title: 44_CLP+a_ACBP_24h

description: Library name: 44


title: MX1157 [206699910050_R03C01]

status: Public on Jan 26 2026

type: genomic

city: Wantirna South

first: Rust

last: Turakulov

state: Victoria

address: u23 105 Mountain Hwy

department: Bioinformatics

country: Australia

institute: AGRF

description:
206699910050_R03C01
BL_EBVN

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

molecule: genomic DNA

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

tag: tissue

value: Burkitt lymphoma

value: Colon

tag: group

value: Ref set

tag: material

value: FFPE

tag: age

tag: Sex

value: M

value: NIH

tag: mcf


title: 40_CLP+IgG_24h

type: SRA

city: PARIS

first: Guido

last: Kroemer

address: 15 rue de L'école de médecine

country: France

institute: Centre de Recherche des Cordeliers

description: Library name: 40

library_source: transcriptomic

data_processing:
Fastq verification by FastQC
Fastq is align on assemble genome by HISAT2 results are write in SAM file
Count is done HTSeq-count
Assembly: mm10
Supplementary files format and content: Result  are present in a tabulate text file, with ensembl ID and gene name associate, raw count gene for each sample.

molecule: total RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
For RNA-sequencing library preparation, RNA was extracted from mouse lungs using RNA Plus Mini Kit (Qiagen) according to manufacturer’s instructions. The concentration and integrity of total RNA was analysed using electrophoretic separation on microfabricated chips in Agilent 2100 Bioanalyzer System (Agilent, CA, USA).
mRNA-sequencing library preparation (1.5 µg total RNA per sample) was carried out on NovaSeq 6000 PE150 instrument (2 x 150 bp, 40 million reads per sample).

treatment_protocol: Eight-week-old male C57Bl/6J mice were randomly assigned to treatment groups and administered either a monoclonal antibody against ACBP/DBI (α-ACBP; 4h and 1h prior to surgery) or its isotype control (IgG), administered 1h before surgery. Sepsis was induced by cecal ligation and puncture (CLP) under isoflurane anesthesia. Briefly, the cecum was exteriorized, ligated at 75% of its length using non-absorbable 4-0 silk suture, and punctured once through-and-through with a 21-gauge needle. A small amount of fecal content was gently extruded, and the cecum was returned to the abdominal cavity. Sham-operated mice underwent the same procedure, including treatment injections, but without ligation or puncture. Mice that died within the first 24h post-surgery were considered to have succumbed to perioperative complications and were excluded from further analysis. For molecular analyses, organs were collected on the day of euthanasia (6h and 24h post-CLP) and immediately snap-frozen in liquid nitrogen.

value: Lung

tag: strain

tag: treatment

value: CLP+IgG

tag: time point

tag: batch


title: 46_CLP+a_ACBP_24h

description: Library name: 46

value: CLP+a-ACBP


title: 31_CLP+IgG_24h

description: Library name: 31


title: AV59 [206530740107_R01C01]

description:
206530740107_R01C01
ENKTL

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

value: Lymph node

value: Test set

value: F


title: AX36 [206530740084_R03C01]

description:
206530740084_R03C01
FTHCL

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


title: 36_CLP+IgG_24h

description: Library name: 36


title: AP06 [206530740067_R05C01]

description:
206530740067_R05C01
FDCS

source_name: Follicular dendritic cell sarcoma

value: Follicular dendritic cell sarcoma


title: 35_CLP+IgG_24h

description: Library name: 35


title: 33_CLP+IgG_24h

description: Library name: 33


title: 32_CLP+IgG_24h

description: Library name: 32


title: AN74 [206530740064_R04C01]

description:
206530740064_R04C01
NMZL

source_name: Nodal marginal zone lymphoma with follicular colonization


title: AR92 [206530740048_R07C01]

description:
206530740048_R07C01
FL_A

source_name: Follicular lymphoma, grade 1-2, BCL2 negative;


title: HP-MX1096 [207019360112_R06C01]

description:
207019360112_R06C01
HG_BCL


title: HP-MX1129 [206699910111_R05C01]

description:
206699910111_R05C01
BL_EBVP


title: HP-MX1097 [207019360112_R07C01]

description:
207019360112_R07C01
BL_EBVP


title: BF64 [206530740084_R08C01]

description:
206530740084_R08C01
TLL_C

source_name: T-lymphoblastic leukemia/lymphoma with histiocytic/dendritic cell component


title: 25_CLP+a_ACBP_6h

description: Library name: 25


title: BX60 [206530740029_R06C01]

description:
206530740029_R06C01
ENKTL

value: Soft tissue


title: AS41 [206530740055_R07C01]

description:
206530740055_R07C01
FL_A

source_name: Follicular lymphoma, grade 1-2, CD10 negative


title: 34_CLP+IgG_24h

description: Library name: 34


title: 30_CLP+a_ACBP_6h

description: Library name: 30


title: HP-MX477 [206382220066_R08C01]

description:
206382220066_R08C01
NMZL

source_name: Nodal marginal zone lymphoma

value: Nodal marginal zone lymphoma


title: HP-CS78 [206535560143_R06C01]

description:
206535560143_R06C01
FTHCL

source_name: Malignant lymphoma, most consistent with Follicular helper T cell lymphoma, NOS, with associated monotypic plasma cell proliferation, EBV negative. See note.

value: Lymph Node


title: HP-TCL37 [203136010021_R08C01]

description:
203136010021_R08C01
ETCL_SETD2

source_name: Monomorphic epitheliotropic intestinal T cell lymphoma (MEITL);

value: small intestine


title: HP-MX1077 [206095950110_R03C01]

description:
206095950110_R03C01
DLBCL_EN

source_name: DLBCL,ABC(Primary testicular DLBCL)

value: DLBCL,ABC(Primary testicular DLBCL)

value: Testis


title: BS81 [206530740029_R01C01]

description:
206530740029_R01C01
FL_A

source_name: Primary cutaneous follicle centre lymphoma

value: FFPE


title: 29_CLP+a_ACBP_6h

description: Library name: 29


title: 23_CLP+a_ACBP_6h

description: Library name: 23


title: 19_CLP+IgG_6h

description: Library name: 19


title: 22_CLP+a_ACBP_6h

description: Library name: 22


title: 24_CLP+a_ACBP_6h

description: Library name: 24


title: 28_CLP+a_ACBP_6h

description: Library name: 28


title: 18_CLP+IgG_6h

description: Library name: 18


title: HP-MX475 [206382220066_R06C01]

description:
206382220066_R06C01
NMZL

value: Nodal marginal zone lymphoma with follicular colonization

value: M


title: 17_CLP+IgG_6h

description: Library name: 17

value: Lung


title: HP-MX1128 [206699910111_R04C01]

description:
206699910111_R04C01
HG_BCL

source_name: Aggressive B-cell lymphoma most consistent with Burkitt lymphoma

value: Adnexal mass

value: Ref set

value: NIH


title: HP-CS10 [206535560068_R01C01]

description:
206535560068_R01C01
ENKTL

source_name: Peripheral T-cell lymphoma, consistent with ALK-negative anaplastic large cell lymphoma (ALCL)

value: Brain

value: Test set


title: BR03 [206530740005_R07C01]

description:
206530740005_R07C01
ETCL_SETD2

source_name: Hepatosplenic T-cell lymphoma  / Hepatosplenic T-cell lymphoma


title: 20_CLP+IgG_6h

description: Library name: 20

value: CLP+IgG


title: HP-MX717 [206530730159_R05C01]

description:
206530730159_R05C01
NMZL

source_name: MZL

value: MZL

value: Lymph node

value: F


title: 26_CLP+a_ACBP_6h

description: Library name: 26

value: CLP+a-ACBP


title: 16_CLP+IgG_6h

description: Library name: 16


title: 27_CLP+a_ACBP_6h

description: Library name: 27


title: 21_CLP+a_ACBP_6h

description: Library name: 21


title: MX1075 [207019360143_R06C01]

description:
207019360143_R06C01
HG_BCL

source_name: DLBCL, NOS GCB

value: DLBCL, NOS GCB

value: Soft tissue


title: 15_CLP+IgG_6h

description: Library name: 15

source_name: Lung


title: CP91 [206537460066_R08C01]

description:
206537460066_R08C01
BLL_NONKMT2A

source_name: B-lymphoblastic leukemia/lymphoma not otherwise specified IN SKIN

value: Skin


title: Z822 [206530740159_R06C01]

description:
206530740159_R06C01
FL_A

source_name: Follicular lymphoma, BCL2 pos (Z822-CREBP, TNFRSF14)

value: FFPE


title: CN18 [206535560055_R04C01]

description:
206535560055_R04C01
FTHCL

source_name: Peripheral T-cell lymphoma, favor Follicular Helper T-cell (TFH), lymphoma

value: Lymph Node


title: 10_Sham+a_ACBP_24h

description: Library name: 10

value: Sham+a-ACBP


title: CN17 [206535560055_R03C01]

description:
206535560055_R03C01
ALCL_A

source_name: ALK-negative anaplastic large cell lymphoma


title: 9_Sham+a_ACBP_24h

description: Library name: 9

value: Lung


title: HP-CK51 [206535560113_R01C01]

description:
206535560113_R01C01
HS

source_name: Histiocytic sarcoma

value: Histiocytic sarcoma

value: Soft Tissue


title: HP-CL80 [206535560127_R01C01]

description:
206535560127_R01C01
FDCS

source_name: Follicular dendritic cell sarcoma in a background of hyaline vascular Castleman disease

value: NIH


title: CQ27 [206537460139_R02C01]

description:
206537460139_R02C01
FL_A

source_name: Follicular lymphoma, BCL2 negative, Grade 1-2

value: Brain


title: 11_CLP+IgG_6h

description: Library name: 11


title: 6_Sham+a_ACBP_24h

description: Library name: 6


title: 13_CLP+IgG_6h

description: Library name: 13


title: HP-CH65 [206382220145_R05C01]

description:
206382220145_R05C01
FDCS

source_name: FDC sarcoma possibly arising in a background of hyaline vascular Castleman disease

value: Test set


title: 7_Sham+a_ACBP_24h

description: Library name: 7


title: 8_Sham+a_ACBP_24h

description: Library name: 8


title: HP-MX1093 [207019360112_R03C01]

description:
207019360112_R03C01
BL_EBVN

source_name: Burkitt lymphoma

value: Burkitt lymphoma

value: Thoracic

value: Ref set

value: M


title: 14_CLP+IgG_6h

description: Library name: 14

value: CLP+IgG


title: 12_CLP+IgG_6h

description: Library name: 12


title: 3_Sham+IgG_24h

description: Library name: 3

value: Sham+IgG


title: HP-MX1092 [207019360112_R02C01]

description:
207019360112_R02C01
BL_EBVN

value: Cecum


title: HP-MX1090 [207019360125_R08C01]

description:
207019360125_R08C01
HG_BCL

value: Appendix


title: HP-Z822 [205379750017_R03C01]

description:
205379750017_R03C01
FL_A

source_name: Follicular lymphoma, grade 1-2; BCL2 positive

value: Lymph node

value: FFPE


title: 1_Sham+IgG_24h

description: Library name: 1


title: 2_Sham+IgG_24h

description: Library name: 2


title: 5_Sham+IgG_24h

description: Library name: 5


title: tdTomato+ hCD2+ cells extracted from different tissues_RNA

city: St. Louis

first: Marco

last: Colonna

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

country: USA

institute: Washington University School of Medicine in St. Louis

description: Library name: tdTomato+ hCD2+ (Sample 1)_RNA

data_processing:
3' scRNAseq data was processed using the cellranger count pipeline (CellRanger version 9.0.1, 10X Genomics).
Assembly: GRCm39
Supplementary files format and content: Four files per sample: barcodes.tsv.gz,  features.tsv.gz and matrix.mtx.gz as well as assignment_confidence_table.csv
Library strategy: CITE-seq

molecule: polyA RNA

source_name: BM, spleen, cLN, mLN and sLN

extract_protocol:
We followed the Chromium Single Cell 3′ Reagent Kit v4 User Guide.
According Material and Methods of corresponding Manuscript

value: BM, spleen, cLN, mLN and sLN

tag: cell type

value: tdTomato+ hCD2+ cells

tag: genotype

value: Gm38411 iCre-hCD2 R26 tdTomato

value: No treatment

tag: library type

value: RNA

tag: hto


title: HP-MX1089 [207019360125_R07C01]

description:
207019360125_R07C01
BL_EBVN

value: NIH


title: tdTomato+ hCD2- cells extracted from different tissues_RNA

description: Library name: tdTomato+ hCD2- (Sample 2)_RNA

value: tdTomato+ hCD2- cells


title: tdTomato+ hCD2+ cells extracted from different tissues_Hashtag

description: Library name: tdTomato+ hCD2+ (Sample 1)_Hashtag

library_source: other

molecule: protein

value: HTO


title: HP-MR0234 [205848670066_R02C01]

description:
205848670066_R02C01
FDCS

source_name: Follicular Dendritic sarcoma

value: Follicular Dendritic sarcoma

value: Soft tissue


title: MX1079 [207019360096_R01C01]

description:
207019360096_R01C01
HG_BCL

source_name: DLBCL NOS GCB

value: DLBCL NOS GCB

value: Soft tissue, mesentry

value: Ref set

value: M


title: HP-AT27 [206382220097_R08C01]

description:
206382220097_R08C01
FL_B

source_name: Follicular lymphoma, low grade    t(14;18) negative

value: Test set


title: 4_Sham+IgG_24h

description: Library name: 4

value: Lung

value: Sham+IgG


title: HP-MX483 [206382220026_R07C01]

description:
206382220026_R07C01
NMZL

source_name: Nodal marginal zone lymphoma with follicular colonisation

value: Lymph node

value: FFPE

value: F


title: In vitro generated ILC3s and RORgt+ DCs_RNA

description:
Library name: In vitro generated cells_RNA
polyA RNA

source_name: BM culture

value: BM culture

value: ILC3s and RORgt+ DCs

value: Gm38411 iCre-hCD2 R26 tdTomato

value: No treatment


title: HP-MX480 [206537460078_R07C01]

description:
206537460078_R07C01
NMZL

source_name: NMZL with follicular colonization

value: NMZL with follicular colonization

value: NIH


title: HP-MX462 [206382220066_R02C01]

description:
206382220066_R02C01
NMZL

source_name: Nodal marginal zone lymphoma with plasmacytic differentiation, lambda light chain restricted.

value: Soft tissue


title: MNK3, control_2, ChIL-seq

city: Fukuoka

first: Shinichiro

last: Sawa

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

description: Library name: MNK3_control_2

library_source: genomic

data_processing:
Raw single-end ChIL-seq reads were trimmed for adapters and filtered for quality using Cutadapt. Trimmed reads were aligned to the mouse genome (mm10) with Bowtie2 (v2.2.5). Non-uniquely mapping reads and reads that aligned to the mitochondrial genome were filtered out using Samtools. Normalized coverage tracks (bigWig) were generated using deepTools bamCoverage with CPM normalization. Reads were extended to 75 bp (--extendReads 75) prior to coverage calculation.
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: MNK-3 cells were cultured in DMEM (Sigma-Aldrich) with 10% fetal bovine serum, 2 mM L-Glutamine (Sigma-Aldrich), 1 mM sodium pyruvate (Gibco, Thermo Fisher), 55 μM 2-mercaptoethanol (Sigma-Aldrich), 10 mM HEPES (Sigma-Aldrich), and 100 μg/ml penicillin and streptomycin. To maintain the property of MNK-3 cells, 10 ng/ml IL-7 (R&D System), 10 ng/ml IL-2 (R&D System), 10 ng/ml IL-15 (Pepro Tech), and 10 ng/ml retinoic acid (Sigma-Aldrich) were added to the culture medium.

extract_protocol:
No extraction performed
Library synthesis and amplification were conducted using a SMART-Seq v4 Ultra Low Input RNA Kit (TaKaRa). All reagents were prepared separately, and reactions were performed according to the manufacturer’s protocol using ChIL Read2 primers together with Ad1 and Ad2 primers. Amplified DNA was purified with AMPure XP beads (Beckman Coulter).

tag: cell line

value: mouse innate lymphoid celll type3

tag: antibody


title: HP-MX473 [206382220066_R04C01]

description:
206382220066_R04C01
FL_B

source_name: Follicular lymphoma, grade 1-2, negative for  BCL2 rearrangement.


title: tdTomato+ hCD2- cells extracted from different tissues_Hashtag

description: Library name: tdTomato+ hCD2- (Sample 2)_Hashtag

value: BM, spleen, cLN, mLN and sLN

value: tdTomato+ hCD2- cells

value: HTO


title: HP-MX1091 [207019360112_R01C01]

description:
207019360112_R01C01
BL_EBVP

value: Burkitt lymphoma

value: Colon

value: Ref set

value: M


title: MNK3, CBFβ_2, ChIL-seq

description: Library name: MNK3_CBFβ_2

value: CBFβ


title: cKO E14.5 fetus, fetal liver, ATAC-seq, HSCMPP-1

description:
Library name: cKO1_FL_HSCMPP
Active Motif

data_processing:
Raw ATAC-seq reads were trimmed and filtered for quality control using Cutadapt with the adapter sequence "CTGTCTCTTATACACATCT". The trimmed reads were then aligned to the mouse genome (mm10 or CNS11mut-modified mm10) using Bowtie2 v2.2.5 with the parameter -X 2000. Non-uniquely mapping reads and reads that aligned to the mitochondrial genome were filtered out using Samtools. Only concordantly mapped reads were used for further analysis. Peaks were called using Genrich with the following parameters: -j (ATAC-seq mode), -q 0.01 (FDR threshold), -y (exclude mitochondrial reads), and -e chrM (exclude mitochondrial chromosome).
Assembly: mm10
Supplementary files format and content: tdf
Supplementary files format and content: bigWig

source_name: fetal liver

extract_protocol:
Fetal liver and fetal thymus were separated under a stereo microscope, and single-cell suspension was generated by robustly pipetting with a 1000-μl pipette. The cell suspension was then filtered through a 100 μm strainer and resuspended in FACS buffer (2% FBS/0.05% NaN3/PBS)　The collected adult intestines were cut into 1 cm pieces and washed with PBS. After opening the intestines along the longitudinal axis, they were incubated in 30mM EDTA-containing PBS at room temperature for 15 minutes and were immediately washed with EDTA-free PBS to remove epithelium. The tissues were then digested by incubating at 37°C in DMEM (Nacalai Tesque) containing 1 mg/mL Collagenase D (SIGMA) and 0.33 mg/mL DNase I (SIGMA) for 30 min. Dissociated cells were collected every 30 min and strained with a 100μm strainer, and then lymphocytes were further enriched on a 40%/80% Percoll gradient. Bone marrow was isolated from the femur and tibia (four bones in total), crushed using the syringe plunger flange, filtered through a 100 µm cell strainer, and resuspended in FACS buffer. After staining by antibodies,  cell sorting were performed with  MA900 (Sony Imaging Products & Solutions).
100-200 cells were used for ATAC-seq following the manufacturer's instructions (Active Motif, #53150).

value: fetal liver

value: Lin- Sca-1high c-Kit high

value: Vav Cre Cbfb flox/flox


title: CNS11mut adult mice, small intestine, ATAC-seq, ILC2-1

description:
Library name: mut1_SI_ILC2
Active Motif

source_name: small intestine

value: small intestine

value: CD3e- B220- CD11b- CD11c- MHC ClassII- NK1.1- KLRG1+


title: HP-MX454 [206381860111_R08C01]

description:
206381860111_R08C01
NMZL

source_name: Low grade B-cell lymphoma, most consistent with nodal marginal zone lymphoma

value: Test set

value: FFPE


title: control E14.5 fetus, fetal liver, ATAC-seq, HSCMPP-1

description:
Library name: control1_FL_HSCMPP
Active Motif

value: Cbfb flox/flox


title: MX1076 [207019360143_R07C01]

description:
207019360143_R07C01
HG_BCL

source_name: DLBCL, GCB

value: DLBCL, GCB

value: Appendix

value: NIH


title: MX723 [206535560158_R05C01]

description:
206535560158_R05C01
NMZL

source_name: Nodal marginal zone lymphoma with prominent monocytoid B-cells

value: Lymph node


title: cKO E14.5 fetus, fetal liver, ATAC-seq, HSCMPP-2

description:
Library name: cKO2_FL_HSCMPP
Active Motif


title: MNK3, control_1, ChIL-seq

description: Library name: MNK3_control_1

value: mouse innate lymphoid celll type3


title: CNS11mut adult mice, small intestine, ATAC-seq, ILC2-2

description:
Library name: mut2_SI_ILC2
Active Motif


title: Z764 [206530740134_R06C01]

description:
206530740134_R06C01
FL_B

source_name: Follicular lymphoma, grade 1-2, t(14;18)-negative

value: Lymph Node


title: HP-MX715 [206382220026_R08C01]

description:
206382220026_R08C01
NMZL

source_name: Nodal marginal zone lymphoma

value: Nodal marginal zone lymphoma


title: adult mice, small intestine, ATAC-seq, ILC2-2

description:
Library name: WT2_SI_ILC2
Active Motif

value: WT


title: adult mice, small intestine, ATAC-seq, ILC2-1

description:
Library name: WT1_SI_ILC2
Active Motif


title: control E14.5 fetus, fetal liver, ATAC-seq, HSCMPP-2

description:
Library name: control2_FL_HSCMPP
Active Motif


title: HP-MX722 [207018680030_R02C01]

description:
207018680030_R02C01
NMZL

source_name: NMZL

value: NMZL

value: Ref set

value: F


title: MNK3, CBFβ_1, ChIL-seq

description: Library name: MNK3_CBFβ_1

value: CBFβ


title: MA1115 [207019360096_R03C01]

description:
207019360096_R03C01
LPL

source_name: LPL

value: LPL

value: Soft tissue


title: HP-MX725 [207018680030_R03C01]

description:
207018680030_R03C01
NMZL


title: In vitro generated ILC3s and RORgt+ DCs_Hashtag

description:
Library name: In vitro generated cells_Hashtag
HTO

value: BM culture

value: ILC3s and RORgt+ DCs

value: Gm38411 iCre-hCD2 R26 tdTomato

value: No treatment

value: HTO

value: TotalSeq™-B0310 anti-mouse Hashtag 10 Antibody, TotalSeq™-B0311 anti-mouse Hashtag 11 Antibody and TotalSeq™-B0312 anti-mouse Hashtag 12 Antibody


title: CNS11 4thmut adult mice, small intestine, ATAC-seq, LTi-2

description:
Library name: 4mut2_SI_LTi
Active Motif

value: small intestine

value: CD3e- B220- TCRb- LTa-EGFP+ c-Kit+ CD4+

value: CNS11 4th/4th


title: HP-AN-07 [206382220043_R08C01]

description:
206382220043_R08C01
FDCS

source_name: Follicular dendritic cell tumor

value: Follicular dendritic cell tumor

value: Brain

value: Test set

value: FFPE

value: NIH


title: MX564 [205624870096_R02C01]

description:
205624870096_R02C01
FL_A

source_name: Follicular lymphoma, BCL2 negative; grade 1-2

value: Lymph node

value: Ref set

value: F


title: HP-AN75 [203723050032_R05C01]

description:
203723050032_R05C01
ETCL_SETD2

source_name: Monomorphic epitheliotropic intestinal T cell lymphoma (MEITL);

value: Colorectal

value: M


title: adult mice, small intestine, ATAC-seq, LTi-1

description:
Library name: WT1_SI_LTi
Active Motif

value: WT


title: HP-MR0251 [205848670066_R07C01]

description:
205848670066_R07C01
FDCS

source_name: Follicular Dendritic sarcoma

value: Follicular Dendritic sarcoma

value: Soft tissue


title: HP-MX478 [206382220048_R05C01]

description:
206382220048_R05C01
NMZL

value: Nodal marginal zone lymphoma


title: adult mice, bone marrow, ATAC-seq, MPP-4

description:
Library name: WT4_BM_MPP
Active Motif

source_name: bone marrow

value: bone marrow

value: Lin- Sca-1high c-Kit high Flt3+


title: CNS11 4thmut adult mice, bone marrow, ATAC-seq, MPP-1

description:
Library name: 4mut1_BM_MPP
Active Motif

value: CNS11 4th/4th


title: CNS11 4thmut adult mice, bone marrow, ATAC-seq, MPP-2

description:
Library name: 4mut2_BM_MPP
Active Motif


title: HP-MX472 [206382220066_R03C01]

description:
206382220066_R03C01
FL_B

source_name: Follicular lymphoma, negative for BCL-2 protein by immunohistochemistry


title: HP-AN-06 [206381860074_R03C01]

description:
206381860074_R03C01
FDCS

source_name: Follicular dendritic cell tumo

value: Follicular dendritic cell tumo


title: HP-MX693 [206084850040_R06C01]

description:
206084850040_R06C01
FL_A

source_name: Follicular lymphoma grade 1-2,BCL2pos

value: Follicular lymphoma grade 1-2,BCL2pos


title: HP-MX479 [206382220026_R03C01]

description:
206382220026_R03C01
NMZL

value: Low grade B-cell lymphoma, most consistent with nodal marginal zone lymphoma

value: Test set


title: MX724 [206535560158_R06C01]

description:
206535560158_R06C01
NMZL

value: NMZL

value: FFPE

value: NIH


title: HP-MX690 [206084850040_R03C01]

description:
206084850040_R03C01
FL_B

source_name: Follicular lymphoma, grade 3A, BCL2R Pos

value: Lymph node

value: F


title: CNS11mut E14.5 fetus, fetal liver, ATAC-seq, ChILP-2

description:
Library name: mut2_FL_ChILP
Active Motif

source_name: fetal liver

value: fetal liver

value: Lin- CD127+ Int.a4b7+ Flt3-  excluding Sca-1high c-Kit high double positive cells


title: CNS11mut adult mice, Thymus, ATAC-seq, DP-1

description:
Library name: mut1_Thymus_DP
Active Motif

source_name: Thymus

value: Thymus

value: Lin- CD4+ CD8a+


title: HP-AN78.1 [203723050032_R06C01]

description:
203723050032_R06C01
ETCL_SETD2

value: Monomorphic epitheliotropic intestinal T cell lymphoma (MEITL);

value: Small intestine

value: Ref set

value: M


title: HP-MR322 [206084850030_R06C01]

description:
206084850030_R06C01
FDCS

source_name: Folliculardendritic cell tumor, apparently arising in Castleman's  disease

value: Soft tissue


title: HP-MX689 [206084850040_R02C01]

description:
206084850040_R02C01
FL_A

source_name: Follicular lymphoma, grade 1-2, BCL2pos

value: Follicular lymphoma, grade 1-2, BCL2pos


title: E14.5 fetus, fetal liver, ATAC-seq, ChILP-2

description:
Library name: WT2_FL_ChILP
Active Motif

value: WT


title: HP-MX1116 [206100370168_R01C01]

description:
206100370168_R01C01
LPL

source_name: Low grade B-cell lymphoma favor lymphoplasmacytic lymphoma


title: HP-MX1084 [207019360125_R05C01]

description:
207019360125_R05C01
HG_BCL

source_name: Burkitt lymphoma

value: Burkitt lymphoma

value: Soft tissue, right axilla


title: HP-AN76 [203136010019_R07C01]

description:
203136010019_R07C01
ETCL_NONSETD2

source_name: Primary intestinal Peripheral T-cell lymphoma, not otherwise specified of  gamma delta T-cell origin,

value: Gastrointestinal

value: FFPE


title: HP-MX1088 [207019360125_R06C01]

description:
207019360125_R06C01
BL_EBVP

value: NIH


title: CNS11mut adult mice, Thymus, ATAC-seq, DP-2

description:
Library name: mut2_Thymus_DP
Active Motif


title: E14.5 fetus, fetal liver, ATAC-seq, HSCMPP-2

description:
Library name: WT2_FL_HSCMPP
Active Motif

value: Lin- Sca-1high c-Kit high


title: HP-MX687 [206103240068_R08C01]

description:
206103240068_R08C01
FL_A

source_name: Follicular lymphoma, grade 1-2

value: Follicular lymphoma, grade 1-2

value: Lymph node

value: Test set

value: F


title: adult mice, Thymus, ATAC-seq, DP-2

description:
Library name: WT2_Thymus_DP
Active Motif

value: Thymus

value: Lin- CD4+ CD8a+


title: adult mice, small intestine, ATAC-seq, LTi-2

description:
Library name: WT2_SI_LTi
Active Motif

source_name: small intestine

value: small intestine

value: CD3e- B220- TCRb- LTa-EGFP+ c-Kit+ CD4+


title: HP-AN-03 [206381860074_R02C01]

description:
206381860074_R02C01
FDCS

source_name: Follicular dendritic cellsarcoma/tumor

value: Follicular dendritic cellsarcoma/tumor

value: Soft tissue

value: M


title: HP-MX686 [206103240068_R07C01]

description:
206103240068_R07C01
FL_A

source_name: Follicular lymphoma, grade 3A,BCL2pos

value: Follicular lymphoma, grade 3A,BCL2pos


title: adult mice, Thymus, ATAC-seq, DP-1

description:
Library name: WT1_Thymus_DP
Active Motif

value: WT


title: CNS11mut E14.5 fetus, fetal liver, ATAC-seq, ChILP-1

description:
Library name: mut1_FL_ChILP
Active Motif

value: fetal liver

value: Lin- CD127+ Int.a4b7+ Flt3-  excluding Sca-1high c-Kit high double positive cells


title: HP-MR0238 [205848670066_R05C01]

description:
205848670066_R05C01
FDCS

source_name: Follicular Dendritic sarcoma

value: Follicular Dendritic sarcoma

value: Ref set

value: FFPE

value: NIH


title: CNS11 4thmut adult mice, small intestine, ATAC-seq, LTi-1

description:
Library name: 4mut1_SI_LTi
Active Motif

value: CNS11 4th/4th


title: CNS11mut adult mice, bone marrow, ATAC-seq, MPP-2

description:
Library name: mut2_BM_MPP
Active Motif

source_name: bone marrow

value: bone marrow

value: Lin- Sca-1high c-Kit high Flt3+


title: adult mice, bone marrow, ATAC-seq, ChILP-1

description:
Library name: WT1_BM_ChILP
Active Motif

value: Lin- CD127+ Int.a4b7+ Flt3- CD25-  excluding Sca-1high c-Kit high double positive cells


title: adult mice, bone marrow, ATAC-seq, MPP-3

description:
Library name: WT3_BM_MPP
Active Motif


title: CNS11mut adult mice, bone marrow, ATAC-seq, MPP-1

description:
Library name: mut1_BM_MPP
Active Motif


title: PC-X411 [205987780142_R06C01]

description:
205987780142_R06C01
FDCS

source_name: Follicular Dendritic cell sarcoma

value: Follicular Dendritic cell sarcoma

value: Test set

value: Frozen


title: HP-MR325 [206084850024_R03C01]

description:
206084850024_R03C01
FDCS

source_name: Malignant spindle cell neoplasm with focal epithelioid appearance, favor stromal tumor, not further subclassified, in  association with Castleman's disease,  hyaline vascular type,

value: Lymph node

value: F


title: CNS11mut E14.5 fetus, fetal liver, ATAC-seq, HSCMPP-1

description:
Library name: mut1_FL_HSCMPP
Active Motif

value: Lin- Sca-1high c-Kit high


title: PC-W274 [205987780142_R03C01]

description:
205987780142_R03C01
HSTCL_GD

source_name: Hepatosplenic T-cell lymphoma

value: Hepatosplenic T-cell lymphoma

value: Spleen

value: M


title: E14.5 fetus, fetal liver, ATAC-seq, ChILP-1

description:
Library name: WT1_FL_ChILP
Active Motif

value: fetal liver

value: Lin- CD127+ Int.a4b7+ Flt3-  excluding Sca-1high c-Kit high double positive cells

value: WT


title: HP-MX451 [206381860111_R05C01]

description:
206381860111_R05C01
NMZL

source_name: Nodal marginal zone lymphoma (NMZL) with follicular colonization

value: Ref set

value: FFPE

value: NIH


title: CNS11mut adult mice, bone marrow, ATAC-seq, HSC-1

description:
Library name: mut1_BM_HSC
Active Motif

value: bone marrow

value: Lin- Sca-1high c-Kit high Flt3-


title: adult mice, bone marrow, ATAC-seq, HSC-2

description:
Library name: WT2_BM_HSC
Active Motif


title: CNS11mut E14.5 fetus, fetal liver, ATAC-seq, HSCMPP-2

description:
Library name: mut2_FL_HSCMPP
Active Motif

source_name: fetal liver


title: adult mice, bone marrow, ATAC-seq, HSC-1

description:
Library name: WT1_BM_HSC
Active Motif


title: HP-MR324 [206084850030_R08C01]

description:
206084850030_R08C01
FDCS

value: Follicular Dendritic sarcoma


title: adult mice, bone marrow, ATAC-seq, ChILP-2

description:
Library name: WT2_BM_ChILP
Active Motif

value: Lin- CD127+ Int.a4b7+ Flt3- CD25-  excluding Sca-1high c-Kit high double positive cells


title: HP-L711 [205848670021_R01C01]

description:
205848670021_R01C01
PTFL

source_name: Pediatric-type follicular lymphoma

value: Pediatric-type follicular lymphoma


title: MX568 [205624870096_R06C01]

description:
205624870096_R06C01
FL_A

source_name: Follicular lymphoma, BCL2 negative; grade 3A

value: Lymph node


title: CLP+DEX/aDBI_4

description:
Library name: 100
F100_EKRN240003486-1A

data_processing:
Quality control by FastQC
Alignment on genome by HISAT2
Raw count by HTSeq-count
Assembly: mm10
Supplementary files format and content: It is a Tabulate Separated Value text file with ensemble gene code and corresponding Gene Name. One sample by columns and one gene by row.

source_name: Spleen

extract_protocol:
For RNA-sequencing library preparation, RNA was extracted from mouse spleens using RNA Plus Mini Kit (Qiagen) according to manufacturer’s instructions. The concentration and integrity of total RNA was analysed using electrophoretic separation on microfabricated chips in Agilent 2100 Bioanalyzer System (Agilent, CA, USA).
mRNA-sequencing library preparation (1.5 µg total RNA per sample) was carried out on NovaSeq 6000 PE150 instrument (2 x 150 bp, 40 million reads per sample).

treatment_protocol: Eight-week-old male C57Bl/6J mice were randomly assigned to treatment groups and administered either a monoclonal antibody against ACBP/DBI (aDBI; 4h and1 h prior to surgery) or its isotype control (IgG), in combination with dexamethasone (DEX) or PBS 1X, administered 1h before CLP. Sepsis was induced by cecal ligation and puncture (CLP) under isoflurane anesthesia. Briefly, the cecum was exteriorized, ligated at 75% of its length using non-absorbable 4-0 silk suture, and punctured once through-and-through with a 21-gauge needle. A small amount of fecal content was gently extruded, and the cecum was returned to the abdominal cavity. Sham-operated mice underwent the same procedure, including treatment injections, but without ligation or puncture. Mice that died within the first 24h post-surgery were considered to have succumbed to perioperative complications and were excluded from further analysis. For molecular analyses, organs were collected on the day of euthanasia (24h post-CLP) and immediately snap-frozen in liquid nitrogen.


title: HP-P085 [203136010021_R07C01]

description:
203136010021_R07C01
ETCL_SETD2

source_name: Monomorphic epitheliotropic intestinal T cell lymphoma (MEITL);

value: Soft tissue

value: F


title: MX570 [205624870096_R08C01]

description:
205624870096_R08C01
FL_A

source_name: Follicular lymphoma, BCL2 negative; grade 1-2


title: CNS11mut adult mice, bone marrow, ATAC-seq, ChILP-2

description:
Library name: mut2_BM_ChILP
Active Motif


title: CLP+DEX/aDBI_3

description:
Library name: 99
F99_EKRN240003464-1A


title: HP-Q032 [205751550152_R08C01]

description:
205751550152_R08C01
NMZL

source_name: Low-grade B-cell lymphoma, consistent with nodal marginal zone lymphoma.  See note.


title: E14.5 fetus, fetal liver, ATAC-seq, HSCMPP-1

description:
Library name: WT1_FL_HSCMPP
Active Motif

value: Lin- Sca-1high c-Kit high


title: CLP+PBS/aDBI_6

description:
Library name: 112
F112_EKRN240003481-1A

value: Spleen


title: CLP+PBS/aDBI_5

description:
Library name: 93
F93_EKRN240003459-1A


title: HP-BT58.1 [206082540131_R01C01]

description:
206082540131_R01C01
NMZL

source_name: B-cell lymphoma consistent with nodal marginal zone lymphoma

value: Test set


title: adult mice, bone marrow, ATAC-seq, MPP-2

description:
Library name: WT2_BM_MPP
Active Motif

value: Lin- Sca-1high c-Kit high Flt3+


title: HP-P484 [205848670021_R02C01]

description:
205848670021_R02C01
PTFL

value: M


title: PC-W878 [205987770176_R05C01]

description:
205987770176_R05C01
ALCL_A

source_name: Primary cutaneous anaplastic large cell lymphoma

value: Frozen


title: CNS11mut adult mice, bone marrow, ATAC-seq, HSC-2

description:
Library name: mut2_BM_HSC
Active Motif


title: CLP+DEX/aDBI_2

description:
Library name: 96
F96_EKRN240003462-1A


title: HP-AN01 [205848670051_R01C01]

description:
205848670051_R01C01
FDCS

source_name: FDCS

value: FDCS

value: Tonsil


title: CLP+PBS/aDBI_2

description:
Library name: 35
F35_EKRN240003484-1A


title: HP-MX1085 [206699910111_R01C01]

description:
206699910111_R01C01
BL_EBVP

source_name: BL, EBV POS

value: BL, EBV POS

value: Ref set

value: FFPE

value: NIH


title: CNS11mut adult mice, bone marrow, ATAC-seq, ChILP-1

description:
Library name: mut1_BM_ChILP
Active Motif

value: bone marrow

value: Lin- CD127+ Int.a4b7+ Flt3- CD25-  excluding Sca-1high c-Kit high double positive cells


title: PC-W160 [205987780030_R03C01]

description:
205987780030_R03C01
ETCL_SETD2

value: Hepatosplenic T-cell lymphoma


title: HP-MX449 [206381860111_R03C01]

description:
206381860111_R03C01
NMZL

source_name: a nodal marginal zone B-cell lymphoma, splenic type, which are usually IgD positive

value: Lymph node


title: PC-Y818 [205987780015_R03C01]

description:
205987780015_R03C01
NMZL

source_name: Marginal zone cell lymphoma

value: Marginal zone cell lymphoma


title: CLP+DEX/IgG_6

description:
Library name: 106
F106_EKRN240003465-1A


title: adult mice, bone marrow, ATAC-seq, MPP-1

description:
Library name: WT1_BM_MPP
Active Motif

source_name: bone marrow

value: WT


title: HP-W861 [205003700039_R06C01]

description:
205003700039_R06C01
LN_NN_A

source_name: Castleman disease, hyaline vascular variant, with a TDT-positive T-lymphoblastic proliferation

value: Soft tissue


title: CLP+DEX/aDBI_6

description:
Library name: 118
F118_EKRN240003456-1A

value: Spleen


title: CLP+DEX/IgG_4

description:
Library name: 89
F89_EKRN240003452-1A


title: HP-MX1082 [207019360125_R03C01]

description:
207019360125_R03C01
BL_EBVP

source_name: Burkitt lymphoma

value: Burkitt lymphoma


title: HP-MX594 [205756360148_R03C01]

description:
205756360148_R03C01
FL_B

source_name: Primary cutaneous follicle center lymphoma

value: Skin

value: F


title: CLP+DEX/IgG_3

description:
Library name: 88
F88_EKRN240003472-1A


title: PC-X413 [205987780006_R07C01]

description:
205987780006_R07C01
FDCS

source_name: Follicular Dendritic cell sarcoma

value: Follicular Dendritic cell sarcoma

value: Bone

value: Test set

value: Frozen

value: M


title: CLP+DEX/aDBI_5

description:
Library name: 116
F116_EKRN240003470-1A


title: CLP+DEX/IgG_1

description:
Library name: 50
F50_EKRN240003467-1A


title: PC-Y787 [205982910150_R02C01]

description:
205982910150_R02C01
ETCL_SETD2

source_name: Monomorphic Epitheliotropic Intestinal T-Cell Lymphoma (MEITL).

value: Small Intestine

value: NIH


title: CLP+PBS/IgG_6

description:
Library name: 84
F84_EKRN240003454-1A


title: HP-MX685 [206084850024_R06C01]

description:
206084850024_R06C01
FL_B

source_name: Follicular lymphoma, grade 3A,bcl2 P(focal colasce to large nodlue no diff sheets)

value: Ref set

value: FFPE


title: CLP+PBS/IgG_5

description:
Library name: 83
F83_EKRN240003460-1A

source_name: Spleen


title: HP-MR0246 [205848670066_R08C01]

description:
205848670066_R08C01
FDCS

source_name: Follicular Dendritic sarcoma

value: Follicular Dendritic sarcoma


title: HP-MX1074 [206095950110_R04C01]

description:
206095950110_R04C01
HG_BCL

source_name: Diffuse large B-cell lymphoma, Germinal center type

value: Nasopharynx mass


title: HP-MX663 [205841320155_R02C01]

description:
205841320155_R02C01
NMZL

source_name: Nodal marginal zone lymphoma

value: Nodal marginal zone lymphoma

value: Lymph node


title: CLP+PBS/IgG_2

description:
Library name: 42
F42_EKRN240003466-1A

value: Spleen


title: HP-MR0236 [205848670066_R04C01]

description:
205848670066_R04C01
FDCS


title: HP-T069 [205841320034_R06C01]

description:
205841320034_R06C01
PTFL

source_name: Pediatric-type Follicular Lymphoma

value: Pediatric-type Follicular Lymphoma


title: CLP+DEX/aDBI_1

description:
Library name: 36
F36_EKRN240003475-1A


title: HP-HP04 [203136010021_R05C01]

description:
203136010021_R05C01
ETCL_SETD2

source_name: Monomorphic epitheliotropic intestinal T cell lymphoma (MEITL);

value: Soft tissue


title: CLP+DEX/IgG_5

description:
Library name: 90
F90_EKRN240003479-1A


title: CLP+PBS/aDBI_1

description:
Library name: 34
F34_EKRN240003491-1A


title: HP-R597 [205841320034_R04C01]

description:
205841320034_R04C01
PTFL

source_name: Pediatric-type follicular lymphoma

value: Pediatric-type follicular lymphoma


title: HP-T607 [205756360067_R06C01]

description:
205756360067_R06C01
HS

source_name: Histiocytic sarcoma,P

value: Histiocytic sarcoma,P

value: Brain


title: HP-MX591 [205724770094_R08C01]

description:
205724770094_R08C01
FL_B

value: Primary cutaneous follicle center lymphoma

value: Skin


title: Sham+DEX/aDBI_2

description:
Library name: 158
F158_EKRN240003488-1A


title: Sham+DEX/aDBI_1

description:
Library name: 156
F156_EKRN240003483-1A


title: CLP+PBS/IgG_1

description:
Library name: 41
F41_EKRN240003471-1A


title: CLP+PBS/aDBI_3

description:
Library name: 53
F53_EKRN240003457-1A


title: HP-MX592 [205756360148_R01C01]

description:
205756360148_R01C01
FL_B

value: M


title: HP-MX653 [205841340029_R08C01]

description:
205841340029_R08C01
NMZL

value: Test set

value: F


title: CLP+PBS/aDBI_4

description:
Library name: 91
F91_EKRN240003461-1A


title: HP-MX609 [205841340029_R02C01]

description:
205841340029_R02C01
FL_B

value: NIH


title: CLP+PBS/IgG_3

description:
Library name: 44
F44_EKRN240003468-1A


title: CLP+DEX/IgG_2

description:
Library name: 86
F86_EKRN240003463-1A


title: Sham+PBS/aDBI_2

description:
Library name: 148
F148_EKRN240003458-1A


title: HP-MX649 [205841340029_R04C01]

description:
205841340029_R04C01
NMZL

value: Ref set

value: FFPE


title: HP-MX667 [205841320155_R06C01]

description:
205841320155_R06C01
NMZL


title: HP-MX688 [206084850040_R01C01]

description:
206084850040_R01C01
FL_A

source_name: Follicular lymphoma, grade 1-2,BCL2R Pos


title: HP-MX606 [205841320026_R07C01]

description:
205841320026_R07C01
FL_B


title: HP-MX595 [205756360148_R04C01]

description:
205756360148_R04C01
FL_A


title: CLP+PBS/IgG_4

description:
Library name: 45
F45_EKRN240003478-1A


title: HP-R160 [205722630146_R06C01]

description:
205722630146_R06C01
HS

source_name: Histiocytic sarcoma, poss P

value: Histiocytic sarcoma, poss P


title: HP-U445 [205756360067_R08C01]

description:
205756360067_R08C01
HS

source_name: Atypical histiocytic infiltrate most consistent with histiocytic sarcoma,S

value: Bone


title: HP-MX659 [205841320154_R06C01]

description:
205841320154_R06C01
NMZL

value: Nodal marginal zone lymphoma

value: Lymph node


title: Sham+DEX/aDBI_3

description:
Library name: 159
F159_EKRN240003473-1A

value: Spleen


title: HP-X413 [205756360149_R01C01]

description:
205756360149_R01C01
FDCS

source_name: Follicular dendritic cell sarcoma

value: Follicular dendritic cell sarcoma

value: Spine


title: HP-T065 [205722630146_R08C01]

description:
205722630146_R08C01
HS

value: Histiocytic sarcoma,P

value: Colorectal


title: Sham+PBS/aDBI_4

description:
Library name: 150
F150_EKRN240003480-1A


title: Sham+DEX/IgG_1

description:
Library name: 142
F142_EKRN240003477-1A


title: Sham+DEX/aDBI_4

description:
Library name: 162
F162_EKRN240003474-1A


title: HP-T949 [205848670021_R04C01]

description:
205848670021_R04C01
PTFL

source_name: Paediatric nodal marginal zone lymphoma

value: Paediatric nodal marginal zone lymphoma

value: Soft tissue


title: Sham+PBS/IgG_3

description:
Library name: 128
F128_EKRN240003490-1A


title: Sham+PBS/aDBI_3

description:
Library name: 149
F149_EKRN240003489-1A


title: HP-U834 [205848670021_R06C01]

description:
205848670021_R06C01
PTFL

value: Pediatric-type follicular lymphoma

value: M


title: HP-MX599 [205756360148_R08C01]

description:
205756360148_R08C01
FL_B

source_name: Primary cutaneous follicle center lymphoma

value: Skin

value: Test set


title: Sham+PBS/aDBI_1

description:
Library name: 147
F147_EKRN240003476-1A


title: Sham+DEX/IgG_4

description:
Library name: 140
F140_EKRN240003482-1A


title: Sham+DEX/IgG_3

description:
Library name: 139
F139_EKRN240003469-1A


title: HP-V097 [205722630146_R04C01]

description:
205722630146_R04C01
ALCL_A

source_name: Primary cutaneous ALCL ALK-

value: Primary cutaneous ALCL ALK-

value: Ref set

value: NIH


title: Sham+DEX/IgG_2

description:
Library name: 144
F144_EKRN240003487-1A


title: Sham+PBS/IgG_2

description:
Library name: 127
F127_EKRN240003455-1A


title: HP-W734 [205751550164_R01C01]

description:
205751550164_R01C01
NMZL

value: FFPE

value: F


title: HP-MX654 [205841320154_R01C01]

description:
205841320154_R01C01
NMZL

value: Nodal marginal zone lymphoma

value: Lymph node


title: HP-MX603 [205841320026_R04C01]

description:
205841320026_R04C01
FL_B

value: Primary cutaneous follicle center lymphoma


title: CLP_aDBI_7

description: Library name: 1086

data_processing:
Alignment  on genome by STAR
Raw count by featureCounts
Analysis on R with DESeq2
Assembly: GRCm38/mm10
Supplementary files format and content: Excel file which contain raw count and DESeq2 analysis follow by genes database’s informations

source_name: Liver

extract_protocol:
For RNA-sequencing library preparation, RNA was extracted from mouse livers using RNA Plus Mini Kit (Qiagen) according to manufacturer’s instructions. The concentration and integrity of total RNA was analysed using electrophoretic separation on microfabricated chips in Agilent 2100 Bioanalyzer System (Agilent, CA, USA).
mRNA-sequencing library preparation (1.5 µg total RNA per sample) was carried out on NovaSeq 6000 PE150 instrument (2 x 150 bp, 40 million reads per sample).

treatment_protocol: Eight-week-old male C57Bl/6J mice were randomly assigned to treatment groups and administered either a monoclonal antibody against ACBP/DBI (α-ACBP; 4 h and 1 h prior to surgery) or its isotype control (IgG), administered 1 h before surgery. Sepsis was induced by cecal ligation and puncture (CLP) under isoflurane anesthesia. Briefly, the cecum was exteriorized, ligated at 75% of its length using non-absorbable 4-0 silk suture, and punctured once through-and-through with a 21-gauge needle. A small amount of fecal content was gently extruded, and the cecum was returned to the abdominal cavity. Sham-operated mice underwent the same procedure, including treatment injections, but without ligation or puncture. Mice that died within the first 24 h post-surgery were considered to have succumbed to perioperative complications and were excluded from further analysis. For molecular analyses, organs were collected on the day of euthanasia (24h post-CLP) and immediately snap-frozen in liquid nitrogen.

value: Liver


title: Sham+PBS/IgG_4

description:
Library name: 129
F129_EKRN240003485-1A

value: Spleen


title: HP-HP22 [203723050032_R07C01]

description:
203723050032_R07C01
ETCL_SETD2

value: Monomorphic epitheliotropic intestinal T cell lymphoma (MEITL);

value: Small intestine


title: HP-MX597 [205756360148_R06C01]

description:
205756360148_R06C01
FL_A


title: CLP_aDBI_9

description: Library name: 1088


title: CLP_aDBI_5

description: Library name: 1084


title: CLP_aDBI_6

description: Library name: 1085


title: CLP_aDBI_3

description: Library name: 1082


title: CLP_aDBI_2

description: Library name: 1081


title: HP-Z306 [205751550164_R07C01]

description:
205751550164_R07C01
NMZL

source_name: Nodal marginal zone lymphoma WITH PROMINENT MONOCYTOID CELLS


title: CLP_aDBI_1

description: Library name: 1080


title: CLP_IgG_8

description: Library name: 1078


title: Sham+PBS/IgG_1

description:
Library name: 126
F126_EKRN240003453-1A

source_name: Spleen


title: HP-MX602 [205841320026_R03C01]

description:
205841320026_R03C01
FL_A


title: CLP_IgG_6

description: Library name: 1076


title: HP-N495 [205751550152_R05C01]

description:
205751550152_R05C01
NMZL

source_name: Nodal marginal zone lymphoma WITH INCREASED LARGE CELLS


title: HP-V143 [203726680058_R03C01]

description:
203726680058_R03C01
ETCL_NONSETD2

source_name: Enteropathy-associated T-cell lymphoma

value: Enteropathy-associated T-cell lymphoma


title: HP-U604 [205751550159_R05C01]

description:
205751550159_R05C01
NMZL

source_name: Nodal marginal zone lymphoma


title: HP-HP23 [203723050032_R08C01]

description:
203723050032_R08C01
ETCL_SETD2


title: CLP_IgG_4

description: Library name: 1074


title: HP-P163 [205751550152_R07C01]

description:
205751550152_R07C01
NMZL

source_name: Low grade B-cell lymphona most consistent with Nodal marginal zone lymphoma


title: HP-MX246 [205751520080_R03C01]

description:
205751520080_R03C01
FL_B

source_name: Follicular lymphoma, BCL2 negative

value: Follicular lymphoma, BCL2 negative

value: Soft tissue


title: PC-Z001 [205987780015_R06C01]

description:
205987780015_R06C01
FL_A

source_name: Follicular lymphoma (FL), grade1-2 BCL2R pos

value: Frozen


title: HP-U221 [205848670021_R05C01]

description:
205848670021_R05C01
PTFL

value: Paediatric nodal marginal zone lymphoma

value: M


title: CLP_IgG_9

description: Library name: 1079


title: HP-MX245 [205751520080_R02C01]

description:
205751520080_R02C01
FL_A

source_name: Follicular lymphoma grade 1-2, BCL2 negative

value: Ref set


title: CLP_aDBI_4

description: Library name: 1083


title: Sham_aDBI_5

description: Library name: 1070


title: HP-AZ16 [205751550155_R02C01]

description:
205751550155_R02C01
ETCL_SETD2

source_name: Peripheral T-cell lymphoma, not otherwise specified

value: Lung

value: Test set

value: NIH


title: HP-MX244 [205751520080_R01C01]

description:
205751520080_R01C01
FL_B

source_name: Follicular lymphoma, grade 1-2, focally follicular and predominantly diffuse,bcl2neg

value: FFPE


title: HP-MX604 [205841320026_R05C01]

description:
205841320026_R05C01
FL_A

value: Skin


title: HP-Z001 [205379750080_R01C01]

description:
205379750080_R01C01
FL_A

source_name: Follicular lymphoma(BCL2 pos by IHC)

value: Follicular lymphoma(BCL2 pos by IHC)

value: Lymph node

value: F


title: CLP_IgG_5

description: Library name: 1075

value: Liver


title: HP-MX247 [205751520080_R04C01]

description:
205751520080_R04C01
FL_B

source_name: Follicular lymphoma, grade 3A, CD10 negative, MUM1 positive,bcl2 neg(Karube)


title: CLP_aDBI_8

description: Library name: 1087


title: Sham_aDBI_1

description: Library name: 1066


title: CLP_IgG_3

description: Library name: 1073


title: Sham_IgG_5

description: Library name: 1065


title: CLP_IgG_7

description: Library name: 1077


title: HP-M308 [205751550152_R01C01]

description:
205751550152_R01C01
NMZL

value: Nodal marginal zone lymphoma


title: Sham_aDBI_4

description: Library name: 1069


title: Sham_IgG_3

description: Library name: 1063


title: HP-P098 [205751550152_R06C01]

description:
205751550152_R06C01
NMZL


title: HP-MX642 [205724770045_R03C01]

description:
205724770045_R03C01
NMZL


title: HP-W513 [205841320034_R08C01]

description:
205841320034_R08C01
PTFL

source_name: Pediatric marginal zone lymphoma

value: Pediatric marginal zone lymphoma


title: CLP_IgG_2

description: Library name: 1072


title: Sham_IgG_2

description: Library name: 1062


title: Sham_aDBI_3

description: Library name: 1068


title: Sham_IgG_1

description: Library name: 1061


title: HP-W005 [206095950017_R08C01]

description:
206095950017_R08C01
PTFL

source_name: Pediatric-Type Follicular Lymphoma

value: Pediatric-Type Follicular Lymphoma


title: Islet, bulk RNA-seq, insulin-depleted, short-read, bio replicate 2

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_bulk_depleted_2
short-read

data_processing:
Raw reads were trimmed using cutadapt (version 4.8, python version 3.10.14) and aligned to the mouse GRCm38 genome using STAR (version 2.7.11b).
Assembly: mm10
Supplementary files format and content: .txt file contains count table for all four samples.

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. RNA was purified using the Qiagen RNeasy micro kit (Qiagen Cat # 74004)
Bulk RNA-seq libraries were prepared using KAPA mRNA Hyper Prep kit (Roche 8098123702), following the KAPA mRNA HyperPrep Kit protocol (KR1352 – v7.21). Insulin depletion was applied between step 8 and 9 in the KAPA library prep protocol.  PacBio MAS-IsoSeq protocol from Jumpcode Genomics. Using the DepleteXTM RNA Depletion Panel (Insulin) kit from Jumpcode Genomics.

value: pancreatic islet

value: male, 8 weeks


title: HP-Y787 [205379750063_R07C01]

description:
205379750063_R07C01
ETCL_SETD2

source_name: Monomorphic epitheliotropic intestinal T-cell lymphoma

value: Small intestine


title: JMML-MT012 [205724770019_R04C01]

description:
205724770019_R04C01
JMML

value: Peripheral blood

value: M


title: JMML-MT015 [205724770019_R07C01]

description:
205724770019_R07C01
JMML

value: Ref set


title: Sham_aDBI_2

description: Library name: 1067

source_name: Liver


title: Sham_IgG_4

description: Library name: 1064


title: HP-AP99 [205724770094_R07C01]

description:
205724770094_R07C01
NMZL

value: Soft tissue

value: Test set


title: CLP_IgG_1

description: Library name: 1071


title: Islet, 3prime, nondepleted, short-read

description:
Library name: islet_3prime_nondepleted
short-read

library_source: transcriptomic single cell

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.

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: male

value: 8 weeks


title: Islet, bulk RNA-seq, non-depleted, short-read, bio replicate 1

description:
Library name: islet_bulk_nondepleted_1
short-read


title: JMML-MT007 [205724770007_R07C01]

description:
205724770007_R07C01
JMML

value: FFPE

value: NIH


title: HP-Q832 [205751550158_R02C01]

description:
205751550158_R02C01
NMZL

value: Lymph node

value: F


title: JMML-MT016 [205724770019_R08C01]

description:
205724770019_R08C01
JMML


title: JMML-MT008 [205724770007_R08C01]

description:
205724770007_R08C01
JMML


title: JMML-MT006 [205724770007_R06C01]

description:
205724770007_R06C01
JMML


title: HP-W349 [205003700039_R02C01]

description:
205003700039_R02C01
ALCL_A

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


title: JMML-MT018 [205724770045_R02C01]

description:
205724770045_R02C01
JMML


title: JMML-MT004 [205724770007_R04C01]

description:
205724770007_R04C01
JMML


title: mouse brain, WT, valproic acid, rep2

city: Wako

first: Yoko

last: Hanno

state: Saitama

address: 2-1 Hirosawa

institute: RIKEN Center for Brain Science

description: Library name: WT-V2

data_processing:
The procedure of raw reads filtering is as follows: (1) Remove reads containing adapters; (2) Remove reads containing N > 10% (N represents base that could not be determined); (3) Remove low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 5.
Mapping the clean reads to the reference genome or the transcriptome is the basis for the next following analysis. Clean reads were mapped to the mouse reference genome (GRCm39/mm39) using the HISAT2.
Assembly: GRCm39/mm39
Supplementary files format and content: csv file includes raw count for each sample

source_name: brain

extract_protocol:
RNA was harvested using Rneasy mini plus kit (QIAGEN). Total RNA was used for the construction of sequencing libraries.
rRNA depletion was performed with the Ribo-Zero rRNA Removal Kit (Illumina, San Diego, CA, USA). The enriched mRNA was randomly fragmented using fragmentation buffer, and cDNA synthesis was carried out using the NEB Next Ultra RNA Library Kit (Illumina) according to the manufacturer’s protocol.

value: brain

value: WT

value: valproic acid


title: JMML-MT002 [205724770007_R02C01]

description:
205724770007_R02C01
JMML


title: JMML-MT005 [205724770007_R05C01]

description:
205724770007_R05C01
JMML


title: mouse brain, htr, valproic acid, rep3

description: Library name: htr-V3

value: htr3a Notch KO


title: mouse brain, htr, rep1

description: Library name: htr1


title: HP-MX605 [205841320026_R06C01]

description:
205841320026_R06C01
FL_B

source_name: Primary cutaneous follicle center lymphoma

value: Skin


title: mouse brain, WT, valproic acid, rep3

description: Library name: WT-V3


title: mouse brain, WT, rep3

description: Library name: WT3


title: HP-T693 [205722630144_R06C01]

description:
205722630144_R06C01
ALCL_A

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

value: Small intestine


title: mouse brain, WT, valproic acid, rep1

description: Library name: WT-V1


title: JMML-MT010 [205724770019_R02C01]

description:
205724770019_R02C01
JMML

value: Peripheral blood

value: M


title: HP-U947 [205722630144_R08C01]

description:
205722630144_R08C01
ALCL_A


title: Islet, bulk RNA-seq, non-depleted, short-read, bio replicate 2

description:
Library name: islet_bulk_nondepleted_2
short-read

value: pancreatic islet

value: male, 8 weeks


title: mouse brain, htr, valproic acid, rep2

description: Library name: htr-V2


title: mouse E14 brain, valproic acid, rep1

description: Library name: V1


title: HP-HS02 [205722630144_R01C01]

description:
205722630144_R01C01
HS

source_name: Histiocytic sarcoma

value: Histiocytic sarcoma

value: Test set


title: MX1068 [207019360143_R04C01]

description:
207019360143_R04C01
DLBCL_EN

source_name: DLBCL, ABCPrimary testicular DLBCL)

value: DLBCL, ABCPrimary testicular DLBCL)

value: Testis

value: Ref set

value: FFPE


title: HP-W863 [205003700039_R07C01]

description:
205003700039_R07C01
FDCS

source_name: Follicular dendritic cell sarcoma arising in a background of Castleman disease

value: Soft tissue

value: NIH


title: mouse E14 brain, poly(I:C), rep3

description: Library name: P3

value: brain


title: Islet, bulk RNA-seq, insulin-depleted, short-read, bio replicate 1

description:
Library name: islet_bulk_depleted_1
short-read


title: mouse E14 brain, valproic acid, rep3

description: Library name: V3

value: valproic acid


title: mouse E14 brain, poly(I:C), rep1

description: Library name: P1


title: mouse brain, htr, rep3

description: Library name: htr3

value: htr3a Notch KO


title: HP-Y672 [205722630146_R05C01]

description:
205722630146_R05C01
ALCL_A

source_name: Primary cutaneous ALCL, ALK negative (unusual coexp of TCR delta and CD4)

value: Skin


title: mouse E14 brain, valproic acid, rep2

description: Library name: V2


title: mouse E14 brain, control, rep2

description: Library name: C2

value: saline


title: mouse E14 brain, control, rep3

description: Library name: C3


title: HP-W678 [205724770094_R01C01]

description:
205724770094_R01C01
FL_A

source_name: Follicular lymphoma,grade 1-2, BCL2R neg

value: Lymph node


title: HP-W878 [205003700039_R08C01]

description:
205003700039_R08C01
ALCL_A

source_name: Primary cutaneous CD30 positive T-cell LPD, c/w primary cutaneous ALCL

value: M


title: HP-MX1086 [206699910111_R02C01]

description:
206699910111_R02C01
BL_EBVN

source_name: Burkitt lymphoma

value: Burkitt lymphoma


title: mouse E14 brain, control, rep1

description: Library name: C1


title: HP-MX1081 [207019360125_R02C01]

description:
207019360125_R02C01
BL_EBVP

value: Thymus

value: F


title: HP-MX1067 [206699910111_R07C01]

description:
206699910111_R07C01
DLBCL_EN

source_name: DLBCL, GCB

value: DLBCL, GCB


title: HP-AR70 [205624900058_R03C01]

description:
205624900058_R03C01
FL_B

source_name: B-cell lymphoma favor follicular lymphoma, grade1-2, BCL2Rneg(BCL6R pos,

value: Test set


title: HP-MX1066 [206699910111_R06C01]

description:
206699910111_R06C01
DLBCL_EN

source_name: DLBCL, ABC

value: DLBCL, ABC

value: Stomach


title: JMML-MT001 [205724770007_R01C01]

description:
205724770007_R01C01
JMML

value: Peripheral blood

value: Ref set

value: FFPE


title: mouse brain, htr, valproic acid, rep1

description: Library name: htr-V1

value: brain


title: HP-MX1080 [207019360125_R01C01]

description:
207019360125_R01C01
BL_EBVP

source_name: Burkitt lymphoma, pos for EBV

value: Burkitt lymphoma, pos for EBV

value: Bowel

value: NIH


title: mouse E14 brain, poly(I:C), rep2

description: Library name: P2


title: mouse brain, WT, rep1

description: Library name: WT1

value: WT


title: C57 mouse WT3

city: Shanghai

first: Zhixin

last: Bai

address: Dongan Road

department: Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences

country: China

institute: Fudan University

data_processing:
The raw data was checked by FastQC v0.11.5
Clean reads were aligned to the Mouse genome using STAR 2.5.3a
The expression of the transcript was calculated by FPKM using Cuffnorm
Differentially expression transcripts were determined using DESeq v1.16.1
Function and signaling pathway enrichment analysis using GO and KEGG database
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: substantia nigra

extract_protocol:
Total RNA was isolated from each substantia nigra sample using Trizol
Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit

value: substantia nigra


title: MX586 [205624890021_R05C01]

description:
205624890021_R05C01
FL_A

value: Primary cutaneous follicle center lymphoma

value: Skin

value: M


title: C57 mouse WT2


title: C57 mouse WT1


title: mouse brain, htr, rep2

description: Library name: htr2

value: htr3a Notch KO


title: mouse brain, WT, rep2

description: Library name: WT2


title: MX582 [205624890021_R01C01]

description:
205624890021_R01C01
FL_A


title: C57 mouse shDNAJB1 3


title: HP-X555 [205724770094_R02C01]

description:
205724770094_R02C01
HS

source_name: Histiocytic sarcoma,S(h/o CLL)

value: Histiocytic sarcoma,S(h/o CLL)

value: Liver


title: HP-MX652 [205841340029_R07C01]

description:
205841340029_R07C01
NMZL

source_name: Nodal marginal zone lymphoma with follicular colonization

value: Lymph node

value: F


title: MR318 [205624880166_R07C01]

description:
205624880166_R07C01
FDCS

source_name: Most consistent follicular dendritic cell sarcoma

value: Test set


title: MX590 [205624890021_R08C01]

description:
205624890021_R08C01
FL_B


title: Sample34_set5_2xTrS_IP

city: Guangzhou

first: Xin

last: Cheng

address: 74 Zhongshaner Rd

institute: Sun Yat-sen University

data_processing:
Base calling: The image data measured by the high- throughput sequencer areconverted into sequence data ( reads) by Illumina CASAVA (v1.7) base recognition.
Quality control: Rawdata( raw reads) of fastq format were firstly processed through in- house perl scripts. In this step, clean data ( clean reads) were obtained by removing readscontaining adapter, reads containing N base and low quality reads fromraw data. At the same time, Q20, Q30 and GC content the cleandata were calculated.
Alignment: Reference genome and gene model annotation files weredownloaded from genome website directly. Index of the referencegenome was built using Hisat2 (v2.0.5) and paired-end cleanreads were aligned to the reference genome using Hisat2(v2.0.5)
Quantification: featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
Assembly: GRCm38.100   Mus musculus
Supplementary files format and content: tab-delimited text files include counts for each Sample

source_name: brain

extract_protocol:
RNA was extracted using RNeasy Micro Kit following the manufacturer's protocols
Libraries were pepared using SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian following the manufacturesr's protocols

tag: sample type

value: IP


title: MX581 [205624870150_R08C01]

description:
205624870150_R08C01
FL_B

source_name: Primary cutaneous follicle center lymphoma

tag: tissue

value: FFPE


title: C57 mouse shDNAJB1 1


title: C57 mouse shDNAJB1 2


title: Sample33_set6_2xTrA_IP

value: brain

tag: group


title: Sample36_set2_2xTrS_IP


title: MR319 [205624880166_R08C01]

description:
205624880166_R08C01
FDCS

source_name: Follicular dendritic cell proliferation likely arising in a background of Castleman disease, hyaline-vascular type

value: Soft tissue

tag: material


title: MX583 [205624890021_R02C01]

description:
205624890021_R02C01
FL_B

tag: age


title: Sample35_set5_2xTrA_IP


title: MX579 [205624870150_R06C01]

description:
205624870150_R06C01
FL_A

tag: Sex


title: MX424 [205624870150_R01C01]

description:
205624870150_R01C01
LN_NN_A

source_name: FH+ Plasmacytosis

value: FH+ Plasmacytosis

value: Ref set

tag: mcf


title: MX423 [205624870098_R08C01]

description:
205624870098_R08C01
LN_NN_B

source_name: Reactive lymphoid hyperplasia with marked plasmacytosis and fibrosis and increased IgG4 positive plasma cells.

value: NIH


title: HP-MX243 [205624870099_R01C01]

description:
205624870099_R01C01
FL_B

source_name: Follicular lymphoma, grade 1-2,BCL2 neg

value: Follicular lymphoma, grade 1-2,BCL2 neg


title: MX575 [205624870150_R02C01]

description:
205624870150_R02C01
FL_B

value: Primary cutaneous follicle center lymphoma


title: Sample32_set3_1xTr_IP


title: Sample29_set6_1xTr_IP


title: Sample28_set4_2xTrA_IP


title: Sample31_set6_2xTrS_IP


title: CT26 tumors from mice treated with Complex 1 and Radiation, rep3

city: Hefei

first: Chen

last: Guiyuan

address: Jinzhai Road

institute: University of Science and Technology of China

description: Library name: Combination3

data_processing:
Bioinformatics analysis was performed on the original sequencing data, mainly differential gene analysis including cluster analysis, GO enrichment analysis and KEGG enrichment analysis. Raw sequencing reads were aligned to the Ensembl Release mm39 reference genome using STAR (version 2.5.3a) with default parameters. Following alignment, HTSeq (version 2.0.1) was employed to quantify read counts for each gene. DESeq2 was utilized for differential expression analysis.
Assembly: mm39
Supplementary files format and content: raw counts for each sample

source_name: CT26 tumor tissues

extract_protocol:
The tumour samples were then subjected to RNA extraction and RNA quality testing immediately followed by library construction, library purification, library detection, and library quantification.
Next® Ultra™ RNA Library Prep Kit for Illumina® (NEB, lot no. E7530) was using for RNA library preparation.

value: CT26 tumor tissues

value: WT


title: MX420 [205624870098_R05C01]

description:
205624870098_R05C01
LN_NN_B

source_name: Reactive lymphoid hyperplasia

value: Reactive lymphoid hyperplasia


title: MX421 [205624870098_R06C01]

description:
205624870098_R06C01
LN_NN_B

source_name: FH

value: FH


title: Sample30_set3_2xTrS_IP


title: Sample27_set1_2xTrA_IP


title: MX573 [205624870098_R03C01]

description:
205624870098_R03C01
FL_A

source_name: Follicular lymphoma, BCL2R negative; grade 1-2


title: HeLa_SOX6_overexpression

type: RNA

city: Beijing

first: Han

last: Zheng

address: 38 Xueyuan Road, Haidian District

institute: Peking University Health Science Center

description: Gene expression data from HeLa cells transfected with SOX6 vector.

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

label: biotin

source_name: HeLa cell line, SOX6 overexpression

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: HeLa cells were cultured and seeded in 10-well plates.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: HeLa cells were transfected with either SOX6 vector or control vector.

value: HeLa


title: MX566 [205624870096_R04C01]

description:
205624870096_R04C01
FL_B

source_name: Follicular lymphoma grade 1-2, predominantly diffuse

value: Lymph node

value: M


title: CT26 tumors from mice treated with Complex 1 and Radiation, rep2

description: Library name: Combination2


title: MX569 [205624870096_R07C01]

description:
205624870096_R07C01
FL_A

value: Follicular lymphoma, BCL2R negative; grade 1-2

value: Test set

value: F


title: Sample25_set2_1xTr_IP

value: brain

value: IP


title: CT26 tumors from mice treated with Radiation, rep2

description: Library name: Radiation2


title: Sample24_set1_2xTrS_IP


title: Sample26_set1_1xTr_IP


title: HP-X812 [205848670021_R08C01]

description:
205848670021_R08C01
PTFL

source_name: Pediatric-type follicular lymphoma

value: Pediatric-type follicular lymphoma

value: FFPE


title: HeLa_negative_control

description: Gene expression data from HeLa cells transfected with control vector.

source_name: HeLa cell line, negative control


title: HP-Y712 [205379750063_R04C01]

description:
205379750063_R04C01
ALCL_A

source_name: Primary cutaneous ALCL, ALK negative (unusual coexp of TCR delta and CD4)

value: Skin

value: Ref set

value: NIH


title: CT26 tumors from mice treated with Radiation, rep3

description: Library name: Radiation3

value: CT26 tumor tissues


title: CT26 tumors from mice treated with Complex 1 and Radiation, rep1

description: Library name: Combination1

value: WT


title: CT26 tumors from mice treated with complex 1, rep2

description: Library name: Chem2


title: HP-Y778 [205379750063_R05C01]

description:
205379750063_R05C01
ETCL_NONSETD2

source_name: Primary cutenaous gamma delta T-cell lymphoma


title: Sample22_set4_2xTrS_IP


title: CT26 tumors from mice in the untreated control group, rep2

description: Library name: Blank2


title: CT26 tumors from mice in the untreated control group, rep3

description: Library name: Blank3


title: CT26 tumors from mice treated with complex 1, rep1

description: Library name: Chem1


title: CT26 tumors from mice treated with Radiation, rep1

description: Library name: Radiation1


title: CT26 tumors from mice in the untreated control group, rep1

description: Library name: Blank1


title: Sample19_set2_2xTrA_IP


title: LayRNA-9

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

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

source_name: lung adenocarcinoma

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

value: lung adenocarcinoma

tag: patient id

tag: cohort

value: validation cohort

tag: novel grade

value: NST

tag: tnm 8th_edition_stage

tag: passed qc

value: TRUE

tag: mean tin

tag: site

value: LHMC

tag: sequence batch


title: Human Coronary Smooth Muscle Cells, H3K27ac HiChIP

city: Singapore

first: Roger

last: Foo

address: 14 Medical Drive, MD6

country: Singapore

institute: National University of Singapore

description:
Library name: HCASMC H3K27ac HiChIP
H3K27ac HiChIP in HCASMC

data_processing:
Raw paired-end reads in Fastq format for respective samples were processed using the HiCuP pipeline (Version 0.7.4). The hg38 human genome was used as reference to generate the HiCuP Digest file using two restriction motifs GATC and GANTC via the hicup_digester command for running the HiCuP pipeline.
Paired contacts were extracted from aligned filtered bam files using Samtools (Version 1.13) and used as input for the pre function in juicer package to generate .hic files
Paired interaction counts at 5kb resolution were extracted from the matrix, and High-confidence chromatin loops were identified using the FitHiChIP tool (Version 11.0) as previously described using default parameters, with loop type = peak-to-all, coverage = bias correction, merge nearby interactions = Yes,  FDR < 0.01, minimum interaction size =20kb, maximum interaction size = 2 mb.
Assembly: hg38
Supplementary files format and content: .HIC file include interaction matrix for each sample
Supplementary files format and content: High-confidence interaction FitHiChIP called loops in bed files for each sample
Library strategy: HiChIP-Seq

source_name: HCASMC

growth_protocol: human healthy coronary artery smooth muscle cells (HCASMC) (Thermo Scientific, Product code C-017-5C, Lot. 1689414) are cultured in human vascular smooth muscle (VSMC) basal medium (Gibco, M231500), in Smooth Muscle Growth Supplement (SMGS) (Gibco, S00725) and 1% penicillin/streptomycin. human healthy coronary artery endothelial cells (HCAEC) (ATCC, Product code PCS-100-020, Lot 62382179) are cultured in Endothelial Cell Growth medium MV2 (PromoCell, C-22022).

extract_protocol:
At least one million cells from the same lot used for HiChIP experiments were crosslinked with 1% Formaldehyde for 10 min at room temperature and quenched with glycine (125mM) for 5 min. The protocol was followed using Arima High Coverage Hi-C Kit (Arima Genomics, A410110), as per manufacturer's instructions.
Library was prepared using NEB Ultra II Library preparation kit (NEB, E7645L) according to manufacturer's protocol and appropriate index primers. 12 PCR cycles were performed using indexed primers, and DNA fragments were cleaned up with Omega MagBind NGS Cleanup Magnetic Beads. Libraries were sequenced by paired-end sequencing with at least 300 million read pairs at 2 X 151 bp read length on illumina HiSeq4000 platforms.

value: Heart

tag: cell type

value: Smooth Muscle Cells

tag: chip antibody

value: anti-H3K27ac (Abcam, ab4729)


title: HP-Z280 [205379750123_R02C01]

description:
205379750123_R02C01
ALCL_A

source_name: Anaplastic large cell lymphoma, ALK-negative;

value: Lymph Node

value: Test set

value: M


title: Sample21_set4_1xTr_IP

source_name: brain

value: brain

tag: treatment

tag: sample type

value: IP


title: Sample23_set5_1xTr_IP

tag: tissue

tag: group


title: LayRNA-7

value: FFPE

value: VI


title: CT26 tumors from mice treated with complex 1, rep3

description: Library name: Chem3

value: CT26 tumor tissues

tag: cell line


title: HP-Z391 [205379750123_R03C01]

description:
205379750123_R03C01
FTHCL

source_name: Angioimmunoblastic T-cell lymphoma COEXISTING cmmL

value: Lymph node

tag: material

tag: age

tag: Sex

value: F

value: NIH


title: HP-W274 [205121980113_R07C01]

description:
205121980113_R07C01
HSTCL_GD

source_name: Hepatosplenic T-cell lymphoma(SPLEEN)

value: Hepatosplenic T-cell lymphoma(SPLEEN)

value: Spleen

value: Ref set

tag: mcf


title: LayRNA-8

value: lung adenocarcinoma

tag: patient id

tag: cohort

value: validation cohort

tag: novel grade

value: NST

value: IB

value: TRUE

value: LHMC


title: LayRNA-4

tag: tnm 8th_edition_stage

tag: passed qc

tag: mean tin


title: Human Coronary Endothelial Cells, H3K27ac HiChIP

description:
Library name: HCAEC H3K27ac HiChIP
H3K27ac HiChIP in HCAEC

source_name: HCAEC

value: Heart

tag: cell type

value: Endothelial

value: anti-H3K27ac (Abcam, ab4729)


title: Sample17_set6_2xTrA_Input

value: brain

value: Input


title: LayRNA-5

value: FFPE

value: LMP

tag: site

tag: sequence batch


title: HP-Z255 [205379750080_R07C01]

description:
205379750080_R07C01
NMZL

source_name: B-cell lymphoma with marked plasmacytic differentiation

value: Lymph node

value: Test set

value: M

value: NIH


title: Sample20_set3_2xTrA_IP

tag: treatment

tag: sample type

value: IP


title: LayRNA-6

tag: tissue

value: lung adenocarcinoma

value: validation cohort


title: Sample16_set6_1xTr_Input

tag: group


title: LayRNA-3

value: NST


title: HP-Z002 [205379750080_R02C01]

description:
205379750080_R02C01
HS

source_name: Histiocytic sarcoma

value: Histiocytic sarcoma

value: Skin

tag: material

value: F


title: Sample18_set6_2xTrS_Input


title: LayRNA-30

value: IB

value: TRUE

value: LHMC


title: LayRNA-27

value: VI


title: LayRNA-26

value: FFPE


title: Sample14_set5_2xTrA_Input

value: brain

value: Input


title: Sample15_set5_2xTrS_Input


title: HP-W160 [205121980113_R04C01]

description:
205121980113_R04C01
ETCL_SETD2

source_name: Hepatosplenic T-cell lymphoma

value: Hepatosplenic T-cell lymphoma

value: Spleen

value: Ref set

tag: age


title: LayRNA-29

value: LMP


title: LayRNA-28

value: lung adenocarcinoma


title: LayRNA-22

value: validation cohort


title: LayRNA-23

value: NST

value: FALSE


title: LayRNA-24


title: LayRNA-21


title: Sample12_set4_2xTrS_Input


title: HP-MX410 [205624900044_R07C01]

description:
205624900044_R07C01
LN_NN_B

source_name: Reactive follicular and paracortical hyperplasia with marked eosinophilia  including eosinophilic microabscesses

value: Lymph node

tag: Sex

value: M

value: NIH


title: Sample13_set5_1xTr_Input


title: LayRNA-20

value: TRUE


title: LayRNA-19

value: LHMC


title: HP-Y299 [205379750043_R04C01]

description:
205379750043_R04C01
FDCS

source_name: Follicular dendritic cell sarcoma

value: Follicular dendritic cell sarcoma

value: Test set

value: F

tag: mcf


title: LayRNA-17

value: FFPE

tag: patient id


title: HP-MX417 [205624900045_R06C01]

description:
205624900045_R06C01
LN_NN_A

source_name: Reactive follicular and paracortical hyperplasia with dermatopathic changes.


title: HP-X411 [205756360002_R08C01]

description:
205756360002_R08C01
FDCS

value: Soft Tissue


title: HP-V612 [205121980113_R02C01]

description:
205121980113_R02C01
FHTCL

source_name: Angioimmunoblastic T-cell lymphoma

value: Angioimmunoblastic T-cell lymphoma


title: LayRNA-15

tag: cohort

value: VI


title: Sample10_set4_1xTr_Input

value: brain

value: Input


title: Sample9_set3_2xTrS_Input


title: LayRNA-2

value: lung adenocarcinoma

value: validation cohort

tag: novel grade


title: LayRNA-25

value: NST

tag: tnm 8th_edition_stage


title: MX565 [205624870096_R03C01]

description:
205624870096_R03C01
FL_B

source_name: B-cell lymphoma favor follicular lymphoma, BCL2 negative

value: Orbit mass

value: Ref set


title: Sample11_set4_2xTrA_Input


title: LayRNA-16

tag: passed qc


title: LayRNA-14

value: LMP

tag: mean tin


title: HP-MX608 [205841340029_R01C01]

description:
205841340029_R01C01
FL_A

source_name: B-cell lymphoma, favor primary cutaneous follicle center lymphoma,

value: Skin

value: NIH


title: HP-MX419 [205624900045_R08C01]

description:
205624900045_R08C01
LN_NN_A

source_name: FH

value: FH

value: Lymph node


title: HP-MX415 [205624900045_R04C01]

description:
205624900045_R04C01
LN_NN_A

source_name: Reactive follicular hyperplasia with follicular lysis

value: M


title: Sample8_set3_2xTrA_Input


title: HP-MX248 [205379750009_R01C01]

description:
205379750009_R01C01
LN_NN_B

source_name: Paracortical hyperplasia

value: Paracortical hyperplasia

value: FFPE


title: LayRNA-12

source_name: lung adenocarcinoma

value: IB

value: TRUE

value: LHMC


title: LayRNA-13


title: Sample6_set2_2xTrS_Input

source_name: brain

value: brain

value: Input


title: LayRNA-10

value: lung adenocarcinoma

value: validation cohort


title: LayRNA-11

value: NST


title: HP-Z743 [205107400093_R07C01]

description:
205107400093_R07C01
FL_B

source_name: Follicular lymphoma, grade 1-2, t(14;18)-negative

value: Ref set


title: Sample4_set2_1xTr_Input


title: FFP-5x-4


title: FFP-5x-25

value: VI


title: Sample7_set3_1xTr_Input


title: LayRNA-18


title: FFP-5x-27


title: Sample5_set2_2xTrA_Input


title: FFP-5x-18

value: LMP


title: LayRNA-1


title: HP-AN-05 [206381860074_R05C01]

description:
206381860074_R05C01
FDCS

source_name: Poorly differentiated spindle cell neoplasm, consistent with follicular dendritic cell sarcoma

value: Soft tissue

value: NIH


title: 9475


title: 915


title: HP-AN-09 [206381860074_R04C01]

description:
206381860074_R04C01
FDCS

value: Follicular dendritic cell sarcoma


title: HP-X209 [205107400091_R02C01]

description:
205107400091_R02C01
FTHCL

source_name: Follicular T-cell lymphoma

value: Follicular T-cell lymphoma

value: Lymph node

value: Test set

value: M


title: HP-Z744 [205107400093_R08C01]

description:
205107400093_R08C01
FL_A

source_name: Follicular lymphoma, grade 3A, negative for t(14;18) translocation

value: FFPE

value: F


title: 3255

value: TRUE

value: LHMC


title: HP-X408 [205107400091_R06C01]

description:
205107400091_R06C01
LN_NN_B

source_name: Unicentric Castleman disease, hyaline vascular variant, with increased TdT-positive cells

value: Colon


title: HP-Z827 [205379750017_R04C01]

description:
205379750017_R04C01
ETCL_SETD2

source_name: Monomorphic epitheliotropic intestinal T-cell lymphoma

value: Small intestine


title: Sample3_set1_2xTrA_Input

value: brain

value: Input


title: 2885

value: lung adenocarcinoma

value: validation cohort

value: VI


title: 611

value: NST


title: wt cardiac macrophage, mi-d3

first: Zhenzhen

last: Zhan

address: Jimo Road 150

department: Research Center for Translational Medicine

institute: Shanghai East Hospital, Tongji University School of Medicine,

description: mi-d3 cMa.txt

data_processing:
We first apply Stringtie (version: 1.3.0) to count the number of Fragments for each gene after Hisat2 alignment.
Then the TMM (trimmed mean of M values) method was used to standardize the expression levels across various samples.
We then use Perl script to calculate the FPKM (Fragments Per Kilobase of transcript per Million mapped fragments) value for each gene.
Apply edgeR for differential gene analysis, obtain p-value, and perform multiple hypothesis testing correction. By controlling the FDR (False Discovery Rate) to determine the threshold of p-value, the corrected p-value is q-value. At the same time, we calculate the differential expression multiple, which is Fold change
Genes that exhibit a fold change in expression level larger than 2.0 and a q-value less than 0.05 are referred to as differentially expressed genes (DEGs).
Assembly: mm10
Supplementary files format and content: matrix table with raw gene counts for every gene and every sample

source_name: heart

extract_protocol:
Mice were sacrificed by CO2 anesthetization. The heart was rapidly excised, cut into little blocks and soaked in digested buffer to get single cell suspension. The cardiac macrophages were enriched using UltraPure Anti-F4/80 Microbeads (130-110-443, Miltenyi Biotec). Total RNA was extracted using MJzol animal RNA Extraction Kit(MagBeads) (Cat#T102096)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 4200 TapeStation (Agilent technologies, Santa Clara, CA, US).
Library construction was perfromed following the steps of mRNA isolation, fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, end repair, adding A at the 3 'end, connecting connectors, enrichment, using Dual-mode mRNA Library Prep Kit(Borroen), Agilent High Sensitivity DNA Kit(Agilent) and Agilent D1000 Reagents(Agilent).

value: heart

tag: cell type

value: cardiac macrophage

tag: genotype

value: WT

tag: disease state

value: myocardial infarction

tag: time

value: Day 3


title: FFP-5x-16

tag: sample type

value: FFPE

tag: site

tag: sequence batch


title: Sample2_set1_2xTrS_Input

tag: tissue

tag: group

tag: treatment


title: 31551

value: IB


title: 24512

value: TRUE


title: 24018

value: LHMC


title: 29063


title: 4225


title: wt cardiac macrophage, mi-d3, biol rep2

description: mi-d3 cMa.txt


title: wt cardiac macrophage, mi-d3, biol rep3

description: mi-d3 cMa.txt


title: 20736

value: LMP


title: wt cardiac macrophage, mi-d3, biol rep4

description: mi-d3 cMa.txt


title: ko cardiac macrophage, mi-d3, biol rep2

description: mi-d3 cMa.txt

value: NPM1 knockout


title: ko cardiac macrophage, mi-d3, biol rep4

description: mi-d3 cMa.txt


title: 23153


title: 30868


title: HP-MX1095 [207019360112_R05C01]

description:
207019360112_R05C01
BL_EBVP

data_processing: BeadStudio software v3.2

source_name: Burkitt lymphoma

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

value: Burkitt lymphoma

value: Tonsil

value: Ref set

tag: material

tag: age

tag: Sex

value: M

value: NIH

tag: mcf


title: 20538

value: lung adenocarcinoma

tag: patient id

tag: cohort

value: validation cohort

tag: novel grade

value: NST

tag: tnm 8th_edition_stage


title: HP-P912 [204809970041_R08C01]

description:
204809970041_R08C01
CLL

source_name: CLL

value: CLL

value: Test set

value: Frozen


title: 18033

value: FFPE

tag: passed qc

tag: mean tin


title: HP-W406 [205003700039_R03C01]

description:
205003700039_R03C01
NMZL

source_name: Marginal zone lymphoma (post transplant setting)

value: Tongue


title: wt cardiac macrophage, mi-d5, biol rep3

description: mi-d5 cMa.txt

value: heart

tag: cell type

value: cardiac macrophage

tag: genotype

value: WT

tag: disease state

value: myocardial infarction

tag: time

value: Day 5


title: 18619

tag: tissue

tag: sample type

value: TRUE

tag: site

value: LHMC

tag: sequence batch


title: HP-G458 [204809970041_R07C01]

description:
204809970041_R07C01
CLL

source_name: Primary cutaneous follicle center lymphoma

tag: group

tag: material

tag: age

value: F


title: 18576

tag: patient id


title: HP-BE97 [206382220099_R02C01]

description:
206382220099_R02C01
FL_B

source_name: Follicular lymphoma, grade 1-2, BCL2 negative

value: Lymph node

value: Ref set

tag: Sex

value: M

value: NIH

tag: mcf


title: Sample1_set1_1xTr_Input

value: brain

tag: treatment

value: Input


title: 26482

value: lung adenocarcinoma

tag: cohort

value: validation cohort

tag: novel grade

value: NST

tag: tnm 8th_edition_stage

tag: passed qc


title: ko cardiac macrophage, mi-d3, biol rep3

description: mi-d3 cMa.txt

value: heart

tag: cell type

tag: genotype

value: NPM1 knockout

tag: disease state

value: Day 3


title: 11980

tag: tissue

tag: sample type

value: FFPE

value: VI

value: IB

tag: mean tin


title: 10152

value: TRUE

tag: site

value: LHMC

tag: sequence batch


title: 11462


title: 21448


title: ko cardiac macrophage, mi-d5, biol rep4

description: mi-d5 cMa.txt

value: cardiac macrophage

value: myocardial infarction

tag: time

value: Day 5


title: SDG724_HA_in_sdg724_HA_rep2, CUT&Tag

first: Jiachen

last: Wang

state: Shanghai

address: No. 2005, Songhu Road

department: Institute of Plant Biology

description:
Library name: SDG724_HA_in_sdg724_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

organism: Oryza sativa

source_name: 14-day-old seedlings

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: 14-day-old seedlings

value: no treatment


title: 14746

tag: patient id


title: 22809


title: SDG724_HA_in_sdg724_HA_rep1, CUT&Tag

description:
Library name: SDG724_HA_in_sdg724_HA_rep1
rep1


title: HP-V208 [204809970142_R04C01]

description:
204809970142_R04C01
CLL

source_name: Unknown

value: Unknown

tag: group

value: Test set

tag: material

value: Frozen

tag: age

tag: Sex

value: M

value: NIH


title: SDG724_HA_in_ehd3sdg724_HA_rep1, CUT&Tag

description:
Library name: SDG724_HA_in_ehd3sdg724_HA_rep1
rep1

value: SDG724-HA/ehd3 sdg724

tag: treatment


title: HP-BH35 [206382220099_R03C01]

description:
206382220099_R03C01
FL_B

source_name: Follicular lymphoma, follicular and diffuse,  grade 1-2, 14,18 neg by FISH

value: Lymph node

value: Ref set

tag: mcf


title: HP-MX250 [205379750009_R03C01]

description:
205379750009_R03C01
LN_NN_B

source_name: Reactive lymphoid hyperplasia

value: Reactive lymphoid hyperplasia

value: FFPE


title: wt cardiac macrophage, mi-d5, biol rep4

description: mi-d5 cMa.txt

value: heart

value: WT


title: ko cardiac macrophage, mi-d5

description: mi-d5 cMa.txt

value: cardiac macrophage

value: NPM1 knockout


title: 20904

source_name: lung adenocarcinoma

value: lung adenocarcinoma

tag: cohort

value: validation cohort

tag: novel grade

value: VI

tag: tnm 8th_edition_stage

tag: passed qc

value: TRUE

value: LHMC


title: 13034

tag: tissue

value: NST

value: IIA


title: HA_Ehd3mu_in_ehd3_1_1_Input_REP1, ChIP-seq

description:
Library name: HA_Ehd3mu_in_ehd3_1_1_Input_REP1
rep1

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

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).

value: 14-day-old seedlings

tag: cell type

tag: genotype

value: no treatment


title: HP-F654 [204809970041_R06C01]

description:
204809970041_R06C01
CLL

source_name: Chronic lymphocytic leukaemia/small lymphocytic lymphoma

value: Test set

value: Frozen

value: M

value: NIH


title: HP-Z850 [205379750017_R05C01]

description:
205379750017_R05C01
ETCL_SETD2

value: Monomorphic epitheliotropic intestinal T-cell lymphoma

value: Small intestine

value: Ref set

value: FFPE


title: wt cardiac macrophage, mi-d5, biol rep2

description: mi-d5 cMa.txt

value: heart

value: cardiac macrophage

value: WT

tag: disease state

value: myocardial infarction

value: Day 5


title: Marrow, replicate 4, 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_4

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

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: HP-MX254 [205379750009_R07C01]

description:
205379750009_R07C01
LN_NN_A

source_name: Follicular hyperplasia and polytypic plasmacytosis

value: Lymph node

value: F


title: HP-AR88 [206382220097_R07C01]

description:
206382220097_R07C01
FL_A

source_name: Follicular lymphoma, grade 1-2 with diffuse pattern,BCL2neg(mutation  in TNFRSF14,crebbp)

value: Left inguinal mass


title: ko cardiac macrophage, mi-d3

description: mi-d3 cMa.txt

value: NPM1 knockout

tag: time

value: Day 3


title: HP-AR69 [205624900058_R02C01]

description:
205624900058_R02C01
FL_A

source_name: Follicular lymphoma grade1-2, clinically recurrent,BCL2 R neg

value: M

value: NIH


title: wt cardiac macrophage, mi-d5

description: mi-d5 cMa.txt


title: Marrow, replicate 3, scRNAseq

description:
10x Genomics
Marrow_3


title: HA_Ehd3_in_ehd3_1_1_Input_REP1, ChIP-seq

description:
Library name: HA_Ehd3_in_ehd3_1_1_Input_REP1
rep1

value: 14-day-old seedlings

value: no treatment


title: NiP_HA_rep2, CUT&Tag

description:
Library name: NiP_HA_rep2
rep2

value: Nipponbare


title: ko cardiac macrophage, mi-d5, biol rep3

description: mi-d5 cMa.txt

value: heart

value: cardiac macrophage


title: HP-D922 [204809970008_R08C01]

description:
204809970008_R08C01
CLL

value: CLL

value: Test set

value: Frozen


title: ko cardiac macrophage, mi-d5, biol rep2

description: mi-d5 cMa.txt

value: myocardial infarction

value: Day 5


title: HA_Ehd3_in_ehd3_1_1_H3K36me2_REP1, ChIP-seq

description:
Library name: HA_Ehd3_in_ehd3_1_1_H3K36me2_REP1
rep1


title: HA_Ehd3_in_ehd3_1_1_Input_REP2, ChIP-seq

description:
Library name: HA_Ehd3_in_ehd3_1_1_Input_REP2
rep2