title: DASLV4_1963

value: CHOP-R

value: N

value: raised


title: DASLV4_1967

status: Public on Jul 30 2021

type: RNA

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: The University of York

hyb_protocol: Standard Illumina protocol

scan_protocol: Arrays were scanned on a BeadArray reader

data_processing: Data were normalised using Lumi for R.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Biopsy

label_protocol: Standard Illumina protocol

extract_protocol: Total RNA was extracted from 5mm paraffin sections using the Ambion RecoverAll kit standard protocol, with the exception of a 16-hour protease digestion. These were routinely collected tissue samples and no attempt was made to standardise fixation or processing protocols

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

tag: reagent

tag: microdissection

value: FALSE

value: ABC

tag: Sex

value: F

tag: marrow

tag: Stage

value: II

tag: ldh

value: normal

tag: albumin

tag: hb

tag: lymphs

tag: monocytes

tag: neutrophils

tag: pcv

tag: plts

tag: wbc

value: Yes

value: TRUE


title: DASLV4_1962

value: GCB

value: Y

value: IV

value: EZB


title: DASLV4_1957

value: MHG


title: DASLV4_1995

value: UNC

value: CHOP-R

value: not done


title: DASLV4_1953

value: DLBCL

value: CHOP

value: No


title: DASLV4_1956

value: Diffuse large B-cell lymphoma, NOS

value: FALSE

value: N

value: NEC


title: DASLV4_1954

value: F

value: III

value: raised

value: Yes


title: DASLV4_1943

value: ABC

value: Y

value: TRUE


title: DASLV4_1952

value: M

value: II

value: unknown


title: DASLV4_1920

value: DLBCL

value: UNC

value: CHOP-R

value: not done


title: DASLV4_1955

value: Diffuse large B-cell lymphoma, NOS

value: FALSE

value: I

value: normal


title: DASLV4_1944

value: F

value: Supportive/palliativeonly

value: IV

value: EZB


title: DASLV4_1909

value: GCB

value: N

value: III

value: Yes


title: DASLV4_1945

value: ABC

value: M

value: GCVP

value: raised

value: NEC


title: DASLV4_1923

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: CHOP-R

value: II

value: not done


title: DASLV4_1921

value: FALSE

value: MHG

value: Y

value: I

value: No

value: TRUE

value: EZB-MYC


title: DASLV4_1919

value: GCB

value: F

value: Yes


title: DASLV4_1930

value: M

value: CHOP-R/Bortezomib

value: III

value: raised


title: DASLV4_1918

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: ABC

value: N

value: Treatment data not available


title: DASLV4_1917

value: FALSE

value: CHOP-R

value: II

value: MCD


title: DASLV4_1916

value: not done

value: TRUE

value: NEC


title: DASLV4_1907

value: GCB

value: Gemcitabine

value: Yes


title: DASLV4_1906

value: F

value: Y

value: IV

value: EZB


title: DASLV4_1908

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: I

value: raised

value: No


title: DASLV4_1894

value: FALSE

value: M

value: CHOP-R

value: N

value: II


title: DASLV4_1898

value: GCB

value: normal

value: TRUE


title: DASLV4_1873

value: Hodgkin

value: Nodular sclerosis classical Hodgkin lymphoma

value: ABC

value: F

value: ABVD

value: Yes


title: DASLV4_1865

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: CHOP-R/Bortezomib

value: Y

value: III


title: DASLV4_1849

value: FALSE

value: CHOP-R

value: IV

value: EZB


title: DASLV4_1845

value: N

value: II

value: normal


title: DASLV4_1834

value: UNC

value: M

value: No

value: TRUE


title: DASLV4_1843

value: Hodgkin

value: Mixed cellularity classical Hodgkin lymphoma

value: ABVD

value: Yes


title: DASLV4_1836

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: GCB

value: F

value: Y


title: DASLV4_1840

value: FALSE

value: CHOP-R/Bortezomib

value: I

value: raised


title: DASLV4_1823

value: Nodular sclerosis classical Hodgkin lymphoma

value: UNC

value: N

value: normal


title: DASLV4_1709

value: TRUE

value: M

value: CHOP-R

value: III

value: No


title: DASLV4_1816

value: Hodgkin

value: ABVD

value: II

value: Yes


title: DASLV4_1785

value: FALSE

value: Y


title: DASLV4_1817

value: I


title: DASLV4_1815

value: raised


title: DASLV4_1690

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: F

value: IV


title: DASLV4_1824

value: Mixed cellularity classical Hodgkin lymphoma

value: ABC

value: N

value: normal


title: DASLV4_1818

value: UNC

value: M


title: DASLV4_1820

value: Hodgkin

value: Nodular sclerosis classical Hodgkin lymphoma

value: GCB

value: ABVD


title: DASLV4_1821

value: FALSE

value: Yes


title: DASLV4_1819

value: Y

value: II


title: DASLV4_1844


title: DASLV4_1789

value: raised


title: DASLV4_1786

value: F


title: DASLV4_1830

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: CHOP-R

value: IV

value: No

value: TRUE


title: DASLV4_1787

value: UNC

value: M

value: normal


title: DASLV4_1846

value: Hodgkin

value: Nodular sclerosis classical Hodgkin lymphoma

value: ABC

value: III


title: DASLV4_1822

value: FALSE

value: ABVD

value: N

value: Yes


title: DASLV4_1671

value: DLBCL

value: GCB

value: raised


title: DASLV4_1641

value: Diffuse large B-cell lymphoma, NOS

value: CHOP-R/Bortezomib


title: DASLV4_1642

value: Y

value: IV

value: TRUE


title: DASLV4_1569

value: F

value: II

value: normal

value: No


title: DASLV4_1504

value: M

value: CHOP-R


title: DASLV4_1442

value: FALSE

value: UNC

value: III


title: DASLV4_1429

value: DLBCL

value: MHG

value: CODOX-M(+/-R)

value: Yes

value: EZB


title: DASLV4_1450

value: Diffuse large B-cell lymphoma, NOS

value: Y

value: raised


title: DASLV4_1427

value: Burkitt

value: Burkitt lymphoma

value: CODOX

value: N

value: not done


title: DASLV4_1345

value: GCB

value: M

value: IV

value: TRUE

value: NEC


title: DASLV4_1377

value: DLBCL

value: FALSE

value: CHOP-R/Bortezomib


title: DASLV4_1425

value: MHG

value: F

value: Supportive/Palliative/None

value: Yes


title: DASLV4_1424

value: Burkitt

value: Y

value: raised


title: DASLV4_1356

value: Diffuse large B-cell lymphoma, NOS

value: CODOX-M(+/-R)

value: N


title: DASLV4_1357

value: GCB

value: M


title: DASLV4_1362

value: CHOP-R

value: III

value: No

value: TRUE


title: DASLV4_1344

value: DLBCL

value: FALSE

value: IV


title: DASLV4_1383

value: UNC

value: F


title: DASLV4_1369

value: Burkitt

value: Burkitt lymphoma

value: MHG

value: CODOX

value: Yes


title: DASLV4_1341

value: Diffuse large B-cell lymphoma, NOS

value: CODOX-M(+/-R)

value: Y

value: raised


title: DASLV4_1371

value: GCB

value: CHOP-R

value: N

value: II

value: normal


title: DASLV4_1319

value: DLBCL

value: FALSE

value: M

value: IV

value: TRUE


title: DASLV4_1321

value: NEC


title: DASLV4_1422

value: Burkitt

value: Burkitt lymphoma

value: MHG

value: F

value: Supportive/Palliative/None


title: DASLV4_1428

value: CODOX

value: Y

value: raised

value: Yes


title: DASLV4_1353

value: Diffuse large B-cell lymphoma, NOS

value: GCB

value: CHOP-R/Bortezomib

value: N

value: III


title: DASLV4_1343

value: DLBCL

value: FALSE

value: CODOX-M(+/-R)

value: IV

value: EZB


title: DASLV4_1416

value: II

value: TRUE


title: DASLV4_1426

value: Burkitt

value: Burkitt lymphoma

value: MHG

value: M

value: Supportive/Palliative/None


title: DASLV4_1364

value: Diffuse large B-cell lymphoma, NOS

value: CHOP-R

value: raised

value: Yes


title: DASLV4_1320

value: N

value: unknown

value: NEC


title: Liolaemus parthenos liver sample

type: SRA

city: Puerto Madryn

first: Martin

middle: Miguel

last: Femenias

state: Chubut

address: Bv. Almte Brown 2915

country: Argentina

institute: IPEEC-CENPAT-CONICET

description:
subfamily_abundancelogCPM_matrix.txt
Raw_subfamily_counts_matrix.txt
Lp_assembly.fasta
references_rule_50_0_80.csv

library_source: transcriptomic

data_processing:
reads quality control: correction of k-mers with rCorrector (Song & Florea 2015), uncorrectable reads remotion with a Python script (available at https://github.com/harvardinformatics/TranscriptomeAssemblyTools). We filtered rRNA using all available rRNA sequences in the SILVA database (https://www.arb-silva.de/, accessed March 25, 2019) and aligned the reads to this reference using Bowtie2 v2.3.4.1 (Langmead & Salzberg 2012).
de novo assembly: Trinity v2.8.4 (Grabherr et al. 2011)
gene annotation:CD-HIT-EST v4.8.1 (Limin Fu et al. 2012), TransDecoder v5.5.0 pipeline (Haas et al. 2013), Swiss-Prot protein database (accessed March 22, 2019) and the Pfam-A v.33.0, HMMSCAN v3.2.1 (Mistry et al. 2013), BLASTX and BLASTP v2.2.29 (parameters: -max_target_seqs 1 -evalue 1e-5). Details in the manuscript
TEs annotation:RepeatModeler v2.0.1 (Flynn et al. 2020), CENSOR v.4.2.22 (Kohany et al. 2006) against RepBase (accessed September 25, 2020, Bao et al. 2015), and in-house RepeatMasker rounds with three libraries (details in manuscript)
TEs refinament and abundance estimation: ExplorATE pipeline
Supplementary_files_format_and_content: normalized counts per TEs class
subfamily_abundancelogCPM_matrix.txt  (abundance measurements, normalized counts per TEs class)
Raw_subfamily_counts_matrix.txt  (raw counts for transposon family)
Lp_brain_raw_counts.sf  (raw counts)
Lp_liver_raw_counts.sf  (raw counts)
Lp_ovary_raw_counts.sf  (raw counts)
Lp_assembly.fasta  (de novo transcriptome)
references_rule_50_0_80.csv  (transposon annotation references)

organism: Liolaemus parthenos

source_name: liver

extract_protocol:
The RNA was extracted with RNeasy Plus Micro kit (QIAGEN, Germantown, MD, USA) according to the manufacturer’s instructions
The libraries were prepared using TruSeq RNA Sample Prep kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions and the libraries were sequenced on a Illumuna HiSeq 2500 platform
RNA-Seq non-stranded

treatment_protocol: One individual was collected in the type locality of the species (El Nihil, Mendoza, Argentina) and dissected to extract the ovary, brain, and liver. Tissues were immediately placed in RNAlater (Ambion, Austin, TX, USA) and stored at -80 °C until RNA extraction.

tag: tissue

value: liver

value: adult


title: Liolaemus parthenos ovary sample

source_name: ovary

value: ovary


title: Liolaemus parthenos brain sample

source_name: brain

value: brain


title: DASLV4_1342

value: DLBCL

value: FALSE

value: UNC

value: CODOX-M(+/-R)

value: Y

value: IV

value: TRUE


title: DASLV4_1318

value: Diffuse large B-cell lymphoma, NOS

value: ABC

value: F

value: not done


title: DASLV4_1296

value: M

value: raised

value: Yes


title: DASLV4_1243

value: GCB

value: CHOP-R

value: III


title: DASLV4_1250

value: DLBCL

value: CHOP-R/Bortezomib

value: N

value: normal


title: nascONT-seq K562 dBET6 2h R2 (OJ51)

city: Innsbruck

first: Univ.-Prof. Dr. Andreas

last: Mayer

address: Innrain 80/82

department: Institute for Genomics and RNomics

country: Austria

institute: Biocenter, Medical University Innsbruck

data_processing:
Library strategy: nascONT-seq
For base calling we applied Guppy v3.2.4 using the kit and flow cell specific parameters '--flowcell FLO-MIN106 --kit SQK-DCS109'.
Next, we aligned the long-reads to the human reference genome (hg38/GRCh38) using minimap2 v2.17 (Li, 2018) with the parameters '-ax splice -ub -k14 --secondary=no -O 12,32 –junc-bonus=19'.
We improved the splice-site detection using a reference splice-junction set based on the GENCODE v28 annotation.
The strand information was derived from Minimap2 for spliced reads. The unspliced reads remained unclassified and are included in the profiles for both strands.
Genome_build: Human (hg38/GRCh38)
Supplementary_files_format_and_content: bigWig files were generated using ‘bedGraphToBigWig’; Scores represent raw read counts.

source_name: bone marrow, CML

growth_protocol: K562 cells were cultured in RPMI containing 10% FBS, 5% penicillin-streptomycin. K562 dTAG-BRD4 cells were diluted to 5 x 10^5 cells/ml every two days.

extract_protocol:
Cells were collected and lysed by incubating on ice in 0.15% NP-40, 25 mM α-amanitin in PBS for 2 min. The following steps of cell fractionation were performed as described by Mayer and Churchman (2016), with only minor modifications. After purification of the chromatin-associated RNA by isopropanol precipitation, and DNase treatment, the RNA way biotinylated using MTSEA biotin-XX linker (Biotinum) and purified using μMACS streptavidin MicroBeads. E. coli poly-A polymerase (Takara) was used to polyadenylate the enriched RNA.
The libraries was prepared using the Direct cDNA Sequencing kit (Oxford Nanopore Technologies), with modifications to improve capture of longer fragments.

treatment_protocol: K562 cells were treated with 100 nM dBET6 or an equivalent volume of DMSO for 1 h 50 min, and for another 10 min in the presence of 500 µM 4-thiouridine (4sU)

tag: cell line

tag: treatment

value: pan-BET degradation

tag: treatment time

tag: molecule subtype

value: nascent RNA


title: DASLV4_1225

tag: reagent

tag: microdissection

value: FALSE

tag: Sex

value: TRUE


title: DASLV4_1298

value: Diffuse large B-cell lymphoma, NOS

value: MHG

tag: marrow

tag: Stage

value: IV

tag: ldh

value: No


title: DASLV4_1213

value: F

value: DHAP-R

value: EZB

value: EZB-MYC


title: DASLV4_1206

value: M

value: CHOP-R

value: III

tag: albumin

tag: hb

tag: lymphs

value: Yes

value: NEC


title: DASLV4_1184

value: DLBCL

value: GCB

value: N

value: raised

tag: monocytes

tag: neutrophils

tag: pcv


title: DASLV4_1193

value: Burkitt

value: Burkitt lymphoma

value: TRUE

value: Supportive/Palliative/None

value: Y

tag: plts

tag: wbc

value: FALSE


title: DASLV4_1309

value: Diffuse large B-cell lymphoma, NOS

value: CODOX-M(+/-R)

value: IV

value: EZB


title: DASLV4_1317

value: F


title: DASLV4_1297

value: UNC

value: M

value: Yes


title: DASLV4_1192

value: MHG

value: CODOX

value: III

value: normal


title: DASLV4_1942

value: DLBCL

value: Vincristine(+/-R)

value: raised

value: NEC


title: DASLV4_1212

value: FALSE

value: GCB

value: CHOP-R

value: N

value: II

value: TRUE


title: DASLV4_1211

value: Diffuse large B-cell lymphoma, NOS

value: ABC

value: F

value: IV

value: No


title: DASLV4_1205

value: MHG

value: M

value: unknown

value: Yes

value: EZB


title: DASLV4_1183

value: DLBCL

value: CHOP-R/Bortezomib

value: III

value: normal


title: nascONT-seq K562 DMSO 2h R2 (OJ52)

tag: cell line

tag: treatment

value: control

value: nascent RNA


title: DASLV4_1209

value: FALSE

value: GCB

value: DHAP-R

value: N

value: TRUE


title: nascONT-seq K562 DMSO 2h R1(OJ48)

tag: treatment time

tag: molecule subtype


title: DASLV4_1208

value: Diffuse large B-cell lymphoma, NOS

tag: reagent

tag: microdissection

value: CHOP-R

value: II

value: raised


title: ExoRNA11250Hy

city: Pozzuoli

first: Claudia

last: Tortiglione

address: Via Campi Flegrei, 34

department: Istituto di Scienze Applicate e Sistemi Intelligenti "E.caianiello"

country: Italy

institute: National Research Council of Italy

data_processing:
Reads were cleaned to remove the first 5 bases of read1, the Illumina adapter sequence 'AGATCGGAAGAGC' and with quality threshold 20 and minimum sequence length 35 using the program TrimGalore!
Pseudoalignment and gene expression quantification was performed with kallisto directly on transcript sequences
Genome_build: GCF_000004095.1_Hydra_RP_1.0_rna
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Hydra vulgaris

source_name: Extracellular vescicle

growth_protocol: For EV collection, 250 polyps were placed in 10 mL of Hydra solution in 6 cm Petri dishes and starved 4 days before processing for RNA extraction

extract_protocol:
Total RNA extraction was performed on EV samples using “Total RNA Purification Kit” (Norgen Biotek Corp.) and following the manufacturer’s supplementary protocol for exosomal RNA purification, with one modification: the optional DNA removal step was carried out using RQ1 RNase-Free DNAse (Promega) at 0.1 U/mL.
Libraries were prepared with the Ovation SoLo RNA-seq system (NuGEN Technologies) according to the manufacturer’s instructions

treatment_protocol: Prior to total RNA extraction, EVs isolated by ultracentrifugation were enzymatically treated to eliminate the free RNA derived from the ribonucleoprotein complexes. Isolated vesicles were treated with 1 mg/mL of proteinase K for 30 min at 37°C, incubated 10 min at 65°C to inactivate the proteinase K and then treated with 10 µg/mL of RNAse A for 15 min at 37°C.

tag: strain

value: Zurich


title: DASLV4_1905

value: ABC

tag: Sex

value: M

value: CHOP

value: Yes

value: MCD


title: DASLV4_1186

value: DLBCL

value: UNC

value: F

tag: Stage

value: IV

tag: ldh


title: DASLV4_1172

value: Burkitt

value: Burkitt lymphoma

value: FALSE

value: MHG

value: CODOX

value: I

tag: albumin

tag: hb


title: DASLV4_1173

value: Diffuse large B-cell lymphoma, NOS

value: Supportive/palliativeonly

value: Y

value: raised

tag: lymphs

value: TRUE

value: NEC


title: DASLV4_1182

value: M

value: CHOP-R

value: N

tag: monocytes

tag: neutrophils

value: No


title: DASLV4_1171

value: Supportive/Palliative/None

value: normal


title: nascONT-seq K562 dBET6 2h R1(OJ47_OJ53)

value: pan-BET degradation

value: nascent RNA


title: Sendai virus-infected 1week

city: Houston

first: Margo

middle: Patricia

last: Cain

state: Texas

address: 6565 MD Anderson Blvd

department: Pulmonary Medicine

country: USA

institute: MD Anderson Cancer Center

data_processing:
Chromium single-cell RNA-seq output was processed with Cell Ranger using “cellranger count” and “cellranger aggr”.
Further analysis was carried out using Loupe Cell Browser (10x Genomics) or an R package Seurat
Genome_build: mm10
Supplementary_files_format_and_content: Cloupe file can be opened with Loupe cell browser to visualize the data.

organism: Mus musculus

source_name: lung

extract_protocol:
FACS-purified whole lung cells were processed through the Chromium Single Cell Gene Expression Solution Platform (10X Genomics) using the Chromium Single Cell 3' Library and Gel Bead Kit in accordance with the manufacturer’s user guide (v2, rev D).
The libraries were sequenced on an Illumina NextSeq500 using a 26X124 sequencing run format with 8 bp index (Read1).

treatment_protocol: animal at 8 weeks of age underwent oropharyngeal instillation of pfu Sendai virus and was sacrificed 1 weeks later

tag: tissue

value: lung

tag: age

value: 9 weeks

tag: genotype

value: wild type


title: Sendai virus-infected 7weeks

treatment_protocol: animal at 8 weeks of age underwent oropharyngeal instillation of pfu Sendai virus and was sacrificed 7 weeks later

value: 15 weeks


title: PBS Control 1week1

treatment_protocol: animal at 8 weeks of age underwent oropharyngeal instillation of PBS and was sacrificed 1 week later


title: DASLV4_1170

value: Burkitt

value: Burkitt lymphoma

value: FALSE

value: MHG

value: COP

value: I

tag: pcv

tag: plts

tag: wbc

value: Yes


title: DASLV4_1150

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

tag: reagent

value: GCB

value: F

value: CHOP-R

value: Y

value: IV

value: not done

value: TRUE

value: EZB


title: PBS Control 7weeks

treatment_protocol: animal at 8 weeks of age underwent oropharyngeal instillation of PBS and was sacrificed 7 weeks later

value: lung

value: 15 weeks

value: wild type


title: Foxn1-cre(+/-).STAG2(fl/fl).Aire(-/-)_#3 [RNA-seq]

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: Thymus

extract_protocol:
Cells were isolated by tissue digestion and fluorescence activated cell sorting for viable CD45-Ly51loMHCIIhi as mTECs.
1,000 mTECs were sorted directly into lysis buffer (TCL with 1% 2-Mercaptoethanol) and Smart-seq2 libraries were prepared by the Broad Technology Labs, and were sequenced using the Broad Genomics Platform. Total RNA was captured on RNAClean XP beads followed by selection of mRNA using an anchored oligo(dT) primer. RNA was converted into cDNA via reverse transcription and first-strand cDNA was subjected to limited PCR amplification followed by transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit. Samples were amplified and barcoded with PCR followed by sequencing.

value: Foxn1-cre(+/-) STAG2(fl/fl) Aire(-/-)

value: Thymus

tag: cell type

value: mTECs


title: WT_NIPBL_Rep_3 [CUT&Tag]

library_source: genomic

data_processing:
library strategy: CUT&Tag
Low-quality reads were removed and adapters were trimmed with Trimmomatic (v0.36).
Reads were mapped to the mouse (mm10) genome using bowtie2 (v2.2.9) and multimapped and duplicate reads were removed with samtools (v1.3.1) and picard (v2.8.0) respectively.
CUT&Tag data was visualized on genome browser using bigwig files which were generated using the bamCoverage function in deeptools (v3.0.2).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

extract_protocol:
Cells were isolated by tissue digestion and fluorescence activated cell sorting for viable CD45-Ly51loMHCIIhi as mTECs.
mTECs bound to magnetic concavalin A beads were incubated overnight at 4°C with anti-NIPBL or IgG control antibodies. Cells were washed and incubated with anti-rabbit secondary antibodies for 1h at room temperature. Cells were washed again and incubated with pA-Tn5 fusion protein for 1h at room temperature followed by tagmentation at 37°C for 30 minutes. Reaction was stopped by addition of EDTA, SDS and proteinase K and tagmented DNA was purified by phenol chloroform extraction. CUT&Tag libraries were amplified and indexed by PCR.

tag: strain background

tag: gentoype

value: Aire+/+


title: Foxn1-cre(+/-).STAG2(fl/fl).Aire(-/-)_#2 [RNA-seq]

tag: strain


title: WT_NIPBL_Rep_1 [CUT&Tag]


title: WT_IgG [CUT&Tag]


title: DASLV4_1156

value: DLBCL

tag: microdissection

value: FALSE

value: ABC

tag: Sex

value: N

tag: marrow

tag: Stage

value: III

tag: ldh

value: raised

value: No


title: DASLV4_1149

value: Diffuse large B-cell lymphoma, NOS

value: GCB

value: M

value: CHOP-R

value: Y

tag: albumin

tag: hb

tag: lymphs

value: Yes


title: DASLV4_1145

value: Supportive/palliativeonly

value: IV


title: DASLV4_1144

value: UNC

value: F

value: TRUE

value: NEC


title: DASLV4_1146

value: DLBCL

value: FALSE

value: MHG

value: EZB


title: DASLV4_1168

value: Burkitt

value: Burkitt lymphoma

value: COP

value: N

value: raised

tag: monocytes

tag: neutrophils


title: WT_NIPBL_Rep_2 [CUT&Tag]

value: Aire+/+

tag: tissue

value: Thymus

value: mTECs


title: Foxn1-cre(+/-).STAG2(fl/fl).Aire(-/-)_#1 [RNA-seq]

tag: genotype

value: Foxn1-cre(+/-) STAG2(fl/fl) Aire(-/-)


title: STAG2(fl/fl).Aire(-/-)_#3 [RNA-seq]

value: Foxn1-cre(-/-) STAG2(fl/fl) Aire(-/-)


title: DASLV4_1169

tag: reagent

value: F

value: Supportive/Palliative/None

value: Yes


title: DASLV4_1147

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: GCB

value: M

value: Supportive/palliativeonly

value: IV

value: not done

tag: wbc


title: DASLV4_1143

value: FALSE

value: CHOP-R

value: N

value: I

value: TRUE

value: EZB


title: STAG2(fl/fl).Aire(-/-)_#2 [RNA-seq]

value: Foxn1-cre(-/-) STAG2(fl/fl) Aire(-/-)

value: Thymus

tag: cell type

value: mTECs


title: Fonx1-cre(+/-).STAG2(fl/fl)_#4 [RNA-seq]

value: Fonx1-cre(+/-) STAG2(fl/fl)


title: DASLV4_1139

value: DLBCL

value: Primary mediastinal (thymic) large B-cell lymphoma

value: Y

value: III

value: normal

tag: pcv

tag: plts

value: Yes

value: NEC


title: Fonx1-cre(+/-).STAG2(fl/fl)_#2 [RNA-seq]

tag: strain


title: Fonx1-cre(+/-).STAG2(fl/fl)_#1 [RNA-seq]


title: WT_CTCF_Rep_2 [ChIP-seq]

data_processing:
Low-quality reads were trimmed using sickle1.2, and short reads (50bp, single end) were aligned to the mouse reference genome (mm10) using bowtie aligner version 2.2.4.
Unmapped reads and reads with multiple alignments were removed with samtools (v1.1) followed by de-duplication with picard (v1.130) MarkDuplicates command.
Peaks in ChIPseq data were identified with HOMER (v4.6) package’s findPeaks command with the ‘histone’ parameter for SMC1 and MED1, while ‘factor’ parameter for CTCF ChIP-seq.
To visualize individual ChIP-seq data on Integrative Genomics Viewer (IGV), bam output files from picard were converted into normalized bigwig format using the bamCoverage function in deepTools (v1.6).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
Cells were isolated by tissue digestion and fluorescence activated cell sorting for viable CD45-Ly51loMHCIIhi as mTECs.
IPed chromatin was eluted from the Protein G beads, treated with DNase-free RNase and proteinase K followed by reverse cross-linking. DNA from reverse cross-linked material was purified with SPRI beads; and sequential steps of end-repair, A-base addition, adaptor-ligation and PCR amplification were performed to prepare the ChIP-seq library for each sample.

tag: strain background

value: Aire+/+


title: STAG2(fl/fl)_#2 [RNA-seq]

value: Foxn1-cre(-/-) STAG2(fl/fl)


title: STAG2(fl/fl)_#1 [RNA-seq]


title: Aire_KO_CTCF_Rep_2 [ChIP-seq]

value: Aire-/-


title: STAG2(fl/fl)_#3 [RNA-seq]


title: WT_CTCF_Rep_1 [ChIP-seq]


title: Aire_KO_CTCF_Rep_1 [ChIP-seq]


title: Aire_KO_SMC1_Rep_2 [ChIP-seq]


title: DASLV4_1138

tag: microdissection

value: FALSE

value: UNC

tag: Sex

value: M

value: CHOP-R

value: N

value: IV

value: raised


title: DASLV4_1142

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: MHG

value: F

tag: Stage

tag: ldh

value: TRUE

value: EZB

value: EZB-MYC


title: STAG2(fl/fl).Aire(-/-)_#1 [RNA-seq]

value: Foxn1-cre(-/-) STAG2(fl/fl) Aire(-/-)

value: Thymus

value: mTECs


title: Fonx1-cre(+/-).STAG2(fl/fl)_#3 [RNA-seq]

value: Fonx1-cre(+/-) STAG2(fl/fl)


title: DASLV4_1137

value: Primary mediastinal (thymic) large B-cell lymphoma

value: FALSE

value: ABC

value: Y

value: II

tag: albumin

tag: hb

value: Yes


title: DASLV4_1136

value: DLBCL

value: CHOP-R

value: raised

tag: lymphs


title: DASLV4_1131

value: Burkitt

value: Burkitt lymphoma

value: GCB

value: M

value: COP

value: N

value: I

tag: monocytes

tag: neutrophils


title: DASLV4_1128

value: MHG

value: F

value: CODOX


title: DASLV4_1130

value: FALSE

tag: marrow

value: IV


title: DASLV4_1132

value: Plasmablastic large B-cell lymphoma

tag: reagent

value: Y

value: II

value: TRUE

value: NEC


title: DASLV4_1127

value: Burkitt

value: CHOP-R

value: not done

tag: wbc

value: Yes


title: DASLV4_1134

value: DLBCL

value: Primary mediastinal (thymic) large B-cell lymphoma

value: GCB


title: WT_SMC1_Rep_2 [ChIP-seq]

tag: genotype

value: Aire+/+

tag: tissue

value: Thymus

tag: cell type

value: mTECs


title: DASLV4_1133

value: FALSE

value: ABC

value: M

value: CODOX-M(+/-R)

value: raised


title: WT_SMC1_Rep_1 [ChIP-seq]


title: DASLV4_1129

value: Burkitt lymphoma

value: MHG

value: COP

value: N

value: IV

tag: pcv

tag: plts


title: DASLV4_1126

value: Burkitt

tag: microdissection

value: Y

value: III

value: Yes


title: Aire_KO_MED1_Rep_1 [ChIP-seq]

tag: strain background

value: Aire-/-


title: DASLV4_1125

tag: Sex

value: F

value: CHOP-R

tag: Stage

value: II


title: Aire_KO_SMC1_Rep_1 [ChIP-seq]

value: Thymus

value: mTECs


title: WT_MED1_Rep_1 [ChIP-seq]

value: Aire+/+


title: WT_MED1_Rep_2 [ChIP-seq]


title: Aire_KO_Rep_2 [Hi-C]

data_processing:
Paired-end reads were aligned to the mouse genome (mm10) using Bowtie2 (v2.2.9) in HiC-Pro (v2.9.0) pipeline. Default settings were used to remove duplicate reads, assign reads to MboI restriction fragments, filter for valid interactions, and generate binned interaction matrices.
Subsequent Hi-C analyses were performed using various open-access programs including Juicer (v1.5), HOMER (v4.6), and Hi-CExplorer (v2.1.1, v2.2 and v3.6).
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

extract_protocol:
Cells were isolated by tissue digestion and fluorescence activated cell sorting for viable CD45-Ly51loMHCIIhi as mTECs.
Formaldehyde-fixed mTECs were suspended in ice-cold Hi-C lysis buffer, and nuclei were isolated. Nuclei were permeabilized by incubation with sodium dodecyl sulfate (SDS) followed by quenching of SDS with Triton X-100. DNA in permeabilized nuclei was digested with MboI overnight on 37°C followed by inactivation of MboI at 62°C. 5’-overhangs were filled with dCTP, dGTP, dTTP, biotin-14-dATP and resulting blunt-end DNA fragments were ligated with T4 DNA ligase followed by digestion of proteins with proteinase K and reverse cross-linking. DNA was precipitated with ethanol and sheared. Biotinylated ligation junctions in sheared DNA were captured with streptavidin beads and IPed DNA fragments were subjected to sequential steps of end repair, A-base addition, adapter-ligation and PCR amplification to prepare Hi-C library.

tag: strain


title: DASLV4_1124

value: FALSE

value: M

tag: ldh

value: raised

tag: albumin

tag: hb


title: Aire_KO_Rep_1 [Hi-C]


title: WT_Rep_2 [Hi-C]


title: Aire_KO_MED1_Rep_2 [ChIP-seq]


title: DASLV4_1106

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: GCB

value: I

tag: lymphs

tag: monocytes

tag: neutrophils

value: TRUE


title: DASLV4_1103

value: Burkitt

value: Burkitt lymphoma

tag: reagent

value: MHG

value: CODOX

value: N

value: normal

tag: wbc


title: DASLV4_1105

value: IV

value: Yes


title: WT_Rep_1 [Hi-C]

tag: genotype

value: Aire+/+

tag: tissue

value: Thymus

value: mTECs


title: DASLV4_1104

value: FALSE

value: M

value: raised

tag: pcv


title: DASLV4_1123

value: Supportive/Palliative/None

value: II


title: DASLV4_1141

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: ABC

value: CHOP-R

value: not done

value: TRUE

value: MCD


title: DASLV4_1102

value: Burkitt

value: Burkitt lymphoma

value: MHG

value: COP

value: N

value: IV

tag: plts


title: DASLV4_1043

tag: microdissection

value: FALSE

value: M

value: CHOP-R/Bortezomib

tag: marrow

value: III

value: normal

value: Yes


title: DASLV4_972

value: Hodgkin

value: Nodular sclerosis classical Hodgkin lymphoma

tag: Sex

value: F

value: ABVD

value: raised


title: DASLV4_1040

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: ABC

value: CHOP-R

tag: Stage

value: II

value: TRUE


title: DASLV4_1096

value: Primary mediastinal (thymic) large B-cell lymphoma

value: FALSE

value: GCB

value: N

value: not done

value: NEC


title: DASLV4_921

value: Y

value: IV

value: Yes


title: DASLV4_922

value: F

value: Supportive/palliativeonly

value: I

value: EZB


title: 89-naivewtT16VIVO06DMD-2018_R1

city: Cinisello Balsamo

first: Simonetta

middle: Andrea

last: Licandro

state: MI

address: Via Dei Lavoratori, 54

institute: ITALFARMACO SPA

data_processing:
Basecalling was performed with bcl2fastq 1.37.0 using the following command:
/opt/illumina/Isas/1.37.0/bcl2fastq2/bin/bcl2fastq  --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --ignore-missing-controls --auto-set-to-zero-barcode-mismatches --find-adapters-with-sliding-window --adapter-stringency 0.9 --mask-short-adapter-reads 35 --minimum-trimmed-read-length 35 --loading-threads 1 -R "/data/scratch/workspace/RunFolder" --sample-sheet "/data/scratch/workspace/RunFolder/SampleSheet.csv" -o "/data/scratch/workspace/RunFolder/Analysis/Temp_01.01-GenerateFASTQ.FastqGeneration
Adapter trimming was performed with cutadapt 1.4.2 using the following parameters:
--discard-untrimmed -m 15 -e 0.15 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Reads were aligned with bowtie 1.0.0 against mm10 using the following parameters:
-k 10 -n 0 -l 25 --best --mm
A matrix with raw miRNA counts based was generated using custom Perl & R scripts that parse bowtie output and perform transcript quantification using miRBase 21.
The raw miR counts matrix was normalised using a custom R script:
data_miR_norm <- data_miR  data_miR_norm[data_miR_norm < 4] <- NA  data_NF       <- apply(data_miR_norm, 2, function(x) sum(x, na.rm=T))  data_miR_norm <- log(scale(data_miR_norm, center = F, scale = data_NF) * median(data_NF), 2)  data_miR_norm <- merge(mirbase_annotation[,c("miRBase_accession_number", "miRNA_name")], data_miR_norm, by.x = "miRBase_accession_number", by.y = "row.names")
Genome_build: mm10
Supplementary_files_format_and_content: matrix_miR.txt: A tab-delimited file representing a matrix with raw miRNA counts. The first column contains the miRBase accession numbers. The second column contains the miRBase names. All other columns represent samples. Each row contains counts for a miRNA accross all samples.
Supplementary_files_format_and_content: matrix_miR_norm.txt: A tab-delimited file containing the normalized miRNA counts derived from the raw counts in matrix_miR.txt

growth_protocol: Plasma samples were from mice treated as described in cell A11.

extract_protocol:
RNA extraction from plasma sample was performed using miRNeasy Serum/Plasma Kit (Qiagen) following the manufacturer’s instructions.
Libraries for small RNA sequencing were prepared using the NEBNext small RNA library prep kit (New England Biolabs) according to the manufacturer’s instructions. Briefly, 5 μl of RNA eluate was used as input for RNA adapter ligation (using 3’ and 5’ RNA adapters) followed by reverse transcription and PCR amplification with bar-coded primers. Size selection of individual libraries was performed on a Pippin Prep system (Sage Science) to recover the ~147-157 nt fractions containing mature miRNAs. Next, qPCR-based normalization was used for pooling of the individual small RNA libraries. Finally, the resulting small RNA pools were concentrated via ethanol precipitation and quantified using the Qubit 2.0 fluorometer (Thermo Fisher Scientific) prior to sequencing with read length of 75 bp on a NextSeq 500 sequencer (Illumina).

treatment_protocol: wild type (wt) mice (C57BL/10J): no treatment; dystrophin deficient mice (C57BL10ScSn-Dmdmdx/J or mdx) untreated (naive mdx) or treated by gavage (p.o.) with both vehicle (0.5% methylcellulose; qdx5x15weeks) and Givinostat at 37.5 mg/kg (qdx5x15weeks).

tag: strain


title: DASLV4_963

value: Hodgkin

value: Nodular sclerosis classical Hodgkin lymphoma

value: UNC

value: M

value: ABVD

value: III

tag: ldh

value: normal


title: 86-naivewtT16VIVO06DMD-2018_R1


title: 40-vehicleT16VIVO06DMD-2018_R1


title: 41-vehicleT16VIVO06DMD-2018_R1


title: 39-naivemdxT16VIVO06DMD-2018_R1


title: 36-naivemdxT16VIVO06DMD-2018_R1


title: DASLV4_1046

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: TRUE

value: ABC

value: CHOP-R/Bortezomib

tag: albumin

value: No

value: FALSE


title: DASLV4_919

value: GCB

value: Supportive/palliativeonly

value: N

value: IV

tag: hb

value: Yes

value: EZB-MYC


title: 31-37.5mgPkgT16VIVO06DMD-2018_R1


title: 34-37.5mgPkgT16VIVO06DMD-2018_R1


title: 42-vehicleT16VIVO06DMD-2018_R1


title: DASLV4_968

value: Hodgkin

value: Nodular sclerosis classical Hodgkin lymphoma

value: MHG

value: M

tag: lymphs


title: DASLV4_1095

value: DLBCL

value: Primary mediastinal (thymic) large B-cell lymphoma

value: F

value: CHOP-R

value: Y

value: raised


title: ExoRNA5000Hy

value: Zurich


title: 37-naivemdxT16VIVO06DMD-2018_R1


title: DASLV4_916

value: Diffuse large B-cell lymphoma, NOS

value: FALSE

value: III

value: TRUE

value: EZB


title: DASLV4_913

value: GCB

value: Supportive/palliativeonly

value: N

value: not done

value: Yes


title: DASLV4_899

value: Burkitt

value: Burkitt lymphoma

value: MHG

value: COP

value: IV

tag: monocytes


title: DASLV4_918

value: DLBCL

value: F

value: CHOP-R


title: 95-naivewtT16VIVO06DMD-2018_R1


title: 35-37.5mgPkgT16VIVO06DMD-2018_R1


title: 43-vehicleT16VIVO06DMD-2018_R1


title: DASLV4_898

value: FALSE

value: M

value: CODOX

value: raised

tag: neutrophils


title: DASLV4_897

tag: reagent

value: Y

value: II


title: DASLV4_894

value: N

tag: wbc


title: DASLV4_892

value: Supportive/Palliative/None

value: not done


title: IgG control 1

city: Birmingham

first: David

last: Bending

address: IBR

department: Institute of Immunology and Immunotherapy

institute: University of Birmingham

description: IgGA

data_processing:
Basecalls by Illumina software on NextSeq
Zipped FASTQC files were generated using illumina BaseSpace, and then uploaded to the Lexogen Bluebee software platform. Briefly, Bbduk was used for trimming, before alignment using STAR v2.5.2a to the mm10 mouse genome before samtools index to create .bam files. Gene read counting was generated using HTSeq-count to generate raw read count files for each sample
Raw count matrix files were read into DESeq2 in R and rows with read counts <10 removed from the analysis. Raw counts were then normalised using the regularised Log2 (rLog) function to generate normalised expression data for each sample.
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes regularised Log2 normalised expression values for each sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Flow sorted T cells

extract_protocol:
CD4+ T cells were sorted based on Nr4a3-Timer expression on a FACS Aria cell sorter and collected into eppendorfs. Cells were lysed in 100uL extraction buffer using PicoPure RNA extraction kit according to manufacturer's instructions. An on column DNase digest was performed.
Libraries were constructed using Lexogen Quantseq 3' mRNA Forward kits according to the manufacturer's instructions using a starting amount of 25ng of RNA
3' mRNA-seq

value: Tg4 Tiger Nr4a3-Tocky

tag: cell type

value: CD4+ T cells

tag: treatment

value: Isotype


title: anti-Lag3 2


title: anti-Lag3 1


title: anti-PD1 2


title: anti-PD1 1


title: IgG control 2

description: IgGB


title: 80ug 24hr 3

extract_protocol:
CD4+ T cells were sorted based on Nr4a3-Timer expression on a FACS Aria cell sorter and collected into eppendorfs. Cells were lysed in 100uL extraction buffer using PicoPure RNA extraction kit according to manufacturer's instructions. An on column DNase digest was performed.
Libraries were constructed using Lexogen Quantseq 3' mRNA Forward kits according to the manufacturer's instructions using a starting amount of 15-20ng of RNA
3' mRNA-seq

value: 80ug 4Y MBP peptide s.c.


title: 80ug 24hr 1


title: 0.8ug 24hr 3

value: 0.8ug 4Y MBP peptide s.c.


title: 0.8ug 24hr 2


title: DASLV4_890

value: Burkitt

value: Burkitt lymphoma

value: MHG

tag: pcv

value: Yes


title: DASLV4_872

value: FALSE

value: M

value: supportivecare

value: IV

tag: plts


title: DASLV4_869

tag: microdissection

value: GCB

value: F

value: CODOX

value: I


title: DASLV4_891

value: COP

value: N

value: raised

value: No


title: DASLV4_861

value: Y


title: 0.8ug 24hr 1

value: Tg4 Tiger Nr4a3-Tocky

value: CD4+ T cells

value: 0.8ug 4Y MBP peptide s.c.


title: DASLV4_871

value: Burkitt

value: Burkitt lymphoma

value: MHG

value: II

value: normal

value: Yes


title: DASLV4_860

value: FALSE

value: GCB

value: F

value: IV


title: DASLV4_889

value: M

value: COP

value: N


title: DASLV4_865

value: CODOX

value: raised


title: DASLV4_849

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: TRUE

value: CHOP-R/Bortezomib

tag: marrow

value: III

value: No


title: DASLV4_783

value: UNC

tag: Sex

value: CHOP-R

value: Y

value: normal


title: DASLV4_896

value: Burkitt

value: Burkitt lymphoma

value: FALSE

value: MHG

value: not done

value: Yes


title: DASLV4_776

value: ABC

value: F

tag: Stage

value: II


title: 80ug 24hr 2

tag: strain

value: Tg4 Tiger Nr4a3-Tocky

value: CD4+ T cells

value: 80ug 4Y MBP peptide s.c.


title: 80ug 12hr 3


title: 80ug 12hr 2


title: 80ug 12hr 1


title: DASLV4_874

value: M

value: Supportive/Palliative/None

value: N

value: I

tag: ldh


title: 0.8ug 12hr 2

value: 0.8ug 4Y MBP peptide s.c.


title: DASLV4_758

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: TRUE

value: GCB

value: CHOP-R

value: Y

value: III

value: raised

tag: albumin

value: No


title: 0.8ug 12hr 3

value: Tg4 Tiger Nr4a3-Tocky


title: 0.8ug 12hr 1

value: CD4+ T cells


title: DASLV4_762

value: FALSE

value: CHOP-R/Bortezomib

value: II

tag: hb

value: Yes


title: 80ug 4hr 3

value: 80ug 4Y MBP peptide s.c.


title: 80ug 4hr 2


title: 0.8ug 4hr 2

value: 0.8ug 4Y MBP peptide s.c.


title: 0.8ug 4hr 3


title: Control 3

value: Untreated


title: 0.8ug 4hr 1


title: Control 2


title: DASLV4_755

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: F

tag: lymphs


title: DASLV4_708

value: ABC

value: CHOP-R

value: N

value: normal

value: TRUE


title: DASLV4_743

value: M

value: III

value: raised


title: anti-parB ChIP-seq of SMChigh cells and parSopt at -304kb and -9kb in exponential phase in SMG at 37°C

city: Lausanne

first: Anna

last: Anchimiuk

state: Vaud

address: UNIL-Sorge District

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

description:
BSG4137_parB_ChIP
processed data file: BSG3790_3805_3815_4083_4091_4100_4137_4143_parB_ChIP_1kb.txt

data_processing:
ChIP-seq data was trimmed using Trimmomatic-0.39 (SE -phred33, ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36), mapped with bowtie2 using --very-sensitive-local setting, sorted with samtools and obtained .bam files were further imported to SeqMonk for Read Count Quantitation.
Sequencing data from 3C-seq experiments was demultiplexed, adapters trimmed, and PCR duplicates removed using custom scripts. If additional sequencing was performed, it is indicated in the sample name as '_reseq' and the data was pooled prior to mapping. Next, data was processed as described at https://github.com/axelcournac/3C_tutorial.
Removal of PCR duplicates based on the 20 first bp of the read containing a 6 nt random tag (home made script).
Iterative alignment, Min-leght=20, step=5, bowtie2 --very-sensitive-local
Filtering, Mapping quality=30, no ambiguous reads
Assignment to restriction fragment
Removal of un-informative events (uncuts, loops etc) as described in Cournac et al. BMC 2012.
3C-seq: binning at 10kb. ChIP-seq: binning at 1kb.
Genome_build: NC_000964 (1A700) or NC_022898 (PY79)
Supplementary_files_format_and_content: 422x422 (for 1A700 strains) and 404x404 (for PY79 strains) normalized contact matrix in txt format for the 3C-seq data. '_pooled' in processed data file name contains a matrix resulting from processing data from sample which was resequenced and both fastq files were combined. Read Count Quantitation and generation of Probe Report in .txt format with SeqMonk (used All Reads, Correct for total read count, Correcct for Milion Reads) for the ChIP-seq data.

organism: Bacillus subtilis

source_name: anti-parB ChIP-seq of SMChigh cells and parSopt at -304kb and –9kb in exponential phase in SMG at 37°C

growth_protocol: strains were grown overnight in SMG, diluted to OD600 0.004 in fresh SMG and grown at 30 or 37°C until reached an OD600 between 0.022-0.026

extract_protocol:
3C-seq:
3C libraries were prepared as previously described (Marbouty et al., 2015). Minimal media (SMG) was used instead of LB. Briefly, cells were grown in 400 ml of SMG medium to exponential phase (OD = 0.022-0.030) and fixed with fresh formaldehyde (3% final concentration) for 30 minutes at RT, followed by 30 minutes at 4°C and quenched for 30 minutes with 0.25 M glycine at 4°C. Fixed cells were harvested by filtering, washed in fresh SMG, frozen in liquid nitrogen and stored at -80°C until further use.
For time-course experiments 2 l preculture was first grown until mid-exponential phase (OD = 0.022-0.030) and next, appropriate culture volumes were added to fresh pre-warmed SMG so that at given time points 2 x 200 ml of culture at mid-exponential could be collected (two technical replicates). The cultures were induced with 2 mM theophylline or 1 mM IPTG, depending on the promoter used, Ptheo or Pspank, respectively. Due to characteristics of the theophylline switch, the pre-culture as well as induction was performed at 30°C.
Frozen pellets were resuspended in 600 µl 1x TE and incubated at RT for 20 minutes with 4 µl of Ready-lyze lysozyme (35U/ul, Tebu Bio). Next, SDS was added to a final concentration of 0.5% and incubated at RT for 10 minutes.
50 µl of lysed cells were aliquoted to 8 tubes containing 450 µl of digestion mix (1x NEB 1 buffer, 1% triton X-100, and 100 U HpaII enzyme (NEB)) and incubated at 37°C for 3 hours with constant shaking. Digested DNA was collected by centrifugation, diluted into 4 tubes containing 8 ml of ligation mix (1x ligation buffer: 50 mM Tris-HCl, 10 mM MgCl2, 10 mM DTT), 1 mM ATP, 0.1 mg/ml BSA, 125 U T4 DNA ligase 5 U/ml) and incubated at 16°C for 4 hours. Ligation reaction was followed by O/N decrosslinking at 65°C in the presence of 250 µg/ml proteinase K (Eurobio) and 5 mM EDTA.
DNA was precipitated with 1 volume of isopropanol and 0.1 Volume of 3 M sodium acetate (pH 5.2, Sigma) at -80°C for 1 hour. After centrifugation, the DNA pellet was resuspended in 1x TE at 30°C for 20 minutes. Next, DNA was extracted once with 400 µl phenol-chloroform-isoamyl alcohol solution and precipitated with 1.5 volume cold 100% ethanol in the presence of 0.1 volume 3 M sodium acetate at -80°C for 30 minutes. The pellet was collected and resuspended in 30 µl TE with RNaseA at 37°C for 30 minutes. All tubes were pooled and the resulting 3C library was quantified on gel using ImageJ.
ChIP-seq:
ChIP samples were prepared as described previously (Bürmann et al., 2017). Briefly, cells were cultured in 200 ml of minimal media (SMG) at 37°C until mid-exponential phase (OD=0.022-0.030) and fixed with buffer F (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 0.5 mM EGTA pH 8.0, 1 mM EDTA pH 8.0, 10% (w/v) formaldehyde) for 30 minutes at RT with occasional shaking. Cells were harvested by filtration and washed in PBS. Each sample was adjusted for 2 OD units (2 ml at OD600 = 1) and resuspended in TSEMS lysis buffer (50 mM Tris pH 7.4, 50 mM NaCl, 10 mM EDTA pH 8.0, 0.5 M sucrose and PIC (Sigma), 6 mg/ml lysozyme from chicken egg white (Sigma)). After 30 minutes of incubation at 37°C with vigorous shaking protoplasts were washed again in 2 ml TSEMS, resuspended in 1 ml TSEMS, split into 3 aliquots, pelleted and, after flash freezing, stored at -80°C until further use.
For time-course experiments 1 l preculture was first grown until mid-exponential phase (OD = 0.022-0.030) and next, appropriate culture volumes were added to fresh pre-warmed SMG so that at given time points 200 ml of culture at mid-exponential could be processed. The cultures were induced with 2 mM theophylline (Ptheo promoter). Due to characteristics of the theophylline switch, the pre-culture as well as induction was performed at 30°C.
For IP of samples for ChIP-seq, each pellet was resuspended in 1 ml of buffer L (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 1% (v/v) Triton X-100, 0.1% (w/v) Na-deoxycholate, 0.1 mg/ml RNaseA and PIC (Sigma)) and transferred to milliTUBE 1ml AFA Fiber and sonicated in a Covaris E220 water bath sonicator for 5 minutes at 4°C, 100 W, 200 cycles, 10% load and water level 5. Next, lysates were transferred into 2 ml tubes and centrifuged 10 minutes at 21000g at 4°C. 800 µl of supernatant was used for IP and 200 µl was kept as WCE (whole cell extract).
For IP, first, antibody serum was incubated with Protein G coupled Dynabeads (Invitrogen) in 1:1 ratio for 2.5 hours at 4°C with rotation. Next, beads were washed in buffer L and 50 µl were aliquoted to each sample tube. Samples were incubated for 2 hours at 4°C with rotation, followed by a series of washes with buffer L, buffer L5 (buffer L containing 500 mM NaCl), buffer W (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% (v/v) NP-40, 0.5% (w/v) sodium deoxycholate, 1 mM EDTA pH 8.0) and buffer TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0). Finally, the beads were resuspended in 520 µl buffer TES (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1% (w/v) SDS). 300 µl of TES and 20 µl of 10% SDS were also added to WCE. Both tubes were incubated O/N at 65°C with vigorous shaking to reverse formaldehyde crosslinks.
Following rabbit polyclonal antibodies (manufactured by Eurogentec) were used:
For anti-scpB ChIP time-course experiment COD3 BsScpB-His6
For other anti-scpB ChIP experiments COD33 BsScpB-His6
For anti-parB ChIP experiments COD11 BsParB-His
Phenol-chloroform extraction was performed to purify the decrosslinked DNA. Samples were transferred to screw cap 1.5-ml tubes and first mixed vigorously with 500 µl of phenol equilibrated with buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). After centrifugation (10 minutes, RT, 13000 rpm), 450 µl of the aqueous phase was transferred to a new screw cap tube and mixed with equal volume of chloroform, followed by centrifugation. 400ul of aqueous phase was recovered for DNA precipitation with 2.5x volume of 100 % ethanol, 0.1x volume of 3M NaOAc and 1.2 µl of GlycoBlue and incubated for 20 minutes at -20°C. Next, samples were centrifuged for 10 minutes at 20000 g at RT and pellets obtained pellets were resuspended in 10 µl of EB (Qiagen) shaking at 55°C for 10 minutes and finally purified with a PCR purification kit, eluting in 50 uL EB.
3C-seq
1 ug of 3C library was suspended in water (final volume 130 µl) and sonicated using Covaris S220 (following manufacturers recommendations to obtain 500 bp target size). Next, DNA was purified with Qiagen PCR purification kit, eluted in 40 µl EB and quantified using NanoDrop. 1 ug of DNA was processed according to manufacturer instructions (Paired-End DNA sample Prep Kit – Illumina – PE-930-1001), except that DNA was ligated to custom-made adapters for 4 hours at RT, followed by inactivation step at 65°C for 20 minutes. DNA was purified with 0.75x AMPure beads and 3 µl were used for 50 µl PCR reaction (12 cycles). Amplified libraries were purified on Qiagen columns and pair end sequenced on an Illumina platform (HiSeq4000 or NextSeq).
ChIP-seq
For deep sequencing, the DNA libraries were prepared by Genomic Facility at CIG, UNIL, Lausanne. Briefly, the DNA was fragmented by sonication (Covaris S2) to fragment sizes ranging from 220–250 bp. DNA libraries were prepared using the Ovation Ultralow Library Systems V2 Kit (NuGEN) including 15 cycles of PCR amplification. Five to ten million single end sequence reads were obtained on a HiSeq2500 (Illumina) with 150-bp read length

tag: strain/genotype information

value: 1A700, Δ6-parS (mtparS334 to parS359), smc::ermB, ΔamyE::smc::CAT, qoxD-specR::scpAB-ywcE

tag: chip antibody

value: anti-parB


title: DASLV4_767

tag: reagent

value: CHOP-R/Bortezomib

value: IV

tag: neutrophils

value: Yes

value: FALSE


title: 80ug 4hr 1

value: Tg4 Tiger Nr4a3-Tocky

tag: cell type

value: CD4+ T cells

value: 80ug 4Y MBP peptide s.c.


title: DASLV4_744

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: GCB

tag: monocytes

tag: wbc


title: Control 1

tag: treatment

value: Untreated


title: anti-parB ChIP-seq of SMChigh cells in exponential phase in SMG at 37°C

description:
BSG4100_parB_ChIP
processed data file: BSG3790_3805_3815_4083_4091_4100_4137_4143_parB_ChIP_1kb.txt

value: 1A700, ΔamyE::smc::CAT, qoxD-specR::scpAB-ywcE, trpC2


title: anti-parB ChIP-seq of del8parS cells in exponential phase in SMG at 37°C

description:
BSG3815_parB_ChIP
processed data file: BSG3790_3805_3815_4083_4091_4100_4137_4143_parB_ChIP_1kb.txt

value: 1A700, Δ8-parS, parAB(mtparS359)::kanR, smc::specR


title: anti-parB ChIP-seq of cells with wtSmc and parSopt at -304kb and +328kb cells in exponential phase in SMG at 37°C

description:
BSG4091_parB_ChIP
processed data file: BSG3790_3805_3815_4083_4091_4100_4137_4143_parB_ChIP_1kb.txt

value: 1A700, Δ6-parS(parS334->359+), parAB::kanR, smc::ermB, ΔamyE::parS-359 + tetO qPCR primer seq::cat


title: anti-parB ChIP-seq of cells with wtSmc and parSopt at -9kb in exponential phase in SMG at 37°C

description:
BSG3790_parB_ChIP
processed data file: BSG3790_3805_3815_4083_4091_4100_4137_4143_parB_ChIP_1kb.txt

source_name: anti-parB ChIP-seq of cells with wtSmc and parSopt at –9kb in exponential phase in SMG at 37°C

value: 1A700, Δ7-parS(parS359+), smc::specR


title: anti-scpB ChIP-seq of del8parS cells in exponential phase in SMG at 37°C

description:
BSG3815_scpB_ChIP
processed data file: BSG3790_3805_3815_4083_4091_4100_4137_4143_scpB_ChIP_1kb.txt

value: anti-scpB


title: DASLV4_567

tag: microdissection

value: TRUE

value: ABC

value: M

value: CHOP-R

value: N

value: raised

tag: pcv

tag: plts


title: anti-parB ChIP-seq of SMChigh cells and parSopt at -9kb in exponential phase in SMG at 37°C

description:
BSG4143_parB_ChIP
processed data file: BSG3790_3805_3815_4083_4091_4100_4137_4143_parB_ChIP_1kb.txt

source_name: anti-parB ChIP-seq of SMChigh cells and parSopt at –9kb in exponential phase in SMG at 37°C

value: 1A700, Δ7-parS(parS359+), smc::ermB, ΔamyE::smc::CAT, qoxD-specR::scpAB-ywcE

value: anti-parB


title: anti-parB ChIP-seq of cells with wtSmc and parSopt at -9kb and +328kb in exponential phase in SMG at 37°C

description:
BSG4083_parB_ChIP
processed data file: BSG3790_3805_3815_4083_4091_4100_4137_4143_parB_ChIP_1kb.txt

source_name: anti-parB ChIP-seq of cells with wtSmc and parSopt at –9kb and +328kb in exponential phase in SMG at 37°C

value: 1A700, Δ6-parS(parS359+), smc::specR, ΔamyE::parS-359 + tetO qPCR primer seq::cat


title: DASLV4_698

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: FALSE

tag: Sex

tag: Stage

value: III

value: Yes


title: anti-parB ChIP-seq of cells with wtSmc and parSopt at -304kb and -9kb cells in exponential phase in SMG at 37°C

description:
BSG3805_parB_ChIP
processed data file: BSG3790_3805_3815_4083_4091_4100_4137_4143_parB_ChIP_1kb.txt

source_name: anti-parB ChIP-seq of cells with wtSmc and parSopt at -304kb and –9kb cells in exponential phase in SMG at 37°C

value: 1A700, Δ6-parS (mtparS334 to parS359), smc::ermB


title: DASLV4_609

value: GCB

value: F

value: CHOP-R/Bortezomib

value: Y

tag: marrow

value: IV

tag: ldh

value: not done


title: DASLV4_654

value: TRUE

value: MHG

value: M

value: N

tag: albumin

tag: hb

value: No


title: DASLV4_560

value: DLBCL

value: CHOP-R

value: normal

tag: lymphs

value: EZB


title: DASLV4_495

value: Diffuse large B-cell lymphoma, NOS

value: ABC

value: I

value: Yes

value: MCD


title: anti-scpB ChIP-seq of SMChigh cells and parSopt at -304kb and -9kb in exponential phase in SMG at 37°C

description:
BSG4137_scpB_ChIP
processed data file: BSG3790_3805_3815_4083_4091_4100_4137_4143_scpB_ChIP_1kb.txt

source_name: anti-scpB ChIP-seq of SMChigh cells and parSopt at -304kb and –9kb in exponential phase in SMG at 37°C

tag: strain/genotype information

value: 1A700, Δ6-parS (mtparS334 to parS359), smc::ermB, ΔamyE::smc::CAT, qoxD-specR::scpAB-ywcE

tag: chip antibody

value: anti-scpB


title: DASLV4_500

tag: reagent

value: FALSE

value: GCB

value: CHOP-R/Bortezomib

value: Y

value: III

value: raised

tag: neutrophils


title: DASLV4_660

value: DLBCL

value: M

value: N

value: IV

value: low

tag: monocytes

value: TRUE


title: DASLV4_693

value: Diffuse large B-cell lymphoma, NOS

value: F

value: CHOP-R

tag: wbc


title: DASLV4_691

value: UNC

value: II

value: normal

value: No


title: DASLV4_603

value: FALSE

value: ABC


title: DASLV4_480

value: Burkitt

value: Burkitt lymphoma

value: GCB

value: CODOX

value: Y

value: unknown

value: Yes


title: DASLV4_478

value: DLBCL

value: Primary mediastinal (thymic) large B-cell lymphoma

value: M

value: DHAP-R

value: N

value: NEC


title: DASLV4_477

value: CHOP-R

value: I

value: normal

value: EZB


title: anti-scpB ChIP-seq of SMChigh cells and parSopt at -9kb in exponential phase in SMG at 37°C

description:
BSG4143_scpB_ChIP
processed data file: BSG3790_3805_3815_4083_4091_4100_4137_4143_scpB_ChIP_1kb.txt

source_name: anti-scpB ChIP-seq of SMChigh cells and parSopt at –9kb in exponential phase in SMG at 37°C

value: 1A700, Δ7-parS(parS359+), smc::ermB, ΔamyE::smc::CAT, qoxD-specR::scpAB-ywcE

value: anti-scpB


title: DASLV4_730

value: FALSE

value: GCB

value: TRUE


title: DASLV4_593

value: Diffuse large B-cell lymphoma, NOS

value: CHOP-R/Bortezomib

value: Y

value: IV

value: raised

value: No


title: anti-scpB ChIP-seq of cells with wtSmc and parSopt at -9kb in exponential phase in SMG at 37°C

description:
BSG3790_scpB_ChIP
processed data file: BSG3790_3805_3815_4083_4091_4100_4137_4143_scpB_ChIP_1kb.txt

source_name: anti-scpB ChIP-seq of cells with wtSmc and parSopt at –9kb in exponential phase in SMG at 37°C

value: 1A700, Δ7-parS(parS359+), smc::specR


title: anti-scpB ChIP-seq of cells with wtSmc and parSopt at -9kb and +328kb in exponential phase in SMG at 37°C

description:
BSG4083_scpB_ChIP
processed data file: BSG3790_3805_3815_4083_4091_4100_4137_4143_scpB_ChIP_1kb.txt

source_name: anti-scpB ChIP-seq of cells with wtSmc and parSopt at –9kb and +328kb in exponential phase in SMG at 37°C

value: 1A700, Δ6-parS(parS359+), smc::specR, ΔamyE::parS-359 + tetO qPCR primer seq::cat


title: anti-scpB ChIP-seq of SMChigh cells in exponential phase in SMG at 37°C

description:
BSG4100_scpB_ChIP
processed data file: BSG3790_3805_3815_4083_4091_4100_4137_4143_scpB_ChIP_1kb.txt

value: 1A700, ΔamyE::smc::CAT, qoxD-specR::scpAB-ywcE, trpC2


title: DASLV4_569

source_name: Biopsy

value: DLBCL

value: ABC

value: M

value: N

value: II

value: Yes

value: MCD


title: DASLV4_476

value: Primary mediastinal (thymic) large B-cell lymphoma

value: FALSE

value: GCB

value: F

value: CVP

value: III

value: TRUE

value: NEC


title: DASLV4_508

value: Diffuse large B-cell lymphoma, NOS

value: MHG

value: CHOP-R

value: Y

value: IV

value: raised

value: No

value: EZB


title: DASLV4_498

value: DLBCL

value: T-cell/histiocyte-rich large B-cell lymphoma

value: UNC

value: M

value: CHOP-R/Bortezomib

value: Yes


title: anti-scpB ChIP-seq of cells with wtSmc and parSopt at -304kb and +328kb cells in exponential phase in SMG at 37°C

description:
BSG4091_scpB_ChIP
processed data file: BSG3790_3805_3815_4083_4091_4100_4137_4143_scpB_ChIP_1kb.txt

source_name: anti-scprB ChIP-seq of cells with wtSmc and parSopt at -304kb and +328kb cells in exponential phase in SMG at 37°C

value: 1A700, Δ6-parS(parS334->359+), parAB::kanR, smc::ermB, ΔamyE::parS-359 + tetO qPCR primer seq::cat

value: anti-parB


title: anti-scpB ChIP-seq of cells with wtSmc and parSopt at -304kb and -9kb cells in exponential phase in SMG at 37°C

description:
BSG3805_scpB_ChIP
processed data file: BSG3790_3805_3815_4083_4091_4100_4137_4143_scpB_ChIP_1kb.txt

source_name: anti-scpB ChIP-seq of cells with wtSmc and parSopt at -304kb and –9kb cells in exponential phase in SMG at 37°C

value: 1A700, Δ6-parS (mtparS334 to parS359), smc::ermB

value: anti-scpB


title: anti-scpB ChIP-seq time course t60 of Smc-CC425 and parS at -9kb cells in exponential phase in SMG at 30°C

description:
BSG3216_t60_ChIP_scpB
processed data file: BSG3216_scpB_ChIP_1kb.txt

source_name: anti-scpB ChIP-seq time course t60 of Smc-CC425 and parS at –9kb cells in exponential phase in SMG at 30°C

value: PY79:Δ7-parS(parS359+), ΔparB::kanR, smc(1-476 SpnSmc(398-768) 695-1186) ftsY::ermB, amyE::(PhbsB short 5'UTR-theo E+ -parB (mtparS))::CAT


title: anti-scpB ChIP-seq time course t40 of Smc-CC425 and parS at -9kb cells in exponential phase in SMG at 30°C

description:
BSG3216_t40_ChIP_scpB
processed data file: BSG3216_scpB_ChIP_1kb.txt

source_name: anti-scpB ChIP-seq time course t40 of Smc-CC425 and parS at –9kb cells in exponential phase in SMG at 30°C


title: DASLV4_419

value: Diffuse large B-cell lymphoma, NOS

value: FALSE

value: GCB

value: CHOP-R

value: N

value: TRUE


title: anti-scpB ChIP-seq time course t20 of Smc-CC425 and parS at -9kb cells in exponential phase in SMG at 30°C

description:
BSG3216_t20_ChIP_scpB
processed data file: BSG3216_scpB_ChIP_1kb.txt

source_name: anti-scpB ChIP-seq time course t20 of Smc-CC425 and parS at –9kb cells in exponential phase in SMG at 30°C


title: anti-scpB ChIP-seq time course t0 of Smc-CC425 and parS at -9kb cells in exponential phase in SMG at 30°C

description:
BSG3216_t0_ChIP_scpB
processed data file: BSG3216_scpB_ChIP_1kb.txt

source_name: anti-scpB ChIP-seq time course t0 of Smc-CC425 and parS at –9kb cells in exponential phase in SMG at 30°C


title: anti-scpB ChIP-seq time course t60 of wtSmc and parS at -9kb cells in exponential phase in SMG at 30°C

description:
BSG3026_t60_ChIP_scpB
processed data file: BSG3026_scpB_ChIP_1kb.txt

source_name: anti-scpB ChIP-seq time course t60 of wtSmc and parS at –9kb cells in exponential phase in SMG at 30°C

value: PY79:Δ7-parS(parS359+), ΔparB::kanR, amyE::(PhbsB short 5'UTR-theo E+ -parB (mtparS))::CAT


title: DASLV4_415

value: DLBCL

value: CVP-R

value: Y

value: IV

value: normal

value: NEC


title: DASLV4_418

value: ABC

value: F

value: Supportive/palliativeonly

value: Yes


title: anti-scpB ChIP-seq time course t40 of wtSmc and parS at -9kb cells in exponential phase in SMG at 30°C

description:
BSG3026_t40_ChIP_scpB
processed data file: BSG3026_scpB_ChIP_1kb.txt

source_name: anti-scpB ChIP-seq time course t40 of wtSmc and parS at –9kb cells in exponential phase in SMG at 30°C

value: anti-scpB


title: anti-scpB ChIP-seq time course t0 of wtSmc and parS at -9kb cells in exponential phase in SMG at 30°C

description:
BSG3026_t0_ChIP_scpB
processed data file: BSG3026_scpB_ChIP_1kb.txt

source_name: anti-scpB ChIP-seq time course t0 of wtSmc and parS at –9kb cells in exponential phase in SMG at 30°C


title: anti-scpB ChIP-seq time course t20 of wtSmc and parS at -9kb cells in exponential phase in SMG at 30°C

description:
BSG3026_t20_ChIP_scpB
processed data file: BSG3026_scpB_ChIP_1kb.txt

source_name: anti-scpB ChIP-seq time course t20 of wtSmc and parS at –9kb cells in exponential phase in SMG at 30°C


title: DASLV4_416

value: DLBCL-HL

value: B-cell lymphoma, intermediate between DLBCL and classical HL

value: FALSE

value: UNC

value: M

value: COP

value: not done


title: DASLV4_366

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: GCB

value: CHOP-R

value: N

value: TRUE


title: DASLV4_397

value: F

value: Y

value: raised

value: No


title: anti-scpB ChIP-seq of cells with Smc-CC425 and parS at -9kb in exponential phase in SMG at 37°C

description:
BSG3803_ChIP_scpB
processed data file: BSG1489_1002_3790_3803_3427_scpB_ChIP_1kb.txt

source_name: anti-scpB ChIP-seq of cells with Smc-CC425 and parS at –9kb in exponential phase in SMG at 37°C

value: anti-scpB


title: anti-scpB ChIP-seq of cells with Smc-CC425 in exponential phase in SMG at 37°C

description:
BSG3427_ChIP_scpB
processed data file: BSG1489_1002_3790_3803_3427_scpB_ChIP_1kb.txt


title: anti-scpB ChIP-seq of cells with wtSmc and parS at -9kb in exponential phase in SMG at 37°C

description:
BSG3790_ChIP_scpB
processed data file: BSG1489_1002_3790_3803_3427_scpB_ChIP_1kb.txt

source_name: anti-scpB ChIP-seq of cells with wtSmc and parS at –9kb in exponential phase in SMG at 37°C

value: 1A700, Δ7-parS(parS359+), smc::specR


title: anti-scpB ChIP-seq of wt cells in exponential phase in SMG at 37°C

description:
BSG1002_ChIP_scpB
processed data file: BSG1489_1002_3790_3803_3427_scpB_ChIP_1kb.txt

value: 1A700, smc ftsY::ermB, trpC2


title: DASLV4_357

value: FALSE

value: ABC

value: IV

value: Yes


title: DASLV4_417

value: DLBCL

value: III


title: DASLV4_350

value: Diffuse large B-cell lymphoma, NOS

value: MHG

value: M

value: Resectiononly(stageI)

value: II


title: DASLV4_128

value: GCB

value: F

value: Supportive/palliativeonly

value: Y

value: not done

value: TRUE

value: EZB


title: DASLV4_96

value: FALSE

value: CHOP-R

value: N

value: raised


title: DASLV4_93

value: DLBCL

value: IV

value: Yes


title: MPRA_Plasmid_Library

city: Stanford

first: Daniel

middle: Sunwook

last: Kim

state: CA

address: 269 Campus Drive, CCSR 2150

institute: Stanford School of Medicine

description: Sequencing of MPRA plasmid library for fractional representation of fragments in library. UMI is first 15 bp of read 1, barcode is the 20 bps after the first 17 bps in read 2

data_processing:
library strategy: Massively parallel reporter assays (MPRA)
MPRA read strategy: single ended reads where UMI is in read name and barcode is on the read (the 20 bps after the first 17 bps)
Reads are trimmed and UMI is associated to matching read such that downstream analysis proceeds with reads as just the barcodes
Reads (barcodes) are matched to original barcodes with BWA alignment with default params to get reads per MPRA fragment
UMIs are used to get unique reads per fragment
Counts are normalized according to the plasmid fractions and then run through DESeq2 rlog transformation for a normalized signal matrix
Genome_build: hg19
Supplementary_files_format_and_content: Master file of all tested fragments with relevant metadata, FASTA file of tested fragments, read counts for each fragment in the plasmid library, MPRA RNA read counts for each fragment per sample

organism: Escherichia coli

source_name: Takara Stellar cells

growth_protocol: Human primary keratinocytes were cultured in 50/50 growth media and induced to differentiate for 6 days as previously describe (Zarnegar 2012)

extract_protocol:
At each timepoint, total RNA was isolated using Qiagen's Rneasy Plus kit
cDNA was synthesized using SuperScript IV using primers containing UMIs, cDNA synthesis reactions were cleaned up witih SPRIselect beads and amplified with PrimeSTAR Max DNA Polymerase, sequennce indices were added, then libraries were ge purified and pooled.

treatment_protocol: Keratinocyes were infected with lentiviral MPRA library, selected for infected cells 24 hours later with puromycin, then induced to differentiate 24 hours later (Zarnegar 2012) for up to 6 days, harvested at days 0, 3, and 6

tag: cell type

value: Takara Stellar cells

tag: molecule subtype

value: Plasmid DNA


title: DASLV4_89

value: Diffuse large B-cell lymphoma, NOS

tag: microdissection

value: UNC

value: M

tag: pcv

value: NEC


title: DASLV4_349

value: GCB

tag: Sex

value: F

value: Y

value: No


title: DASLV4_92

value: FALSE

tag: Stage

value: III

value: normal

value: TRUE


title: DASLV4_132

value: DLBCL

value: Primary mediastinal (thymic) large B-cell lymphoma

value: CHOP-R

value: I

tag: plts

value: EZB


title: DASLV4_88

value: Diffuse large B-cell lymphoma, NOS

value: N

tag: ldh

value: Yes


title: WT_left_ventricle_TAC, rep2

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

data_processing:
Library strategy: 4C-seq
4C-seq reads were mapped to mm9 and sequence depth normalized to 1 million intrachromosomal reads after exclusion of the two most captured fragment ends using pipe4C (Krijger et al, 2020 and github.com/deLaatLab/pipe4C). 4C-seq coverage for each individual experiment was calculated by averaging mapped reads in running windows of 21 4C-seq fragment-ends. The median coverage of the replicates was plotted as the combined 4C profile.
Genome_build: mm9
Supplementary_files_format_and_content: wig

source_name: WT

growth_protocol: Animal care and experiments conform to the Directive 2010/63/EU of the European Parliament. All animal work was approved by the Animal Experimental Committee of the Amsterdam University Medical Centers, location AMC, Amsterdam, and was carried out in compliance with the Dutch government guidelines, approved by the Central Committee Animal Experiments.

extract_protocol:
4C templates were prepared as previously described (de Krijger et al., 2020). In short, snap frozen adult left ventricle were crushed, dissociated and dounce homogenized to obtain single cell suspension. Chromatin was cross-linked with 2% formaldehyde in PBS with 10% FCS for 10 minutes at room temperature. Nuclei were isolated and cross-linked DNA was digested with DpnII, followed by proximity ligation. Cross-links were removed and a secondary restriction digestion with Csp6I performed, followed again by proximity ligation. Per viewpoint, 8 PCR reactions were performed on 200 ng of 4C template each, to a total of 1.6 µg.
PCR reactions were pooled and purified for next generation sequencing. The 4C-seq PCRs were essentially performed as previously described (de Krijfer et al., 2020) using reading primers (Nppa promoter – GCCCTAGGAGAGCTATGATC) as 4C viewpoints combined with non-reading primer ( Nppa promoter –TAACAGGGACATCTAGGGTG). The primers were extended with Illumina adapter sequences and the samples were sequenced on the MiSeq.

tag: strain

value: FVB

tag: genotype

value: WT

tag: age

value: 8-12 weeks

tag: stress

value: TAC

tag: tissue

value: Left ventricle


title: WT_left_ventricle_MI, rep1

value: MI


title: WT_left_ventricle_TAC, rep3


title: DASLV4_83

tag: reagent

value: FALSE

value: ABC

value: M

value: Y

value: IV

value: raised

tag: albumin

tag: hb

tag: lymphs

value: NEC


title: WT_left_ventricle_TAC, rep1


title: WT_left_ventricle_control, rep3

value: control


title: WT_left_ventricle_MI, rep3


title: DASLV4_84

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: PmitCEBO/Rituximab

value: III

tag: wbc

value: TRUE


title: WT_left_ventricle_control, rep1

value: FVB

value: WT

value: 8-12 weeks


title: WT_left_ventricle_control, rep2

value: Left ventricle


title: RE3_KO_Nppa_C

data_processing:
library strategy: 4C-seq
4C-seq reads were mapped to mm9 and sequence depth normalized to 1 million intrachromosomal reads after exclusion of the two most captured fragment ends using pipe4C (Krijger et al, 2020 and github.com/deLaatLab/pipe4C). 4C-seq coverage for each individual experiment was calculated by averaging mapped reads in running windows of 21 4C-seq fragment-ends. The median coverage of the replicates was plotted as the combined 4C profile.
Genome_build: mm9
Supplementary_files_format_and_content: wig

extract_protocol:
4C templates were prepared as previously described (de Krijger et al., 2020). In short, snap frozen adult mouse hearts of Scn5a RE6-9 mutant mice and wildtype littermates were crushed, dissociated and dounce homogenized to obtain single cell suspension. Chromatin was cross-linked with 2% formaldehyde in PBS with 10% FCS for 10 minutes at room temperature. Nuclei were isolated and cross-linked DNA was digested with DpnII, followed by proximity ligation. Cross-links were removed and a secondary restriction digestion with Csp6I performed, followed again by proximity ligation. Per viewpoint, 8 PCR reactions were performed on 200 ng of 4C template each, to a total of 1.6 µg.
PCR reactions were pooled and purified for next generation sequencing. The 4C-seq PCRs were essentially performed as previously described (de Krijfer et al., 2020) using reading primers (CTCF left – AAAAGCTCAGAGTGGAGATC and Nppa promoter – GCCCTAGGAGAGCTATGATC) as 4C viewpoints combined with non-reading primers (CTCF left – ATTCTACTGATGCTGCATGG and Nppa promoter –TAACAGGGACATCTAGGGTG). The primers were extended with Illumina adapter sequences and the samples were sequenced on the Nextseq.

tag: strain background

tag: genotype/variation

value: CRISPR/Cas9 deletion RE3


title: WT_left_ventricle_MI, rep2

value: MI


title: RE3_KO_Nppa_B


title: DASLV4_727

tag: microdissection

value: FALSE

value: ABC

value: F

value: CHOP-R/Bortezomib

value: N

value: II

tag: monocytes

tag: neutrophils

tag: pcv

value: Yes


title: DASLV4_86

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: GCB

tag: Sex

value: CHOP-R

tag: Stage

value: IV

tag: ldh

value: normal

value: NEC


title: DASLV4_81

value: M

value: Y

value: III

value: raised

value: TRUE


title: DASLV4_80

value: FALSE

value: UNC

value: F


title: DASLV4_68

value: N

value: II

tag: plts


title: DASLV4_82

value: DLBCL

value: ABC

value: unknown

value: Yes

value: MCD


title: DASLV4_61

value: Diffuse large B-cell lymphoma, NOS

value: CHOP

value: I

value: normal


title: WT_Nppa_B

value: FVB

value: WT

tag: age

value: 8-12 weeks

value: Left ventricle


title: DASLV4_79

value: FALSE

value: GCB

value: M

value: CHOP-R

value: Y

value: raised

value: TRUE

value: NEC


title: DASLV4_67

value: DLBCL

value: F

value: IV

value: Yes


title: WT_Nppa_C

tag: tissue


title: DASLV4_62

value: Diffuse large B-cell lymphoma, NOS

tag: reagent

value: ABC

value: N

value: I

value: MCD


title: DASLV4_55

value: FALSE

value: normal

tag: albumin


title: WT_Nppa_A

value: FVB

value: WT

value: 8-12 weeks

value: Left ventricle


title: DASLV4_58

value: MHG

value: Supportive/palliativeonly

value: not done

tag: hb

value: TRUE

value: EZB


title: RE3_KO_CTCF_left_B

value: CRISPR/Cas9 deletion RE3


title: RE3_KO_CTCF_left_A


title: WT_CTCF_left_C


title: DASLV4_52

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: GCB

value: M

value: CVP-R

value: Y

value: IV

value: raised

tag: lymphs

value: Yes


title: DASLV4_46

value: FALSE

value: UNC

value: F

value: CHOP-R

value: N

value: I

tag: wbc


title: DASLV4_50

value: III

value: TRUE

value: NEC


title: WT_CTCF_left_B

tag: strain background

value: FVB

value: WT

value: 8-12 weeks

value: Left ventricle


title: RE3_KO_Nppa_A

tag: genotype/variation

value: CRISPR/Cas9 deletion RE3


title: RE3_KO_CTCF_left_C


title: DASLV4_51

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

tag: microdissection

value: ABC

value: M

value: Supportive/palliativeonly

value: IV

value: not done

value: MCD


title: DASLV4_44

value: FALSE

value: GCB

value: CHOP-R

value: N

value: normal

value: Yes


title: DASLV4_43

value: III

value: TRUE

value: NEC


title: DASLV4_42

value: DLBCL

value: F

value: II

value: raised


title: DASLV4_37

value: Diffuse large B-cell lymphoma, NOS


title: WT_CTCF_left_A

value: FVB

value: WT

value: 8-12 weeks

value: Left ventricle


title: OC9.1

city: Baltimore

first: Carrie

last: McCracken

state: MD

address: 670 W. Baltimore St

department: Institute for Genome Sciences

institute: Institute of Genome

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software
The STAR aligner uses a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes.
Genome_build: The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Supplementary_files_format_and_content: tab-delimted text files include counts values for each sample

source_name: Oseochondroma

growth_protocol: Cartilage caps were microdissected from human osteochondromas obtained at surgery, miced into 3-5 mm cubic and cultured inside a diffusion chamber

extract_protocol:
Osteochondroma explants were washed with PBS, stored in RNAlator and kept at -80C. The explants were placed on clean Kimwipe to absorb excess RNAlater solution and then were snap-frozen in liquid nitrogen. Frozen tissue fragments were placed on pre-chilled carbon steel block and crashed into powder by the steel hammer. We then purified total RNA using Qiagen RNeasy fibrous tissue mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Osteochondroma explants were treated with NRX202467 or Palovarotene at 50-300nM.

tag: patient

value: Patient #9

tag: treated drug

value: Vehicle ethanol

tag: concentration


title: OC9.2


title: OC9.4


title: OC7.6

value: Patient #7


title: G56 KD_14hpf_rep1

city: Nanjing

first: Wenshuang

last: Jia

address: NO.129 Jiangjun Road

country: China

institute: Nanjing University

description: Gene expression after gata5/gata6 MO injection

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities, and normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Danio rerio

source_name: zebrafish embryos_gata5/gata6 MO

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany)

growth_protocol: Zebrafish were housed in the zebrafish room of Model Animal Research Center, Nanjing University, in accordance with IACUC-approved protocol. All methods were performed in accordance with the relevant guidelines and regulations.

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 integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Morpholinos (MOs) were purchased from Gene Tools (http://www.gene-tools.com). MOs were dissolved in nanopure water and microinjected into the embryos at 1-cell stages. The microinjection amount was 1 nl solution containing 6.25 ng gata5 MO and 1.25 ng gata6 MO, or 7.5 ng control MO per embryo. Because it is reported that morpholinos against gata5 and gata6 also lead to a loss of gata4 expression in zebrafish, we used a combination microinjection of gata5 and gata6 morpholinos for knocking down all the three genes. The embryos microinjected with control MO or gata5/6 MOs at 1-cell stage were collected at 14 hpf for analyzing the gene expression changes affected by knocking down gata4/5/6.

value: gata5/6 knock down

value: embryos


title: OC7.5


title: DASLV4_34

data_processing: Data were normalised using Lumi for R.

source_name: Biopsy

extract_protocol: Total RNA was extracted from 5mm paraffin sections using the Ambion RecoverAll kit standard protocol, with the exception of a 16-hour protease digestion. These were routinely collected tissue samples and no attempt was made to standardise fixation or processing protocols

value: FALSE

value: MHG

tag: Sex

value: M

value: CHOP-R

value: N

value: III

value: normal

value: Yes


title: OC7.4


title: G56 KD_14hpf_rep2

tag: Stage


title: DASLV4_23

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: TRUE

value: GCB

value: I

tag: ldh


title: Ctl_14hpf_rep3

description: Gene expression after control MO injection

source_name: zebrafish embryos_control MO

value: control


title: DASLV4_26

value: Y

value: NEC


title: DASLV4_35

value: II


title: ETO_ChIP_Kasumi-1_plusKTS

first: Salam

middle: Adli

last: Assi

department: Institute for Cancer and Genomic Sciences

data_processing:
Quality of reads was verified using FASTQC analysis
Sequences reads in fastq format were mapped onto the reference human genome version hg38, Genome Reference Consortium GRCh38. The Illumina reads were aligned to the human genome using Bowtie2
Reads that were uniquely aligned to chromosomal positions were retained and duplicate reads were removed from the aligned data using Picard tools.
The filtered aligned reads were used to generate density profiles using “genomeCoverageBed” function from bedtools
Genome_build: hg38
Supplementary_files_format_and_content: wiggle

extract_protocol:
Cells were crosslinked in 1% formaldehyde for 10 minutes before being quenched by 0.4M Glycine. For EGR-1 ChIP, cells were also double-crosslinked with Di(N-succinimidyl) glutarate (DSG) for 45 minutes. Cells were lysed for 10 minutes in cell lysis buffer (5mM PIPES pH 8.0, 85mM KCl, 0.5% NP-40, 1:200 Protease Inhibitory Cocktail [PIC] before undergoing nuclear lysis for 10 minutes in nuclear lysis buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS, 1:100 PIC). Nuclei were then sonicated in a Bioruptor Pico (Diagenode) until chromatin was sheared to a 200-600bp fragment size and then diluted in blocking buffer (16.7mM Tris pH 8.0, 167mM NaCl, 1.2mM EDTA, 1.1% Triton X-100, 0.01% SDS and 1:100 PIC). 15ul of Dynabeads G were pre-blocked for 2 hours at 4oC with blocking buffer consisting of 0.5% BSA, 30µg glycogen and ChIP grade antibody at a suitable concentration, before being incubated overnight 4oC with the diluted chromatin. See Key Resources table for details of antibodies used. Then the beads were washed in sonication wash buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS), twice in Buffer A (20mM Tris, pH 8.0, 0.1% SDS, 1% Triton-X 100, 2mM EDTA, 150mM NaCl), twice in Buffer B (20mM Tris, pH 8.0, 0.1% SDS, 1% Triton-X 100, 2mM EDTA, 150mM NaCl), with Lithium buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA pH 8.0, 0.5 % NP-40 and 0.5 % sodium deoxycholate). Beads were then washed once in 1xTE. Chromatin was then eluted in 100mM NaHCO3 and 1% SDS and reverse crosslinked for 4-16 hours at 65oC with 50μg Proteinase K. DNA was then cleaned up with 1.8x SPRI beads. qPCR amplification of immunoprecipitated DNA was compared to input at several loci of putative protein binding sites as well as non-binding sites to assess the success of ChIP. See Supplementary file 5 for qPCR primer sequences.
Libraries for high throughput sequencing were prepared using the Kapa HyperPrep kit (Kapa biosystems, USA), as per manufacturer’s protocol. 16 cycles of PCR was performed and 200-400 bp fragments were size selected by running the samples in an agarose gel. Libraries were validated by qPCR, with an analysis of the ChIP signal of a positive control region (e.g. PU.1 14 3H enhancer) over a negative control region (e.g. IVL). Finally, libraries were quantified by Kapa library quantification kit (Kapa biosystems, USA) and run in a pool of four indexed libraries in one lane of a HiSeq 2500 (Illumina, USA) or 12 indexed libraries in one lane of a NextSeq 500 (Illumina, USA) using 50 cycle single-end reads.

tag: cell type

value: Kasumi-1 cells

tag: genotype

value: overexpression WT1 +KTS

tag: antibody

value: ETO (C-terminus)

tag: company

value: Santa Cruz

tag: identifier

value: cat# sc9737


title: Ctl_14hpf_rep1

tag: tissue

value: embryos


title: Ctl_14hpf_rep2


title: DASLV4_31

tag: reagent

value: FALSE

value: M

value: DHAP-R

value: III

value: raised

tag: albumin

tag: hb

tag: lymphs


title: DASLV4_7

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

tag: microdissection

value: GCB

value: CVP-R

tag: wbc

value: Yes

value: TRUE


title: DASLV4_29

value: ABC

value: radiotherapyonly

value: N


title: ETO_ChIP_Kasumi-1_minusKTS

value: Kasumi-1 cells

value: overexpression WT1 -KTS

value: ETO (C-terminus)

value: Santa Cruz


title: OC7.2

tag: patient

value: Patient #7

tag: treated drug

value: Vehicle ethanol


title: OC7.3

tag: concentration


title: DASLV4_33

value: FALSE

value: MHG

tag: Sex

value: M

value: CHOP-R

value: Y

tag: Stage

value: III

value: NEC

value: EZB


title: DASLV4_4

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

value: F

value: IV

tag: ldh

value: raised

tag: monocytes

tag: neutrophils

tag: pcv

tag: plts

value: Yes

value: TRUE


title: DASLV4_20

value: GCB

value: II

value: normal


title: ETO_ChIP_Kasumi-1_EV

tag: cell type

value: Kasumi-1 cells

tag: genotype

value: Control Empty vector

tag: antibody

value: ETO (C-terminus)

tag: company

value: Santa Cruz

tag: identifier

value: cat# sc9737


title: DASLV4_1

tag: reagent

tag: microdissection

value: FALSE

value: MHG

value: CHOP-R

value: N

tag: albumin

tag: hb

tag: lymphs


title: OC7.1

tag: patient

value: Patient #7

tag: treated drug

value: Vehicle ethanol

tag: concentration


title: DASLV4_2

value: DLBCL

value: Diffuse large B-cell lymphoma, NOS

tag: Sex

value: M

tag: Stage

tag: ldh

value: raised

tag: monocytes

tag: wbc


title: OC6.6

value: Patient #6


title: EGR1_ChIP_Kasumi-1_shWT1_plusDox

tag: cell type

tag: genotype

value: shWT1 with Dox

value: Cell Signaling


title: DASLV4_6

value: GCB

value: F

value: IV

value: Yes

value: TRUE

value: NEC


title: EGR1_ChIP_Kasumi-1_shWT1_noDox

value: Kasumi-1 cells

value: shWT1 wothout dox

tag: antibody

tag: company


title: OC6.5


title: OC6.4


title: OC6.2


title: OC6.3


title: OC6.1


title: EGR1_ChIP_Kasumi-1_shRE_plusDox

value: shRE with Dox

tag: identifier


title: OC5.8

value: Patient #5


title: EGR1_ChIP_Kasumi-1_minusKTS

value: overexpression WT1 -KTS


title: OC5.6


title: EGR1_ChIP_Kasumi-1_plusKTS

value: overexpression WT1 +KTS


title: t8.21_primary_shNTC_ATAC

data_processing:
Quality of reads was verified using FASTQC analysis
Sequences reads in fastq format were mapped onto the reference human genome version hg38, Genome Reference Consortium GRCh38. The Illumina reads were aligned to the human genome using Bowtie2
Reads that were uniquely aligned to chromosomal positions were retained for downstream analysis
The filtered aligned reads were used to generate density profiles using “genomeCoverageBed” function from bedtools
Genome_build: hg38
Supplementary_files_format_and_content: wiggle

extract_protocol:
ATAC-seq was performed  as described in Corces et al. 20162. Briefly, cells were harvested and 50,000 cells pelleted prior to resuspension in 50 µl ATAC transposition reaction mix containing 2x Tagment DNA Buffer (Illumina), Tn5 transposase (Illumina) and 0.5 µl 1% Digitonin (Promega). DNA was purified using a MinElute Reaction Clean up kit (Qiagen). DNA was PCR amplified using Nextera custom primers and saturation of the PCR reaction avoided by monitoring the reaction to prevent overamplification as described in Buenrostro et al.3,4. Amplified DNA was subsequently purified using MinElute columns or Ampure Beads (Beckman Coulter) prior to validation. Libraries were sequenced in a pool of 12 indexed libraries using a NextSeq 500/550 High Output Kit v2 (150 cycles) for paired end sequencing (Illumina) at the Genomics Birmingham sequencing facility.
ATAC-seq libraries were prepared essentially as described in Corces, M. R. et al. 2016 and in Buenrostro et al.2015. Libraries were sequenced in a pool of 12 indexed libraries using a NextSeq 500/550 High Output Kit v2 (150 cycles) for paired end sequencing (Illumina) at the Genomics Birmingham sequencing facility.

value: t(8;21) AML cells

value: shNTC


title: t8.21_primary_minusKTS_ATAC


title: OC5.5


title: t8.21_primary_plusKTS_ATAC


title: EGR1_ChIP_Kasumi-1_EV

value: Control Empty vector


title: OC5.4

value: Vehicle ethanol


title: OC5.1


title: Healthy_primary_shWT1_ATAC

value: CD34+ primary cells

value: shWT1 with Dox


title: Healthy_primary_shNTC_ATAC


title: OC5.2


title: Healthy_primary_plusKTS_ATAC


title: OC5.3


title: EGR1_ChIP_Kasumi-1_shRE_noDox

value: shRE wothout dox

value: Cell Signaling


title: t8.21_primary_shWT1_ATAC


title: OC5.7


title: shCHERP_1

city: Barcelona

last: Vivori

address: Carrer Dr Aiguader 88

country: Spain

institute: Centre for Genomic Regulation

data_processing:
AS events for each knockdown:
Reads alignment and alternative splicing analysis performed with vast-tools v2.2.2.
Differentially spliced events: abs(∆PSI) >= 15, range >= 5
differentially expressed genes for each knockdown:
Reads alignment performed with STAR
Differential gene expression analysis performed with CuffDiff: abs(log2(Fold Change)) >= 0.6, ∆FPKM >1, status OK, significant YES
Genome_build: hg19
Supplementary_files_format_and_content: text files with AS events for each knockdown
Supplementary_files_format_and_content: comma separated files with differentially expressed genes for each knockdown

growth_protocol: HeLa cells were cultured in Glutamax Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS), 500U/mL penicillin and 500µg/mL streptomycin.

extract_protocol:
For RNA-seq experiments, total RNA extraction was carried out using RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.
Stranded RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For lentiviral infections, cells were incubated with concentrated lentivirus overnight and subcultured with fresh medium the following day. 48h after infection cells were selected with puromycin (1μg/mL for U2OS, 2μg/mL for HeLa) for 2 days.

tag: cell line

value: HeLa

tag: genotype/variation

value: shCHERP


title: shCHERP_2


title: shSR140_2


title: shSR140_1


title: Healthy_primary_EV_ATAC

value: Control


title: FLT3ITD_primary_shWT1_ATAC

value: FLT3-ITD AML cells


title: FLT3ITD_primary_shNTC_ATAC


title: FLT3ITD_primary_plusKTS_ATAC


title: t8.21_primary_EV_ATAC


title: shSPF45_2


title: shSPF45_1


title: FLT3ITD_primary_minusKTS_ATAC


title: shCNT_2

value: shCNT


title: shCNT_1


title: 150-16 + Abx NO PTL

city: Los Angeles

first: Suhas

middle: G

last: Kallapur

address: 10833 Le Conte Avenue

institute: UCLA

data_processing:
The reads were mapped with STAR 2.5.3a to the Macaca mulatta genome (Mmul 8.0.1).
The counts for each gene were obtained by using quantMode GeneCounts in the STAR commands, and only counts for the featured genes were reserved.
Genome_build: mmul 8.0.1
Supplementary_files_format_and_content: Deseq2 normalized count : normalized_counts_txt
Supplementary_files_format_and_content: Raw counts : raw_counts.txt

organism: Macaca mulatta

source_name: chorioamniondecidua

extract_protocol:
chorioamnion decidua samples were collected right after delivery, sna-frozen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: intra-amniontic injection of live E coli, LPS or saline

value: chorioamniondecidua cells

tag: preterm labor (ptl)

value: no

tag: treatment

value: intra-amniotic injection of live E coli + intra-amniotic/intra-muscular antibiotics (Abx)


title: 149-16 + Abx NO PTL


title: 146-16 + Abx PTL

value: yes


title: stool small RNA-Seq VOV98

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

institute: University of Turin

data_processing:
Fastq files were quality-controlled with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Reads shorter than 14 nt were discarded.
The QC-passed reads were clipped from the adapter sequences using Cutadapt v1.10 by imposing a maximum error rate in terms of mismatches, insertions, and deletions equal to 0.15.
Trimmed reads were mapped against a miRNA reference based on miRBase v22 annotations using the small RNA-Seq module of Docker4Seq. The alignment was performed using BWA algorithm v0.7.127 with the default settings
The human miRNAs were annotated and quantified using two methods called the "knowledge-based" and "position-based". miRNAs whose assigned arms were derived from the "position-based" methodology were indicated in italics. The results generated by the annotation and quantification methods were merged into a unique mature miRNA count matrix. In the case of mature miRNAs processed from different precursors but characterized by the same mature sequence, the read counts were summed.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Stool

extract_protocol:
RNA was extracted using the Stool Total RNA Purification Kit (Norgen Biotek Corp).
Small RNA (sRNA) transcripts were converted into barcoded cDNA libraries. Library preparation was performed with the NEBNext Multiplex Small RNA Library Prep Set for Illumina (Protocol E7330, New England BioLabs Inc., USA). The obtained libraries were subjected to the Illumina sequencing pipeline, passing through clonal cluster generation on a single-read flow cell (Illumina Inc., USA) by bridge amplification on the cBot (TruSeq SR Cluster Kit v3-cBOT-HS, Illumina Inc., USA) and 50 cycles sequencing-by-synthesis on the HiSeq 2000 (Illumina Inc., USA).

tag: diet

value: Vegan


title: stool small RNA-Seq VOV96

value: Vegetarian


title: stool small RNA-Seq VOV97


title: stool small RNA-Seq VOV95

value: Omnivorous


title: stool small RNA-Seq VOV09


title: stool small RNA-Seq VOV94


title: Healthy_primary_minusKTS_ATAC

value: overexpression WT1 -KTS


title: 17-13 LPS 48h

value: intra-amniotic injection of lipopolysaccharide (LPS)


title: 141-16  (preterm labor) PTL

value: intra-amniotic injection of live E coli


title: 15-13 LPS 48h


title: stool small RNA-Seq VOV90


title: stool small RNA-Seq VOV08


title: 18-13 LPS 48h


title: stool small RNA-Seq VOV88


title: 20-13 ctrl

value: intra-amniotic injection of saline


title: FLT3ITD_primary_EV_ATAC


title: stool small RNA-Seq VOV85


title: 09-12 ctrl


title: 19-13 ctrl


title: stool small RNA-Seq VOV87


title: stool small RNA-Seq VOV84


title: 147-16 PTL


title: stool small RNA-Seq VOV82


title: stool small RNA-Seq VOV80


title: stool small RNA-Seq VOV07


title: stool small RNA-Seq VOV78


title: Med16-AID, TBP-ChEC (DMSO) rep-2

city: Bloomington

first: Gabriel

middle: E

last: Zentner

state: IN

address: 915 E 3rd St

department: Biology

institute: Indiana University

data_processing:
Library strategy: ChEC-seq
Alignment with Bowtie2 (default settings plus "--no-unal --dovetail –no-discordant --no-mixed")
samtools view (default settings)
samtools sort (default settings)
samtools index (default settings)
Deeptools bamCoverage (default settings plus "--ignoreDuplicates -bs 10 --normalizeUsing CPM" )
Genome_build: sacCer3
Supplementary_files_format_and_content: bigWig

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown at 30℃ in YPD to an OD600 of 0.7-1.0

extract_protocol:
ChEC was performed as described in Donczew et al. 2020, PMID: 31913117
NEB Next Ultra II DNA Library Prep Kit for Illumina

treatment_protocol: For the Med16-AID strains, 3-IAA treated samples were treated with 3-IAA in DMSO at a final concentration of 0.5mM for 30 minutes. DMSO-treated samples were treated with DMSO (1:2000 by culture volume) for 30 minutes

tag: chec tag

tag: auxin-inducible degron (aid) tag

tag: background


title: Med16-AID, TBP-ChEC (IAA) rep-2


title: stool small RNA-Seq VOV75


title: stool small RNA-Seq VOV74


title: Wi38 S2

city: Berlin

first: Clemens

last: Schmitt

address: Augustenburger Platz 1

department: Hematology, Oncology, Tumorimmunology

country: Germany

institute: Charite

description:
OIS Wi38
AS-401826-LR-46699
OIS_norm_counts

data_processing:
Transcript quantification using salmon (Patro et al.)
Transcript import using tximeta (Love et al.) or tximport packages (Soneson et al.).
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with normalized transcript counts for every gene and every sample

growth_protocol: A549 and Wi38 cells were cultivated in DMEM supplemented with 10% FBS and Pen-Strep antibiotics; THP-1 cells were cultivated in RPMI-1640 supplemented with 10% FBS and Pen-Strep antibiotics

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus Mini Kit
Libraries were prepared by BGI or DKFZ sequencing core facility according to Illumina's TruSeq RNA kit (RS-122-2001) instructions.

treatment_protocol: Cells were infected with virus or cultivated in conditioned medium for 5 days (THP-1: 3 days) and cell pellets were collected for RNA extraction. THP1 VIS samples were split into CD86+ and CD86- fractions using surface labelung with a CD86-biotin antibody and anti-biotin Microbeads from Miltenyi, following the manufacturer´s instructions.

tag: condition


title: Wi38 S3

description:
OIS Wi38
AS-401827-LR-46699
OIS_norm_counts


title: stool small RNA-Seq VOV73


title: EAT 54

city: London

first: Paula

last: Longhi

address: William Harvey Research Institute

institute: Queen Mary, University of London

description: RawCounts.tsv

data_processing:
Pseudo-alignment and count abundance via salmon v1.4.0
Import to R via tximport v1.16.1
Normalisation of raw counts via DESeq2v1.28.1
n/a
n/a
Genome_build: GENCODE v37
Supplementary_files_format_and_content: TSV; raw count

source_name: EPICARDIAL ADIPOSE TISSUE

extract_protocol:
Total RNA was extracted from the adipose tissue using QIAzol (QIAGEN) and the RNeasy Lipid Tissue Mini Kits (QIAGEN) following the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: metabolic status

value: Obese/overweight

tag: tissue

value: Epicardial adipose tissue (EAT)


title: stool small RNA-Seq VOV71


title: EAT 46

description: RawCounts.tsv


title: stool small RNA-Seq VOV70


title: Wi38 S1

description:
OIS Wi38
AS-401825-LR-46699
OIS_norm_counts


title: stool small RNA-Seq VOV06


title: Wi38 P3

description:
control Wi38 proliferating
AS-401824-LR-46699
OIS_norm_counts