title: Desmoid type fibromatosis12

description:
D12
190109_13)Expression_Profile.GRCh38.gene.txt
190109_13)Expression_Profile.GRCh38.transcript.txt

value: Thigh


title: YZ-10

status: Public on Sep 09 2025

type: SRA

city: Chicago

first: Thomas

last: Gajewski

state: IL

address: 929 E 57th St

country: USA

institute: University of Chicago

description: Library name: YZ-10

library_source: transcriptomic

data_processing:
Kallisto and tximport were used to align to gencode primary assembly sequence (release 39) and export sequencing data while Limma and edgeR R packages were used to process the count matrices. Samples were filtered by a minimum of 5,100,000 reads and genes were filtered using the following cutoffs: a minimum of 30 samples were required to express a given gene and with a minimum counts per million (CPM) of 1. Normalization was done using the “calcNormFactors” function, using the TMM method. Count data was transformed using “limmavoom” and data was centered using the scale function in R.
Assembly: gencode primary assembly sequence (release 39)
Supplementary files format and content: tab-delimited count matrix with samples in columns and transcripts in rows

molecule: total RNA

organism: Homo sapiens

source_name: skin

extract_protocol:
Patients donated a single 18g core biopsy which was either formalin-fixed paraffin-embedded (FFPE) or fresh frozen (FF). RNA was isolated using Qiagen RNeasy FFPE kit (Qiagen, 73504) for FFPE samples, or Qiagen RNeasy kit (Qiagen, 74104) for FF samples.
RNA QC (quality and quantity) was performed using an Agilent 2100 Bio-analyzer using Agilent reagents and protocols. RNA-SEQ libraries were generated using Illumina TruSEQ TotalRNA stranded library making kits using Illumina protocols. Library QC (quality and quantity) was performed using an Agilent 2100 Bio-analyzer using Agilent reagents and protocols. RNA-SEQ libraries were sequenced with paired-end 100 bp reads using an Illumina HiSEQ40000 with Illumina reagents and protocols.

tag: tissue

value: skin


title: Day 3 Cocultured FB rep3

city: Kowloon

first: Sin Yen

last: Tan

address: Clear Water Bay

country: Hong Kong

institute: HKUST

data_processing:
Quality of all raw FASTQ files was checked using Fastqc.
Reads were aligned to the human reference genome GRCh38 using STAR with default parameters.
Gene counts were made using featureCounts.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for each sample.

source_name: Fibroblasts (FB)

extract_protocol:
RNA were isolated using TRIzol reagent along with DNase application to purify the samples.
RNA libraries were prepared for sequencing using Smart-seq2 protocol and Illumina Nextera XT DNA Library Prep Kit.

tag: cell type

value: Normal Human Lung Fibroblasts

tag: time

value: day 3

tag: condition

value: Cocultured with EC


title: YZ-1

description: Library name: YZ-1


title: U1 HSV-1 rep1

city: Suzhou

first: Fan

last: Zhang

address: 100 Chongwen Road

country: China

institute: Suzhou Institute of Systems Medicine

data_processing:
Reads were treated using fastp software with parameter '-n 10 -q 5 -u 50' to discard reads which are short or in poor quality
The treated reads then mapped to mm10 reference genome using CLC Genomic Workbench 12 to get expression of genes
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each sample

organism: Mus musculus

source_name: BMDM

extract_protocol:
The cell samples were lysed in TRIzol and extract total RNA for RNA-seq
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: BMDM

value: Bone-marrow-derived macrophage

tag: genotype

value: U1 snRNA knock-in

tag: treatment

value: HSV-1 infection


title: Desmoid type fibromatosis11

city: Seoul

first: Eun-jin

last: Jeong

address: 81 Ilwon-ro, Gangnam-gu

country: South Korea

institute: Samsung Advanced Institute for Health Sciences & Technolohy, Sungkyunkwan University

description:
D11
190109_13)Expression_Profile.GRCh38.gene.txt
190109_13)Expression_Profile.GRCh38.transcript.txt

data_processing:
Trimmomatic v0.38 was used to remove adapter sequences and trim bases with poor base quality.
The cleaned reads were aligned to the Homo sapiens (GRCh37) using HISAT v2.1.0 (KIM et al, 2015), based on the HISAT and Bowtie2 implementations.
Aligned data (SAM file format) were sorted and indexed using SAMtools v 1.9. After alignment, the transcripts were assembled and quantified using StringTie v2.1.3b (Pertea, Mihaela, et al., 2015, 2016).
Assembly: GRCh37
Supplementary files format and content: Gene-level and Transcript-level quantification were calculated as raw read count, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Million).

source_name: abdominal wall

extract_protocol:
Total RNA was extracted from the samples using an RNeasy FFPE Kit (Qiagen, 73504) according to the manufacturer’s instructions.
A total of 100 ng of total RNA was subjected to a sequencing library construction using the Agilent SureSelectXT RNA Direct kit according to the manufacturer’s protocol.

value: abdominal wall


title: Day 3 Cocultured FB rep2


title: U1 mock rep3

value: mock


title: hepithelial carcinoma cells, TGF-β treated (T4), 48h

city: HYDERABAD

first: Swati

last: Singh

state: TELANGANA

address: BITS PILANI HYDERABAD CAMPUS, JAWAHAR NAGAR, KAPRA MANDAL, MEDCHAL

department: BIOLOGICAL SCIENCES

country: India

institute: BITS PILANI HYDERABAD CAMPUS

data_processing:
The following data analysis flow was followed: Data QC, Contamination removal, Read alignment, expression estimation, differential expression, gene ontology and pathway analysis; The QC passed paired end reads were aligned to the reference human genome (hg19) and alignment was performed using HISAT2 (2.1.0)
Unwanted sequences, including nonpolyA tailed RNAs, mitochondrial genome sequences, ribosomal RNAs, transfer RNAs, adapter sequences were removed using Bowtie2 (2.2.4)
Assembly: Reference human genome (hg19)
Supplementary files format and content: Excel sheet of expression count file with following description is provided: Ensemble ID, expression counts (control and TGF-β treated), gene symbol, gene biotype, transcript biotype, chromosomal location

source_name: Pharynx

extract_protocol:
Total RNA was isolated using an MN Nucleo Spin RNA Plus isolation kit (Cat. No. 740984.5)
RNA-seq libraries were made with NEB Ultra II Directional RNA-seq Library prep kit according to the manufacturer's instructions.

value: Pharynx

value: FaDu

value: Epithelial

value: WT

value: TGF-β treated


title: Desmoid type fibromatosis10

description:
D10
190109_13)Expression_Profile.GRCh38.gene.txt
190109_13)Expression_Profile.GRCh38.transcript.txt


title: U1 mock rep2


title: Desmoid type fibromatosis9

description:
D9
187416_13)Expression_Profile.GRCh37.gene.txt
187416_13)Expression_Profile.GRCh37.transcript.txt

source_name: small bowel

value: small bowel


title: Day 1 Monocultured FB rep7

value: day 1

value: Monocultured


title: hepithelial carcinoma cells, TGF-β treated (T3), 48h


title: hepithelial carcinoma cells, TGF-β treated (T2), 48h


title: U1 mock rep1


title: WT HSV-1 rep3


title: Desmoid type fibromatosis7

description:
D7
187416_13)Expression_Profile.GRCh37.gene.txt
187416_13)Expression_Profile.GRCh37.transcript.txt


title: Day 1 Monocultured FB rep5

value: Normal Human Lung Fibroblasts


title: Day 3 Cocultured FB rep5

value: day 3


title: WT HSV-1 rep2


title: hepithelial carcinoma cells, Control (C3), 48h

value: Mock treated


title: Desmoid type fibromatosis6

description:
D6
187416_13)Expression_Profile.GRCh37.gene.txt
187416_13)Expression_Profile.GRCh37.transcript.txt


title: Desmoid type fibromatosis5

description:
D5
187416_13)Expression_Profile.GRCh37.gene.txt
187416_13)Expression_Profile.GRCh37.transcript.txt

source_name: Retroperitoenum

value: Retroperitoenum


title: Day 1 Monocultured FB rep4


title: Day 1 Monocultured FB rep3


title: WT HSV-1 rep1

value: BMDM

value: Bone-marrow-derived macrophage


title: WT mock rep3


title: Desmoid type fibromatosis4

description:
D4
187416_13)Expression_Profile.GRCh37.gene.txt
187416_13)Expression_Profile.GRCh37.transcript.txt

source_name: pelvic cavity

value: pelvic cavity


title: Day 1 Monocultured FB rep2


title: Rat nucleus RNA-seq, IH group, replicate 3

city: Zhangzhou

first: Li-Da

last: Chen

address: No 59, Shenglixiroad, Xiangcheng district

institute: Zhangzhou Affiliated Hospital of Fujian Medical University

description: Library name: CIH_3

library_source: transcriptomic single cell

data_processing:
Raw reads from sncRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline. Briefly, raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v1.17 to trim poly-A tail and adapter sequences. Cell barcode and UMI were extracted. After that, we used STAR v2.6.1a  to map reads to the reference genome mRatBN7.2 (rattus_enemebl_111). UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1software, and used to generate expression matrix files for subsequent analysis.
Assembly: mRatBN7.2
Supplementary files format and content: Filtered gene-barcode matrix files in Matrix Market Exchange format (MTX), including matrix.mtx.gz

molecule: nuclear RNA

organism: Rattus norvegicus

source_name: Kiney

extract_protocol:
3 renal tissue samples were randomly selected from each group and then subjected for sequencing. Renal tissues were harvested and washed in pre-cooled PBSE (PBS buffer containing 2 mM EGTA). Nuclei isolation was carried out using GEXSCOPE® Nucleus Separation Solution (Singleron Biotechnologies, Nanjing, China) refer to the manufacturer's product manual. Isolated nuclei were resuspended in PBSE to 106 nuclei per 400μl, filtered through a 40μm cell strainer, and counted with Trypan blue. Nuclei enriched in PBSE were stained with DAPI (1:1,000) (Thermo Fisher Scientific). Nuclei were considered as DAPI-positive singlets.
The concentration of single nucleus suspension was adjusted to 3-4 × 105 nuclei/mL in PBS. Single nucleus suspension was then loaded onto a microfluidic chip (GEXSCOPE® Single Nucleus RNA-seq Kit, Singleron Biotechnologies) and snRNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron Biotechnologies). The resulting snRNA-seq libraries were sequenced on an Illumina novaseq 6000 instrument with 150 bp paired end reads.

value: Kiney

tag: strain

value: Sprague-Dawley

tag: Sex

value: male

value: Mixed renal cells

value: CIH


title: Day 3 Cocultured FB rep1

value: Cocultured with EC


title: Desmoid type fibromatosis8

description:
D8
187416_13)Expression_Profile.GRCh37.gene.txt
187416_13)Expression_Profile.GRCh37.transcript.txt


title: Day 1 Monocultured FB rep1


title: Rat nucleus RNA-seq, IH group, replicate 2

description: Library name: CIH_2


title: WT mock rep1

value: WT

value: mock


title: Desmoid type fibromatosis2

description:
D2
187416_13)Expression_Profile.GRCh37.gene.txt
187416_13)Expression_Profile.GRCh37.transcript.txt

value: small bowel


title: Desmoid type fibromatosis3

description:
D3
187416_13)Expression_Profile.GRCh37.gene.txt
187416_13)Expression_Profile.GRCh37.transcript.txt


title: hepithelial carcinoma cells, Control (C4), 48h

value: Pharynx

value: FaDu

value: Epithelial


title: Day 1 Monocultured FB rep6

value: Normal Human Lung Fibroblasts

value: day 1

value: Monocultured


title: Rat nucleus RNA-seq, IH group, replicate 1

description: Library name: CIH_1


title: Rat nucleus RNA-seq, NC group, replicate 3

description: Library name: NC_3

value: NC


title: Desmoid type fibromatosis1

description:
D1
187416_13)Expression_Profile.GRCh37.gene.txt
187416_13)Expression_Profile.GRCh37.transcript.txt


title: Bone tissue of control mice replicate (second replicate)

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

data_processing:
Single-cell sequencing datasets were analysed by package CellRanger (v6.0.0, 10× Genomics) and Seurat (v4.1.0). The 10× Genomics pre-built mouse genome for mm10-3.0.0 was used as reference.
Assembly: mm10
Supplementary files format and content: cell barcodes (tab-separated text file)
Supplementary files format and content: cell features (tab-separated text file)
Supplementary files format and content: Cell Ranger Feature Barcode Matrices (MEX Format)

source_name: Bone

extract_protocol:
Mice were treated with control (n = 2) and tail-suspended (n = 2)for 28 days. After that, tibiae and femurs were flushed with a 2 mL syringe using ice-cold PBS to remove bone marrow cells. The tissues were enzymatically digested and dissociated into single cell for further single-cell RNA sequencing analysis.
According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1. The libraries were finally sequenced using an  Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp  (PE150) reading strategy.

value: Bone

value: Wild-type mice

value: No treatment


title: Day 1 Cocultured FB rep9


title: Day 1 Cocultured FB rep8


title: Bone tissue of control mice replicate (first replicate)


title: Rat nucleus RNA-seq, NC group, replicate 2

description: Library name: NC_2

value: Kiney

value: Sprague-Dawley

value: male


title: hepithelial carcinoma cells, Control (C2), 48h

value: Mock treated


title: M1 [M1_c]

city: Debrecen

first: Laszlo Attila

last: Papp

state: Hajdú-Bihar Vármegye

address: Egyetem tér 1.

department: Department of Genetics and Applied Microbiology

country: Hungary

institute: University of Debrecen

description:
M1_vs_K1_ModT-Test_with_BH-FDR.xlsx
K1_vs_M1_featureCount.out.txt

data_processing:
Alignment with HISAT2 aligner
Generation of BAM files
FeatureCount values were generated using Liao Y, Smyth GK and Shi W (2014). featureCounts software.
Quantification and normalization using StrandNGS with DeSeq algorithm
Assembly: In case of co-culture experiment S. pombe ASM294v2 assembly was used.
Assembly: In case of F. verticillioides ASM14955v1 was used.
Supplementary files format and content: in the co-culture experiment: pombe_count.out.txt file contains the tab delimited raw count values of S. pombe control (14) vs S. pombe co-cultured (6-Fv3). co-culture_vs_control-pombe_Moderated T-Test.xlsx file contains the normalized data with statistics (moderated T-test, BH-FDR)
Supplementary files format and content: in the co-culture experiment: fusarium_count file contains the tab delimited raw count values of F. verticillioides control vs F. verticillioides co-cultured (6-Fv3). co-culture_vs_control-fusarium_Moderated T-Test.xlsx file contains the normalized data with statistics (moderated T-test, BH-FDR)
Supplementary files format and content: in the fumonisin B1 experiment: K1_vs_M1_featureCount.out.txt file contains tab delimited raw count values of S. pombe control (K1) vs S. pombe+0.5ppm fumonisin B1 (M1). M1_vs_K1_ModT-Test_with_BH-FDR.xlsx file contains the normalized data with statistics (moderated T-test, BH-FDR)

organism: Schizosaccharomyces pombe

growth_protocol: Control S. pombe cells were grown on YEA (yeast-extract agar) media. Control F. verticillioides were grown on MXGB media. Both strains were cultured at 25°C.

extract_protocol:
RNA were extracted from cells using the method described by Lyne et al. (2003).RNA quality was checked with Agilent BioAnalyzer.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep kit for Illumina

treatment_protocol:
The S. pombe cells treated with FB1 (0.5 ppm) for 1hour in MXGB media at 30°C.
In case of co-culturing conditions: 100 µl.of overnight S. pombe cells were inoculated into 150ml MXGB. We excised 5x5 mm of F. verticillioides hyphaes were transferred from another pre-cultured F. verticillioides flask. S. pombe and F. verticillioides were co-cultured for 2 days at 25°C without shaking. Then the cells were separated and submitted to RNA extraction respectively.

value: WT

value: 0.5 ppm fuminisin B1


title: Day 1 Cocultured FB rep7

value: Cocultured with EC


title: Rat nucleus RNA-seq, NC group, replicate 1

description: Library name: NC_1

value: Mixed renal cells


title: M1 [M1_b]


title: Bone tissue of hindlimb unloading mice (second replicate)

value: Hindlimb unlloading


title: Day 1 Cocultured FB rep6


title: WT mock rep2

value: BMDM

value: Bone-marrow-derived macrophage

value: mock


title: Bone tissue of hindlimb unloading mice (first replicate)


title: Day 1 Cocultured FB rep5

value: Normal Human Lung Fibroblasts

value: day 1


title: M1 [M1_a]


title: Day 1 Cocultured FB rep4


title: K1, control [K1_c]


title: 7dpr_rep2

first: Hui

address: 167 Beilishi Road, Xicheng District

institute: Fuwai hospital

data_processing:
SpaceRanger (version: 2.0.0), Seurat (version: 3.2.2)
Sequencing read alignment, tissue detection, and spot barcode/UMI counting of the spatial transcriptomic data were performed separately for each section using the 10× Genomics official tool kit SpaceRanger with an H&E-stained bright-field image and FASTQ files as inputs.
After filtering out low-quality spots manually using Loupe Browser (v.6.0.0), a total of 17,541 spots with 31,053 genes were obtained.
Gene-spot matrix extraction and performed using Seurat.
Assembly: refdata-cellranger-mm10-3.0.0
Supplementary files format and content: tab-delimited text file includeds barcodes, gene name, and raw counts for each sample
Supplementary files format and content: tab-delimited text file includeds origin identity, replication, number of count, number of gene, and group information

molecule: polyA RNA

source_name: heart

extract_protocol:
The Visium Spatial Gene Expression Reagents Kits (10x Genomics) were employed to perform a spatial transcriptome analysis on heart sections, adhering to the manufacture’s guidelines. Briefly, mouse hearts were dissected and expeditious embedded in an OCT-filled tissue embedding mold, which was then immersed in a blend of isopentane and liquid nitrogen. The OCT-embedded heart tissue blocks were subsequently cryosectioned using a cryostat to aquire sections of suitable dimensions for the Visium Spatial slides. Sections of AR hearts and their corresponding positions in sham hearts were obtained and placed onto the capture areas of the Visium Spatial slides.
Sections from the same heart were collected in a Eppendorf tube to evaluate the quality of RNA. After confirming the RNA quality using an Agilent 2100 TapeStation, the tissue sections on the Gene Expression Spatial slides were fixed in methanol and stained with Hematoxylin and Eosin. The tissue sections were then imaged. The heart sections were subject to permeabilization for a duration of 18 minutes, followed by RNA reverse transcription. The determination of the optimal permeabilization time was conducted using the Visum Spatial Tissue Optimization Kit (10x Genomics) in accordance with the manufacturer’s protocol. Subsequently, second strand cDNA synthesis was performed on the tissue sections and transferred to an Eppendorf tube after denaturation. The cDNA obtained from the spatially barcode tissue slide underwent PCR amplification and enzymatic fragmentation. The final sequencing library was generated by incorporating indexes through the processes of End Repair, A-tailing, Adaptor ligation, and PCR.

value: heart

value: Apex resection


title: 7dpr_rep1


title: K1, control [K1_b]


title: Day 1 Cocultured FB rep3


title: K1, control [K1_a]


title: Day 1 Cocultured FB rep2


title: 7dwt

value: Wild type


title: 14, control [14-rep2]

description:
co-culture_vs_control-pombe_Moderated T-Test.xlsx
pombe_count.out.txt


title: 6dsh

value: Sham


title: Day 1 Cocultured FB rep1


title: Developing_Root_Cortex 3 mM KCl experiment 3

city: Malaga

first: Rafael

middle: A

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

country: Spain

institute: Universidad de Málaga

description: Library name: CRDC_3

data_processing:
Base calling was made with the NovaSeq 6000 RTA3 software (Illumina). Conversion of cbcl files to fastq files were made with bcl2fastq2 Conversion Software (Illumina)
The raw reads were trimmed (quality and contamination) using SeqTrimBB software (https://github.com/rafnunser/seqtrimbb). Only the pairs in which both reads passed the quality test were further analysed (Q>20).
The Pinus pinaster transcriptome from Genbank (GenBank: GJFX00000000.1) was used as the reference for the read mapping that was performed with BWA using the MEM option (Li and Durbin, 2009, Bioinformatics 25: 1754-1760). The read count was obtained with the phyton script sam2counts (https://github.com/vsbuffalo/sam2counts).
The transcript expression was normalised by cpm. Finally the transcripts were filtered; 2 cpm in at least 2 samples (Robinson et al., 2010, Bioinformatics 26: 139-140).
Assembly: TSA: Pinus pinaster, transcriptome shotgun assembly (GenBank: GJFX00000000.1)
Supplementary files format and content: Tab-delimited text files include CPM normalized counts for each sample (CRC_1, CRC_2, CRC_3, NRC_1, NRC_2, NRC_3, CRM_1, CRM_2, CRM_3, NRM_1, NRM_2, NRM_3, CRDV_1, CRDV_2, CRDV_3, NRDV_1, NRDV_2, NRDV_3, CRDC_1, CRDC_2, CRDC_3, NRDC_1, NRDC_2, NRDC_3).The column id is the sequence identifier.

organism: Pinus pinaster

growth_protocol: Seeds from maritime pine (Pinus pinaster Ait.) from “Sierra Segura y Alcaraz” (Albacete, Spain) were provided by from the Área de Recursos Genéticos Forestales of the Spanish Ministerio de Agricultura, Pesca y Alimentación. Seeds were imbibed in distilled water for 24 h under continuous aeration and germinated in a plastic tray with vermiculite as a substrate. Seedlings were grown in vermiculite in plant growth chambers under 16 h light photoperiod, a luminal intensity of 100 μmol m−2 s−1, a constant temperature of 25 °C and watered twice a week with distilled water.

extract_protocol:
All the RNA extractions from the microdissection procedure were carried out using manufacturer’s instruction protocol (non‐LCM) for the RNAqueous‐Micro RNA Isolation Kit (Ambion, USA). RNA quality, DNA contamination and first quantification were performed via RNA Pico Assay for the 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). Quantification was verified via a Qubit RNA BR (Broad-Range) Assay Kit (Invitrogen, Paisley, UK).  RNA samples with RNA integrity number (RIN) higher than 7 were used for subsequent RNA sequencing.
The low input RNA-seq was carried out by Novogen. The cDNA synthesis and amplification, and the library preparation was made with the SMART-Seq™ v4 Ultra™ Low Input RNA Kit for Sequencing (Takara, Mountain View, CA, USA) following the manufacturer’s instructions. RNA sequencing was made in a NovaSeq 6000 sequencer according to the manufacturer’s instructions for paired-end reads (Illumina, San Diego, CA, USA). The 24 samples were sequenced producing paired-end reads of 150 bp length.

treatment_protocol: One-month old maritime pine seedlings were used for this experiment. Pine seedlings were randomly subdivided into three different groups, relocated into forestall seedbeds and irrigated with 80 mL of a solution that contains macro- and micronutrients without any nitrogen source (1.16 mM KCl; 0.63 mM KH2PO4; 0.35 mM MgSO4·7H2O; 0.17 mM CaCl2·H2O; 80 μM EDTA-FeSO4; 25.9 μM H3BO3; 10.2 μM MnCl2·4H2O; 1.3 μM ZnSO4·7H2O; 0.7 μM CuSO4·5H2O; 0.1 μM Na2MoO4·2H2O). After three days of acclimation, the control group was irrigated with 80 mL of KCl (C), the second group was supplied with 80 mL of 3 mM NO3K. Root samples were collected 2 hours after the irrigation. Seedling’s root tips were cut and tissues of 5 - 6 mm were imbibed in a specimen holder with Tissue‐Tek optimal cutting temperature embedding medium (Sakura Finetek, Alphen aan den Rijn, The Netherlands) and immediately frozen in liquid nitrogen for cryostat sectioning. LCM procedure:  1 day before cryosectioning, root tip samples were tempered at -20°C. Thirty micrometers thick sections were cut using a cryostat (CM1950, Leica Biosysyems, Wetzlar, Germany) at -20°C and mounted on PET-membrane 1.4 µm steel frame (Leica Biosysyems, Wetzlar, Germany). The PET-membrane containing samples were stored at −80°C until use. Before microdissection, samples were fixed in cold 70% ethanol for 30 seconds, embedding medium was removed in DEPC-treated water for 2 minutes and refixed in cold 100% ethanol for 2 minutes. Afterwards, samples were air dried and used for microdissection. A laser microdissector (LMD 7000, Leica, Wetzlar, Germany) was used for microdissection. The samples obtained were placed into 0.5 mL tube caps containing 20 μL of lysis buffer from the RNAqueous-Micro RNA Isolation Kit (Ambion, USA) and all samples were placed at −80°C. Four different tissue areas were isolated by microdissection approximatively corresponding to the root cap (RC), meristem (RM), developing cortex (RDC) and developing vessels (RDV) areas.

tag: provenance

value: Segura-Alcaraz

tag: developmental stage

value: 1 month-old seedling

value: 3 mM KCl

value: 2 hours

tag: experimental replicate


title: 14, control [14-rep1]

value: WT


title: Developing_Root_Cortex 3 mM KCl experiment 2

description: Library name: CRDC_2


title: Developing_Root_Cortex 3 mM KCl experiment 1

description: Library name: CRDC_1


title: Developing_Root_Cortex 3 mM NO3K experiment 2

description: Library name: NRDC_2

value: 3 mM NO3K


title: 6dpr


title: Developing_Root_Cortex 3 mM NO3K experiment 1

description: Library name: NRDC_1


title: Day 5 Cocultured EC rep15

source_name: Endothelial Cells (EC)

value: HUVEC

value: day 5

value: Monocultured


title: Developing_Root_Cortex 3 mM NO3K experiment 3

description: Library name: NRDC_3


title: 862T, ACC

city: La Jolla

first: Kuniaki

last: Sato

state: CA

address: 3855 Health Sciences Dr Room 2345

department: Moores Cancer Center

institute: University of California San Diego

description: Library name: 862T

data_processing:
Raw sequencing data includnig adapter sequences or low-quality sequences was filtered using SOAPnuke software with the following parameters: " -n 0.001 -l 20 -q 0.4 --adaMR 0.25 --ada_trim".
The filtered sequenced reads were aligned to the human reference genome hg38 using STAR v2.7.9a with Gencode v38 annotations.
Read count data for each gene was calculated usng RSEM v1.3.1.
Assembly: hg38
Supplementary files format and content: tab-deliminated text files containing read count data for each gene. Gene names are represented as Ensembl Gene IDs.

source_name: ACC

extract_protocol:
The extraction of RNA from skin tissues and tumor tissues were performed using a NucleoSpin RNA plus kit.
Library preparation was performed using DNBSEQ Eukaryotic Strand-specific mRNA library kit.

value: ACC

value: Adenoid Cystic Carcinoma


title: 5dpr_rep2


title: Day 5 Cocultured EC rep14


title: 5dpr_rep1


title: Developing_Root_Vascular 3 mM NO3K experiment 2

description: Library name: NRDV_2


title: 399T, ACC

description: Library name: 399T


title: Day 5 Cocultured EC rep13


title: 4dsh


title: 293T, EACSCC

description: Library name: 293T

source_name: EACSCC

value: EACSCC

value: Squamous Cell Carcinoma


title: Developing_Root_Vascular 3 mM NO3K experiment 1

description: Library name: NRDV_1


title: Day 5 Cocultured EC rep12


title: 4dpr

value: heart


title: 168T, EACSCC

description: Library name: 168T


title: Developing_Root_Vascular 3 mM KCl experiment 3

description: Library name: CRDV_3


title: Day 5 Cocultured EC rep11


title: Developing_Root_Vascular 3 mM KCl experiment 2

description: Library name: CRDV_2


title: Day 5 Cocultured EC rep10


title: 854T, EACSCC

description: Library name: 854T


title: 3dpr

value: Apex resection


title: 2dpr


title: Developing_Root_Vascular 3 mM KCl experiment 1

description: Library name: CRDV_1


title: Day 5 Cocultured EC rep9


title: 040T, EACSCC

description: Library name: 040T


title: 596T, EACSCC

description: Library name: 596T


title: Developing_Root_Vascular 3 mM NO3K experiment 3

description: Library name: NRDV_3


title: Day 5 Cocultured EC rep8


title: 1dwt

value: Wild type


title: Root meristem 3 mM NO3K experiment 3

description: Library name: NRM_3

source_name: Root meristem

value: Root meristem


title: 1dpr


title: Day 5 Cocultured EC rep7

value: Cocultured with FB


title: U1 HSV(MOI=0.1) 8h rep2

data_processing:
Reads were treated using fastp software with parameter '-n 10 -q 5 -u 50' to discard reads which are short or in poor quality
The treated reads then mapped to mm10 reference genome using CLC Genomic Workbench 12 to get expression of genes
Assembly: mm10

value: BMDM

value: Bone-marrow-derived macrophage

value: wild type

value: U1 transfection,HSV infection


title: Root meristem 3 mM NO3K experiment 2

description: Library name: NRM_2

value: Segura-Alcaraz

value: 1 month-old seedling

value: 3 mM NO3K

value: 2 hours


title: Root meristem 3 mM NO3K experiment 1

description: Library name: NRM_1


title: 433T, EACSCC

description: Library name: 433T


title: Day 5 Cocultured EC rep6

value: HUVEC

value: day 5


title: RFP HSV(MOI=0.1) 8h rep2

value: RFP transfection,HSV infection


title: 266T, EACSCC

description: Library name: 266T

value: EACSCC

value: Squamous Cell Carcinoma


title: Root meristem 3 mM KCl experiment 3

description: Library name: CRM_3

value: 3 mM KCl


title: Root meristem 3 mM KCl experiment 2

description: Library name: CRM_2


title: U1 HSV(MOI=0.1) 4h rep2


title: Day 5 Cocultured EC rep5


title: 156T, EACSCC

description: Library name: 156T


title: RFP HSV(MOI=0.1) 4h rep2


title: Root meristem 3 mM KCl experiment 1

description: Library name: CRM_1


title: 911T, EACSCC

description: Library name: 911T


title: Day 5 Cocultured EC rep3


title: U1 HSV(MOI=1) 8h rep2


title: 473T, EACSCC

description: Library name: 473T


title: 291T, EACSCC

description: Library name: 291T


title: Root cap 3 mM NO3K experiment 2

description: Library name: NRC_2

source_name: Root cap

value: Root cap


title: Day 5 Cocultured EC rep1


title: Root cap 3 mM NO3K experiment 3

description: Library name: NRC_3


title: RFP HSV(MOI=1) 8h rep2


title: Day 5 Cocultured EC rep2


title: Root cap 3 mM NO3K experiment 1

description: Library name: NRC_1


title: 858T, EACSCC

description: Library name: 858T


title: 289T, EACSCC

description: Library name: 289T


title: U1 HSV(MOI=1) 4h rep2


title: Root cap 3 mM KCl experiment 3

description: Library name: CRC_3


title: Day 3 Monocultured EC rep7

value: day 3

value: Monocultured


title: 102T, EACSCC

description: Library name: 102T


title: Day 3 Monocultured EC rep8


title: RFP HSV(MOI=1) 4h rep2

value: BMDM


title: U1 mock rep2

value: Bone-marrow-derived macrophage

value: U1 transfection


title: Root cap 3 mM KCl experiment 2

description: Library name: CRC_2


title: 986T, EACSCC

description: Library name: 986T


title: Day 5 Cocultured EC rep4

value: Cocultured with FB


title: Day 3 Monocultured EC rep6


title: 140T, EACSCC

description: Library name: 140T


title: Root cap 3 mM KCl experiment 1

description: Library name: CRC_1

value: Segura-Alcaraz


title: U1 HSV(MOI=0.1) 8h rep1

value: wild type

value: U1 transfection,HSV infection


title: Ccl28-KO_4

city: Hangzhou

first: Rifeng

last: Gao

state: Zhejiang

address: No. 88 Jiefang Road

institute: Zhejiang University

description: Library name: Samples 6

data_processing:
RNA quantification and qualification:RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) . RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
Library preparation for Transcriptome sequencing:A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.  Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.  Briefly, mRNA was purified from total RNA using poly-T oligo attached magnetic beads.  Fragmentation was carried out using divalent cations under elevated temperature  in NEBNext First Strand Synthesis Reaction Buffer(5X).  First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-).  Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities.  After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization.  In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).  Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR.  Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer.  Atlast, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
Clustering and sequencing: The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.
Data Analysis: 1. Data quality control Use fastp v 0.19.3 to filter the original data, mainly to remove reads with adapters; when the N content in any sequencing reads exceeds 10% of the base number of the reads, remove the paired reads; when any sequencing reads When the number of low quality (Q<=20) bases contained in reads exceeds 50% of the bases of the reads, this paired reads will be removed. All subsequent analyses are based on clean reads. 2. Reads mapping to the reference genome Download the reference genome and its annotation files from the designated website, use HISAT v2.1.0 to construct the index, and compare clean reads to the reference genome. 3. New transcript prediction Use StringTie v1.3.4d for new gene prediction. StringTie applies network streaming algorithms and optional de novo to splice transcripts. Compared with Cufflinks and other software, StringTie can splice a more complete and accurate transcript, and the splicing speed is faster. 4. Quantification of gene expression levels Use featureCounts v1.6.2 to calculate the gene alignment, and then calculate the FPKM of each gene based on the gene length. FPKM is currently the most commonly used method to estimate gene expression levels. 5. Difference analysis DESeq2 v1.22.1 was used to analyze the differential expression between the two groups, and the P value was corrected using the Benjamini & Hochberg method. The corrected P value and |log2foldchange| are used as the threshold for significant difference expression. 6. Differential gene enrichment analysis The enrichment analysis is performed based on the hypergeometric test. For KEGG, the hypergeometric distribution test is performed with the unit of pathway; for GO, it is performed based on the GO term. 7. Differential AS analysis Use rMATS v3.1.0 to analyze variable splicing events, including five alternative splicing events: SE, RI, MXE, A5SS, and A3SS. 8. SNP analysis Use GATK v4.0.11.0 to analyze the variant sites, and use annovar to annotate the variant sites. 9. Differential gene protein interaction analysis The protein interaction analysis of differentially expressed genes is based on the STRING database of known and predicted protein--protein interactions. For the species existing in the database, we construct the network by extracting the target gene list from the database; otherwise, use blast v2.7.1+ to compare the target gene sequence with the selected reference protein sequence, and then according to the selected reference species Know the interaction to build a network. 10. GSEA Use gsea--3.0.jar for gene set enrichment analysis. 11. WGCNA Use WGCNA v1.69 for weighted gene co--expression network analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Mus

source_name: cardiac microvascular endothelial cells

growth_protocol: RNA-seq was performed on CD45-CD31+ ECs magnetic bead sorted from WT and Ccl28-KO mice

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer's protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
Then the libraries were constructed using TruSeq Stranded mRNALTSample Prep Kit(Ilumina,San Diego, CA, USA) .

treatment_protocol: Left coronary artery ligation surgery

value: cardiac microvascular endothelial cells

value: Left coronary artery ligation surgery


title: 354T, EACSCC

description: Library name: 354T


title: Day 3 Monocultured EC rep4

value: HUVEC


title: RFP HSV(MOI=0.1) 8h rep1

value: RFP transfection,HSV infection


title: Day 3 Monocultured EC rep3


title: U1 HSV(MOI=0.1) 4h rep1


title: 145S, skin

description: Library name: 145S

source_name: Noncancerous Ear Skin

value: Noncancerous Ear Skin

value: Skin Tissue


title: Ccl28-KO_3

description: Library name: Samples 5


title: 432S, skin

description: Library name: 432S


title: Ccl28-KO_2

description: Library name: Samples 4


title: RFP HSV(MOI=0.1) 4h rep1


title: Day 3 Monocultured EC rep1


title: 320S, skin

description: Library name: 320S


title: Ccl28-WT_4

description: Library name: Samples 3

value: wild-type


title: Day 3 Monocultured EC rep2


title: U1 HSV(MOI=1) 8h rep1


title: Ccl28-WT_3

description: Library name: Samples 2


title: 398S, skin

description: Library name: 398S


title: RFP HSV(MOI=1) 8h rep1


title: RFP mock rep2

value: RFP transfection


title: Day 3 Cocultured EC rep8

value: day 3


title: 266S, skin

description: Library name: 266S


title: Day 3 Cocultured EC rep7


title: Ccl28-WT_2

description: Library name: Samples 1


title: Day 3 Monocultured EC rep5

value: Monocultured


title: U1 HSV(MOI=1)  4h rep1

value: BMDM


title: 442S, skin

description: Library name: 442S


title: C3HeB/FeJ_aIFNAR_HN878_d26_4

city: London

first: Anne

last: O'Garra

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

description: Library name: aIFNAR_d26_4

data_processing:
nf-core/rnaseq pipeline v3.16.1; default parameters
Assembly: mm10
Supplementary files format and content: csv of DESeq2 noramalised expression values

source_name: Lung

extract_protocol:
RNA was extracted from lung homogenates using the DirectZol Mini Kit with on-column DNase I digestion (Zymo), as per manufacturer’s instructions. BAL cell pellets were resuspended in TRI reagent and vortexed at high speed for ≥10 seconds to lyse. RNA was extracted from BAL lysates using the DirectZol Mini Kit with on-column DNase I digestion (Zymo), as per manufacturer’s instructions. RNA integrity of all samples was determined to range from 5.7 – 9.4 (median 7.9)
RNA-seq libraries from whole BAL and lung of HN878-infected C57BL/6 and C3HeB/FeJ mice and from lung tissue samples obtained from anti-IFNAR-treated HN878-infected C3HeB/FeJ mice were prepared using the total RNA library prep kit with Polaris ribosomal RNA depletion (Watchmaker Genomics)

value: Lung

tag: antibody

value: aIFNAR

value: HN878 Infected Day 26


title: RFP HSV(MOI=1) 4h rep1

source_name: BMDM

value: Bone-marrow-derived macrophage


title: C3HeB/FeJ_aIFNAR_HN878_d26_3

description: Library name: aIFNAR_d26_3


title: 945S, skin

description: Library name: 945S


title: Day 3 Cocultured EC rep5

value: Cocultured with FB


title: U1 mock rep1

value: wild type

value: U1 transfection


title: C3HeB/FeJ_aIFNAR_HN878_d26_2

description: Library name: aIFNAR_d26_2


title: RFP mock rep1


title: C3HeB/FeJ_aIFNAR_HN878_d26_1

description: Library name: aIFNAR_d26_1


title: 203S, skin

description: Library name: 203S


title: Day 3 Cocultured EC rep4


title: 6-Fv3 [6-Fv3-rep2]

description: co-culture_vs_control-pombe_Moderated T-Test.xlsx, co-culture_vs_control-fusarium_Moderated T-Test.xlsx

organism:
Schizosaccharomyces pombe
Fusarium verticillioides

value: WT

value: co-culture


title: Mus musculus, 500uM treat, rep2

city: Zhengzhou

first: yanyong

last: cao

state: henan

address: No. 116, Huayuan Road

institute: Henan Academy of Agricultural Sciences

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts.
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software (version2.20).
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).
The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Mus musculus, Ensembl_v101
Supplementary files format and content: 1_genes_fpkm_expression.xlsx: Excel file includes FPKM values for each Sample.

source_name: cranial bone

growth_protocol: We introduced a Mus musculus cranial defect with a diameter of 5 mm as an experimental defect model.

extract_protocol:
Total RNA was extracted using Trizol reagent (Thermo Fisher, 15596018) following the manufacturer's procedure. The RNA amount and purity of each sample were quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
We performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: Micro-computed tomography, hematoxylin and eosin staining, Masson staining, and immunohistochemical staining were used to determine the effectiveness of the composite as a scaffold in a Mus musculus skull defect model. The composite material loaded with 500 μM of metformin had the strongest osteoinduction ability under these conditions.

value: cranial bone

value: treatment (Met/alpha-CSH/nHA scaffold, 500uM)


title: Mus musculus, 500uM treat, rep3


title: Day 3 Cocultured EC rep2

value: HUVEC


title: Day 3 Cocultured EC rep3


title: C3HeB/FeJ_isotype_HN878_d26_3

description: Library name: Iso_d26_3

value: Isotype


title: Day 3 Cocultured EC rep1


title: 6-Fv3 [6-Fv3-rep1]


title: C3HeB/FeJ_isotype_HN878_d26_2

description: Library name: Iso_d26_2


title: HFF.hicar.50kPa.rep2

city: Durham

first: Charles

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

institute: Duke University

description: Library name: HFF.hicar.50kPa.rep2 (stiff rep2)

library_source: genomic

data_processing:
HiCAR libraries were processed with the nf-core pipeline that can be found at https://nf-co.re/hicar/1.0.0 with the following parameters: `--genome GrCh38, --profile singularity, --ensyme ‘MseI’, --restriction_sites ‘^TAA’, --resample_pairs, --qval_thresh 0.01`
Quality reads were determined using FASTQC
Adapters were trimmed using cutadapt
Reads were aligned to the reference genome using bwa mem
Aligned reads were then processed using pairtools and quality control was performed using pairsqc
MACS2 was used to call peaks and MAPS was used to find genomic interaction loops.
Differential analysis was performed using edgeR and files for visualization were generated using Cooler and Juicer
To compare the chromatin loops between ECM stiffness conditions, we used bedtools pairtopair with the -type parameter set to both, either, or neither
To compare the chromatin loops with the differentially accessible ATAC-seq peaks, we used bedtools pairtobed
Assembly: GRCh38
Supplementary files format and content: BWA aligned reads in BAM file format
Supplementary files format and content: Index of BWA aligned reads in BAI file format
Supplementary files format and content: Loop calls (combining both replicates) for 5kb and 10kb resolution in BEDPE file format

molecule: genomic DNA

source_name: HFF

growth_protocol: HFF cells were seeded on Matrigen T75 flasks (1 kPa and 50 kPa) at slightly variable densities to account for reduced cell attachment on softer substrates (2 million and 1.25 million).

extract_protocol:
200,000 crosslinked cells were used for each replicate. Nuclei were isolated using NPB buffer (5% BSA in PBS, 1mM DTT, 0.2% IGEPAL, Protease Inhibitor) and incubated with assembled Tn5 transposase in 1X TB buffer (33 mM Tris-AC pH 7.8, 66 mM KCl-AC, 10 mM Mg-AC, 16% DMF) at 37C on a rotator for 1 hour. Chromatin digestion was performed with MseI, followed by in situ ligation with T4 DNA ligase and DNA purification.
Purified genomic DNA was further digested with NlaIII and circularized with T4 DNA ligase, followed by DNA purification and PCR amplification. After size selection, the libraries were sequenced using the Illumina Novaseq X.

treatment_protocol: After 20 hours glycine was added to a final concentration of 0.125 M and incubated at room temperature for 5 minutes to quench formaldehyde. This protocol included a rapid fixation step prior to Tn5 transposition.

value: HFF

value: Human foreskin fibroblasts

value: 50kPa surface


title: Mus musculus, 500uM treat, rep1


title: HFF.hicar.50kPa.rep1

description: Library name: HFF.hicar.50kPa.rep1 (stiff rep1)


title: C3HeB/FeJ_isotype_HN878_d26_1

description: Library name: Iso_d26_1


title: Day 3 Cocultured EC rep6

value: day 3


title: Day 1 Monocultured EC rep9

value: day 1

value: Monocultured


title: HFF.hicar.1kPa.rep2

description: Library name: HFF.hicar.1kPa.rep2 (soft rep2)

value: 1kPa surface


title: C3HeB/FeJ_isotype_uninfected_3

description: Library name: Iso_uninf_3

value: Lung

value: Uninfected


title: Day 1 Monocultured EC rep8


title: HFF.hicar.1kPa.rep1

description: Library name: HFF.hicar.1kPa.rep1 (soft rep1)


title: Day 1 Monocultured EC rep7


title: Mus musculus, control, rep1

value: control (0uM)


title: C3HeB/FeJ_isotype_uninfected_1

description: Library name: Iso_uninf_1


title: Day 1 Monocultured EC rep6


title: SPANXA2-OT1 ASO3

city: Boston

first: Masanori

last: Aikawa

state: Massachusetts

address: 77 Avenue Louis Pasteur, NRB741

institute: Brigham and Women's Hospital

description: Library name: Sample 7

data_processing:
VIPER analysis pipeline for mapping and read counts
We normalized the raw read count data using DESeq2
The Wald test of DESeq2 was used to compare the RNA abundances and identify transcripts that were differentially abundant (increase/decrease by 2-fold) between two groups (NC_ASO versusSPANXA2-OT1_ASO) (adjusted p-values <0.05).
The FDR was used for adjusted p-values. The data were imported into Excel to make the volcano plot. We used Qlucore for drawing principal component analysis (PCA) plots and heatmaps
Assembly: GRCH38/hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: PBMC

growth_protocol: Monocytes were isolated from PBMC and were differentiated in presence of M-CSF for 10 days in RPMI 1640 containing 5% human serum and antibiotics in humidified atmosphere with 5% CO2 at 37C to derived human primary macrophage cells

extract_protocol:
RNA was harvested using Qiagen RNA Mini kit
TotalRNAseq QiaSelect rRNA removal

treatment_protocol: 10 ng/ml human recombinant M-CSF

value: PBMC

value: Primary cell

value: PBMC derived macrophage

value: IL1β; SPANXA2-OT1 ASO


title: SPANXA2-OT1 ASO4

description: Library name: Sample 8


title: IEC4.1cells, U90926KO + IFNγ, rep3

first: Aiyu

last: Gong

address: 1735 W. Harrison St

department: MPI

institute: Rush University

data_processing:
Base-calling sofeware, version, parameters;
BGI SOAPnuke v1.5.2 software used for basecalling.
Sequencing data filtering:this project uses the filtering software SOAPnuke developed by BGI independently for filtering. Software Information:  SOAPnuke:Version v1.5.2; Parameters -l 15 -q 0.2 -n 0.05
Data filtering steps; 1) Remove the reads containing the adaptor (adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" are saved in FASTQ format.
Read alignment: Align to the reference genome: After getting clean reads, used HISAT to align the clean reads to the reference genome. Software Information: HISAT2;  Version：v2.0.4; Parameters：--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF
Assembly: mm10; Reference species: Species：Mus_musculus; Source：NCBI;  Reference Genome Version：GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include gene expression FPKM values and Read counts for each Sample

extract_protocol:
IEC 4.1 cells were harvested, and RNA were extract using Rneasy Mini Kit (QIAGEN Cat. No. 74104).  Agilent 2100 or Fragment Analyzer was used to detect thequality of RNA. 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using DNBSEQ platform

value: CRISPR/Cas9 U90926KO

value: IFNγ


title: SPANXA2-OT1 ASO2

description: Library name: Sample 6


title: IEC4.1cells, U90926KO + IFNγ, rep2


title: Day 1 Monocultured EC rep4

data_processing:
Quality of all raw FASTQ files was checked using Fastqc.
Reads were aligned to the human reference genome GRCh38 using STAR with default parameters.
Gene counts were made using featureCounts.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for each sample.

value: HUVEC


title: Mus musculus, control, rep3

value: cranial bone


title: Day 1 Monocultured EC rep3


title: IEC4.1cells, U90926KO, rep3

value: Control


title: SPANXA2-OT1 ASO1

description: Library name: Sample 5


title: Mus musculus, control, rep2


title: Negative control ASO3

description: Library name: Sample 3

value: IL1β; Negative control ASO


title: IEC4.1cells, U90926KO, rep2


title: C3HeB/FeJ_isotype_uninfected_2

description: Library name: Iso_uninf_2

value: Isotype


title: Negative control ASO4

description: Library name: Sample 4


title: Day 1 Monocultured EC rep1

value: day 1


title: IEC4.1cells, U90926KO, rep1


title: Negative control ASO2

description: Library name: Sample 2


title: Day 1 Monocultured EC rep5

value: Monocultured


title: IEC4.1cells, Ctrl + IFNγ, rep3

value: control


title: Day 1 Cocultured EC rep6

value: Cocultured with FB


title: Day 1 Cocultured EC rep5


title: IEC4.1cells, U90926KO + IFNγ, rep1


title: Day 1 Monocultured EC rep2


title: Day 1 Cocultured EC rep4


title: chronic active AMR_58058

city: Loma Linda

first: Yan

last: Chen Wongworawat

address: 11234 Anderson Street, Room 2516

institute: Loma Linda University

description:
Library name: chronic active AMR_58058
FFPE spatial transcriptome seuqencing

data_processing:
Raw sequencing data were processed using 10xGenomic Space Ranger pipeline to generate FASTQ files.
Sequences were aligned to grch38 reference genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using space ranger's default setting
Assembly: grch38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: gene expression count data in Matri Market Exchanges Format
Library strategy: Spatial Transcriptomics

source_name: Kidney allograft biopsy tissue

extract_protocol:
Section FFPE embeded tissues onto charged glass slides
Spatial transcriptomic sequencing libraries were prepared with 10xGenomics Visium Sptatial Gene Expression Slides & REagent kit according to manufacturer's instruction.

value: Kidney allograft biopsy tissue

tag: group

value: chronic active AMR


title: Day 1 Cocultured EC rep3

first: Sin Yen

address: Clear Water Bay

institute: HKUST

extract_protocol:
RNA were isolated using TRIzol reagent along with DNase application to purify the samples.
RNA libraries were prepared for sequencing using Smart-seq2 protocol and Illumina Nextera XT DNA Library Prep Kit.


title: IEC4.1cells, Ctrl + IFNγ, rep1


title: acute TCMR_58057

description:
Library name: acute TCMR_58057
FFPE spatial transcriptome seuqencing

value: acute TCMR


title: Day 1 Cocultured EC rep2


title: IEC4.1cells, Ctrl, rep3


title: IEC4.1cells, Ctrl, rep2


title: NIF_rep3

type: RNA

city: Stanford

first: Melanie

middle: J

last: Barnett

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

description: The nitrogen fixation zone of 47 day old root nodules was collected by laser-capture microdissection.

hyb_protocol: Five micrograms of the amplified cDNA were biotin labeled with the Biotin Labeling Kit for 3’ arrays (Genisphere) and hybridized to our chip at 45 degree centigrade as described in the Genisphere Biotin Labeling Kit for 3’ arrays.

scan_protocol: Chips were scanned at the Stanford PAN facility using an Affymetrix scanner 3000 7G

data_processing: Affymetrix CEL files were analyzed using R and BIOCONDUCTOR software packages (Gentleman et al. 2004, Genome Biol 5:R80). Probe summarization and normalization were carried out with the AFFY package and the RMA algorithm (Irizarry et al. 2003, Biostatistics 4: 249-264). To account for varying plant to bacterial RNA ratios in different samples, normalization was done separately for M. truncatula and S. meliloti probe sets.

label: biotin

organism:
Sinorhizobium meliloti
Medicago truncatula

label_protocol: RNA from LCM samples (25–40 ng total RNA) was amplified with the Sensation RNA amplification kit (Genisphere).

growth_protocol: Medicago truncatula [Gaertn.] cv Jemalong were lightly scratched with sandpaper and sterilized in undiluted bleach for 5 min. Seeds were rinsed with sterile water and imbibed for 8 h at room temperature and 48 h at 4°C, germinated overnight in inverted petri dishes in the dark, and planted into pre-sterilized vermiculite in cone-tainer tubes (Stuewe & Sons). Plants were watered every third day with 5 ml 0.1x BNM. Five day old seedlings were inoculated with 5 ml of a suspension (OD600 = 0.1) of CL150 in 0.1x Buffered Nodulation Medium (BNM) (Ehrhardt et al. 1992)(Barnett et al. 2004 Proc Natl Acad Sci USA 101:16636-16641). Cultures of S. meliloti CL150 were prepared for plant inoculation as described previously (Mitra and Long 2004, Plant Physiol.134: 595-604).

extract_protocol: Total RNA was extracted using the RNeasy Plus Micro Kit (Qiagen). To remove genomic DNA, we eluted the samples consecutively through three gDNA eliminator columns (RNeasy Plus Micro Kit, Qiagen).

treatment_protocol: 47 days after inoculation root nodules were harvested. Ten nodules from three plants were embedded in OCT (Sakura Tissue-Tek), frozen on liquid nitrogen, and stored at -80 degree centigrade. For each sample and each of the three replicates 9-10 plants were used. OCT embedded, frozen root nodules were longitudinally sectioned at 14 µm in a cryostat (Microm HM550, Thermo Fisher Scientific) at -20 degree C.. The sections were transferred to adhesive coated microscopic slides (CFSA CS-1/2X, Instrumedics) using the CryoJane Tape-Transfer System (Instrumedics). Slides were placed in 70% (v/v) ethanol at 20 degree C. for 5 min and dehydrated using a graded ethanol series (70%, 95%, 100% (v/v) for 30s each), followed by three incubations in xylene for 2 min each. The slides were air-dried and processed with a PALM Microbeam LCM system (Carl Zeiss Microscopy) equipped with a Hitachi HV-D30 camera within 3 hours. Tissue zones of interest were selected using a 5x objective lens magnification and LCM was carried out using a 20x objective lens and the AutoLPC function. The LCM parameters were: focus, 77; energy, 93; autocircle, 4 µm; distance between dots, 8 µm; distance from line, 4 µm; LCM speed, 200 µm/s. The tissue was collected into 50 µl RLT plus buffer (Qiagen), frozen on dry ice, and stored at -80 degree centigrade.

value: Root nodule

tag: nodule region

value: NIF


title: NIF_rep1

source_name: The nitrogen fixation zone of 47 day old root nodules was collected by laser-capture microdissection.


title: NIF_rep2


title: active AMR_58056

description:
Library name: active AMR_58056
FFPE spatial transcriptome seuqencing

value: active AMR


title: DIFF_rep1

description: The first layer of enlarged, bacteroid-filled plant cells in 47 day old root nodules was collected by laser-capture microdissection.

value: DIFF


title: DIFF_rep2

source_name: The first layer of enlarged, bacteroid-filled plant cells in 47 day old root nodules was collected by laser-capture microdissection.


title: control_58055

description:
Library name: control_58055
FFPE spatial transcriptome seuqencing


title: Negative control ASO1

description: Library name: Sample 1

value: PBMC

value: Primary cell

value: PBMC derived macrophage


title: EARLY_rep3

description: The small, mostly uninvaded plant cells at the tip of a 47 day old root nodule and the first layer of enlarged, bacteroid-filled plant cells were collected by laser-capture microdissection.

value: EARLY


title: EARLY_rep2

source_name: The small, mostly uninvaded plant cells at the tip of a 47 day old root nodule and the first layer of enlarged, bacteroid-filled plant cells were collected by laser-capture microdissection.


title: IEC4.1cells, Ctrl, rep1

city: Chicago

value: Control


title: DIFF_rep3


title: control8

status: Public on Sep 08 2025

city: Nishi-Shinbashi, Minato-ku

first: Tomohiro

last: Aoki

state: Tokyo

department: Pharmacology

country: Japan

institute: Jikei University School of Medicine

description: rat 10sample, rna-seq, edge test, all gene.xlsx

data_processing:
CLC genomics workbench (version 11,QIAGEN
Supplementary files format and content: Differential expression analyses, including principal component analysis and gene ontology (GO)analysis, were performed using the RNA-Seq tool, one similar to the DESeq and the edgeR package, in CLCgenomics workbench.

source_name: intracranial artery

extract_protocol:
The total RNA was isolated from homogenized samples using an RNeasy fibrous tissuemini kit (QIAGEN, Hilden, Germany) with an on-column DNase treatment, according to the manufacturer’s instructions.
The quantity of each total RNA sample was measured using a NanoDrop (Thermofisher, Waltham,MA), and its quality was assessed by using the RNA integrity number (RIN) on an Agilent 4200 TapeStation(Agilent, Santa Clara, CA). The libraries obtained from the purified RNA samples (500ng) were then preparedusing a TruSeq stranded mRNA sample preparation kit (Illumina, San Diego, CA), for the RNA sequencinganalyses. Paired-end sequencing (2 × 75 base pair) was performed on a NextSeq500 (Illumina). Each read wasthen ma

value: intracranial artery

value: rat control intracranial artery

value: WT


title: TIP_rep3

description: The small, mostly uninvaded plant cells at the tip of a 47 day old root nodule were collected by laser-capture microdissection.

value: TIP


title: IEC4.1cells, Ctrl + IFNγ, rep2

value: control

value: IFNγ


title: TIP_rep2

source_name: The small, mostly uninvaded plant cells at the tip of a 47 day old root nodule were collected by laser-capture microdissection.


title: EARLY_rep1


title: control6


title: control5


title: control7


title: control4


title: TIP_rep1


title: aneurysm8

value: rat intracranial aneurysm


title: aneurysm6


title: aneurysm7


title: aneurysm5


title: aneurysm4


title: Breast_Cancer_cfDNA_2_DeepSeq

city: Grand Forks

first: Motoki

last: Takaku

state: ND

address: W221 Biomedical Sciences 1301 N. Columbia Road

institute: University of North Dakota

description:
Library name: Breast_Cancer_cfDNA_2_DeepSeq
BC2_DeepSeq

data_processing:
Raw reads were filtered based on a mean base quality score greater than 20. Adapter sequences were removed using Cutadapt, and the reads were subsequently mapped to the hg19 genome using Bowtie 1.2.2. Duplicate reads were eliminated using the MarkDuplicates tool from the Picard-tools-2.26.4 package. Paired-end reads were converted into single fragments for metaplot analyses and visualization on the UCSC Genome Browser. After normalization within each dataset, bigWig files were generated to visualize genomic coverage.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: Plasma

extract_protocol:
NEXTFLEX Rapid DNA-Seq Kit 2.0 (Approximately650µL of blood plasma from cancer patients or healthy donors was used for cfDNA purification utilizing the SubXTM-Exo-DNA kit (Capital Biosciences). The purified cfDNA was then quantified using the Qubit dsDNA HS Assay kit.
Libraries were prepared using the NEXTFLEX Rapid DNA-Seq Kit 2.0 (Revvity). Half the volume of purified cfDNAs, ranging from approximately 1 ng to 10 ng, was utilized. After adapter ligation, a total of 11 PCR cycles were performed.

value: Plasma

value: cfDNA

tag: cancer type

value: breast cancer

tag: data ids


title: ESL DNA-seq

city: seattle

first: Samantha

last: Koplik

email: skoplik@uw.edu, kopliksam@gmail.com

state: Washington

address: 185 Stevens Way

department: Electrical and Computer Engineering

institute: University of Washington

description:
Library name: DNA_seq_concat_2023_09_19
MPRA library DNA-Seq

library_source: other

data_processing:
DNA-seq reads were used to extract 20-nt barcodes from R2, anchored by a required 20-bp forward shared region (allowing up to 5 mismatches). Barcodes were clustered with starcode (distance = 1), and consensus barcode+insert sequences supported by ≥5 reads were assembled into a FASTA reference for STAR indexing. Reference FASTA entries were assembled from each unique 20-nt barcode cluster. For each barcode cluster and library member combination, the reference sequence consisted of the last 25 nt of Citrine exon 1, SMN2 intron 6, the variable exon and intronic flanks, SMN2 intron 7, Citrine exon 2, and the 20-nt barcode. The matched barcode+insert references were used to build STAR genome indexes for RNA-seq mapping.
RNA-seq reads were split based on barcode and mapped to the barcode+insert reference FASTA using STAR. Unique molecular identifiers (UMIs) were collapsed to remove PCR duplicates, and reads were remapped with STAR after collapsing. Splice isoform abundance was quantified by counting junction-spanning reads, from which percent spliced-in (PSI) values were calculated. PSI values were clipped to be [0.01, 0.99] and then logit-transformed to obtain logit(PSI), and ΔPSI and Δlogit(PSI) were computed relative to the corresponding wild-type reference sequence.
Assembly: Synthetic plasmid backbone reference sequence (Citrine exon 1 – SMN2 intron 6 – variable intron flank-exon-intron flank – SMN2 intron 7 – Citrine exon 2). Human genome build hg38 was used only for annotation of exons and their variants
Supplementary files format and content: Processed PSI values are provided in tab-delimited text/CSV format. Each row corresponds to a variant with columns for reference ID (1-indexed), event_id, gene_exon, gene_name, cell line, replicate, and computed values including inclusion reads, exclusion reads, PSI, clipped PSI (0.01–0.99), logit(PSI), ΔPSI, and Δlogit(PSI).

molecule: other

source_name: plasmid

growth_protocol: Cells were cultured under standard conditions. HEK293, HeLa, K562, MCF7, and HMC3 cells were seeded at 200,000 cells/mL in 10 cm plates in appropriate growth medium supplemented with 10% FBS.

extract_protocol:
Total RNA was extracted from cells 36–48 h after transfection using the Monarch RNA cleanup kit (NEB). Poly(A)+ mRNA was isolated with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). mRNA was reverse transcribed with SuperScript IV Reverse Transcriptase (Thermo Fisher) to generate cDNA using a primer downstream of the barcode region.
cDNA was amplified with KAPA HiFi HotStart ReadyMix using primers flanking the Citrine exon 1 splice junction and barcode region, which included offset sequences to increase base diversity. Following amplification, Illumina P5/P7 adapters were added via qPCR to selectively enrich for adapter-containing fragments and prevent over-amplification. Libraries were size-selected to retain fragments ≥100 nt, quantified with Qubit and qPCR, pooled with PhiX, and sequenced on an Illumina NextSeq 500 using 300-cycle kits and custom primers.

treatment_protocol: Cells were transfected with 15 µg of the plasmid MPRA library using Lipofectamine 3000 (Thermo Fisher). Cells were harvested 36–48 h post-transfection.

value: plasmid


title: Day 1 Cocultured EC rep1

city: Kowloon

last: Tan

source_name: Endothelial Cells (EC)

value: HUVEC

value: day 1

value: Cocultured with FB


title: MPS_1

city: Yangzhou City

first: jin

last: li

address: No.88, Daxue South Road

institute: Yangzhou University

description: Library name: sample4

data_processing:
Quality control and Read mapping:The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference- based approach.
Differential expression analysis and Functional enrichment: To identify DEGs ( differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads ( TPM) method. RSEM was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2 or DEGseq. DEGs with |log2FC| ≧ 1 and FDR≤ 0.05(DESeq2 ) or FDR ≤0.001(DEGseq) were considered to be significantly different expressed genes. In addition, functional- enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni- corrected P-value ≤0.05 compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools and KOBAS, respectively.
Alternative Splice events Identification: All the alternative splice events that occurred in our sample were identified by using recently releases program rMATS. Only the isoforms that were similar to the reference or comprised novel splice junctions were considered, and the splicing differences were detected as exon inclusion, exclusion, alternative 5′, 3′, and intron retention events.
Assembly: GRCh38
Supplementary files format and content: The PROCESSED DATA FILES.xlsx file contains RAW count for each sample

source_name: lung cancer

growth_protocol: Cells were cultured in a humidified incubator with 5% CO₂ at 37°C, using Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’ s instructions. Then RNA quality was determined by 53 0 0 Bioanalyser(Agilent) and quantified using the ND- 2 0 0 0 ( NanoDrop Technologies). Only high-quality RNA sample was used to construct sequencing library
RNA purification, reverse transcription, library construction and sequencing were performed at Hangzhou Cosmos Wisdom Biotech Co., Ltd. (Hangzhou, China) according to the manufacturer’s instructions (Illumina, San Diego, CA). The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep Ligation from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyAselection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double- stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, paired-end RNA-seq sequencing library was sequenced with the NovaSeq X plus sequencer (2 × 150bp read length).

treatment_protocol: PS-MPs (20 mg/mL) were added to A549 cells for 48h.

tag: tissue

value: lung cancer

value: PS MPs (20 mg/mL)


title: ctr_1

description: Library name: sample1

tag: cell type

value: none; control


title: MPS_3

description: Library name: sample6


title: ctr_3

description: Library name: sample3


title: PSOR2098.1

city: New York City

first: Florencia

last: Schlamp

state: New York

address: 435 East 30th Street

institute: NYU Langone Health

description: Library name: PSOR2098.1_S324

data_processing:
Quality control of sequencing reads was assessed using FastQC (v0.11.7) and MultiQC (v1.10.1).
Reads were then mapped to the hg38 genome using STAR (v2.6.1d).
Read count tables were generated using featureCounts from Subread (v1.6.3) and normalized based upon library size using DESeq2 R package (v1.34.0) followed by differential expression analysis  adjusting for age and sex.
Assembly: hg38
Supplementary files format and content: space-delimited text file includes raw counts per sample per gene

source_name: platelet

extract_protocol:
citrated blood was collected, spun, and platelet-rich plasma was collected. ACD was added 1:10 to resting citrated blood samples and spun at 1000g for 10 minutes. The pellet was resuspended in Easysep buffer (STEMCELL) and subjected to negative selection using human CD45+ and Glycophorin A+. A relative purity of platelet/leukocyte ratio of 1x107 was confirmed by flow cytometry. Samples were lysed in TRIzol (ThermoFisher) and stored at -80oC until use.  RNA was extracted using Direct-zol microspin columns (Zymo Research). Yield, quantity, and quality of the RNA were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Libraries were prepared utilizing the Clontech SMART-Seq HT with Nxt HT kit (Takara Bio USA), and sequenced single end on an Illumina NovaSeq 6000.

value: platelet

value: Male

tag: age

value: PSOR

tag: batch


title: MPS_2

description: Library name: sample5

tag: cell line


title: PSOR2099.1

description: Library name: PSOR2099.1_S325


title: PSOR2094.1

description: Library name: PSOR2094.1_S320

value: Female


title: PSOR2095.1

description: Library name: PSOR2095.1_S321


title: PSOR2096.1

description: Library name: PSOR2096.1_S322

value: CONTROL


title: PSOR2084.1

description: Library name: PSOR2084.1_S318


title: PSOR2083.1

description: Library name: PSOR2083.1_S317


title: PSOR2081.1

description: Library name: PSOR2081.1_S315


title: PSOR2080.1

description: Library name: PSOR2080.1_S314


title: PSOR2079.1

description: Library name: PSOR2079.1_S313


title: PSOR2078.1

description: Library name: PSOR2078.1_S312


title: PSOR2075.1

description: Library name: PSOR2075.1_S311


title: PSOR2074.1

description: Library name: PSOR2074.1_S309


title: PSOR2073.1

description: Library name: PSOR2073.1_S308


title: ctr_2

description: Library name: sample2


title: PSOR2072.1

description: Library name: PSOR2072.1_S307


title: PSOR2070.1

description: Library name: PSOR2070.1_S305


title: PSOR2068.1

description: Library name: PSOR2068.1_S302


title: PSOR2065.1

description: Library name: PSOR2065.1_S300


title: PSOR2064.1

description: Library name: PSOR2064.1_S299


title: PSOR2097.1

description: Library name: PSOR2097.1_S323


title: PSOR2093.1

description: Library name: PSOR2093.1_S319


title: PSOR2062.1

description: Library name: PSOR2062.1_S288


title: PSOR2060.1

description: Library name: PSOR2060.1_S296


title: PSOR2056.1

description: Library name: PSOR2056.1_S292


title: PSOR2082.1

description: Library name: PSOR2082.1_S316


title: PSOR2063.1

description: Library name: PSOR2063.1_S298


title: PSOR2057.1

description: Library name: PSOR2057.1_S293


title: PSOR2059.1

description: Library name: PSOR2059.1_S295


title: PSOR2050.1

description: Library name: PSOR2050.1_S285


title: PSOR2058.1

description: Library name: PSOR2058.1_S294


title: PSOR2055.1

description: Library name: PSOR2055.1_S290


title: PSOR2054.1

description: Library name: PSOR2054.1_S289


title: PSOR2048.1

description: Library name: PSOR2048.1_S283


title: PSOR2047.1

description: Library name: PSOR2047.1_S282


title: PSOR2052.1

description: Library name: PSOR2052.1_S2


title: PSOR2051.1

description: Library name: PSOR2051.1_S286


title: PSOR2071.1

description: Library name: PSOR2071.1_S306


title: PSOR2045.1

description: Library name: PSOR2045.1_S280


title: PSOR2049.1

description: Library name: PSOR2049.1_S284


title: PSOR2046.1

description: Library name: PSOR2046.1_S1


title: PSOR2043.1

description: Library name: PSOR2043.1_S277


title: PSOR2041.1

description: Library name: PSOR2041.1_S275


title: PSOR2042.1

description: Library name: PSOR2042.1_S276


title: PSOR2040.1

description: Library name: PSOR2040.1_S274


title: PSOR2037.1

description: Library name: PSOR2037.1_S270


title: PSOR2035.1

description: Library name: PSOR2035.1_S268


title: PSOR2034.1

description: Library name: PSOR2034.1_S267


title: PSOR2069.1

description: Library name: PSOR2069.1_S304


title: PSOR2053.1

description: Library name: PSOR2053.1_S297


title: PSOR2033.1

description: Library name: PSOR2033.1_S266


title: PSOR2031.1

description: Library name: PSOR2031.1_S264


title: PSOR2028.1

description: Library name: PSOR2028.1_S260


title: PSOR2032.1

description: Library name: PSOR2032.1_S265


title: PSOR2027.1

description: Library name: PSOR2027.1_S257


title: PSOR2029.1

description: Library name: PSOR2029.1_S261


title: PSOR2025.1

description: Library name: PSOR2025.1_S253


title: PSOR2023.1

description: Library name: PSOR2023.1_S251


title: PSOR2024.1

description: Library name: PSOR2024.1_S252


title: PSOR2019.1

description: Library name: PSOR2019.1_S243


title: PSOR2017.1

description: Library name: PSOR2017.1_S241


title: PSOR2044.1

description: Library name: PSOR2044.1_S279


title: PSOR2018.1

description: Library name: PSOR2018.1_S242


title: PSOR2016.1

description: Library name: PSOR2016.1_S240


title: PSOR2021.1

description: Library name: PSOR2021.1_S245


title: PSOR2014.1

description: Library name: PSOR2014.1_S236


title: PSOR2011.1

description: Library name: PSOR2011.1_S234


title: PSOR2010.1

description: Library name: PSOR2010.1_S233


title: PSOR2007.1

description: Library name: PSOR2007.1_S228


title: PSOR2006.1

description: Library name: PSOR2006.1_S227


title: PSOR2005.1

description: Library name: PSOR2005.1_S226


title: PSOR2004.1

description: Library name: PSOR2004.1_S225


title: PSOR2003.1

description: Library name: PSOR2003.1_S224


title: PSOR2002.1

description: Library name: PSOR2002.1_S223


title: PSOR2030.1

description: Library name: PSOR2030.1_S262


title: PSOR2026.1

description: Library name: PSOR2026.1_S256


title: PSOR2001.1

description: Library name: PSOR2001.1_S222


title: CRD117.1

description: Library name: CRD117.1_S219

value: CHORD


title: PSOR2022.1

description: Library name: PSOR2022.1_S248


title: CRD084.1

description: Library name: CRD084.1_S174


title: CRD086.1

description: Library name: CRD086.1_S398


title: CRD112.1

description: Library name: CRD112.1_S209


title: CRD075.1

description: Library name: CRD075.1_S384


title: CRD080.1

description: Library name: CRD080.1_S392


title: CRD068.1

description: Library name: CRD068.1_S164


title: CRD064.1

description: Library name: CRD064.1_S376


title: CRD007.1

description: Library name: CRD007.1_S427


title: PSOR2009.1

description: Library name: PSOR2009.1_S232


title: CKDL220016674

city: New York

first: Caleb

last: Lareau

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

description: Library name: CKDL220016674

library_source: genomic single cell

data_processing:
Fastqs were aligned using the CellRanger-ATAC v2.0 pipeline
Mitochondrial heteroplasmy was inferred using mgatk v0.7.0
All data was processed with the hg38 reference genome (for mitochondrial, the rCRS contig is the default reference)
Assembly: hg38
Supplementary files format and content: Nuclear accessible chromatin files with corresponding single-cell barcodes (.fragments.tsv.gz)
Supplementary files format and content: Mitochondrial heteroplasmy per cell of high-quality mtDNA (variant_stats.tsv.gz and cell_heteroplasmic_df.tsv.gz)

source_name: Lung normal

extract_protocol:
Whole cells were isolated from primary human tissues/tumors and optionally flow sorted for specific populations
10x Genomics Single-cell ATAC-seq

value: Lung normal

tag: sorting

tag: donor

tag: diagnosis

value: NSCLC


title: CKDL220016675

description: Library name: CKDL220016675

value: PBMC

value: ALL


title: CKDL220016673

description: Library name: CKDL220016673


title: CRD083.1

description: Library name: CRD083.1_S396

tag: Sex


title: PSOR2013.1

description: Library name: PSOR2013.1_S235


title: CKDL220016672

description: Library name: CKDL220016672

source_name: Lung tumor

value: Lung tumor


title: CKDL220016671

description: Library name: CKDL220016671


title: CKDL220016668

description: Library name: CKDL220016668


title: CKDL220016669

description: Library name: CKDL220016669


title: CRD062.1

description: Library name: CRD062.1_S158


title: CKDL220016667

description: Library name: CKDL220016667


title: PSOR2020.1

description: Library name: PSOR2020.1_S244


title: CKDL220016670

description: Library name: CKDL220016670


title: CKDL220016666

description: Library name: CKDL220016666


title: CKDL220016665

description: Library name: CKDL220016665


title: CKDL220016664

description: Library name: CKDL220016664


title: CKDL220016663

description: Library name: CKDL220016663


title: CKDL220016662

description: Library name: CKDL220016662


title: CKDL220016661

description: Library name: CKDL220016661


title: CKDL220016659

description: Library name: CKDL220016659


title: CKDL220016660

description: Library name: CKDL220016660


title: CKDL220016658

description: Library name: CKDL220016658


title: CKDL220016657

description: Library name: CKDL220016657


title: CKDL210028094

description: Library name: CKDL210028094


title: CKDL220016656

description: Library name: CKDL220016656


title: CKDL210028090

description: Library name: CKDL210028090


title: CKDL210028093

description: Library name: CKDL210028093


title: CKDL210028091

description: Library name: CKDL210028091


title: CKDL210028089

description: Library name: CKDL210028089


title: CKDL210012696

description: Library name: CKDL210012696

value: HGSC


title: CKDL210028092

description: Library name: CKDL210028092


title: CKDL210012694

description: Library name: CKDL210012694

source_name: Ovarian tumor

value: Ovarian tumor


title: CKDL210012692

description: Library name: CKDL210012692


title: CKDL210028088

description: Library name: CKDL210028088


title: CKDL210012691

description: Library name: CKDL210012691


title: CKDL210012684

description: Library name: CKDL210012684

value: LGSC


title: CKDL210012679

description: Library name: CKDL210012679


title: CKDL210012672

description: Library name: CKDL210012672

value: Endometriosis


title: CKDL210012693

description: Library name: CKDL210012693


title: CKDL210012690

description: Library name: CKDL210012690


title: induced_neurons,B7D12_2089,truncating_d12,rep2

city: Nijmegen

first: Maggie MK

last: Wong

address: Wundtlaan 1

department: Language and Genetics

country: Netherlands

institute: Max Planck Institute for Psycholinguistics

description:
Library name: B7D12_2089
Column name in tpm_filt_counts_noOutlier.csv:B7D12_2089

data_processing:
Reads with adapter contamination, reads when uncertain nucleotides constitute more than 10 per cent of either read (N > 10%) and reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50 per cent of the read were removed.
Image processing and basecall was performed using the Illumina Real Time Analysis Software
Fastq files were aligned to the human genome (GRCh38/hg39, Ensembl) using HISAT266 v.2.0.5 software together with the corresponding splice junctions Ensembl GTF annotation.
For induced neuron samples, at least 88% of the reads for each sample were uniquely mapped to the human genome, entailing at least 39.9 million unique reads in the sample with the lowest sequencing depth.
Data pre-processing and analysis were performed using R Statistical Software v4.1.267.
Count table was created using featureCounts in Rsubread68. Transcripts that have no reads in all samples were removed.
Assembly: GRCh38/hg39, Ensembl
Supplementary files format and content: file includes raw counts for each sample: tpm_filt_counts_noOutlier.csv

growth_protocol: Human dermal fibroblasts were cultured in DMEM supplemented with 20% FBS, 100 U/ml Penicillin-Streptomycin and 1% sodium pyruvate (Thermo-Fisher) at 37°C and 5% CO2. Human dermal fibroblasts were differentiated into induced neurons according to Yang et al.42 with modifications. In brief, on day -1, fibroblasts were first cultured on Matrigel (1:100)-coated Ibidi 8-well removable chamber polymer slide flask with 14,684 cells in 400 µl of medium per well and 6-well plates with 15,1578 cells in 2 ml of medium per well. Cells were maintained in fibroblast medium [DMEM high-glucose medium (Invitrogen) consisting of 10% fetal bovine serum (Gibco), 1% nonessential amino acids (Gibco), and 1 mM GlutaMAX (Gibco)] for 24 hours. On day 0, medium was completely replaced by neuronal induction medium (NIM) consisting of DMEM/F12:neurobasal medium (1:1) supplemented with 1% N-2, 2% B-27, 40 ng/mL brain-derived neurotrophic factor, 20 ng/mL glial cell-derived neurotrophic factor, 20 ng/mL insulin-like growth factor 1, and 1 mM GlutaMAX. NIM also contained small molecules or 1% DMSO in differentiation control groups. From day 0, fibroblasts were treated with NIM containing small molecule combination A (CA: 3 μM CHIR99021, 0.25 μM LDN193189, 10 μM RG108, 1 μM dorsomorphin, 3 μM P7C3-A20, 0.5 μM A83-01, and 5 μM ISX9) for three days. On day 3, half the medium was changed to NIM containing small molecule combination B (CB: 10 μM forskolin, 5 μM Y27632, 1 μM DAPT, 1 μM PD0325901, 0.5 μM A83-01, 1 μM purmorphamine, and 3 μM P7C3-A20) for another 3 days. On day 6, half of the medium was again changed with NIM containing CA and on day 9 with NIM supplemented with CB. On days 10 and 12, neurons were harvested as pellets for downstream analyses.

extract_protocol:
Total RNA was extracted from one to two million cells using a Qiagen Rneasy kit and performed by sequencing company Novogene.
1 μg of total RNA extracted (Qiagen) was used to generate RNA libraries using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (New England Biolabs) following the manufacturer’s protocol and index codes were added to attribute sequences to each sample. These steps are performed by sequencing company Novogene.

treatment_protocol: No treatment was performed.

value: induced neurons

tag: genotype

tag: treatment

tag: condition

value: Truncating

value: M


title: CKDL210012687-D2

description: Library name: CKDL210012687-D2

value: OC


title: CKDL210012695

description: Library name: CKDL210012695

source_name: Omentum met

value: Omentum met


title: induced_neurons,B8D10_2081,truncating_d10,rep3

description:
Library name: B8D10_2081
Column name in tpm_filt_counts_noOutlier.csv:B8D10_2081

value: F


title: induced_neurons,B7D10_2080b,control_d10,rep2

description:
Library name: B7D10_2080b
Column name in tpm_filt_counts_noOutlier.csv:B7D10_2080b

value: WT

value: Control


title: induced_neurons,B6D12_1225b,within_degron_d12,rep1

description:
Library name: B6D12_1225b
Column name in tpm_filt_counts_noOutlier.csv:B6D12_1225b


title: induced_neurons,B6D12_1914b,outside_degron_d12,rep1

description:
Library name: B6D12_1914b
Column name in tpm_filt_counts_noOutlier.csv:B6D12_1914b


title: induced_neurons,B6D10_1225b,within_degron_d10,rep1

description:
Library name: B6D10_1225b
Column name in tpm_filt_counts_noOutlier.csv:B6D10_1225b


title: induced_neurons,B7D10_1225b,within_degron_d10,rep2

description:
Library name: B7D10_1225b
Column name in tpm_filt_counts_noOutlier.csv:B7D10_1225b


title: induced_neurons,B7D12_2081,truncating_d12,rep2

description:
Library name: B7D12_2081
Column name in tpm_filt_counts_noOutlier.csv:B7D12_2081


title: induced_neurons,B8D12_19115,outside_degron_d12,rep3

description:
Library name: B8D12_19115
Column name in tpm_filt_counts_noOutlier.csv:B8D12_19115


title: induced_neurons,B8D12_1914,outside_degron_d12,rep3

description:
Library name: B8D12_1914
Column name in tpm_filt_counts_noOutlier.csv:B8D12_1914


title: induced_neurons,B8D12_2080,control_d12,rep3

description:
Library name: B8D12_2080
Column name in tpm_filt_counts_noOutlier.csv:B8D12_2080


title: induced_neurons,B8D12_1225,within_degron_d12,rep3

description:
Library name: B8D12_1225
Column name in tpm_filt_counts_noOutlier.csv:B8D12_1225


title: induced_neurons,B8D10_19115,outside_degron_d10,rep3

description:
Library name: B8D10_19115
Column name in tpm_filt_counts_noOutlier.csv:B8D10_19115


title: induced_neurons,B8D12_1166,control_d12,rep3

description:
Library name: B8D12_1166
Column name in tpm_filt_counts_noOutlier.csv:B8D12_1166


title: induced_neurons,B8D10_1914,outside_degron_d10,rep3

description:
Library name: B8D10_1914
Column name in tpm_filt_counts_noOutlier.csv:B8D10_1914


title: induced_neurons,B8D10_2080,control_d10,rep3

description:
Library name: B8D10_2080
Column name in tpm_filt_counts_noOutlier.csv:B8D10_2080


title: induced_neurons,B7D12_1914,outside_degron_d12,rep2

description:
Library name: B7D12_1914
Column name in tpm_filt_counts_noOutlier.csv:B7D12_1914


title: induced_neurons,B7D12_2080,control_d12,rep2

description:
Library name: B7D12_2080
Column name in tpm_filt_counts_noOutlier.csv:B7D12_2080


title: induced_neurons,B7D12_1166,control_d12,rep2

description:
Library name: B7D12_1166
Column name in tpm_filt_counts_noOutlier.csv:B7D12_1166


title: induced_neurons,B7D10_1914,outside_degron_d10,rep2

description:
Library name: B7D10_1914
Column name in tpm_filt_counts_noOutlier.csv:B7D10_1914


title: induced_neurons,B7D10_19115,outside_degron_d10,rep2

description:
Library name: B7D10_19115
Column name in tpm_filt_counts_noOutlier.csv:B7D10_19115


title: induced_neurons,B6D12_2089,truncating_d12,rep1

description:
Library name: B6D12_2089
Column name in tpm_filt_counts_noOutlier.csv:B6D12_2089


title: induced_neurons,B7D10_1223,within_degron_d10,rep2

description:
Library name: B7D10_1223
Column name in tpm_filt_counts_noOutlier.csv:B7D10_1223


title: induced_neurons,B6D12_2081,truncating_d12,rep1

description:
Library name: B6D12_2081
Column name in tpm_filt_counts_noOutlier.csv:B6D12_2081


title: induced_neurons,B6D12_2080,control_d12,rep1

description:
Library name: B6D12_2080
Column name in tpm_filt_counts_noOutlier.csv:B6D12_2080


title: induced_neurons,B6D12_19115,outside_degron_d12,rep1

description:
Library name: B6D12_19115
Column name in tpm_filt_counts_noOutlier.csv:B6D12_19115


title: induced_neurons,B6D12_1166,control_d12,rep1

description:
Library name: B6D12_1166
Column name in tpm_filt_counts_noOutlier.csv:B6D12_1166


title: induced_neurons,B8D10_1225b,within_degron_d10,rep3

description:
Library name: B8D10_1225b
Column name in tpm_filt_counts_noOutlier.csv:B8D10_1225b


title: induced_neurons,B6D10_1914,outside_degron_d10,rep1

description:
Library name: B6D10_1914
Column name in tpm_filt_counts_noOutlier.csv:B6D10_1914


title: induced_neurons,B6D10_19115,outside_degron_d10,rep1

description:
Library name: B6D10_19115
Column name in tpm_filt_counts_noOutlier.csv:B6D10_19115


title: induced_neurons,B6D10_1223,within_degron_d10,rep1

description:
Library name: B6D10_1223
Column name in tpm_filt_counts_noOutlier.csv:B6D10_1223


title: induced_neurons,B8D0_2080,control_d0,rep3

description:
Library name: B8D0_2080
Column name in tpm_filt_counts_noOutlier.csv:B8D0_2080


title: induced_neurons,B6D10_1166,control_d10,rep1

description:
Library name: B6D10_1166
Column name in tpm_filt_counts_noOutlier.csv:B6D10_1166


title: induced_neurons,B8D0_1166,control_d0,rep3

description:
Library name: B8D0_1166
Column name in tpm_filt_counts_noOutlier.csv:B8D0_1166


title: induced_neurons,B7D0_2080,control_d0,rep2

description:
Library name: B7D0_2080
Column name in tpm_filt_counts_noOutlier.csv:B7D0_2080


title: induced_neurons,B8D12_1223,within_degron_d12,rep3

description:
Library name: B8D12_1223
Column name in tpm_filt_counts_noOutlier.csv:B8D12_1223


title: induced_neurons,B7D0_1166,control_d0,rep2

description:
Library name: B7D0_1166
Column name in tpm_filt_counts_noOutlier.csv:B7D0_1166


title: induced_neurons,B6D0_1166,control_d0,rep1

description:
Library name: B6D0_1166
Column name in tpm_filt_counts_noOutlier.csv:B6D0_1166


title: induced_neurons,B8D12_2089,truncating_d12,rep3

description:
Library name: B8D12_2089
Column name in tpm_filt_counts_noOutlier.csv:B8D12_2089


title: induced_neurons,B8D12_2081,truncating_d12,rep3

description:
Library name: B8D12_2081
Column name in tpm_filt_counts_noOutlier.csv:B8D12_2081


title: induced_neurons,B8D10_2089,truncating_d10,rep3

description:
Library name: B8D10_2089
Column name in tpm_filt_counts_noOutlier.csv:B8D10_2089


title: induced_neurons,B8D10_1166,control_d10,rep3

description:
Library name: B8D10_1166
Column name in tpm_filt_counts_noOutlier.csv:B8D10_1166


title: induced_neurons,B6D10_2089,truncating_d10,rep1

description:
Library name: B6D10_2089
Column name in tpm_filt_counts_noOutlier.csv:B6D10_2089


title: induced_neurons,B7D10_1166,control_d10,rep2

description:
Library name: B7D10_1166
Column name in tpm_filt_counts_noOutlier.csv:B7D10_1166


title: induced_neurons,B7D12_19115,outside_degron_d12,rep2

description:
Library name: B7D12_19115
Column name in tpm_filt_counts_noOutlier.csv:B7D12_19115


title: induced_neurons,B7D10_2081,truncating_d10,rep2

description:
Library name: B7D10_2081
Column name in tpm_filt_counts_noOutlier.csv:B7D10_2081


title: induced_neurons,B7D10_2089,truncating_d10,rep2

description:
Library name: B7D10_2089
Column name in tpm_filt_counts_noOutlier.csv:B7D10_2089


title: induced_neurons,B6D10_2081,truncating_d10,rep1

description:
Library name: B6D10_2081
Column name in tpm_filt_counts_noOutlier.csv:B6D10_2081


title: induced_neurons,B6D10_2080,control_d10,rep1

description:
Library name: B6D10_2080
Column name in tpm_filt_counts_noOutlier.csv:B6D10_2080


title: I822Y_fs*13_3

description:
Library name: CL2089_M_3
Column name in tpm_filt_counts.csv: CL2089_M_3.bam

data_processing:
Image processing and basecall was performed using the Illumina Real Time Analysis Software
Reads with adapter contamination, reads when uncertain nucleotides constitute more than 10 per cent of either read (N > 10%) and reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50 per cent of the read were removed.
Fastq files were aligned to the human genome (GRCh38/hg39, Ensembl) using HISAT266 v. 2.0.5 software together with the corresponding splice junctions Ensembl GTF annotation.
At least 89% of the reads for each sample were uniquely mapped to the human genome entailing at least 36.4 million unique reads in the sample with the lowest sequencing depth for fibroblast samples.
Data pre-processing and analysis were performed using R Statistical Software v4.1.267.
Count table was created using featureCounts in Rsubread68. Transcripts that have no reads in all samples were removed.
Assembly: GRCh38/hg39, Ensembl
Supplementary files format and content: filtered raw counts: tpm_filt_counts.csv

source_name: primary human skin fibroblasts

growth_protocol: Human dermal fibroblasts were cultured in DMEM supplemented with 20% FBS, 100 U/ml Penicillin-Streptomycin and 1% sodium pyruvate (Thermo-Fisher) at 37°C and 5% CO2.

value: primary human skin fibroblasts

tag: age at_sampling

value: teenager

value: truncating


title: I822Y_fs*13_1

description:
Library name: CL2089_M_1
Column name in tpm_filt_counts.csv: CL2089_M_1.bam


title: induced_neurons,B6D12_1223,within_degron_d12,rep1

description:
Library name: B6D12_1223
Column name in tpm_filt_counts_noOutlier.csv:B6D12_1223


title: G15R_fs*47_2

description:
Library name: CL2078_M_2
Column name in tpm_filt_counts.csv: CL2078_M_2.bam


title: K693P_fs*86_2

description:
Library name: CL2080_F_2
Column name in tpm_filt_counts.csv: CL2080_F_2.bam


title: I822Y_fs*13_2

description:
Library name: CL2089_M_2
Column name in tpm_filt_counts.csv: CL2089_M_2.bam


title: G15R_fs*47_3

description:
Library name: CL2078_M_3
Column name in tpm_filt_counts.csv: CL2078_M_3.bam


title: G15R_fs*47_1

description:
Library name: CL2078_M_1
Column name in tpm_filt_counts.csv: CL2078_M_1.bam


title: S867R_3

description:
Library name: GM_F_3
Column name in tpm_filt_counts.csv: GM_F_3.bam

value: kid


title: induced_neurons,B6D0_2080,control_d0,rep1

description:
Library name: B6D0_2080
Column name in tpm_filt_counts_noOutlier.csv:B6D0_2080


title: S867R_2

description:
Library name: GM_F_2
Column name in tpm_filt_counts.csv: GM_F_2.bam


title: S867R_1

description:
Library name: GM_F_1
Column name in tpm_filt_counts.csv: GM_F_1.bam


title: P995L_1

description:
Library name: CL2087_M_1
Column name in tpm_filt_counts.csv: CL2087_M_1.bam


title: P995L_2

description:
Library name: CL2087_M_2
Column name in tpm_filt_counts.csv: CL2087_M_2.bam


title: E858K_2_3

description:
Library name: CL2046_F_3
Column name in tpm_filt_counts.csv: CL2046_F_3.bam


title: E858K_2_2

description:
Library name: CL2046_F_2
Column name in tpm_filt_counts.csv: CL2046_F_2.bam


title: D868N_3

description:
Library name: CL1225_M_3
Column name in tpm_filt_counts.csv: CL1225_M_3.bam


title: E858K_2_1

description:
Library name: CL2046_F_1
Column name in tpm_filt_counts.csv: CL2046_F_1.bam


title: I871T_2

description:
Library name: CL1223_M_2
Column name in tpm_filt_counts.csv: CL1223_M_2.bam


title: I871T_1

description:
Library name: CL1223_M_1
Column name in tpm_filt_counts.csv: CL1223_M_1.bam


title: I871T_3

description:
Library name: CL1223_M_3
Column name in tpm_filt_counts.csv: CL1223_M_3.bam


title: ControlM5_8

description:
Library name: CL2090_M_3
Column name in tpm_filt_counts.csv: CL2090_M_3.bam

value: adult


title: ControlM5_7

description:
Library name: CL2090_M_2
Column name in tpm_filt_counts.csv: CL2090_M_2.bam


title: ControlM5_6

description:
Library name: CL2090_M_1
Column name in tpm_filt_counts.csv: CL2090_M_1.bam


title: D868N_1

description:
Library name: CL1225_M_1
Column name in tpm_filt_counts.csv: CL1225_M_1.bam


title: ControlM4_6

description:
Library name: CL2088_M_3
Column name in tpm_filt_counts.csv: CL2088_M_3.bam


title: K693P_fs*86_3

description:
Library name: CL2080_F_3
Column name in tpm_filt_counts.csv: CL2080_F_3.bam


title: K693P_fs*86_1

description:
Library name: CL2080_F_1
Column name in tpm_filt_counts.csv: CL2080_F_1.bam


title: ControlM3_6

description:
Library name: CL2079_M_3
Column name in tpm_filt_counts.csv: CL2079_M_3.bam


title: ControlM4_5

description:
Library name: CL2088_M_2
Column name in tpm_filt_counts.csv: CL2088_M_2.bam


title: ControlM2_6

description:
Library name: CL1166_M_3
Column name in tpm_filt_counts.csv: CL1166_M_3.bam


title: ControlM2_5

description:
Library name: CL1166_M_2
Column name in tpm_filt_counts.csv: CL1166_M_2.bam


title: ControlM3_5

description:
Library name: CL2079_M_2
Column name in tpm_filt_counts.csv: CL2079_M_2.bam


title: ControlM3_4

description:
Library name: CL2079_M_1
Column name in tpm_filt_counts.csv: CL2079_M_1.bam


title: ControlM4_4

description:
Library name: CL2088_M_1
Column name in tpm_filt_counts.csv: CL2088_M_1.bam


title: ControlM2_4

description:
Library name: CL1166_M_1
Column name in tpm_filt_counts.csv: CL1166_M_1.bam


title: P995L_3

description:
Library name: CL2087_M_3
Column name in tpm_filt_counts.csv: CL2087_M_3.bam


title: ControlM1_5

description:
Library name: CL1163_M_2
Column name in tpm_filt_counts.csv: CL1163_M_2.bam


title: ControlM1_6

description:
Library name: CL1163_M_3
Column name in tpm_filt_counts.csv: CL1163_M_3.bam


title: D868N_2

description:
Library name: CL1225_M_2
Column name in tpm_filt_counts.csv: CL1225_M_2.bam


title: ControlM1_4

description:
Library name: CL1163_M_1
Column name in tpm_filt_counts.csv: CL1163_M_1.bam


title: ControlF3_2

description:
Library name: CL2081_F_2
Column name in tpm_filt_counts.csv: CL2081_F_2.bam


title: ControlF3_3

description:
Library name: CL2081_F_3
Column name in tpm_filt_counts.csv: CL2081_F_3.bam


title: ControlF2_6

description:
Library name: CL1009_F_3
Column name in tpm_filt_counts.csv: CL1009_F_3.bam


title: ControlF2_5

description:
Library name: CL1009_F_2
Column name in tpm_filt_counts.csv: CL1009_F_2.bam


title: ControlF3_1

description:
Library name: CL2081_F_1
Column name in tpm_filt_counts.csv: CL2081_F_1.bam


title: ControlF2_4

description:
Library name: CL1009_F_1
Column name in tpm_filt_counts.csv: CL1009_F_1.bam