title: PMc1_peripheral blood_90237

description:
Library name: PMc1_MF_peripheral blood_169
Column name in raw_counts_PMc1_358.txt: 90237

value: Peripheral blood

tag: cell type

tag: age at_sample_collection

value: Post ET-MF

tag: os status_at_last_follow_up

tag: os time_at_last_follow_up_(days)

tag: mpn24 score


title: PMc1_peripheral blood_90674

status: Public on Dec 02 2025

type: SRA

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_170
Column name in raw_counts_PMc1_358.txt: 90674

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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.

tag: tissue

value: mononuclear cells

tag: Sex

value: Male

tag: diagnosis

value: PMF, prefibrotic/early stage

tag: calr

tag: mpl

tag: dipss category

value: Alive

tag: transplant time_(days)

tag: transform time_(days)


title: PMc1_peripheral blood_90116

description:
Library name: PMc1_MF_peripheral blood_168
Column name in raw_counts_PMc1_358.txt: 90116

value: PMF, overt fibrotic stage

value: Positive

value: Negative

value: Dead


title: MSK_peripheral blood_186619

type: RNA

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: myelofibrosis

tag: age at sample collection

value: High

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: MSK_peripheral blood_99391

description: custom codeset

tag: mpn24 score


title: MSK_peripheral blood_185533

description: custom codeset

value: Female

value: Post-ET MF

value: unknown

value: Low


title: PMc1_peripheral blood_80474

description:
Library name: PMc1_MF_peripheral blood_167
Column name in raw_counts_PMc1_358.txt: 80474

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_80348

description:
Library name: PMc1_MF_peripheral blood_166
Column name in raw_counts_PMc1_358.txt: 80348

tag: Sex

tag: diagnosis

tag: calr

tag: mpl

tag: dipss category


title: PMc1_peripheral blood_100187

description:
Library name: PMc1_MF_peripheral blood_175
Column name in raw_counts_PMc1_358.txt: 100187

tag: transplant time_(days)

tag: transform time_(days)


title: MSK_peripheral blood_180454

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_181053

description: custom codeset

tag: transplant_time (days)

tag: transform_time (days)

tag: mpn24 score

tag: mpn24 category


title: PMc1_peripheral blood_125

description:
Library name: PMc1_MF_peripheral blood_164
Column name in raw_counts_PMc1_358.txt: 125

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: MSK_peripheral blood_181415

description: custom codeset

tag: Sex

tag: diagnosis

tag: calr

tag: mpl

tag: dipss category


title: PMc1_peripheral blood_140561

description:
Library name: PMc1_MF_peripheral blood_163
Column name in raw_counts_PMc1_358.txt: 140561

tag: transplant time_(days)

tag: transform time_(days)


title: PMc1_peripheral blood_161812

description:
Library name: PMc1_MF_peripheral blood_162
Column name in raw_counts_PMc1_358.txt: 161812


title: MSK_peripheral blood_178261

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_179107

description: custom codeset

tag: transplant_time (days)

tag: transform_time (days)

tag: mpn24 score

tag: mpn24 category


title: MSK_peripheral blood_182781

description: custom codeset


title: MSK_peripheral blood_168704

description: custom codeset

value: Post-PV MF


title: MSK_peripheral blood_167918

description: custom codeset


title: PMc1_peripheral blood_161359

description:
Library name: PMc1_MF_peripheral blood_160
Column name in raw_counts_PMc1_358.txt: 161359

tag: tissue

value: Peripheral blood

tag: cell type

tag: age at_sample_collection

tag: os status_at_last_follow_up

tag: os time_at_last_follow_up_(days)


title: MSK_peripheral blood_166908

description: custom codeset

tag: Sex

tag: diagnosis

tag: calr

tag: mpl

tag: dipss category


title: MSK_peripheral blood_162873

description: custom codeset

tag: disease

tag: age at sample collection

tag: mipss70 category


title: PMc1_peripheral blood_120951

description:
Library name: PMc1_MF_peripheral blood_158
Column name in raw_counts_PMc1_358.txt: 120951

tag: transplant time_(days)

tag: transform time_(days)


title: PMc1_peripheral blood_160974

description:
Library name: PMc1_MF_peripheral blood_157
Column name in raw_counts_PMc1_358.txt: 160974

tag: mpn24 score


title: PMc1_peripheral blood_151177

description:
Library name: PMc1_MF_peripheral blood_156
Column name in raw_counts_PMc1_358.txt: 151177


title: PMc1_peripheral blood_555

description:
Library name: PMc1_MF_peripheral blood_165
Column name in raw_counts_PMc1_358.txt: 555


title: MSK_peripheral blood_159065

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)

tag: mpn24 category


title: MSK_peripheral blood_160575

description: custom codeset


title: MSK_peripheral blood_150354

description: custom codeset


title: PMc1_peripheral blood_160641

description:
Library name: PMc1_MF_peripheral blood_154
Column name in raw_counts_PMc1_358.txt: 160641

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: MSK_peripheral blood_150167

description: custom codeset

tag: Sex

tag: diagnosis

tag: calr

tag: mpl

tag: dipss category


title: MSK_peripheral blood_153593

description: custom codeset

tag: disease

tag: age at sample collection

tag: mipss70 category


title: PMc1_peripheral blood_160507

description:
Library name: PMc1_MF_peripheral blood_152
Column name in raw_counts_PMc1_358.txt: 160507

tag: transplant time_(days)

tag: transform time_(days)

tag: mpn24 score


title: PMc1_peripheral blood_160464

description:
Library name: PMc1_MF_peripheral blood_151
Column name in raw_counts_PMc1_358.txt: 160464


title: PMc1_peripheral blood_161438

description:
Library name: PMc1_MF_peripheral blood_161
Column name in raw_counts_PMc1_358.txt: 161438

value: Post ET-MF


title: PMc1_peripheral blood_151452

description:
Library name: PMc1_MF_peripheral blood_149
Column name in raw_counts_PMc1_358.txt: 151452

value: mononuclear cells


title: PMc1_peripheral blood_160134

description:
Library name: PMc1_MF_peripheral blood_150
Column name in raw_counts_PMc1_358.txt: 160134

value: Male


title: PMc1_peripheral blood_151348

description:
Library name: PMc1_MF_peripheral blood_148
Column name in raw_counts_PMc1_358.txt: 151348

value: Post PV-MF


title: PMc1_peripheral blood_151336

description:
Library name: PMc1_MF_peripheral blood_147
Column name in raw_counts_PMc1_358.txt: 151336

value: Alive


title: PMc1_peripheral blood_161164

description:
Library name: PMc1_MF_peripheral blood_159
Column name in raw_counts_PMc1_358.txt: 161164

value: PMF, overt fibrotic stage


title: MSK_peripheral blood_123854

description: custom codeset

value: Positive

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: MSK_peripheral blood_134709

description: custom codeset

value: Negative


title: MSK_peripheral blood_133381

description: custom codeset


title: PMc1_peripheral blood_10077

description:
Library name: PMc1_MF_peripheral blood_145
Column name in raw_counts_PMc1_358.txt: 10077

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: PMc1_peripheral blood_140764

description:
Library name: PMc1_MF_peripheral blood_155
Column name in raw_counts_PMc1_358.txt: 140764

tag: Sex

tag: diagnosis

tag: calr

tag: mpl

tag: dipss category


title: PMc1_peripheral blood_150578

description:
Library name: PMc1_MF_peripheral blood_144
Column name in raw_counts_PMc1_358.txt: 150578

tag: transplant time_(days)

tag: transform time_(days)


title: MSK_peripheral blood_148582

description: custom codeset

tag: disease

value: myelofibrosis

tag: age at sample collection

tag: mipss70 category

tag: os_status_at last follow up

tag: mpn24 score


title: MSK_peripheral blood_147276

description: custom codeset

tag: os_time_at last follow up (days)

tag: transplant_time (days)

tag: transform_time (days)

tag: mpn24 category


title: MSK_peripheral blood_13897

description: custom codeset

value: High


title: MSK_peripheral blood_123194

description: custom codeset


title: MSK_peripheral blood_141921

description: custom codeset

value: Female


title: MSK_peripheral blood_112587

description: custom codeset


title: PMc1_peripheral blood_140892

description:
Library name: PMc1_MF_peripheral blood_143
Column name in raw_counts_PMc1_358.txt: 140892

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: MSK_peripheral blood_112112

description: custom codeset

tag: Sex

tag: diagnosis

tag: calr

tag: mpl

tag: dipss category


title: PMc1_peripheral blood_140272

description:
Library name: PMc1_MF_peripheral blood_142
Column name in raw_counts_PMc1_358.txt: 140272

tag: transplant time_(days)

tag: transform time_(days)


title: PMc1_peripheral blood_140999

description:
Library name: PMc1_MF_peripheral blood_140
Column name in raw_counts_PMc1_358.txt: 140999

tag: mpn24 score


title: MSK_peripheral blood_110886

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_110581

description: custom codeset

tag: transplant_time (days)

tag: transform_time (days)

tag: mpn24 category


title: MSK_peripheral blood_137908

description: custom codeset


title: MSK_peripheral blood_137909

description: custom codeset


title: MSK_peripheral blood_139454

description: custom codeset


title: MSK_peripheral blood_110295

description: custom codeset


title: PMc1_peripheral blood_150778

description:
Library name: PMc1_MF_peripheral blood_146
Column name in raw_counts_PMc1_358.txt: 150778

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: MSK_peripheral blood_109590

description: custom codeset

tag: Sex

tag: diagnosis

tag: calr

tag: mpl

tag: dipss category


title: MSK_peripheral blood_107905

description: custom codeset

tag: disease

tag: age at sample collection

tag: mpn24 score


title: MSK_peripheral blood_106964

description: custom codeset

tag: mipss70 category

tag: os_status_at last follow up

tag: os_time_at last follow up (days)


title: PMc1_peripheral blood_140828

description:
Library name: PMc1_MF_peripheral blood_137
Column name in raw_counts_PMc1_358.txt: 140828

tag: transplant time_(days)

tag: transform time_(days)


title: PMc1_peripheral blood_140765

description:
Library name: PMc1_MF_peripheral blood_135
Column name in raw_counts_PMc1_358.txt: 140765

tag: tissue

tag: cell type


title: PMc1_peripheral blood_120737

description:
Library name: PMc1_MF_peripheral blood_136
Column name in raw_counts_PMc1_358.txt: 120737

tag: age at_sample_collection

tag: os status_at_last_follow_up


title: PMc1_peripheral blood_110188

description:
Library name: PMc1_MF_peripheral blood_134
Column name in raw_counts_PMc1_358.txt: 110188

tag: Sex

tag: os time_at_last_follow_up_(days)


title: PMc1_peripheral blood_140123

description:
Library name: PMc1_MF_peripheral blood_131
Column name in raw_counts_PMc1_358.txt: 140123

tag: diagnosis

tag: calr


title: PMc1_peripheral blood_120413

description:
Library name: PMc1_MF_peripheral blood_133
Column name in raw_counts_PMc1_358.txt: 120413

tag: mpl

tag: dipss category


title: PMc1_peripheral blood_140321

description:
Library name: PMc1_MF_peripheral blood_132
Column name in raw_counts_PMc1_358.txt: 140321


title: PMc1_peripheral blood_140089

description:
Library name: PMc1_MF_peripheral blood_130
Column name in raw_counts_PMc1_358.txt: 140089


title: PMc2_peripheral blood_962593

description: custom codeset

tag: disease

tag: age at sample collection

value: Intermediate

tag: transplant_time (days)

tag: transform_time (days)

tag: mpn24 category


title: PMc1_peripheral blood_150104

description:
Library name: PMc1_MF_peripheral blood_141
Column name in raw_counts_PMc1_358.txt: 150104

tag: transplant time_(days)

tag: mpn24 score


title: MSK_peripheral blood_100800

description: custom codeset

tag: mipss70 category

tag: os_status_at last follow up

tag: os_time_at last follow up (days)


title: MSK_peripheral blood_101020

description: custom codeset

value: Post-ET MF


title: MSK_peripheral blood_101375

description: custom codeset

value: unknown


title: PMc1_peripheral blood_140082

description:
Library name: PMc1_MF_peripheral blood_129
Column name in raw_counts_PMc1_358.txt: 140082

tag: tissue

tag: cell type

tag: age at_sample_collection

tag: os status_at_last_follow_up

tag: transform time_(days)


title: PMc1_peripheral blood_140977

description:
Library name: PMc1_MF_peripheral blood_139
Column name in raw_counts_PMc1_358.txt: 140977

tag: Sex

tag: diagnosis

tag: calr

tag: mpl

tag: os time_at_last_follow_up_(days)


title: PMc1_peripheral blood_130715

description:
Library name: PMc1_MF_peripheral blood_128
Column name in raw_counts_PMc1_358.txt: 130715

tag: dipss category

value: Low


title: PMc1_peripheral blood_151172

description:
Library name: PMc1_MF_peripheral blood_138
Column name in raw_counts_PMc1_358.txt: 151172

value: Peripheral blood


title: PMc1_peripheral blood_130402

description:
Library name: PMc1_MF_peripheral blood_127
Column name in raw_counts_PMc1_358.txt: 130402


title: PMc1_peripheral blood_120176

description:
Library name: PMc1_MF_peripheral blood_153
Column name in raw_counts_PMc1_358.txt: 120176


title: PMc2_peripheral blood_959413

description: custom codeset

tag: disease

tag: age at sample collection

value: Pre-fibrotic MF

tag: transplant_time (days)

tag: transform_time (days)

tag: mpn24 category


title: PMc2_peripheral blood_962555

description: custom codeset

tag: mipss70 category

tag: os_status_at last follow up

tag: os_time_at last follow up (days)

tag: mpn24 score


title: PMc1_peripheral blood_130376

description:
Library name: PMc1_MF_peripheral blood_126
Column name in raw_counts_PMc1_358.txt: 130376

tag: tissue

tag: cell type

value: mononuclear cells

tag: age at_sample_collection

value: Post ET-MF

tag: os status_at_last_follow_up

tag: transplant time_(days)


title: PMc2_peripheral blood_961797

description: custom codeset

tag: Sex

value: Male

tag: diagnosis

tag: calr

tag: mpl


title: PMc2_peripheral blood_959293

description: custom codeset

tag: disease

tag: age at sample collection

value: Post PV-MF

tag: dipss category


title: PMc1_peripheral blood_130291

description:
Library name: PMc1_MF_peripheral blood_125
Column name in raw_counts_PMc1_358.txt: 130291

value: PMF, overt fibrotic stage

tag: os time_at_last_follow_up_(days)

tag: transform time_(days)


title: PMc2_peripheral blood_952061

description: custom codeset

value: Positive

tag: mipss70 category

tag: os_status_at last follow up

value: Alive

tag: transplant_time (days)

tag: transform_time (days)

tag: mpn24 category


title: PMc2_peripheral blood_958496

description: custom codeset

value: Negative

value: Dead

tag: os_time_at last follow up (days)

tag: mpn24 score


title: PMc2_peripheral blood_952060

description: custom codeset

value: myelofibrosis

value: High


title: PMc1_peripheral blood_130084

description:
Library name: PMc1_MF_peripheral blood_124
Column name in raw_counts_PMc1_358.txt: 130084

tag: tissue

tag: cell type

tag: age at_sample_collection

value: Female

tag: os status_at_last_follow_up

tag: transplant time_(days)


title: PMc2_peripheral blood_951964

description: custom codeset

tag: disease

tag: Sex

tag: diagnosis

tag: calr

tag: mpl


title: PMc2_peripheral blood_949655

description: custom codeset

tag: age at sample collection

tag: dipss category

tag: mipss70 category

value: Intermediate


title: PMc2_peripheral blood_946461

description: custom codeset

tag: os_status_at last follow up

tag: transplant_time (days)

tag: transform_time (days)


title: PMc1_peripheral blood_161104

description:
Library name: PMc1_MF_peripheral blood_120
Column name in raw_counts_PMc1_358.txt: 161104

tag: os time_at_last_follow_up_(days)

tag: transform time_(days)

tag: mpn24 score


title: PMc2_peripheral blood_946462

description: custom codeset

tag: os_time_at last follow up (days)

tag: mpn24 category


title: PMc1_peripheral blood_120414

description:
Library name: PMc1_MF_peripheral blood_122
Column name in raw_counts_PMc1_358.txt: 120414

tag: tissue

tag: cell type

tag: age at_sample_collection

tag: os status_at_last_follow_up

tag: transplant time_(days)


title: PMc1_peripheral blood_120125

description:
Library name: PMc1_MF_peripheral blood_119
Column name in raw_counts_PMc1_358.txt: 120125

tag: Sex

tag: diagnosis

tag: calr

tag: mpl


title: PMc2_peripheral blood_940851

description: custom codeset

tag: disease

tag: age at sample collection

tag: dipss category

tag: mipss70 category

tag: os_status_at last follow up


title: PMc1_peripheral blood_150518

description:
Library name: PMc1_MF_peripheral blood_117
Column name in raw_counts_PMc1_358.txt: 150518

tag: os time_at_last_follow_up_(days)

tag: transform time_(days)

tag: mpn24 score


title: PMc1_peripheral blood_110559

description:
Library name: PMc1_MF_peripheral blood_116
Column name in raw_counts_PMc1_358.txt: 110559

tag: tissue


title: PMc1_peripheral blood_120236

description:
Library name: PMc1_MF_peripheral blood_121
Column name in raw_counts_PMc1_358.txt: 120236

tag: cell type


title: PMc1_peripheral blood_150642

description:
Library name: PMc1_MF_peripheral blood_118
Column name in raw_counts_PMc1_358.txt: 150642

tag: age at_sample_collection


title: PMc2_peripheral blood_936673

description: custom codeset

tag: os_time_at last follow up (days)

tag: transplant_time (days)

tag: transform_time (days)

tag: mpn24 category


title: PMc2_peripheral blood_936897

description: custom codeset

tag: Sex

tag: diagnosis

tag: calr


title: PMc1_peripheral blood_110294

description:
Library name: PMc1_MF_peripheral blood_113
Column name in raw_counts_PMc1_358.txt: 110294

tag: mpl

tag: os status_at_last_follow_up

tag: transplant time_(days)


title: PMc2_peripheral blood_933586

description: custom codeset

tag: disease

tag: age at sample collection

tag: dipss category

tag: mipss70 category

tag: os_status_at last follow up


title: PMc1_peripheral blood_150662

description:
Library name: PMc1_MF_peripheral blood_114
Column name in raw_counts_PMc1_358.txt: 150662

tag: tissue

tag: cell type

tag: os time_at_last_follow_up_(days)

tag: transform time_(days)

tag: mpn24 score


title: PMc1_peripheral blood_100266

description:
Library name: PMc1_MF_peripheral blood_110
Column name in raw_counts_PMc1_358.txt: 100266

tag: age at_sample_collection


title: PMc1_peripheral blood_100459

description:
Library name: PMc1_MF_peripheral blood_111
Column name in raw_counts_PMc1_358.txt: 100459

tag: Sex


title: PMc1_peripheral blood_120950

description:
Library name: PMc1_MF_peripheral blood_123
Column name in raw_counts_PMc1_358.txt: 120950

tag: diagnosis


title: PMc2_peripheral blood_923004

description: custom codeset

tag: calr

tag: os_time_at last follow up (days)

tag: transplant_time (days)

tag: transform_time (days)

tag: mpn24 category


title: PMc2_peripheral blood_924171

description: custom codeset

tag: disease

tag: age at sample collection

tag: mpl


title: PMc2_peripheral blood_925307

description: custom codeset

tag: dipss category

tag: mipss70 category

tag: os_status_at last follow up


title: PMc2_peripheral blood_923003

description: custom codeset


title: PMc2_peripheral blood_921948

description: custom codeset


title: PMc1_peripheral blood_90774

description:
Library name: PMc1_MF_peripheral blood_109
Column name in raw_counts_PMc1_358.txt: 90774

tag: tissue

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_140681

description:
Library name: PMc1_MF_peripheral blood_112
Column name in raw_counts_PMc1_358.txt: 140681

tag: age at_sample_collection

tag: Sex

tag: diagnosis

tag: transform time_(days)

tag: mpn24 score


title: PMc2_peripheral blood_916873

description: custom codeset

tag: calr

tag: os_time_at last follow up (days)

tag: transplant_time (days)

tag: transform_time (days)

tag: mpn24 category


title: PMc1_peripheral blood_90737

description:
Library name: PMc1_MF_peripheral blood_108
Column name in raw_counts_PMc1_358.txt: 90737

tag: mpl

tag: dipss category


title: PMc2_peripheral blood_919934

description: custom codeset

tag: disease

tag: age at sample collection

tag: mipss70 category

tag: os_status_at last follow up


title: PMc2_peripheral blood_937657

description: custom codeset


title: PMc1_peripheral blood_90624

description:
Library name: PMc1_MF_peripheral blood_107
Column name in raw_counts_PMc1_358.txt: 90624

tag: tissue

tag: cell type

tag: os status_at_last_follow_up

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)


title: PMc2_peripheral blood_917825

description: custom codeset

tag: Sex

tag: diagnosis

tag: mpn24 score


title: PMc1_peripheral blood_140495

description:
Library name: PMc1_MF_peripheral blood_115
Column name in raw_counts_PMc1_358.txt: 140495

tag: age at_sample_collection

tag: calr

tag: transform time_(days)


title: PMc1_peripheral blood_90595

description:
Library name: PMc1_MF_peripheral blood_106
Column name in raw_counts_PMc1_358.txt: 90595

tag: mpl


title: PMc1_peripheral blood_90117

description:
Library name: PMc1_MF_peripheral blood_105
Column name in raw_counts_PMc1_358.txt: 90117

tag: dipss category


title: PMc1_peripheral blood_422

description:
Library name: PMc1_MF_peripheral blood_103
Column name in raw_counts_PMc1_358.txt: 422


title: PMc1_peripheral blood_411

description:
Library name: PMc1_MF_peripheral blood_102
Column name in raw_counts_PMc1_358.txt: 411


title: PMc1_peripheral blood_130739

description:
Library name: PMc1_MF_peripheral blood_100
Column name in raw_counts_PMc1_358.txt: 130739


title: PMc1_peripheral blood_120505

description:
Library name: PMc1_MF_peripheral blood_99
Column name in raw_counts_PMc1_358.txt: 120505


title: PMc1_peripheral blood_9823

description:
Library name: PMc1_MF_peripheral blood_101
Column name in raw_counts_PMc1_358.txt: 9823


title: PMc2_peripheral blood_909502

description: custom codeset

tag: disease

tag: os_time_at last follow up (days)

tag: transplant_time (days)

tag: transform_time (days)

tag: mpn24 category


title: PMc1_peripheral blood_80367

description:
Library name: PMc1_MF_peripheral blood_98
Column name in raw_counts_PMc1_358.txt: 80367

tag: tissue

tag: cell type


title: PMc2_peripheral blood_916130

description: custom codeset

tag: age at sample collection

tag: mipss70 category

tag: os_status_at last follow up


title: PMc2_peripheral blood_916817

description: custom codeset

tag: Sex

tag: diagnosis


title: PMc2_peripheral blood_911460

description: custom codeset

tag: mpn24 score


title: PMc1_peripheral blood_160445

description:
Library name: PMc1_MF_peripheral blood_97
Column name in raw_counts_PMc1_358.txt: 160445

tag: age at_sample_collection

tag: calr

tag: os status_at_last_follow_up

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)


title: PMc2_peripheral blood_912762

description: custom codeset

tag: disease

tag: mpl

tag: dipss category

tag: os_time_at last follow up (days)


title: PMc1_peripheral blood_150958

description:
Library name: PMc1_MF_peripheral blood_96
Column name in raw_counts_PMc1_358.txt: 150958

tag: tissue

tag: transform time_(days)


title: PMc2_peripheral blood_905711

description: custom codeset

tag: age at sample collection

tag: transplant_time (days)

tag: transform_time (days)

tag: mpn24 category


title: PMc1_peripheral blood_161217

description:
Library name: PMc1_MF_peripheral blood_95
Column name in raw_counts_PMc1_358.txt: 161217

tag: cell type

tag: Sex

tag: diagnosis


title: PMc1_peripheral blood_161194

description:
Library name: PMc1_MF_peripheral blood_94
Column name in raw_counts_PMc1_358.txt: 161194

tag: age at_sample_collection

tag: calr

tag: mpn24 score


title: PMc2_peripheral blood_902338

description: custom codeset

tag: mipss70 category

tag: os_status_at last follow up


title: PMc1_peripheral blood_161128

description:
Library name: PMc1_MF_peripheral blood_93
Column name in raw_counts_PMc1_358.txt: 161128

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_140033

description:
Library name: PMc1_MF_peripheral blood_104
Column name in raw_counts_PMc1_358.txt: 140033

tag: tissue

tag: dipss category

tag: transform time_(days)


title: PMc1_peripheral blood_140585

description:
Library name: PMc1_MF_peripheral blood_92
Column name in raw_counts_PMc1_358.txt: 140585


title: PMc2_peripheral blood_894396

description: custom codeset

tag: disease

tag: age at sample collection

tag: os_time_at last follow up (days)

tag: transplant_time (days)

tag: transform_time (days)


title: PMc1_peripheral blood_160907

description:
Library name: PMc1_MF_peripheral blood_90
Column name in raw_counts_PMc1_358.txt: 160907

tag: cell type

tag: age at_sample_collection

tag: Sex

tag: diagnosis


title: PMc1_peripheral blood_150348

description:
Library name: PMc1_MF_peripheral blood_89
Column name in raw_counts_PMc1_358.txt: 150348

tag: calr

tag: mpn24 score


title: PMc2_peripheral blood_892832

description: custom codeset

tag: mpl

tag: mipss70 category

tag: os_status_at last follow up

tag: mpn24 category


title: PMc1_peripheral blood_140499

description:
Library name: PMc1_MF_peripheral blood_88
Column name in raw_counts_PMc1_358.txt: 140499

tag: tissue

tag: dipss category

tag: os status_at_last_follow_up

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)


title: PMc1_peripheral blood_130130

description:
Library name: PMc1_MF_peripheral blood_87
Column name in raw_counts_PMc1_358.txt: 130130

tag: transform time_(days)


title: PMc2_peripheral blood_892199

description: custom codeset

tag: disease

tag: age at sample collection

tag: os_time_at last follow up (days)

tag: transplant_time (days)

tag: transform_time (days)


title: PMc1_peripheral blood_130673

description:
Library name: PMc1_MF_peripheral blood_85
Column name in raw_counts_PMc1_358.txt: 130673

tag: cell type

tag: age at_sample_collection

tag: Sex

tag: diagnosis

tag: calr


title: PMc2_peripheral blood_890985

description: custom codeset

tag: mpl

tag: mipss70 category

tag: os_status_at last follow up

tag: mpn24 score

tag: mpn24 category


title: PMc1_peripheral blood_150949

description:
Library name: PMc1_MF_peripheral blood_84
Column name in raw_counts_PMc1_358.txt: 150949

tag: tissue

tag: dipss category

tag: os status_at_last_follow_up

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)


title: PMc2_peripheral blood_887242

description: custom codeset

tag: disease

tag: age at sample collection

tag: os_time_at last follow up (days)

tag: transplant_time (days)


title: PMc2_peripheral blood_890652

description: custom codeset

tag: Sex

tag: transform_time (days)


title: PMc1_peripheral blood_11277

description:
Library name: PMc1_MF_peripheral blood_83
Column name in raw_counts_PMc1_358.txt: 11277

tag: cell type

tag: age at_sample_collection

tag: diagnosis

tag: calr

tag: transform time_(days)


title: PMc1_peripheral blood_120948

description:
Library name: PMc1_MF_peripheral blood_82
Column name in raw_counts_PMc1_358.txt: 120948

tag: mpl

tag: mpn24 score


title: PMc2_peripheral blood_884532

description: custom codeset

tag: dipss category

tag: mipss70 category

tag: os_status_at last follow up

tag: mpn24 category


title: PMc2_peripheral blood_898259

description: custom codeset

tag: disease


title: PMc2_peripheral blood_900813

description: custom codeset

tag: age at sample collection


title: PMc1_peripheral blood_140680

description:
Library name: PMc1_MF_peripheral blood_91
Column name in raw_counts_PMc1_358.txt: 140680

tag: tissue

tag: os status_at_last_follow_up

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)


title: PMc2_peripheral blood_883865

description: custom codeset

tag: Sex

tag: os_time_at last follow up (days)

tag: transplant_time (days)

tag: transform_time (days)


title: PMc1_peripheral blood_160594

description:
Library name: PMc1_MF_peripheral blood_86
Column name in raw_counts_PMc1_358.txt: 160594

tag: cell type

tag: age at_sample_collection

tag: diagnosis

tag: calr

tag: transform time_(days)


title: PMc1_peripheral blood_150658

description:
Library name: PMc1_MF_peripheral blood_81
Column name in raw_counts_PMc1_358.txt: 150658

tag: mpl

tag: dipss category

tag: mpn24 score


title: PMc2_peripheral blood_884039

description: custom codeset

tag: disease

tag: age at sample collection

tag: mipss70 category

tag: os_status_at last follow up

tag: mpn24 category


title: PMc2_peripheral blood_910441

description: custom codeset

tag: Sex


title: PMc1_peripheral blood_110784

description:
Library name: PMc1_MF_peripheral blood_80
Column name in raw_counts_PMc1_358.txt: 110784

tag: tissue

tag: os status_at_last_follow_up

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)


title: PMc1_peripheral blood_80541

description:
Library name: PMc1_MF_peripheral blood_79
Column name in raw_counts_PMc1_358.txt: 80541

tag: cell type

tag: age at_sample_collection

value: PMF, prefibrotic/early stage


title: PMc1_peripheral blood_140389

description:
Library name: PMc1_MF_peripheral blood_77
Column name in raw_counts_PMc1_358.txt: 140389

tag: diagnosis

tag: calr


title: PMc1_peripheral blood_150055

description:
Library name: PMc1_MF_peripheral blood_78
Column name in raw_counts_PMc1_358.txt: 150055

tag: mpl

tag: transform time_(days)


title: PMc2_peripheral blood_886495

description: custom codeset

tag: dipss category

tag: os_time_at last follow up (days)

tag: transplant_time (days)

tag: transform_time (days)

tag: mpn24 score

value: Low


title: PMc1_peripheral blood_140365

description:
Library name: PMc1_MF_peripheral blood_76
Column name in raw_counts_PMc1_358.txt: 140365

value: Peripheral blood


title: PMc2_peripheral blood_880984

description: custom codeset

tag: disease

tag: age at sample collection

value: Pre-fibrotic MF

tag: mipss70 category

tag: os_status_at last follow up

tag: mpn24 category


title: PMc2_peripheral blood_881006

description: custom codeset

tag: Sex


title: PMc1_peripheral blood_140029

description:
Library name: PMc1_MF_peripheral blood_74
Column name in raw_counts_PMc1_358.txt: 140029

tag: tissue

tag: cell type

value: mononuclear cells

tag: os status_at_last_follow_up

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)


title: PMc1_peripheral blood_140203

description:
Library name: PMc1_MF_peripheral blood_75
Column name in raw_counts_PMc1_358.txt: 140203

tag: age at_sample_collection

tag: diagnosis

value: Post ET-MF

tag: calr

tag: mpl

tag: transform time_(days)


title: PMc1_peripheral blood_130463

description:
Library name: PMc1_MF_peripheral blood_73
Column name in raw_counts_PMc1_358.txt: 130463

tag: dipss category

tag: mpn24 score


title: PMc2_peripheral blood_897500

description: custom codeset

tag: disease

tag: age at sample collection

value: Male

tag: os_time_at last follow up (days)

tag: transplant_time (days)

tag: transform_time (days)


title: PMc2_peripheral blood_895338

description: custom codeset

tag: Sex

value: Post PV-MF

tag: mipss70 category

tag: os_status_at last follow up

tag: mpn24 category


title: PMc2_peripheral blood_900982

description: custom codeset


title: PMc2_peripheral blood_865090

description: custom codeset

value: PMF, overt fibrotic stage


title: PMc1_peripheral blood_130400

description:
Library name: PMc1_MF_peripheral blood_72
Column name in raw_counts_PMc1_358.txt: 130400

tag: tissue

tag: cell type

value: Positive

tag: os status_at_last_follow_up

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)


title: PMc2_peripheral blood_866763

description: custom codeset

tag: diagnosis

tag: calr

tag: mpl

value: Alive


title: PMc2_peripheral blood_867551

description: custom codeset

tag: disease

value: Negative

tag: dipss category

tag: mpn24 score


title: PMc2_peripheral blood_866108

description: custom codeset

tag: age at sample collection

tag: os_time_at last follow up (days)

tag: transplant_time (days)


title: PMc1_peripheral blood_130139

description:
Library name: PMc1_MF_peripheral blood_71
Column name in raw_counts_PMc1_358.txt: 130139

tag: age at_sample_collection

tag: Sex

tag: transform time_(days)


title: PMc2_peripheral blood_868030

description: custom codeset

tag: mipss70 category

tag: os_status_at last follow up

tag: transform_time (days)

tag: mpn24 category


title: PMc2_peripheral blood_880087

description: custom codeset


title: PMc1_peripheral blood_130066

description:
Library name: PMc1_MF_peripheral blood_70
Column name in raw_counts_PMc1_358.txt: 130066

tag: tissue

tag: cell type

tag: os status_at_last_follow_up

value: Dead

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)


title: PMc2_peripheral blood_876224

description: custom codeset

tag: disease

value: myelofibrosis

tag: diagnosis

tag: calr

tag: mpl

tag: dipss category


title: PMc2_peripheral blood_856059

description: custom codeset

tag: age at sample collection

tag: os_time_at last follow up (days)

tag: transplant_time (days)

tag: mpn24 score


title: PMc2_peripheral blood_862076

description: custom codeset

tag: Sex

tag: mipss70 category

tag: os_status_at last follow up

value: High


title: PMc2_peripheral blood_863704

description: custom codeset

value: Female

tag: transform_time (days)

tag: mpn24 category


title: PMc1_peripheral blood_110626

description:
Library name: PMc1_MF_peripheral blood_68
Column name in raw_counts_PMc1_358.txt: 110626

tag: tissue

tag: cell type

tag: age at_sample_collection

tag: os status_at_last_follow_up

tag: transform time_(days)


title: PMc2_peripheral blood_854193

description: custom codeset

tag: disease

tag: diagnosis

tag: calr

value: Intermediate


title: PMc1_peripheral blood_130243

description:
Library name: PMc1_MF_peripheral blood_66
Column name in raw_counts_PMc1_358.txt: 130243

tag: mpl

tag: dipss category

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)


title: PMc1_peripheral blood_120501

description:
Library name: PMc1_MF_peripheral blood_67
Column name in raw_counts_PMc1_358.txt: 120501

tag: Sex

tag: mpn24 score


title: PMc1_peripheral blood_130009

description:
Library name: PMc1_MF_peripheral blood_69
Column name in raw_counts_PMc1_358.txt: 130009


title: PMc2_peripheral blood_854765

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: transplant_time (days)


title: PMc2_peripheral blood_853569

description: custom codeset

tag: transform_time (days)

tag: mpn24 category


title: PMc1_peripheral blood_120072

description:
Library name: PMc1_MF_peripheral blood_65
Column name in raw_counts_PMc1_358.txt: 120072

tag: tissue

tag: cell type

tag: age at_sample_collection

tag: os status_at_last_follow_up

tag: transform time_(days)


title: PMc2_peripheral blood_852435

description: custom codeset

tag: disease

tag: diagnosis

tag: calr

tag: mpl

tag: dipss category


title: PMc2_peripheral blood_851080

description: custom codeset

tag: age at sample collection

tag: Sex

tag: mpn24 score


title: PMc1_peripheral blood_120012

description:
Library name: PMc1_MF_peripheral blood_64
Column name in raw_counts_PMc1_358.txt: 120012

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)


title: PMc1_peripheral blood_110455

description:
Library name: PMc1_MF_peripheral blood_63
Column name in raw_counts_PMc1_358.txt: 110455


title: PMc1_peripheral blood_110084

description:
Library name: PMc1_MF_peripheral blood_62
Column name in raw_counts_PMc1_358.txt: 110084


title: PMc1_peripheral blood_110055

description:
Library name: PMc1_MF_peripheral blood_61
Column name in raw_counts_PMc1_358.txt: 110055


title: PMc1_peripheral blood_100870

description:
Library name: PMc1_MF_peripheral blood_60
Column name in raw_counts_PMc1_358.txt: 100870


title: PMc2_peripheral blood_906984

description: custom codeset

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)


title: PMc2_peripheral blood_908151

description: custom codeset

tag: mpn24 category


title: PMc2_peripheral blood_908912

description: custom codeset


title: PMc2_peripheral blood_908087

description: custom codeset


title: PMc1_peripheral blood_100073

description:
Library name: PMc1_MF_peripheral blood_59
Column name in raw_counts_PMc1_358.txt: 100073

tag: tissue

tag: cell type

tag: age at_sample_collection

tag: os status_at_last_follow_up

tag: transform time_(days)


title: PMc2_peripheral blood_849052

description: custom codeset

tag: disease

tag: diagnosis

tag: calr

tag: mpl

tag: dipss category


title: PMc2_peripheral blood_851075

description: custom codeset

tag: age at sample collection

tag: Sex

tag: mpn24 score


title: PMc2_peripheral blood_848217

description: custom codeset

tag: mipss70 category

tag: os_status_at last follow up

tag: os_time_at last follow up (days)


title: PMc2_peripheral blood_846620

description: custom codeset

tag: transplant_time (days)

tag: transform_time (days)

tag: mpn24 category


title: PMc2_peripheral blood_845989

description: custom codeset


title: PMc2_peripheral blood_844783

description: custom codeset


title: PMc1_peripheral blood_90215

description:
Library name: PMc1_MF_peripheral blood_57
Column name in raw_counts_PMc1_358.txt: 90215

tag: tissue

tag: cell type

tag: age at_sample_collection

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)


title: PMc1_peripheral blood_140472

description:
Library name: PMc1_MF_peripheral blood_53
Column name in raw_counts_PMc1_358.txt: 140472

tag: diagnosis

tag: calr

tag: os status_at_last_follow_up

tag: transform time_(days)


title: PMc1_peripheral blood_130945

description:
Library name: PMc1_MF_peripheral blood_55
Column name in raw_counts_PMc1_358.txt: 130945

tag: Sex

value: PMF, prefibrotic/early stage

tag: mpl

tag: dipss category


title: PMc1_peripheral blood_90749

description:
Library name: PMc1_MF_peripheral blood_58
Column name in raw_counts_PMc1_358.txt: 90749

tag: mpn24 score


title: PMc1_peripheral blood_90131

description:
Library name: PMc1_MF_peripheral blood_56
Column name in raw_counts_PMc1_358.txt: 90131


title: PMc1_peripheral blood_160843

description:
Library name: PMc1_MF_peripheral blood_54
Column name in raw_counts_PMc1_358.txt: 160843


title: PMc1_peripheral blood_140127

description:
Library name: PMc1_MF_peripheral blood_52
Column name in raw_counts_PMc1_358.txt: 140127


title: PMc2_peripheral blood_839981

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: PMc2_peripheral blood_838766

description: custom codeset

tag: transplant_time (days)

tag: transform_time (days)

tag: mpn24 category


title: PMc2_peripheral blood_840101

description: custom codeset

value: Low


title: PMc1_peripheral blood_267944

description:
Library name: PMc1_MF_peripheral blood_51
Column name in raw_counts_PMc1_358.txt: 267944

tag: tissue

value: Peripheral blood

tag: cell type

tag: age at_sample_collection

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)


title: PMc1_peripheral blood_242485

description:
Library name: PMc1_MF_peripheral blood_50
Column name in raw_counts_PMc1_358.txt: 242485

tag: Sex

tag: diagnosis

tag: calr

tag: os status_at_last_follow_up

tag: transform time_(days)


title: PMc2_peripheral blood_837775

description: custom codeset

tag: disease

tag: age at sample collection

tag: mpl

tag: dipss category

tag: mpn24 score


title: PMc1_peripheral blood_234352

description:
Library name: PMc1_MF_peripheral blood_48
Column name in raw_counts_PMc1_358.txt: 234352


title: PMc1_peripheral blood_232458

description:
Library name: PMc1_MF_peripheral blood_46
Column name in raw_counts_PMc1_358.txt: 232458


title: PMc1_peripheral blood_233124

description:
Library name: PMc1_MF_peripheral blood_47
Column name in raw_counts_PMc1_358.txt: 233124


title: PMc1_peripheral blood_235619

description:
Library name: PMc1_MF_peripheral blood_49
Column name in raw_counts_PMc1_358.txt: 235619


title: PMc2_peripheral blood_828430

description: custom codeset

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)


title: PMc1_peripheral blood_226660

description:
Library name: PMc1_MF_peripheral blood_45
Column name in raw_counts_PMc1_358.txt: 226660

tag: tissue

tag: cell type

tag: age at_sample_collection

tag: os time_at_last_follow_up_(days)


title: PMc2_peripheral blood_830276

description: custom codeset

tag: Sex

tag: diagnosis

tag: calr

tag: mpn24 category


title: PMc1_peripheral blood_225418

description:
Library name: PMc1_MF_peripheral blood_44
Column name in raw_counts_PMc1_358.txt: 225418

tag: os status_at_last_follow_up

tag: transplant time_(days)

tag: transform time_(days)


title: PMc2_peripheral blood_828262

description: custom codeset

tag: disease

tag: age at sample collection

tag: mpl

tag: dipss category

tag: mpn24 score


title: PMc2_peripheral blood_835210

description: custom codeset

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)


title: PMc2_peripheral blood_827710

description: custom codeset

tag: Sex


title: PMc2_peripheral blood_827438

description: custom codeset

tag: diagnosis


title: PMc2_peripheral blood_826375

description: custom codeset

tag: calr


title: PMc2_peripheral blood_826888

description: custom codeset

tag: mpn24 category


title: PMc2_peripheral blood_837445

description: custom codeset


title: PMc1_peripheral blood_219358

description:
Library name: PMc1_MF_peripheral blood_42
Column name in raw_counts_PMc1_358.txt: 219358

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_218903

description:
Library name: PMc1_MF_peripheral blood_41
Column name in raw_counts_PMc1_358.txt: 218903

tag: mpl

tag: transplant time_(days)

tag: transform time_(days)


title: PMc1_peripheral blood_214690

description:
Library name: PMc1_MF_peripheral blood_40
Column name in raw_counts_PMc1_358.txt: 214690

tag: dipss category

tag: mpn24 score


title: PMc1_peripheral blood_209652

description:
Library name: PMc1_MF_peripheral blood_38
Column name in raw_counts_PMc1_358.txt: 209652


title: PMc1_peripheral blood_222475

description:
Library name: PMc1_MF_peripheral blood_43
Column name in raw_counts_PMc1_358.txt: 222475


title: PMc2_peripheral blood_821089

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: PMc1_peripheral blood_213440

description:
Library name: PMc1_MF_peripheral blood_39
Column name in raw_counts_PMc1_358.txt: 213440

tag: Sex

tag: diagnosis

tag: calr


title: PMc1_peripheral blood_207413

description:
Library name: PMc1_MF_peripheral blood_36
Column name in raw_counts_PMc1_358.txt: 207413

tag: tissue

tag: cell type


title: PMc2_peripheral blood_827468

description: custom codeset

tag: transplant_time (days)

tag: transform_time (days)

tag: mpn24 category


title: PMc1_peripheral blood_200122

description:
Library name: PMc1_MF_peripheral blood_33
Column name in raw_counts_PMc1_358.txt: 200122

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_202811

description:
Library name: PMc1_MF_peripheral blood_34
Column name in raw_counts_PMc1_358.txt: 202811

tag: dipss category

tag: transform time_(days)

tag: mpn24 score


title: PMc1_peripheral blood_208839

description:
Library name: PMc1_MF_peripheral blood_37
Column name in raw_counts_PMc1_358.txt: 208839


title: PMc2_peripheral blood_829468

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: PMc2_peripheral blood_817748

description: custom codeset

tag: Sex

tag: diagnosis

tag: calr


title: PMc2_peripheral blood_816517

description: custom codeset

tag: transplant_time (days)

tag: transform_time (days)

tag: mpn24 category


title: PMc2_peripheral blood_815462

description: custom codeset

tag: mpl


title: PMc2_peripheral blood_816908

description: custom codeset


title: PMc2_peripheral blood_813609

description: custom codeset


title: PMc1_peripheral blood_200120

description:
Library name: PMc1_MF_peripheral blood_32
Column name in raw_counts_PMc1_358.txt: 200120

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: PMc2_peripheral blood_814064

description: custom codeset

tag: disease

tag: dipss category

tag: mpn24 score


title: PMc2_peripheral blood_812401

description: custom codeset

tag: age at sample collection

tag: mipss70 category

tag: os_status_at last follow up


title: PMc2_peripheral blood_807715

description: custom codeset

tag: Sex

tag: diagnosis

tag: os_time_at last follow up (days)


title: PMc2_peripheral blood_812518

description: custom codeset

value: Pre-fibrotic MF

tag: calr

tag: transplant_time (days)

tag: transform_time (days)


title: PMc2_peripheral blood_809975

description: custom codeset

tag: mpl

tag: mpn24 category


title: PMc1_peripheral blood_198577

description:
Library name: PMc1_MF_peripheral blood_31
Column name in raw_counts_PMc1_358.txt: 198577

tag: tissue

tag: cell type

value: mononuclear cells

tag: age at_sample_collection

tag: transplant time_(days)

tag: transform time_(days)


title: PMc1_peripheral blood_206120

description:
Library name: PMc1_MF_peripheral blood_35
Column name in raw_counts_PMc1_358.txt: 206120

value: Post ET-MF

tag: dipss category

tag: os status_at_last_follow_up

tag: os time_at_last_follow_up_(days)

tag: mpn24 score


title: PMc2_peripheral blood_807518

description: custom codeset

tag: disease

tag: age at sample collection

tag: Sex

value: Male

tag: mipss70 category

tag: os_status_at last follow up


title: PMc2_peripheral blood_818901

description: custom codeset

tag: diagnosis

tag: calr

tag: os_time_at last follow up (days)

tag: transplant_time (days)

tag: transform_time (days)


title: PMc1_peripheral blood_193949

description:
Library name: PMc1_MF_peripheral blood_30
Column name in raw_counts_PMc1_358.txt: 193949

tag: tissue

tag: cell type

tag: age at_sample_collection

tag: mpl


title: PMc2_peripheral blood_806386

description: custom codeset

value: Post PV-MF

tag: dipss category

tag: mpn24 category


title: PMc1_peripheral blood_193010

description:
Library name: PMc1_MF_peripheral blood_29
Column name in raw_counts_PMc1_358.txt: 193010

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 score


title: PMc2_peripheral blood_805587

description: custom codeset

tag: disease

tag: age at sample collection

tag: Sex

tag: mipss70 category

tag: os_status_at last follow up


title: PMc1_peripheral blood_190127

description:
Library name: PMc1_MF_peripheral blood_27
Column name in raw_counts_PMc1_358.txt: 190127

tag: diagnosis

tag: calr


title: PMc2_peripheral blood_802371

description: custom codeset

tag: os_time_at last follow up (days)

tag: transplant_time (days)

tag: transform_time (days)


title: PMc1_peripheral blood_189422

description:
Library name: PMc1_MF_peripheral blood_26
Column name in raw_counts_PMc1_358.txt: 189422

tag: tissue

tag: cell type

tag: age at_sample_collection

value: PMF, overt fibrotic stage

tag: mpl

tag: dipss category


title: PMc1_peripheral blood_192150

description:
Library name: PMc1_MF_peripheral blood_28
Column name in raw_counts_PMc1_358.txt: 192150

value: Positive

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_188498

description:
Library name: PMc1_MF_peripheral blood_24
Column name in raw_counts_PMc1_358.txt: 188498

tag: Sex

value: Alive

tag: mpn24 score


title: PMc2_peripheral blood_332948

description: custom codeset

tag: disease

tag: age at sample collection

value: Negative

tag: mipss70 category

tag: os_status_at last follow up

tag: mpn24 category


title: PMc1_peripheral blood_188706

description:
Library name: PMc1_MF_peripheral blood_25
Column name in raw_counts_PMc1_358.txt: 188706

tag: diagnosis

tag: calr


title: PMc1_peripheral blood_183195

description:
Library name: PMc1_MF_peripheral blood_23
Column name in raw_counts_PMc1_358.txt: 183195

tag: tissue

tag: cell type

value: Dead


title: PMc1_peripheral blood_203521

description:
Library name: PMc1_MF_peripheral blood_21
Column name in raw_counts_PMc1_358.txt: 203521

tag: age at_sample_collection

tag: mpl


title: PMc1_peripheral blood_179600

description:
Library name: PMc1_MF_peripheral blood_20
Column name in raw_counts_PMc1_358.txt: 179600

tag: dipss category

tag: os status_at_last_follow_up


title: PMc2_peripheral blood_332795

description: custom codeset

value: myelofibrosis

tag: os_time_at last follow up (days)

tag: transplant_time (days)

tag: transform_time (days)


title: PMc1_peripheral blood_182937

description:
Library name: PMc1_MF_peripheral blood_22
Column name in raw_counts_PMc1_358.txt: 182937

tag: Sex

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)

tag: transform time_(days)

tag: mpn24 score


title: PMc1_peripheral blood_179523

description:
Library name: PMc1_MF_peripheral blood_19
Column name in raw_counts_PMc1_358.txt: 179523


title: PMc1_peripheral blood_176503

description:
Library name: PMc1_MF_peripheral blood_18
Column name in raw_counts_PMc1_358.txt: 176503


title: PMc1_peripheral blood_175999

description:
Library name: PMc1_MF_peripheral blood_17
Column name in raw_counts_PMc1_358.txt: 175999


title: PMc2_peripheral blood_331821

description: custom codeset

tag: disease

tag: age at sample collection

tag: mipss70 category

tag: os_status_at last follow up

tag: mpn24 category


title: PMc2_peripheral blood_330808

description: custom codeset

tag: diagnosis

tag: calr


title: PMc2_peripheral blood_330851

description: custom codeset

tag: mpl

tag: dipss category


title: PMc2_peripheral blood_799472

description: custom codeset

tag: os_time_at last follow up (days)


title: PMc2_peripheral blood_331879

description: custom codeset

tag: transplant_time (days)


title: PMc1_peripheral blood_174839

description:
Library name: PMc1_MF_peripheral blood_15
Column name in raw_counts_PMc1_358.txt: 174839

tag: tissue

tag: cell type

tag: age at_sample_collection

tag: os status_at_last_follow_up


title: PMc1_peripheral blood_175898

description:
Library name: PMc1_MF_peripheral blood_16
Column name in raw_counts_PMc1_358.txt: 175898

tag: Sex

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)

tag: transform time_(days)


title: PMc2_peripheral blood_327670

description: custom codeset

tag: disease

tag: age at sample collection

tag: mipss70 category

value: High

tag: transform_time (days)

tag: mpn24 score


title: PMc2_peripheral blood_330700

description: custom codeset

value: Female

tag: diagnosis

tag: calr

tag: mpl

tag: os_status_at last follow up

tag: mpn24 category


title: PMc1_peripheral blood_173218

description:
Library name: PMc1_MF_peripheral blood_14
Column name in raw_counts_PMc1_358.txt: 173218

tag: tissue

tag: cell type

tag: dipss category


title: PMc1_peripheral blood_172723

description:
Library name: PMc1_MF_peripheral blood_13
Column name in raw_counts_PMc1_358.txt: 172723

tag: age at_sample_collection

tag: Sex

tag: os status_at_last_follow_up


title: PMc2_peripheral blood_326384

description: custom codeset

tag: os_time_at last follow up (days)

tag: transplant_time (days)


title: PMc2_peripheral blood_327616

description: custom codeset

tag: disease

tag: age at sample collection

value: Intermediate


title: PMc1_peripheral blood_172543

description:
Library name: PMc1_MF_peripheral blood_12
Column name in raw_counts_PMc1_358.txt: 172543

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)

tag: transform time_(days)


title: PMc2_peripheral blood_326381

description: custom codeset

tag: diagnosis

tag: calr

tag: mipss70 category

tag: transform_time (days)

tag: mpn24 score


title: PMc1_peripheral blood_167198

description:
Library name: PMc1_MF_peripheral blood_11
Column name in raw_counts_PMc1_358.txt: 167198

tag: tissue

tag: cell type

tag: mpl


title: PMc1_peripheral blood_165597

description:
Library name: PMc1_MF_peripheral blood_10
Column name in raw_counts_PMc1_358.txt: 165597

tag: age at_sample_collection

tag: Sex

tag: dipss category


title: PMc2_peripheral blood_324851

description: custom codeset

tag: os_status_at last follow up

tag: os_time_at last follow up (days)

tag: transplant_time (days)

tag: mpn24 category


title: PMc1_peripheral blood_164312

description:
Library name: PMc1_MF_peripheral blood_9
Column name in raw_counts_PMc1_358.txt: 164312

tag: os status_at_last_follow_up

tag: os time_at_last_follow_up_(days)

tag: transplant time_(days)


title: PMc2_peripheral blood_324855

description: custom codeset

tag: disease

tag: age at sample collection

tag: diagnosis

tag: calr


title: PMc1_peripheral blood_211698

description:
Library name: PMc1_MF_peripheral blood_7
Column name in raw_counts_PMc1_358.txt: 211698

tag: tissue

tag: transform time_(days)

tag: mpn24 score


title: PMc1_peripheral blood_164165

description:
Library name: PMc1_MF_peripheral blood_8
Column name in raw_counts_PMc1_358.txt: 164165

tag: cell type

tag: age at_sample_collection

tag: mpl


title: PMc2_peripheral blood_323560

description: custom codeset

tag: Sex

tag: dipss category

tag: mipss70 category

tag: os_status_at last follow up

tag: transform_time (days)


title: PMc1_peripheral blood_7322

description:
Library name: PMc1_MF_peripheral blood_5
Column name in raw_counts_PMc1_358.txt: 7322

tag: os status_at_last_follow_up

tag: os time_at_last_follow_up_(days)


title: PMc1_peripheral blood_9596

description:
Library name: PMc1_MF_peripheral blood_6
Column name in raw_counts_PMc1_358.txt: 9596

value: PMF, prefibrotic/early stage

tag: transplant time_(days)


title: PMc1_peripheral blood_7323

description:
Library name: PMc1_MF_peripheral blood_4
Column name in raw_counts_PMc1_358.txt: 7323


title: PMc1_peripheral blood_4174

description:
Library name: PMc1_MF_peripheral blood_3
Column name in raw_counts_PMc1_358.txt: 4174


title: PMc2_peripheral blood_332794

description: custom codeset

tag: disease

tag: age at sample collection

tag: os_time_at last follow up (days)

tag: transplant_time (days)

tag: mpn24 category


title: PMc2_peripheral blood_328562

description: custom codeset

tag: diagnosis

tag: calr

tag: mpn24 score

value: Low


title: PMc2_peripheral blood_315961

description: custom codeset

tag: mpl


title: PMc2_peripheral blood_313127

description: custom codeset

tag: Sex


title: PMc2_peripheral blood_314592

description: custom codeset

tag: dipss category


title: RiSi07_Hu_2_CD4_9D_CITE

city: La Jolla

first: Emil

last: Johansson

state: California

address: 9420 Athena Cir

department: Center for Autoimmunity and Inflammation

country: USA

institute: La Jolla Institute for Immunology

description:
Library name: RiSi07_Hu_2_CD4_9D_CITE
CITE

library_source: other

data_processing:
The Cellranger multi pipeline (v8.0.1) was used to perform alignment to the pre-built GRCh38 human genome reference (2020-A), UMI counting, sample deconvolution, and TCR clonotype calling. The Seurat toolkit (v5.2.1) was employed in R (v4.4.1) to perform quality control (QC), unbiased clustering, dimensionality reduction and cluster annotation on each aggregated dataset. The following QC criteria were enforced to minimize doublets and eliminate low-quality transcriptomes: 1,500 ≥ unique molecular identifier (UMI) count ≤20,000; 800 ≥ gene count ≤4,400; and mitochondrial UMI percentage ≤7%. As we had previously found that MAIT cells are captured among AIM+ cells26, we excluded cells expressing the known MAIT TCRα chain segment TRAV1-2-TRAJ33/12/20, and the TCRβ chain segment TRBV6-1/6-4/20-165. To prevent donor-specific gene expression of individual TCR genes to influence gene expression-based clustering, TCRA/B/D/G genes were pulled from the gene expression matrix and counts were aggregated into a single gene feature for each gene66. Samples were normalized using the SCTransform function (“V2” regularization, v0.4.2) with mitochondrial content as the variable to regress and 3000 variable features. Samples were thereafter integrated using the RunHarmony function (v1.2.3), with sequencing batch and donor ID specified as covaries. For CD4 T cells 20 PCA dimensions were used as cell embedding features, while 15 PCA dimensions were used for the CD8 T cells. FindNeighbors and RunUMAP were performed using 30 dimensions, and FindClusters was performed using a resolution of 0.2 for CD4 T cells and 0.3 for CD8 T cells. The Clustree package (v0.5.1) was used to plot cluster number and cell distribution at different cluster resolutions.
The FindAllMarkers function from Seurat67 (v3.2.3) was used to perform differential gene expression analysis (DGEA) with MAST (v1.32.0) employed as the statistical framework for differential expression analysisv68. The function was used to identify transcripts enriched in T cell clusters, as well to compare transcriptome of the same cluster between two study groups. Mitochondrial and ribosomal genes were excluded for cluster DGEA between study groups. A gene was considered as differentially expressed if Benjamini-Hochberg adjusted p-value <0.05 and either log2 fold change (LFC) ≥ 0.25 or LFC ≤ −0.25. Metascape69 (http://metascape.org) was used for gene set overrepresentation analyses.
The immunarch R package (v0.9.1) was used to calculate the TCR repertoire diversity of cells with paired TCRα and TCRβ chains. To identify cells with TCR sequences with known antigen-specificity, CDR3 amino acid sequence, V-segment, and J-segments from paired TCRα and TCRβ chain sequences, as well as individual TCRα and TCRβ chains, were mapped to sequences deposited at the VDJ database (Table S6). The scRepertoire (v2.2.1) package was used to visualize the frequency of expansion from paired TCRα and TCRβ clones per cluster and make circle plot showing clonal sharing among clusters.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: .RDS file containig the Seurat object used for all analyses in the paper. It contains both RNA and TCR data for CD4 and CD8 T cells

molecule: protein

source_name: Peripheral blood mononuclear cells

extract_protocol:
According to the previously described AIM assay protocol, PBMCs were thawed and stimulated for 24 h with the S MP. Cells were washed and stained with an antibody cocktail containing the antibodies described above for 30 min at 4°C, protected from light. TotalSeqTM-C oligonucleotide-conjugated antibodies (BioLegend, San Diego, CA) were also added at this step at 0.01mg/mL final concentration (one distinct antibody per sample). After two washes in PBS, cells were resuspended into 500 μL of FACS buffer (PBS containing 2mM EDTA (pH 8.0) and 0.5% BSA) and stored at 4°C until flow cytometry acquisition. S-specific CD4+ and CD8+ AIM+ T cells were subsequently sorted using a BD FACSAria Fusion cell sorter (Becton Dickinson), as previously described26. On average 20,000–40,000 AIM+ T cells per subject were sorted for single-cell RNA-seq assays (10x Genomics, Pleasantown). Cells were collected directly into low-retention, sterile 1.5 mL collection tubes (Thermo-fisher) pre-chilled on ice and containing 500 μL of PBS:FBS solution (1:1, vol:vol) supplemented with RNAse inhibitor (1:100, Takara Bio). 5 to 6 different samples were multiplexed, each labeled with distinct TotalSeq-C DNA-oligo barcoded, totaling approximately 60,000 cells per 10X lane (equivalent to one well of the 10X chip). Samples were centrifuged at 600 ×g for 10 min at 4°C, and the supernatant was carefully removed, leaving behind 10–12 μL of residual volume. Cell pellets were resuspended in 25 μL of 10x Genomics-compatible resuspension buffer (0.22 μm filtered PBS containing 0.04% ultrapure bovine serum albumin, Sigma-Aldrich). 33 μL of the resuspended cells was transferred to an 8-strip PCR tube for downstream processing as per the 10x Genomics protocol. Remaining cells were used for a cell-counting quality control.
Following the manufacturer’s recommendations, single-cell RNA libraries were generated using the 10x Genomics standard 5′TAG v2 chemistry. Both cDNA amplification and library preparation were carried out using 13 PCR cycles. Barcoded cDNA products were collected, quantified, and pooled at equimolar concentrations. The libraries were sequenced on the Illumina Novaseq6000 platform with paired-end sequencing (S4 100x100cycle, Illumina) configured as follows: read length: read 1, 100 cycles; read 2, 100 cycles; i7 index, 10 cycles and i5 index 10 cycles. Size and quantity quality controls were performed throughout the procedure by capillary DNA high sensitivity electrophoresis (HS NGS Fragment Kit, 1-6000bp, Fragment Analyzer, Agilent) and Picogreen assay (Quant-iT PicoGreen dsDNA Assay Kits and dsDNA Reagents). Sequencing depth was aimed to reach 30,000 reads per cell for gene expressions, 8,000 reads/cell for TCR, and antibody-feature sequencing (multiplexing analysis).

tag: cell type

value: Peripheral blood mononuclear cells


title: PMc2_peripheral blood_321346

description: custom codeset

tag: mipss70 category

tag: os_status_at last follow up


title: PMc2_peripheral blood_313240

description: custom codeset

tag: transform_time (days)


title: PMc2_peripheral blood_308053

description: custom codeset


title: RiSi07_Hu_1_CD4_9D_CITE

description:
Library name: RiSi07_Hu_1_CD4_9D_CITE
CITE


title: PMc2_peripheral blood_310619

description: custom codeset


title: PMc2_peripheral blood_321247

description: custom codeset


title: PMc2_peripheral blood_312842

description: custom codeset


title: RiSi06_Hu_3_CD8_9D_CITE

description:
Library name: RiSi06_Hu_3_CD8_9D_CITE
CITE


title: PMc2_peripheral blood_306447

description: custom codeset


title: PMc2_peripheral blood_304708

description: custom codeset

value: Pre-fibrotic MF


title: RiSi05_Hu_3_CD8_9D_CITE

description:
Library name: RiSi05_Hu_3_CD8_9D_CITE
CITE


title: PMc1_peripheral blood_3803

description:
Library name: PMc1_MF_peripheral blood_2
Column name in raw_counts_PMc1_358.txt: 3803

tag: tissue

value: Peripheral blood

value: mononuclear cells

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: RiSi06_Hu_1_CD4_9D_CITE

description:
Library name: RiSi06_Hu_1_CD4_9D_CITE
CITE


title: PMc1_peripheral blood_323584

description:
Library name: PMc1_MF_peripheral blood_1
Column name in raw_counts_PMc1_358.txt: 323584

value: Male

tag: transplant time_(days)


title: RiSi05_Hu_2_CD4_9D_CITE

description:
Library name: RiSi05_Hu_2_CD4_9D_CITE
CITE


title: PMc2_peripheral blood_303635

description: custom codeset

tag: disease

tag: age at sample collection

tag: os_time_at last follow up (days)

tag: transplant_time (days)

tag: mpn24 category


title: RiSi05_Hu_1_CD4_9D_CITE

description:
Library name: RiSi05_Hu_1_CD4_9D_CITE
CITE


title: PMc2_peripheral blood_302551

description: custom codeset

tag: Sex

tag: diagnosis

tag: calr

tag: mpl

tag: mpn24 score


title: PMc2_peripheral blood_299477

description: custom codeset

tag: dipss category

tag: mipss70 category

tag: os_status_at last follow up

tag: transform_time (days)


title: PMc2_peripheral blood_311973

description: custom codeset


title: PMc2_peripheral blood_298183

description: custom codeset


title: RiSi04_Hu_4_CD8_9D_CITE

description:
Library name: RiSi04_Hu_4_CD8_9D_CITE
CITE

tag: cell type


title: PMc2_peripheral blood_298179

description: custom codeset


title: PMc2_peripheral blood_306454

description: custom codeset


title: RiSi04_Hu_1_CD4_9D_CITE

description:
Library name: RiSi04_Hu_1_CD4_9D_CITE
CITE


title: PMc2_peripheral blood_295473

description: custom codeset


title: RiSi04_Hu_3_CD8_9D_CITE

description:
Library name: RiSi04_Hu_3_CD8_9D_CITE
CITE


title: RiSi06_Hu_4_CD8_9D_CITE

description:
Library name: RiSi06_Hu_4_CD8_9D_CITE
CITE


title: RiSi03_Hu_spike_CD4_9_b_CITE

description:
Library name: RiSi03_Hu_spike_CD4_9_b_CITE
CITE


title: PMc2_peripheral blood_291085

description: custom codeset

value: Post ET-MF


title: RiSi06_Hu_2_CD4_9D_CITE

description:
Library name: RiSi06_Hu_2_CD4_9D_CITE
CITE


title: RiSi03_Hu_spike_CD4_9_a_CITE

description:
Library name: RiSi03_Hu_spike_CD4_9_a_CITE
CITE


title: PMc2_peripheral blood_288779

description: custom codeset


title: PMc2_peripheral blood_300119

description: custom codeset

value: PMF, overt fibrotic stage


title: RiSi02_Hu_spike_CD8_9_a_CITE

description:
Library name: RiSi02_Hu_spike_CD8_9_a_CITE
CITE


title: PMc2_peripheral blood_288676

description: custom codeset

value: Positive


title: RiSi02_Hu_spike_CD4_9_b_CITE

description:
Library name: RiSi02_Hu_spike_CD4_9_b_CITE
CITE


title: PMc2_peripheral blood_283581

description: custom codeset


title: RiSi02_Hu_spike_CD4_9_a_CITE

description:
Library name: RiSi02_Hu_spike_CD4_9_a_CITE
CITE


title: RiSi01_Hu_4_CD8_9D_CITE

description:
Library name: RiSi01_Hu_4_CD8_9D_CITE
CITE


title: RiSi01_Hu_3_CD8_9D_CITE

description:
Library name: RiSi01_Hu_3_CD8_9D_CITE
CITE


title: PMc2_peripheral blood_282782

description: custom codeset

value: Post PV-MF

value: Alive


title: RiSi01_Hu_2_CD4_9D_CITE

description:
Library name: RiSi01_Hu_2_CD4_9D_CITE
CITE


title: PMc2_peripheral blood_280057

description: custom codeset

value: Negative

value: Dead


title: PMc2_peripheral blood_270544

description: custom codeset

value: myelofibrosis

value: High


title: PMc2_peripheral blood_280787

description: custom codeset

value: Intermediate


title: RiSi01_Hu_1_CD4_9D_CITE

description:
Library name: RiSi01_Hu_1_CD4_9D_CITE
CITE


title: RiSi03_Hu_spike_CD8_9_b_CITE

description:
Library name: RiSi03_Hu_spike_CD8_9_b_CITE
CITE


title: PMc2_peripheral blood_266434

description: custom codeset

value: Female


title: PMc2_peripheral blood_264181

description: custom codeset


title: PMc2_peripheral blood_314997

description: custom codeset

value: Low


title: PMc2_peripheral blood_291530

description: custom codeset


title: RiSi06_Hu_4_CD8_9D_TCR

description:
Library name: RiSi06_Hu_4_CD8_9D_TCR
TCR

molecule: other

value: Peripheral blood mononuclear cells


title: RiSi06_Hu_2_CD4_9D_TCR

description:
Library name: RiSi06_Hu_2_CD4_9D_TCR
TCR


title: RiSi06_Hu_3_CD8_9D_TCR

description:
Library name: RiSi06_Hu_3_CD8_9D_TCR
TCR


title: RiSi02_Hu_spike_CD8_9_b_CITE

description:
Library name: RiSi02_Hu_spike_CD8_9_b_CITE
CITE


title: PMc2_peripheral blood_264175

description: custom codeset

value: Pre-fibrotic MF


title: PMc2_peripheral blood_261431

description: custom codeset


title: RiSi06_Hu_1_CD4_9D_TCR

description:
Library name: RiSi06_Hu_1_CD4_9D_TCR
TCR


title: PMc2_peripheral blood_260994

description: custom codeset


title: RiSi05_Hu_3_CD8_9D_TCR

description:
Library name: RiSi05_Hu_3_CD8_9D_TCR
TCR


title: PMc2_peripheral blood_290046

description: custom codeset


title: PMc2_peripheral blood_261126

description: custom codeset


title: RiSi05_Hu_2_CD4_9D_TCR

description:
Library name: RiSi05_Hu_2_CD4_9D_TCR
TCR


title: PMc2_peripheral blood_259812

description: custom codeset


title: RiSi05_Hu_1_CD4_9D_TCR

description:
Library name: RiSi05_Hu_1_CD4_9D_TCR
TCR


title: RiSi04_Hu_4_CD8_9D_TCR

description:
Library name: RiSi04_Hu_4_CD8_9D_TCR
TCR


title: RiSi04_Hu_1_CD4_9D_TCR

description:
Library name: RiSi04_Hu_1_CD4_9D_TCR
TCR


title: PMc2_peripheral blood_259745

description: custom codeset


title: PMc2_peripheral blood_256736

description: custom codeset


title: PMc2_peripheral blood_257810

description: custom codeset


title: RiSi02_Hu_spike_CD8_9_b_TCR

description:
Library name: RiSi02_Hu_spike_CD8_9_b_TCR
TCR


title: RiSi03_Hu_spike_CD4_9_a_TCR

description:
Library name: RiSi03_Hu_spike_CD4_9_a_TCR
TCR


title: RiSi03_Hu_spike_CD4_9_b_TCR

description:
Library name: RiSi03_Hu_spike_CD4_9_b_TCR
TCR


title: PMc2_peripheral blood_247968

description: custom codeset


title: RiSi03_Hu_spike_CD8_9_b_TCR

description:
Library name: RiSi03_Hu_spike_CD8_9_b_TCR
TCR


title: RiSi02_Hu_spike_CD8_9_a_TCR

description:
Library name: RiSi02_Hu_spike_CD8_9_a_TCR
TCR


title: PMc2_peripheral blood_254705

description: custom codeset


title: RiSi02_Hu_spike_CD4_9_b_TCR

description:
Library name: RiSi02_Hu_spike_CD4_9_b_TCR
TCR


title: PMc2_peripheral blood_246348

description: custom codeset


title: PMc2_peripheral blood_249134

description: custom codeset


title: PMc2_peripheral blood_243685

description: custom codeset


title: RiSi01_Hu_4_CD8_9D_TCR

description:
Library name: RiSi01_Hu_4_CD8_9D_TCR
TCR


title: RiSi02_Hu_spike_CD4_9_a_TCR

description:
Library name: RiSi02_Hu_spike_CD4_9_a_TCR
TCR


title: PMc1_peripheral blood_90237

description: custom codeset


title: RiSi04_Hu_3_CD8_9D_TCR

description:
Library name: RiSi04_Hu_3_CD8_9D_TCR
TCR


title: RiSi01_Hu_3_CD8_9D_TCR

description:
Library name: RiSi01_Hu_3_CD8_9D_TCR
TCR


title: RiSi01_Hu_1_CD4_9D_TCR

description:
Library name: RiSi01_Hu_1_CD4_9D_TCR
TCR


title: PMc1_peripheral blood_7322

description: custom codeset


title: PMc1_peripheral blood_80474_rep2

description: custom codeset


title: RiSi07_Hu_4_CD8_9D_Gex

description:
Library name: RiSi07_Hu_4_CD8_9D_Gex
GEX

library_source: transcriptomic single cell

molecule: polyA RNA


title: PMc1_peripheral blood_555

description: custom codeset

value: PMF, prefibrotic/early stage


title: RiSi07_Hu_3_CD8_9D_Gex

description:
Library name: RiSi07_Hu_3_CD8_9D_Gex
GEX


title: RiSi01_Hu_2_CD4_9D_TCR

description:
Library name: RiSi01_Hu_2_CD4_9D_TCR
TCR


title: PMc1_peripheral blood_422

description: custom codeset


title: PMc1_peripheral blood_3803

description: custom codeset


title: RiSi07_Hu_2_CD4_9D_Gex

description:
Library name: RiSi07_Hu_2_CD4_9D_Gex
GEX


title: PMc2_peripheral blood_245729

description: custom codeset


title: RiSi06_Hu_4_CD8_9D_Gex

description:
Library name: RiSi06_Hu_4_CD8_9D_Gex
GEX


title: RiSi07_Hu_1_CD4_9D_Gex

description:
Library name: RiSi07_Hu_1_CD4_9D_Gex
GEX


title: PMc1_peripheral blood_200120_rep3

description: custom codeset


title: PMc1_peripheral blood_218903

description: custom codeset


title: PMc1_peripheral blood_90351

description: custom codeset


title: RiSi06_Hu_1_CD4_9D_Gex

description:
Library name: RiSi06_Hu_1_CD4_9D_Gex
GEX


title: PMc1_peripheral blood_233124

description: custom codeset


title: RiSi06_Hu_3_CD8_9D_Gex

description:
Library name: RiSi06_Hu_3_CD8_9D_Gex
GEX


title: RiSi05_Hu_3_CD8_9D_Gex

description:
Library name: RiSi05_Hu_3_CD8_9D_Gex
GEX


title: RiSi06_Hu_2_CD4_9D_Gex

description:
Library name: RiSi06_Hu_2_CD4_9D_Gex
GEX


title: PMc1_peripheral blood_200120_rep2

description: custom codeset


title: PMc1_peripheral blood_80474_rep1

description: custom codeset


title: PMc1_peripheral blood_200120_rep1

description: custom codeset


title: RiSi05_Hu_2_CD4_9D_Gex

description:
Library name: RiSi05_Hu_2_CD4_9D_Gex
GEX


title: RiSi05_Hu_1_CD4_9D_Gex

description:
Library name: RiSi05_Hu_1_CD4_9D_Gex
GEX


title: RiSi04_Hu_4_CD8_9D_Gex

description:
Library name: RiSi04_Hu_4_CD8_9D_Gex
GEX


title: RiSi04_Hu_3_CD8_9D_Gex

description:
Library name: RiSi04_Hu_3_CD8_9D_Gex
GEX


title: PMc1_peripheral blood_188706_rep3

description: custom codeset


title: RiSi04_Hu_1_CD4_9D_Gex

description:
Library name: RiSi04_Hu_1_CD4_9D_Gex
GEX


title: PMc1_peripheral blood_162243

description: custom codeset


title: PMc1_peripheral blood_162277

description: custom codeset


title: PMc1_peripheral blood_183195

description: custom codeset


title: PMc1_peripheral blood_188706_rep1

description: custom codeset


title: PMc1_peripheral blood_188706_rep2

description: custom codeset


title: PMc1_peripheral blood_188498

description: custom codeset


title: RiSi03_Hu_spike_CD4_9_b_Gex

description:
Library name: RiSi03_Hu_spike_CD4_9_b_Gex
GEX


title: RiSi03_Hu_spike_CD4_9_a_Gex

description:
Library name: RiSi03_Hu_spike_CD4_9_a_Gex
GEX


title: PMc1_peripheral blood_161272

description: custom codeset


title: RiSi02_Hu_spike_CD4_9_b_Gex

description:
Library name: RiSi02_Hu_spike_CD4_9_b_Gex
GEX


title: PMc1_peripheral blood_161105

description: custom codeset


title: RiSi02_Hu_spike_CD8_9_a_Gex

description:
Library name: RiSi02_Hu_spike_CD8_9_a_Gex
GEX


title: RiSi02_Hu_spike_CD4_9_a_Gex

description:
Library name: RiSi02_Hu_spike_CD4_9_a_Gex
GEX


title: RiSi02_Hu_spike_CD8_9_b_Gex

description:
Library name: RiSi02_Hu_spike_CD8_9_b_Gex
GEX


title: PMc1_peripheral blood_151360

description: custom codeset


title: PMc1_peripheral blood_151413

description: custom codeset


title: PMc1_peripheral blood_160686

description: custom codeset


title: PMc1_peripheral blood_160782

description: custom codeset


title: PMc1_peripheral blood_160015

description: custom codeset


title: RiSi01_Hu_4_CD8_9D_Gex

description:
Library name: RiSi01_Hu_4_CD8_9D_Gex
GEX


title: RiSi01_Hu_3_CD8_9D_Gex

description:
Library name: RiSi01_Hu_3_CD8_9D_Gex
GEX


title: PMc1_peripheral blood_151336_rep2

description: custom codeset


title: RiSi01_Hu_2_CD4_9D_Gex

description:
Library name: RiSi01_Hu_2_CD4_9D_Gex
GEX


title: RiSi03_Hu_spike_CD8_9_b_Gex

description:
Library name: RiSi03_Hu_spike_CD8_9_b_Gex
GEX


title: PMc1_peripheral blood_161783

description: custom codeset


title: RiSi01_Hu_1_CD4_9D_Gex

description:
Library name: RiSi01_Hu_1_CD4_9D_Gex
GEX


title: Patient B992, peripheral blood, CD19+ and  CD3+ cells

city: Bethesda

first: Chi-Ping

last: Day

state: Maryland

address: Bldg 15C1, NIH-Bethesda

department: National Cancer Institute

institute: National Institutes of HEalth

description: Library name: RG05

data_processing:
Isolated cells from HCLv and HCL patients, both with unmutated IGHV4-34, were sequenced. Upon obtaining FASTQ files containing reads of RNA from 42 leukemic B cells sequenced on the SmartSeq2 platform, we used Rsem to align the read data and estimate expression counts for each transcript. After using GATK’s Best Practices for mutation calling from single-cell RNA sequencing data, we constructed a binary genotype matrix for each mutation and cell, entering a “1” where a mutation is observed, “0” where a mutation is absent, and “N/A” where a mutation is missing/unobservable due to low sequencing coverage. We used ScisTree 11 and PhISCS 12, two well-known tumor phylogeny reconstruction methods, to construct the most likely phylogeny from this genotype matrix. For the second patient C435, we obtained sequencing data from 380 single cells (320 leukemic B cells and 60 non-leukemic T cells) sequenced on the NovaSeq platform and performed the same downstream analysis, using the non-leukemic RNA as a germline control for somatic mutation calling. Prior to constructing each phylogeny, we removed “private” mutations, or mutations that occur in only one cell.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files.

extract_protocol:
PBMCs were purified from peripheral blood using Ficoll-PlaqueTM Plus (Cytiva, Uppsala, Sweden) and then frozen. On the day of sorting, the PBMC sample was thawed, washed twice in PBS, and resuspended in a FACS buffer containing 1% BSA and 0.1% sodium azide. Three million PBMCs were stained with CD19-FITC (SJ25C1, BD Bioscience, San Jose, CA) and CD3-APC (SK7, BD Bioscience, San Jose, CA) in FACS buffer, using the concentrations recommended by the manufacturer, for 30 minutes. After incubation, the cells were washed, resuspended in a FACS buffer, and stained with DAPI. Single cells positive for either CD19 or CD3 were sorted into a 96-well plate by BD FACSAria II Cell Sorter (BD Bioscience, San Jose, CA) containing PlexWell sample preparation buffer and the libraries were prepared following the manufacturer’s instruction (Part No. PW096, seqWell Inc, Beverly MA).
The sorted cells were lysed and full-length cDNA was generated from total RNA. cDNA was then purified, quantitated, and diluted to equal concentration across each plate. Diluted cDNA samples from each plate were then individually barcoded using the plexWell Sample Barcode Plate (SBL96). After stopping the sample barcoding (SB) reaction, each plate of 96 samples was pooled into a single tube and purified, and a pool barcoding (PB) reaction was performed using a different PB reagent for each SB reaction pool . The barcoded samples were purified and the libraries were amplified, followed by a final library purification. Agilent 2100 Bioanalyzer High Sensitivity DNA Assays were used to check the concentration and quality of the libraries prior to sequencing. The libraries were pooled in one run by the NovaSeq 6000 S1 system for sequencing.

tag: tissue

value: Peripheral blood

tag: cell line

value: tissue

value: CD19+ and CD3+ cells


title: PMc1_peripheral blood_151172_rep1

description: custom codeset

tag: disease


title: PMc1_peripheral blood_150507

description: custom codeset

tag: age at sample collection

value: Male

value: PMF, overt fibrotic stage


title: PMc1_peripheral blood_151336_rep1

description: custom codeset

value: Post PV-MF

value: Positive

tag: os_time_at last follow up (days)


title: ttc_OG_rep2

city: Columbus

first: Rachel

middle: D

last: Dreher

state: OH

address: 575 Children's Crossroad

institute: Nationwide Children's Hospital

description: Library name: sample 113

data_processing:
Low quality and adapter sequences were trimmed using Trim_galore
Trimmed sequences were mapped to hg38 using STAR with 2-pass approach
Reads were assigned to features using featureCounts
Normalization, differential analysis and statistical reports were done using DESeq2 and SARTools
Assembly: hg38
Supplementary files format and content: tab-delimited text file include log2FoldChange, p-values adjusted and other the statistics generated by DESeq2 for each sample

growth_protocol: A673 cells were grown in DMEM + 10% FBS + PSQ + 1% Sodium Pyruvate. TTC466 cells were grown in RPMI-1640 + 10% FBS + PSQ. CHP-100 cells were grown in McCoys 5A Medium + 10% heat inactivated FBS + PSQ.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen). 300ng of total RNA was used for library prep.
NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol:
Cells were seeded at 30% confluency and left to adhere overnight. After 24 hours, cells were dosed with DMSO or UM171, or OG-L002. Cells were harvested for RNA extraction after designated treatment time
KO cell lines were generated via CRISPR/Cas9 gene editing and electroporation delivery and are stable polyclonal populations that were seeded at 30% then harvested once confluent.

value: Ewing sarcoma

tag: genotype

value: LSD1 inhibition

tag: treatment

tag: batch


title: PMc1_peripheral blood_150658

description: custom codeset

value: myelofibrosis

tag: Sex

tag: diagnosis

value: Negative

value: Dead

tag: transplant_time (days)

tag: mpn24 category


title: ttc_96hrUM_rep3

description: Library name: sample 111

value: LSD1 knockdown


title: PMc1_peripheral blood_150778

description: custom codeset

tag: calr

tag: mpl

tag: dipss category

tag: mpn24 score


title: Patient C435, peripheral blood, CD19+ and  CD3+ cells

description: Library name: C435

tag: cell type


title: ttc_96hrUM_rep2

description: Library name: sample 110


title: PMc1_peripheral blood_150394

description: custom codeset

value: Female

value: Low

tag: mipss70 category

tag: os_status_at last follow up

value: Alive

tag: transform_time (days)


title: PMc1_peripheral blood_150155

description: custom codeset

tag: disease

tag: age at sample collection

value: Post ET-MF

value: High


title: PMc1_peripheral blood_151172_rep2

description: custom codeset

tag: os_time_at last follow up (days)


title: ttc_24hrUM_rep3

description: Library name: sample 108

tag: cell line

tag: genotype

tag: treatment


title: ttc_24hrUM_rep2

description: Library name: sample 107

tag: batch


title: PMc1_peripheral blood_140797

description: custom codeset

tag: Sex

tag: diagnosis

tag: transplant_time (days)


title: PMc1_peripheral blood_140960

description: custom codeset

tag: calr

tag: mpl

tag: mpn24 category


title: PMc1_peripheral blood_140736

description: custom codeset

tag: dipss category

tag: mpn24 score


title: PMc1_peripheral blood_140499

description: custom codeset

tag: mipss70 category

tag: os_status_at last follow up


title: PMc1_peripheral blood_140235

description: custom codeset

tag: disease

tag: transform_time (days)


title: ttc_6hrUM_rep2

description: Library name: sample 104

tag: cell type


title: ttc_6hrUM_rep3

description: Library name: sample 105

tag: cell line


title: ttc_6hrUM_rep1

description: Library name: sample 103

tag: genotype


title: ttc_OG_rep3

description: Library name: sample 114

tag: treatment


title: PMc1_peripheral blood_140203

description: custom codeset

tag: age at sample collection

tag: os_time_at last follow up (days)


title: ttc_24hrUM_rep1

description: Library name: sample 106

tag: batch


title: ttc_DMSO_rep3

description: Library name: sample 102

value: wildtype

value: DMSO


title: ttc_OG_rep1

description: Library name: sample 112


title: ttc_DMSO_rep2

description: Library name: sample 101


title: PMc1_peripheral blood_140089

description: custom codeset

tag: Sex

tag: diagnosis

tag: transplant_time (days)


title: PMc1_peripheral blood_140082

description: custom codeset

tag: calr

tag: mpl

tag: mpn24 category


title: PMc1_peripheral blood_130326

description: custom codeset

tag: dipss category

tag: mipss70 category

tag: mpn24 score


title: ttc_DMSO_rep1

description: Library name: sample 100


title: ttc_CRWT_rep1

description: Library name: sample 97

value: CRISPR WT


title: PMc1_peripheral blood_130780

description: custom codeset

tag: disease

value: Male

value: PMF, overt fibrotic stage

tag: os_status_at last follow up

tag: transform_time (days)


title: PMc1_peripheral blood_130332

description: custom codeset

value: Post PV-MF

value: Positive


title: PMc1_peripheral blood_130291

description: custom codeset


title: ttc_CRKO_rep2

description: Library name: sample 95

tag: cell line

tag: cell type

value: Ewing sarcoma

tag: genotype

value: LSD1 KO

value: CRISPR KO


title: ttc_CRWT_rep3

description: Library name: sample 99

tag: treatment


title: ttc_96hrUM_rep1

description: Library name: sample 109

tag: batch


title: PMc1_peripheral blood_120843

description: custom codeset

value: myelofibrosis

tag: age at sample collection

tag: Sex

value: Negative

tag: os_time_at last follow up (days)


title: ttc_CRWT_rep2

description: Library name: sample 98


title: CHP100_iEF714_rep2

description: Library name: sample 92

value: EWS::FLI rescue

value: iEWS::FLI shRNA, 714 EWS::FLI rescue


title: PMc1_peripheral blood_120948

description: custom codeset

value: Female

tag: diagnosis

tag: calr

value: Dead

tag: transplant_time (days)


title: PMc1_peripheral blood_120526

description: custom codeset

value: PMF, prefibrotic/early stage

tag: mpl

tag: dipss category

tag: mpn24 category


title: PMc1_peripheral blood_130168

description: custom codeset

tag: disease

tag: mipss70 category

tag: mpn24 score


title: CHP100_iEF714_rep3

description: Library name: sample 93

tag: cell line


title: PMc1_peripheral blood_130066_rep1

description: custom codeset

value: High

tag: os_status_at last follow up

tag: transform_time (days)


title: ttc_CRKO_rep1

description: Library name: sample 94

tag: cell type

tag: genotype

tag: treatment


title: ttc_CRKO_rep3

description: Library name: sample 96


title: CHP100_iEF197_rep3

description: Library name: sample 90

value: EWS::FLI knockdown

value: iEWS::FLI shRNA, empty pMSCV


title: PMc1_peripheral blood_120236

description: custom codeset

tag: age at sample collection

tag: Sex

value: Post ET-MF


title: CHP100_iEF714_rep1

description: Library name: sample 91


title: CHP100_iEF197_rep1

description: Library name: sample 88


title: CHP100_iEF197_rep2

description: Library name: sample 89


title: PMc1_peripheral blood_130259

description: custom codeset

tag: diagnosis

value: Alive

tag: os_time_at last follow up (days)


title: PMc1_peripheral blood_120072

description: custom codeset

value: Post PV-MF

tag: calr

tag: transplant_time (days)


title: PMc1_peripheral blood_110849

description: custom codeset

value: Male

value: Positive

tag: mpl

tag: dipss category


title: PMc1_peripheral blood_120204

description: custom codeset

tag: disease

value: PMF, overt fibrotic stage

tag: mpn24 category


title: CHP100_iLuc197_rep1

description: Library name: sample 85

value: Ewing sarcoma

value: wildtype

value: iLuc shRNA, empty pMSCV


title: CHP100_iLuc197_rep3

description: Library name: sample 87


title: PMc1_peripheral blood_130066_rep2

description: custom codeset

value: myelofibrosis

tag: mipss70 category

tag: mpn24 score


title: PMc1_peripheral blood_110559

description: custom codeset

value: Negative

tag: os_status_at last follow up


title: chp_KQ_AEresc_rep2

description: Library name: sample 83

tag: cell line

value: K661Q/A539E LSD1 rescue


title: chp_KQ_AEresc_rep3

description: Library name: sample 84

tag: cell type


title: CHP100_iLuc197_rep2

description: Library name: sample 86

tag: genotype


title: PMc1_peripheral blood_110294

description: custom codeset

value: Dead

tag: transform_time (days)


title: PMc1_peripheral blood_110268

description: custom codeset

tag: age at sample collection


title: chp_KQ_AEresc_rep1

description: Library name: sample 82

tag: treatment


title: chp_Nullresc_rep3

description: Library name: sample 81

value: wt LSD1 rescue


title: PMc1_peripheral blood_110655

description: custom codeset

tag: Sex

tag: diagnosis


title: PMc1_peripheral blood_120334

description: custom codeset

tag: calr

tag: os_time_at last follow up (days)


title: chp_Nullresc_rep2

description: Library name: sample 80


title: chp_Nullresc_rep1

description: Library name: sample 79


title: AB5075 SP total RNA replicate C

city: Iowa City

first: Michael

middle: J

last: Gebhardt

state: IA

address: 431 Newton Road, 200A EMRB

department: Department of Microbiology and Microbiology

institute: University of Iowa

description: Library name: Sample 8C

data_processing:
Demultiplexing, quality control and adapter trimming was perfromed with bcl-convert (v3.9.3).
Raw reads were mapped with bowtie2 version 2.4.5.
Alignment files (sam format) were converted to bam files and sorted with samtools (v 1.16.1).
Bam files were converted to bed format with bedtools (v 2.30.0) and normalized to a read depth of 10 million reads per sample
Bed files were converted to bigwig format using bedGraphToBigWig program (v 2.9)
Assembly: A. baumannii AB5075-UW chromosome and 3 plasmids; NZ_CP008706.1, NZ_CP008707.1, NZ_CP008708.1, and NZ_CP008709.1
Supplementary files format and content: Bigwig format files for viewing in genome browser.

organism: Acinetobacter baumannii

growth_protocol: Bacterial strains were grown at 37˚C , shaking at 200 rpm, in LB rich medium and samples 1&2 were collected at OD ≈ 0.6, samples 3&4 were collected at OD ≈ 2.0.

extract_protocol:
Standard TRI Reagent LS protocol was used for RNA extraction
Samples were treated with DNAse (Invitrogen)
Library preparation was performed with Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10 bp IDT for Illumina Indicies

treatment_protocol: Cells were harvested by centrifugation, washed with 1X PBS, and cell pellets snap frozen in a dry ice - ethanol bath.

value: WT

value: Growth:OD ≈ 2.0 in LB


title: AB5075 SP total RNA replicate A

description: Library name: Sample 8A


title: AB5075 SP total RNA replicate B

description: Library name: Sample 8B


title: AB5075 hfq-V SP total RNA replicate C

description: Library name: Sample 7C

value: hfq-VSVG


title: AB5075 hfq-V SP total RNA replicate B

description: Library name: Sample 7B


title: PMc1_peripheral blood_100266

description: custom codeset

tag: mpl

tag: transplant_time (days)


title: PMc1_peripheral blood_100032

description: custom codeset

tag: disease

tag: dipss category

value: High


title: chp_WTresc_rep3

description: Library name: sample 78

value: pMSCV_puro empty vector


title: chp_WTresc_rep1

description: Library name: sample 76


title: AB5075 hfq-V SP total RNA replicate A

description: Library name: Sample 7A


title: chp_WTresc_rep2

description: Library name: sample 77


title: AB5075 EP total RNA replicate B

description: Library name: Sample 6B

value: Growth:OD ≈ 0.6 in LB


title: AB5075 EP total RNA replicate C

description: Library name: Sample 6C


title: chp_KOresc_rep2

description: Library name: sample 74

value: LSD1 KO


title: AB5075 EP total RNA replicate A

description: Library name: Sample 6A


title: chp_KOresc_rep3

description: Library name: sample 75


title: AB5075 hfq-V EP total RNA replicate C

description: Library name: Sample 5C


title: chp_OG_rep3

description: Library name: sample 72

value: LSD1 inhibition

tag: batch


title: AB5075 hfq-V EP total RNA replicate B

description: Library name: Sample 5B


title: chp_OG_rep2

description: Library name: sample 71


title: AB5075 hfq-V EP total RNA replicate A

description: Library name: Sample 5A


title: chp_96hr_UM_rep3

description: Library name: sample 69

value: LSD1 knockdown


title: chp_OG_rep1

description: Library name: sample 70

value: Ewing sarcoma


title: Protoplast,cotyledonic somatic embryos (CSE),rep1

city: Guangzhou

first: xiaobing

last: wang

address: Higher Education Mega center, Panyu, Guangzhou

country: China

institute: Guangzhou University of Chinese Medicine

description:
Library name: Sample2
10x Genomics

data_processing:
The raw data was filtered, compared, quantified, and analyzed using the official Cell Ranger software to obtain the gene expression matrix for each cell. Subsequently, Seurat was employed for cell filtering, normalization, cluster classification, differential expression gene analysis of each cluster, and marker gene screening. Cell Ranger was utilized for quality control of sequencing data, where reads with low sequencing quality were removed. Preliminary statistical analyses were performed on the number of reads measured and the sequencing quality of each sample. Cell Ranger software harnessed the Spliced Transcripts Alignment to a Reference (STAR) tool to align cDNA sequence fragments to the reference genome of P. cablin.
Assembly: GZUCM_PCab_1.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Pogostemon cablin

source_name: cotyledonic somatic embryos

extract_protocol:
Protoplast suspensions were prepared from P. cablin GSE and CSE using the enzymatic hydrolysis method. To prepare the protoplast cleaning solution, 20 μL of 500× BSA and 3.43 mL of ddH2O were added to 6.25 mL of 0.8 M mannitol. The solution was then pre-cooled in a refrigerator at 4°C. To prepare the enzyme solution, cellulose R10 (0.075 g), pectinase (0.025 g), 3.125 mL of 0.8 M mannitol, 500 μL of 0.1 M MES (pH 5.7), 500 μL of 0.2 M KCl, and 870 μL of ddH2O were weighed or measured and put into a 15 mL centrifuge tube and incubate the tube in a 55℃-water bath for 10 minutes, with vortexing and mixing performed twice during this period. Once the solution had cooled to room temperature, 25 μL of 500× BSA and 50 μL of 1 M CaCl2 were added. The solution was then mixed thoroughly and filtered through a 0.22 μm filter into another 15 mL centrifuge tube. The P. cablin GSE and CSE were washed twice with protoplast washing solution. Subsequently, they were transferred to centrifuge tubes containing enzyme solution and incubated on a shaking table at 30 ℃ with 75 rpm in the dark for 0.5-24 h. A 5 μL aliquot of 0.4% trypan blue staining solution was mixed with 5 μL of protoplast suspension. Cell concentration and viability rates were then determined using the Countess® II automated cell counter. Protoplasts with greater than 80% viability were used for 10x single-cell library construction within 30 min.
To construct scRNA-seq library, barcode-encoded gel beads were mixed with a blend of cells and enzymes and subsequently separated by oil to form Gel Beads-In-Emulsions (GEMs) within a reservoir. After being dissolved, the gel beads freed the capture sequence that incorporated the barcode sequence, and this sequence was later converted into cDNA through reverse transcription. The samples were then labeled. The gel beads were crushed, and the oil droplets were broken up, after which PCR amplification was performed, with the cDNA serving as the template. All GEMs were then mixed to construct sequencing library. The cDNA was enzymatically cleaved into 200-300 bp fragments and subjected to second-generation sequencing library construction steps, followed by PCR to obtain the DNA library. The Illumina HiSeq2500 sequencing platform (Genedenovo Biotechnology Co., Ltd, Guangzhou, China) was utilized to conduct high-throughput sequencing of the prepared libraries.

tag: tissue

value: cotyledonic somatic embryos

tag: sample type

value: Protoplast


title: chp_96hr_UM_rep1

description: Library name: sample 67

tag: cell line


title: chp_24hr_UM_rep3

description: Library name: sample 66

tag: cell type