title: HA_Ehd3mu_in_ehd3_1_1_H3K36me3_REP1, ChIP-seq

description:
Library name: HA_Ehd3mu_in_ehd3_1_1_H3K36me3_REP1
rep1


title: HA_Ehd3mu_in_ehd3_1_1_Input_REP2, ChIP-seq

status: Public on Jan 26 2026

type: SRA

city: Shanghai

first: Jiachen

last: Wang

state: Shanghai

address: No. 2005, Songhu Road

department: Institute of Plant Biology

country: China

institute: Fudan University

description:
Library name: HA_Ehd3mu_in_ehd3_1_1_Input_REP2
rep2

library_source: genomic

data_processing:
Raw reads were trimmed to remove the adapters and take out the reads with low sequencing quality score using TrimGalore/Cutadapt.
Clean reads were aligned to the rice reference genome (MSU7) using Bowtie2.
Reads mapped to the chromosome genome were preserved and tools of SAMtools were used to obtain high quality alignment results.
After deduplication, MACS3 and MAnorm were used for peak-calling and differential peaks detection, respectively.
Reads were normalized by the bamCoverage tool in deepTools. To obtain the enrichment signal around the gene body, TSS and TTS, computeMatrix tool in deepTools was employed.
Assembly: MSU7
Supplementary files format and content: BigWig

molecule: genomic DNA

organism: Oryza sativa

source_name: 14-day-old seedlings

growth_protocol: Rice were grown in artificial growth chambers under an LD photoperiod for 14 days.

extract_protocol:
Rice seedlings were harvested and fixed with the buffer containing 0.4 M sucrose, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 1% formaldehyde, and 1 mM PMSF.Chromatin was sonicated into DNA fragments around 150~500-bp in size using lysis buffer containing 50 mM HEPES (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM PMSF, 1% SDS, 0.1% Na deoxycholate, 1% Triton X-100 and Protease Inhibitor cocktail.
The ChIP-seq libraries were constructed by following the manufacturer’s instructions of VAHTSTM Universal DNA Library Prep Kit (Vazyme).

tag: tissue

value: 14-day-old seedlings

tag: cell type

tag: genotype

tag: treatment

value: no treatment


title: HP-MX1083 [207019360125_R04C01]

type: genomic

city: Wantirna South

first: Rust

last: Turakulov

state: Victoria

address: u23 105 Mountain Hwy

department: Bioinformatics

country: Australia

institute: AGRF

description:
207019360125_R04C01
HG_BCL

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

organism: Homo sapiens

source_name: Burkitt lymphoma

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: Burkitt lymphoma

value: Soft tissue, right maxilary sinus

tag: group

value: Ref set

tag: material

value: FFPE

tag: age

tag: Sex

value: M

value: NIH

tag: mcf


title: NiP_Input_REP2, ChIP-seq

description:
Library name: NiP_Input_REP2
rep2

value: Nipponbare


title: HP-AP06 [205724770094_R04C01]

description:
205724770094_R04C01
FDCS

source_name: Follicular Dendritic sarcoma

value: Follicular Dendritic sarcoma


title: Marrow, replicate 5, scRNAseq

city: SYDNEY

first: Peter

last: Croucher

state: NSW

address: 384 VICTORIA ST, DARLINGHURST NSW 2010

institute: Garvan Institute of Medical Research

description:
10x Genomics
Marrow_5

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.2.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: Marrow, femur

extract_protocol:
Cells of the bone microenvironment were isolated from the femurs of C57BL6/J mice. The femurs were separated into diaphysis and metaphysis with the epiphysis removed. Marrow cells were collected by flushing the diaphysis with PBS. Endosteal cells were isolated from marrow-depleted diaphyseal and metaphyseal bone fractions by gently crushing and cutting bones and digested in 2mg/ml of collagenase A and 2.5mg/ml of trypsin for 30 mins at 37ºC. After digestion, bone fractions were vortexed for 10s and the supernatant containing digested cells was filtered through a 100um filter into collection tubes containing 10% FCS. Marrow cells and endosteal cells were then centrifuged at 400 G for 5 mins. Cells of the bone microenvironment were isolated by FACS sorting by enriching for non-erythroid (Ter119-) and live cells (DAPI-).
Libraries were prepared as according to the manufacturer’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in master mix before loading with partitioning oil and gel beads onto a 10X Chromium Next GEM Chip G to partition cells into GEMs (Gel Bead-In EMulsions). Gel beads were then dissolved to release primers (containing TruSeq Read 1 primer sequence, 10X Barcode and Unique Molecular Identifier, or UMI) and co-partitioned cells were lysed before incubating with reverse transcription reagents to generate barcoded, full-length cDNA. GEMs were then broken and the resulting cDNA pooled and purified using silane magnetic beads before amplifying via PCR. cDNA amplicon size was optimized by enzymatic fragmentation and subsequent fragment selection. Final libraries were generated by adding TruSeq Read 2 primer sequence, P5, P7 and a sample index via End Repair, A-tailing, Adaptor Ligation and PCR.

value: Bone microenvironment cells

value: Marrow, femur

tag: strain

value: 8 weeks old


title: HA_Ehd3mu_in_ehd3_1_1_H3K36me3_REP2, ChIP-seq

description:
Library name: HA_Ehd3mu_in_ehd3_1_1_H3K36me3_REP2
rep2


title: HA_Ehd3mu_in_ehd3_1_1_H3K36me2_REP1, ChIP-seq

description:
Library name: HA_Ehd3mu_in_ehd3_1_1_H3K36me2_REP1
rep1


title: W926 [203730640105_R01C01]

description:
203730640105_R01C01
DLBCL_EN

source_name: Diffuse large B-cell lymphoma

value: Diffuse large B-cell lymphoma

value: Brain

value: Test set


title: HA_Ehd3mu_in_ehd3_1_1_H3K36me2_REP2, ChIP-seq

description:
Library name: HA_Ehd3mu_in_ehd3_1_1_H3K36me2_REP2
rep2


title: HA_Ehd3_in_ehd3_1_1_H3K36me3_REP2, ChIP-seq

description:
Library name: HA_Ehd3_in_ehd3_1_1_H3K36me3_REP2
rep2


title: HP-AR92 [205624900058_R07C01]

description:
205624900058_R07C01
FL_A

source_name: Follicular lymphoma, BCL2 neg

value: Follicular lymphoma, BCL2 neg

value: Soft tissue

value: F


title: Marrow, replicate 1, scRNAseq

description:
10x Genomics
Marrow_1


title: HA_Ehd3_in_ehd3_1_1_H3K36me2_REP2, ChIP-seq

description:
Library name: HA_Ehd3_in_ehd3_1_1_H3K36me2_REP2
rep2

value: 14-day-old seedlings

value: no treatment


title: ehd3_H3K36me3_REP, ChIP-seq

description:
Library name: ehd3_H3K36me3_REP
replicate


title: Metaphysis, replicate 5, scRNAseq

description:
10x Genomics
Metaphysis_5

source_name: Metaphysis, femur

value: Metaphysis, femur


title: HP-AS41 [205624900059_R07C01]

description:
205624900059_R07C01
FL_A

source_name: Follicular lymphoma,BCL2 pos

value: Follicular lymphoma,BCL2 pos

value: Lymph node

value: Ref set

value: FFPE


title: HP-AV28 [205722630146_R02C01]

description:
205722630146_R02C01
ALCL_A

source_name: Anaplastic large T-cell lymphoma, ALK-positive

value: M

value: NIH


title: AZ25 [206530740091_R04C01]

description:
206530740091_R04C01
HS

source_name: Histiocytic sarcoma

value: Histiocytic sarcoma

value: Ascending colon


title: NiP_H3K36me2_REP2, ChIP-seq

description:
Library name: NiP_H3K36me2_REP2
rep2

value: Nipponbare


title: NiP_H3K36me2_REP1, ChIP-seq

description:
Library name: NiP_H3K36me2_REP1
rep1


title: HP-BD12 [206382220099_R01C01]

description:
206382220099_R01C01
FL_A

source_name: B-cell lymphoma favor follicular lymphoma, grade 1-2,BCL2 neg(FISH BCL2neg, BCL6Rp, CREBBP arid1b)


title: Metaphysis, replicate 1, scRNAseq

description:
10x Genomics
Metaphysis_1

value: Bone microenvironment cells

value: 8 weeks old


title: NiP_H3K36me3_REP1, ChIP-seq

description:
Library name: NiP_H3K36me3_REP1
rep1


title: Metaphysis, replicate 4, scRNAseq

description:
10x Genomics
Metaphysis_4


title: ehd3_Input_REP, ChIP-seq

description:
Library name: ehd3_Input_REP
replicate


title: NiP_Input_REP1, ChIP-seq

description:
Library name: NiP_Input_REP1
rep1


title: HP-AN-11 [206381860074_R01C01]

description:
206381860074_R01C01
FDCS

source_name: Spindle andepithelioid neoplasm consistent with follicular dendritic cell tumor

value: Brain


title: ehd3_H3K36me2_REP, ChIP-seq

description:
Library name: ehd3_H3K36me2_REP
replicate


title: NiP_H3K36me3_REP2, ChIP-seq

description:
Library name: NiP_H3K36me3_REP2
rep2


title: ehd3_Input_for_HA_rep2, ChIP-seq

description: Library name: ehd3_Input_for_HA_rep2

data_processing:
Raw reads were trimmed to remove the adapters and take out the reads with low sequencing quality score using TrimGalore/Cutadapt.
Clean reads were aligned to the rice reference genome (MSU7) using Bowtie2.
Reads mapped to the chromosome genome were preserved and tools of SAMtools were used to obtain high quality alignments.
After deduplication, we used the bamCoverage tool in deepTools to normalize sequencing reads signals.
We performed peaks calling for the overexpression samples using SICER (W200-G600-FDR0.05), with NiP samples as controls.
The enrichment signals of Ehd or SDG724 were obtained by subtracting the corresponding NiP controls from the antibody-enriched overexpression samples.
Assembly: MSU7
Supplementary files format and content: BigWig (BW)

extract_protocol:
Rice seedlings were harvested and fixed with the buffer containing 0.4 M sucrose, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 1% formaldehyde, and 1 mM PMSF. Chromatin was sonicated into DNA fragments around 150~500-bp in size using lysis buffer containing 50 mM HEPES (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM PMSF, 1% SDS, 0.1% Na deoxycholate, 1% Triton X-100 and Protease Inhibitor cocktail.
The ChIP-seq libraries were constructed by following the manufacturer’s instructions of VAHTSTM Universal DNA Library Prep Kit (Vazyme).

tag: cell line

value: Nipponbare (NiP)


title: Diaphysis, replicate 4, scRNAseq

description:
10x Genomics
Diaphysis_4

source_name: Diaphysis, femur

value: Diaphysis, femur


title: ehd3_Input_for_HA_rep1, ChIP-seq

description: Library name: ehd3_Input_for_HA_rep1

value: 14-day-old seedlings


title: ehd3_HA_rep2, ChIP-seq

description: Library name: ehd3_HA_rep2

value: no treatment


title: Metaphysis, replicate 2, scRNAseq

description:
10x Genomics
Metaphysis_2

value: Metaphysis, femur


title: ehd3_HA_rep1, ChIP-seq

description: Library name: ehd3_HA_rep1


title: HA_Ehd3_Input_rep1, ChIP-seq

description: Library name: HA_Ehd3_Input_rep1


title: Diaphysis, replicate 5, scRNAseq

description:
10x Genomics
Diaphysis_5


title: HP-BQ66 [206084850030_R03C01]

description:
206084850030_R03C01
DLBCL_EN

source_name: Diffuse large B-cell lymphoma, non-GCB (Hans)

value: Soft tissue


title: HP-BQ11 [206084850024_R08C01]

description:
206084850024_R08C01
ETCL_NONSETD2

source_name: Primary cutaneous gamma delta T cell lymphoma

value: Skin

value: F


title: HA_Ehd3_HA_rep3, ChIP-seq

description: Library name: HA_Ehd3_HA_rep3


title: HA_Ehd3_Input_rep2, ChIP-seq

description: Library name: HA_Ehd3_Input_rep2


title: Diaphysis, replicate 2, scRNAseq

description:
10x Genomics
Diaphysis_2


title: Diaphysis, replicate 3, scRNAseq

description:
10x Genomics
Diaphysis_3


title: HA_Ehd3_HA_rep2, ChIP-seq

description: Library name: HA_Ehd3_HA_rep2


title: HA_Ehd3_HA_rep1, ChIP-seq

description: Library name: HA_Ehd3_HA_rep1


title: HP-AN-04 [203726680015_R05C01]

description:
203726680015_R05C01
HS

source_name: Histiocytic sarcoma,P

value: Histiocytic sarcoma,P

value: Tonsil

value: Test set

value: FFPE


title: BR05 [206530740007_R07C01]

description:
206530740007_R07C01
NMZL

source_name: Nodal marginal zone lymphoma with follicular colonization

value: Lymph node

value: Ref set

value: NIH


title: NiP_Input_for_GFP_for_Ehd3_rep1, ChIP-seq

description: Library name: NiP_Input_for_GFP_for_Ehd3_rep1

source_name: 14-day-old seedlings

value: wild-type (NiP)


title: NiP_GFP_for_Ehd3_rep1, ChIP-seq

description: Library name: NiP_GFP_for_Ehd3_rep1


title: HP-BS81 [206084850022_R04C01]

description:
206084850022_R04C01
FL_A

source_name: Primary cutaneous follicle centre lymphoma


title: NiP_GFP_for_Ehd3_rep2, ChIP-seq

description: Library name: NiP_GFP_for_Ehd3_rep2


title: Diaphysis, replicate 1, scRNAseq

description:
10x Genomics
Diaphysis_1

value: Bone microenvironment cells

value: 8 weeks old


title: SDG724_HA_in_ehd3sdg724_HA_rep2, CUT&Tag

description:
Library name: SDG724_HA_in_ehd3sdg724_HA_rep2
rep2

data_processing:
Raw reads were trimmed to remove the adapters and take out the reads with low sequencing quality score using TrimGalore/Cutadapt.
Clean reads were aligned to the rice reference genome (MSU7) using Bowtie2.
Reads mapped to the chromosome genome were preserved and tools of SAMtools were used to obtain high quality alignment results.
After deduplication, regions of non-specific cutting signal resulting from the inherent affinity of the transposome to the genome (blacklists) were excluded, as defined by peaks called from the NiP sample using SICER (W200-G200-E100).
Reads were normalized by the bamCoverage tool in deepTools. To obtain the enrichment signal around the gene body, TSS and TTS, computeMatrix tool in deepTools was employed.
Assembly: MSU7
Supplementary files format and content: BigWig
Supplementary files format and content: BED
Library strategy: CUT&Tag

growth_protocol: Fourteen-day-old Oryza sativa seedlings (2 g) grown on MS medium were ground in liquid nitrogen and resuspended in ChIP isolation buffer containing 0.1% (v/v) formaldehyde.

extract_protocol:
Rice nuclei were extracted by isolation buffer (0.25 M sucrose, 15 mM PIPES, 5 mM MgCl2, 60 mM KCl, 15 mM NaCl, 1 mM CaCl2, 0.9% (v/v) Triton X-100, 1 mM PMSF, 0.1% (v/v) formaldehyde, and proteinase inhibitor cocktail (Roche), pH 6.8).
Cross-linking was quenched by adding 2.5 M Glycine. Nuclei were bound to Concanavalin A (ConA) beads and incubated overnight at 4 °C with an anti-HA  antibody. After washing, samples were incubated with an anti-rabbit IgG H&L antibody for 1 h at room temperature, followed by incubation with Tn5 transposase for 1 h at room temperature. Target chromatin was fragmented at 37 °C for 1 h, and reverse cross-linking was performed at 55 °C for 3 h. DNA was purified, and libraries were constructed and amplified.

value: SDG724-HA/ehd3 sdg724


title: EGFP_Ehd3_GFP_rep2, ChIP-seq

description: Library name: EGFP_Ehd3_GFP_rep2

value: 14-day-old seedlings

value: Nipponbare (NiP)


title: NiP_Input_for_GFP_for_Ehd3_rep2, ChIP-seq

description: Library name: NiP_Input_for_GFP_for_Ehd3_rep2

value: no treatment


title: BS76.1 [206530740021_R01C01]

description:
206530740021_R01C01
FHTCL

source_name: PTCL_TFH with expansion of clonal B cells

value: Soft tissue

value: M


title: SS_Syn with Penicillium with EM2

city: Bangkok

first: Jidapa

last: Leksingto

country: Thailand

institute: Chulalongkorn

description: Library name: SS_Syn with Penicillium with EM replicate2 R1, SS_Syn with Penicillium with EM replicate2 R2

library_source: transcriptomic

data_processing:
cDNA libraries were quantified using a DeNovix fluorometer (DeNovix).
Pair-end 125 nucleotides read sequencing on an Illumina HiSeq sequencer was done with cluster creation.
The quality of the raw read data was examined using the FASTQC software.
Fastp software was used to delete adapters and low-quality reads.
Salmon software was used to compare high-quality reads to the reference genome sequence (Synechocystis sp. PCC 6803, accession number: ASM972v1). DESeq2 was used for the differential gene expression analysis (FDR 0.05, log2 fold change > 1.0)
Assembly: mm10, Synechocystis sp. PCC 6803, accession number: ASM972v1
Supplementary files format and content: fold-change
Supplementary files format and content: fold-change of transcript level

organism: Synechocystis sp. PCC 6803

source_name: total cell

growth_protocol: BG11 medium cultured for 5 day

extract_protocol:
TRIzol reagent (Life Technologies, Carlsbad, CA, USA) was used to extract RNA
. In brief, RNA strand-specific RNA-Seq libraries were created using the QIAseq FastSelect RNA removal and QIAseq stranded total RNA library preparation kits (QIAGEN).

treatment_protocol: with and without erythromycin

value: total cell

value: wild type


title: EGFP_Ehd3_GFP_rep1, ChIP-seq

description: Library name: EGFP_Ehd3_GFP_rep1


title: HA_Ehd3_in_ehd3_1_1_H3K36me3_REP1, ChIP-seq

description:
Library name: HA_Ehd3_in_ehd3_1_1_H3K36me3_REP1
rep1


title: NiP_Input_for_GFP_for_SDG724_rep4, ChIP-seq

description: Library name: NiP_Input_for_GFP_for_SDG724_rep4


title: HP-8293 [204551190109_R02C01]

description:
204551190109_R02C01
HCL

source_name: Hairy cell leukemia

value: Hairy cell leukemia

value: Peripheral blood

value: Frozen


title: NiP_GFP_for_SDG724_rep2, ChIP-seq

description: Library name: NiP_GFP_for_SDG724_rep2


title: HP-BW36 [206082540131_R03C01]

description:
206082540131_R03C01
PCN

source_name: Plasma cell neoplasm

value: Plasma cell neoplasm

value: Lymph node

value: FFPE

value: F


title: NiP_GFP_for_SDG724_rep1, ChIP-seq

description: Library name: NiP_GFP_for_SDG724_rep1

value: wild-type (NiP)


title: SS_Syn with Penicillium with EM3

description: Library name: SS_Syn with Penicillium with EM replicate3 R1, SS_Syn with Penicillium with EM replicate3 R2


title: SS_Syn with Penicillium with EM1

description: Library name: SS_Syn with Penicillium with EM replicate1 R1, SS_Syn with Penicillium with EM replicate1 R2


title: NiP_Input_for_GFP_for_SDG724_rep2, ChIP-seq

description: Library name: NiP_Input_for_GFP_for_SDG724_rep2


title: CQ07 [206530730100_R08C01]

description:
206530730100_R08C01
FL_A

source_name: Follicular Lymphoma Grade 3B (CD10 negative, MUM1 positive and reported BCL2 gene translocation negative).

value: Lymph nodes, left inguinal and left axillary, excisional biopsy

value: Ref set

value: NIH


title: Syn with EM3

description: Library name: Syn with EM replicate3 R1, Syn with EM replicate3 R2


title: NiP_Input_for_GFP_for_SDG724_rep1, ChIP-seq

description: Library name: NiP_Input_for_GFP_for_SDG724_rep1

value: 14-day-old seedlings

value: Nipponbare (NiP)


title: Syn with EM1

description: Library name: Syn with EM replicate1 R1, Syn with EM replicate1 R2


title: HP-BQ41 [206084850030_R02C01]

description:
206084850030_R02C01
DLBCL_EN

source_name: Primary cutaneous diffuse large B-cell lymphoma, leg type

value: Skin


title: HP-BX60 [206381860062_R05C01]

description:
206381860062_R05C01
ENKTL

source_name: Extranodal NK/T-cell lymphoma, nasal type

value: Left adrenal gland

value: M


title: NiP_GFP_for_SDG724_rep4, ChIP-seq

description: Library name: NiP_GFP_for_SDG724_rep4

value: no treatment


title: LR_Syn with Penicillium with EM2

description: Library name: LR_Syn with Penicillium with EM replicate2 R1, LR_Syn with Penicillium with EM replicate2 R2

value: total cell

value: wild type


title: LR_Syn with Penicillium with EM3

description: Library name: LR_Syn with Penicillium with EM replicate3 R1, LR_Syn with Penicillium with EM replicate3 R2


title: HP-E620 [204809970041_R02C01]

description:
204809970041_R02C01
CLL

source_name: Chronic lymphocytic leukaemia/small lymphocytic lymphoma

value: Test set

value: Frozen


title: Syn without EM3

description: Library name: Syn without EM_3


title: YFP_SDG724_Input_rep4, ChIP-seq

description: Library name: YFP_SDG724_Input_rep4


title: NiP_GFP_for_SDG724_rep3, ChIP-seq

description: Library name: NiP_GFP_for_SDG724_rep3


title: YFP_SDG724_Input_rep2, ChIP-seq

description: Library name: YFP_SDG724_Input_rep2


title: NiP_Input_for_GFP_for_SDG724_rep3, ChIP-seq

description: Library name: NiP_Input_for_GFP_for_SDG724_rep3


title: CO36 [206535560055_R08C01]

description:
206535560055_R08C01
ETCL_NONSETD2

value: Primary cutaneous gamma delta T cell lymphoma

value: Soft tissue


title: YFP_SDG724_Input_rep1, ChIP-seq

description: Library name: YFP_SDG724_Input_rep1


title: YFP_SDG724_GFP_rep2, ChIP-seq

description: Library name: YFP_SDG724_GFP_rep2


title: ehd3_Input_rep2, ChIP-seq

description: Library name: ehd3_Input_rep2

data_processing:
Raw reads were trimmed to remove the adapters and take out the reads with low sequencing quality score using TrimGalore/Cutadapt.
Clean reads were aligned to the rice reference genome (MSU7) using Bowtie2.
Reads mapped to the chromosome genome were preserved and tools of SAMtools were used to obtain high quality alignments.
After deduplication, MACS3 and MAnorm were used for peak-calling and differential peaks detection, respectively.
Reads were normalized by the bamCoverage tool in deepTools. To obtain the enrichment signal around the gene body, TSS and TTS, computeMatrix tool in deepTools was employed.
Assembly: MSU7
Supplementary files format and content: BigWig

extract_protocol:
Rice seedlings were harvested and fixed with the buffer containing 0.4 M sucrose, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 1% formaldehyde, and 1 mM PMSF.Chromatin was sonicated into DNA fragments around 150~500-bp in size using lysis buffer containing 50 mM HEPES (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM PMSF, 1% SDS, 0.1% Na deoxycholate, 1% Triton X-100 and Protease Inhibitor cocktail.
Genome enrichment/distribution profiling by high throughput sequencing
The ChIP-seq libraries were constructed by following the manufacturer’s instructions of VAHTSTM Universal DNA Library Prep Kit (Vazyme).

tag: replicate


title: HP-AN74 [203723050032_R04C01]

description:
203723050032_R04C01
ETCL_SETD2

source_name: Nodal marginal zone lymphoma

value: Nodal marginal zone lymphoma

value: Lymph node

value: FFPE


title: YFP_SDG724_GFP_rep3, ChIP-seq

description: Library name: YFP_SDG724_GFP_rep3


title: YFP_SDG724_Input_rep3, ChIP-seq

description: Library name: YFP_SDG724_Input_rep3


title: Syn without EM2

description: Library name: Syn without EM_2


title: ehd3_Input_rep3, ChIP-seq

description: Library name: ehd3_Input_rep3


title: Syn with Penicillium without EM3

description: Library name: Syn with Penicillium replicate3 R1, Syn with Penicillium replicate3 R2


title: LR_Syn with Penicillium with EM1

description: Library name: LR_Syn with Penicillium with EM replicate1 R1, LR_Syn with Penicillium with EM replicate1 R2


title: YFP_SDG724_GFP_rep4, ChIP-seq

description: Library name: YFP_SDG724_GFP_rep4


title: osldl3_Input_rep1, ChIP-seq

description:
Library name: osldl3_Input_rep1
rep1

extract_protocol:
Rice seedlings were harvested and fixed with the buffer containing 0.4 M sucrose, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 1% formaldehyde, and 1 mM PMSF.Chromatin was sonicated into DNA fragments around 150~500-bp in size using lysis buffer containing 50 mM HEPES (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM PMSF, 1% SDS, 0.1% Na deoxycholate, 1% Triton X-100 and Protease Inhibitor cocktail.
Genome enrichment/distribution profiling by high throughput sequencing.
The ChIP-seq libraries were constructed by following the manufacturer’s instructions of VAHTSTM Universal DNA Library Prep Kit (Vazyme).

tag: chip antibody


title: Syn with EM2

description: Library name: Syn with EM replicate2 R1, Syn with EM replicate2 R2


title: Syn with Penicillium without EM2

description: Library name: Syn with Penicillium replicate2 R1, Syn with Penicillium replicate2 R2


title: DQ64 [206699910050_R05C01]

description:
206699910050_R05C01
BL_EBVN

source_name: High grade B-cell lymphoma, consistent with Burkitt lymphoma

value: Ref set


title: YFP_SDG724_GFP_rep1, ChIP-seq

description: Library name: YFP_SDG724_GFP_rep1


title: DQ63 [206699910050_R04C01]

description:
206699910050_R04C01
FTHCL

source_name: Peripheral T-cell lymphoma

value: Peripheral T-cell lymphoma

value: NIH


title: NiP_HA_rep1, CUT&Tag

description:
Library name: NiP_HA_rep1
rep1

value: 14-day-old seedlings

value: Nipponbare


title: Syn with Penicillium without EM1

description: Library name: Syn with Penicillium replicate1 R1, Syn with Penicillium replicate1 R2


title: BQ49 [206530740013_R06C01]

description:
206530740013_R06C01
FHTCL

source_name: Manual Override - Nodal Peripheral T cell lymphoma with T follicular helper cell (TFH) phenotype(lack of FDC meshwork so no AITL) with associated monoclonal B-cell / plasma cell proliferation.


title: osldl3_H3_rep2, ChIP-seq

description:
Library name: osldl3_H3_rep2
rep2


title: NiP_Input_rep2, ChIP-seq

description: Library name: NiP_Input_rep2

value: wild-type


title: Syn without EM1

description: Library name: Syn without EM_1


title: ehd3_Input_rep1, ChIP-seq

description: Library name: ehd3_Input_rep1


title: osldl3_H3_rep1, ChIP-seq

description:
Library name: osldl3_H3_rep1
rep1


title: HP-Z051 [205379750080_R03C01]

description:
205379750080_R03C01
HS

source_name: Malignant sarcomatoid neoplasm with epithelioid morphology, a histiocytic sarcoma.

value: Colorectal

value: M


title: osldl3_H3K4me2_rep2, ChIP-seq

description:
Library name: osldl3_H3K4me2_rep2
rep2

value: no treatment


title: osldl3_H3K4me3_rep1, ChIP-seq

description:
Library name: osldl3_H3K4me3_rep1
rep1


title: HP-AN54 [203136010021_R01C01]

description:
203136010021_R01C01
ETCL_SETD2

source_name: meitl

value: meitl

value: Gastrointestinal


title: HP-CA92 [206382220073_R04C01]

description:
206382220073_R04C01
ETCL_NONSETD2

source_name: Primary cutaneous gamma delta T cell lymphoma

value: Skin


title: osldl3_Input_rep2, ChIP-seq

description:
Library name: osldl3_Input_rep2
rep2

source_name: 14-day-old seedlings


title: NiP_Input_rep3, ChIP-seq

description: Library name: NiP_Input_rep3


title: NiP_Input_rep1, ChIP-seq

description: Library name: NiP_Input_rep1


title: osldl3_H3K4me1_rep2, ChIP-seq

description:
Library name: osldl3_H3K4me1_rep2
rep2


title: TR16 [202135260046_R05C01]

description:
202135260046_R05C01
TLL_C

source_name: T-lymphoblastic leukemia/lymphoma

value: T-lymphoblastic leukemia/lymphoma

value: Bone marrow

value: Frozen


title: D-6

city: zhengzhou

first: Deqian

last: Kong

state: henan

address: No.1 Longhu Zhonghuan Road, Jinshui District

institute: The First Affiliated Hospital of Zhengzhou University

description:
Library name: D-6
lncRNA GAS5 KO group, replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DM 1-3 516 R44 (v6.1)  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes gene counts and fpkm for each sample

source_name: cell culture

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: cell culture


title: BL82 [205841330048_R03C01]

description:
205841330048_R03C01
HS

source_name: Histiocytic sarcoma

value: Histiocytic sarcoma

value: Brain

value: FFPE

value: F


title: TR15 [202135260046_R04C01]

description:
202135260046_R04C01
TLL_A

value: Lymph node

value: Ref set


title: D-4

description:
Library name: D-4
lncRNA GAS5 KO group, replicate biosample 1


title: Control-6

description:
Library name: Control-6
lncRNA GAS5 control group, replicate biosample 3


title: osldl3_H3K4me2_rep1, ChIP-seq

description:
Library name: osldl3_H3K4me2_rep1
rep1

value: 14-day-old seedlings


title: osldl3_H3K4me3_rep2, ChIP-seq

description:
Library name: osldl3_H3K4me3_rep2
rep2


title: NiP_H3K4me2_for_osldl3, tech replicate, ChIP-seq

description:
Library name: NiP_H3K4me2_for_osldl3_techrep
Technical replicates

value: Nipponbare

value: wild-type


title: TP8 [202135260016_R07C01]

description:
202135260016_R07C01
TLL_B

value: Soft tissue

value: M


title: osldl3_H3K4me1_rep1, ChIP-seq

description:
Library name: osldl3_H3K4me1_rep1
rep1

value: no treatment


title: CN96 [206537460072_R08C01]

description:
206537460072_R08C01
LCH

source_name: Langerhans cell histocytosis

value: Langerhans cell histocytosis

value: NIH


title: NiP_H3_for_osldl3, tech replicate, ChIP-seq

description:
Library name: NiP_H3_for_osldl3_techrep
Technical replicates


title: NiP_Input_for_osldl3, tech replicate, ChIP-seq

description:
Library name: NiP_Input_for_osldl3_techrep
Technical replicates


title: Control-4

description:
Library name: Control-4
lncRNA GAS5 control group, replicate biosample 1


title: NiP_H3K4me3_for_osldl3, tech replicate, ChIP-seq

description:
Library name: NiP_H3K4me3_for_osldl3_techrep
Technical replicates


title: Control-5

description:
Library name: Control-5
lncRNA GAS5 control group, replicate biosample 2


title: NiP_H3K4me2_for_osldl3, ChIP-seq

description:
Library name: NiP_H3K4me2_for_osldl3
Technical replicates


title: D-5

description:
Library name: D-5
lncRNA GAS5 KO group, replicate biosample 2


title: HP-CI48 [206382220028_R03C01]

description:
206382220028_R03C01
DLBCL_EN

source_name: Partial involvement by DLBCL, GCB

value: Partial involvement by DLBCL, GCB

value: tonsil


title: TR12 [202135260046_R01C01]

description:
202135260046_R01C01
TLL_A

value: T-lymphoblastic leukemia/lymphoma

value: Blood

value: Frozen


title: D-3

description:
Library name: D-3
lncRNA GAS5 KO group, replicate biosample 3

value: cell culture


title: NiP_H3K4me1_for_osldl3, ChIP-seq

description:
Library name: NiP_H3K4me1_for_osldl3
Technical replicates


title: NiP_H3K4me1_for_osldl3, tech replicate, ChIP-seq

description:
Library name: NiP_H3K4me1_for_osldl3_techrep
Technical replicates


title: NiP_Input_for_osldl3, ChIP-seq

description:
Library name: NiP_Input_for_osldl3
Technical replicates


title: D-2

description:
Library name: D-2
lncRNA GAS5 KO group, replicate biosample 2


title: NiP_H3_for_osldl3, ChIP-seq

description:
Library name: NiP_H3_for_osldl3
Technical replicates


title: NiP_H3K4me3_for_osldl3, ChIP-seq

description:
Library name: NiP_H3K4me3_for_osldl3
Technical replicates


title: TP7 [202135260016_R06C01]

description:
202135260016_R06C01
TLL_B


title: ehd3sdg724_rep1, RNA-seq

data_processing:
Raw reads were cleaned by Cutadapt v3.5 to remove low quality bases and sequencing adapters.
Then trimmed reads were mapped to rice reference genome MSU7 using HISAT2 v2.1.0.
Samtools v1.17 was used to remove the low mapping quality (MAPQ<20) reads and then featureCounts v2.0.1 was used to count the number of reads that were aligned to exons.
Assembly: MSU7
Supplementary files format and content: Binary bw files (bigwig)
Supplementary files format and content: Tab-delimited text files including featureCounts value and TPM (Transcripts per million) for each Sample

molecule: polyA RNA

extract_protocol:
RNA was extracted using an RNAprep pure Plant Kit (Tiangen Biotech).
The strand-specific RNA-seq libraries were constructed by following the KAPA stranded mRNA-seq Kit instructions (Illumina® Platforms, KR0960-v5.17), according to the manufacturer’s instructions.

value: ehd3 sdg724


title: ehd3sdg724_rep2, RNA-seq


title: TP4 [202135260016_R03C01]

description:
202135260016_R03C01
TLL_A

value: Bone marrow

value: Test set


title: Control-1

description:
Library name: Control-1
control group, replicate biosample 1


title: Control-3

description:
Library name: Control-3
control group, replicate biosample 3


title: D-1

description:
Library name: D-1
lncRNA GAS5 KO group, replicate biosample 1


title: TP5 [202135260016_R04C01]

description:
202135260016_R04C01
TLL_B

value: Ref set


title: Control-2

description:
Library name: Control-2
control group, replicate biosample 2


title: ehd3_rep3, RNA-seq

value: 14-day-old seedlings

value: Nipponbare


title: TP6 [202135260016_R05C01]

description:
202135260016_R05C01
TLL_B

value: Soft tissue


title: Periostin-treated human nasal epithelial cells (replicate 3)

city: Sakado

first: Yusuke

last: Ando

state: Saitama

address: 1-1, Keyaki-dai

country: Japan

institute: Josai University

description: Library name: hNEC_POSTN_rep3

data_processing:
Raw sequencing reads were quality-controlled and aligned to the human reference genome. Gene-level read counts were generated. Transcript abundance was normalized and expressed as TPM values.
Assembly: GRCh38
Supplementary files format and content: hNEC_RNAseq_raw_counts.tsv: gene-level raw read counts for all samples hNEC_RNAseq_TPM.tsv: gene-level TPM values for all samples

source_name: nasal epithelium

growth_protocol: Primary human nasal epithelial cells were cultured under standard submerged conditions according to the supplier’s instructions.

extract_protocol:
Total RNA was extracted using a commercial RNA extraction kit according to the manufacturer’s protocol.
RNA-seq libraries were prepared using a poly(A) selection-based library preparation kit following the manufacturer’s instructions.

treatment_protocol: Cells were treated with recombinant human periostin or vehicle control for the indicated duration prior to RNA extraction.

value: nasal epithelium

value: primary human nasal epithelial cells

value: recombinant human periostin


title: TP3 [202135260016_R02C01]

description:
202135260016_R02C01
TLL_A

value: Effusion

value: F


title: ehd3sdg724_rep3, RNA-seq

value: no treatment


title: sdg724_rep1, RNA-seq


title: sdg724_rep3, RNA-seq


title: TR11 [202110250045_R08C01]

description:
202110250045_R08C01
TLL_B

value: T-lymphoblastic leukemia/lymphoma

value: M


title: NiP_rep2, RNA-seq

value: wild type


title: NiP_rep3, RNA-seq


title: ehd3_rep2, RNA-seq


title: TP2 [202135260016_R01C01]

description:
202135260016_R01C01
TLL_B

value: Frozen


title: ehd3_rep1, RNA-seq


title: sdg724_rep2, RNA-seq


title: ehd3sdg724_Input_rep3, ChIP-seq

value: ehd3 sdg724


title: ehd3sdg724_Input_rep2, ChIP-seq


title: Periostin-treated human nasal epithelial cells (replicate 2)

description: Library name: hNEC_POSTN_rep2


title: NiP_rep1, RNA-seq


title: TP16 [202110250045_R07C01]

description:
202110250045_R07C01
TLL_C

value: Bone marrow


title: ehd3sdg724_Input_rep4, ChIP-seq


title: Control human nasal epithelial cells (replicate 2)

description: Library name: hNEC_Control_rep2

value: vehicle control


title: ehd3sdg724_H3_rep2, ChIP-seq


title: ehd3sdg724_H3_rep1, ChIP-seq


title: Control human nasal epithelial cells (replicate 3)

description: Library name: hNEC_Control_rep3


title: Control human nasal epithelial cells (replicate 1)

description: Library name: hNEC_Control_rep1


title: ehd3sdg724_Input_rep1, ChIP-seq


title: TP15 [202110250045_R06C01]

description:
202110250045_R06C01
TLL_A

value: Test set


title: ehd3sdg724_H3K36me2_rep2, ChIP-seq

value: 14-day-old seedlings


title: ehd3sdg724_H3K36me2_rep1, ChIP-seq

value: Nipponbare


title: ehd3sdg724_H3K36me3_rep1, ChIP-seq


title: Periostin-treated human nasal epithelial cells (replicate 1)

description: Library name: hNEC_POSTN_rep1


title: TP12 [202110250045_R03C01]

description:
202110250045_R03C01
TLL_A


title: TP13 [202110250045_R04C01]

description:
202110250045_R04C01
TLL_A

value: Lymph node


title: ehd3sdg724_H3K36me2_rep4, ChIP-seq


title: ehd3sdg724_H3K36me3_rep2, ChIP-seq


title: Cr_rep3, mRNA-seq

data_processing:
Raw reads were cleaned by Cutadapt v3.5 to remove low quality bases and sequencing adapters.
Then trimmed reads were mapped to the reference genome Chlamydomonas_reinhardtii_v5.5 (Ensembl Plants)  using HISAT2 v2.1.0.
Samtools v1.17 was used to remove the low mapping quality (MAPQ<20) reads and then featureCounts v2.0.1 was used to count the number of reads that were aligned to exons.
Assembly: Chlamydomonas_reinhardtii_v5.5 (Ensembl Plants)
Supplementary files format and content: Binary bw files (bigwig)
Supplementary files format and content: Tab-delimited text files including featureCounts value and TPM (Transcripts per million) for each Sample

organism: Chlamydomonas reinhardtii

source_name: cells

growth_protocol: Chlamydomonas reinhardtii were grown in Tris-acetate-phosphate medium on a rotary shaker at 24°C to a density of 4-8 × 10^6 cells/ml.

value: cells

value: wild-type


title: Metaphysis, replicate 3, scRNAseq

description:
10x Genomics
Metaphysis_3

source_name: Metaphysis, femur

value: Bone microenvironment cells

value: Metaphysis, femur

value: 8 weeks old


title: TP14 [202110250045_R05C01]

description:
202110250045_R05C01
TLL_A

value: Effusion


title: Cr_Input_rep1, ChIP-seq

data_processing:
Raw reads were trimmed to remove the adapters and take out the reads with low sequencing quality score using TrimGalore/Cutadapt.
Clean reads were aligned to the Arabidopsis thaliana reference genome Chlamydomonas_reinhardtii_v5.5 (Ensembl Plants) using Bowtie2.
Reads mapped to the chromosome genome were preserved and tools of SAMtools were used to obtain high quality alignments.
Sequencing signals were normalized by the bamCoverage tool in deepTools. To obtain the enrichment signal around the gene body, TSS and TTS, computeMatrix tool in deepTools was employed.
Assembly: Chlamydomonas_reinhardtii_v5.5 (Ensembl Plasnts)
Supplementary files format and content: bigwig

source_name: cell

extract_protocol:
Cells were harvested and fixed with the buffer containing 0.4 M sucrose, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 1% formaldehyde, and 1 mM PMSF. Chromatin was sonicated into DNA fragments around 150~500-bp in size using lysis buffer containing 50 mM HEPES (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM PMSF, 1% SDS, 0.1% Na deoxycholate, 1% Triton X-100 and Protease Inhibitor cocktail.
ChIP-seq libraries were constructed by following the manufacturer’s instructions of VAHTSTM Universal DNA Library Prep Kit (Vazyme).

value: cell

value: no treatment


title: ehd3sdg724_H3K36me3_rep3, ChIP-seq


title: Cr_H3K36me3_rep2, ChIP-seq


title: X9.2 [200340580162_R05C01]

description:
200340580162_R05C01
BLL_KMT2A

source_name: Infant B-cell precursor acute lymphoblastic leukemia

value: Ref set

value: F


title: Cr_rep1, mRNA-seq


title: X4.36 [200340580162_R03C01]

description:
200340580162_R03C01
BLL_KMT2A

value: Infant B-cell precursor acute lymphoblastic leukemia

value: Frozen


title: ehd3sdg724_H3K36me1_rep2, ChIP-seq

value: ehd3 sdg724


title: Cr_rep2, mRNA-seq


title: ehd3sdg724_H3K4me3_rep3, ChIP-seq


title: ehd3sdg724_H3K4me2_rep1, ChIP-seq


title: ehd3sdg724_H3K36me2_rep3, ChIP-seq


title: Cr_H3K36me2_rep2, ChIP-seq


title: TP1 [202110250006_R08C01]

description:
202110250006_R08C01
TLL_B

value: T-lymphoblastic leukemia/lymphoma

value: Test set

value: M


title: ehd3sdg724_H3K36me1_rep3, ChIP-seq

value: 14-day-old seedlings

value: Nipponbare


title: TP11 [202110250045_R02C01]

description:
202110250045_R02C01
TLL_B


title: Cr_H3K36me1_rep2, ChIP-seq

value: wild-type


title: Cr_Input_rep2, ChIP-seq


title: ehd3sdg724_H3K36me1_rep1, ChIP-seq


title: ehd3sdg724_H3K4me3_rep2, ChIP-seq


title: TP10 [202110250045_R01C01]

description:
202110250045_R01C01
TLL_B


title: ehd3sdg724_H3K4me2_rep2, ChIP-seq


title: sdg724_Input_rep1, ChIP-seq


title: X9.1 [200340580161_R05C01]

description:
200340580161_R05C01
BLL_KMT2A

value: Bone marrow


title: Cr_H3K4me3_rep2, ChIP-seq


title: ehd3sdg724_H3K4me1_rep3, ChIP-seq


title: X4.24 [200340580162_R02C01]

description:
200340580162_R02C01
BLL_KMT2A


title: X4.11 [200340580161_R01C01]

description:
200340580161_R01C01
BLL_KMT2A


title: Cr_H3K36me3_rep1, ChIP-seq


title: ehd3sdg724_H3K4me3_rep1, ChIP-seq


title: sdg724_H3K36me3_rep3, ChIP-seq


title: M.21 [200340580160_R05C01]

description:
200340580160_R05C01
BLL_NONKMT2A


title: sdg724_Input_rep4, ChIP-seq


title: sdg724_H3K36me3_rep2, ChIP-seq


title: sdg724_H3K36me3_rep1, ChIP-seq


title: X4.34 [200340580160_R03C01]

description:
200340580160_R03C01
BLL_KMT2A


title: sdg724_Input_rep3, ChIP-seq


title: ehd3sdg724_H3K4me1_rep2, ChIP-seq


title: M.10 [200340580161_R04C01]

description:
200340580161_R04C01
BLL_NONKMT2A


title: sdg724_H3K36me2_rep2, ChIP-seq


title: ehd3sdg724_H3K4me2_rep3, ChIP-seq


title: X4.35 [200340580161_R03C01]

description:
200340580161_R03C01
BLL_KMT2A


title: sdg724_H3K36me2_rep3, ChIP-seq


title: MCL-082 [9007217084_R01C01]

description:
9007217084_R01C01
MCL_SOX11P

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

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

value: Lymph node


title: sdg724_H3_rep2, ChIP-seq


title: sdg724_Input_rep2, ChIP-seq


title: ehd3sdg724_H3K4me1_rep1, ChIP-seq


title: X4.23 [200340580161_R02C01]

description:
200340580161_R02C01
BLL_KMT2A


title: sdg724_H3K4me3_rep1, ChIP-seq


title: MCL-081 [9007217084_R01C02]

description:
9007217084_R01C02
MCL_SOX11P

source_name: Mantle Cell Lymphoma. SOX11: NegativeMCL_morphology: , Nodal: Yes, Series_origin: Kiel

value: Mantle Cell Lymphoma. SOX11:NegativeMCL_morphology:, Nodal:Yes, Series_origin:Kiel


title: Cr_H3K4me2_rep2, ChIP-seq

value: cell


title: Cr_H3K36me2_rep1, ChIP-seq

value: no treatment


title: MCL-080 [9007217084_R06C01]

description:
9007217084_R06C01
MCL_SOX11P

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

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

value: Ref set


title: sdg724_H3K4me2_rep2, ChIP-seq


title: sdg724_H3K36me2_rep1, ChIP-seq


title: Cr_H3K4me2_rep1, ChIP-seq


title: X4.22 [200340580160_R02C01]

description:
200340580160_R02C01
BLL_KMT2A

value: Infant B-cell precursor acute lymphoblastic leukemia


title: X4.32 [200340580083_R03C01]

description:
200340580083_R03C01
BLL_KMT2A

value: Frozen


title: Cr_H3K4me3_rep1, ChIP-seq


title: sdg724_H3K4me1_rep3, ChIP-seq


title: X4.10 [200340580160_R01C01]

description:
200340580160_R01C01
BLL_KMT2A


title: Cr_H3K4me1_rep2, ChIP-seq


title: X4.20 [200340580083_R02C01]

description:
200340580083_R02C01
BLL_KMT2A

value: F


title: MCL-079 [9007217084_R05C01]

description:
9007217084_R05C01
MCL_SOX11P

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

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


title: sdg724_H3K4me1_rep1, ChIP-seq


title: sdg724_H3K36me1_rep3, ChIP-seq


title: sdg724_H3_rep1, ChIP-seq


title: Cr_H3K36me1_rep1, ChIP-seq


title: MCL-078 [9007217069_R01C02]

description:
9007217069_R01C02
MCL_SOX11P


title: sdg724_H3K36me2_rep4, ChIP-seq


title: sdg724_H3K36me1_rep2, ChIP-seq


title: M.18 [200340580079_R05C01]

description:
200340580079_R05C01
BLL_NONKMT2A


title: MCL-077 [9007217068_R06C01]

description:
9007217068_R06C01
MCL_SOX11P

source_name: Mantle Cell Lymphoma. SOX11: PositiveMCL_morphology: , Nodal: Yes, Series_origin: Kiel

value: Mantle Cell Lymphoma. SOX11:PositiveMCL_morphology:, Nodal:Yes, Series_origin:Kiel


title: ehd3_H3K36me3_rep2, ChIP-seq


title: ehd3_H3K36me3_rep3, ChIP-seq


title: sdg724_H3K4me3_rep3, ChIP-seq


title: X9.10 [200340580083_R06C01]

description:
200340580083_R06C01
BLL_KMT2A


title: Cr_H3K4me1_rep1, ChIP-seq


title: ehd3_H3K36me2_rep4, ChIP-seq


title: X4.19 [200340580079_R02C01]

description:
200340580079_R02C01
BLL_KMT2A

value: M


title: MCL-074 [9007217084_R04C01]

description:
9007217084_R04C01
MCL_SOX11P


title: sdg724_H3K4me3_rep2, ChIP-seq

value: 14-day-old seedlings


title: ehd3_H3K36me2_rep3, ChIP-seq

value: Nipponbare


title: M.19 [200340580083_R05C01]

description:
200340580083_R05C01
BLL_NONKMT2A


title: M.7 [200340580083_R04C01]

description:
200340580083_R04C01
BLL_NONKMT2A


title: sdg724_H3K4me2_rep3, ChIP-seq


title: ehd3_H3K36me1_rep3, ChIP-seq


title: ehd3_H3K36me1_rep2, ChIP-seq


title: ehd3_H3K36me1_rep1, ChIP-seq


title: sdg724_H3K4me1_rep2, ChIP-seq


title: X4.30 [200340580070_R03C01]

description:
200340580070_R03C01
BLL_KMT2A


title: sdg724_H3K36me1_rep1, ChIP-seq


title: X4.8 [200340580083_R01C01]

description:
200340580083_R01C01
BLL_KMT2A


title: ehd3_H3K36me3_rep1, ChIP-seq


title: ehd3_H3_rep1, ChIP-seq


title: sdg724_H3K4me2_rep1, ChIP-seq


title: MCL-075 [9007217084_R02C02]

description:
9007217084_R02C02
MCL_SOX11N_A

value: Test set

value: Kiel


title: ehd3_H3K4me2_rep2, ChIP-seq


title: MCL-069 [9007217069_R02C02]

description:
9007217069_R02C02
MCL_SOX11P


title: MCL-076 [9007217069_R05C02]

description:
9007217069_R05C02
MCL_SOX11P


title: X4.7 [200340580079_R01C01]

description:
200340580079_R01C01
BLL_KMT2A

value: Bone marrow


title: ehd3_H3K4me2_rep1, ChIP-seq


title: MCL-073 [9007217068_R01C01]

description:
9007217068_R01C01
MCL_SOX11P

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

value: Lymph node


title: X4.31 [200340580079_R03C01]

description:
200340580079_R03C01
BLL_KMT2A


title: X9.7 [200340580050_R06C01]

description:
200340580050_R06C01
BLL_KMT2A


title: ehd3_H3K36me2_rep2, ChIP-seq


title: ehd3_H3K4me1_rep2, ChIP-seq


title: ehd3_H3K36me2_rep1, ChIP-seq


title: MCL-071 [9007217084_R02C01]

description:
9007217084_R02C01
MCL_SOX11P


title: ehd3_H3K4me1_rep1, ChIP-seq


title: MCL-072 [9007217084_R04C02]

description:
9007217084_R04C02
MCL_SOX11P


title: ehd3_H3K4me3_rep3, ChIP-seq


title: M.17 [200340580070_R05C01]

description:
200340580070_R05C01
BLL_NONKMT2A


title: X4.18 [200340580070_R02C01]

description:
200340580070_R02C01
BLL_KMT2A


title: X4.29 [200340580050_R03C01]

description:
200340580050_R03C01
BLL_KMT2A


title: MCL-070 [9007217068_R05C01]

description:
9007217068_R05C01
MCL_SOX11P


title: NiP_H3K36me3_rep3, ChIP-seq

value: wild-type


title: NiP_H3_rep1, ChIP-seq

value: no treatment


title: ehd3_H3K4me3_rep1, ChIP-seq


title: M.16 [200340580050_R05C01]

description:
200340580050_R05C01
BLL_NONKMT2A


title: ehd3_H3K4me3_rep2, ChIP-seq


title: MCL-068 [9007217068_R03C02]

description:
9007217068_R03C02
MCL_SOX11P

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


title: MCL-065 [9007217068_R04C01]

description:
9007217068_R04C01
MCL_SOX11P

value: Ref set


title: NiP_H3K36me2_rep4, ChIP-seq


title: X4.6 [200340580070_R01C01]

description:
200340580070_R01C01
BLL_KMT2A

value: Infant B-cell precursor acute lymphoblastic leukemia


title: ehd3_H3_rep2, ChIP-seq


title: NiP_H3K36me2_rep2, ChIP-seq


title: ehd3_H3K4me2_rep3, ChIP-seq


title: M.3 [200340580035_R04C01]

description:
200340580035_R04C01
BLL_NONKMT2A

value: Frozen


title: MCL-066 [9007217069_R06C02]

description:
9007217069_R06C02
MCL_SOX11P


title: X4.5 [200340580050_R01C01]

description:
200340580050_R01C01
BLL_KMT2A

value: F


title: NiP_H3K36me3_rep1, ChIP-seq


title: NiP_H3K36me2_rep1, ChIP-seq


title: MCL-064 [9007217068_R02C01]

description:
9007217068_R02C01
MCL_SOX11P


title: NiP_H3_rep2, ChIP-seq


title: MCL-063 [9007217068_R01C02]

description:
9007217068_R01C02
MCL_SOX11P

value: MG1 :Kiel


title: X4.28 [200340580035_R03C01]

description:
200340580035_R03C01
BLL_KMT2A


title: X4.17 [200340580050_R02C01]

description:
200340580050_R02C01
BLL_KMT2A


title: X4.16 [200340580035_R02C01]

description:
200340580035_R02C01
BLL_KMT2A


title: NiP_H3K36me3_rep2, ChIP-seq


title: NiP_H3K36me1_rep1, ChIP-seq


title: NiP_H3K36me2_rep3, ChIP-seq


title: NiP_H3K36me1_rep3, ChIP-seq


title: ehd3_H3K4me1_rep3, ChIP-seq


title: X4.4 [200340580035_R01C01]

description:
200340580035_R01C01
BLL_KMT2A


title: MCL-060 [9007217084_R03C02]

description:
9007217084_R03C02
MCL_SOX11N_B

value: Mantle Cell Lymphoma. SOX11:NegativeMCL_morphology:, Nodal:Yes, Series_origin:Kiel


title: NiP_H3K36me1_rep2, ChIP-seq


title: NiP_H3K4me3_rep3, ChIP-seq


title: MCL-062 [9007217069_R04C02]

description:
9007217069_R04C02
MCL_SOX11P

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

value: M


title: MCL-061 [9007217068_R02C02]

description:
9007217068_R02C02
MCL_SOX11P


title: X9.5 [200340580017_R06C01]

description:
200340580017_R06C01
BLL_KMT2A


title: NiP_H3K4me3_rep1, ChIP-seq

value: 14-day-old seedlings

value: Nipponbare


title: NiP_H3K4me2_rep2, ChIP-seq


title: NiP_H3K4me3_rep2, ChIP-seq


title: MCL-067 [9007217084_R06C02]

description:
9007217084_R06C02
MCL_SOX11P


title: I571B

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

country: USA

institute: Boston University School of Medicine

description: Library name: I571B

data_processing:
Sample sequencing was performed on the Illumina NextSeq 2000 to generate paired-end 100-nucleotide reads.
BaseSpace (Illumina) was used for demultiplexing and FASTQ file generation.
A Nextflow (v21.10.6) RNA-Seq pipeline (https://github.com/compbiomed/RNA_Seq/) was used to align reads with hg38 and STAR v2.6.0c.
Counts were calculated using RSEM v1.3.1 and Ensembl annotation build 108.
Quality metrics were calculated with FastQC v0.11.7, STAR v2.6.0c, and RSeQC v3.0.0.
Assembly: hg38
Supplementary files format and content: biopsies_exp_count.txt: whitespace-delimited text file with raw expected counts for each sample

source_name: lung adenocarcinoma

extract_protocol:
Total RNA was extracted from FFPE tissue with the Qiagen miRNeasy FFPE kit.
Libraries were prepared using Illumina RNA Prep with Enrichment with IDT® for Illumina® DNA/RNA UD Indexes Set A (Catalog # 20027213).

value: lung adenocarcinoma

tag: sample type

value: FFPE

tag: patient id

tag: cohort

value: biopsy cohort

tag: characteristics

value: novel grade:VI

tag: tnm 8th edition stage

value: IB

tag: gender

value: Male

tag: race

value: White

tag: smoking status

value: Former

tag: procedure

value: Lobectomy

tag: biopsy type

value: Needle

tag: site

value: Inova


title: MCL-057 [9007217084_R03C01]

description:
9007217084_R03C01
MCL_SOX11P

tag: tissue

value: Lymph node

tag: group

value: Ref set

tag: material

value: Frozen

tag: age

tag: Sex


title: X4.15 [200340580017_R02C01]

description:
200340580017_R02C01
BLL_KMT2A

value: Infant B-cell precursor acute lymphoblastic leukemia

value: Bone marrow

value: F

tag: mcf


title: MCL-059 [9007217084_R05C02]

description:
9007217084_R05C02
MCL_SOX11P

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

value: M


title: hiPSC, heart organoid, PDGFBB

city: Cantanhede

first: Jacek

middle: Dariusz

last: Marzec

address: Biocant Park

country: Portugal

institute: CoLAB AccelBio

description: Library name: Sample PDGFBB

data_processing:
Raw sequencing data were processed using the Cell Ranger pipeline (v9.0.1, 10x Genomics). Reads were demultiplexed to produce paired FASTQ files for each library and aligned to the human reference transcriptome (GRCh38, Ensembl annotation). PCR duplicates were removed by collapsing reads with identical unique molecular identifiers (UMIs), 10x barcodes, and gene annotations into a single UMI count. The output gene–barcode UMI count matrices were used for downstream analyses.
Assembly: GRCh38
Supplementary files format and content: RDS file containing processed and annotated Seurat object used for downstream analyses (counts and normalized data, dimensionality reductions (PCA, UMAP, t-SNE) and metadata including cell types)
Supplementary files format and content: cloupe file for Loupe Browser (10x Genomics) with information on gene expression, cell types, and dimensionality reduction plots (t-SNE) for each sample
Supplementary files format and content: HDF5 files (10x Genomics v3 format) containing gene–barcode matrices, feature annotations, and cell barcodes for individual samples
Supplementary files format and content: csv files, associated with corresponding HDF5 files, containing metadata for individual cells, including cell types

source_name: Heart Organoid

extract_protocol:
V-EMOs and P-EMOs were dissociated into single cells using 0.25% Trypsin-EDTA and incubated for 10 min at 37 °C. After centrifugation for 3 min at 200 × g, suspended cells were stained with LIVE/DEAD™ Fixable Near-IR Dead Cell Stain (Thermo Fisher Scientific, USA) for 15 min. Cells were washed with PBS, centrifuged at 200 × g for 3 min, and resuspended in 300 µl of 0.5% BSA in PBS. Stained cells were sorted using an Aurora CS spectral cell sorter (Cytek Biosciences, USA) at the Flow Cytometry Platform of the Gulbenkian Institute for Molecular Medicine. Sorting was performed with a 100 µm nozzle in Purity mode (100% Purity Mask, 25% Yield Mask) with the sort chamber cooled to 4 °C. After exclusion of debris and doublets, live cells (negative for the Dead Cell Stain) were collected into 1.5 mL tubes containing 30 µL PBS with 2% BSA. Sorted cells were gently homogenized with a micropipette, centrifuged at 4 °C and 200 × g for 3 min, resuspended in PBS, and quantified using the Trypan Blue exclusion method.
Single-cell 3′ gene expression libraries were prepared using the Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (10x Genomics) according to the manufacturer’s protocol. Final libraries were quantified using a Qubit fluorometer (Thermo Fisher Scientific) and assessed for size distribution on an Agilent TapeStation (Agilent Technologies). Libraries were pooled and sequenced on an Illumina NextSeq 2000 using paired-end reads with the following configuration: 28 bp (Read 1, cell barcode and UMI), 8 bp (i7 index), and 91 bp (Read 2, transcript). Libraries were sequenced to a depth of 30,000–50,000 reads per cell.

treatment_protocol: Organoids were treated with vascular endothelial growth factor (VEGF) or platelet-derived growth factor-BB (PDGF-BB) during the cardiac differentiation phase.

value: Heart Organoid

tag: cell line

tag: cell type

value: in vitro differentiated human induced pluriotent stem cells (hiPSC)

tag: treatment

value: PDGFBB


title: I64B

description: Library name: I64B

value: lung adenocarcinoma

tag: sample type

value: FFPE

tag: patient id

tag: cohort

value: biopsy cohort

tag: characteristics

value: novel grade:NST

value: Female


title: MCL-058 [9007217069_R06C01]

description:
9007217069_R06C01
MCL_SOX11P


title: NiP_H3K4me2_rep3, ChIP-seq

source_name: 14-day-old seedlings

value: 14-day-old seedlings

value: Nipponbare

tag: genotype

value: wild-type

value: no treatment

tag: chip antibody


title: M.2 [200340580017_R04C01]

description:
200340580017_R04C01
BLL_NONKMT2A

value: Infant B-cell precursor acute lymphoblastic leukemia

value: Ref set

value: Frozen


title: X4.3 [200340580017_R01C01]

description:
200340580017_R01C01
BLL_KMT2A

value: Bone marrow


title: MCL-056 [9007217068_R03C01]

description:
9007217068_R03C01
MCL_SOX11P

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

value: Lymph node

value: M


title: I55B

description: Library name: I55B

tag: tnm 8th edition stage

tag: gender

tag: race

value: Asian

tag: smoking status

value: Never

tag: procedure

value: Lobectomy

tag: biopsy type

value: Needle

value: Inova


title: I571R

description: Library name: I571R

tag: tissue

value: lung adenocarcinoma

value: FFPE

value: biopsy cohort

value: novel grade:VI

value: IB

tag: age

value: Male

value: White

value: Former

tag: site


title: MCL-055 [9007217068_R04C02]

description:
9007217068_R04C02
MCL_SOX11P

tag: group

value: Ref set

tag: material

value: Frozen

tag: Sex

value: F

tag: mcf


title: NiP_H3K4me2_rep1, ChIP-seq

value: 14-day-old seedlings

tag: cell line

value: Nipponbare

tag: cell type

value: wild-type

tag: treatment

value: no treatment


title: I519B

description: Library name: I519B

tag: sample type

tag: patient id

tag: cohort

tag: characteristics

value: Female

value: Never

value: Wedge

value: Needle


title: M.13 [200340580016_R05C01]

description:
200340580016_R05C01
BLL_NONKMT2A

value: Infant B-cell precursor acute lymphoblastic leukemia

value: Bone marrow


title: MCL-054 [9007217068_R06C02]

description:
9007217068_R06C02
MCL_SOX11P

value: Mantle Cell Lymphoma. SOX11:PositiveMCL_morphology:, Nodal:Yes, Series_origin:Kiel

value: Lymph node

value: M


title: I509R

description: Library name: I509R

value: lung adenocarcinoma

value: FFPE

value: biopsy cohort

value: novel grade:VI

tag: tnm 8th edition stage

tag: gender

tag: race

value: White

tag: smoking status

value: Former

value: Lobectomy

value: Fine needle aspiration

value: Inova


title: NiP_H3K4me1_rep2, ChIP-seq

tag: tissue

value: 14-day-old seedlings

value: Nipponbare

tag: genotype

value: wild-type

value: no treatment

tag: chip antibody


title: M.1 [200340580016_R04C01]

description:
200340580016_R04C01
BLL_NONKMT2A

value: Infant B-cell precursor acute lymphoblastic leukemia

value: Bone marrow

tag: group

value: Ref set

tag: material

value: Frozen

tag: age

value: F


title: MCL-053 [6929671157_R01C02]

description:
6929671157_R01C02
MCL_SOX11N_B

source_name: Mantle Cell Lymphoma. SOX11: Negative, Diagnosis, Pre-treatment, MCL_morphology: PAMPLONA

value: Mantle Cell Lymphoma. SOX11:Negative, Diagnosis, Pre-treatment, MCL_morphology:PAMPLONA

tag: Sex

value: M

tag: mcf


title: X4.27 [200340580017_R03C01]

description:
200340580017_R03C01
BLL_KMT2A


title: I509B

description: Library name: I509B

value: lung adenocarcinoma

value: FFPE

value: biopsy cohort

value: novel grade:VI

value: Female

tag: procedure

tag: biopsy type

tag: site


title: X4.26 [200340580016_R03C01]

description:
200340580016_R03C01
BLL_KMT2A


title: Islet, 5prime, insulin-depleted, modified protocol, long-read, rep2

city: Aurora

first: Maria

middle: Skjoett

last: Hansen

state: CO

address: 1775 Aurora Ct

department: Pediatrics

institute: University of Colorado Anschutz Medical Campus

description:
Library name: islet_5prime_mod_rep2
long-read

data_processing:
Single cell libraries were processed using the EPI2ME single cell workflow v1.1.0 from Oxford Nanopore Technologies for the identification of cell and UMI barcodes. Only the reads that had a sequence quality higher than 7 were input into this pipeline. We manually created a gene count matrix from the BAM outputs that were produced by the EPI2ME pipeline, then utilized the emptyDrops function from the DropletUtils package.
Assembly: mm10
Supplementary files format and content: csv files contains nCounts and nFeatures for both RNA and Transcripts. As well as cluster information for both gene-based clustering and transcript-based clustering. One csv file contains metadata from the 5' mod replicate 2 seurat object, and one csv file contains metadata from the rep1/rep2 merged 5' mod seurat object used for paper figures. .tsv files contain gene and transcript count matrices.

source_name: pancreatic islet

extract_protocol:
Pancreatic islets were isolated from mice under ketamine/xylazine/acepromazine anesthesia by collagenase delivery into the pancreas via injection into the bile duct. The collagenase-inflated pancreas was surgically removed and digested. After isolation, islets were dissociated using Accutase in a 37°C bead bath for 25-30 minutes. Single-cell suspension was filtered through a 40 mm filter and quenched in RPMI media with 10% FBS. Single-cell suspensions were loaded into a Genomics Chromium targeting 4000 cells per sample.
Single-cell 3' libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Kit v3.1 following the protocol up to and including step 2.4, stopping just before fragmentation. Single-cell 5' libraries were prepared using the Chromium Next GEM Single Cell 5' Kit v2  following the protocol up to and including step 2.4, stopping just before fragmentation.  For the optimized libraries, the following modifications were applied to the 5’ library preparation: 1 ul 10 mM dNTP solution (Thermo Scientific FERR0191) was added to the reaction in step 1.1. The extension time was increased from 45 minutes to 2 hours in step 1.5. 1 ul 10 mM dNTP solution was added to the reaction in step 2.2 and the extension time was increased from 1 minute to 3 minutes. Insulin depletion was performed on cDNA from step 2.4 of the 10X Genomics Chromium library preparation using the DepleteXTM RNA Depletion Panel (Insulin) kit from Jumpcode Genomics. We followed the PacBio MAS-IsoSeq protocol (December 2022, Version 1.0) with the following modifications: During RNP Complex Formation (Step A), we used 0.9 ul Cas9 instead of 2.3 ul, and 1.6 ul Insulin Guide RNA instead of 4.0 ul Single Cell Boost Guide RNA. During Bead Cleanup (Step D), we used 50 ul (1X) AMPure XP Beads instead of 75 ul 1.5X SMRTbell Cleanup Beads. Long-read libraries were prepared from the cDNA using Sequencing Kit V14 (Nanopore SQK-LSK114) and the PCR Expansion (Nanopore EXP-PCA001). For 3’ libraries, the Ligation sequencing V14 — single-cell transcriptomics with 3' cDNA prepared using 10X Genomics on PromethION (SQK-LSK114) protocol was used.  For 5’ libraries, the Ligation sequencing V14 - Single-cell transcriptomics with 5' cDNA prepared using 10X Genomics on PromethION (SQK-LSK114) protocol was used. Short Fragment Buffer (SFB) was used for library preparation instead of Long Fragment buffer (LFB). Library Beads (LIB) were used for the flow cell priming mix stead of Library Solution (LIS). Libraries were sequenced on R10.4.1 flow cells on either a PromethION 2 Solo (P2S) or PromethION  2 Integrated (P2i).

value: pancreatic islet

value: female

value: 10 weeks


title: NiP_H3K4me1_rep3, ChIP-seq

value: 14-day-old seedlings

tag: cell line

value: Nipponbare

tag: cell type

value: wild-type

tag: treatment


title: MCL-050 [6929671153_R03C01]

description:
6929671153_R03C01
MCL_SOX11P


title: MCL-051 [6929671153_R04C01]

description:
6929671153_R04C01
MCL_SOX11P

source_name: Mantle Cell Lymphoma. SOX11: Positive, Diagnosis, Pre-treatment, MCL_morphology: PAMPLONA

value: Mantle Cell Lymphoma. SOX11:Positive, Diagnosis, Pre-treatment, MCL_morphology:PAMPLONA

value: Bone marrow


title: I500B

description: Library name: I500B

tag: sample type

tag: patient id

tag: cohort

tag: characteristics

tag: tnm 8th edition stage

tag: gender

value: Male

value: White

value: Former

value: Lobectomy

value: Needle

value: Inova


title: Islet, 5prime, insulin-depleted, long-read, rep2

description:
Library name: islet_5prime_rep2
long-read

tag: tissue


title: Islet, 3prime, insulin-depleted, long-read, rep2

description:
Library name: islet_3prime_rep2
long-read


title: NiP_H3K4me1_rep1, ChIP-seq

tag: genotype

value: no treatment

tag: chip antibody


title: X4.14 [200340580016_R02C01]

description:
200340580016_R02C01
BLL_KMT2A

value: Infant B-cell precursor acute lymphoblastic leukemia

tag: group

value: Ref set

tag: material

value: Frozen

tag: age

tag: Sex

value: M


title: MCL-049 [6929671153_R02C01]

description:
6929671153_R02C01
MCL_SOX11P

tag: mcf


title: hiPSC, heart organoid, VEGF

description: Library name: Sample VEGF

value: Heart Organoid

tag: cell line

value: in vitro differentiated human induced pluriotent stem cells (hiPSC)

value: VEGFA


title: X9.3 [200340580008_R06C01]

description:
200340580008_R06C01
BLL_KMT2A


title: X4.2 [200340580016_R01C01]

description:
200340580016_R01C01
BLL_KMT2A


title: Spleen, 5prime, modified protocol, long-read, rep2

description:
Library name: spleen_5prime_mod_rep2
long-read

source_name: spleen

value: spleen

value: female

value: 10 weeks


title: M.12 [200340580008_R05C01]

description:
200340580008_R05C01
BLL_NONKMT2A

value: Bone marrow


title: MCL-047 [6929671139_R01C01]

description:
6929671139_R01C01
MCL_SOX11N_A

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

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

value: Peripheral Blood

value: F


title: MCL-048 [6929671153_R01C01]

description:
6929671153_R01C01
MCL_SOX11N_A

value: Mantle Cell Lymphoma. SOX11:Negative, Diagnosis, Pre-treatment, MCL_morphology:PAMPLONA


title: I375B

description: Library name: I375B

value: lung adenocarcinoma

value: FFPE

value: biopsy cohort

value: novel grade:VI

value: Female

tag: race

value: Other

tag: smoking status

value: Current

tag: procedure

value: Lobectomy

tag: biopsy type

value: Forceps

tag: site

value: Inova


title: I375R

description: Library name: I375R

tag: sample type

tag: patient id

tag: cohort

tag: characteristics


title: I363R

description: Library name: I363R

tag: tissue

tag: tnm 8th edition stage

value: IB

tag: gender

value: White


title: Spleen, 3prime, long-read, rep2

description:
Library name: spleen_3prime_rep2
long-read

value: spleen

value: female

value: 10 weeks


title: Islet, 5prime, insulin-depleted, modified protocol, long-read

description:
Library name: islet_5prime_mod
long-read

data_processing:
Single cell libraries were processed using the EPI2ME single cell workflow v1.1.0 from Oxford Nanopore Technologies for the identification of cell and UMI barcodes. Only the reads that had a sequence quality higher than 7 were input into this pipeline. We manually created a gene count matrix from the BAM outputs that were produced by the EPI2ME pipeline, then utilized the emptyDrops function from the DropletUtils package.
Assembly: mm10
Supplementary files format and content: csv file contains nCounts and nFeatures for both RNA and Transcripts. As well as cluster information for both gene-based clustering and transcript-based clustering. .tsv files contain gene and transcript count matrices.

value: pancreatic islet


title: Islet, 5prime, insulin-depleted, long-read

description:
Library name: islet_5prime
long-read


title: MCL-042 [6929671128_R01C01]

description:
6929671128_R01C01
MCL_SOX11N_B

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

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

value: Peripheral Blood

tag: group

value: Ref set

tag: material

value: Frozen

value: M


title: X4.1 [200340580008_R01C01]

description:
200340580008_R01C01
BLL_KMT2A

value: Infant B-cell precursor acute lymphoblastic leukemia

value: Bone marrow

tag: age

tag: Sex


title: I355B

description: Library name: I355B

value: lung adenocarcinoma

value: FFPE

value: biopsy cohort

value: novel grade:LMP

value: Female

value: Never

value: Needle


title: X4.37 [200340580008_R04C01]

description:
200340580008_R04C01
BLL_KMT2A

tag: mcf


title: I500R

description: Library name: I500R

value: novel grade:VI

value: Male

tag: race

value: White

value: Former

value: Lobectomy

value: Inova


title: X9.11 [200325580100_R06C01]

description:
200325580100_R06C01
BLL_KMT2A

value: Ref set

value: Frozen


title: Islet, 3prime, insulin-depleted, long-read

description:
Library name: islet_3prime
long-read

value: pancreatic islet

value: female

value: 10 weeks


title: MCL-041 [6929689010_R01C02]

description:
6929689010_R01C02
MCL_SOX11P

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

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

value: Peripheral Blood

value: M


title: X4.13 [200340580008_R02C01]

description:
200340580008_R02C01
BLL_KMT2A

value: Infant B-cell precursor acute lymphoblastic leukemia

value: Bone marrow


title: MCL-043 [6929689005_R04C01]

description:
6929689005_R04C01
MCL_SOX11P

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

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


title: MCL-045 [6929689010_R06C01]

description:
6929689010_R06C01
MCL_SOX11P

source_name: Mantle Cell Lymphoma. SOX11: Positive, Diagnosis, Pre-treatment, MCL_morphology: classic, Nodal: No, Series_origin: NIH

value: Mantle Cell Lymphoma. SOX11:Positive, Diagnosis, Pre-treatment, MCL_morphology:classic, Nodal:No, Series_origin:NIH


title: I363B

description: Library name: I363B

value: lung adenocarcinoma

value: FFPE

value: biopsy cohort

value: novel grade:VI

value: IB

value: Female

tag: smoking status

value: Current

value: Forceps


title: I351B

description: Library name: I351B

value: Male

value: Other

value: Former

tag: procedure

value: Lobectomy

value: Inova


title: I293R

description: Library name: I293R

value: novel grade:NST

value: White

tag: biopsy type

value: Needle


title: I418B

description: Library name: I418B

tag: site


title: MCL-040 [6929671116_R05C01]

description:
6929671116_R05C01
MCL_SOX11P

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

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

value: Peripheral Blood

value: Ref set

value: Frozen

value: M


title: M.20 [200325580100_R05C01]

description:
200325580100_R05C01
BLL_NONKMT2A

source_name: Infant B-cell precursor acute lymphoblastic leukemia

value: Bone marrow

value: F


title: MCL-038 [6929689005_R03C01]

description:
6929689005_R03C01
MCL_SOX11P

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


title: Spleen, 5prime, long-read

description:
Library name: spleen_5prime
long-read

data_processing:
Single cell libraries were processed using the EPI2ME single cell workflow v1.1.0 from Oxford Nanopore Technologies for the identification of cell and UMI barcodes. Only the reads that had a sequence quality higher than 7 were input into this pipeline. We manually created a gene count matrix from the BAM outputs that were produced by the EPI2ME pipeline, then utilized the emptyDrops function from the DropletUtils package.
Assembly: mm10
Supplementary files format and content: .tsv files contain count matrices for spleen samples.

extract_protocol:
Spleens were isolated from mice under ketamine/xylazine/acepromazine anesthesia. Spleens were dissociated through a 70 µm strainer in cIMDM using a 3 mL syringe plunger. Cells were washed, centrifuged (400 × g, 5 min), and treated with 1 mL ACK lysis buffer for 30 seconds, followed by dilution in cIMDM and a second spin. After one additional wash, cells were resuspended in 6 mL FACS buffer. Viable cells were counted by trypan blue exclusion.
Single-cell 3' libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Kit v3.1 following the protocol up to and including step 2.4, stopping just before fragmentation. Single-cell 5' libraries were prepared using the Chromium Next GEM Single Cell 5' Kit v2  following the protocol up to and including step 2.4, stopping just before fragmentation.  For the optimized libraries, the following modifications were applied to the 5’ library preparation: 1 ul 10 mM dNTP solution (Thermo Scientific FERR0191) was added to the reaction in step 1.1. The extension time was increased from 45 minutes to 2 hours in step 1.5. 1 ul 10 mM dNTP solution was added to the reaction in step 2.2 and the extension time was increased from 1 minute to 3 minutes. Long-read libraries were prepared from the cDNA using Sequencing Kit V14 (Nanopore SQK-LSK114) and the PCR Expansion (Nanopore EXP-PCA001). For 3’ libraries, the Ligation sequencing V14 — single-cell transcriptomics with 3' cDNA prepared using 10X Genomics on PromethION (SQK-LSK114) protocol was used.  For 5’ libraries, the Ligation sequencing V14 - Single-cell transcriptomics with 5' cDNA prepared using 10X Genomics on PromethION (SQK-LSK114) protocol was used. Short Fragment Buffer (SFB) was used for library preparation instead of Long Fragment buffer (LFB). Library Beads (LIB) were used for the flow cell priming mix stead of Library Solution (LIS). Libraries were sequenced on R10.4.1 flow cells on either a PromethION 2 Solo (P2S) or PromethION  2 Integrated (P2i).

value: spleen

value: female

value: 10 weeks


title: M.8 [200325580100_R04C01]

description:
200325580100_R04C01
BLL_NONKMT2A

value: Infant B-cell precursor acute lymphoblastic leukemia


title: Spleen, 3prime, long-read

description:
Library name: spleen_3prime
long-read


title: I293B

description: Library name: I293B

value: lung adenocarcinoma

tag: sample type

value: FFPE

value: biopsy cohort

value: IB

value: Female

value: Former

value: Lobectomy


title: X4.21 [200325580100_R02C01]

description:
200325580100_R02C01
BLL_KMT2A

value: Ref set


title: X4.25 [200340580008_R03C01]

description:
200340580008_R03C01
BLL_KMT2A

value: Frozen


title: X4.33 [200325580100_R03C01]

description:
200325580100_R03C01
BLL_KMT2A


title: MCL-036 [6929689010_R05C01]

description:
6929689010_R05C01
MCL_SOX11P

value: Peripheral Blood

value: M


title: MCL-037 [6929671116_R06C01]

description:
6929671116_R06C01
MCL_SOX11P

value: F


title: I284B

description: Library name: I284B

tag: patient id

value: novel grade:VI

value: Black

value: Inova


title: Endometrium, d16, saline infused-cow1

city: Gainesville

first: John

middle: James

last: Bromfield

state: FL

address: 2250 Shealy Drive, Dept of Animal Sciences, Rm 108

department: Animal Sciences

institute: University of Florida

description: Library name: A3

data_processing:
Original data files generated from high-throughput sequencing were transformed into raw reads by CASAVA base recognition and stored in FASTQ format files. Individual reads were filtered to remove adaptors, poly-N reads, and low-quality reads from the raw data. The Q20, Q30, and GC content were calculated for the cleaned data during this step. All downstream analyses were based on the clean data with high quality reads. After data filtering, paired-end clean reads of each sample were aligned to the latest bovine reference genome (ARS-UCD2.0) using HISAT2 v2.0.5. Quantification was performed using the FeatureCounts v1.5.0-p3 to count the read numbers mapped to each gene.
Assembly: Sample were aligned to the latest bovine reference genome (ARS-UCD2.0)
Supplementary files format and content: All raw files are FASTQ format

organism: Bos taurus

source_name: Endometrium

extract_protocol:
RNA was extracted using the RNeasy Mini kit (Qiagen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by a second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The non-directional library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

treatment_protocol: Cows were infused with either bacteria or PBS on day 0. Endometrial amples were collected on day 41 (corresponding to day 16 of the estrous cycle).

value: Endometrium

tag: treatment

value: Saline


title: DIPGXIII_RNAseq_GSK4027.3

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_GSK4027.3

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).

value: glioma

tag: cell line

value: SU-DIPGXIII

tag: cell type

value: diffuse midline glioma

tag: genotype

value: WT


title: DIPGXIII_RNAseq_GSK4027.2

description: Library name: XIII_RNAseq_GSK4027.2

tag: tissue


title: Endometrium, d16, saline infused-cow3

description: Library name: A10


title: I256B

description: Library name: I256B

value: lung adenocarcinoma

value: FFPE

tag: cohort

value: biopsy cohort

tag: characteristics

value: novel grade:NST

tag: tnm 8th edition stage

tag: gender

value: Male

value: White

value: Needle


title: Spleen, 5prime, modified protocol, long-read

description:
Library name: spleen_5prime_mod
long-read

value: spleen

tag: Sex

value: female

tag: age

value: 10 weeks


title: Endometrium, d16, saline infused-cow2

description: Library name: A7


title: I200R

description: Library name: I200R

value: novel grade:LMP

value: Female

tag: race

tag: smoking status

value: Former

value: Lobectomy

value: Inova


title: I200B

description: Library name: I200B

tag: procedure

tag: biopsy type


title: Endometrium, d16, bacteria infused-cow5

description: Library name: A9

value: Endometrium

value: Bacteria


title: MCL-039 [6929671157_R04C02]

description:
6929671157_R04C02
MCL_SOX11P

data_processing: BeadStudio software v3.2

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, Diagnosis, Pre-treatment, MCL_morphology:classic, Nodal:Yes, Series_origin:NIH

value: Peripheral Blood

tag: group

value: Ref set

tag: material

value: Frozen

value: M

tag: mcf


title: X4.9 [200325580100_R01C01]

description:
200325580100_R01C01
BLL_KMT2A

value: Infant B-cell precursor acute lymphoblastic leukemia

value: Bone marrow


title: MCL-034 [6929671157_R05C02]

description:
6929671157_R05C02
MCL_SOX11P


title: I249B

description: Library name: I249B

value: lung adenocarcinoma

tag: sample type

value: FFPE

tag: patient id

value: biopsy cohort

value: novel grade:VI

value: Other

value: Never

value: Needle

tag: site


title: MCL-035 [6929671116_R04C01]

description:
6929671116_R04C01
MCL_SOX11P

tag: tissue

value: Mantle Cell Lymphoma. SOX11:Positive, Diagnosis, Pre-treatment, MCL_morphology:classic, Nodal:No, Series_origin:NIH

value: Test set

value: BCN


title: MCL-032 [6929689005_R06C01]

description:
6929689005_R06C01
MCL_SOX11P

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


title: I187R

description: Library name: I187R

tag: cohort

value: novel grade:LMP

value: IB

value: Female

value: White

value: Former

value: Lobectomy

value: Inova


title: Endometrium, d16, bacteria infused-cow7

description: Library name: A12

value: Endometrium

tag: treatment

value: Bacteria


title: Spleen, 5prime, long-read, rep2

description:
Library name: spleen_5prime_rep2
long-read

value: spleen

value: female

value: 10 weeks


title: DIPGXIII_RNAseq_CPTH2.3

description: Library name: XIII_RNAseq_CPTH2.3

value: glioma

tag: cell line

value: SU-DIPGXIII

tag: cell type

value: diffuse midline glioma

tag: genotype

value: WT

value: 10 uM CPTH2


title: DIPGXIII_RNAseq_GSK4027.1

description: Library name: XIII_RNAseq_GSK4027.1


title: Endometrium, d16, bacteria infused-cow4

description: Library name: A8


title: MCL-033 [6929671128_R03C01]

description:
6929671128_R03C01
MCL_SOX11N_A

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

value: Peripheral Blood

value: Test set

value: Frozen

tag: age

tag: Sex

value: M

value: BCN


title: I355R

description: Library name: I355R

value: lung adenocarcinoma

value: FFPE

value: biopsy cohort

tag: characteristics

value: novel grade:LMP

tag: tnm 8th edition stage

tag: gender

value: Female

tag: race

value: White

tag: smoking status

value: Never

value: Lobectomy

value: Needle

value: Inova


title: MCL-030 [6929671157_R03C02]

description:
6929671157_R03C02
MCL_SOX11P

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

tag: group

value: Ref set

tag: material

value: F

tag: mcf


title: Endometrium, d16, bacteria infused-cow6

description: Library name: A11

value: Endometrium

value: Bacteria


title: Endometrium, d16, bacteria infused-cow3

description: Library name: A6


title: I149B

description: Library name: I149B

tag: sample type

tag: patient id

value: novel grade:NST

value: Male

value: Former

tag: procedure

tag: biopsy type

tag: site


title: DIPGXIII_RNAseq_DMSO.1

description: Library name: XIII_RNAseq_DMSO.1

tag: tissue

value: glioma

tag: cell line

value: SU-DIPGXIII

tag: cell type

value: diffuse midline glioma

value: WT

tag: treatment

value: DMSO


title: I149R

description: Library name: I149R

value: lung adenocarcinoma

value: FFPE

tag: cohort

value: biopsy cohort

tag: characteristics

tag: age

value: White


title: DIPGXIII_RNAseq_CPTH2.2

description: Library name: XIII_RNAseq_CPTH2.2

tag: genotype

value: 10 uM CPTH2


title: I183B

description: Library name: I183B

value: novel grade:LMP

tag: tnm 8th edition stage

tag: gender

tag: race

tag: smoking status

value: Wedge

value: Needle

value: Inova


title: MCL-026 [6929671137_R05C02]

description:
6929671137_R05C02
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

value: Lymph node

tag: group

value: Ref set

tag: material

value: Frozen

tag: Sex

value: M

tag: mcf


title: DIPGXIII_RNAseq_CPTH2.1

description: Library name: XIII_RNAseq_CPTH2.1

value: glioma

value: SU-DIPGXIII

value: diffuse midline glioma


title: I166B

description: Library name: I166B

source_name: lung adenocarcinoma

value: lung adenocarcinoma

tag: sample type

tag: patient id

value: Male

value: Former

tag: procedure

tag: biopsy type

tag: site


title: I144B

description: Library name: I144B

tag: tissue

value: FFPE

tag: cohort

value: biopsy cohort

value: novel grade:VI

value: White

value: Lobectomy


title: DIPGXIII_RNAseq_SGF29sgC.3

description: Library name: XIII_RNAseq_SGF29sgC.3

tag: cell line

tag: cell type

value: SGF29 KO


title: I187B

description: Library name: I187B

tag: characteristics

value: novel grade:LMP

tag: tnm 8th edition stage

value: IB

tag: age

value: Female

value: Needle

value: Inova


title: MCL-031 [6929671157_R02C02]

description:
6929671157_R02C02
MCL_SOX11P

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

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

value: Peripheral Blood

value: Ref set

value: Frozen

value: M


title: MCL-025 [6929671137_R04C02]

description:
6929671137_R04C02
MCL_SOX11P

source_name: Mantle Cell Lymphoma. SOX11: PositiveMCL_morphology: , Nodal: Yes, Series_origin: HCP

value: Mantle Cell Lymphoma. SOX11:PositiveMCL_morphology:, Nodal:Yes, Series_origin:HCP

value: Spleen

value: F


title: MCL-028 [7990895143_R01C02]

description:
7990895143_R01C02
MCL_SOX11N_A

source_name: Mantle Cell Lymphoma. SOX11: Negative, Diagnosis, Pre-treatment, MCL_morphology: , Nodal: Yes, Series_origin: GRECIA

value: Mantle Cell Lymphoma. SOX11:Negative, Diagnosis, Pre-treatment, MCL_morphology:, Nodal:Yes, Series_origin:GRECIA


title: DIPGXIII_RNAseq_DMSO.3

description: Library name: XIII_RNAseq_DMSO.3

value: glioma

value: SU-DIPGXIII

value: diffuse midline glioma

tag: genotype

value: WT

tag: treatment

value: DMSO


title: MCL-024 [6929671137_R03C02]

description:
6929671137_R03C02
MCL_SOX11P

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

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

value: Soft tissue

tag: group

tag: material


title: Endometrium, d16, bacteria infused-cow1

description: Library name: A1

value: Endometrium

value: Bacteria


title: DIPGXIII_RNAseq_DMSO.2

description: Library name: XIII_RNAseq_DMSO.2


title: H3K14Ac G217B 50Ent RT C

city: San Francisco

first: Mark

last: Voorhies

state: CA

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

description: Library name: H3K14Ac_RT_50Ent_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. 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.

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: replicate

value: C

tag: temperature

value: RT

tag: antibody

value: fungal cell


title: MCL-027 [6929671137_R06C02]

description:
6929671137_R06C02
MCL_SOX11N_B

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

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

value: Lymph node

value: Ref set

value: Frozen

tag: Sex

value: M

tag: mcf


title: H3K14Ac G217B DMSO RT C

description: Library name: H3K14Ac_RT_DMSO_C


title: H3K14Ac G217B 50Ent RT A

description: Library name: H3K14Ac_RT_50Ent_A

value: A


title: DIPGXIII_RNAseq_SGF29sgA.3

description: Library name: XIII_RNAseq_SGF29sgA.3

value: glioma

value: SU-DIPGXIII

value: SGF29 KO


title: Endometrium, d16, bacteria infused-cow2

description: Library name: A2


title: H3K14Ac G217B DMSO RT B

description: Library name: H3K14Ac_RT_DMSO_B

value: B

value: DMSO


title: MCL-021 [6929671131_R03C01]

description:
6929671131_R03C01
MCL_SOX11P

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

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

value: F


title: H3K14Ac G217B DMSO RT A

description: Library name: H3K14Ac_RT_DMSO_A


title: MCL-029 [6929671116_R01C02]

description:
6929671116_R01C02
MCL_SOX11N_A

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

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

value: Peripheral Blood


title: I144R

description: Library name: I144R

value: lung adenocarcinoma

tag: sample type

value: FFPE

tag: patient id

value: biopsy cohort

value: novel grade:VI

tag: gender

value: Male

tag: race

value: White

tag: smoking status

value: Former

tag: procedure

value: Lobectomy

tag: biopsy type

tag: site

value: Inova


title: MCL-023 [6929671139_R02C01]

description:
6929671139_R02C01
MCL_SOX11P

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

tag: tissue

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

value: Lymph node

value: Test set

value: Frozen

tag: age

value: M

value: BCN


title: H3K14Ac G217B 50Ent RT B

description: Library name: H3K14Ac_RT_50Ent_B

tag: genotype

value: B

value: RT

tag: treatment

tag: cell type

value: fungal cell


title: DIPGXIII_RNAseq_SGF29sgC.1

description: Library name: XIII_RNAseq_SGF29sgC.1

value: glioma

tag: cell line

value: SU-DIPGXIII

value: diffuse midline glioma

value: SGF29 KO


title: DIPGXIII_RNAseq_SGF29sgA.2

description: Library name: XIII_RNAseq_SGF29sgA.2


title: DIPGXIII_RNAseq_SGF29sgC.2

description: Library name: XIII_RNAseq_SGF29sgC.2


title: I100B

description: Library name: I100B

value: lung adenocarcinoma

value: FFPE

tag: cohort

value: biopsy cohort

tag: characteristics

value: novel grade:LMP

tag: tnm 8th edition stage

value: Female

value: White

value: Needle


title: I123B

description: Library name: I123B

tag: sample type

value: novel grade:NST

value: Male

value: Former

value: Wedge

value: Inova


title: DIPGXIII_RNAseq_SGF29sgA.1

description: Library name: XIII_RNAseq_SGF29sgA.1


title: H3K9Ac G217B 50Ent RT C

description: Library name: H3K9Ac_RT_50Ent_C

tag: replicate

value: C

tag: temperature

value: RT

tag: antibody

value: fungal cell


title: MCL-022 [6929671131_R04C01]

description:
6929671131_R04C01
MCL_SOX11P

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

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

value: Spleen

tag: group

value: Ref set

tag: material

value: Frozen

tag: Sex

value: M

tag: mcf


title: DIPGXIII_RNAseq_CTL.3

description: Library name: XIII_RNAseq_CTLsg.3

tag: tissue

value: glioma

value: SU-DIPGXIII

value: diffuse midline glioma

value: WT


title: MCL-020 [6929689010_R03C02]

description:
6929689010_R03C02
MCL_SOX11N_A

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

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

value: Peripheral Blood

tag: age


title: H3K9Ac G217B 50Ent RT B

description: Library name: H3K9Ac_RT_50Ent_B

tag: genotype

value: B


title: I100R

description: Library name: I100R

value: lung adenocarcinoma

value: FFPE

tag: patient id

value: biopsy cohort

value: novel grade:LMP

tag: gender

value: Female

tag: race

value: White

tag: smoking status

value: Former

tag: procedure

value: Lobectomy

tag: biopsy type

value: Needle

tag: site


title: I110B

description: Library name: I110B

tag: sample type

tag: cohort

tag: characteristics

value: novel grade:VI

tag: tnm 8th edition stage

value: IB

value: Male

value: Never

value: Inova