, Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation
FASTQ files were trimmed using "fastp" (0.23.4) (default mode)
Trimmed paired-end reads were aligned to the human reference genome GRCh38/hg38 using RNA STAR (2.7.11a).
genome-coverage (generation of bigwig wiles) was conducted using "bamcoverage" (default mode)
Mapped reads were quantified using featureCounts (2.0.3) against the corresponding GTF annotation file.
Differential gene expression analysis was carried out using DESeq2 (2.11.40.8), and genes with an adjusted p-value < 0.05 and a fold change >2 were considered significantly differentially expressed.
Assembly: hg38
Supplementary files format and content: .bigwig file encoding coverage data for visualization in genome browser for all samples
Supplementary files format and content: .txt files containing normalized gene counts for HEL cells and MPN-BP1 primary patient cells
Supplementary files format and content: .xlsx file contains differentiall expression analysis (DESeq2 output) for HEL cells (all comparisons)
Supplementary files format and content: . Txt file  contains differentiall expression analysis (DESeq2 output) for MPN-BP1 primary patient cells (DOT1L-shRNA vs. scr control)

source_name: hematopoietic

growth_protocol: The human MPN-BP cell line HEL was grown in RPMI+10%FBS+5%Pen/Strep (Gibco) at 5% CO2 and 37°C. Primary MPN-BP patient cells were cultured in fully-supplemented human methylcellulose medium (H4034 Optimum)

extract_protocol:
RNA was extracted using the RNeasy Mini kit (Qiagen) accoding to the manufacturer's instructions
Poly-A tail selection and library preparation were performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA).

treatment_protocol: Drug treatment of HEL cells was performed using the LSD1-inhibitor Bomedemstat at a concentration of 150nM for 24h or 5d. DOT1L-knockouts in HEL cells were performed using the CRISPR-Cas9 system by stable expression of Cas9 and the sgRNA construct and continous selection with blasticidin (10µg/ml) and puromycin (1µg/ml). RNAi-mediated knockdown of DOT1L in primary human MPN-BP cell was performed by stable expression of a commercial shRNA construct (Sigma, Mission shRNAs) and continous selection with puromycine (1µg/ml).

value: hematopoietic

value: MPN-BP patient bone marrow

value: blast-phase MPN (MPN-BP)

value: JAK2-V617F / TP53-loss


title: Col0_S+HS_Rep3

value: Salt and heat stress together


title: NIPBL-D7_STAG1-2-WT_DMSO_4hr_R1_HiC

description: Library name: AP90

value: DMSO 4hr


title: Myobacterium tuberculosis, UNT, 4 hrs, Biological Replicate 3

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: 4 hrs

value: UNT


title: Myobacterium tuberculosis, UNT, 0 hrs, Biological Replicate 3, Plate Control

value: 0 hrs


title: Myobacterium tuberculosis, RIF, 4 hrs, Biological Replicate 3

value: RIF


title: Jurkat_2G5_TripleKO_H3K27ac

description:
Library name: Sample2
column name in H3K27Ac_normalized_counts.txt = 2G5_K27Ac

value: Jurkat

value: Thymocyte

value: H3K27ac (Abcam, #AB4729)


title: Myobacterium tuberculosis, RFP, 4 hrs, Biological Replicate 3

value: RFP


title: MPN-BP_patient_SCR-shRNA_rep3

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

description: Library name: MPN-BP_patient_SCR-shRNA_rep3


title: Myobacterium tuberculosis, ETH, 24 hrs, Biological Replicate 3

value: 24 hrs

value: ETH


title: Col0_HL+HS_Rep3

value: Seedlings

value: Columbia 0

value: High light and heat stress together


title: MPN-BP_patient_SCR-shRNA_rep1

description: Library name: MPN-BP_patient_SCR-shRNA_rep1

value: hematopoietic

value: MPN-BP patient bone marrow

value: blast-phase MPN (MPN-BP)

value: JAK2-V617F / TP53-loss


title: Col0_HS_Rep3

value: Heat stress


title: MPN-BP_patient_DOT1L-shRNA_rep3

description: Library name: MPN-BP_patient_DOT1L-shRNA_rep3


title: Myobacterium tuberculosis, PRE, 4 hrs, Biological Replicate 3

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: 4 hrs

value: PRE


title: Jurkat_D2bis_Electroporated

description:
Library name: Sample5
column name in normalized_count_CRISPR.txt = D2bis

value: Jurkat

value: WT Electroporated


title: Jurkat_D2_Electroporated

description:
Library name: Sample4
column name in normalized_count_CRISPR.txt = D2

value: Thymocyte


title: Myobacterium tuberculosis, PZA, 4 hrs, Biological Replicate 3

value: PZA


title: MPN-BP_patient_DOT1L-shRNA_rep2

description: Library name: MPN-BP_patient_DOT1L-shRNA_rep2


title: Col0_HL_Rep3

value: High light


title: Jurkat_3B6_TripleKO

description:
Library name: Sample3
column name in normalized_count_CRISPR.txt = 3B6

value: Triple KO BEX1 | BEX2 | BEX5


title: Col0_S+HL+HS_Rep2

value: Seedlings

value: Salt, high light and heat stress together


title: Myobacterium tuberculosis, LIN, 4 hrs, Biological Replicate 3

value: LIN


title: Jurkat_2G5_TripleKO

description:
Library name: Sample2
column name in normalized_count_CRISPR.txt = 2G5


title: Jurkat_1D9_TripleKO

description:
Library name: Sample1
column name in normalized_count_CRISPR.txt = 1D9


title: Col0_Control_Rep3

value: Columbia 0

value: No treatment


title: Col0_S+HS_Rep2

value: Salt and heat stress together


title: Myobacterium tuberculosis, ETH, 4 hrs, Biological Replicate 3

value: ETH


title: HEL_NTC_Bomedemstat_24h_rep2

description: Library name: HEL_NTC_Bomedemstat_24h_rep2

value: hematopoietic

value: HEL

value: blast-phase MPN (MPN-BP)

value: JAK2-V617F / TP53-loss


title: Jurkat_WT

description:
Library name: Sample6
column name in normalized_count_CRISPR.txt = Jkt

value: Jurkat

value: WT


title: Myobacterium tuberculosis, MOX, 4 hrs, Biological Replicate 3

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: 4 hrs

value: MOX


title: HEL_NTC_Bomedemstat_24h_rep3

description: Library name: HEL_NTC_Bomedemstat_24h_rep3


title: Myobacterium tuberculosis, INH, 4 hrs, Biological Replicate 3

value: INH


title: G402, anlotinib resistant, replicate 2

city: Sutton

first: Paul

middle: H

last: Huang

address: 15 Cotswold Road

institute: The Institute of Cancer Research

description:
Library name: G402AnloR_n2
Column name in gene_fpkm.txt: G402AnloR_n2

data_processing:
Adapter trimming and low-quality sequence removal was performed using trimmomatic
Mapping to hg38 reference genome was performed using HISAT2
Read count quantification was undertaken using featureCounts
Raw count normalisation and fpkm generation was undertaken using edgeR
Assembly: hg38
Supplementary files format and content: Tab-delimited text file contains FPKM values per sample

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen) according to manufacturer's instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: Anlotinib


title: Col0_S+HL_Rep2

value: Seedlings

value: Salt and high light stress together


title: Myobacterium tuberculosis, CLZ, 4 hrs, Biological Replicate 3

value: CLZ


title: Col0_S_Rep2

value: Columbia 0

value: Salt stress


title: G402, anlotinib resistant, replicate 1

description:
Library name: G402AnloR_n1
Column name in gene_fpkm.txt: G402AnloR_n1


title: Myobacterium tuberculosis, BDQ, 4 hrs, Biological Replicate 3

value: BDQ


title: HEL_NTC_Bomedemstat_5d_rep3

description: Library name: HEL_NTC_Bomedemstat_5d_rep3

value: hematopoietic


title: A549 not treatment 48 h 2

value: A549 cell line


title: CBS138_RPMI_VORI_A

value: A


title: HEL_NTC_Bomedemstat_5d_rep2

description: Library name: HEL_NTC_Bomedemstat_5d_rep2

value: HEL

value: blast-phase MPN (MPN-BP)

value: JAK2-V617F / TP53-loss


title: Col0_HS_Rep2

value: Heat stress


title: Myobacterium tuberculosis, UNT, 0 hrs, Biological Replicate 3

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: 0 hrs

value: UNT


title: G402, sitravatinib resistant, replicate 1

description:
Library name: G402_SitR_n1
Column name in gene_fpkm.txt: G402_SitR_n1

value: Sitravatinib


title: Col0_HL_Rep2

value: Seedlings

value: High light


title: G402, regorafenib resistant, replicate 2

description:
Library name: G402_RegR_n2
Column name in gene_fpkm.txt: G402_RegR_n2

value: Regorafenib


title: Col0_Control_Rep2

value: Columbia 0

value: No treatment


title: HEL_NTC_DMSO_rep3

description: Library name: HEL_NTC_DMSO_rep3

value: DMSO


title: Myobacterium tuberculosis, RIF, 24 hrs, Biological Replicate 2

value: 24 hrs

value: RIF


title: Myobacterium tuberculosis, UNT, 24 hrs, Biological Replicate 2


title: G402, regorafenib resistant, replicate 1

description:
Library name: G402_RegR_n1
Column name in gene_fpkm.txt: G402_RegR_n1


title: HEL_NTC_DMSO_rep2

description: Library name: HEL_NTC_DMSO_rep2

value: hematopoietic


title: Col0_S+HL+HS_Rep1

value: Salt, high light and heat stress together


title: G402, pazopanib resistant, replicate 2

description:
Library name: G402_PazR_n2
Column name in gene_fpkm.txt: G402_PazR_n2

value: Pazopanib


title: HEL_NTC_DMSO_rep1

description: Library name: HEL_NTC_DMSO_rep1

value: HEL

value: blast-phase MPN (MPN-BP)

value: JAK2-V617F / TP53-loss


title: Myobacterium tuberculosis, RFP, 24 hrs, Biological Replicate 2

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: RFP


title: G402, pazopanib resistant, replicate 1

description:
Library name: G402_PazR_n1
Column name in gene_fpkm.txt: G402_PazR_n1


title: Myobacterium tuberculosis, PZA, 24 hrs, Biological Replicate 2

value: PZA


title: Col0_S+HS_Rep1

value: Seedlings

value: Salt and heat stress together


title: HEL_DOT1L-ko_Bomedemstat_24h_rep3

description: Library name: HEL_DOT1L-ko_Bomedemstat_24h_rep3


title: Myobacterium tuberculosis, PRE, 24 hrs, Biological Replicate 2

value: PRE


title: Col0_HL+HS_Rep2

value: Columbia 0

value: High light and heat stress together


title: G402, sitravatinib resistant, replicate 2

description:
Library name: G402_SitR_n2
Column name in gene_fpkm.txt: G402_SitR_n2

value: Sitravatinib


title: Col0_S+HL_Rep1

value: Salt and high light stress together


title: G402, parental, replicate 2

description:
Library name: G402_n2
Column name in gene_fpkm.txt: G402_n2


title: HEL_NTC_Bomedemstat_5d_rep1

description: Library name: HEL_NTC_Bomedemstat_5d_rep1


title: HEL_DOT1L-ko_Bomedemstat_24h_rep2

description: Library name: HEL_DOT1L-ko_Bomedemstat_24h_rep2


title: Myobacterium tuberculosis, MOX, 24 hrs, Biological Replicate 2

value: 24 hrs

value: MOX


title: Col0_S_Rep1

value: Salt stress


title: G402, parental, replicate 1

description:
Library name: G402_n1
Column name in gene_fpkm.txt: G402_n1


title: Myobacterium tuberculosis, LIN, 24 hrs, Biological Replicate 2

value: LIN


title: Col0_HL+HS_Rep1


title: A204, anlotinib resistant, replicate 2

description:
Library name: A204AnloR_n2
Column name in gene_fpkm.txt: A204AnloR_n2

value: Anlotinib


title: Myobacterium tuberculosis, ETH, 24 hrs, Biological Replicate 2

value: ETH


title: Myobacterium tuberculosis, CLZ, 24 hrs, Biological Replicate 2

value: CLZ


title: A204, sitravatinib resistant, replicate 1

description:
Library name: A204_SitR_n1
Column name in gene_fpkm.txt: A204_SitR_n1


title: HEL_DOT1L-ko_Bomedemstat_5d_rep2

description: Library name: HEL_DOT1L-ko_Bomedemstat_5d_rep2

value: hematopoietic

value: HEL

value: blast-phase MPN (MPN-BP)

value: JAK2-V617F / TP53-loss


title: Col0_HL_Rep1

value: Seedlings

value: High light


title: Myobacterium tuberculosis, INH, 24 hrs, Biological Replicate 2

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: INH


title: Myobacterium tuberculosis, BDQ, 24 hrs, Biological Replicate 2

value: BDQ