title: H3K9Ac G217B 50Ent RT A

description: Library name: H3K9Ac_RT_50Ent_A

tag: replicate

value: A

tag: temperature

value: RT

tag: treatment

tag: antibody

tag: cell type

value: fungal cell


title: H3K9Ac G217B DMSO RT C

status: Public on Jan 26 2026

type: SRA

city: San Francisco

first: Mark

last: Voorhies

state: CA

address: 513 Parnassus, S472

department: Microbiology and Immunology

country: USA

institute: University of California

description: Library name: H3K9Ac_RT_DMSO_C

library_source: genomic

data_processing:
Paired-end reads were aligned to the Histoplasma ohiense G217B genome (GCA_017607445.1) using BOWTIE2 version 2.4.2 with default parameters. Per sample promoter signal was quantified by counting read pairs in each promoter, log2 transforming with pseudocount of 1 to handle missing data, and normalizing to the signal in the NPS1 negative control region. This negative control region was defined as the middle 500 bp of NPS1 (I7I48_05472, JAEVHH010000002: 444765..449764 (+)). Differential enrichment was then calculated as the difference of the means of the log2 signal over replicates from each condition.
Assembly: GCA_017607445.1
Supplementary files format and content: Processed data file for each sample is in Excel-compatible tab-delimited text conforming to JavaTreeView extended CDT format.  Each row represents the promoter of one gene with the systematic gene name given redundantly in the GID, UNIQID, and NAME columns.  The next columns give normalized read density (D_f), read counts (R_f), and promoter size (1kb 5' of CDS ATG in all cases), and log2 normalized read density.  A GWEIGHT column is included for JavaTreeView compatibility.  A combined table of differential histone modification ChIP enrichment over all experiments is given in the accompanying paper as Table S11.

molecule: genomic DNA

organism: Histoplasma ohiense

source_name: fungal cell

growth_protocol: Cultures used for growth assays, RNA-seq and ChIP-seq studies were set up in triplicate biological replicates. When possible, inoculum from a single colony grown at 37 °C was used to start a liquid culture in HMM media. This liquid culture was passaged every 2-3 days in HMM media for a total of 2 passages before being used to inoculate a master culture in HMM + GlcNAc at an OD600 of 0.2 that was then aliquoted into replicates with equal volumes of each HDACi concentration being tested or DMSO. Cultures were incubated for 2 days at 37 °C and 5 % CO2 or at RT with shaking. Microscopy samples were harvested and fixed for 30 minutes with a solution of 4 % paraformaldehyde (PFA) every 24 hours for up to 3 days following incubation and stored long-term at 4 °C in PBS. Samples for genomic DNA isolation were harvested through centrifugation. Cell pellets used for isolating RNA, and protein samples were harvested through filtration using SFCA Membrane Nalgene Rapid-Flow Sterile Disposable Bottle Top Filters (Fisher 09-740-22G). 10-25 mL of culture was harvested from each flask and immediately flash frozen in liquid nitrogen before being stored at -80 °C.

extract_protocol:
Cultures processed for ChIP-seq were crosslinked with formaldehyde (Polysciences 18814-10) added to a final concentration of 1 % and kept under culture conditions (shaking at 37 °C with 5 % CO2 or ambient RT) for 20 minutes to allow fixing to take place. Crosslinking was quenched with glycine added to a final concentration of 125 mM for 5 minutes at RT. Fixed cells were pelleted at 3000 g for 10 minutes at 4 °C and washed twice with TBS (20 mM Tris-HCl (pH 7.5), 150 mM NaCl). Washed cells were harvested through filtration, aliquoted into pellets of equal mass (between 150-300 mg/tube) and flash frozen in liquid nitrogen as described above. Frozen pellets were resuspended in lysis buffer (50 mM Hepes/KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % sodium deoxycholate, protease/phosphatase inhibitors) at 4 °C before being bead beat with 500 µL of 0.5 mm zirconia beads in 5 x 1 minute cycles at RT with 2 minute rests on ice in between. The resulting lysate was then spun down at 8000 rpm for 10 minutes at 4 °C to isolate the insoluble chromatin fraction. This chromatin pellet was resuspended in 600-900 µL of lysis buffer and sonicated at 4 °C using the Diagenode Bioruptor® Pico for 30-35 cycles (30s on, 30s off). Sonicated samples were spun down for 5 min at 14,000 rpm at 4 °C to pellet cell debris and aliquots for input DNA were reserved at -20 °C in TE + 1 % SDS. Input samples were also used to assess shearing using a High Sensitivity DNA Bioanalyzer chip from Agilent. Equal lysate volumes were aliquoted for each IP to be performed and brought to a final volume of 500 µL with lysis buffer and 20 µg of each polyclonal ⍺-Ryp antibody (Ryp1: 3873, Ryp2: 387, and Ryp3: 356) or 3 µg of a ChIP-grade monoclonal ⍺-histone-acetyl antibody (H3K9Ac: ab177177 , H3K14Ac: ab52946, H4K16Ac: ab109463). Samples were incubated overnight with agitation at 4 °C before being incubated with 50 µL of a 50% slurry of Protein A Dynabeads (Life Technologies Corporation 10002D) pre-washed 2x with TBS and 3x lysis buffer for 2 hours at 4 °C with agitation.  Immunoprecipitated DNA was recovered through pulldown on Protein A beads using a magnetic rack. Pellets containing DNA-protein complexes were washed 2x in lysis buffer, 2x with high-salt (500 mM NaCl) lysis buffer, 2x with wash buffer (10 mM Tris/HCl (pH 8.0), 250 mM LiCl, 0.5 % NP-40, 0.5 % Na-deoxycholate, 1 mM EDTA) and 1x with TE before adding elution buffer (50 mM Tris/HCl (pH 8.0), 10 mM EDTA, 1 % SDS) and incubating at 65 °C for 10 minutes. DNA was eluted using a magnetic rack and the resulting beads were subjected to second round of resuspension and elution with 150 µl TE + 0.65 % SDS and pooled with the initial eluate to maximize total yield of DNA. IP and input samples were treated with 1 µL of Proteinase K (20 mg/mL Qiagen 19131) and incubated at 65 °C for approximately 16 hours. IP and Input DNA samples were then treated with 2 µg of RNase A (Qiagen) and incubated at 37 °C for 1 hour. DNA was then purified using the Zymo ChIP DNA Clean & Concentrator Kit (D5205) and eluted in 31 µL of ddH2O or TE.
Purified IP and input DNA were used for Illumina library preparation using the NEBNext Ultra II DNA Library Prep Kit (NEB E7103S) and Illumina dual-indexed primer pairs sourced from the UCSF CAT. The quality and size distribution of each library was assessed using the Agilent High Sensitivity DNA Bioanalyzer Kit (Agilent Technologies 5067-4626) to ensure proper fragment size and the absence of contaminating adapters. Final library concentrations were measured using a Qubit HS dsDNA assay kit (Life Technologies Q33230) and used to pool equimolar amounts of each sample into final libraries for sequencing. Pooled libraries were used for paired-end sequencing using one NovaSeq X 10B lane at the UCSF CAT.

tag: genotype

value: C

value: DMSO


title: LM_SD_15

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

library_source: transcriptomic

data_processing:
The 10x SpaceRanger pipeline (Space Ranger v1.3.1, bcl2fastq v2.20) was used to demultiplex and generate FASTQ files. FASTQ files were input into the SpaceRanger FFPE count algorithm along with matching H&E .tiff images for alignment to the reference probe set and generation of count matrices for each Visium capture area.
H&E images of sections captured for stRNA-seq analysis were annotated for pathological features of interest by an experienced thoracic pathologist (EB) using Loupe Browser v6 (10x Genomics).
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes filtered after Space Ranger tissue detection
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial transcriptomics

molecule: polyA RNA

organism: Homo sapiens

source_name: lung adenocarcinoma

extract_protocol:
New 5 𝜇m tissue sections were cut by a microtome, placed in a 42°C RNase-free water bath and manually transferred onto 6.5 x 6.5 mm tissue capture areas on Visium Spatial Gene Expression Slides (PN-1000185, 10x Genomics). Tissues were deparaffinized, H&E stained, imaged with a Leica Aperio AT2, and de-crosslinked according to the manufacturer’s recommended protocol, with the following user modifications made to deparaffinization to prevent tissue detachment: 1) the 15 min incubation step during deparaffinization was removed, 2) after immersion in 96% ethanol, one 85%, one 70% and one 50% ethanol immersion for 3 min each was added.
Probe hybridization was performed with the Visium Human Transcriptome Probe Kit (PN-1000364), followed by probe ligation, extension and elution for downstream qPCR cycle determination and 10x library construction with the Visium FFPE Reagent Kit (PN-1000362).

tag: tissue

value: lung adenocarcinoma

tag: sample type

value: FFPE

tag: patient id

tag: block id

tag: sample id

tag: slide id

tag: cohort

value: validation cohort

tag: novel grade

value: NST

tag: tnm 8th_edition_stage

tag: age

tag: gender

value: F

tag: smoking status

value: Former

tag: capture frame_vi

tag: sequence batch

tag: passed qc

value: TRUE

tag: site

value: LHMC

tag: dual index_id


title: DIPGXIII_RNAseq_CTL.2

city: Houston

first: Jamie

middle: N.

last: Anastas

state: TX

address: 1 Baylor Plaza

department: Neurosurgery

institute: Baylor College of Medicine

description: Library name: XIII_RNAseq_CTLsg.2

data_processing:
RNAseq reads were aligned to hg38 using STAR
Counts tables were generated using featureCounts
Assembly: hg38
Supplementary files format and content: tab-delimited text files with transcript counts

source_name: glioma

growth_protocol: SU-DIPGXIII cells were maintained as gliomaspheres in DMG media (50:50 DMEM/F12 and Neurobasal A, supplements with B27 minus Vitamin A, heparin, sodium pyruvate, GlutaMAX, MEM non-essential amino acids,  HEPES, Antibiotic-Antimyotic, Heparin, hPDGF-AA, hPDGF-BB, hFGF154, and hEGF) in a humidified chamber with 5% CO2 at 37C

extract_protocol:
RNA was extracted using TRIzol reagent and polyA transcripts were purified.
Paired-end libraries were generated from RNAseq cDNA using an Illumina DNA-Seq library preparation kits (Illumina Technologies).

treatment_protocol: For RNAseq following treatment with drugs to inhibit KAT2A/KAT2B, 250,000 live SU-DIPGXIII cells were collected after 25 hours of treatment with DMSO, 10 µM GSK4027 (bromodomain inhibitor), or 10 µM CPTH2 (catalytic HAT inhibitor).

tag: tissue

value: glioma

tag: cell line

value: SU-DIPGXIII

tag: cell type

value: diffuse midline glioma

tag: genotype

value: WT


title: MCL-017 [6929671111_R04C02]

type: genomic

city: Wantirna South

first: Rust

last: Turakulov

state: Victoria

address: u23 105 Mountain Hwy

department: Bioinformatics

country: Australia

institute: AGRF

description:
6929671111_R04C02
MCL_SOX11P

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: Mantle Cell Lymphoma. SOX11: Positive, Post-treatment, MCL_morphology: classic, Nodal: Yes, Series_origin: PAMPLONA

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

value: Mantle Cell Lymphoma. SOX11:Positive, Post-treatment, MCL_morphology:classic, Nodal:Yes, Series_origin:PAMPLONA

value: Lymph node

tag: group

value: Ref set

tag: material

value: Frozen

tag: Sex

value: M

tag: mcf


title: MCL-015 [6929671111_R02C02]

description:
6929671111_R02C02
MCL_SOX11P

source_name: Mantle Cell Lymphoma. SOX11: Positive, Diagnosis, Pre-treatment, MCL_morphology: blastoid, Nodal: Yes, Series_origin: HCP

value: Mantle Cell Lymphoma. SOX11:Positive, Diagnosis, Pre-treatment, MCL_morphology:blastoid, Nodal:Yes, Series_origin:HCP


title: H3K9Ac G217B DMSO RT B

description: Library name: H3K9Ac_RT_DMSO_B

tag: replicate

value: B

tag: temperature

value: RT

tag: treatment

value: DMSO

tag: antibody

value: fungal cell


title: LM_SD_9

value: lung adenocarcinoma

tag: sample type

value: FFPE

tag: patient id

tag: block id

tag: sample id

tag: slide id

tag: cohort

value: validation cohort

tag: novel grade

value: VI

tag: tnm 8th_edition_stage

tag: age

tag: gender

value: F

tag: smoking status

value: Current

tag: capture frame_vi


title: MCL-019 [6929671131_R02C01]

description:
6929671131_R02C01
MCL_SOX11P

source_name: Mantle Cell Lymphoma. SOX11: NegativeMCL_morphology: classic

tag: tissue

value: Mantle Cell Lymphoma. SOX11:NegativeMCL_morphology:classic

value: Soft tissue

tag: group

tag: material

tag: Sex

tag: mcf

value: MG1 :BCN


title: LM_SD_1216_12

tag: sample type

value: NST

value: IIA

value: Former

tag: sequence batch

tag: passed qc

value: TRUE

tag: site

value: LHMC

tag: dual index_id


title: Patient RRx_034, cells from human femoral neck cortical region isolated using collagenase A + dispase

city: SYDNEY

first: Peter

last: Croucher

state: NSW

address: 384 VICTORIA ST, DARLINGHURST NSW 2010

institute: Garvan Institute of Medical Research

description: Library name: RRx_034_FNG_cort_v2

library_source: transcriptomic single cell

data_processing:
Single-cell sequencing data was demultiplexed, aligned and quantified using Cell Ranger (10x Genomics) against the human reference genome (10x Genomics, July 7, 2020 release) with default parameters.
Filtering and quality control was performed using Seurat (Stuart et al., 2019) on raw data where cells were retained satisfying thresholds of both <10% mitochondria content and number of genes of at least 300. ‘Log Normalisation’ was used for normalization.
Cell types were identified using the Seurat clustering algorithm as described above, using both discrete and continuous variations in gene expression across cell clusters. Cell types were annotated based on canonical markers and markers identified in published bulk RNAseq and scRNA-seq datasets. For cell clusters without previous annotations from the literature, we used cluster-specific gene programs detailed below to annotate cells at the resolution of Leiden clusters.
Assembly: Human GRCh38 (July 7 2020 release)
Supplementary files format and content: Barcodes, features and matrix files generated from Cell Ranger
Supplementary files format and content: Seurat object saved as Rds format

source_name: Femoral neck

extract_protocol:
Single cell transcriptomic libraries were generated using the Chromium Single Cell 3’ v2 Reagent Kit. Up to 20,000 cells were loaded into each lane of Chromium Next GEM Chip K Single Cell Kit (10x Genomics) to achieve a recovery cell number of approximately 10,000 cells.
cDNA libraries were generated according to manufacturer’s instructions (10x Genomics).

treatment_protocol: Femoral head bone samples were obtained from patients with osteoarthritis undergoing total hip arthroplasty. Femoral head samples were collected in RPMI medium and stored at 4°C for up to 18 hours prior to cell isolation. Bone cores were isolated from the femoral head using an electric core drill. Bone fragments from the femoral neck regions were obtained by cutting using secateurs. Bone cores and fragments were cut up into smaller bone chips using surgical blades and scissors.  Cells were removed from the bone chips using 2mg/ml of collagenase A, or 2mg/ml collagenase IV and 2.5mg/ml of dispase for 30 mins at 37ºC. After digestion, bone chips were vortexed for 10s and the supernatant containing digested cells was filtered through a 100μm filter into collection tubes containing 10% fetal calf serum (FCS; Bovogen Biologicals). Cells were then stained with anti-human CD235a (RBC marker), anti-human CD45, DAPI and FAC-sorted. DAPI-CD235a-CD45- were pooled with DAPI-CD235a-CD45+ 1:1 prior to capture.

value: Femoral neck

tag: sample preparation

value: Tissue digested with collagenase A and dispase

value: Adult


title: LM_SD_1216_14

value: lung adenocarcinoma

tag: patient id

tag: block id

tag: sample id

tag: slide id

tag: cohort

tag: novel grade


title: Input G217B 50Ent RT C

description: Library name: input_RT_50Ent_C

tag: genotype

tag: replicate

value: C

tag: temperature

value: RT

tag: treatment

tag: antibody

value: Input

tag: cell type

value: fungal cell


title: MCL-014 [9297953080_R06C02]

description:
9297953080_R06C02
MCL_SOX11N_A

source_name: Mantle Cell Lymphoma. SOX11: Negative, Diagnosis, Pre-treatment, MCL_morphology: smallcell, Nodal: No, Series_origin: HCP

tag: tissue

value: Mantle Cell Lymphoma. SOX11:Negative, Diagnosis, Pre-treatment, MCL_morphology:smallcell, Nodal:No, Series_origin:HCP

value: Peripheral Blood

tag: group

value: Ref set

tag: material

value: Frozen

tag: age

tag: Sex

value: F

tag: mcf


title: LM_SD_13

tag: sample type

value: FFPE

tag: patient id

tag: block id

value: validation cohort

value: NST

tag: tnm 8th_edition_stage

value: IB

tag: gender

tag: smoking status

tag: capture frame_vi

tag: sequence batch

tag: passed qc

tag: site

tag: dual index_id


title: H3K9Ac G217B DMSO RT A

description: Library name: H3K9Ac_RT_DMSO_A

tag: genotype

tag: replicate

value: A

tag: temperature

tag: treatment

value: DMSO

tag: antibody

tag: cell type


title: MCL-016 [6929671111_R03C02]

description:
6929671111_R03C02
MCL_SOX11P

source_name: Mantle Cell Lymphoma. SOX11: Positive, Diagnosis, Pre-treatment, MCL_morphology: pleomorphic, Nodal: Yes, Series_origin: HCP

tag: tissue

value: Mantle Cell Lymphoma. SOX11:Positive, Diagnosis, Pre-treatment, MCL_morphology:pleomorphic, Nodal:Yes, Series_origin:HCP

value: Lymph node

tag: group

tag: material

tag: age

tag: Sex

value: M

tag: mcf


title: Patient RRx_034, cells from human femoral neck isolated using collagenase A + dispase

description: Library name: RRx_034_FNG

value: Femoral neck

tag: sample preparation

value: Tissue digested with collagenase A and dispase

value: Adult


title: Patient RRx_030, cells from human femoral neck cortical region isolated using collagenase A + dispase

description: Library name: RRx_030_FNG_cort


title: Patient RRx_032, cells from human femoral neck cortical region isolated using collagenase A + dispase

description: Library name: RRx_032_FNG_cort


title: Patient RRx_032, cells from human femoral neck isolated using collagenase A + dispase

description: Library name: RRx_032_FNG


title: MCL-018 [6929671111_R02C01]

description:
6929671111_R02C01
MCL_SOX11P

source_name: Mantle Cell Lymphoma. SOX11: Positive, Diagnosis, Pre-treatment, MCL_morphology: classic, Nodal: Yes, Series_origin: HCP

value: Mantle Cell Lymphoma. SOX11:Positive, Diagnosis, Pre-treatment, MCL_morphology:classic, Nodal:Yes, Series_origin:HCP


title: Input G217B DMSO RT C

description: Library name: input_RT_DMSO_C

value: C

value: RT

value: Input

value: fungal cell


title: LM_SD_1216_8

value: lung adenocarcinoma

tag: sample type

value: FFPE

tag: patient id

tag: block id

tag: sample id

tag: slide id

tag: cohort

tag: novel grade

value: VI

tag: tnm 8th_edition_stage

tag: gender

tag: smoking status

value: Former

tag: capture frame_vi

tag: sequence batch

value: TRUE

value: LHMC


title: MCL-013 [6929671111_R01C02]

description:
6929671111_R01C02
MCL_SOX11P

source_name: Mantle Cell Lymphoma. SOX11: Positive, Diagnosis, Pre-treatment, MCL_morphology: classic, Nodal: Yes, Series_origin: TOLEDO

tag: tissue

value: Mantle Cell Lymphoma. SOX11:Positive, Diagnosis, Pre-treatment, MCL_morphology:classic, Nodal:Yes, Series_origin:TOLEDO

tag: group

value: Ref set

tag: material

value: Frozen

value: F


title: Input G217B 50Ent RT A

description: Library name: input_RT_50Ent_A

tag: genotype

tag: replicate

value: A

tag: temperature

tag: treatment

tag: antibody

tag: cell type


title: DIPGXIII_RNAseq_CTL.1

description: Library name: XIII_RNAseq_CTLsg.1

value: glioma

tag: cell line

value: SU-DIPGXIII

value: diffuse midline glioma

value: WT


title: LM_SD_7

tag: sample type

tag: patient id

tag: block id

tag: sample id

tag: slide id

tag: cohort

value: validation cohort

value: LMP

tag: age

value: Current

tag: passed qc

tag: site

tag: dual index_id


title: MCL-012 [9341679044_R05C02]

description:
9341679044_R05C02
MCL_SOX11P

tag: tissue

value: Mantle Cell Lymphoma. SOX11:Positive, Diagnosis, Pre-treatment, MCL_morphology:classic, Nodal:Yes, Series_origin:HCP

value: Peripheral Blood

tag: group

tag: material

tag: Sex

tag: mcf


title: LM_SD_10

value: lung adenocarcinoma

value: FFPE

tag: novel grade

value: NST

tag: tnm 8th_edition_stage

tag: gender

value: M

tag: smoking status

value: Former

tag: capture frame_vi

tag: sequence batch


title: Input G217B DMSO RT B

description: Library name: input_RT_DMSO_B

tag: genotype

tag: replicate

value: B

tag: temperature

value: RT

tag: treatment

value: DMSO

tag: antibody

value: Input

tag: cell type

value: fungal cell


title: MCL-010 [9341679044_R04C02]

description:
9341679044_R04C02
MCL_SOX11N_A

source_name: Mantle Cell Lymphoma. SOX11: Negative, Pre-treatment, Pre-treatment, MCL_morphology: smallcell, Nodal: No, Series_origin: HCP

tag: tissue

value: Mantle Cell Lymphoma. SOX11:Negative, Pre-treatment, Pre-treatment, MCL_morphology:smallcell, Nodal:No, Series_origin:HCP

value: Ref set

value: Frozen

tag: age


title: LM_SD_6

tag: sample type

tag: patient id

tag: block id

tag: sample id

tag: slide id

tag: cohort

value: validation cohort

value: VI

value: IB

tag: passed qc

value: FALSE

tag: site

value: LHMC

tag: dual index_id


title: MCL-011 [9341679044_R06C02]

description:
9341679044_R06C02
MCL_SOX11P

source_name: Mantle Cell Lymphoma. SOX11: Positive, Diagnosis, Pre-treatment, MCL_morphology: blastoid/pleomorphic, Nodal: No, Series_origin: HCP

value: Mantle Cell Lymphoma. SOX11:Positive, Diagnosis, Pre-treatment, MCL_morphology:blastoid/pleomorphic, Nodal:No, Series_origin:HCP

value: Peripheral Blood

tag: group

tag: material

tag: Sex

tag: mcf


title: Patient RRx_026, cells from human femoral neck cortical region isolated using collagenase A + dispase

description: Library name: RRx_026_FNG_cort

value: Femoral neck

tag: sample preparation

value: Tissue digested with collagenase A and dispase

value: Adult


title: LM_SD_5

value: lung adenocarcinoma

value: FFPE

tag: novel grade

value: NST

tag: tnm 8th_edition_stage

tag: gender

value: M

tag: smoking status

value: Former

tag: capture frame_vi

tag: sequence batch

value: TRUE


title: MCL-009 [7990895143_R02C02]

description:
7990895143_R02C02
MCL_SOX11P

tag: tissue

value: Mantle Cell Lymphoma. SOX11:Positive, Diagnosis, Pre-treatment, MCL_morphology:classic, Nodal:Yes, Series_origin:HCP

value: Test set

value: Frozen

tag: age

value: BCN


title: LM_SD_2

tag: sample type

tag: patient id

tag: block id

tag: sample id

tag: slide id

tag: cohort

value: validation cohort

value: VI

value: F

value: Current


title: LM_SD_3

tag: passed qc

tag: site

value: LHMC

tag: dual index_id


title: Patient RRx_026, cells from human femoral neck isolated using collagenase A + dispase

description: Library name: RRx_026_FNG

value: Femoral neck

tag: sample preparation

value: Tissue digested with collagenase A and dispase


title: H3K14Ac G217B 50Ent 37 C

description: Library name: H3K14Ac_37_50Ent_C

tag: genotype

tag: replicate

value: C

tag: temperature

tag: treatment

tag: antibody

tag: cell type

value: fungal cell


title: LM_SD_4

tag: tissue

value: lung adenocarcinoma

value: FFPE

tag: novel grade

tag: tnm 8th_edition_stage

value: IB

tag: age

tag: gender

tag: smoking status

tag: capture frame_vi

tag: sequence batch


title: MCL-008 [7990895143_R01C01]

description:
7990895143_R01C01
MCL_SOX11N_A

value: Mantle Cell Lymphoma. SOX11:Negative, Diagnosis, Pre-treatment, MCL_morphology:smallcell, Nodal:No, Series_origin:HCP

value: Peripheral Blood

tag: group

value: Ref set

tag: material

tag: Sex

value: M

tag: mcf


title: Input G217B DMSO RT A

description: Library name: input_RT_DMSO_A

tag: genotype

tag: replicate

value: A

value: RT

value: DMSO

value: Input


title: MCL-006 [7990895143_R02C01]

description:
7990895143_R02C01
MCL_SOX11N_B

source_name: Mantle Cell Lymphoma. SOX11: Negative, Pre-treatment, Pre-treatment, MCL_morphology: smallcell, Nodal: No, Series_origin: GIRONA

value: Mantle Cell Lymphoma. SOX11:Negative, Pre-treatment, Pre-treatment, MCL_morphology:smallcell, Nodal:No, Series_origin:GIRONA

value: Frozen


title: H3K14Ac G217B DMSO 37 C

description: Library name: H3K14Ac_37_DMSO_C

tag: temperature

tag: treatment


title: Patient RRx_024, ALPL-high cells from human femoral neck isolated using collagenase A + dispase

description: Library name: RRx_024_FNG_ALPLhi

value: Femoral neck

tag: sample preparation

value: Adult


title: MCL-007 [7990895143_R05C01]

description:
7990895143_R05C01
MCL_SOX11N_B

tag: tissue

value: Mantle Cell Lymphoma. SOX11:Negative, Pre-treatment, Pre-treatment, MCL_morphology:smallcell, Nodal:No, Series_origin:HCP

value: F


title: Patient RRx_024, ALPL-negative cells from human femoral neck isolated using collagenase A + dispase

description: Library name: RRx_024_FNG_ALPLneg_CD45pos

value: Tissue digested with collagenase A and dispase


title: H3K14Ac G217B 50Ent 37 B

description: Library name: H3K14Ac_37_50Ent_B

value: B

tag: antibody

tag: cell type

value: fungal cell


title: Patient RRx_024, ALPL-low cells from human femoral neck isolated using collagenase A + dispase

description: Library name: RRx_024_FNG_ALPLlo

tag: age


title: LM_SD_11

value: lung adenocarcinoma

tag: sample type

value: FFPE

tag: patient id

tag: block id

tag: sample id

tag: slide id

tag: cohort

value: validation cohort

tag: novel grade

value: VI

tag: tnm 8th_edition_stage

tag: gender

value: Current

tag: passed qc

value: TRUE

tag: site

value: LHMC

tag: dual index_id


title: MCL-416

data_processing:
Sample sequencing was performed on the Illumina NextSeq 500 to generate paired-end 50- nucleotide reads (discovery cohort) or Illumina HiSeq 2500 to generate paired-end 75-nucleotide reads (validation cohort).
Basespace (Illumina) was used for demultiplexing and FASTQ file generation.
A Nextflow v21.10.6 RNA-Seq pipeline aligned reads using hg38 and STAR v2.6.0c.
Counts were calculated using RSEM v1.3.1 using Ensembl v108 annotation. Quality metrics were calculated with STAR and RSeQC. RNA-seq processing pipeline software (https://github.com/compbiomed/RNA_Seq/blob/master/RNA_Seq.nf): nextflow v21.10.16, star v2.6.0c, rsem v1.3.1, FastQC v0.11.7, Picard tools v2.18.11, GATK v3.8-1, rseqc v3.0.0, multiqc v1.6, samtools v1.9.
Assembly: hg38
Supplementary files format and content: exp_count.txt: tab-delimited text file with raw expected counts for each sample

molecule: total RNA

extract_protocol:
Total RNA was extracted from FFPE tissue with the Qiagen AllPrep DNA/RNA Universal Kit.
Exome-targeted sequencing libraries were prepared with the Illumina TruSeq RNA Exome Library Prep Kit.

value: discovery cohort

tag: mean tin

value: BMC

tag: sequence batch


title: MCL-004 [6929689010_R02C02]

description:
6929689010_R02C02
MCL_SOX11N_A

source_name: Mantle Cell Lymphoma. SOX11: Negative, Post-treatment, MCL_morphology: smallcell, Nodal: No, Series_origin: HCP

tag: tissue

value: Mantle Cell Lymphoma. SOX11:Negative, Post-treatment, MCL_morphology:smallcell, Nodal:No, Series_origin:HCP

value: Peripheral Blood

tag: group

value: Ref set

tag: material

value: Frozen

tag: Sex

tag: mcf


title: Patient RRx_024, cells from human femoral head isolated using collagenase A + dispase, from region affected by OA

description: Library name: RRx_024_FHG_Dis

source_name: Femoral head

value: Femoral head

tag: sample preparation

tag: age

value: Adult


title: Patient RRx_030, cells from human femoral neck isolated using collagenase A + dispase

description: Library name: RRx_030_FNG

value: Femoral neck

value: Tissue digested with collagenase A and dispase


title: MCL-005 [7990895143_R03C02]

description:
7990895143_R03C02
MCL_SOX11P

value: Mantle Cell Lymphoma. SOX11:Positive, Diagnosis, Pre-treatment, MCL_morphology:classic, Nodal:Yes, Series_origin:HCP

value: Lymph node

value: F


title: LM_SD_1216_1

value: lung adenocarcinoma

tag: sample type

value: FFPE

tag: patient id

tag: block id

tag: sample id

tag: slide id

value: validation cohort

value: VI

value: IB

value: M

tag: smoking status

value: Former

tag: capture frame_vi


title: Patient RRx_024, cells from human femoral head isolated using collagenase A + dispase, from region unaffected by OA

description: Library name: RRx_024_FHG_Normal


title: H3K14Ac G217B DMSO 37 B

description: Library name: H3K14Ac_37_DMSO_B

tag: genotype

tag: replicate

value: B

tag: temperature

tag: treatment

value: DMSO

tag: antibody

tag: cell type

value: fungal cell


title: LM_SD_16

tag: tissue

tag: cohort

tag: novel grade

tag: tnm 8th_edition_stage

tag: gender

tag: sequence batch

tag: passed qc

value: TRUE

tag: site

value: LHMC

tag: dual index_id


title: Patient RRx_022, ALPL-negative cells from human femoral neck isolated using collagenase A + dispase

description: Library name: RRx_022_FNG_ALPLneg_CD45pos

value: Femoral neck

tag: sample preparation

tag: age

value: Adult


title: Input G217B 50Ent RT B

description: Library name: input_RT_50Ent_B

tag: genotype

value: RT

value: Input


title: H3K14Ac G217B 50Ent 37 A

description: Library name: H3K14Ac_37_50Ent_A

tag: replicate

value: A


title: MCL-003 [7990895143_R04C01]

description:
7990895143_R04C01
MCL_SOX11N_A

source_name: Mantle Cell Lymphoma. SOX11: Negative, Pre-treatment, Pre-treatment, MCL_morphology: classic, Nodal: No, Series_origin: HCP

value: Mantle Cell Lymphoma. SOX11:Negative, Pre-treatment, Pre-treatment, MCL_morphology:classic, Nodal:No, Series_origin:HCP

value: Peripheral Blood

tag: group

value: Ref set

tag: material

value: Frozen

tag: Sex

tag: mcf


title: H3K14Ac G217B DMSO 37 A

description: Library name: H3K14Ac_37_DMSO_A

source_name: fungal cell

tag: temperature

tag: treatment

tag: antibody

tag: cell type


title: H3K9Ac G217B 50Ent 37 A

description: Library name: H3K9Ac_37_50Ent_A


title: MCL-392

source_name: lung adenocarcinoma

tag: tissue

value: lung adenocarcinoma

tag: sample type

value: FFPE

tag: patient id

tag: cohort

value: discovery cohort

tag: novel grade

value: NST

tag: tnm 8th_edition_stage

value: IB

tag: mean tin

value: BMC


title: MCL-001 [9721365200_R01C02]

description:
9721365200_R01C02
MCL_SOX11P

source_name: Mantle Cell Lymphoma.SOX11: Positive, Diagnosis, Pre-treatment, MCL_morphology: classic/blastic, Nodal: Yes, Series_origin: TERRASSA

value: Mantle Cell Lymphoma.SOX11:Positive, Diagnosis, Pre-treatment, MCL_morphology:classic/blastic, Nodal:Yes, Series_origin:TERRASSA

value: Lymph node

tag: age

value: M


title: MCL-189

value: LMP

tag: passed qc

value: FALSE

tag: site

tag: sequence batch


title: MCL-002 [7990895143_R03C01]

description:
7990895143_R03C01
MCL_SOX11N_A

source_name: Mantle Cell Lymphoma. SOX11: Negative, Diagnosis, Pre-treatment, MCL_morphology: pleomorphic, Nodal: No, Series_origin: HCP

value: Mantle Cell Lymphoma. SOX11:Negative, Diagnosis, Pre-treatment, MCL_morphology:pleomorphic, Nodal:No, Series_origin:HCP

tag: group

tag: material

tag: Sex


title: H3K9Ac G217B DMSO 37 C

description: Library name: H3K9Ac_37_DMSO_C

tag: genotype

tag: replicate

value: C

tag: temperature

tag: treatment

value: DMSO

value: fungal cell


title: Patient RRx_022, cells from human femoral head isolated using collagenase A + dispase, from region unaffected by OA

description: Library name: RRx_022_FH_Normal_G_repeat

tag: tissue

value: Femoral neck

tag: sample preparation

value: Tissue digested with collagenase A and dispase

value: Adult


title: Patient RRx_022, ALPL-low cells from human femoral neck isolated using collagenase A + dispase

description: Library name: RRx_022_FNG_ALPLlo


title: CH2_PCNSL_24 [200109350098_R06C02]

description:
200109350098_R06C02
DLBCL_EN

source_name: primary central nervous system lymphoma

value: primary central nervous system lymphoma

value: Brain

value: Ref set

value: Frozen

value: F

tag: mcf


title: MCL-187

value: lung adenocarcinoma

tag: sample type

value: FFPE

tag: patient id

tag: cohort

value: discovery cohort

tag: novel grade

value: NST

value: TRUE

value: LHMC


title: CH2_PCNSL_22 [200109350098_R05C02]

description:
200109350098_R05C02
DLBCL_EN

tag: age

value: M


title: Patient RRx_022, ALPL-high cells from human femoral neck isolated using collagenase A + dispase

description: Library name: RRx_022_FNG_ALPLhi


title: H3K9Ac G217B 50Ent 37 C

description: Library name: H3K9Ac_37_50Ent_C

value: C

tag: antibody

tag: cell type


title: MCL-186

tag: tnm 8th_edition_stage

tag: passed qc

tag: mean tin

tag: site

value: BMC

tag: sequence batch


title: MCL-182

value: LMP


title: H3K9Ac G217B DMSO 37 B

description: Library name: H3K9Ac_37_DMSO_B

tag: genotype

tag: replicate

value: B

tag: temperature

value: DMSO

value: fungal cell


title: H3K9Ac G217B 50Ent 37 B

description: Library name: H3K9Ac_37_50Ent_B

tag: treatment


title: CH2_PCNSL_20 [200109350098_R04C02]

description:
200109350098_R04C02
DLBCL_EN

tag: tissue

value: primary central nervous system lymphoma

value: Brain

tag: group

tag: material

tag: Sex

tag: mcf


title: Patient RRx_020, cells from human femoral neck isolated using collagenase IV + dispase

description: Library name: RRx_020_FN_R

value: Femoral neck

tag: sample preparation

value: Tissue digested with collagenase IV and dispase

tag: age

value: Adult


title: MCL-179

value: lung adenocarcinoma

tag: sample type

value: FFPE

tag: patient id

tag: cohort

tag: novel grade


title: MCL-177

value: discovery cohort

value: VI

tag: tnm 8th_edition_stage

tag: passed qc

tag: mean tin

tag: site


title: Input G217B 50Ent 37 B

description: Library name: input_37_50Ent_B

tag: genotype

tag: replicate

tag: temperature

tag: antibody

value: Input

tag: cell type


title: CH2_PCNSL_19 [200109350098_R04C01]

description:
200109350098_R04C01
DLBCL_EN

tag: tissue

tag: group

value: Ref set

tag: material

value: Frozen

tag: Sex

value: F


title: Input G217B 50Ent 37 A

description: Library name: input_37_50Ent_A

value: A

tag: treatment


title: H3K9Ac G217B DMSO 37 A

description: Library name: H3K9Ac_37_DMSO_A


title: CH2_PCNSL_15 [200109350098_R02C01]

description:
200109350098_R02C01
DLBCL_EN

tag: age

value: M

tag: mcf


title: Patient RRx_014, cells from human femoral neck isolated using collagenase IV + dispase

description: Library name: RRx_014_FN_R

tag: sample preparation


title: MCL-184

tag: sample type

tag: patient id

tag: cohort

tag: novel grade

value: LMP

tag: tnm 8th_edition_stage

value: TRUE

value: BMC

tag: sequence batch


title: MCL-171

value: IB

tag: passed qc

tag: mean tin

tag: site


title: Patient RRx_020, cells from human femoral neck isolated using collagenase A + dispase

description: Library name: RRx_020_FN_G

tag: tissue

value: Femoral neck

value: Tissue digested with collagenase A and dispase


title: CH2_PCNSL_17 [200109350098_R03C01]

description:
200109350098_R03C01
DLBCL_EN

value: primary central nervous system lymphoma

value: Brain

tag: group


title: Patient RRx_014, cells from human femoral neck isolated using collagenase A + dispase

description: Library name: RRx_014_FN_G

value: Adult


title: MCL-176

value: lung adenocarcinoma

value: FFPE

value: discovery cohort

value: LHMC


title: MCL-169

value: NST


title: CH2_PCNSL_18 [200109350098_R03C02]

description:
200109350098_R03C02
DLBCL_EN

value: Ref set

tag: material

value: Frozen


title: Patient RRx_014, cells from human femoral head isolated using collagenase IV + dispase

description: Library name: RRx_014_FH_R

value: Femoral head

value: Tissue digested with collagenase IV and dispase


title: CH2_PCNSL_10 [200109350097_R05C02]

description:
200109350097_R05C02
DLBCL_EN

tag: Sex

value: M


title: MCL-149

value: LMP

value: TRUE

value: BMC


title: Input G217B 50Ent 37 C

description: Library name: input_37_50Ent_C

tag: genotype

tag: replicate

value: C

tag: temperature

tag: treatment

tag: antibody

value: Input

tag: cell type

value: fungal cell


title: CH2_PCNSL_14 [200109350098_R01C02]

description:
200109350098_R01C02
DLBCL_EN

value: primary central nervous system lymphoma

value: Brain

tag: age

value: F

tag: mcf


title: Input G217B DMSO 37 B

description: Library name: input_37_DMSO_B

value: B

value: DMSO


title: Patient RRx_012, cells from human femoral head isolated using collagenase IV + dispase

description: Library name: RRx_012_FH_R

tag: sample preparation

value: Adult


title: Input rpd3delta C

description: Library name: rpd3_input_C


title: Input G217B DMSO 37 C

description: Library name: input_37_DMSO_C


title: Patient RRx_022, cells from human femoral head isolated using collagenase A + dispase, from region affected by OA

description: Library name: RRx_022_FH_Dis_G

value: Femoral neck

value: Tissue digested with collagenase A and dispase


title: Patient RRx_014, cells from human femoral head isolated using collagenase A + dispase

description: Library name: RRx_014_FH_G

value: Femoral head


title: CH2_PCNSL_8 [200109350097_R04C02]

description:
200109350097_R04C02
DLBCL_EN

value: Ref set

value: Frozen


title: H4K5Ac rpd3delta C

description: Library name: rpd3_H4K5Ac_C


title: MCL-142

value: lung adenocarcinoma

tag: sample type

value: FFPE

tag: patient id

tag: cohort

value: discovery cohort

tag: novel grade

value: VI

tag: tnm 8th_edition_stage

value: IB

tag: sequence batch


title: Patient RRx_012, cells from human femoral neck isolated using collagenase A + dispase

description: Library name: RRx_012_FN_G

tag: tissue


title: H3K9Ac rpd3delta C

description: Library name: rpd3_H3K9Ac_C

value: C

value: fungal cell


title: Input G217B DMSO 37 A

description: Library name: input_37_DMSO_A

value: A

value: Input


title: CH2_PCNSL_9 [200109350097_R05C01]

description:
200109350097_R05C01
DLBCL_EN

value: primary central nervous system lymphoma

value: Brain

tag: group

tag: material

tag: Sex

value: M


title: Patient RRx_012, cells from human femoral head isolated using collagenase A + dispase

description: Library name: RRx_012_FH_G

value: Adult


title: H3K14Ac rpd3delta C

description: Library name: rpd3_H3K14Ac_C

tag: genotype

tag: replicate


title: MCL-155

tag: passed qc

value: TRUE

tag: mean tin

tag: site

value: BMC


title: MCL-140

value: LMP

value: LHMC


title: MCL-141

value: lung adenocarcinoma

value: NST


title: Patient RRx_012, cells from human femoral neck isolated using collagenase IV + dispase

description: Library name: RRx_012_FN_R

value: Femoral neck

value: Tissue digested with collagenase IV and dispase

tag: age


title: MCL-138

value: FFPE

value: discovery cohort


title: H4K5Ac rpd3delta B

description: Library name: rpd3_H4K5Ac_B

value: B

tag: antibody

tag: cell type

value: fungal cell


title: CH2_PCNSL_7 [200109350097_R04C01]

description:
200109350097_R04C01
DLBCL_EN

value: Ref set

value: Frozen

tag: mcf


title: CH2_PCNSL_2 [200109350097_R01C02]

description:
200109350097_R01C02
DLBCL_EN

value: primary central nervous system lymphoma

value: Brain


title: CH2_PCNSL_1 [9370847123_R02C01]

description:
9370847123_R02C01
DLBCL_EN

value: F


title: H3K14Ac rpd3delta B

description: Library name: rpd3_H3K14Ac_B


title: Patient RRx_011, cells from human femoral neck isolated using collagenase IV + dispase

description: Library name: RRx_011_FN_R

tag: sample preparation

value: Adult


title: H3K9Ac rpd3delta B

description: Library name: rpd3_H3K9Ac_B


title: MCL-125

tag: sample type

tag: patient id

tag: cohort

tag: novel grade

value: TRUE

value: BMC


title: CH2_T3 [7990895106_R05C01]

description:
7990895106_R05C01
ALCL_A

source_name: Anaplastic large cell lymphoma, ALK-positive

tag: tissue

tag: group


title: Input rpd3delta A

description: Library name: rpd3_input_A

value: A

value: Input


title: Patient RRx_011, cells from human femoral neck isolated using collagenase A + dispase

description: Library name: RRx_011_FN_G

source_name: Femoral neck

value: Tissue digested with collagenase A and dispase


title: Patient RRx_011, cells from human femoral head isolated using collagenase IV + dispase

description: Library name: RRx_011_FH_R

value: Femoral head


title: CH2_T4 [7990895106_R03C02]

description:
7990895106_R03C02
ALCL_A

value: Anaplastic large cell lymphoma, ALK-positive

tag: material

tag: Sex


title: Patient RRx_011, cells from human femoral head isolated using collagenase A + dispase

description: Library name: RRx_011_FH_G


title: MCL-119

value: lung adenocarcinoma

value: FFPE

value: NST

tag: tnm 8th_edition_stage

tag: sequence batch


title: human keratinocytes treated with base editor mRNA and TGM1 sgRNA, replicate 2

city: Berlin

first: Benedikt

last: Obermayer

address: Chariteplatz 1

department: Core Unit Bioinformatics

country: Germany

institute: Berlin Institute of Health

description: Library name: Treated_KC_2

data_processing:
Sequencing data were processed with CellRanger (v9.0.1) and the GRCh38 reference augmented by custom probe sequences against EGFP.
Assembly: GRCh38
Supplementary files format and content: Cellranger h5 output
Supplementary files format and content: feature_counts

source_name: skin

growth_protocol: All keratinocyte cultures, including skin biopsies maintained at the air–liquid interface (ALI), were cultured in EpiLife medium (Gibco, Cat. No. MEPI500CA) supplemented with human keratinocyte growth supplement (HKGS, Gibco, Cat. No. S0015).

extract_protocol:
For primary cell isolation, residual adipose and connective tissue were carefully trimmed from the skin specimens, which were subsequently minced into small fragments using a scalpel. The tissue pieces were then incubated overnight at 4°C in dispase solution (Worthington, Cat. No. LS02100, 1 mg/ml), with the epidermal side oriented upwards and not fully submerged. On the following day, the epidermis was mechanically separated and transferred into a fresh 50 mL conical tube containing 5 mL Trypsin/EDTA. Epidermal fragments were incubated for 25 min at 37°C, with gentle agitation of the tube every 5 min to facilitate cell dissociation. Trypsin activity was quenched by adding 15 mL fibroblast growth medium (FGM, see above). The resulting cell suspension was filtered through a 70 µm cell strainer, centrifuged at 130 g for 5 min at room temperature, and resuspended in 1 mL supplemented EpiLife medium. Cells were quantified and seeded at a density of 1 × 10⁷ cells per T75 culture flask, and expanded to approximately 70% confluence prior to cryopreservation.
Isolated live cells were then prepped with the GEM-X Flex Sample Preparation (10X Genomics, CatNr. 1000781) kit as per manufacturer SOP. Fixed cells were processed with the GEM-X Flex assay for fixed RNA (10X Genomics).

treatment_protocol: scRNASeq: Freshly excised human skin was obtained with written informed consent under approval of the Charité ethics committee (EA1/356/21). Tissue originated from female donors aged 35–63 years (mean age 45 years) undergoing elective abdominoplasty at the Clinic for Plastic and Aesthetic Surgery, Helios-Klinikum Buch, Berlin, Germany. Only donor sex and age were disclosed. Upon collection, skin samples were sectioned into approximately 10 × 10 cm pieces and briefly cleansed using ethanol wipes. Residual adipose and connective tissue were carefully removed from abdominal biopsies prior to further processing. The tissue was subsequently cut into 1 × 1 cm explants and placed into transwell inserts (Corning Life Sciences, Cat. No. 353093). Inserts were maintained in 6-well companion plates containing 1.8 mL EpiLife medium in the outer chamber (Corning Life Sciences, Cat. No. 353502), supplemented with penicillin and streptomycin at final concentrations of 1% each. Laser-assisted microporation was performed using the P.L.E.A.S.E. device to achieve an average depth of 23-25 µm, following which lipid nanoparticles were topically applied and incubated overnight. For Bulk-RNASeq: cells were electroporated as per manufacturer instructions (NeonNXT, Thermofisher)

value: skin

tag: treatment

value: Base editor mRNA and TGM1 sgRNA


title: H3K14Ac rpd3delta A

description: Library name: rpd3_H3K14Ac_A

tag: genotype

tag: replicate

value: fungal cell


title: CH2_T7 [101032560165_R04C01]

description:
101032560165_R04C01
ALCL_A

source_name: Anaplastic large cell lymphoma, ALK-negative

value: Ref set

value: Frozen

tag: age


title: MCL-124

value: discovery cohort

value: VI

tag: passed qc

tag: mean tin

tag: site

value: LHMC


title: CH2_PCNSL_5 [200109350097_R03C01]

description:
200109350097_R03C01
DLBCL_EN

value: primary central nervous system lymphoma

value: Brain

value: F

tag: mcf


title: human keratinocytes, replicate 1

description: Library name: Ctrl_KC_1

value: untreated


title: MCL-112

tag: sample type

tag: patient id

value: LMP

value: TRUE


title: human keratinocytes treated with base editor mRNA and TGM1 sgRNA, replicate 1

description: Library name: Treated_KC_1


title: CH2_T2 [7990895106_R04C01]

description:
7990895106_R04C01
ALCL_B

value: Anaplastic large cell lymphoma, ALK-positive

value: M


title: CH2_PCNSL_3 [200109350097_R02C01]

description:
200109350097_R02C01
DLBCL_EN


title: H4K5Ac rpd3delta A

description: Library name: rpd3_H4K5Ac_A

value: A

tag: antibody

tag: cell type


title: MCL-123

tag: tissue

value: lung adenocarcinoma

value: FFPE

tag: cohort

tag: novel grade

value: NST

value: BMC


title: CH2_WZ_12 [7796814006_R06C02]

description:
7796814006_R06C02
SZ

source_name: Sezary syndrome

value: Sezary syndrome

tag: group

value: Ref set

tag: material

value: Frozen

tag: Sex


title: human keratinocytes from ARCI patient treated with base editor mRNA and TGM1 sgRNA, replicate 2

description: Library name: Treated_ARCI_2

value: skin

tag: treatment

value: Base editor mRNA and TGM1 sgRNA


title: human keratinocytes from ARCI patient treated with base editor mRNA and TGM1 sgRNA, replicate 1

description: Library name: Treated_ARCI_1


title: MCL-095

value: discovery cohort

value: VI

tag: tnm 8th_edition_stage

value: IB

tag: sequence batch


title: human keratinocytes, replicate 2

description: Library name: Ctrl_KC_2

value: untreated


title: H4K5Ac G217B C

description: Library name: WT_H4K5Ac_C

tag: genotype

tag: replicate

value: C

value: fungal cell


title: human keratinocytes from ARCI patient, replicate 2

description: Library name: Ctrl_ARCI_2


title: CH2_WZ_10 [7796814006_R04C02]

description:
7796814006_R04C02
SZ

tag: age

value: F


title: H3K14Ac G217B C

description: Library name: WT_H3K14Ac_C


title: human skin cells treated with EGFP mRNA-loaded LNPs from donor GS167

description: Library name: GS167

value: EGFP mRNA-loaded LNP


title: CH2_WZ_4 [7796814006_R04C01]

description:
7796814006_R04C01
SZ

tag: mcf


title: MCL-091

value: lung adenocarcinoma

tag: sample type

value: LMP

tag: passed qc

value: TRUE

tag: mean tin

tag: site


title: H3K9Ac rpd3delta A

description: Library name: rpd3_H3K9Ac_A

value: A

tag: antibody

tag: cell type


title: human keratinocytes from ARCI patient, replicate 1

description: Library name: Ctrl_ARCI_1

tag: tissue


title: human skin cells treated with EGFP mRNA-loaded LNPs from donor GS163

description: Library name: GS163


title: MCL-097

value: FFPE

tag: patient id

tag: cohort

tag: novel grade

value: LHMC


title: MCL-120

value: NST

value: BMC


title: CH2_WZ_3 [7796814006_R03C01]

description:
7796814006_R03C01
SZ

value: Sezary syndrome

tag: group

value: Ref set

tag: material

value: Frozen

tag: Sex


title: MCL-080

value: discovery cohort

tag: tnm 8th_edition_stage

tag: sequence batch


title: MCL-075


title: CH2_WZ_6 [7796814006_R06C01]

description:
7796814006_R06C01
SZ

tag: age


title: MCL-107


title: Input G217B C

description: Library name: WT_input_C

tag: genotype

tag: replicate

value: Input


title: CH2_WZ_9 [7796814006_R03C02]

description:
7796814006_R03C02
SZ

value: M

tag: mcf


title: H3K9Ac G217B C

description: Library name: WT_H3K9Ac_C

value: C

value: fungal cell


title: Input G217B B

description: Library name: WT_input_B

value: B


title: human skin cells treated with EGFP mRNA-loaded LNPs from donor GS157

description: Library name: GS157

value: skin

tag: treatment

value: EGFP mRNA-loaded LNP


title: Input rpd3delta B

description: Library name: rpd3_input_B


title: H3K14Ac G217B B

description: Library name: WT_H3K14Ac_B


title: H3K9Ac G217B B

description: Library name: WT_H3K9Ac_B


title: human skin cells treated with EGFP mRNA-loaded LNPs from donor GS162

description: Library name: GS162


title: Endocervical, PUT, GV, replicate 3

city: Hanover

first: Olha

last: Kholod

state: NH

address: 15 Thayer Drive

institute: Dartmouth College

description: Library name: ENDO_PUTaddGV-3_S97

data_processing:
Transcript quantification from RNA-seq data was performed using Salmon and release 44 (GRCh38.p13) of the human genome. QC analyses were done with Fastqc for the raw fastq files. Several Bioconductor (v3.17) packages in R (v4.32) were used for subsequent steps. The transcriptome count data was annotated and summarized to the gene level with tximeta and further annotated with biomaRt.
Assembly: GRCh38.p13
Supplementary files format and content: combined count matrix and metadata file

source_name: Endo

extract_protocol:
Cell culture media was collected for cell death assays, metabolomics analysis and Luminex and/or the cells were collected in Trizol for RNA extraction and RNA sequencing.
RNA-sequencing libraries were generated according to manufacturer’s instructions for the CORALL Total RNA-Seq Library Prep kit (Lexogen GmbH). Unique Dual Indexes Primer Pair Set were incorporated for multiplexed high-throughput sequencing.

tag: cell line

value: Endo

value: Endocervical

value: GV


title: MCL-070

value: lung adenocarcinoma

tag: sample type

value: FFPE

tag: passed qc

value: TRUE

tag: mean tin

tag: site


title: CH2_WZ_7 [7796814006_R01C02]

description:
7796814006_R01C02
SZ

tag: tissue

value: Sezary syndrome


title: CH2_WZ_15 [7796814012_R03C01]

description:
7796814012_R03C01
SZ

value: Ref set


title: CH2_WZ_8 [7796814006_R02C02]

description:
7796814006_R02C02
SZ

value: Frozen

value: F


title: MCL-065

tag: patient id

tag: cohort

value: discovery cohort

tag: novel grade

value: NST

value: BMC


title: Endocervical, SPD, GV, replicate 3

description: Library name: ENDO_SPDaddGV-3_S95

tag: cell type


title: CH2_WZ_1 [7796814006_R01C01]

description:
7796814006_R01C01
SZ

tag: group

tag: material

tag: Sex

value: M


title: Input G217B A

description: Library name: WT_input_A

tag: genotype

value: A

tag: antibody

value: Input

value: fungal cell


title: Vaginal, PUT, GV, replicate 3

description: Library name: VK_PUTaddGV-3_S96

value: Vaginal


title: H4K5Ac G217B B

description: Library name: WT_H4K5Ac_B

tag: replicate

value: B


title: H4K5Ac G217B A

description: Library name: WT_H4K5Ac_A


title: MCL-058

value: VI

tag: tnm 8th_edition_stage

tag: sequence batch


title: MCL-088

value: lung adenocarcinoma

tag: sample type

value: IB


title: CH2_WZ_13 [7796814012_R01C01]

description:
7796814012_R01C01
SZ

tag: age

tag: mcf


title: MCL-052

value: FFPE

tag: passed qc

value: TRUE

tag: mean tin

tag: site


title: CH2_TENOMIC037 [9007217027_R05C01]

description:
9007217027_R05C01
ETCL_SETD2

source_name: Hepatosplenic T-cell lymphoma, gamma-delta T-cell subset

tag: tissue

value: Spleen

value: Ref set


title: MCL-060

tag: patient id

tag: cohort

tag: novel grade


title: MCL-045

value: LHMC


title: CH2_WZ_14 [7796814012_R02C01]

description:
7796814012_R02C01
SZ

value: Sezary syndrome

tag: group

tag: material

value: Frozen


title: MCL-063

value: discovery cohort

value: NST

value: BMC


title: Ectocervical, PUT, GV, replicate 3

description: Library name: ECTO_PUTaddGV-3_S94

source_name: Ecto

tag: cell line

value: Ecto

tag: cell type

value: Ectocervical

tag: treatment

value: GV


title: Ectocervical, SPD, GV, replicate 3

description: Library name: ECTO_SPDaddGV-3_S91


title: MCL-044

tag: tnm 8th_edition_stage


title: H3K14Ac G217B A

description: Library name: WT_H3K14Ac_A

tag: genotype

tag: replicate

value: A

tag: antibody

value: fungal cell


title: Input DMSO C

description: Library name: DMSO_input_C

data_processing:
Paired-end reads were aligned to the Histoplasma ohiense G217B genome (GCA_017607445.1) using BOWTIE2 version 2.4.2 with default parameters.  Peaks were called for each individual replicate with MACS2 version 2.2.7.1 with default parameters except that min-length was set to 100 for paired-end reads as recommended by Gaspar 2018.  Aggregate peaks were defined by taking the union of the coordinates of overlapping peaks among replicates for regions where peaks were called for at least two replicates. The aggregate peaks defined for 37 °C samples for a given TF were used for quantification of all samples for that TF.  Per peak signal was quantified by counting reads or read pairs in each aggregate peak, log2 transforming with pseudocount of 1 to handle missing data, and normalizing to the signal in the NPS1 negative control region. This negative control region was defined as the middle 500 bp of NPS1 (I7I48_05472, JAEVHH010000002: 444765..449764 (+)). Differential enrichment was then calculated as the difference of the means of the log2 signal over replicates from each condition. Peaks were assigned to individual genes if any part of the peak fell in the intergenic region between the stop codon of the upstream gene and before the start codon for that gene, limiting the intergenic size to a maximum of 10 kb as described in Homer et al [PMID:40233121].
Single or paired-end reads were aligned to the Histoplasma ohiense G217B genome (GCA_017607445.1) using BOWTIE2 version 2.4.2 with default parameters. Per sample promoter signal was quantified by counting reads or read pairs in each promoter, log2 transforming with pseudocount of 1 to handle missing data, and normalizing to the signal in the NPS1 negative control region. This negative control region was defined as the middle 500 bp of NPS1 (I7I48_05472, JAEVHH010000002: 444765..449764 (+)). Differential enrichment was then calculated as the difference of the means of the log2 signal over replicates from each condition.
Assembly: GCA_017607445.1
Supplementary files format and content: Processed data file for each sample is in Excel-compatible tab-delimited text conforming to JavaTreeView extended CDT format.  Each row represents the promoter of one gene with the systematic gene name given redundantly in the GID, UNIQID, and NAME columns.  The next columns give normalized read density (D_f), read counts (R_f), and promoter size (1kb 5' of CDS ATG in all cases), and log2 normalized read density.  A GWEIGHT column is included for JavaTreeView compatibility.  A combined table of differential histone modification ChIP enrichment over all experiments is given in the accompanying paper as Table S11.

extract_protocol:
Cultures processed for ChIP-seq were crosslinked with formaldehyde (Polysciences 18814-10) added to a final concentration of 1 % and kept under culture conditions (shaking at 37 °C with 5 % CO2 or ambient RT) for 20 minutes to allow fixing to take place. Crosslinking was quenched with glycine added to a final concentration of 125 mM for 5 minutes at RT. Fixed cells were pelleted at 3000 g for 10 minutes at 4 °C and washed twice with TBS (20 mM Tris-HCl (pH 7.5), 150 mM NaCl). Washed cells were harvested through filtration, aliquoted into pellets of equal mass (between 150-300 mg/tube) and flash frozen in liquid nitrogen as described above. Frozen pellets were resuspended in lysis buffer (50 mM Hepes/KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % sodium deoxycholate, protease/phosphatase inhibitors) at 4 °C before being bead beat with 500 µL of 0.5 mm zirconia beads in 5 x 1 minute cycles at RT with 2 minute rests on ice in between. The resulting lysate was then spun down at 8000 rpm for 10 minutes at 4 °C to isolate the insoluble chromatin fraction. This chromatin pellet was resuspended in 600-900 µL of lysis buffer and sonicated at 4 °C using the Diagenode Bioruptor® Pico for 30-35 cycles (30s on, 30s off). Sonicated samples were spun down for 5 min at 14,000 rpm at 4 °C to pellet cell debris and aliquots for input DNA were reserved at -20 °C in TE + 1 % SDS. Input samples were also used to assess shearing using a High Sensitivity DNA Bioanalyzer chip from Agilent. Equal lysate volumes were aliquoted for each IP to be performed and brought to a final volume of 500 µL with lysis buffer and 20 µg of each polyclonal ⍺-Ryp antibody (Ryp1: 3873, Ryp2: 387, and Ryp3: 356) or 3 µg of a ChIP-grade monoclonal ⍺-histone-acetyl antibody (H3K9Ac: ab177177 , H3K14Ac: ab52946, H4K16Ac: ab109463). Samples were incubated overnight with agitation at 4 °C before being incubated with 50 µL of a 50% slurry of Protein A Dynabeads (Life Technologies Corporation 10002D) pre-washed 2x with TBS and 3x lysis buffer for 2 hours at 4 °C with agitation.  Immunoprecipitated DNA was recovered through pulldown on Protein A beads using a magnetic rack. Pellets containing DNA-protein complexes were washed 2x in lysis buffer, 2x with high-salt (500 mM NaCl) lysis buffer, 2x with wash buffer (10 mM Tris/HCl (pH 8.0), 250 mM LiCl, 0.5 % NP-40, 0.5 % Na-deoxycholate, 1 mM EDTA) and 1x with TE before adding elution buffer (50 mM Tris/HCl (pH 8.0), 10 mM EDTA, 1 % SDS) and incubating at 65 °C for 10 minutes. DNA was eluted using a magnetic rack and the resulting beads were subjected to second round of resuspension and elution with 150 µl TE + 0.65 % SDS and pooled with the initial eluate to maximize total yield of DNA. IP and input samples were treated with 1 µL of Proteinase K (20 mg/mL Qiagen 19131) and incubated at 65 °C for approximately 16 hours. IP and Input DNA samples were then treated with 2 µg of RNase A (Qiagen) and incubated at 37 °C for 1 hour. DNA was then purified using the Zymo ChIP DNA Clean & Concentrator Kit (D5205) and eluted in 31 µL of ddH2O or TE.
Purified IP and input DNA were used for Illumina library preparation using the NEBNext Ultra II DNA Library Prep Kit (NEB E7103S) and Illumina dual-indexed primer pairs sourced from the UCSF CAT. The quality and size distribution of each library was assessed using the Agilent High Sensitivity DNA Bioanalyzer Kit (Agilent Technologies 5067-4626) to ensure proper fragment size and the absence of contaminating adapters. Final library concentrations were measured using a Qubit HS dsDNA assay kit (Life Technologies Q33230) and used to pool equimolar amounts of each sample into final libraries for sequencing. Pooled libraries were used for single-end sequencing using one NovaSeq X 10B lane at the UCSF CAT.

tag: additive

value: DMSO

value: C

value: Input


title: CH2_TENOMIC014 [9007217027_R04C01]

description:
9007217027_R04C01
HSTCL_GD

value: Hepatosplenic T-cell lymphoma, gamma-delta T-cell subset

tag: age

tag: Sex

value: M

tag: mcf


title: Endocervical, NT, GV, replicate 3

description: Library name: ENDO_GV-3_S89

value: Endo

value: Endocervical


title: Endocervical, SPM, GV, replicate 3

description: Library name: ENDO_SPMaddGV-3_S92


title: Input 50uM Entinostat C

description: Library name: 50Ent_input_C

value: 50uM Entinostat


title: H3K9Ac G217B A

description: Library name: WT_H3K9Ac_A


title: MCL-032

tag: tissue

value: lung adenocarcinoma

tag: sample type

value: FFPE

value: LMP

tag: passed qc

value: TRUE

tag: mean tin

tag: site

tag: sequence batch


title: CH2_TENOMIC179 [9007217027_R06C01]

description:
9007217027_R06C01
ETCL_SETD2

tag: group

value: Ref set

tag: material

value: Frozen

value: F


title: Vaginal, SPD, GV, replicate 3

description: Library name: VK2_SPDaddGV-3_S93

tag: cell line

tag: cell type

value: Vaginal

tag: treatment

value: GV


title: CH2_TENOMIC181 [9007217027_R01C02]

description:
9007217027_R01C02
HSTCL_GD

value: Spleen


title: Vaginal, SPM, GV, replicate 3

description: Library name: VK_SPMaddGV-3_S90


title: CH2_Uk17 [6969568046_R05C02]

description:
6969568046_R05C02
ETCL_SETD2

value: bonemarrow


title: Ectocervical, SPM, GV, replicate 3

description: Library name: ECTO_SPMaddGV-3_S88

value: Ecto

value: Ectocervical


title: CH2_TENOMIC184 [9007217027_R04C02]

description:
9007217027_R04C02
HSTCL_AB

source_name: Hepatosplenic T-cell lymphoma, alpha-beta T-cell subset

value: M


title: CH2_TENOMIC446 [9007217027_R05C02]

description:
9007217027_R05C02
HSTCL_AB

value: Hepatosplenic T-cell lymphoma, alpha-beta T-cell subset


title: MCL-017

tag: patient id

tag: cohort

value: discovery cohort

tag: novel grade

value: NST

tag: tnm 8th_edition_stage

value: BMC


title: Input DMSO B

description: Library name: DMSO_input_B

tag: genotype

tag: additive

value: DMSO

tag: replicate

value: B

tag: antibody

value: Input

value: fungal cell


title: Input 50uM Entinostat A

description: Library name: 50Ent_input_A

value: 50uM Entinostat

value: A


title: MCL-018

tag: tissue

value: lung adenocarcinoma

tag: sample type

value: FFPE

tag: passed qc

value: TRUE

value: LHMC


title: Endocervical, PUT, noGV, replicate 3

description: Library name: ENDO_PUT-3_S86

value: Endo

value: Endocervical

value: noGV


title: Input 50uM Entinostat B

description: Library name: 50Ent_input_B


title: Input DMSO A

description: Library name: DMSO_input_A


title: MCL-016

value: IB

tag: mean tin

tag: site

tag: sequence batch


title: CH2_TENOMIC663 [9007217027_R06C02]

description:
9007217027_R06C02
HSTCL_AB

source_name: Hepatosplenic T-cell lymphoma

value: Hepatosplenic T-cell lymphoma

value: bone marrow

tag: group

value: Ref set

tag: material

value: Frozen

tag: age

tag: Sex

value: M

tag: mcf


title: H3K9Ac 50uM Entinostat B

description: Library name: 50Ent_H3K9_B

value: B

tag: cell type


title: MCL-043

tag: patient id

tag: cohort

value: discovery cohort

tag: novel grade

value: NST

tag: tnm 8th_edition_stage

value: BMC


title: Ectocervical, NT, GV, replicate 3

description: Library name: ECTO_GV-3_S85

tag: cell line

value: Ecto

value: Ectocervical

tag: treatment

value: GV


title: Vaginal, PUT, noGV, replicate 3

description: Library name: VK2_PUT-3_S84

value: Vaginal


title: CH2_TENOMIC183 [9007217027_R03C02]

description:
9007217027_R03C02
HSTCL_AB

tag: tissue

value: Hepatosplenic T-cell lymphoma, alpha-beta T-cell subset

value: Spleen


title: CH2_LYMPHO_09 [9878820030_R04C01]

description:
9878820030_R04C01
DLBCL_EN

source_name: diffuse large B-cell lymphoma

value: diffuse large B-cell lymphoma

value: Brain

value: FFPE

value: F

value: Capper Nature 2018, Siewert_T-Cell_Lymphoma


title: H3K9Ac 50uM Entinostat A

description: Library name: 50Ent_H3K9_A

tag: genotype

tag: additive

value: 50uM Entinostat

tag: replicate

value: A

tag: antibody

value: fungal cell


title: MCL-009

value: lung adenocarcinoma

tag: sample type

value: discovery cohort

value: VI

value: IB

tag: passed qc

value: TRUE

tag: mean tin

tag: site

value: LHMC

tag: sequence batch


title: H3K9Ac 50uM Entinostat C

description: Library name: 50Ent_H3K9_C

value: C

tag: cell type


title: CH2_LYMPHO_10 [9406921039_R04C02]

description:
9406921039_R04C02
DLBCL_EN

tag: group

value: Ref set

tag: material

tag: age

tag: Sex

value: M

tag: mcf


title: Endocervical, SPD, noGV, replicate 3

description: Library name: ENDO_SPD-3_S83

tag: cell line

value: Endo

value: Endocervical

tag: treatment

value: noGV


title: Vaginal, NT, GV, replicate 3

description: Library name: VK_GV-3_S87

value: Vaginal

value: GV


title: CH2_LYMPHO_06 [9007217153_R01C01]

description:
9007217153_R01C01
DLBCL_EN

tag: tissue

value: diffuse large B-cell lymphoma

value: Brain

value: FFPE

value: F

value: Capper Nature 2018, Siewert_T-Cell_Lymphoma


title: CH2_LYMPHO_07 [9007217153_R02C01]

description:
9007217153_R02C01
DLBCL_EN


title: Ectocervical, PUT, noGV, replicate 3

description: Library name: ECTO_PUT-3_S82

value: Ecto

value: Ectocervical


title: H3K9Ac DMSO B

description: Library name: DMSO_H3K9_B

tag: genotype

tag: additive

value: DMSO

value: B

value: fungal cell


title: MCL-012

value: lung adenocarcinoma

tag: patient id

tag: cohort

value: discovery cohort

tag: novel grade

value: NST

tag: tnm 8th_edition_stage

value: TRUE

value: BMC


title: MCL-035

tag: sample type

value: IB

tag: passed qc

tag: mean tin

tag: site


title: H3K9Ac DMSO A

description: Library name: DMSO_H3K9_A

tag: replicate

value: A

tag: antibody

tag: cell type


title: MCL-003

value: LHMC

tag: sequence batch


title: H3K9Ac DMSO C

description: Library name: DMSO_H3K9_C

value: C


title: MCL-175

value: FFPE

value: VI


title: MCL-172


title: MCL-166


title: Endocervical, NT, noGV, replicate 3

description: Library name: ENDO_NT-3_S68

tag: cell line

value: Endo

value: Endocervical

value: noGV


title: Vaginal, SPD, noGV, replicate 3

description: Library name: VK2_SPD-3_S81

value: Vaginal

tag: treatment


title: dkfz_hem200 [9855358003_R05C02]

description:
9855358003_R05C02
PCN

source_name: Plasmazytoma

tag: tissue

value: Plasmazytoma

tag: group

value: Test set

tag: material

tag: age

tag: Sex

value: M

tag: mcf


title: H4K16Ac DMSO B

description: Library name: DMSO_H4K16_B

source_name: fungal cell

tag: genotype

tag: additive

value: DMSO

value: B

value: fungal cell


title: CH2_LYMPHO_04 [8963311099_R06C02]

description:
8963311099_R06C02
DLBCL_EN

value: diffuse large B-cell lymphoma

value: Brain

value: Ref set

value: F

value: Capper Nature 2018, Siewert_T-Cell_Lymphoma


title: Ectocervical, SPD, noGV, replicate 3

description: Library name: ECTO_SPD-3_S79

value: Ecto

value: Ectocervical


title: dkfz_hem201 [9855358003_R06C01]

description:
9855358003_R06C01
PCN

value: FFPE


title: CH2_LYMPHO_13 [6929718009_R05C01]

description:
6929718009_R05C01
DLBCL_EN

value: Frozen


title: dkfz_hem198 [9741950027_R06C01]

description:
9741950027_R06C01
PCN


title: MCL-164

source_name: lung adenocarcinoma

value: lung adenocarcinoma

tag: sample type

tag: patient id

tag: cohort

value: discovery cohort

tag: novel grade

value: NST

tag: tnm 8th_edition_stage

tag: passed qc

value: TRUE

value: BMC


title: H4K16Ac 50uM Entinostat B

description: Library name: 50Ent_H4K16_B

value: 50uM Entinostat

tag: replicate

tag: antibody

tag: cell type


title: Ectocervical, NT, noGV, replicate 3

description: Library name: ECTO_NT-3_S56

tag: cell line

tag: treatment

value: noGV


title: Vaginal, NT, noGV, replicate 3

description: Library name: VK2_NT-3_S57

value: Vaginal


title: dkfz_hem195 [3999308205_R02C01]

description:
3999308205_R02C01
BLL_NONKMT2A

source_name: B-ALL

tag: tissue

value: B-ALL

tag: group

value: Test set

tag: material


title: Input rpd3delta C

description: Library name: rpd3_input_C

data_processing:
Paired-end reads were aligned to the Histoplasma ohiense G217B genome (GCA_017607445.1) using BOWTIE2 version 2.4.2 with default parameters.  Peaks were called for each individual replicate with MACS2 version 2.2.7.1 with default parameters except that min-length was set to 100 for paired-end reads as recommended by Gaspar 2018.  Aggregate peaks were defined by taking the union of the coordinates of overlapping peaks among replicates for regions where peaks were called for at least two replicates. The aggregate peaks defined for 37 °C samples for a given TF were used for quantification of all samples for that TF.  Per peak signal was quantified by counting reads or read pairs in each aggregate peak, log2 transforming with pseudocount of 1 to handle missing data, and normalizing to the signal in the NPS1 negative control region. This negative control region was defined as the middle 500 bp of NPS1 (I7I48_05472, JAEVHH010000002: 444765..449764 (+)). Differential enrichment was then calculated as the difference of the means of the log2 signal over replicates from each condition. Peaks were assigned to individual genes if any part of the peak fell in the intergenic region between the stop codon of the upstream gene and before the start codon for that gene, limiting the intergenic size to a maximum of 10 kb as described in Homer et al [PMID:40233121].
Assembly: GCA_017607445.1
Supplementary files format and content: Processed data file for each non-input sample is in MACS2 tab delimited text peaks format
Supplementary files format and content: Supplementary file Table_S10.txt is an Excel-compatible tab-delimited text conforming to JavaTreeView extended CDT format.  Each row represents a gene associated with at least one Ryp as given in the UNIQID column.  The NAME column gives short names taken from Data S1 of [PMID:35089059] with additional names and corrections based on human curation. This is followed by Ryp-specific peak coordinates; where more than one peak exists for a given gene, the peak with the best MACS2 score is given.  Description and HcG217B_pred (WUSTL G217B predicted gene accessions), HcG217B_rc (Edwards et al G217B transcript accessions [PMID: 24112604]), HcG217B_acc (UCSF1 gene accessions [PMID:35089059]), and HcG217B (Gilmore et al transcript accessions [PMID: 26177267]); and Ryp1_ChIP, Ryp2_ChIP, Ryp3_ChIP, and Ryp4_ChIP (indicating genes with promoters bound by Ryp TFs in [PMID: 23935449]) are taken from Data S1 of [PMID:35089059].  Following a GWEIGHT column, included for JavaTreeView compatibility, is log2 differential ChIP enrichment between WT and rpd3 samples for each Ryp.

extract_protocol:
Cultures processed for ChIP-seq were crosslinked with formaldehyde (Polysciences 18814-10) added to a final concentration of 1 % and kept under culture conditions (shaking at 37 °C with 5 % CO2 or ambient RT) for 20 minutes to allow fixing to take place. Crosslinking was quenched with glycine added to a final concentration of 125 mM for 5 minutes at RT. Fixed cells were pelleted at 3000 g for 10 minutes at 4 °C and washed twice with TBS (20 mM Tris-HCl (pH 7.5), 150 mM NaCl). Washed cells were harvested through filtration, aliquoted into pellets of equal mass (between 150-300 mg/tube) and flash frozen in liquid nitrogen as described above. Frozen pellets were resuspended in lysis buffer (50 mM Hepes/KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % sodium deoxycholate, protease/phosphatase inhibitors) at 4 °C before being bead beat with 500 µL of 0.5 mm zirconia beads in 5 x 1 minute cycles at RT with 2 minute rests on ice in between. The resulting lysate was then spun down at 8000 rpm for 10 minutes at 4 °C to isolate the insoluble chromatin fraction. This chromatin pellet was resuspended in 600-900 µL of lysis buffer and sonicated at 4 °C using the Diagenode Bioruptor® Pico for 30-35 cycles (30s on, 30s off). Sonicated samples were spun down for 5 min at 14,000 rpm at 4 °C to pellet cell debris and aliquots for input DNA were reserved at -20 °C in TE + 1 % SDS. Input samples were also used to assess shearing using a High Sensitivity DNA Bioanalyzer chip from Agilent. Equal lysate volumes were aliquoted for each IP to be performed and brought to a final volume of 500 µL with lysis buffer and 20 µg of each polyclonal ⍺-Ryp antibody (Ryp1: 3873, Ryp2: 387, and Ryp3: 356) or 3 µg of a ChIP-grade monoclonal ⍺-histone-acetyl antibody (H3K9Ac: ab177177 , H3K14Ac: ab52946, H4K16Ac: ab109463). Samples were incubated overnight with agitation at 4 °C before being incubated with 50 µL of a 50% slurry of Protein A Dynabeads (Life Technologies Corporation 10002D) pre-washed 2x with TBS and 3x lysis buffer for 2 hours at 4 °C with agitation.  Immunoprecipitated DNA was recovered through pulldown on Protein A beads using a magnetic rack. Pellets containing DNA-protein complexes were washed 2x in lysis buffer, 2x with high-salt (500 mM NaCl) lysis buffer, 2x with wash buffer (10 mM Tris/HCl (pH 8.0), 250 mM LiCl, 0.5 % NP-40, 0.5 % Na-deoxycholate, 1 mM EDTA) and 1x with TE before adding elution buffer (50 mM Tris/HCl (pH 8.0), 10 mM EDTA, 1 % SDS) and incubating at 65 °C for 10 minutes. DNA was eluted using a magnetic rack and the resulting beads were subjected to second round of resuspension and elution with 150 µl TE + 0.65 % SDS and pooled with the initial eluate to maximize total yield of DNA. IP and input samples were treated with 1 µL of Proteinase K (20 mg/mL Qiagen 19131) and incubated at 65 °C for approximately 16 hours. IP and Input DNA samples were then treated with 2 µg of RNase A (Qiagen) and incubated at 37 °C for 1 hour. DNA was then purified using the Zymo ChIP DNA Clean & Concentrator Kit (D5205) and eluted in 31 µL of ddH2O or TE.
Purified IP and input DNA were used for Illumina library preparation using the NEBNext Ultra II DNA Library Prep Kit (NEB E7103S) and Illumina dual-indexed primer pairs sourced from the UCSF CAT. The quality and size distribution of each library was assessed using the Agilent High Sensitivity DNA Bioanalyzer Kit (Agilent Technologies 5067-4626) to ensure proper fragment size and the absence of contaminating adapters. Final library concentrations were measured using a Qubit HS dsDNA assay kit (Life Technologies Q33230) and used to pool equimolar amounts of each sample into final libraries for sequencing. Pooled libraries were used for paired-end sequencing  using one NovaSeq X 10B lane at the UCSF CAT.

value: Input

value: C

value: fungal cell


title: MCL-154

value: LMP

tag: mean tin

tag: site

tag: sequence batch


title: dkfz_hem193 [3999100065_R02C01]

description:
3999100065_R02C01
BLL_NONKMT2A

tag: age

tag: Sex

value: F

tag: mcf


title: Ryp3 rpd3delta C

description: Library name: rpd3_Ryp3_C

tag: genotype


title: MCL-162

tag: sample type

value: FFPE

tag: patient id

tag: cohort

tag: novel grade

tag: tnm 8th_edition_stage


title: Endocervical, SPM, noGV, replicate 3

description: Library name: ENDO_SPM-3_S80

tag: cell line

value: Endo

tag: cell type

value: Endocervical


title: dkfz_hem191 [3999078134_R06C02]

description:
3999078134_R06C02
BLL_NONKMT2A

tag: tissue

value: M


title: MCL-161

value: lung adenocarcinoma

value: discovery cohort

value: VI

value: IB

tag: passed qc


title: Vaginal, PUT, GV, replicate 2

description: Library name: VK_PUTaddGV-2_S47

tag: treatment

value: GV


title: H4K16Ac DMSO A

description: Library name: DMSO_H4K16_A

tag: additive

value: DMSO

tag: replicate

value: A

tag: antibody


title: MCL-174

value: NST

value: TRUE

tag: mean tin

tag: site

value: BMC

tag: sequence batch


title: H4K16Ac 50uM Entinostat C

description: Library name: 50Ent_H4K16_C

tag: genotype

value: 50uM Entinostat

value: C

value: fungal cell


title: Endocervical, PUT, GV, replicate 2

description: Library name: ENDO_PUTaddGV-2_S48


title: Ectocervical, SPM, noGV, replicate 3

description: Library name: ECTO_SPM-3_S67

value: Ecto

value: Ectocervical

value: noGV


title: dkfz_hem190 [3998920105_R01C01]

description:
3998920105_R01C01
BLL_KMT2A

value: B-ALL

tag: group

value: Test set

tag: material

value: FFPE

tag: age

tag: Sex

value: M

tag: mcf


title: MCL-151

value: lung adenocarcinoma

tag: sample type

tag: patient id

tag: cohort

value: discovery cohort

tag: novel grade

value: VI

tag: tnm 8th_edition_stage


title: Vaginal, SPM, noGV, replicate 3

description: Library name: VK2_SPM-3_S78

tag: cell line

tag: cell type

value: Vaginal

tag: treatment


title: MCL-152

tag: tissue

value: NST

value: IB

tag: passed qc

tag: mean tin


title: MCL-136

value: TRUE

tag: site

value: BMC

tag: sequence batch


title: Ryp3 rpd3delta B

description: Library name: rpd3_Ryp3_B

tag: genotype

tag: antibody

tag: replicate

value: B


title: Vaginal, SPD, GV, replicate 2

description: Library name: VK2_SPDaddGV-2_S44

value: GV


title: MCL-118

value: LMP


title: H4K16Ac 50uM Entinostat A

description: Library name: 50Ent_H4K16_A

tag: additive

value: 50uM Entinostat

value: A

value: fungal cell


title: Ryp2 rpd3delta B

description: Library name: rpd3_Ryp2_B


title: Ryp1 rpd3delta B

description: Library name: rpd3_Ryp1_B


title: MCL-106

tag: sample type


title: H4K16Ac DMSO C

description: Library name: DMSO_H4K16_C

value: DMSO

value: C


title: Vaginal, SPM, GV, replicate 2

description: Library name: VK_SPMaddGV-2_S41


title: Ryp2 rpd3delta C

description: Library name: rpd3_Ryp2_C


title: dkfz_hem001 [200397870025_R01C02]

description:
200397870025_R01C02
BLL_NONKMT2A

value: B-ALL

tag: group

value: Test set

tag: material

value: FFPE

tag: age

tag: Sex

value: M

tag: mcf


title: MCL-150

value: lung adenocarcinoma

tag: patient id

tag: cohort

value: discovery cohort

tag: novel grade

value: VI

tag: tnm 8th_edition_stage


title: dkfz_hem189 [3998523077_R01C02]

description:
3998523077_R01C02
BLL_NONKMT2A

tag: tissue


title: MCL-117

tag: passed qc

value: TRUE

tag: mean tin

tag: site


title: Ryp1 rpd3delta C

description: Library name: rpd3_Ryp1_C

tag: genotype

tag: antibody

tag: cell type


title: UPN2178 [9482801024_R01C02]

description:
9482801024_R01C02
JMML

source_name: Juvenile Myelomonocytic Leukemia

value: Juvenile Myelomonocytic Leukemia

value: PB

value: F


title: Input rpd3delta A

description: Library name: rpd3_input_A

value: Input

tag: replicate


title: MCL-089

tag: sample type

value: LMP

value: BMC

tag: sequence batch


title: Ectocervical, PUT, GV, replicate 2

description: Library name: ECTO_PUTaddGV-2_S45

tag: cell line

value: Ecto

value: Ectocervical

tag: treatment

value: GV


title: UPN2528 [9482801024_R02C02]

description:
9482801024_R02C02
JMML

tag: group

tag: material

tag: age

tag: Sex

tag: mcf


title: UPN2497 [9482801024_R04C02]

description:
9482801024_R04C02
JMML

tag: tissue


title: Input rpd3delta B

description: Library name: rpd3_input_B

value: B

value: fungal cell


title: UPN2099 [9482801069_R06C02]

description:
9482801069_R06C02
JMML

source_name: Juvenile Myelomonocytic Leukemia, low quality excluded from paper

value: Test set


title: Ryp2 rpd3delta A

description: Library name: rpd3_Ryp2_A

value: A


title: Endocervical, SPM, GV, replicate 2

description: Library name: ENDO_SPMaddGV-2_S43

value: Endo

value: Endocervical


title: Endocervical, SPD, GV, replicate 2

description: Library name: ENDO_SPDaddGV-2_S46


title: MCL-121

value: lung adenocarcinoma

value: FFPE

tag: patient id

tag: cohort

value: discovery cohort

tag: novel grade

value: NST

tag: tnm 8th_edition_stage

tag: passed qc


title: UPN2026 [9761749087_R06C01]

description:
9761749087_R06C01
JMML

value: Juvenile Myelomonocytic Leukemia

value: PB

value: F


title: Input G217B C

description: Library name: WT_input_C

tag: genotype

tag: antibody

value: Input

value: C

tag: cell type


title: Ectocervical, SPD, GV, replicate 2

description: Library name: ECTO_SPDaddGV-2_S42

value: Ecto

value: Ectocervical


title: MCL-079

tag: sample type

value: TRUE

tag: mean tin

tag: site

value: BMC

tag: sequence batch


title: MCL-086


title: Vaginal, PUT, noGV, replicate 2

description: Library name: VK2_PUT-2_S35

tag: cell line

value: Vaginal

tag: treatment

value: noGV


title: UPN2531 [9482801024_R05C02]

description:
9482801024_R05C02
JMML

value: BM

tag: group

value: Test set

tag: material

tag: age

tag: Sex

value: M


title: Ryp3 rpd3delta A

description: Library name: rpd3_Ryp3_A

tag: replicate

value: A

value: fungal cell


title: Vaginal, NT, GV, replicate 2

description: Library name: VK_GV-2_S38

value: GV


title: UPN2309 [9482801024_R03C02]

description:
9482801024_R03C02
JMML

tag: tissue

value: Juvenile Myelomonocytic Leukemia

tag: mcf


title: Ryp2 G217B C

description: Library name: WT_Ryp2_C


title: Ectocervical, SPM, GV, replicate 2

description: Library name: ECTO_SPMaddGV-2_S39


title: Endocervical, PUT, GV, replicate 1

description: Library name: ENDO_PUTaddGV-1_S33

value: Endo

value: Endocervical


title: Input G217B B

description: Library name: WT_input_B

value: Input

value: B


title: Endocervical, NT, GV, replicate 2

description: Library name: ENDO_GV-2_S40


title: UPN1804 [9761749080_R06C01]

description:
9761749080_R06C01
JMML

value: PB


title: MCL-067

value: lung adenocarcinoma

value: FFPE

tag: patient id

tag: cohort

value: discovery cohort

tag: novel grade

value: LMP

tag: tnm 8th_edition_stage

tag: passed qc


title: MCL-056

tag: sample type

value: NST

value: TRUE

tag: mean tin

value: BMC


title: Ectocervical, PUT, noGV, replicate 2

description: Library name: ECTO_PUT-2_S31

value: Ecto

tag: cell type

value: Ectocervical

value: noGV


title: UPN2025 [9482801024_R06C01]

description:
9482801024_R06C01
JMML

value: Test set

value: M


title: UPN2301 [9761749087_R02C02]

description:
9761749087_R02C02
JMML

value: Juvenile Myelomonocytic Leukemia

value: F


title: UPN1778 [9482801024_R03C01]

description:
9482801024_R03C01
JMML

value: BM


title: Ectocervical, NT, GV, replicate 2

description: Library name: ECTO_GV-2_S36

tag: cell line

value: GV


title: MCL-105

value: IB

tag: site

tag: sequence batch


title: UPN1974 [9761749087_R05C01]

description:
9761749087_R05C01
JMML

value: PB

tag: group

tag: material


title: Ryp1 G217B B

description: Library name: WT_Ryp1_B

tag: genotype

tag: antibody

value: B

value: fungal cell


title: Endocervical, PUT, noGV, replicate 2

description: Library name: ENDO_PUT-2_S37

value: Endo

value: Endocervical

tag: treatment


title: MCL-087

tag: tissue

value: lung adenocarcinoma

value: FFPE

value: discovery cohort

value: NST

value: TRUE


title: Endocervical, SPM, noGV, replicate 2

description: Library name: ENDO_SPM-2_S29

value: noGV


title: Ryp1 rpd3delta A

description: Library name: rpd3_Ryp1_A

tag: replicate

value: A


title: Endocervical, SPD, noGV, replicate 2

description: Library name: ENDO_SPD-2_S34


title: Ryp3 G217B C

description: Library name: WT_Ryp3_C

value: C


title: UPN1970 [9761749087_R04C01]

description:
9761749087_R04C01
JMML

value: Juvenile Myelomonocytic Leukemia

value: Test set

tag: age

tag: Sex

value: F

tag: mcf


title: UPN1646 [9761749087_R02C01]

description:
9761749087_R02C01
JMML

value: M


title: MCL-068

tag: patient id

tag: cohort

tag: novel grade

tag: tnm 8th_edition_stage

tag: passed qc

value: BMC


title: UPN1740 [9482801024_R02C01]

description:
9482801024_R02C01
JMML

value: PB


title: MCL-023

tag: sample type

tag: mean tin

tag: site


title: Ryp3 G217B A

description: Library name: WT_Ryp3_A

tag: cell type

value: fungal cell


title: MCL-021

value: VI

tag: sequence batch


title: Ryp1 G217B C

description: Library name: WT_Ryp1_C

tag: genotype

tag: antibody


title: UPN1941 [9482801024_R04C01]

description:
9482801024_R04C01
JMML

tag: tissue

tag: group

tag: material


title: UPN1603 [9761749080_R05C01]

description:
9761749080_R05C01
JMML

tag: age

tag: Sex


title: MCL-069

tag: patient id

value: LMP


title: Vaginal, SPM, noGV, replicate 2

description: Library name: VK2_SPM-2_S27

tag: cell line

value: Vaginal

tag: treatment


title: UPN1595 [9482801069_R05C02]

description:
9482801069_R05C02
JMML

tag: mcf


title: Endocervical, NT, noGV, replicate 2

description: Library name: ENDO_NT-2_S26

value: Endo

value: Endocervical


title: MCL-001

value: lung adenocarcinoma

value: FFPE

tag: cohort

value: discovery cohort

tag: novel grade

value: NST

tag: tnm 8th_edition_stage

tag: passed qc


title: UPN1431 [9482801069_R02C02]

description:
9482801069_R02C02
JMML


title: Ryp3 G217B B

description: Library name: WT_Ryp3_B

tag: replicate

value: B

tag: cell type


title: MCL-055

tag: sample type

value: TRUE

tag: mean tin

tag: site

tag: sequence batch


title: Vaginal, SPD, noGV, replicate 2

description: Library name: VK2_SPD-2_S30

value: noGV


title: Input G217B A

description: Library name: WT_input_A

tag: genotype

tag: antibody

value: Input

value: A


title: UPN1348 [9761749080_R03C01]

description:
9761749080_R03C01
JMML

tag: tissue

value: Juvenile Myelomonocytic Leukemia

value: BM

tag: group

value: Test set

tag: material

tag: age

tag: Sex

value: M


title: MCL-188

tag: patient id

tag: cohort

value: LMP

value: BMC


title: Ryp2 G217B B

description: Library name: WT_Ryp2_B

value: fungal cell


title: Ryp2 50uM Entinostat C

description: Library name: 6B

data_processing:
Single or paired-end reads were aligned to the Histoplasma ohiense G217B genome (GCA_017607445.1) using BOWTIE2 version 2.4.2 with default parameters.  Peaks were called for each individual replicate with MACS2 version 2.2.7.1 with default parameters except that min-length was set to 100 for paired-end reads as recommended by Gaspar 2018.  Aggregate peaks were defined by taking the union of the coordinates of overlapping peaks among replicates for regions where peaks were called for at least two replicates. The aggregate peaks defined for 37 °C samples for a given TF were used for quantification of all samples for that TF.  Per peak signal was quantified by counting reads or read pairs in each aggregate peak, log2 transforming with pseudocount of 1 to handle missing data, and normalizing to the signal in the NPS1 negative control region. This negative control region was defined as the middle 500 bp of NPS1 (I7I48_05472, JAEVHH010000002: 444765..449764 (+)). Differential enrichment was then calculated as the difference of the means of the log2 signal over replicates from each condition. Peaks were assigned to individual genes if any part of the peak fell in the intergenic region between the stop codon of the upstream gene and before the start codon for that gene, limiting the intergenic size to a maximum of 10 kb as described in.
Assembly: GCA_017607445.1
Supplementary files format and content: Processed data file for each non-input sample is in MACS2 tab delimited text peaks format
Supplementary files format and content: Supplementary file Table_S8_S9.tar.gz is a tarball of two tab delimited text files, one for Ryp1 ChIP and one for Ryp2 ChIP.  Each file is Excel-compatible tab-delimited text conforming to JavaTreeView extended CDT format.  Each row represents a unique gene to peak association as given in the UNIQID column.  The NAME column gives short names taken from Data S1 of [PMID:35089059] with additional names and corrections based on human curation. Description and HcG217B_pred (WUSTL G217B predicted gene accessions), HcG217B_rc (Edwards et al G217B transcript accessions [PMID: 24112604]), HcG217B_acc (UCSF1 gene accessions [PMID:35089059]), and HcG217B (Gilmore et al transcript accessions [PMID: 26177267]); and Ryp1_ChIP, Ryp2_ChIP, Ryp3_ChIP, and Ryp4_ChIP (indicating genes with promoters bound by Ryp TFs in [PMID: 23935449]) are taken from Data S1 of [PMID:35089059].  Following a GWEIGHT column, included for JavaTreeView compatibility, is ChIP enrichment for each sample followed by mean enrichment over all samples (A) and differential enrichment (DMSO/Ent50), with all enrichment values on a log2 scale.

tag: additive

value: 50uM Entinostat

value: C


title: UPN1312 [9482801069_R06C01]

description:
9482801069_R06C01
JMML

value: Juvenile Myelomonocytic Leukemia, low quality excluded from paper

value: PB

tag: mcf


title: Ryp1 50uM Entinostat C

description: Library name: 6A

tag: replicate


title: MCL-181

value: lung adenocarcinoma

value: FFPE

value: discovery cohort

tag: novel grade

value: VI

tag: tnm 8th_edition_stage

tag: passed qc


title: Ryp1 G217B A

description: Library name: WT_Ryp1_A

tag: cell type


title: Vaginal, NT, noGV, replicate 2

description: Library name: VK2_NT-2_S24

tag: cell line

value: Vaginal

tag: treatment

value: noGV


title: MCL-006

tag: sample type

value: IB

value: TRUE

tag: mean tin

tag: site

tag: sequence batch


title: Ectocervical, SPD, noGV, replicate 2

description: Library name: ECTO_SPD-2_S28

value: Ecto

value: Ectocervical


title: Vaginal, PUT, GV, replicate 1

description: Library name: VK_PUTaddGV-1_S32

value: GV


title: MCL-013

tag: tissue

value: LMP

value: BMC


title: UPN1550 [9482801069_R04C02]

description:
9482801069_R04C02
JMML

value: Juvenile Myelomonocytic Leukemia

tag: group

value: Test set

tag: material

tag: age

tag: Sex

value: M


title: MCL-111

tag: patient id

tag: cohort

value: NST


title: Ectocervical, PUT, GV, replicate 1

description: Library name: ECTO_PUTaddGV-1_S21


title: Input 50uM Entinostat C

description: Library name: 6D

tag: genotype

tag: additive

value: 50uM Entinostat

tag: replicate

value: C

tag: antibody

value: Input

value: fungal cell


title: Ectocervical, NT, noGV, replicate 2

description: Library name: ECTO_NT-2_S23

tag: cell line

tag: cell type


title: Ectocervical, SPD, GV, replicate 1

description: Library name: ECTO_SPDaddGV-1_S18

tag: treatment


title: Ryp3 50uM Entinostat C

description: Library name: 6C


title: Ectocervical, SPM, noGV, replicate 2

description: Library name: ECTO_SPM-2_S25


title: UPN1142 [9482801069_R04C01]

description:
9482801069_R04C01
JMML

value: PB

tag: mcf


title: Vaginal, SPD, GV, replicate 1

description: Library name: VK2_SPDaddGV-1_S20

value: Vaginal


title: Input 50uM Entinostat B

description: Library name: 5D

value: B


title: Ryp2 G217B A

description: Library name: WT_Ryp2_A

value: A


title: MCL-159

value: lung adenocarcinoma

tag: sample type

value: FFPE

value: discovery cohort

tag: novel grade

tag: tnm 8th_edition_stage

tag: passed qc

value: TRUE

tag: mean tin

tag: site


title: MCL-093

tag: tissue

value: LMP

value: BMC

tag: sequence batch


title: Endocervical, SPM, GV, replicate 1

description: Library name: ENDO_SPMaddGV-1_S19

value: Endo

value: Endocervical

value: GV


title: UPN0647 [9761749080_R02C01]

description:
9761749080_R02C01
JMML

value: Juvenile Myelomonocytic Leukemia

value: BM

tag: group

value: Test set

tag: material

tag: age

tag: Sex

value: M


title: UPN1330 [9482801069_R01C02]

description:
9482801069_R01C02
JMML

value: PB

value: F


title: MCL-059

tag: patient id

tag: cohort

value: NST

value: IB


title: Endocervical, SPD, GV, replicate 1

description: Library name: ENDO_SPDaddGV-1_S22

tag: cell line

tag: cell type


title: UPN0969 [9761749076_R02C01]

description:
9761749076_R02C01
JMML

tag: mcf


title: Ryp2 50uM Entinostat B

description: Library name: 5B

tag: genotype

tag: additive

value: 50uM Entinostat

tag: replicate

value: B

tag: antibody

value: fungal cell


title: MCL-039

value: lung adenocarcinoma

tag: sample type

value: FFPE

value: discovery cohort

tag: novel grade

tag: tnm 8th_edition_stage

tag: passed qc

value: TRUE

tag: mean tin


title: UPN1043 [9482801069_R03C01]

description:
9482801069_R03C01
JMML

tag: tissue

tag: group

tag: material


title: MCL-074

tag: patient id

tag: site

value: BMC

tag: sequence batch


title: Ryp3 50uM Entinostat A

description: Library name: 4C

value: A

tag: cell type


title: MCL-047

tag: cohort


title: Ryp3 50uM Entinostat B

description: Library name: 5C

tag: genotype


title: Ectocervical, SPM, GV, replicate 1

description: Library name: ECTO_SPMaddGV-1_S15

tag: cell line

value: Ecto

value: Ectocervical

tag: treatment

value: GV


title: TCGA-RQ-AAAT-01 [9828653044_R06C01]

description:
9828653044_R06C01
DLBCL_N

source_name: Diffuse large B-cell lymphoma GCB(CD10, BCL6,MUM1)

value: Brain

value: Ref set

value: Frozen

tag: age

tag: Sex

value: TCGA

value: TCGA-RQ-AAAT

tag: mcf


title: MCL-042

tag: sample type

tag: novel grade

value: NST

tag: tnm 8th_edition_stage


title: UPN0906 [9482801069_R02C01]

description:
9482801069_R02C01
JMML

tag: tissue

value: Juvenile Myelomonocytic Leukemia

value: PB

value: Test set

value: M


title: UPN0424 [9761749076_R01C01]

description:
9761749076_R01C01
JMML

value: BM

tag: group

value: F


title: Vaginal, SPM, GV, replicate 1

description: Library name: VK_SPMaddGV-1_S17

value: Vaginal


title: Input DMSO C

description: Library name: 3D

tag: additive

value: DMSO

tag: replicate

value: C

tag: antibody

value: Input

value: fungal cell


title: Vaginal, NT, GV, replicate 1

description: Library name: VK_GV-1_S14

value: GV


title: Ryp2 50uM Entinostat A

description: Library name: 4B

value: 50uM Entinostat

value: A


title: Ryp2 DMSO C

description: Library name: 3B


title: UPN0868 [9482801069_R01C01]

description:
9482801069_R01C01
JMML

tag: material


title: MCL-020

value: lung adenocarcinoma

value: FFPE

tag: patient id

value: discovery cohort

tag: passed qc

value: TRUE

tag: mean tin

tag: site

value: BMC

tag: sequence batch


title: Vaginal, PUT, noGV, replicate 1

description: Library name: VK2_PUT-1_S11

tag: cell line

tag: cell type

tag: treatment

value: noGV


title: TCGA-FF-A7CW-01 [9828653043_R03C01]

description:
9828653043_R03C01
DLBCL_EN

source_name: Diffuse large B-cell lymphoma

value: Diffuse large B-cell lymphoma

value: Lymph node

value: Ref set

value: Frozen

tag: age

tag: Sex

value: M

value: TCGA

tag: mcf


title: MCL-046

tag: tissue

tag: sample type

tag: cohort

tag: novel grade

value: NST

tag: tnm 8th_edition_stage


title: Endocervical, PUT, noGV, replicate 1

description: Library name: ENDO_PUT-1_S13

value: Endo

value: Endocervical


title: Input DMSO B

description: Library name: 2D

tag: genotype

tag: additive

value: DMSO

tag: replicate

value: B

tag: antibody

value: Input

value: fungal cell


title: Endocervical, NT, GV, replicate 1

description: Library name: ENDO_GV-1_S16

value: GV


title: MCL-083

value: lung adenocarcinoma

value: FFPE

tag: patient id

value: discovery cohort

value: VI

value: IB

tag: passed qc

value: TRUE

tag: mean tin

tag: site


title: TCGA-FF-A7CQ-01 [9828653029_R05C02]

description:
9828653029_R05C02
DLBCL_EN

source_name: Diffuse large B-cell lymphoma, ABC

value: Diffuse large B-cell lymphoma, ABC

value: Lymph node

tag: group

value: Ref set

tag: material

value: Frozen


title: TCGA-GS-A9TY-01 [9828653044_R01C02]

description:
9828653044_R01C02
DLBCL_N

source_name: Diffuse large B-cell lymphoma GCB

value: Diffuse large B-cell lymphoma GCB

tag: age

tag: Sex

value: F

value: TCGA


title: MCL-041

tag: tissue

value: NST

value: BMC

tag: sequence batch


title: Input 50uM Entinostat A

description: Library name: 4D

value: 50uM Entinostat

value: A

value: Input

tag: cell type

value: fungal cell


title: Ryp3 DMSO B

description: Library name: 2C

value: DMSO

value: B


title: Ryp1 50uM Entinostat B

description: Library name: 5A


title: Ryp1 50uM Entinostat A

description: Library name: 4A


title: MCL-178

value: lung adenocarcinoma

tag: sample type

value: FFPE

tag: cohort

value: discovery cohort

tag: novel grade

value: VI

value: IB

value: LHMC


title: TCGA-FA-A7Q1-01 [9828653029_R05C01]

description:
9828653029_R05C01
DLBCL_N

source_name: Diffuse large B-cell lymphoma NA

value: Diffuse large B-cell lymphoma NA

value: Lymph node

value: Ref set

value: Frozen

tag: mcf


title: MCL-168

value: LMP

tag: tnm 8th_edition_stage

value: TRUE

value: BMC


title: Ectocervical, NT, GV, replicate 1

description: Library name: ECTO_GV-1_S12

tag: cell line

value: Ecto

value: Ectocervical

tag: treatment

value: GV


title: MCL-158

tag: patient id

tag: passed qc


title: TCGA-GS-A9TU-01 [9828653029_R04C02]

description:
9828653029_R04C02
DLBCL_N

value: Diffuse large B-cell lymphoma

value: M

value: TCGA


title: TCGA-FA-A7DS-01 [9828653043_R05C01]

description:
9828653043_R05C01
DLBCL_EN

source_name: Diffuse large B-cell lymphoma, IPT NA

value: Diffuse large B-cell lymphoma, IPT NA

value: Breast

value: F


title: MCL-040

value: lung adenocarcinoma

value: FFPE

value: discovery cohort

value: NST

tag: mean tin

tag: site


title: TCGA-GS-A9TT-01 [9828653029_R02C02]

description:
9828653029_R02C02
DLBCL_EN

value: Diffuse large B-cell lymphoma, ABC

value: Testis

tag: group

value: Ref set

tag: material

value: Frozen


title: Ryp3 DMSO C

description: Library name: 3C

tag: genotype

tag: additive

value: DMSO

tag: replicate

value: C

tag: antibody

value: fungal cell


title: MCL-002

tag: tissue

tag: sample type

value: TRUE

value: BMC

tag: sequence batch


title: MCL-005

tag: cohort

tag: novel grade

value: IB


title: MCL-147

value: VI

tag: tnm 8th_edition_stage

value: FALSE


title: Ryp1 DMSO C

description: Library name: 3A

tag: cell type


title: Ryp2 DMSO A

description: Library name: 1B

value: A


title: TCGA-GS-A9TQ-01 [9828653029_R06C01]

description:
9828653029_R06C01
DLBCL_N

value: Diffuse large B-cell lymphoma GCB

value: Lymph node

tag: age

tag: Sex

value: F

value: TCGA

tag: mcf


title: Vaginal, SPD, noGV, replicate 1

description: Library name: VK2_SPD-1_S8

tag: cell line

value: Vaginal

tag: treatment

value: noGV


title: Ectocervical, PUT, noGV, replicate 1

description: Library name: ECTO_PUT-1_S9

value: Ecto

value: Ectocervical


title: Ryp2 DMSO B

description: Library name: 2B

value: DMSO

value: B


title: TCGA-FF-A7CR-01 [9828653043_R01C01]

description:
9828653043_R01C01
DLBCL_EN

value: Diffuse large B-cell lymphoma

tag: group

value: Ref set

tag: material

value: Frozen

value: M


title: Vaginal, NT, noGV, replicate 1

description: Library name: VK2_NT-1_S2


title: Ectocervical, SPD, noGV, replicate 1

description: Library name: ECTO_SPD-1_S6


title: Ryp1 DMSO B

description: Library name: 2A

tag: genotype

tag: additive

value: fungal cell


title: Endocervical, SPM, noGV, replicate 1

description: Library name: ENDO_SPM-1_S7

source_name: Endo

value: Endo

value: Endocervical


title: Endocervical, NT, noGV, replicate 1

description: Library name: ENDO_NT-1_S4


title: Vaginal, SPM, noGV, replicate 1

description: Library name: VK2_SPM-1_S5