title: A375 HOXD13 RNA-seq rep1

description: Library name: Sample 13


title: HL+HS+S_rep3

status: Public on Dec 03 2025

type: SRA

city: Columbia

first: Sameep

last: Dhakal

state: MO

address: 1201 Rollins St.

department: Institute for data science and Informatics

country: USA

institute: University of Missouri

description:
Library name: HLHSS_3
Combination of High light stress, Heat stress, and Salinity stress, replicate 3

library_source: transcriptomic

data_processing:
Read quality control was performed using Trim Galore v0.6.10 and FastQC v0.12.1. Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence. Subsequently, the processed reads were mapped to the Gmax_880_v6.0 whole genome using Hisat2 v2.2.1. Samtools v1.18 was used to sort the bam files which were subjected toranscript assembly and quantification using Cufflinks v2.2.1. Differential expression analysis was performed later using Cuffdiff v2.2.1, comparing control conditions with each combined stress condition.
Assembly: reference gemnome used is slycopersicum_691_SL4.0.fa gene model used is Slycopersicum_691_ITAG4.0.gene.gff3
Supplementary files format and content: processed data files are in format txt and it contains the gene names along with the fpkm values for each of the replicates.

molecule: total RNA

organism: Solanum lycopersicum

source_name: leaves

growth_protocol: Moneymaker tomato seeds, purchased from a commercial nursery (Clemente Viven, Semillas Clemente S.A., Vitoria, Alava, Spain), were sown in seedling trays filled with a mixture of peat moss, perlite, and vermiculite (80:10:10) under greenhouse conditions (70% relative humidity with natural photoperiod, 200 µmol photons m−2 s−1 light intensity, and day and night temperature averaging 25.0 ± 3.0◦C and 18.0 ± 3.0◦C, respectively). After germination, seedlings were transplanted to 10-cm diameter pots filled with perlite, maintained under greenhouse conditions as described above, and watered three times a week with half-strength Hoagland solution. Temperature and relative humidity were recorded regularly with a portable USB datalogger (OM-EL-WI- N-USB, Omega, NJ, United States).

extract_protocol:
Total RNA was isolated using Plant RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The experimental design to study wild-type tomato (Moneymaker) responses to MFSC included the following stresses: Nitrogen deficiency (N-), heat stress (HS), salinity (S), high light (HL), heavy metal as cadmium treatment (Cd), and the herbicide paraquat (PQ) were applied up to a combination of all six factors. HL, HS, S and PQ were combined in all their possible combinations of 2-, 3- and 4-factors and Cd and N- were added to 4-factor combination to generate 2 different groups of 5-factor stresses, and all of them simultaneously generate the 6-MFSC. N deficiency was applied by watering plants with a half strength Hoagland solution with 10% of N (Ca(NO₃)₂) content one week after transplanting the plants. One week after the starting of the N-deficiency stress, plants with and without N deficiency were watered with half strength Hoagland solution containing each stressor(s): S (75 mM NaCl), PQ (1 µM PQ), Cd (10 µM CdSO4), S+PQ (75 mM NaCl + 1 µM PQ), S+PQ+N- (75 mM NaCl + 1 µM PQ + 10% N), S+PQ+Cd (75 mM NaCl + 1 µM PQ + 10 µM CdSO4) and S+PQ+Cd+N- (75 mM NaCl + 1 µM PQ + 10 µM CdSO4 + 10% N). Following 15 days of stress treatments, a group of CT plants and a group of plants subjected to each of the individual and combined stresses were transferred to growth chambers and were subjected to HL (700 µmol m-2s-1) and/or HS (37ºC). The tissue sampled from tomato plants were young leaves. All experiments were repeated three times with at least 8 plants per stress treatment.

tag: tissue

value: leaves

tag: variety

value: Moneymaker

tag: genotype

value: wild type


title: 11629-JD-2_D1_Healthy

type: RNA

city: Ann Arbor

first: Joseph

middle: S

last: Durgin

state: MI

address: 1500 E Medical Center Dr

department: Dermatology

institute: University of Michigan

description: FFPE Xenium spatial transcriptomics

hyb_protocol: Probe ligation generates a circular DNA probe which is enzymatically amplified. Slides are placed in the Xenium Analyzer (instrument software version 2.0.1.0) where the sample undergoes successive rounds of fluorescent probe hybridization, imaging, and removal.

data_processing:
Resegment KRT5 (keratin 5) positive cells based on transcript coordinates.
Filtered cells to those with at least 10 measured transcripts
Filtered genes to those present in at least 5 cells
Normalize each cell by total counts over all genes, so that every cell has the same total count after normalization
Logarithmize the data matrix.
Xenium probes are designed to be compatible with the GRCh38 reference genome for human samples
The anndata_global.h5ad file contains the filtered, normalized, log-transformed transcript counts for all samples, annotated by disease state. The bulk_labels field contains cell-type annotations.

organism: Homo sapiens

source_name: Skin

extract_protocol: FFPE tissue is sectioned onto a Xenium slide (each slide has an imageable area of 12mm x 24mm). Sections are treated to access the RNA for labeling with circularizable DNA probes.

value: Skin

tag: age

tag: Sex

value: M

tag: disease state

value: Healthy

tag: batch


title: root-LN51,treated with low nitrogen for 336 hours,biol rep 1

city: Harbin City

first: Chenghao

last: Li

state: HeiLongJiang Province

address: No. 51 HeXing Road,Xiangfang District

department: College of Forestry

country: China

institute: Northeast Forestry University

description:
Library name: LN51_low nitrogen 336h
treated with low nitrogen for 336 hours,biol rep 1

data_processing:
Raw reads were converted to high-fidelity clean data through rigorous filtering of low-quality bases and adapter sequences
The reference genomes and the annotation file were downloaded from  the Populus genome (version3.0,https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa ). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Assembly: Populus trichocarpa v3.0 (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: csv files include FPKM valus for each sample

organism: Populus ussuriensis

source_name: root

growth_protocol: Clonally propagated Populus ussuriensis plantlets were maintained in vitro on Woody Plant Medium supplemented with 25 g/L sucrose and 6 g/L agar. Cultures were incubated under a 16 h light/8 h dark photoperiod at 23°C, with a light intensity of 46 μmol photons m⁻² s⁻¹ provided by cool white fluorescent lights. The upper three internodes were excised from 4-week-old plantlets and transferred via micro-cutting to normal nitrogen WPM(NN), which contains 10 mM NO₃⁻ and 5 mM NH₄⁺.

extract_protocol:
All samples were rapidly frozen in liquid nitrogen and subsequently stored at −80 °C for RNA-seq and RNA was isolated using cetyltrimethyl ammonium bromide reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After three weeks of rooting, the rooted plantlets were subjected to low-nitrogen (LN) treatment by transferring them to modified WPM containing 0.05 mM NO₃⁻ and 0.025 mM NH₄⁺. Root samples were collected at 0, 6, 12, 24, 48, 96, and 336 hours after LN.

value: root

tag: cell type

value: whole root system

tag: treatment

value: treated with low nitrogen for 336 hours

value: low nitrogen 336h batch


title: 11629-JD-1_C3_Nonlesional

description: FFPE Xenium spatial transcriptomics

value: F

value: Non-lesional


title: 1094077_Donor1-1_none

city: Tarrytown

first: Kaitlyn

last: Gayvert

state: NY

address: 777 Old Saw Mill River Rd

department: Molecular Profiling & Data Science

institute: Regeneron Pharmaceuticals

description:
Library name: 1094077
4147.10023.1094077.S33.W111102

data_processing:
FASTQ files were aligned and quantified using Omicsoft ArrayStudio
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include read counts for  each Sample

source_name: blood

extract_protocol:
Tissues/Cells were homogenized in TRIzol and chloroform was used for phase separation. The aqueous phase, containing total RNA, was purified using MagMAX™-96 for Microarrays Total RNA Isolation Kit (Ambion by Life Technologies) according to manufacturer’s specifications. Genomic DNA was removed using RNase-Free DNase Set (Qiagen) on the Kingfisher Flex machine (Thermofisher).
The strand-specific RNA-seq libraries were prepared from 500 ng RNA using KAPA stranded mRNA-Seq Kit (KAPA Biosystems). The libraries were amplified by twelve-cycle PCR. Sequencing was performed on Illumina HiSeq®2000 (Illumina) by multiplexed single-read run with 33 cycles.

value: blood

value: eosinophils

tag: donor

value: Donor 1

value: no cytokine


title: root-LN43,treated with low nitrogen for 96 hours,biol rep 3

description:
Library name: LN43_low nitrogen 96h
treated with low nitrogen for 96 hours,biol rep 3

value: treated with low nitrogen for 96 hours

value: low nitrogen 96h batch


title: A375 GFP RNA-seq rep2

city: New York

first: Pietro

last: Berico

address: 550 1st Ave Smilow 305

department: Pathology

institute: NYU Langone Health

description: Library name: Sample 11

data_processing:
Fastq were trimmed using trim galore and reads were aligned to human (gencode v44) or murine (gencode v10) transcriptome using STAR.
Counts were merged across conditions using R and normalized using edgeR.
Differential expression analysis was conducted using Deseq2.
Assembly: Hg38, mm10
Supplementary files format and content: tab-delimited text file containing raw and normalized (counts per million) couts for each sample

source_name: skin

growth_protocol: Cells were grown in 6 well plates in 2D for 72hr in complete media supplemented with 1ug/ml of doxycyline to induce shRNA or overexpressing constructs.

extract_protocol:
Macherey-Nagel Nucleospin RNA Plus kit following manufacture instructions.
RNA libraries for RNA-seq were prepared using automated TruSeq stranded total RNA RiboZero Gold library preparation.

value: skin

tag: cell line

value: melanoma

tag: sample group

value: A375 GFP


title: 11629-JD-2_A1_Nonlesional

description: FFPE Xenium spatial transcriptomics

value: Skin


title: HL+HS+S_rep1

description:
Library name: HLHSS_1
Combination of High light stress, Heat stress, and Salinity stress, replicate 1

value: leaves

value: Moneymaker

value: wild type


title: root-LN42,treated with low nitrogen for 96 hours,biol rep 2

description:
Library name: LN42_low nitrogen 96h
treated with low nitrogen for 96 hours,biol rep 2

value: root

value: whole root system


title: A375 shHOXD13-3 RNA-seq rep3

description: Library name: Sample 9

value: A375 shHOXD13-3


title: HL+HS_rep3

description:
Library name: HLHS_3
High light stress and Heat stress, replicate 3


title: 11629-JD-2_A2_Pustule

description: FFPE Xenium spatial transcriptomics

value: F

value: Pustule


title: A375 GFP RNA-seq rep1

description: Library name: Sample 10


title: HL+HS_rep2

description:
Library name: HLHS_2
High light stress and Heat stress, replicate 2


title: root-LN41,treated with low nitrogen for 96 hours,biol rep 1

description:
Library name: LN41_low nitrogen 96h
treated with low nitrogen for 96 hours,biol rep 1


title: HL+HS_rep1

description:
Library name: HLHS_1
High light stress and Heat stress, replicate 1


title: 11629-JD-1_C1_Comedone

description: FFPE Xenium spatial transcriptomics

value: Comedo


title: HL+HS+PQ_rep1

description:
Library name: HLHSPQ_1
Combination of High light stress, Heat stress, and Paraquat stress, replicate 1


title: root-LN33,treated with low nitrogen for 48 hours,biol rep 3

description:
Library name: LN33_low nitrogen 48h
treated with low nitrogen for 48 hours,biol rep 3

value: treated with low nitrogen for 48 hours

value: low nitrogen 48h batch


title: 11629-JD-2_B2_Nonlesional

description: FFPE Xenium spatial transcriptomics

value: Non-lesional


title: A375 shHOXD13-3 RNA-seq rep2

description: Library name: Sample 8


title: root-LN52,treated with low nitrogen for 336 hours,biol rep 2

description:
Library name: LN52_low nitrogen 336h
treated with low nitrogen for 336 hours,biol rep 2

value: treated with low nitrogen for 336 hours

value: low nitrogen 336h batch


title: A375 shHOXD13-3 RNA-seq rep1

description: Library name: Sample 7

value: skin

value: melanoma


title: 11629-JD-2_D2_Comedone

description: FFPE Xenium spatial transcriptomics

value: Skin


title: A375 shHOXD13-2 RNA-seq rep3

description: Library name: Sample 6

value: A375 shHOXD13-2


title: HL+HS+S_rep2

description:
Library name: HLHSS_2
Combination of High light stress, Heat stress, and Salinity stress, replicate 2

value: leaves

value: Moneymaker


title: A375 GFP RNA-seq rep3

description: Library name: Sample 12

value: A375 GFP


title: 11629-JD-2_C2_Comedone

description: FFPE Xenium spatial transcriptomics


title: HL+S+PQ_rep3

description:
Library name: HLSPQ_3
Combination of High light stress, Salinity stress, and Paraquat stress, replicate 3

value: wild type


title: A375 shHOXD13-2 RNA-seq rep2

description: Library name: Sample 5


title: root-LN32,treated with low nitrogen for 48 hours,biol rep 2

description:
Library name: LN32_low nitrogen 48h
treated with low nitrogen for 48 hours,biol rep 2

value: root

value: whole root system


title: root-LN31,treated with low nitrogen for 48 hours,biol rep 1

description:
Library name: LN31_low nitrogen 48h
treated with low nitrogen for 48 hours,biol rep 1


title: root-LN23,treated with low nitrogen for 24 hours,biol rep 3

description:
Library name: LN23_low nitrogen 24h
treated with low nitrogen for 24 hours,biol rep 3

value: treated with low nitrogen for 24 hours

value: low nitrogen 24h batch


title: A375 shHOXD13-2 RNA-seq rep1

description: Library name: Sample 4


title: root-LN22,treated with low nitrogen for 24 hours,biol rep 2

description:
Library name: LN22_low nitrogen 24h
treated with low nitrogen for 24 hours,biol rep 2


title: HL+PQ_rep3

description:
Library name: HLPQ_3
High light stress and Paraquat stress, replicate 3


title: HL+S+PQ_rep2

description:
Library name: HLSPQ_2
Combination of High light stress, Salinity stress, and Paraquat stress, replicate 2


title: 11629-JD-2_C1_Comedone

description: FFPE Xenium spatial transcriptomics

value: F

value: Comedo


title: A375 shNTC RNA-seq rep3

description: Library name: Sample 3

value: A375 shNTC


title: 11629-JD-1_C2_Pustule

description: FFPE Xenium spatial transcriptomics

value: M

value: Pustule


title: HL+PQ_rep2

description:
Library name: HLPQ_2
High light stress and Paraquat stress, replicate 2


title: root-LN21,treated with low nitrogen for 24 hours,biol rep 1

description:
Library name: LN21_low nitrogen 24h
treated with low nitrogen for 24 hours,biol rep 1


title: HL+PQ_rep1

description:
Library name: HLPQ_1
High light stress and Paraquat stress, replicate 1


title: root-LN12,treated with low nitrogen for 12 hours,biol rep 2

description:
Library name: LN12_low nitrogen 12h
treated with low nitrogen for 12 hours,biol rep 2

value: treated with low nitrogen for 12 hours

value: low nitrogen 12h batch


title: A375 shNTC RNA-seq rep2

description: Library name: Sample 2

value: skin

value: melanoma


title: 11629-JD-1_A1_Nonlesional

description: FFPE Xenium spatial transcriptomics

value: Skin

value: Non-lesional


title: root-LN11,treated with low nitrogen for 12 hours,biol rep 1

description:
Library name: LN11_low nitrogen 12h
treated with low nitrogen for 12 hours,biol rep 1


title: root-LN13,treated with low nitrogen for 12 hours,biol rep 3

description:
Library name: LN13_low nitrogen 12h
treated with low nitrogen for 12 hours,biol rep 3


title: A375 shNTC RNA-seq rep1

description: Library name: Sample 1


title: HL+S+PQ_rep1

description:
Library name: HLSPQ_1
Combination of High light stress, Salinity stress, and Paraquat stress, replicate 1

value: leaves

value: Moneymaker


title: HL+S_rep2

description:
Library name: HLS_2
High light stress and Salinity stress, replicate 2

value: wild type


title: root-C3,treated with low nitrogen for 0 hours,biol rep 3

description:
Library name: C3_low nitrogen 0h
treated with low nitrogen for 0 hours,biol rep 3

value: root

value: whole root system

value: treated with low nitrogen for 0 hours

value: low nitrogen 0h batch


title: HL+S_rep1

description:
Library name: HLS_1
High light stress and Salinity stress, replicate 1


title: 10305_D1_Comedo

description: FFPE Xenium spatial transcriptomics

value: Comedo


title: SKMEL-5 HiC

description: Library name: Sample 7

library_source: genomic

data_processing:
Fastq were processed using HiC-Pro pipeline to obtain valid pairs and generate contact matrix. Hi-Chipper was used to call Hi-ChIP loops. Domaincaller and Peakachu were used to identify topological associated domains and loops respectively.
Differential loop analysis was conducted using Diffloop R package.
Assembly: Hg38, mm10
Supplementary files format and content: Bigwig tracks, MACS2 narrow and summit peak calling outputs.

molecule: genomic DNA

growth_protocol: Cells were grown in plates in 2D for 72hr in complete media with or without supplementation of 1ug/ml of doxycyline to induce shRNA.

extract_protocol:
Cells were double crosslinked in PFA and EGS and processed for HiC and Hi-ChIP using the Arima kit (Arima Genomics, A101020) according to manufacture protocols.
HiC and Hi-ChIP libraries were prepared using the Arima Library kit (Arima Genomics, A510008, A303011).


title: A375 shNTC H3K27ac HiChIP rep2

description: Library name: Sample 6


title: 11629-JD-1_B3_Pustule

description: FFPE Xenium spatial transcriptomics


title: 11629-JD-1_B1_Nonlesional

description: FFPE Xenium spatial transcriptomics


title: root-C2,treated with low nitrogen for 0 hours,biol rep 2

description:
Library name: C2_low nitrogen 0h
treated with low nitrogen for 0 hours,biol rep 2


title: HL_rep3

description:
Library name: HL_3
High light stress, replicate 3


title: 10305_B1_Comedo

description: FFPE Xenium spatial transcriptomics


title: A375 shHOXD13-3 H3K27ac HiChIP

description: Library name: Sample 4


title: ID_1284

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

description: Library name: Sample_20

data_processing:
The read qualities for each fastq file were accessed with FastQC (V 0.11.9), and low-quality bases and adapters were removed with Trimmomatic.
The sequenced reads were mapped to the bovine reference genome (bosTau 9) with the STAR aligner (V 2.7.0b), generating the genome index with the ARS-UCD2.0 assembly.
Read counts were estimated at the gene level, and the counting was done with featureCounts, part of the Subread software (V 2.0.3).
Assembly: bosTau 9
Supplementary files format and content: tab delimited text file containing raw read counts for each sample.

molecule: polyA RNA

organism: Bos taurus

source_name: maternal blood

extract_protocol:
Blood samples were shipped on dry ice to Macrogen Europe (Amsterdam, Netherlands), which performed the RNA extraction, quality control, library preparation, and sequencing.
Libraries were prepared with the SMARTer Stranded RNA kit, followed by PE100 sequencing with the NovaSeq platform, generating ~30 million raw reads per sample in FASQ format.

value: maternal blood

value: female

tag: gestational age

value: 63 days

tag: calf birth_weight

value: 45 kg


title: A375 shNTC H3K27ac HiChIP rep1

description: Library name: Sample 5


title: 10305_A1_Nonlesional

description: FFPE Xenium spatial transcriptomics

value: M


title: 11629-JD-1_A2_Nonlesional

description: FFPE Xenium spatial transcriptomics


title: root-C1,treated with low nitrogen for 0 hours,biol rep 1

description:
Library name: C1_low nitrogen 0h
treated with low nitrogen for 0 hours,biol rep 1


title: ID_1039

description: Library name: Sample_18

value: 56 kg


title: HL_rep1

description:
Library name: HL_1
High light stress, replicate 1


title: ID_1273

description: Library name: Sample_19

value: 46 kg


title: CT2_rep3

description:
Library name: CT2_3
Control (CT2, HL/HLHS conditions), replicate 3


title: 11027_C2_Healthy

description: FFPE Xenium spatial transcriptomics

value: Skin

value: F

value: Healthy


title: SKMEL-147 HiC

description: Library name: Sample 8

value: skin

value: melanoma


title: A375 IgG HiChIP

description: Library name: Sample 2


title: HL_rep2

description:
Library name: HL_2
High light stress, replicate 2

value: leaves

value: Moneymaker

value: wild type


title: 501mel HiC

description: Library name: Sample 1


title: A375 shHOXD13-2 H3K27ac HiChIP

description: Library name: Sample 3


title: CT2_rep1

description:
Library name: CT2_1
Control (CT2, HL/HLHS conditions), replicate 1


title: ID_3975

description: Library name: Sample_17


title: CT2_rep2

description:
Library name: CT2_2
Control (CT2, HL/HLHS conditions), replicate 2


title: ID_3639

description: Library name: Sample_16

value: 39 kg


title: HL+S_rep3

description:
Library name: HLS_3
High light stress and Salinity stress, replicate 3


title: S+PQ+HS_rep3

description:
Library name: SPQHS_3
Combination of Salinity stress, Paraquat stress, and Heat stress, replicate 3


title: SKMEL-147-ATAC

description: Library name: Sample 21

data_processing:
Fastq were trimmed using trim galore and reads were aligned to human genome using bowtie2. Samtools was used to generate bam alignments which were used for peakcalling (MACS2) and bigwig generation (deeptools).
Assembly: Hg38
Supplementary files format and content: Bigwig tracks, MACS2 narrow and summit peak calling outputs.

growth_protocol: Cells were grown in plates in 2D for 72hr in complete media with or without supplementation of 1ug/ml of doxycyline to induce shRNA or overexpressing constructs.


title: 11027_D2_Nonlesional

description: FFPE Xenium spatial transcriptomics


title: 11027_C1_Healthy

description: FFPE Xenium spatial transcriptomics


title: 11027_B2_Nonlesional

description: FFPE Xenium spatial transcriptomics

value: Non-lesional


title: ID_3418

description: Library name: Sample_15

value: maternal blood


title: SKMEL-147-K27ac

description: Library name: Sample 20


title: S+PQ+HS_rep2

description:
Library name: SPQHS_2
Combination of Salinity stress, Paraquat stress, and Heat stress, replicate 2


title: ID_2320

description: Library name: Sample_14

value: female

value: 30 kg


title: SKMEL-147-IgG

description: Library name: Sample 19


title: 11027_B1_Nonlesional

description: FFPE Xenium spatial transcriptomics


title: 11027_A2_Healthy

description: FFPE Xenium spatial transcriptomics


title: ID_2130

description: Library name: Sample_13

value: 63 days

value: 40 kg


title: B16F10 shHoxd13-4 CD45 positive

description: Library name: Sample 4

library_source: transcriptomic single cell

data_processing:
Fastq were processed using PIPseeker to obtain the final matrix, features and barcodes files.
Next, seurat objects were generated and analyzed using Seurat v5 and implementations.
Assembly: mm10
Supplementary files format and content: Barcodes, features and matrix raw files.

organism: Mus musculus

growth_protocol: C57BL/6J mice were injected intradermal with 50k B16F10 cells in 50%PBS + 50% Matrigel.

extract_protocol:
B16F10 tumors were excised and minced with a scalpel. Next, single cell suspension was generated using a cocktail of Collagenase I and DNAseI. CD45 positive and negative were sorted by flow cytometry.
PIP-seq libraries were produced based on manufacture instructions (Fluent BioScience).

treatment_protocol: Mice were feeded with doxycycline chew (200mg/kg) to induce the expression of shRNA in B16F10 cells.

value: B16F10 shHoxd13-4

tag: fraction

value: CD45 positive


title: SKMEL-5-K27ac

description: Library name: Sample 18


title: S+PQ+HS_rep1

description:
Library name: SPQHS_1
Combination of Salinity stress, Paraquat stress, and Heat stress, replicate 1


title: SKMEL-5-IgG

description: Library name: Sample 17


title: PQ+HS_rep3

description:
Library name: PQHS_3
Paraquat stress and Heat stress, replicate 3


title: ID_1985

description: Library name: Sample_12

value: 36 kg


title: B16F10 shHoxd13-4 CD45 negative

description: Library name: Sample 3

value: CD45 negative


title: 10305_C1_Comedo

description: FFPE Xenium spatial transcriptomics

value: Skin

value: M

value: Comedo


title: SKMEL-5-CTCF

description: Library name: Sample 16

data_processing:
Fastq were trimmed using trim galore and reads were aligned to human genome using bowtie2. Samtools was used to generate bam alignments which were used for peakcalling (MACS2) and bigwig generation (deeptools).
Assembly: Hg38
Supplementary files format and content: Bigwig tracks, MACS2 narrow and summit peak calling outputs.
Library strategy: CUT&Tag

value: skin

value: melanoma


title: PQ+HS_rep1

description:
Library name: PQHS_1
Paraquat stress and Heat stress, replicate 1

value: leaves

value: Moneymaker

value: wild type


title: PQ+HS_rep2

description:
Library name: PQHS_2
Paraquat stress and Heat stress, replicate 2


title: ID_1625

description: Library name: Sample_11

value: maternal blood

value: 37 kg


title: B16F10 shNTC CD45 negative

description: Library name: Sample 1

value: B16F10 shNTC


title: ID_2734

description: Library name: Sample_9

value: female

value: 63 days

value: 43 kg


title: S+HS_rep3

description:
Library name: SHS_3
Salinity stress and Heat stress, replicate 3


title: ID_1475

description: Library name: Sample_10

value: 53 kg


title: ID_2686

description: Library name: Sample_8


title: SKMEL-5-ATAC

description: Library name: Sample 15


title: B16F10 shNTC CD45 positive

description: Library name: Sample 2

value: CD45 positive


title: A375-shNTC-IgG

description: Library name: Sample 12


title: ID_2266

description: Library name: Sample_7

value: 38 kg


title: S+HS_rep1

description:
Library name: SHS_1
Salinity stress and Heat stress, replicate 1


title: YUMM1.7 HOXD13 RNA-seq rep2

description: Library name: Sample 41

value: YUMM1.7 HOXD13


title: YUMM1.7 HOXD13 RNA-seq rep3

description: Library name: Sample 42


title: S+HS_rep2

description:
Library name: SHS_2
Salinity stress and Heat stress, replicate 2


title: YUMM1.7 HOXD13 RNA-seq rep1

description: Library name: Sample 40


title: A375-shNTC-K27ac-rep1

description: Library name: Sample 13


title: S+PQ_rep3

description:
Library name: SPQ_3
Salinity stress and Paraquat stress, replicate 3


title: ID_9609

description: Library name: Sample_6

value: 50 kg


title: A375-shH2-K27ac

description: Library name: Sample 10


title: YUMM1.7 EMPTY RNA-seq rep2

description: Library name: Sample 38

value: YUMM1.7 EMPTY


title: YUMM1.7 EMPTY RNA-seq rep3

description: Library name: Sample 39

value: skin


title: A375-shNTC-K27ac-rep2

description: Library name: Sample 14

value: melanoma


title: S+PQ_rep2

description:
Library name: SPQ_2
Salinity stress and Paraquat stress, replicate 2

value: leaves


title: A375-shH3-K27ac

description: Library name: Sample 11


title: YUMM1.7 EMPTY RNA-seq rep1

description: Library name: Sample 37


title: ID_726

description: Library name: Sample_3

value: 35 kg


title: ID_728

description: Library name: Sample_4

value: 54 kg


title: HCmel1274 shHoxd13-4 RNA-seq rep3

description: Library name: Sample 36

value: HCmel1274 shHoxd13-4


title: S+PQ_rep1

description:
Library name: SPQ_1
Salinity stress and Paraquat stress, replicate 1

value: Moneymaker

value: wild type


title: Cd_rep2

description:
Library name: CD_2
Cadmium stress, replicate 2


title: ID_298

description: Library name: Sample_2

value: maternal blood

value: female


title: A375-HOXD13-HA

description: Library name: Sample 9


title: A375-GFP-ATAC

description: Library name: Sample 8


title: HCmel1274 shHoxd13-4 RNA-seq rep1

description: Library name: Sample 34


title: ID_55

description: Library name: Sample_1

value: 63 days

value: 55 kg


title: N_rep3

description:
Library name: N_3
Nitrogen deficiency, replicate 3


title: HCmel1274 shHoxd13-3 RNA-seq rep3

description: Library name: Sample 33

value: HCmel1274 shHoxd13-3


title: HCmel1274 shHoxd13-4 RNA-seq rep2

description: Library name: Sample 35


title: Cd_rep1

description:
Library name: CD_1
Cadmium stress, replicate 1


title: Cd_rep3

description:
Library name: CD_3
Cadmium stress, replicate 3


title: HCmel1274 shHoxd13-3 RNA-seq rep2

description: Library name: Sample 32


title: HONE1 EBV cells, overexpressing VILL, biol rep3

city: Guangzhou

first: Zhongxi

last: Huang

state: Guangdong

address: NO.1023 Shatai South Road

institute: Southern Medical University

description:
Library name: HONE1 EBV VILL3
Column name in HONE1EBV OE count.csv: HONE1.EBV.VILL.3

data_processing:
Sequence reads were mapped to the human genome version hg38 by using Illumina sequence analysis pipeline.
Assembly: hg38
Supplementary files format and content: Sample
Supplementary files format and content: csv files include count values for each Sample

source_name: HONE1 EBV

growth_protocol: HONE1 EBV cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Vigonob, Guangzhou, China) with 10% fetal bovine serum (Vigonob, Guangzhou, China) in humidified 5% (v/v) CO2 atmosphere at 37°C.

extract_protocol:
Total RNA was extracted from cells and tissues using Trizol (Invitrogen, USA) according to the manufacturer’s instruction.
RNA-seq was processed according to the instructions of NEB Next Ultra RNA Library Prep Kit for Illumina (New England BioLabs).

treatment_protocol: The pTSB02-VILL-GFP-3FLAG-PURO (Cat.TSB180954-1) and the vector were purchased from TranSheep Biotech (Shanghai, China). Lentiviral vectors were co-transfected into HEK293T cells with packaging vectors psPAX2 (Cat.12260, Addgene) and pMD2.G (Cat.12259, Addgene) using Lipofectamine 2000 (Invitrogen, USA). Infectious lentivirus particles were harvested at 48h after transfection, filtered through 0.45μm PVDF filters (Cat.SLHV033RB, Millipore), and transduced into cells. Stable clones were then selected using 0.5 μg/mL puromycin (Cat.ST551, Beyotime).

value: HONE1 EBV

value: nasopharyngeal carcinoma cells

value: overexpressing VILL


title: HONE1 EBV cells, overexpressing VILL, biol rep2

description:
Library name: HONE1 EBV VILL2
Column name in HONE1EBV OE count.csv: HONE1.EBV.VILL.2


title: HONE1 EBV cells, overexpressing VILL, biol rep1

description:
Library name: HONE1 EBV VILL1
Column name in HONE1EBV OE count.csv: HONE1.EBV.VILL.1


title: 501mel-K27ac

description: Library name: Sample 4


title: 501mel-IgG

description: Library name: Sample 3


title: A375-GFP-HA

description: Library name: Sample 5


title: ID_9289

description: Library name: Sample_5

value: 32 kg


title: N_rep2

description:
Library name: N_2
Nitrogen deficiency, replicate 2


title: A375-GFP-K27ac

description: Library name: Sample 7

value: skin


title: HCmel1274 shHoxd13-3 RNA-seq rep1

description: Library name: Sample 31

value: melanoma


title: PQ_rep3

description:
Library name: PQ_3
Paraquat stress, replicate 3

value: leaves


title: N_rep1

description:
Library name: N_1
Nitrogen deficiency, replicate 1


title: PQ_rep2

description:
Library name: PQ_2
Paraquat stress, replicate 2


title: A375-GFP-IgG

description: Library name: Sample 6


title: HCmel1274 shNTC RNA-seq rep3

description: Library name: Sample 30

value: HCmel1274 shNTC


title: PQ_rep1

description:
Library name: PQ_1
Paraquat stress, replicate 1


title: HONE1 EBV cells, vector, biol rep1

description:
Library name: HONE1 EBV CON1
Column name in HONE1EBV OE count.csv: HONE1.EBV.CON.1

value: vector


title: HCmel1274 shNTC RNA-seq rep2

description: Library name: Sample 29


title: 501mel-CTCF

description: Library name: Sample 2


title: HONE1 EBV cells, vector, biol rep2

description:
Library name: HONE1 EBV CON2
Column name in HONE1EBV OE count.csv: HONE1.EBV.CON.2


title: HCmel1274 shNTC RNA-seq rep1

description: Library name: Sample 28


title: Murine lacrimal gland, 3 months, 18 hours post-abrasion, replicate #3

city: Montpellier

first: Frederic

last: Michon

address: 80, rue Augustin Fliche

department: Institute for Neurosciences of Montpellier

country: France

institute: Inserm

description: Library name: 18h post-wound_ICR_3_S9

data_processing:
bcl2fastq2 Conversion Software was used to convert BCL files to FASTQ file format and demultiplex samples.
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence using Trimmomatic. Parameters used: :2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were mapped to GENCODE mouse Release M30 reference genome (GRCm39) and annotation files using STAR aligner with parameters  --runThreadN 20 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJstitchMismatchNmax 5 -1 5 5 --outFilterType BySJout --outFilterMismatchNmax 999 --outSAMattributes NH HI NM MD AS nM jM jI XS --outSAMtype BAM SortedByCoordinate --outSAMmapqUnique 60 --quantMode GeneCounts --twopassMode Basic
Counts per gene were calculated using featureCounts software. Parameters used: -s 2 -T 20 -t exon -g gene_id
Differential expression analysis used the DESeq2 software in R environment. Procedures included: Normalization of count values between samples using a geometric means, using negative binomial linear model and Wald test to produce p-values, removal of low-expression outliers (using Cook's distance)  to optimize for p-value adjustment and finally, multiple testing adjustment of p-values with Benjamini-Hochberg procedure.
Assembly: GENCODE Mus Musculus Release M17 reference genome (GRCm38.p6)
Supplementary files format and content: tab delimited files

source_name: Lacrimal gland

extract_protocol:
Trizol + QIAGEN Rneasy extraction kit
NEBNext® Ultra™ Directional RNA Library Prep Kit

value: Lacrimal gland

value: 18 hours after mechanical abrasion


title: 501mel-ATAC

description: Library name: Sample 1


title: HOXA9+SIX1_4

city: Manchester

first: Georges

last: Lacaud

state: England

address: Wilmslow Raod

department: Stem Cell Biology

country: United Kingdom

institute: Cancer Research UK Manchester Institute

description: Library name: HOXA9+SIX1_R4

data_processing:
Raw fastqc sequencing files were run through nextflow on the CRUK-MI (Manchester institute) server to generate merged salmon gene counts
DESeq2 R package was run to infer differentially expressed genes accross samples
Assembly: mm10
Supplementary files format and content: Salon merged gene counts were generared by nextflow. All counts concatenated on same tsv file

source_name: bone marrow

growth_protocol: All retrovirally transduced lines were serially replated every week for 3 weeks in MeC media. Following line establishment cells were maintained in MT2 media

extract_protocol:
Direct RNA isolation with RNeasy Mini Kit [Qiagen Ref. 74004]
RNA was sent to BMKGENE for library preperation and sequencing

value: bone marrow

value: HOXA9+SIX1 transfomed

value: transformed c-kit+ cells (mAML)


title: Ferret PBMCs, male, untreated, replicate 3

city: Rochester

first: Christian

middle: Karl

last: Pfaller

state: MN

address: 200 First Street SW

department: Molecular Medicine

institute: Mayo Clinic

description: Library name: Ferret_PBMC_3

data_processing:
Raw FASTQ files were quality trimmed with fastp (v. 0.23.1): -M 30 -3 -5 -n 0 -l 35 -q 30 -u 15 -w 16 -f 1 -F 1
Trimmmed FASTQ files were aligned to reference genomes with STAR (v. 2.7.9a): --runThreadN 30 --outSAMmapqUnique 60 --outSAMtype BAM SortedByCoordinate --twopassMode Basic --outFilterType Normal --outFilterMultimapNmax 10 --alignSJoverhangMin 5 --alignSJDBoverhangMin 3 --outFilterMismatchNmax 10 --outFilterMismatchNoverReadLmax 1 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --alignIntronMin 21 --alignIntronMax 0 --alignMatesGapMax 0
Optical duplicates were marked and removed with PICARD MarkDuplicates (v. 2.27.5): CREATE_INDEX=true REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT
Reads spanning exon/exon junctions were split using GATK SplitNCigarReads (v. 4.3.0.0) using default settings
Reads were re-aligned with GATK LeftAlignIndels (v. 4.3.0.0): --disable-read-filter WellformedReadFilter
For deNovo analysis: BAM alignments were analyzed with TSniffer deNovo: -wSize 100 -minCov 4 -chunkSize 5000000 -primary (The primary parameter was omitted for analysis of ferret data); https://github.com/maiher/tsniffer_1.0
For Regio analysis: BAM alignments were analyzed with TSniffer Regio using a filtered and cleaned-up set of regions derived from deNovo analysis using default parameters; https://github.com/maiher/tsniffer_1.0
Assembly: hg38 (GCA_000001405.15_GRCh38)
Assembly: MusPutFur1.0 (GCF_000215625.1)
Supplementary files format and content: deNovo analysis: gff file with detected transition regions; annotation column includes transition type, relative transition frequencies, p-value from Fisher's exact test, transition sites count, and nucleotide positions
Supplementary files format and content: Regio analysis: gff file with detected transition regions; annotation column includes transition type, relative transition frequencies, p-value from Fisher's exact test, transition sites count, and nucleotide positions

organism: Mustela putorius furo

source_name: PBMC

growth_protocol: HeLa cells were grown in standard growth medium in 6 well plates and harvested at confluency; ferret PBMCs were isolated from fresh whole blood and cultivated in standard growth medium for 3 days before RNA extraction.

extract_protocol:
HeLa/Ferret samples: Total RNA was extracted using Trizol; for HeLa cells, genomic DNA was removed by two Dnase I treatment steps and RNA was cleaned up using phenol/chloroform/isoamyl alcohol
HeLa/Ferret samples: RNA integrity numbers (RIN) were assessed by fragment analyzer and only RNAs with RIN=10 were further  processed; ribosomal RNA was removed before RNA-seq library preparation; strand-specific libraries were generated using a custom protocol at the Paul-Ehrlich-Institute (PMID 35952673) or a standard protocol by Azenta (Leipzig, Germany)
HeLa, Ferret samples: Libraries were sequenced at 2x 150 bp paired-end reads

value: PBMC

value: male


title: HS_rep3

description:
Library name: HS_3
Heat stress, replicate 3

value: Moneymaker

value: wild type


title: HS_rep2

description:
Library name: HS_2
Heat stress, replicate 2


title: Ferret PBMCs, male, untreated, replicate 1

description: Library name: Ferret_PBMC_1


title: Murine lacrimal gland, 3 months, 18 hours post-abrasion, replicate #2

description: Library name: 18h post-wound_ICR_2_S8


title: HONE1 EBV cells, vector, biol rep3

description:
Library name: HONE1 EBV CON3
Column name in HONE1EBV OE count.csv: HONE1.EBV.CON.3

value: HONE1 EBV

value: nasopharyngeal carcinoma cells


title: Ferret PBMCs, male, untreated, replicate 2

description: Library name: Ferret_PBMC_2


title: HS_rep1

description:
Library name: HS_1
Heat stress, replicate 1


title: Murine lacrimal gland, 3 months, 18 hours post-abrasion, replicate #1

description: Library name: 18h post-wound_ICR_1_S7


title: High exopher number, biol rep 3

city: Warsaw

first: Michal

last: Turek

address: Pwinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

description: Library name: 3M

data_processing:
Following quality assessment of the raw sequencing data, reads were trimmed to remove potential adapter sequences and low-quality nucleotides using Trimmomatic v0.36.
Assembly: The cleaned reads were then aligned to the Caenorhabditis elegans reference genome from ENSEMBL using the STAR aligner v2.5.2b. STAR is a splice-aware aligner that identifies splice junctions and integrates them into the alignment process to enhance the accuracy of read mapping. This step resulted in the generation of BAM files. Unique gene hit counts were calculated using the featureCounts function from the Subread package v1.5.2, considering only reads uniquely aligned to exon regions.
Supplementary files format and content: The gene hit counts were subsequently used for downstream differential expression analysis. DESeq2 was employed to compare gene expression levels between different sample groups. The Wald test was used to calculate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and an absolute log2 fold change > 1 were considered differentially expressed in each comparison.

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: C. elegans strains were maintained at 20°C on nematode growth medium (NGM) plates seeded with Escherichia coli OP50 as a food source

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus mini kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions.
RNA samples were quantified using the Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA), and their integrity was assessed with the Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina, following the manufacturer’s protocol (NEB, Ipswich, MA, USA). In brief, mRNA was enriched using Oligo(dT) beads and subsequently fragmented at 94°C for 15 minutes. First and second-strand cDNA synthesis was performed, followed by end repair and adenylation of the cDNA fragments at their 3' ends. Universal adapters were then ligated to the cDNA fragments, and libraries were enriched through a limited-cycle PCR with the addition of indexing sequences. The resulting sequencing libraries were validated using the Agilent TapeStation and quantified with both the Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA) and quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The libraries were multiplexed and loaded onto the Illumina NovaSeq 6000 platform according to the manufacturer’s instructions. Sequencing was performed with a 2×150 paired-end (PE) configuration using v1.5 reagents. Image analysis and base calling were carried out using the NovaSeq Control Software v1.7. The raw sequence data (.bcl files) generated were converted into fastq files and de-multiplexed using the Illumina bcl2fastq software (version 2.20), allowing for one mismatch in index sequence identification

value: whole organism

value: hermaphrodite


title: HOXA9+SIX1_2

description: Library name: HOXA9+SIX1_R2


title: S_rep3

description:
Library name: S_3
Salinity stress, replicate 3


title: S_rep2

description:
Library name: S_2
Salinity stress, replicate 2


title: Murine lacrimal gland, 3 months, 6 hours post-abrasion, replicate #2

description: Library name: 6h post-wound_ICR_2_S5

value: 6 hours after mechanical abrasion


title: High exopher number, biol rep 1

description: Library name: 1M


title: Murine lacrimal gland, 3 months, 6 hours post-abrasion, replicate #3

description: Library name: 6h post-wound_ICR_3_S6


title: HOXA9_4

description: Library name: HOXA9_R4

value: HOXA9 transformed


title: High exopher number, biol rep 2

description: Library name: 2M


title: Murine lacrimal gland, 3 months, 6 hours post-abrasion, replicate #1

description: Library name: 6h post-wound_ICR_1_S4


title: HOXA9+SIX1_1

description: Library name: HOXA9+SIX1_R1


title: CT1_rep3

description:
Library name: CT1_3
Control (CT1, HS conditions), replicate 3

value: leaves


title: S_rep1

description:
Library name: S_1
Salinity stress, replicate 1


title: Low exopher number, biol rep 3

description: Library name: 3F


title: HOXA9_3

description: Library name: HOXA9_R3


title: Murine lacrimal gland, 3 months, before abrasion, replicate #3

description: Library name: Pre-wound_ICR_3_S3

value: Before mechanical abrasion


title: CT1_rep2

description:
Library name: CT1_2
Control (CT1, HS conditions), replicate 2


title: HOXA9_2

description: Library name: HOXA9_R2


title: HOXA9+SIX1_3

description: Library name: HOXA9+SIX1_R3


title: HOXA9_1

description: Library name: HOXA9_R1


title: CT1_rep1

description:
Library name: CT1_1
Control (CT1, HS conditions), replicate 1


title: Murine lacrimal gland, 3 months, before abrasion, replicate #1

description: Library name: Pre-wound_ICR_1_S1

value: Lacrimal gland


title: TM-1 1 DPA epidermis and fiber nuclei

status: Public on Dec 02 2025

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

description: Library name: TM1-1DPA

library_source: genomic single cell

data_processing:
Initial mapping and processing was carried out using the  Cellranger-atac  pipeline. Detailed analysis was carried out in R using the Signac package using default protocol.  Cells  were filltered to exclude those with a  transcriptional start site enrichment score below 2.
Assembly: Gossypium hirsutum v2.1 VKGJ00000000
Supplementary files format and content: Processed ouput from the 10x cellranger-atac pipeline  with default setting for each sample with the peaks.bed barcodes.tsv and matrix.mtx files readable by Signac packge in R.

organism: Gossypium hirsutum

source_name: Cotton Ovule

growth_protocol: All plants were grown under field conditions at Texas A&M, College Station in the summer of 2024.

extract_protocol:
Ovules were digested in a enzyme mix of cellulase and macerase in 450 mM mannitol for 15 minutes to release protoplasts from the epidermal layers. The ovules were then strained out and the protoplasts were allowed to continue digesting for an additional hour to remove any remaining cell wall debris. To recover the protoplasts, we used density gradient flotation: samples were centrifuged for 2 minutes at 200 g at 4°C to gently pellet the protoplasts, after which all but ~100 l of the protoplasting buffer was removed, which was mixed with 0.25 volumes chilled Iodixanol (OptiPrep, Sigma-Aldritch, St. Louis, MO) and used to gently resuspend the pellet. 100 l of chilled 450 mM mannitol was layered atop the denser layer containing iodixanol, and the samples were centrifuged at 200g and 4°C, followed by collecting protoplasts from the top layer. Protoplasts were then treated with nuclei isolation buffer and centrifuged, and nucli were washed with 450 mM mannitol,  pelleted, and resuspended in 10 ATAC buffer.
Libraries were constructed acording to the manufacturer's instructions using the Chromium NextGEM SingleCell ATACKit v2 (10x)

value: Cotton Ovule

value: 1 DPA


title: TM-1 2 DPA epidermis and fiber nuclei

description: Library name: TM1-2DPA

value: 2 DPA


title: TM-1 0 DPA epidermis and fiber nuclei

description: Library name: TM1-0DPA

value: 0 DPA


title: HEK293T_PRM1, 3

type: genomic

city: Aachen

first: Deepika

last: Puri

address: Pauwelsstraße 20

country: Germany

institute: Helmholtz Institute For Biomedical Engineering, Uniklinik Aachen

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard recommended Illumina scan protocol

data_processing:
The R packages minfi (v.1.48.0) , SeSAMe (V 1.20.0) , limma , and missMethyl were used for data import, preprocessing, quality control, and analysis, respectively.
Beta Value

label: Cy3 and Cy5

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using the MN tissue kit

value: PRM1 transfection


title: HEK293T_PRM1, 2


title: HEK293T_PRM1, 1


title: HEK293T_Empty vector, 3

value: Empty vector transfection


title: HEK293T_Empty vector, 1


title: CD271cKO skin_2

city: Modena

first: Elisabetta

last: Palazzo

address: Via del Pozzo

country: Italy

institute: Unimore

description: Library name: K2

data_processing:
The library was quantified by using the Ion Library TaqMan Quantitation kit (Thermofisher) in Real-Time PCR. For each sample, 70 pM were pooled for templating on One Touch 2 (OT2).
After emulsion PCR and subsequent Enrichment, the Ion Sphere enriched was loaded onto Chip 540 for the sequencing
The reads have been aligned with the Mouse genome (Ensembl GRCh38) using Torrent Suite™ Software 5.8.1.
The Coverage Analysis plugin has been used to create amplicon counts that have been imported into the TAC (Transcriptome Analysis Console) platform.
Assembly: Ensembl GRCh38
Supplementary files format and content: RPKM and ANOVA Results

extract_protocol:
Quick-DNA/RNA MiniPrep Plus Kit (Zymo Research)
Ion AmpliseqTM 517 Transcriptome Mouse Gene Expression kit

value: skin

value: KO


title: Low exopher number, biol rep 2

description: Library name: 2F


title: HEK293T_Empty vector, 2


title: Wild-type skin_2

description: Library name: F4

value: WT


title: Murine lacrimal gland, 3 months, before abrasion, replicate #2

description: Library name: Pre-wound_ICR_2_S2


title: Wild-type skin_3

description: Library name: F2


title: CD271cKO skin_3

description: Library name: K5


title: experiment 2, si73 depleted

city: Oslo

first: Randi

last: Gussgard Syljuåsen

address: Ullernchausseen 70

department: Department of Radiation Biology, Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

description: Library name: w32_si73_S10_unsorted.sorted

data_processing:
Read mapping of the paired-end RNAseq libraries was carried out using STAR alignment tool GRCh38.p13 reference genome version was used for the mapping together with Gencode v38 full annotation. Quantification of readthrough levels was carried out using ARTDeco.  Genes with the biggest difference in readthrough between WDR82 depleted cells and scrambled control, were inspected and visualized with integrative genomics viewer (IGV) using the GRCh38/hg38 genome reference. Readthrough levels of either the top 2000 expressed genes or all expressed genes were compared across individual libraries. Expressed genes were defined as those with FPKM > 1, a commonly accepted threshold in the field. From the expressed genes, we further selected genes with detectable read density in the read-through region (Log2Ratio > -5). In a more stringent subset, we selected genes with substantial read-through transcription, where the read-through level was comparable to or exceeded that in the gene body region (Log2Ratio > –2). For each of these genes, we computed the proportion of reads containing the canonical polyA signal (AAUAAA), corresponding to AATAAA on the forward strand and TTTATT on the reverse strand in cDNA sequences, separately for gene body and read-through regions. Read-through regions were defined as the 10 kb immediately downstream of the annotated gene body, truncated if another annotated gene occurred within 10 kb, and excluding any overlapping regions. Reads were assigned to either the gene body or read-through region only if at least 90% of their length overlapped the target region.
Assembly: GRCh38.p13 reference genome version was used for the mapping together with Gencode v38 full annotation.
Supplementary files format and content: Tab-delimited text files containing raw expression counts, FPKMs, read-in and read-through levels as computed by ARTDeco.

source_name: Human cervical cancer HeLa Kyoto

extract_protocol:
For chromatin RNA sequencing, cells were harvested and washed in PBS. Soluble RNA was released by resuspending the cell pellet in ice-cold extraction buffer (described above) with 1U/µl of RNAse inhibitor (New England Biolabs) and incubating on ice for 5 min. Extracted cells were spun down at 1300 g for 4 min and lyzed in qiazol (Qiagen). Cells were shredded using the QIAshredder homogenizer, and separated into organic and aqueous phases after the addition of chloroform and spinning in phase lock gel tubes (Tiangen). Ethanol was added to the aqueous phase containing RNA, and the RNA was collected in RNeasy Mini kit columns (Qiagen). RNA was washed and diluted according to the RNeasy kit protocol. The quality of RNA was verified using nanodrop and by bioanalyser measurements.
Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus was used for library preparation. Samples were paired-end sequenced using Illumina NovaSeq6000.

value: Human cervical cancer HeLa Kyoto


title: experiment 2, WDR82 depleted

description: Library name: w32_siw82_S8_unsorted.sorted


title: Low exopher number, biol rep 1

description: Library name: 1F

value: whole organism


title: experiment 2, si73 and WDR82 co-depleted

description: Library name: w32_siw82_si73_S9_unsorted.sorted


title: experiment 1, si73 and WDR82 co-depleted

description: Library name: w25_siw82_si73_S4_unsorted.sorted


title: CD271cKO skin_1

description: Library name: K1


title: experiment 1, si73 depleted

description: Library name: w25_si73_S5_unsorted.sorted


title: experiment 1, scrambled control, sample 2

description: Library name: w25_scr2_S2_unsorted.sorted


title: Wild-type skin_1

description: Library name: F3


title: experiment 1, scrambled control, sample 1

description: Library name: w25_scr1_S1_unsorted.sorted


title: experiment 2, scrambled control, sample 2

description: Library name: w32_scr2_S7_unsorted.sorted


title: HEK293T_PRM2, 2

value: PRM2 transfection


title: HEK293T_PRM2, 1


title: HEK293T_PRM2, 3


title: PMc1_peripheral blood_151582

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

description:
Library name: PMc1_MF_peripheral blood_357
Column name in raw_counts_PMc1_358.txt: 151582

data_processing:
RNA-seq data was aligned to GRCh38 with STAR v2.7.9a using the two-pass mode. The following parameters were set: chimSegmentMin=12, chimJunctionOverhangMin=8, alignSJDBoverhangMin=10, alignIntronMax=100000, alignSJstitchMismatchNmax=5 -1 5 5, alignSplicedMateMapLminOverLmate=0, alignSplicedMateMapLmin=30, chimMultimapScoreRange=3, chimScoreJunctionNonGTAG=-4, chimMultimapNmax=20, chimNonchimScoreDropMin=10 peOverlapNbasesMin=12 and peOverlapMMp=0.1.
Reads were annotated with Ensembl v103.
Count data was obtained using HTSeq v0.7.2 using default settings.
General stats were obtained using picard v2.10.9.
The RNAseq data was processed through DESeq2 v1.32.0. Genes with less than 1 read were removed prior to normalization using variance stabilizing transformation (VST).
Assembly: GRCh38
Supplementary files format and content: HTSeq counts over GRCh38.
Supplementary files format and content: raw count read counts

source_name: Peripheral blood

extract_protocol:
Total RNA was extracted from patient cells using the RNeasy Minikit (Qiagen) following the “Quick-Start Protocol” with “On-Column DNase Digestion”. RNA was eluted in 30ul of molecular-grade water (Sigma, cat #W4502).
NEBNext Ultra Directional polyA mRNA Library Prep using 500ng of total RNA.

treatment_protocol: Peripheral blood mononuclear cells from myelofibrosis patients were thawed.

value: Peripheral blood

value: mononuclear cells

tag: age at_sample_collection

value: Female

tag: diagnosis

value: PMF, overt fibrotic stage

value: Positive

tag: calr

value: Negative

tag: mpl

tag: dipss category

tag: os status_at_last_follow_up

value: Alive

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)

tag: transform time_(days)

tag: mpn24 score


title: PMc1_peripheral blood_100032

description:
Library name: PMc1_MF_peripheral blood_358
Column name in raw_counts_PMc1_358.txt: 100032

tag: tissue

tag: cell type

tag: Sex

value: Male

value: High


title: PMc1_peripheral blood_120843

description:
Library name: PMc1_MF_peripheral blood_354
Column name in raw_counts_PMc1_358.txt: 120843


title: PMc1_peripheral blood_160041

description:
Library name: PMc1_MF_peripheral blood_355
Column name in raw_counts_PMc1_358.txt: 160041

value: Post ET-MF

value: Dead


title: PMc1_peripheral blood_141063

description:
Library name: PMc1_MF_peripheral blood_352
Column name in raw_counts_PMc1_358.txt: 141063

value: PMF, prefibrotic/early stage

value: Low


title: PMc1_peripheral blood_130332

description:
Library name: PMc1_MF_peripheral blood_351
Column name in raw_counts_PMc1_358.txt: 130332

value: Post PV-MF


title: PMc1_peripheral blood_140088

description:
Library name: PMc1_MF_peripheral blood_349
Column name in raw_counts_PMc1_358.txt: 140088


title: PMc1_peripheral blood_140736

description:
Library name: PMc1_MF_peripheral blood_350
Column name in raw_counts_PMc1_358.txt: 140736


title: experiment 2, scrambled control, sample 1

description: Library name: w32_scr1_S6_unsorted.sorted

tag: cell line

value: Human cervical cancer HeLa Kyoto


title: PMc1_peripheral blood_130909

description:
Library name: PMc1_MF_peripheral blood_348
Column name in raw_counts_PMc1_358.txt: 130909


title: PMc1_peripheral blood_120525

description:
Library name: PMc1_MF_peripheral blood_347
Column name in raw_counts_PMc1_358.txt: 120525


title: PMc1_peripheral blood_100779

description:
Library name: PMc1_MF_peripheral blood_346
Column name in raw_counts_PMc1_358.txt: 100779


title: PMc1_peripheral blood_100699

description:
Library name: PMc1_MF_peripheral blood_345
Column name in raw_counts_PMc1_358.txt: 100699


title: PMc1_peripheral blood_130548

description:
Library name: PMc1_MF_peripheral blood_344
Column name in raw_counts_PMc1_358.txt: 130548


title: experiment 1, WDR82 depleted

description: Library name: w25_siw82_S3_unsorted.sorted


title: PMc1_peripheral blood_162277

description:
Library name: PMc1_MF_peripheral blood_342
Column name in raw_counts_PMc1_358.txt: 162277


title: PMc1_peripheral blood_162163

description:
Library name: PMc1_MF_peripheral blood_340
Column name in raw_counts_PMc1_358.txt: 162163


title: PMc1_peripheral blood_162368

description:
Library name: PMc1_MF_peripheral blood_343
Column name in raw_counts_PMc1_358.txt: 162368


title: PMc1_peripheral blood_162164

description:
Library name: PMc1_MF_peripheral blood_339
Column name in raw_counts_PMc1_358.txt: 162164


title: PMc1_peripheral blood_162180

description:
Library name: PMc1_MF_peripheral blood_338
Column name in raw_counts_PMc1_358.txt: 162180


title: PMc1_peripheral blood_141134

description:
Library name: PMc1_MF_peripheral blood_356
Column name in raw_counts_PMc1_358.txt: 141134


title: PMc1_peripheral blood_160015

description:
Library name: PMc1_MF_peripheral blood_336
Column name in raw_counts_PMc1_358.txt: 160015


title: PMc1_peripheral blood_90351

description:
Library name: PMc1_MF_peripheral blood_337
Column name in raw_counts_PMc1_358.txt: 90351


title: PMc1_peripheral blood_150129

description:
Library name: PMc1_MF_peripheral blood_333
Column name in raw_counts_PMc1_358.txt: 150129


title: PMc1_peripheral blood_150263

description:
Library name: PMc1_MF_peripheral blood_334
Column name in raw_counts_PMc1_358.txt: 150263


title: PMc1_peripheral blood_130780

description:
Library name: PMc1_MF_peripheral blood_331
Column name in raw_counts_PMc1_358.txt: 130780


title: PMc1_peripheral blood_140202

description:
Library name: PMc1_MF_peripheral blood_353
Column name in raw_counts_PMc1_358.txt: 140202


title: PMc1_peripheral blood_120842

description:
Library name: PMc1_MF_peripheral blood_330
Column name in raw_counts_PMc1_358.txt: 120842


title: PMc1_peripheral blood_140343

description:
Library name: PMc1_MF_peripheral blood_332
Column name in raw_counts_PMc1_358.txt: 140343


title: PMc1_peripheral blood_150507

description:
Library name: PMc1_MF_peripheral blood_335
Column name in raw_counts_PMc1_358.txt: 150507


title: PMc1_peripheral blood_110003

description:
Library name: PMc1_MF_peripheral blood_327
Column name in raw_counts_PMc1_358.txt: 110003


title: PMc1_peripheral blood_120204

description:
Library name: PMc1_MF_peripheral blood_329
Column name in raw_counts_PMc1_358.txt: 120204


title: PMc1_peripheral blood_120153

description:
Library name: PMc1_MF_peripheral blood_328
Column name in raw_counts_PMc1_358.txt: 120153


title: PMc1_peripheral blood_161995

description:
Library name: PMc1_MF_peripheral blood_325
Column name in raw_counts_PMc1_358.txt: 161995


title: PMc1_peripheral blood_161974

description:
Library name: PMc1_MF_peripheral blood_324
Column name in raw_counts_PMc1_358.txt: 161974


title: PMc1_peripheral blood_160913

description:
Library name: PMc1_MF_peripheral blood_323
Column name in raw_counts_PMc1_358.txt: 160913


title: PMc1_peripheral blood_160018

description:
Library name: PMc1_MF_peripheral blood_321
Column name in raw_counts_PMc1_358.txt: 160018


title: PMc1_peripheral blood_160333

description:
Library name: PMc1_MF_peripheral blood_322
Column name in raw_counts_PMc1_358.txt: 160333


title: PMc1_peripheral blood_151247

description:
Library name: PMc1_MF_peripheral blood_320
Column name in raw_counts_PMc1_358.txt: 151247


title: PMc1_peripheral blood_151248

description:
Library name: PMc1_MF_peripheral blood_317
Column name in raw_counts_PMc1_358.txt: 151248


title: PMc1_peripheral blood_162243

description:
Library name: PMc1_MF_peripheral blood_341
Column name in raw_counts_PMc1_358.txt: 162243


title: PMc1_peripheral blood_151107

description:
Library name: PMc1_MF_peripheral blood_318
Column name in raw_counts_PMc1_358.txt: 151107


title: PMc1_peripheral blood_151231

description:
Library name: PMc1_MF_peripheral blood_319
Column name in raw_counts_PMc1_358.txt: 151231


title: PMc1_peripheral blood_151094

description:
Library name: PMc1_MF_peripheral blood_316
Column name in raw_counts_PMc1_358.txt: 151094


title: PMc1_peripheral blood_150343

description:
Library name: PMc1_MF_peripheral blood_315
Column name in raw_counts_PMc1_358.txt: 150343


title: PMc1_peripheral blood_150128

description:
Library name: PMc1_MF_peripheral blood_314
Column name in raw_counts_PMc1_358.txt: 150128


title: PMc1_peripheral blood_140236

description:
Library name: PMc1_MF_peripheral blood_312
Column name in raw_counts_PMc1_358.txt: 140236


title: PMc1_peripheral blood_151271

description:
Library name: PMc1_MF_peripheral blood_313
Column name in raw_counts_PMc1_358.txt: 151271


title: PMc1_peripheral blood_140234

description:
Library name: PMc1_MF_peripheral blood_311
Column name in raw_counts_PMc1_358.txt: 140234


title: PMc1_peripheral blood_151232

description:
Library name: PMc1_MF_peripheral blood_310
Column name in raw_counts_PMc1_358.txt: 151232


title: PMc1_peripheral blood_130326

description:
Library name: PMc1_MF_peripheral blood_309
Column name in raw_counts_PMc1_358.txt: 130326


title: PMc1_peripheral blood_130259

description:
Library name: PMc1_MF_peripheral blood_307
Column name in raw_counts_PMc1_358.txt: 130259


title: PMc1_peripheral blood_197947

description:
Library name: PMc1_MF_peripheral blood_305
Column name in raw_counts_PMc1_358.txt: 197947


title: PMc1_peripheral blood_120851

description:
Library name: PMc1_MF_peripheral blood_306
Column name in raw_counts_PMc1_358.txt: 120851


title: PMc1_peripheral blood_120976

description:
Library name: PMc1_MF_peripheral blood_304
Column name in raw_counts_PMc1_358.txt: 120976


title: PMc1_peripheral blood_120654

description:
Library name: PMc1_MF_peripheral blood_303
Column name in raw_counts_PMc1_358.txt: 120654


title: PMc1_peripheral blood_120526

description:
Library name: PMc1_MF_peripheral blood_302
Column name in raw_counts_PMc1_358.txt: 120526


title: PMc1_peripheral blood_120175

description:
Library name: PMc1_MF_peripheral blood_299
Column name in raw_counts_PMc1_358.txt: 120175


title: PMc1_peripheral blood_110558

description:
Library name: PMc1_MF_peripheral blood_298
Column name in raw_counts_PMc1_358.txt: 110558


title: PMc1_peripheral blood_90041

description:
Library name: PMc1_MF_peripheral blood_326
Column name in raw_counts_PMc1_358.txt: 90041


title: PMc1_peripheral blood_110053

description:
Library name: PMc1_MF_peripheral blood_297
Column name in raw_counts_PMc1_358.txt: 110053


title: PMc1_peripheral blood_100144

description:
Library name: PMc1_MF_peripheral blood_296
Column name in raw_counts_PMc1_358.txt: 100144


title: PMc1_peripheral blood_150485

description:
Library name: PMc1_MF_peripheral blood_295
Column name in raw_counts_PMc1_358.txt: 150485


title: PMc1_peripheral blood_162019

description:
Library name: PMc1_MF_peripheral blood_292
Column name in raw_counts_PMc1_358.txt: 162019


title: PMc1_peripheral blood_161582

description:
Library name: PMc1_MF_peripheral blood_291
Column name in raw_counts_PMc1_358.txt: 161582


title: PMc1_peripheral blood_120992

description:
Library name: PMc1_MF_peripheral blood_293
Column name in raw_counts_PMc1_358.txt: 120992


title: PMc1_peripheral blood_161272

description:
Library name: PMc1_MF_peripheral blood_290
Column name in raw_counts_PMc1_358.txt: 161272


title: PMc1_peripheral blood_160811

description:
Library name: PMc1_MF_peripheral blood_288
Column name in raw_counts_PMc1_358.txt: 160811


title: PMc1_peripheral blood_160512

description:
Library name: PMc1_MF_peripheral blood_286
Column name in raw_counts_PMc1_358.txt: 160512


title: PMc1_peripheral blood_160686

description:
Library name: PMc1_MF_peripheral blood_287
Column name in raw_counts_PMc1_358.txt: 160686


title: PMc1_peripheral blood_150168

description:
Library name: PMc1_MF_peripheral blood_283
Column name in raw_counts_PMc1_358.txt: 150168


title: PMc1_peripheral blood_602

description:
Library name: PMc1_MF_peripheral blood_284
Column name in raw_counts_PMc1_358.txt: 602


title: PMc1_peripheral blood_130309

description:
Library name: PMc1_MF_peripheral blood_308
Column name in raw_counts_PMc1_358.txt: 130309


title: PMc1_peripheral blood_140960

description:
Library name: PMc1_MF_peripheral blood_285
Column name in raw_counts_PMc1_358.txt: 140960


title: PMc1_peripheral blood_161105

description:
Library name: PMc1_MF_peripheral blood_289
Column name in raw_counts_PMc1_358.txt: 161105


title: PMc1_peripheral blood_120334

description:
Library name: PMc1_MF_peripheral blood_300
Column name in raw_counts_PMc1_358.txt: 120334


title: PMc1_peripheral blood_160045

description:
Library name: PMc1_MF_peripheral blood_282
Column name in raw_counts_PMc1_358.txt: 160045


title: PMc1_peripheral blood_151413

description:
Library name: PMc1_MF_peripheral blood_281
Column name in raw_counts_PMc1_358.txt: 151413


title: PMc1_peripheral blood_151096

description:
Library name: PMc1_MF_peripheral blood_278
Column name in raw_counts_PMc1_358.txt: 151096


title: PMc1_peripheral blood_150891

description:
Library name: PMc1_MF_peripheral blood_277
Column name in raw_counts_PMc1_358.txt: 150891


title: PMc1_peripheral blood_151180

description:
Library name: PMc1_MF_peripheral blood_279
Column name in raw_counts_PMc1_358.txt: 151180


title: PMc1_peripheral blood_150324

description:
Library name: PMc1_MF_peripheral blood_280
Column name in raw_counts_PMc1_358.txt: 150324


title: PMc1_peripheral blood_150646

description:
Library name: PMc1_MF_peripheral blood_274
Column name in raw_counts_PMc1_358.txt: 150646


title: PMc1_peripheral blood_120357

description:
Library name: PMc1_MF_peripheral blood_301
Column name in raw_counts_PMc1_358.txt: 120357


title: PMc1_peripheral blood_150715

description:
Library name: PMc1_MF_peripheral blood_276
Column name in raw_counts_PMc1_358.txt: 150715


title: PMc1_peripheral blood_150466

description:
Library name: PMc1_MF_peripheral blood_272
Column name in raw_counts_PMc1_358.txt: 150466


title: PMc1_peripheral blood_150155

description:
Library name: PMc1_MF_peripheral blood_270
Column name in raw_counts_PMc1_358.txt: 150155


title: PMc1_peripheral blood_90120

description:
Library name: PMc1_MF_peripheral blood_294
Column name in raw_counts_PMc1_358.txt: 90120


title: PMc1_peripheral blood_120695

description:
Library name: PMc1_MF_peripheral blood_269
Column name in raw_counts_PMc1_358.txt: 120695


title: PMc1_peripheral blood_140645

description:
Library name: PMc1_MF_peripheral blood_268
Column name in raw_counts_PMc1_358.txt: 140645


title: PMc1_peripheral blood_140390

description:
Library name: PMc1_MF_peripheral blood_267
Column name in raw_counts_PMc1_358.txt: 140390


title: PMc1_peripheral blood_130202

description:
Library name: PMc1_MF_peripheral blood_266
Column name in raw_counts_PMc1_358.txt: 130202


title: PMc1_peripheral blood_140055

description:
Library name: PMc1_MF_peripheral blood_264
Column name in raw_counts_PMc1_358.txt: 140055


title: PMc1_peripheral blood_130265

description:
Library name: PMc1_MF_peripheral blood_262
Column name in raw_counts_PMc1_358.txt: 130265


title: PMc1_peripheral blood_130393

description:
Library name: PMc1_MF_peripheral blood_263
Column name in raw_counts_PMc1_358.txt: 130393


title: PMc1_peripheral blood_140204

description:
Library name: PMc1_MF_peripheral blood_265
Column name in raw_counts_PMc1_358.txt: 140204


title: PMc1_peripheral blood_130203

description:
Library name: PMc1_MF_peripheral blood_261
Column name in raw_counts_PMc1_358.txt: 130203


title: PMc1_peripheral blood_121011

description:
Library name: PMc1_MF_peripheral blood_258
Column name in raw_counts_PMc1_358.txt: 121011


title: PMc1_peripheral blood_140867

description:
Library name: PMc1_MF_peripheral blood_255
Column name in raw_counts_PMc1_358.txt: 140867


title: PMc1_peripheral blood_100341

description:
Library name: PMc1_MF_peripheral blood_256
Column name in raw_counts_PMc1_358.txt: 100341


title: PMc1_peripheral blood_161704

description:
Library name: PMc1_MF_peripheral blood_257
Column name in raw_counts_PMc1_358.txt: 161704


title: PMc1_peripheral blood_120237

description:
Library name: PMc1_MF_peripheral blood_254
Column name in raw_counts_PMc1_358.txt: 120237


title: PMc1_peripheral blood_110651

description:
Library name: PMc1_MF_peripheral blood_250
Column name in raw_counts_PMc1_358.txt: 110651


title: PMc1_peripheral blood_150692

description:
Library name: PMc1_MF_peripheral blood_275
Column name in raw_counts_PMc1_358.txt: 150692


title: PMc1_peripheral blood_110035

description:
Library name: PMc1_MF_peripheral blood_251
Column name in raw_counts_PMc1_358.txt: 110035


title: PMc1_peripheral blood_120026

description:
Library name: PMc1_MF_peripheral blood_253
Column name in raw_counts_PMc1_358.txt: 120026


title: PMc1_peripheral blood_110275

description:
Library name: PMc1_MF_peripheral blood_248
Column name in raw_counts_PMc1_358.txt: 110275


title: PMc1_peripheral blood_150520

description:
Library name: PMc1_MF_peripheral blood_273
Column name in raw_counts_PMc1_358.txt: 150520


title: PMc1_peripheral blood_110732

description:
Library name: PMc1_MF_peripheral blood_252
Column name in raw_counts_PMc1_358.txt: 110732


title: PMc1_peripheral blood_110076

description:
Library name: PMc1_MF_peripheral blood_246
Column name in raw_counts_PMc1_358.txt: 110076


title: PMc1_peripheral blood_110268

description:
Library name: PMc1_MF_peripheral blood_247
Column name in raw_counts_PMc1_358.txt: 110268


title: PMc1_peripheral blood_100335

description:
Library name: PMc1_MF_peripheral blood_243
Column name in raw_counts_PMc1_358.txt: 100335


title: PMc1_peripheral blood_141035

description:
Library name: PMc1_MF_peripheral blood_244
Column name in raw_counts_PMc1_358.txt: 141035


title: PMc1_peripheral blood_100150

description:
Library name: PMc1_MF_peripheral blood_241
Column name in raw_counts_PMc1_358.txt: 100150


title: PMc1_peripheral blood_100062

description:
Library name: PMc1_MF_peripheral blood_240
Column name in raw_counts_PMc1_358.txt: 100062


title: PMc1_peripheral blood_110054

description:
Library name: PMc1_MF_peripheral blood_245
Column name in raw_counts_PMc1_358.txt: 110054


title: PMc1_peripheral blood_90757

description:
Library name: PMc1_MF_peripheral blood_239
Column name in raw_counts_PMc1_358.txt: 90757


title: PMc1_peripheral blood_150364

description:
Library name: PMc1_MF_peripheral blood_271
Column name in raw_counts_PMc1_358.txt: 150364


title: PMc1_peripheral blood_130025

description:
Library name: PMc1_MF_peripheral blood_259
Column name in raw_counts_PMc1_358.txt: 130025


title: PMc1_peripheral blood_130129

description:
Library name: PMc1_MF_peripheral blood_260
Column name in raw_counts_PMc1_358.txt: 130129


title: PMc1_peripheral blood_90134

description:
Library name: PMc1_MF_peripheral blood_237
Column name in raw_counts_PMc1_358.txt: 90134


title: PMc1_peripheral blood_90671

description:
Library name: PMc1_MF_peripheral blood_238
Column name in raw_counts_PMc1_358.txt: 90671


title: PMc1_peripheral blood_151360

description:
Library name: PMc1_MF_peripheral blood_236
Column name in raw_counts_PMc1_358.txt: 151360


title: PMc1_peripheral blood_110586

description:
Library name: PMc1_MF_peripheral blood_249
Column name in raw_counts_PMc1_358.txt: 110586


title: PMc1_peripheral blood_140676

description:
Library name: PMc1_MF_peripheral blood_235
Column name in raw_counts_PMc1_358.txt: 140676


title: PMc1_peripheral blood_609

description:
Library name: PMc1_MF_peripheral blood_234
Column name in raw_counts_PMc1_358.txt: 609


title: HD_peripheral blood_221880

description: custom codeset

hyb_protocol: Elements hybridization reactions were completed using 7ul of RNA per sample (140ng) incubated with Probe A mix, Probe B mix and Elements TagSets at 67 °C for 16-24 hours to create complete Tag Complexes on the nCounter Prep Station (version 4.0.11.1).

scan_protocol: After hybridization, excess probes were washed out using a 2-step magnetic bead-based purification strategy according to the manufacturer’s protocol and purified target/probe complexes (i.e. Tag Complexes) were immobilized on the NanoString cartridge for data collection. Transcript counts were determined using the nCounter Digital Analyzer (version 2.1.2.3) at the high-resolution setting (FOV set to 555). Specifically, digital images were processed with final barcode counts tabulated in reporter code count (RCC) output files.

data_processing: RCC output files were loaded into the nSolver software, wherein mRNA transcript abundance values of MPN24 genes were reported and subsequently normalized. For each sample, a normalization factor was computed based on the geometric mean of twelve reference genes (ZDHHC6, NRL, FDXACB1, KLHL26, DAP3, SNRNP35, DDX19A, EIF2B1, INTS12, PAPOLA, EIF4H and HNRNPA2B1). This normalization factor was applied to the gene expression counts of each target gene, and normalized counts were subsequently log transformed. No background subtraction or thresholding was performed.

label: Elements TagSet reagents from the manufacturer

label_protocol: Elements TagSet-36 provided by NanoString Technologies for the custom codeset

extract_protocol: Total RNA was extracted from patient cells using the RNeasy Minikit (Qiagen) following the “Quick-Start Protocol” with “On-Column DNase Digestion”. RNA was eluted in 30ul of molecular-grade water (Sigma, cat #W4502).

tag: disease

value: NA; healthy donor

tag: age at sample collection

tag: mipss70 category

tag: os_status_at last follow up

tag: os_time_at last follow up (days)

tag: transplant_time (days)

tag: transform_time (days)

tag: mpn24 category


title: PMc1_peripheral blood_140844

description:
Library name: PMc1_MF_peripheral blood_233
Column name in raw_counts_PMc1_358.txt: 140844

tag: age at_sample_collection

tag: diagnosis

tag: calr

tag: mpl

tag: dipss category

tag: os status_at_last_follow_up


title: PMc1_peripheral blood_130330

description:
Library name: PMc1_MF_peripheral blood_231
Column name in raw_counts_PMc1_358.txt: 130330

tag: tissue

tag: cell type

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)

tag: transform time_(days)

tag: mpn24 score


title: HD_peripheral blood_242117

description: custom codeset

tag: disease

tag: age at sample collection

tag: Sex

tag: mipss70 category

tag: os_status_at last follow up


title: HD_peripheral blood_172385

description: custom codeset

tag: os_time_at last follow up (days)

tag: transplant_time (days)

tag: transform_time (days)

tag: mpn24 category


title: PMc1_peripheral blood_162090

description:
Library name: PMc1_MF_peripheral blood_230
Column name in raw_counts_PMc1_358.txt: 162090

tag: age at_sample_collection

tag: diagnosis

tag: calr

tag: mpl

tag: dipss category


title: HD_peripheral blood_162169

description: custom codeset


title: MSK_peripheral blood_31748

description: custom codeset

value: myelofibrosis


title: PMc1_peripheral blood_161935

description:
Library name: PMc1_MF_peripheral blood_229
Column name in raw_counts_PMc1_358.txt: 161935

tag: tissue

value: Peripheral blood

tag: cell type

tag: os status_at_last_follow_up

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)


title: PMc1_peripheral blood_161840

description:
Library name: PMc1_MF_peripheral blood_228
Column name in raw_counts_PMc1_358.txt: 161840

value: mononuclear cells

tag: Sex

tag: transform time_(days)

tag: mpn24 score


title: PMc1_peripheral blood_100325

description:
Library name: PMc1_MF_peripheral blood_242
Column name in raw_counts_PMc1_358.txt: 100325

value: Female


title: PMc1_peripheral blood_130550

description:
Library name: PMc1_MF_peripheral blood_232
Column name in raw_counts_PMc1_358.txt: 130550


title: MSK_peripheral blood_97505

description: custom codeset

tag: disease

tag: age at sample collection

value: Post-ET MF

tag: mipss70 category

tag: os_status_at last follow up

tag: os_time_at last follow up (days)


title: MSK_peripheral blood_97507

description: custom codeset

tag: diagnosis

value: PMF, overt fibrotic stage

tag: transplant_time (days)

tag: transform_time (days)

tag: mpn24 category


title: PMc1_peripheral blood_161783

description:
Library name: PMc1_MF_peripheral blood_227
Column name in raw_counts_PMc1_358.txt: 161783

tag: tissue

tag: age at_sample_collection

value: Positive

tag: calr

value: Negative

tag: mpl

tag: dipss category


title: PMc1_peripheral blood_161648

description:
Library name: PMc1_MF_peripheral blood_226
Column name in raw_counts_PMc1_358.txt: 161648

tag: cell type

tag: Sex

value: Male

tag: os status_at_last_follow_up

value: Alive

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)


title: MSK_peripheral blood_90933

description: custom codeset

tag: disease

tag: age at sample collection

value: Post-PV MF

tag: mipss70 category

tag: mpn24 score

value: High


title: MSK_peripheral blood_89814

description: custom codeset

tag: diagnosis

tag: os_status_at last follow up

tag: os_time_at last follow up (days)

tag: transplant_time (days)


title: PMc1_peripheral blood_161218

description:
Library name: PMc1_MF_peripheral blood_225
Column name in raw_counts_PMc1_358.txt: 161218

tag: tissue

tag: age at_sample_collection

value: Dead

tag: transform time_(days)


title: MSK_peripheral blood_88582

description: custom codeset

tag: calr

tag: mpl

tag: dipss category

tag: transform_time (days)

tag: mpn24 category

value: Low


title: PMc1_peripheral blood_151120

description:
Library name: PMc1_MF_peripheral blood_224
Column name in raw_counts_PMc1_358.txt: 151120

tag: cell type

tag: Sex

tag: os status_at_last_follow_up

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)


title: PMc1_peripheral blood_160143

description:
Library name: PMc1_MF_peripheral blood_223
Column name in raw_counts_PMc1_358.txt: 160143

tag: diagnosis

tag: mpn24 score


title: PMc1_peripheral blood_160852

description:
Library name: PMc1_MF_peripheral blood_222
Column name in raw_counts_PMc1_358.txt: 160852


title: MSK_peripheral blood_85193

description: custom codeset

tag: disease

tag: age at sample collection

tag: mipss70 category

tag: os_status_at last follow up

tag: os_time_at last follow up (days)


title: MSK_peripheral blood_83614

description: custom codeset

tag: calr

tag: transplant_time (days)


title: PMc1_peripheral blood_160782

description:
Library name: PMc1_MF_peripheral blood_221
Column name in raw_counts_PMc1_358.txt: 160782

tag: tissue

tag: age at_sample_collection

tag: mpl

tag: dipss category

tag: transform time_(days)


title: MSK_peripheral blood_82966

description: custom codeset

tag: Sex

tag: transform_time (days)

tag: mpn24 category


title: PMc1_peripheral blood_160496

description:
Library name: PMc1_MF_peripheral blood_218
Column name in raw_counts_PMc1_358.txt: 160496

tag: cell type

tag: diagnosis

tag: os status_at_last_follow_up

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)


title: PMc1_peripheral blood_160576

description:
Library name: PMc1_MF_peripheral blood_220
Column name in raw_counts_PMc1_358.txt: 160576

tag: mpn24 score


title: PMc1_peripheral blood_130805

description:
Library name: PMc1_MF_peripheral blood_219
Column name in raw_counts_PMc1_358.txt: 130805


title: MSK_peripheral blood_71196

description: custom codeset

tag: disease

tag: age at sample collection

tag: mipss70 category

tag: os_status_at last follow up

tag: os_time_at last follow up (days)


title: MSK_peripheral blood_78875

description: custom codeset

tag: calr

tag: mpl

tag: transplant_time (days)


title: MSK_peripheral blood_82913

description: custom codeset

tag: Sex

tag: dipss category


title: PMc1_peripheral blood_140611

description:
Library name: PMc1_MF_peripheral blood_217
Column name in raw_counts_PMc1_358.txt: 140611

tag: tissue

tag: age at_sample_collection

tag: transform time_(days)


title: PMc1_peripheral blood_110317

description:
Library name: PMc1_MF_peripheral blood_215
Column name in raw_counts_PMc1_358.txt: 110317

tag: cell type

tag: diagnosis

tag: os status_at_last_follow_up


title: PMc1_peripheral blood_151472

description:
Library name: PMc1_MF_peripheral blood_216
Column name in raw_counts_PMc1_358.txt: 151472

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)

tag: mpn24 score


title: PMc1_peripheral blood_151028

description:
Library name: PMc1_MF_peripheral blood_214
Column name in raw_counts_PMc1_358.txt: 151028

value: Post PV-MF


title: MSK_peripheral blood_68183

description: custom codeset

tag: disease

tag: age at sample collection

tag: mipss70 category

tag: transform_time (days)

tag: mpn24 category


title: MSK_peripheral blood_68528

description: custom codeset

tag: calr

tag: mpl

tag: os_status_at last follow up

tag: os_time_at last follow up (days)

tag: transplant_time (days)


title: MSK_peripheral blood_87760

description: custom codeset

tag: Sex

tag: dipss category


title: MSK_peripheral blood_65995

description: custom codeset

tag: diagnosis


title: MSK_peripheral blood_65090

description: custom codeset


title: MSK_peripheral blood_64012

description: custom codeset

value: unknown


title: PMc1_peripheral blood_150808

description:
Library name: PMc1_MF_peripheral blood_213
Column name in raw_counts_PMc1_358.txt: 150808

tag: tissue

tag: cell type

tag: age at_sample_collection

tag: os status_at_last_follow_up

tag: transform time_(days)


title: MSK_peripheral blood_57936

description: custom codeset

tag: disease

tag: age at sample collection

tag: mpn24 score


title: PMc1_peripheral blood_141072

description:
Library name: PMc1_MF_peripheral blood_212
Column name in raw_counts_PMc1_358.txt: 141072

value: Post ET-MF

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)


title: PMc1_peripheral blood_141132

description:
Library name: PMc1_MF_peripheral blood_211
Column name in raw_counts_PMc1_358.txt: 141132

tag: calr

tag: mpl


title: MSK_peripheral blood_5475

description: custom codeset

value: myelofibrosis

tag: mipss70 category

tag: os_status_at last follow up

tag: os_time_at last follow up (days)

tag: transform_time (days)

tag: mpn24 category


title: PMc1_peripheral blood_150512

description:
Library name: PMc1_MF_peripheral blood_210
Column name in raw_counts_PMc1_358.txt: 150512

tag: tissue

value: Peripheral blood

tag: Sex

tag: diagnosis

tag: dipss category


title: MSK_peripheral blood_82684

description: custom codeset

tag: transplant_time (days)


title: HD_peripheral blood_162376

description: custom codeset

tag: disease

value: NA; healthy donor


title: PMc1_peripheral blood_110852

description:
Library name: PMc1_MF_peripheral blood_209
Column name in raw_counts_PMc1_358.txt: 110852

tag: cell type

value: mononuclear cells

tag: age at_sample_collection

value: Female

tag: os status_at_last_follow_up

tag: transform time_(days)


title: PMc1_peripheral blood_150394

description:
Library name: PMc1_MF_peripheral blood_208
Column name in raw_counts_PMc1_358.txt: 150394

value: PMF, overt fibrotic stage

tag: calr

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)

tag: mpn24 score


title: MSK_peripheral blood_54675

description: custom codeset

tag: age at sample collection

value: Positive

tag: mpl

tag: mipss70 category

tag: os_status_at last follow up

tag: os_time_at last follow up (days)


title: MSK_peripheral blood_51575

description: custom codeset

tag: Sex

tag: diagnosis

tag: transform_time (days)

tag: mpn24 category


title: MSK_peripheral blood_44875

description: custom codeset

tag: disease

tag: dipss category

tag: transplant_time (days)


title: PMc1_peripheral blood_130168

description:
Library name: PMc1_MF_peripheral blood_207
Column name in raw_counts_PMc1_358.txt: 130168

tag: tissue

tag: cell type

tag: age at_sample_collection

value: Negative

tag: os status_at_last_follow_up

tag: transform time_(days)


title: MSK_peripheral blood_48299

description: custom codeset

tag: age at sample collection

value: Male

tag: calr

tag: mpn24 score


title: PMc1_peripheral blood_141109

description:
Library name: PMc1_MF_peripheral blood_206
Column name in raw_counts_PMc1_358.txt: 141109

tag: mpl

value: Alive

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)


title: PMc1_peripheral blood_110655

description:
Library name: PMc1_MF_peripheral blood_205
Column name in raw_counts_PMc1_358.txt: 110655

tag: Sex

tag: diagnosis


title: MSK_peripheral blood_43756

description: custom codeset

tag: mipss70 category

tag: os_status_at last follow up

tag: os_time_at last follow up (days)

tag: transform_time (days)

tag: mpn24 category


title: PMc1_peripheral blood_140913

description:
Library name: PMc1_MF_peripheral blood_204
Column name in raw_counts_PMc1_358.txt: 140913

tag: tissue

tag: cell type

tag: dipss category


title: MSK_peripheral blood_34008

description: custom codeset

tag: disease

tag: transplant_time (days)


title: PMc1_peripheral blood_140852

description:
Library name: PMc1_MF_peripheral blood_203
Column name in raw_counts_PMc1_358.txt: 140852

tag: age at_sample_collection

tag: calr

tag: os status_at_last_follow_up

tag: transform time_(days)


title: PMc1_peripheral blood_140797

description:
Library name: PMc1_MF_peripheral blood_201
Column name in raw_counts_PMc1_358.txt: 140797

tag: mpl

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)

tag: mpn24 score


title: PMc1_peripheral blood_140806

description:
Library name: PMc1_MF_peripheral blood_202
Column name in raw_counts_PMc1_358.txt: 140806

tag: Sex

tag: diagnosis


title: PMc1_peripheral blood_140739

description:
Library name: PMc1_MF_peripheral blood_199
Column name in raw_counts_PMc1_358.txt: 140739


title: MSK_peripheral blood_37935

description: custom codeset

tag: age at sample collection

tag: mipss70 category

tag: os_status_at last follow up

tag: os_time_at last follow up (days)

tag: transform_time (days)


title: PMc1_peripheral blood_100506

description:
Library name: PMc1_MF_peripheral blood_198
Column name in raw_counts_PMc1_358.txt: 100506

tag: tissue

tag: cell type

tag: dipss category


title: MSK_peripheral blood_37195

description: custom codeset

tag: disease

tag: calr

tag: transplant_time (days)

tag: mpn24 category


title: PMc1_peripheral blood_130582

description:
Library name: PMc1_MF_peripheral blood_200
Column name in raw_counts_PMc1_358.txt: 130582

tag: age at_sample_collection

value: PMF, prefibrotic/early stage

tag: mpl

tag: os status_at_last_follow_up

tag: os time_at_last_follow_up_(days)

tag: transform time_(days)


title: MSK_peripheral blood_31955

description: custom codeset

tag: age at sample collection

tag: Sex

tag: diagnosis

tag: mpn24 score

value: High


title: MSK_peripheral blood_32197

description: custom codeset

tag: mipss70 category

tag: os_status_at last follow up

tag: os_time_at last follow up (days)

tag: transform_time (days)


title: PMc1_peripheral blood_140550

description:
Library name: PMc1_MF_peripheral blood_197
Column name in raw_counts_PMc1_358.txt: 140550

tag: tissue

tag: cell type

tag: dipss category

tag: transplant time_(days)


title: MSK_peripheral blood_29175

description: custom codeset

tag: disease

value: Post-ET MF

tag: calr

tag: transplant_time (days)

tag: mpn24 category


title: MSK_peripheral blood_26262

description: custom codeset

tag: mpl

value: Dead


title: PMc1_peripheral blood_140470

description:
Library name: PMc1_MF_peripheral blood_196
Column name in raw_counts_PMc1_358.txt: 140470

tag: age at_sample_collection

tag: os status_at_last_follow_up

tag: os time_at_last_follow_up_(days)

tag: transform time_(days)


title: MSK_peripheral blood_24654

description: custom codeset

tag: age at sample collection

tag: Sex

tag: diagnosis

tag: mipss70 category

tag: mpn24 score


title: PMc1_peripheral blood_140460

description:
Library name: PMc1_MF_peripheral blood_195
Column name in raw_counts_PMc1_358.txt: 140460

tag: tissue

tag: cell type


title: MSK_peripheral blood_217364

description: custom codeset

tag: dipss category

tag: os_status_at last follow up

tag: os_time_at last follow up (days)

tag: transform_time (days)


title: MSK_peripheral blood_224734

description: custom codeset

tag: disease

tag: calr

tag: transplant_time (days)

tag: mpn24 category

value: Low


title: PMc1_peripheral blood_140306

description:
Library name: PMc1_MF_peripheral blood_194
Column name in raw_counts_PMc1_358.txt: 140306

tag: age at_sample_collection

tag: mpl

tag: os status_at_last_follow_up

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)


title: PMc1_peripheral blood_130919

description:
Library name: PMc1_MF_peripheral blood_192
Column name in raw_counts_PMc1_358.txt: 130919

tag: Sex

tag: diagnosis

tag: transform time_(days)


title: MSK_peripheral blood_215929

description: custom codeset

tag: age at sample collection

tag: mipss70 category

value: unknown

tag: mpn24 score


title: PMc1_peripheral blood_140235

description:
Library name: PMc1_MF_peripheral blood_193
Column name in raw_counts_PMc1_358.txt: 140235

tag: tissue

tag: cell type

tag: dipss category


title: PMc1_peripheral blood_130737

description:
Library name: PMc1_MF_peripheral blood_191
Column name in raw_counts_PMc1_358.txt: 130737

tag: calr


title: MSK_peripheral blood_213731

description: custom codeset

tag: disease

tag: os_status_at last follow up

tag: os_time_at last follow up (days)

tag: transplant_time (days)

tag: transform_time (days)


title: PMc1_peripheral blood_130688

description:
Library name: PMc1_MF_peripheral blood_190
Column name in raw_counts_PMc1_358.txt: 130688

tag: age at_sample_collection

tag: mpl

tag: os status_at_last_follow_up

tag: os time_at_last_follow_up_(days)


title: PMc1_peripheral blood_130672

description:
Library name: PMc1_MF_peripheral blood_189
Column name in raw_counts_PMc1_358.txt: 130672

tag: Sex

tag: diagnosis

value: Post ET-MF

tag: transplant time_(days)

tag: transform time_(days)


title: PMc1_peripheral blood_130649

description:
Library name: PMc1_MF_peripheral blood_188
Column name in raw_counts_PMc1_358.txt: 130649

tag: tissue

tag: mpn24 score


title: MSK_peripheral blood_209904

description: custom codeset

value: myelofibrosis

tag: age at sample collection

tag: dipss category

tag: mipss70 category

tag: mpn24 category


title: MSK_peripheral blood_209983

description: custom codeset

tag: disease

tag: calr

tag: os_status_at last follow up

tag: os_time_at last follow up (days)


title: MSK_peripheral blood_207266

description: custom codeset

tag: mpl

tag: transplant_time (days)

tag: transform_time (days)


title: PMc1_peripheral blood_130545

description:
Library name: PMc1_MF_peripheral blood_187
Column name in raw_counts_PMc1_358.txt: 130545

value: Peripheral blood

tag: cell type

tag: age at_sample_collection

tag: Sex

tag: os status_at_last_follow_up

tag: os time_at_last_follow_up_(days)


title: PMc1_peripheral blood_160441

description:
Library name: PMc1_MF_peripheral blood_186
Column name in raw_counts_PMc1_358.txt: 160441

tag: tissue

tag: diagnosis

value: Post PV-MF

tag: transplant time_(days)

tag: transform time_(days)

tag: mpn24 score


title: MSK_peripheral blood_207195

description: custom codeset

tag: disease

tag: age at sample collection

tag: dipss category

tag: mipss70 category

tag: mpn24 category


title: MSK_peripheral blood_27395

description: custom codeset

tag: calr

tag: mpl

tag: os_status_at last follow up

tag: os_time_at last follow up (days)

tag: transplant_time (days)


title: PMc1_peripheral blood_130061

description:
Library name: PMc1_MF_peripheral blood_184
Column name in raw_counts_PMc1_358.txt: 130061

tag: cell type

value: mononuclear cells

tag: age at_sample_collection

tag: Sex

tag: os status_at_last_follow_up


title: MSK_peripheral blood_206443

description: custom codeset

tag: diagnosis

tag: transform_time (days)


title: PMc1_peripheral blood_130069

description:
Library name: PMc1_MF_peripheral blood_185
Column name in raw_counts_PMc1_358.txt: 130069

tag: tissue

value: Female

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)

tag: transform time_(days)

tag: mpn24 score


title: MSK_peripheral blood_205487

description: custom codeset

tag: disease

tag: age at sample collection

value: PMF, overt fibrotic stage

tag: dipss category

tag: mipss70 category

tag: mpn24 category


title: PMc1_peripheral blood_120270

description:
Library name: PMc1_MF_peripheral blood_183
Column name in raw_counts_PMc1_358.txt: 120270

tag: calr

value: Positive

tag: mpl


title: PMc1_peripheral blood_120106

description:
Library name: PMc1_MF_peripheral blood_182
Column name in raw_counts_PMc1_358.txt: 120106

tag: cell type

tag: age at_sample_collection


title: MSK_peripheral blood_204519

description: custom codeset

tag: Sex

value: Negative

tag: os_status_at last follow up

tag: os_time_at last follow up (days)

tag: transplant_time (days)


title: MSK_peripheral blood_203126

description: custom codeset

tag: diagnosis

tag: transform_time (days)


title: MSK_peripheral blood_214796

description: custom codeset

value: Male


title: PMc1_peripheral blood_110450

description:
Library name: PMc1_MF_peripheral blood_180
Column name in raw_counts_PMc1_358.txt: 110450

tag: tissue

tag: os status_at_last_follow_up

value: Alive

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)

tag: transform time_(days)


title: PMc1_peripheral blood_110849

description:
Library name: PMc1_MF_peripheral blood_181
Column name in raw_counts_PMc1_358.txt: 110849

tag: dipss category

tag: mpn24 score


title: PMc1_peripheral blood_110168

description:
Library name: PMc1_MF_peripheral blood_179
Column name in raw_counts_PMc1_358.txt: 110168

value: PMF, prefibrotic/early stage

tag: calr


title: MSK_peripheral blood_202959

description: custom codeset

tag: disease

tag: age at sample collection

tag: mpl

tag: mipss70 category

tag: mpn24 category


title: MSK_peripheral blood_196889

description: custom codeset

tag: Sex

tag: os_status_at last follow up

tag: os_time_at last follow up (days)


title: MSK_peripheral blood_196382

description: custom codeset

tag: diagnosis

tag: transplant_time (days)

tag: transform_time (days)


title: MSK_peripheral blood_191345

description: custom codeset


title: MSK_peripheral blood_193952

description: custom codeset

value: High


title: PMc1_peripheral blood_110018

description:
Library name: PMc1_MF_peripheral blood_178
Column name in raw_counts_PMc1_358.txt: 110018

tag: tissue

tag: cell type

tag: age at_sample_collection

tag: os status_at_last_follow_up

tag: os time_at_last_follow_up_(days)


title: PMc1_peripheral blood_100671

description:
Library name: PMc1_MF_peripheral blood_177
Column name in raw_counts_PMc1_358.txt: 100671

tag: calr

tag: dipss category

tag: transplant time_(days)

tag: transform time_(days)

tag: mpn24 score


title: PMc1_peripheral blood_100295

description:
Library name: PMc1_MF_peripheral blood_176
Column name in raw_counts_PMc1_358.txt: 100295

tag: mpl


title: MSK_peripheral blood_205279

description: custom codeset

tag: disease

tag: age at sample collection

tag: Sex

value: Post-PV MF

tag: mipss70 category

tag: mpn24 category


title: MSK_peripheral blood_191270

description: custom codeset

tag: diagnosis

tag: os_status_at last follow up

tag: os_time_at last follow up (days)

tag: transplant_time (days)

tag: transform_time (days)


title: PMc1_peripheral blood_100160

description:
Library name: PMc1_MF_peripheral blood_174
Column name in raw_counts_PMc1_358.txt: 100160

tag: tissue

tag: cell type

tag: age at_sample_collection

tag: os status_at_last_follow_up

value: Dead

tag: os time_at_last_follow_up_(days)


title: MSK_peripheral blood_190766

description: custom codeset

value: Post-ET MF

tag: calr

tag: dipss category

tag: mpn24 score


title: PMc1_peripheral blood_100111

description:
Library name: PMc1_MF_peripheral blood_173
Column name in raw_counts_PMc1_358.txt: 100111

tag: mpl

tag: transplant time_(days)

tag: transform time_(days)


title: PMc1_peripheral blood_90781

description:
Library name: PMc1_MF_peripheral blood_172
Column name in raw_counts_PMc1_358.txt: 90781

tag: Sex


title: MSK_peripheral blood_190763

description: custom codeset

tag: disease

tag: age at sample collection

tag: diagnosis

tag: mipss70 category

value: unknown

tag: mpn24 category


title: PMc1_peripheral blood_90748

description:
Library name: PMc1_MF_peripheral blood_171
Column name in raw_counts_PMc1_358.txt: 90748

tag: tissue


title: MSK_peripheral blood_188621

description: custom codeset

tag: os_status_at last follow up

tag: os_time_at last follow up (days)

tag: transplant_time (days)

tag: transform_time (days)

value: Low


title: MSK_peripheral blood_183845

description: custom codeset

value: myelofibrosis

tag: calr


title: MSK_peripheral blood_189007

description: custom codeset

tag: dipss category